James Whelan

Alternative Splicing Plays a Critical Role in Maintaining Mineral Nutrient Homeostasis in Rice (Oryza sativa)

Publisher: Oxford University Press (OUP)

Date: 25-09-2018

DOI: 10.1105/TPC.18.00051

Transcriptional variation is associated with differences in shoot sodium accumulation in distinct barley varieties

Publisher: Elsevier BV

Date: 10-2019

DOI: 10.1016/J.ENVEXPBOT.2019.103812

Differential Expression of the Multigene Family Encoding the Soybean Mitochondrial Alternative Oxidase

Publisher: Oxford University Press (OUP)

Date: 06-1997

DOI: 10.1104/PP.114.2.455

Abstract: The alternative oxidase (AOX) of the soybean (Glycine max L.) inner mitochondrial membrane is encoded by a multigene family (Aox) with three known members. Here, the Aox2 and Aox3 primary translation products, deduced from cDNA analysis, were found to be 38.1 and 36.4 kD, respectively. Direct N-terminal sequencing of partially purified AOX from cotyledons demonstrates that the mature proteins are 31.8 and 31.6 kD, respectively, implying that processing occurs upon import of these proteins into the mitochondrion. Sequence comparisons show that the processing of plant AOX proteins occurs at a characteristic site and that the AOX2 and AOX3 proteins are more similar to one another than to other AOX proteins, including soybean AOX1. Transcript analysis using a polymerase chain reaction-based assay in conjunction with immunoblot experiments indicates that soybean Aox genes are differentially expressed in a tissue-dependent manner. Moreover, the relative abundance of both Aox2 transcripts and protein in cotyledons increase upon greening of dark-grown seedlings. These results comprehensively explain the multiple AOX-banding patterns observed on immunoblots of mitochondrial proteins isolated from various soybean tissues by matching protein bands with gene products.

The Mitochondrial Protein Import Machinery of Plants (MPIMP) database

Publisher: Oxford University Press (OUP)

Date: 2003

DOI: 10.1093/NAR/GKG055

Abstract: The Mitochondrial Protein Import Machinery of Plants database (MPIMP) is an Internet-accessible database containing detailed information on the protein import apparatus of plant mitochondria. The Arabidopsis genome was searched for com-ponents of the mitochondrial protein import apparatus using components from the well-characterized model system of Saccharomyces cerevisiae. Twenty six homologues of 34 components could be found, encompassing the essential components for the general and carrier import pathways. The database is available through the Internet at millar3.biochem.uwa.edu.au/~lister/index.html.

Root Cell-Specific Regulators of Phosphate-Dependent Growth

Publisher: Oxford University Press (OUP)

Date: 02-05-2017

DOI: 10.1104/PP.16.01698

The Mitochondrial Protein Import Component, TRANSLOCASE OF THE INNER MEMBRANE17-1, Plays a Role in Defining the Timing of Germination in Arabidopsis

Publisher: Oxford University Press (OUP)

Date: 24-09-2014

DOI: 10.1104/PP.114.245928

Nutrient stress-induced chromatin changes in plants

Publisher: Elsevier BV

Date: 10-2017

DOI: 10.1016/J.PBI.2017.04.001

Abstract: The ability of plants to appropriately respond to the soil nutrient availability is of primary importance for their development and to complete their life cycle. Deciphering these multifaceted adaptive mechanisms remains a major challenge for scientists to date. Recent technological breakthroughs now enable to assess the dynamism and complexity of these processes at unprecedented resolution. In this review, we present some of the most recent findings on the involvement of histone modifications, histone variants and DNA methylation in response to nutrient stresses as well as discussing the potential roles these chromatin changes could serve as priming or as trans-generational stress memory mechanisms.

Superoxide Stimulates a Proton Leak in Potato Mitochondria That Is Related to the Activity of Uncoupling Protein

Publisher: Elsevier BV

Date: 06-2003

DOI: 10.1074/JBC.M301075200

Mitochondrial Defects Confer Tolerance against Cellulose Deficiency

Publisher: Oxford University Press (OUP)

Date: 19-08-2016

DOI: 10.1105/TPC.16.00540

Next generation sequencing and de novo transcriptomics to study gene evolution

Publisher: Springer Science and Business Media LLC

Date: 20-10-2014

DOI: 10.1186/1746-4811-10-34

Sequencing of a Soybean Alternative Oxidase cDNA Clone

Publisher: Oxford University Press (OUP)

Date: 12-1993

DOI: 10.1104/PP.103.4.1481

Knockdown of Succinate Dehydrogenase Assembly Factor 2 Induces Reactive Oxygen Species–Mediated Auxin Hypersensitivity Causing pH-Dependent Root Elongation

Publisher: Oxford University Press (OUP)

Date: 26-05-2021

DOI: 10.1093/PCP/PCAB061

Abstract: Metabolism, auxin signaling and reactive oxygen species (ROS) all contribute to plant growth, and each is linked to plant mitochondria and the process of respiration. Knockdown of mitochondrial succinate dehydrogenase assembly factor 2 (SDHAF2) in Arabidopsis thaliana lowered succinate dehydrogenase activity and led to pH-inducible root inhibition when the growth medium pH was poised at different points between 7.0 and 5.0, but this phenomenon was not observed in wildtype (WT). Roots of sdhaf2 mutants showed high accumulation of succinate, depletion of citrate and malate and up-regulation of ROS-related and stress-inducible genes at pH 5.5. A change of oxidative status in sdhaf2 roots at low pH was also evidenced by low ROS staining in root tips and altered root sensitivity to H2O2. sdhaf2 had low auxin activity in root tips via DR5-GUS staining but displayed increased indole-3-acetic acid (IAA, auxin) abundance and IAA hypersensitivity, which is most likely caused by the change in ROS levels. On this basis, we conclude that knockdown of SDHAF2 induces pH-related root elongation and auxin hyperaccumulation and hypersensitivity, mediated by altered ROS homeostasis. This observation extends the existing evidence of associations between mitochondrial function and auxin by establishing a cascade of cellular events that link them through ROS formation, metabolism and root growth at different pH values.

Linking mitochondrial and chloroplast retrograde signalling in plants

Publisher: The Royal Society

Date: 04-05-2020

DOI: 10.1098/RSTB.2019.0410

Abstract: Retrograde signalling refers to the regulation of nuclear gene expression in response to functional changes in organelles. In plants, the two energy-converting organelles, mitochondria and chloroplasts, are tightly coordinated to balance their activities. Although our understanding of components involved in retrograde signalling has greatly increased in the last decade, studies on the regulation of the two organelle signalling pathways have been largely independent. Thus, the mechanism of how mitochondrial and chloroplastic retrograde signals are integrated is largely unknown. Here, we summarize recent findings on the function of mitochondrial signalling components and their links to chloroplast retrograde responses. From this, a picture emerges showing that the major regulators are integrators of both organellar retrograde signalling pathways. This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.

GWAS on multiple traits identifies mitochondrial ACONITASE3 as important for acclimation to submergence stress

Publisher: Oxford University Press (OUP)

Date: 19-01-2022

DOI: 10.1093/PLPHYS/KIAC011

Abstract: Flooding causes severe crop losses in many parts of the world. Genetic variation in flooding tolerance exists in many species however, there are few ex les for the identification of tolerance genes and their underlying function. We conducted a genome-wide association study (GWAS) in 387 Arabidopsis (Arabidopsis thaliana) accessions. Plants were subjected to prolonged submergence followed by desubmergence, and seven traits (score, water content, Fv/Fm, and concentrations of nitrate, chlorophyll, protein, and starch) were quantified to characterize their acclimation responses. These traits showed substantial variation across the range of accessions. A total of 35 highly significant single-nucleotide polymorphisms (SNPs) were identified across the 20 GWA datasets, pointing to 22 candidate genes, with functions in TCA cycle, DNA modification, and cell ision. Detailed functional characterization of one candidate gene, ACONITASE3 (ACO3), was performed. Chromatin immunoprecipitation followed by sequencing showed that a single nucleotide polymorphism in the ACO3 promoter co-located with the binding site of the master regulator of retrograde signaling ANAC017, while subcellular localization of an ACO3-YFP fusion protein confirmed a mitochondrial localization during submergence. Analysis of mutant and overexpression lines determined changes in trait parameters that correlated with altered submergence tolerance and were consistent with the GWAS results. Subsequent RNA-seq experiments suggested that impairing ACO3 function increases the sensitivity to submergence by altering ethylene signaling, whereas ACO3 overexpression leads to tolerance by metabolic priming. These results indicate that ACO3 impacts submergence tolerance through integration of carbon and nitrogen metabolism via the mitochondrial TCA cycle and impacts stress signaling during acclimation to stress.

The Arabidopsis glutathione transferase gene family displays complex stress regulation and co‐silencing multiple genes results in altered metabolic sensitivity to oxidative stress

Publisher: Wiley

Date: 26-03-2009

DOI: 10.1111/J.1365-313X.2008.03761.X

Analysis of Posttranslational Activation of Alternative Oxidase Isoforms

Publisher: Oxford University Press (OUP)

Date: 08-06-2017

DOI: 10.1104/PP.17.00681

Nucleotide and RNA metabolism prime translational initiation in the earliest events of mitochondrial biogenesis during arabidopsis germination

Publisher: Oxford University Press (OUP)

Date: 16-02-2012

DOI: 10.1104/PP.111.192351

Abstract: Mitochondria play a crucial role in germination and early seedling growth in Arabidopsis (Arabidopsis thaliana). Morphological observations of mitochondria revealed that mitochondrial numbers, typical size, and oval morphology were evident after 12 h of imbibition in continuous light (following 48 h of stratification). The transition from a dormant to an active metabolic state was punctuated by an early molecular switch, characterized by a transient burst in the expression of genes encoding mitochondrial proteins. Factors involved in mitochondrial transcription and RNA processing were overrepresented among these early-expressed genes. This was closely followed by an increase in the transcript abundance of genes encoding proteins involved in mitochondrial DNA replication and translation. This burst in the expression of factors implicated in mitochondrial RNA and DNA metabolism was accompanied by an increase in transcripts encoding components required for nucleotide biosynthesis in the cytosol and increases in transcript abundance of specific members of the mitochondrial carrier protein family that have previously been associated with nucleotide transport into mitochondria. Only after these genes peaked in expression and largely declined were typical mitochondrial numbers and morphology observed. Subsequently, there was an increase in transcript abundance for various bioenergetic and metabolic functions of mitochondria. The coordination of nucleus- and organelle-encoded gene expression was also examined by quantitative reverse transcription-polymerase chain reaction, specifically for components of the mitochondrial electron transport chain and the chloroplastic photosynthetic machinery. Analysis of protein abundance using western-blot analysis and mass spectrometry revealed that for many proteins, patterns of protein and transcript abundance changes displayed significant positive correlations. A model for mitochondrial biogenesis during germination is proposed, in which an early increase in the abundance of transcripts encoding biogenesis functions (RNA metabolism and import components) precedes a later cascade of gene expression encoding the bioenergetic and metabolic functions of mitochondria.

Phosphate homeostasis in the yeast Saccharomyces cerevisiae, the key role of the SPX domain‐containing proteins

Publisher: Wiley

Date: 26-01-2012

DOI: 10.1016/J.FEBSLET.2012.01.036

Abstract: In the yeast Saccharomyces cerevisiae, a working model for nutrient homeostasis in eukaryotes, inorganic phosphate (Pi) homeostasis is regulated by the PHO pathway, a set of phosphate starvation induced genes, acting to optimize Pi uptake and utilization. Among these, a subset of proteins containing the SPX domain has been shown to be key regulators of Pi homeostasis. In this review, we summarize the recent progresses in elucidating the mechanisms controlling Pi homeostasis in yeast, focusing on the key roles of the SPX domain-containing proteins in these processes, as well as describing the future challenges and opportunities in this fast-moving field.

Type II NAD(P)H dehydrogenases are targeted to mitochondria and chloroplasts or peroxisomes in Arabidopsis thaliana

Publisher: Wiley

Date: 12-08-2008

DOI: 10.1016/J.FEBSLET.2008.07.061

Abstract: We found that four type II NAD(P)H dehydrogenases (ND) in Arabidopsis are targeted to two locations in the cell NDC1 was targeted to mitochondria and chloroplasts, while NDA1, NDA2 and NDB1 were targeted to mitochondria and peroxisomes. Targeting of NDC1 to chloroplasts as well as mitochondria was shown using in vitro and in vivo uptake assays and dual targeting of NDC1 to plastids relies on regions in the mature part of the protein. Accumulation of NDA type dehydrogenases to peroxisomes and mitochondria was confirmed using Western blot analysis on highly purified organelle fractions. Targeting of ND proteins to mitochondria and peroxisomes is achieved by two separate signals, a C-terminal signal for peroxisomes and an N-terminal signal for mitochondria.

Dissecting the Metabolic Role of Mitochondria during Developmental Leaf Senescence

Publisher: Oxford University Press (OUP)

Date: 15-10-2016

DOI: 10.1104/PP.16.01463

The genetic origin of evolidine, the first cyclopeptide discovered in plants, and related orbitides

Publisher: Cold Spring Harbor Laboratory

Date: 12-06-2020

DOI: 10.1101/2020.06.10.145326

Abstract: Cyclic peptides are reported to have antibacterial, antifungal and other bioactivities. Several genera of the Rutaceae family are known to produce orbitides, which are small head-to-tail cyclic peptides composed of proteinogenic amino acids and lacking disulfide bonds. Melicope xanthoxyloides is an Australian rain forest tree of the Rutaceae family in which evolidine - the first plant cyclic peptide - was discovered. Evolidine (cyclo-SFLPVNL) has subsequently been all but forgotten in the academic literature, but here we use tandem mass spectrometry to rediscover evolidine and using de novo transcriptomics we show its biosynthetic origin to be from a short precursor just 48 residues in length. In all, seven M. xanthoxyloides orbitides were found and they had atypically erse C-termini consisting of residues not recognized by either of the known proteases plants use to macrocyclize peptides. Two of the novel orbitides were studied by nuclear magnetic resonance spectroscopy and although one had definable structure, the other did not. By mining RNA-seq and whole genome sequencing data from other species, it was apparent that a large and erse family of peptides is encoded by sequences like these across the Rutaceae.

Mitochondrial Protein Import: Convergent Solutions for Receptor Structure

Publisher: Elsevier BV

Date: 03-2006

DOI: 10.1016/J.CUB.2006.02.024

Abstract: Complex machinery has evolved to recognise and import nuclear-encoded proteins into mitochondria. Recent work now shows that the plant Tom20 mitochondrial protein import receptor has a similar tertiary structure to animal Tom20, although the proteins are evolutionarily distinct, representing an elegant ex le of convergent evolution.

Phosphorylation and Dephosphorylation of the Presequence of Precursor MULTIPLE ORGANELLAR RNA EDITING FACTOR3 during Import into Mitochondria from Arabidopsis

Publisher: Oxford University Press (OUP)

Date: 24-08-2015

DOI: 10.1104/PP.15.01115

Coordinated regulation of the mitochondrial retrograde response by circadian clock regulators and ANAC017

Publisher: Elsevier BV

Date: 2023

DOI: 10.1016/J.XPLC.2022.100501

Accumulation of Newly Synthesized F1 in Vivo in Arabidopsis Mitochondria Provides Evidence for Modular Assembly of the Plant F1Fo ATP Synthase

Publisher: Elsevier BV

Date: 07-2012

DOI: 10.1074/JBC.M112.373506

Developmental Normalization of Phenomics Data Generated by High Throughput Plant Phenotyping Systems

Publisher: Cold Spring Harbor Laboratory

Date: 19-05-2020

DOI: 10.1101/2020.05.17.100917

Abstract: Sowing time is commonly used as the temporal reference for Arabidopsis thaliana (Arabidopsis) experiments in high throughput plant phenotyping (HTPP) systems. This relies on the assumption that germination and seedling establishment are uniform across the population. However, in idual seeds have different development trajectories even under uniform environmental conditions. This leads to increased variance in quantitative phenotyping approaches. We developed the Digital Adjustment of Plant Development (DAPD) normalization method. It normalizes time-series HTPP measurements by reference to an early developmental stage and in an automated manner. The timeline of each measurement series is shifted to a reference time. The normalization is determined by cross-correlation at multiple time points of the time-series measurements, which may include rosette area, leaf size, and number. The DAPD method improved the accuracy of phenotyping measurements by decreasing the statistical dispersion of quantitative traits across a time-series. We applied DAPD to evaluate the relative growth rate in A. thaliana plants and demonstrated that it improves uniformity in measurements, permitting a more informative comparison between in iduals. Application of DAPD decreased variance of phenotyping measurements by up to 2.5 times compared to sowing-time normalization. The DAPD method also identified more outliers than any other central tendency technique applied to the non-normalized dataset.

A Transcriptomic and Proteomic Characterization of the Arabidopsis Mitochondrial Protein Import Apparatus and Its Response to Mitochondrial Dysfunction  

Publisher: Oxford University Press (OUP)

Date: 02-2004

DOI: 10.1104/PP.103.033910

Abstract: Mitochondria import hundreds of cytosolically synthesized proteins via the mitochondrial protein import apparatus. Expression analysis in various organs of 19 components of the Arabidopsis mitochondrial protein import apparatus encoded by 31 genes showed that although many were present in small multigene families, often only one member was prominently expressed. This was supported by comparison of real-time reverse transcriptase-polymerase chain reaction and microarray experimental data with expressed sequence tag numbers and massive parallel signature sequence data. Mass spectrometric analysis of purified mitochondria identified 17 import components, their mitochondrial sub-compartment, and verified the presence of TIM8, TIM13, TIM17, TIM23, TIM44, TIM50, and METAXIN proteins for the first time, to our knowledge. Mass spectrometry-detected isoforms correlated with the most abundant gene transcript measured by expression data. Treatment of Arabidopsis cell culture with mitochondrial electron transport chain inhibitors rotenone and antimycin A resulted in a significant increase in transcript levels of import components, with a greater increase observed for the minor isoforms. The increase was observed 12 h after treatment, indicating that it was likely a secondary response. Microarray analysis of rotenone-treated cells indicated the up-regulation of gene sets involved in mitochondrial chaperone activity, protein degradation, respiratory chain assembly, and ision. The rate of protein import into isolated mitochondria from rotenone-treated cells was halved, even though rotenone had no direct effect on protein import when added to mitochondria isolated from untreated cells. These findings suggest that transcription of import component genes is induced when mitochondrial function is limited and that minor gene isoforms display a greater response than the predominant isoforms.

Defining reference genes in Oryza sativausing organ, development, biotic and abiotic transcriptome datasets

Publisher: Springer Science and Business Media LLC

Date: 31-03-2010

DOI: 10.1186/1471-2229-10-56

Abstract: Reference genes are widely used to normalise transcript abundance data determined by quantitative RT-PCR and microarrays. However, the approaches taken to define reference genes can be variable. Although Oryza sativa (rice) is a widely used model plant and important crop specie, there has been no comprehensive analysis carried out to define superior reference genes. Analysis of 136 Affymetrix transcriptome datasets comprising of 373 genome microarrays from studies in rice that encompass tissue, developmental, abiotic, biotic and hormonal transcriptome datasets identified 151 genes whose expression was considered relatively stable under all conditions. A sub-set of 12 of these genes were validated by quantitative RT-PCR and were seen to be stable under a number of conditions. All except one gene that has been previously proposed as a stably expressed gene for rice, were observed to change significantly under some treatment. A new set of reference genes that are stable across tissue, development, stress and hormonal treatments have been identified in rice. This provides a superior set of reference genes for future studies in rice. It confirms the approach of mining large scale datasets as a robust method to define reference genes, but cautions against using gene orthology or counterparts of reference genes in other plant species as a means of defining reference genes.

RNA-seq analysis of laser micro-dissected Arabidopsis thaliana leaf epidermis, mesophyll and vasculature defines tissue-specific transcriptional responses to multiple stress treatments

Publisher: Cold Spring Harbor Laboratory

Date: 02-11-2020

DOI: 10.1101/2020.11.01.364257

Abstract: Acclimation of plants to adverse environmental conditions requires the coordination of gene expression and signalling pathways between tissues and cell types. As the energy and carbon capturing organs, leaves are significantly affected by abiotic and biotic stresses. However, tissue- or cell type-specific analyses of stress responses have largely focussed on the Arabidopsis root. Here, we comparatively explore the transcriptomes of three leaf tissues (epidermis, mesophyll, vasculature) after induction of erse stress pathways by chemical stimuli (antimycin A, 3-amino-1,2,4-triazole, methyl viologen, salicylic acid) and UV light in Arabidopsis. Profiling stimuli-dependent changes after treatments revealed an overall reduction in the tissue-specific expression of genes, with only a limited number gaining or changing their tissue-specificity. We find no evidence of a common stress response, with only a few genes responsive to two or more treatments in the analysed tissues. However, differentially expressed genes overlap across tissues for in idual treatments. Further analyses provided evidence for an interaction of auxin and ethylene that mediates retrograde signalling during mitochondrial dysfunction specifically in the epidermis, and a gene regulatory network defined the hierarchy of interactions. Taken together, we generated an extensive reference data set and results enable the tailoring of the tissue-specific engineering of stress tolerant plants.

Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana

Publisher: Springer Science and Business Media LLC

Date: 05-2005

DOI: 10.1007/S11103-005-5514-7

Abstract: Plant mitochondria contain non-phosphorylating bypasses of the respiratory chain, catalysed by the alternative oxidase (AOX) and alternative NADH dehydrogenases (NDH), as well as uncoupling (UCP) protein. Each of these components either circumvents or short-circuits proton translocation pathways, and each is encoded by a small gene family in Arabidopsis. Whole genome microarray experiments were performed with suspension cell cultures to examine the effects of various 3 h treatments designed to induce abiotic stress. The expression of over 60 genes encoding components of the classical, phosphorylating respiratory chain and tricarboxylic acid cycle remained largely constant when cells were subjected to a broad range of abiotic stresses, but expression of the alternative components responded differentially to the various treatments. In detailed time-course quantitative PCR analysis, specific members of both AOX and NDH gene families displayed coordinated responses to treatments. In particular, the co-expression of AOX1a and NDB2 observed under a number of treatments suggested co-regulation that may be directed by common sequence elements arranged hierarchically in the upstream promoter regions of these genes. A series of treatment sets were identified, representing the response of specific AOX and NDH genes to mitochondrial inhibition, plastid inhibition and abiotic stresses. These treatment sets emphasise the multiplicity of pathways affecting alternative electron transport components in plants.

Isolation of Intact Mitochondria from the Model Plant Species Arabidopsis thaliana and Oryza sativa

Publisher: Springer New York

Date: 2015

DOI: 10.1007/978-1-4939-2639-8_1

Differential Gene Expression and Subcellular Targeting of Arabidopsis Glutathione S-Transferase F8 Is Achieved through Alternative Transcription Start Sites

Publisher: Elsevier BV

Date: 09-2007

DOI: 10.1074/JBC.M702207200

RNA‐seq analysis of laser microdissected Arabidopsis thaliana leaf epidermis, mesophyll and vasculature defines tissue‐specific transcriptional responses to multiple stress treatments

Publisher: Wiley

Date: 17-06-2021

DOI: 10.1111/TPJ.15314

Abstract: Acclimation of plants to adverse conditions requires the coordination of gene expression and signalling pathways between tissues and cell types. As the energy and carbon capturing organs, leaves are significantly affected by abiotic and biotic stresses. However, tissue‐ or cell type‐specific analyses of stress responses have focussed on the Arabidopsis root. Here, we comparatively explore the transcriptomes of three leaf tissues (epidermis, mesophyll, vasculature) after induction of erse stress pathways by chemical stimuli (antimycin A, 3‐amino‐1,2,4‐triazole, methyl viologen, salicylic acid) and ultraviolet light in Arabidopsis using laser capture microdissection followed by RNA sequencing. Stimulation of stress pathways caused an overall reduction in the number of genes expressed in a tissue‐specific manner, though a small subset gained or changed their tissue specificity. We find no evidence of a common stress response, with only a few genes consistently responsive to two or more treatments in the analysed tissues. However, differentially expressed genes overlap between tissues for in idual treatments. A focussed analysis provided evidence for an interaction of auxin and ethylene that mediates retrograde signalling during mitochondrial dysfunction specifically in the epidermis, and a gene regulatory network defined the hierarchy of interactions. Taken together, we have generated an extensive reference dataset that will be valuable for future experiments analysing transcriptional responses on a tissue or single‐cell level. Our results will enable the tailoring of the tissue‐specific engineering of stress‐tolerant plants.

Accumulation of endogenous peptides triggers a pathogen stress response in Arabidopsis thaliana

Publisher: Wiley

Date: 11-2018

DOI: 10.1111/TPJ.14100

Abstract: The stepwise degradation of peptides to amino acids in plant mitochondria and chloroplasts is catalyzed by a network of oligopeptidases (presequence protease PreP, organellar oligopeptidase OOP) and aminopeptidases. In the present report, we show that the lack of oligopeptidase activity in Arabidopsis thaliana results in the accumulation of endogenous free peptides, mostly of chloroplastic origin (targeting peptides and degradation products). Using mRNA sequencing and deep coverage proteomics, allowing for the identification of 17 000 transcripts and 11 000 proteins, respectively, we uncover a peptide-stress response occurring in plants lacking PreP and OOP oligopeptidase activity. The peptide-stress response results in the activation of the classical plant defense pathways in the absence of pathogenic challenge. The constitutive activation of the pathogen-defense pathways imposes a strong growth penalty and a reduction of the plants reproductive fitness. Our results indicate that the absence of organellar oligopeptidases PreP1/2 and OOP results in the accumulation of peptides that are perceived as pathogenic effectors and activate the signaling pathways of plant-defense response.

AgriSeqDB: an online RNA-Seq database for functional studies of agriculturally relevant plant species

Publisher: Springer Science and Business Media LLC

Date: 19-09-2018

DOI: 10.1186/S12870-018-1406-2

Approaches to defining dual‐targeted proteins in Arabidopsis

Publisher: Wiley

Date: 03-2009

DOI: 10.1111/J.1365-313X.2008.03745.X

Cloning of an Additional cDNA for the Alternative Oxidase in Tobacco

Publisher: Oxford University Press (OUP)

Date: 04-1995

DOI: 10.1104/PP.107.4.1469

Gene transfer from mitochondrion to nucleus: novel mechanisms for gene activation from Cox2

Publisher: Wiley

Date: 04-2002

DOI: 10.1046/J.1365-313X.2002.01263.X

Abstract: The evolutionarily recent transfer of the gene for cytochrome c oxidase subunit 2 (cox2) from the mitochondrion to the nucleus in legumes is shown to have involved novel gene-activation steps. The acquired mitochondrial targeting presequence is bordered by two introns. Characterization of the import of soybean Cox2 indicates that the presequence is cleaved in a three-step process which is independent of assembly. The final processing step takes place only in the mitochondria of legume species, and not in several non-legume plants. The unusually long presequence of 136 amino acids consists of three regions: the first 20 amino acids are required for mitochondrial targeting and can be replaced by another presequence the central portion of the presequence is required for efficient import of the Cox2 protein into mitochondria and the last 12 amino acids, derived from the mitochondrially encoded protein, are required for correct maturation of the imported protein. The acquisition of a unique presequence, and the capacity for legume mitochondria to remove this presequence post-import, are considered to be essential adaptations for targeting of Cox2 to the mitochondrion and therefore activation of the transferred gene in the nucleus.

Spatiotemporal Deposition of Cell Wall Polysaccharides in Oat Endosperm during Grain Development

Publisher: Oxford University Press (OUP)

Date: 20-10-2023

DOI: 10.1093/PLPHYS/KIAD566

Antagonistic, overlapping and distinct responses to biotic stress in rice (Oryza sativa) and interactions with abiotic stress

Publisher: Springer Science and Business Media LLC

Date: 2013

DOI: 10.1186/1471-2164-14-93

Alternative Oxidase Is Positive for Plant Performance

Publisher: Elsevier BV

Date: 07-2018

DOI: 10.1016/J.TPLANTS.2018.03.012

Abstract: The alternative pathway of mitochondrial electron transport, which terminates in the alternative oxidase (AOX), uncouples oxidation of substrate from mitochondrial ATP production, yet plant performance is improved under adverse growth conditions. AOX is regulated at different levels. Identification of regulatory transcription factors shows that Arabidopsis thaliana AOX1a is under strong transcriptional suppression. At the protein level, the primary structure is not optimised for activity. Maximal activity requires the presence of various metabolites, such as tricarboxylic acid-cycle intermediates that act in an isoform-specific manner. In this opinion article we propose that the regulatory mechanisms that keep AOX activity suppressed, at both the gene and protein level, are positive for plant performance due to the flexible short- and long-term fine-tuning.

Exploring the Function-Location Nexus: Using Multiple Lines of Evidence in Defining the Subcellular Location of Plant Proteins

Publisher: Oxford University Press (OUP)

Date: 06-2009

DOI: 10.1105/TPC.109.066019

Decreasing Electron Flux through the Cytochrome and/or Alternative Respiratory Pathways Triggers Common and Distinct Cellular Responses Dependent on Growth Conditions  

Publisher: Oxford University Press (OUP)

Date: 06-11-2014

DOI: 10.1104/PP.114.249946

Abstract: Diverse signaling pathways are activated by perturbation of mitochondrial function under different growth conditions.Mitochondria have emerged as an important organelle for sensing and coping with stress in addition to being the sites of important metabolic pathways. Here, responses to moderate light and drought stress were examined in different Arabidopsis (Arabidopsis thaliana) mutant plants lacking a functional alternative oxidase (alternative oxidase1a [aox1a]), those with reduced cytochrome electron transport chain capacity (T3/T7 bacteriophage-type RNA polymerase, mitochondrial, and plastidial [rpoTmp]), and double mutants impaired in both pathways (aox1a:rpoTmp). Under conditions considered optimal for growth, transcriptomes of aox1a and rpoTmp were distinct. Under adverse growth conditions, however, transcriptome changes in aox1a and rpoTmp displayed a highly significant overlap and were indicative of a common mitochondrial stress response and down-regulation of photosynthesis. This suggests that the role of mitochondria to support photosynthesis is provided through either the alternative pathway or the cytochrome pathway, and when either pathway is inhibited, such as under environmental stress, a common, dramatic, and succinct mitochondrial signal is activated to alter energy metabolism in both organelles. aox1a:rpoTmp double mutants grown under optimal conditions showed dramatic reductions in biomass production compared with aox1a and rpoTmp and a transcriptome that was distinct from aox1a or rpoTmp. Transcript data indicating activation of mitochondrial biogenesis in aox1a:rpoTmp were supported by a proteomic analysis of over 200 proteins. Under optimal conditions, aox1a:rpoTmp plants seemed to switch on many of the typical mitochondrial stress regulators. Under adverse conditions, aox1a:rpoTmp turned off these responses and displayed a biotic stress response. Taken together, these results highlight the erse signaling pathways activated by the perturbation of mitochondrial function under different growth conditions.

Characterization of Mitochondrial Alternative NAD(P)H Dehydrogenases in Arabidopsis: Intraorganelle Location and Expression

Publisher: Oxford University Press (OUP)

Date: 2006

DOI: 10.1093/PCP/PCI221

Abstract: The intramitochondrial location of putative type II NAD(P)H dehydrogenases (NDs) in Arabidopsis was investigated by measuring the ability of isolated mitochondria to take up precursor proteins generated from cDNAs using an in vitro translation system. The mature proteins of NDA1, NDA2 and NDC1 were judged to be located on the inside of the inner membrane because they were protected from protease added after the mitochondrial outer membrane had been ruptured. In contrast, NDB1, NDB2 and NDB4 were not protected from protease digestion in mitochondria with ruptured outer membranes and were deemed to be located on the outside of the inner membrane. Expression of all ND genes was measured using quantitative reverse transcription-PCR (RT-PCR) to determine transcript abundance, and compared with expression of alternative oxidase, uncoupler proteins and selected components of the oxidative phosphorylation complexes. NDA1 and NDB2 were the most prominently expressed members in a variety of tissues, and were up-regulated in the early daytime in a diurnal manner. Analysis of array data suggested that NDA1 clustered closest to the gene encoding the P-subunit of glycine decarboxylase. Taken together with the diurnal regulation of NDA1 observed here and in other studies, this suggests that NDA1 plays a role in integrating metabolic activities of chloroplasts and mitochondria. NDA2, NDB2 and Aox1a were up-regulated in a coordinated manner under various treatments, potentially forming a complete respiratory chain capable of oxidizing matrix and cytosolic NAD(P)H. NDB1 and NDC1 were down-regulated under the same conditions and may be regarded as housekeeping genes.

Ethylene is involved in the regulation of iron homeostasis by regulating the expression of iron-acquisition-related genes in Oryza sativa

Publisher: Oxford University Press (OUP)

Date: 26-11-2010

DOI: 10.1093/JXB/ERQ301

A molecular link between mitochondrial preprotein transporters and respiratory chain complexes

Publisher: Informa UK Limited

Date: 12-2012

DOI: 10.4161/PSB.22250

The function of the Medicago truncatula ZIP transporter MtZIP14 is linked to arbuscular mycorrhizal fungal colonization

Publisher: Wiley

Date: 29-01-2023

DOI: 10.1111/PCE.14545

Abstract: Soil micronutrient availability, including zinc (Zn), is a limiting factor for crop yield. Arbuscular mycorrhizal (AM) fungi can improve host plant growth and nutrition through the mycorrhizal pathway of nutrient uptake. Although the physiology of Zn uptake through the mycorrhizal pathway is well established, the identity of the related molecular components are unknown. Here, RNA‐seq analysis was used to identify genes differentially‐regulated by AM colonization and soil Zn concentration in roots of Medicago truncatula . The putative Zn transporter gene MtZIP14 was markedly up‐regulated in M. truncatula roots when colonized by Rhizophagus irregularis . MtZIP14 restored yeast growth under low Zn availability. Loss‐of‐function mutant plants ( mtzip14 ) had reduced shoot biomass compared to the wild‐type when colonized by AM fungi and grown under low and sufficient soil Zn concentration at high soil Zn concentration, there were no genotypic differences in shoot biomass. The vesicular and arbuscular colonization of roots was lower in the mtzip14 plants regardless of soil Zn concentration. We propose that MtZIP14 is linked to AM colonization in M. truncatula plants, with the possibility that MtZIP14 function with AM colonization is linked to plant Zn nutrition.

Genome-Wide Analysis of mRNA Decay Rates and Their Determinants inArabidopsis thaliana

Publisher: Oxford University Press (OUP)

Date: 25-05-2011

DOI: 10.1105/TPC.107.055046

Abstract: To gain a global view of mRNA decay in Arabidopsis thaliana, suspension cell cultures were treated with a transcriptional inhibitor, and microarrays were used to measure transcript abundance over time. The deduced mRNA half-lives varied widely, from minutes to & h. Three features of the transcript displayed a correlation with decay rates: (1) genes possessing at least one intron produce mRNA transcripts significantly more stable than those of intronless genes, and this was not related to overall length, sequence composition, or number of introns (2) various sequence elements in the 3′ untranslated region are enriched among short- and long-lived transcripts, and their multiple occurrence suggests combinatorial control of transcript decay and (3) transcripts that are microRNA targets generally have short half-lives. The decay rate of transcripts correlated with subcellular localization and function of the encoded proteins. Analysis of transcript decay rates for genes encoding orthologous proteins between Arabidopsis, yeast, and humans indicated that yeast and humans had a higher percentage of transcripts with shorter half-lives and that the relative stability of transcripts from genes encoding proteins involved in cell cycle, transcription, translation, and energy metabolism is conserved. Comparison of decay rates with changes in transcript abundance under a variety of abiotic stresses reveal that a set of transcription factors are downregulated with similar kinetics to decay rates, suggesting that inhibition of their transcription is an important early response to abiotic stress.

TGD1, -2, and -3 Proteins Involved in Lipid Trafficking Form ATP-binding Cassette (ABC) Transporter with Multiple Substrate-binding Proteins

Publisher: Elsevier BV

Date: 06-2012

DOI: 10.1074/JBC.M112.370213

Temporal tissue‐specific regulation of transcriptomes during barley ( Hordeum vulgare ) seed germination

Publisher: Wiley

Date: 03-12-2019

DOI: 10.1111/TPJ.14574

Abstract: The distinct functions of in idual cell types require cells to express specific sets of genes. The germinating seed is an excellent model to study genome regulation between cell types since the majority of the transcriptome is differentially expressed in a short period, beginning from a uniform, metabolically inactive state. In this study, we applied laser-capture microdissection RNA-sequencing to small numbers of cells from the plumule, radicle tip and scutellum of germinating barley seeds every 8 h, over a 48 h time course. Tissue-specific gene expression was notably common 25% (910) of differentially expressed transcripts in plumule, 34% (1876) in radicle tip and 41% (2562) in scutellum were exclusive to that organ. We also determined that tissue-specific storage of transcripts occurs during seed development and maturation. Co-expression of genes had strong spatiotemporal structure, with most co-expression occurring within one organ and at a subset of specific time points during germination. Overlapping and distinct enrichment of functional categories were observed in the tissue-specific profiles. We identified candidate transcription factors amongst these that may be regulators of spatiotemporal gene expression programs. Our findings contribute to the broader goal of generating an integrative model that describes the structure and function of in idual cells within seeds during germination.

A Membrane-Bound NAC Transcription Factor, ANAC017, Mediates Mitochondrial Retrograde Signaling in Arabidopsis    

Publisher: Oxford University Press (OUP)

Date: 09-2013

DOI: 10.1105/TPC.113.113985

Abstract: Plants require daily coordinated regulation of energy metabolism for optimal growth and survival and therefore need to integrate cellular responses with both mitochondrial and plastid retrograde signaling. Using a forward genetic screen to characterize regulators of alternative oxidase1a (rao) mutants, we identified RAO2/Arabidopsis NAC domain-containing protein17 (ANAC017) as a direct positive regulator of AOX1a. RAO2/ANAC017 is targeted to connections and junctions in the endoplasmic reticulum (ER) and F-actin via a C-terminal transmembrane (TM) domain. A consensus rhomboid protease cleavage site is present in ANAC017 just prior to the predicted TM domain. Furthermore, addition of the rhomboid protease inhibitor N-p-Tosyl-l-Phe chloromethyl abolishes the induction of AOX1a upon antimycin A treatment. Simultaneous fluorescent tagging of ANAC017 with N-terminal red fluorescent protein (RFP) and C-terminal green fluorescent protein (GFP) revealed that the N-terminal RFP domain migrated into the nucleus, while the C-terminal GFP tag remained in the ER. Genome-wide analysis of the transcriptional network regulated by RAO2/ANAC017 under stress treatment revealed that RAO2/ANAC017 function was necessary for & % of the changes observed as a primary response to cytosolic hydrogen peroxide (H2O2), but only ∼33% of transcriptional changes observed in response to antimycin A treatment. Plants with mutated rao2/anac017 were more stress sensitive, whereas a gain-of-function mutation resulted in plants that had lower cellular levels of H2O2 under untreated conditions.

The dual targeting ability of type II NAD(P)H dehydrogenases arose early in land plant evolution

Publisher: Springer Science and Business Media LLC

Date: 10-07-2013

DOI: 10.1186/1471-2229-13-100

Abstract: Type II NAD(PH) dehydrogenases are located on the inner mitochondrial membrane of plants, fungi, protists and some primitive animals. However, recent observations have been made which identify several Arabidopsis type II dehydrogenases as dual targeted proteins. Targeting either mitochondria and peroxisomes or mitochondria and chloroplasts. Members of the ND protein family were identified in various plant species. Phylogenetic analyses and subcellular targeting predictions were carried out for all proteins. All ND proteins from three model plant species Arabidopsis, rice and Physcomitrella were cloned as N- and C-terminal GFP fusions and subcellular localisations were determined. Dual targeting of plant type II dehydrogenases was observed to have evolved early in plant evolution and to be widespread throughout different plant species. In all three species tested dual targeting to both mitochondria and peroxisomes was found for at least one NDA and NDB type protein. In addition two NDB type proteins from Physcomitrella were also found to target chloroplasts. The dual targeting of NDC type proteins was found to have evolved later in plant evolution. The functions of type II dehydrogenases within plant cells will have to be re-evaluated in light of this newly identified subcellular targeting information.

Mapping Metabolic and Transcript Temporal Switches during Germination in Rice Highlights Specific Transcription Factors and the Role of RNA Instability in the Germination Process    

Publisher: Oxford University Press (OUP)

Date: 12-12-2008

DOI: 10.1104/PP.108.129874

Abstract: Transcriptome and metabolite profiling of rice (Oryza sativa) embryo tissue during a detailed time course formed a foundation for examining transcriptional and posttranscriptional processes during germination. One hour after imbibition (HAI), independent of changes in transcript levels, rapid changes in metabolism occurred, including increases in hexose phosphates, tricarboxylic acid cycle intermediates, and γ-aminobutyric acid. Later changes in the metabolome, including those involved in carbohydrate, amino acid, and cell wall metabolism, appeared to be driven by increases in transcript levels, given that the large group (over 6,000 transcripts) observed to increase from 12 HAI were enriched in metabolic functional categories. Analysis of transcripts encoding proteins located in the organelles of primary metabolism revealed that for the mitochondrial gene set, a greater proportion of transcripts peaked early, at 1 or 3 HAI, compared with the plastid set, and notably, many of these transcripts encoded proteins involved in transport functions. One group of over 2,000 transcripts displayed a unique expression pattern beginning with low levels in dry seeds, followed by a peak in expression levels at 1 or 3 HAI, before markedly declining at later time points. This group was enriched in transcription factors and signal transduction components. A subset of these transiently expressed transcription factors were further interrogated across publicly available rice array data, indicating that some were only expressed during the germination process. Analysis of the 1-kb upstream regions of transcripts displaying similar changes in abundance identified a variety of common sequence motifs, potential binding sites for transcription factors. Additionally, newly synthesized transcripts peaking at 3 HAI displayed a significant enrichment of sequence elements in the 3′ untranslated region that have been previously associated with RNA instability. Overall, these analyses reveal that during rice germination, an immediate change in some metabolite levels is followed by a two-step, large-scale rearrangement of the transcriptome that is mediated by RNA synthesis and degradation and is accompanied by later changes in metabolite levels.

How do plants make mitochondria?

Publisher: Springer Science and Business Media LLC

Date: 14-09-2012

DOI: 10.1007/S00425-012-1762-3

Abstract: Plant mitochondria can differ in size, shape, number and protein content across different tissue types and over development. These differences are a result of signaling and regulatory processes that ensure mitochondrial function is tuned in a cell-specific manner to support proper plant growth and development. In the last decade, the processes involved in mitochondrial biogenesis are becoming clearer, including how dormant seeds transition from empty promitochondria to fully functional mitochondria with extensive cristae structures and various biochemical activities, the regulation of nuclear genes encoding mitochondrial proteins via regulators of the diurnal cycle in plants, the mitochondrial stress response, the targeting of proteins to mitochondria and other organelles and connections between the respiratory chain and protein import complexes. All these findings indicate that mitochondrial function is a part of an integrated cellular network, and communication between mitochondria and other cellular processes extends beyond the known exchange or transport of metabolites. Our current knowledge now needs to be used to gain more insight into the molecular components at various levels of this hierarchical and complex regulatory and communication network, so that mitochondrial function can be predicted and modified in a rational manner.

Molecular Definition of the Ascorbate-Glutathione Cycle in Arabidopsis Mitochondria Reveals Dual Targeting of Antioxidant Defenses in Plants

Publisher: Elsevier BV

Date: 11-2003

DOI: 10.1074/JBC.M307525200

What happens to plant mitochondria under low oxygen? An omics review of the responses to low oxygen and reoxygenation

Publisher: Wiley

Date: 11-05-2014

DOI: 10.1111/PCE.12312

Abstract: Floods can rapidly submerge plants, limiting oxygen to the extent that oxidative phosphorylation no longer generates adequate ATP supplies. Low-oxygen tolerant plants, such as rice, are able to adequately respond to low oxygen by successfully remodelling primary and mitochondrial metabolism to partially counteract the energy crisis that ensues. In this review, we discuss how plants respond to low-oxygen stress at the transcriptomic, proteomic, metabolomic and enzyme activity levels, particularly focusing on mitochondria and interacting pathways. The role of reactive oxygen species and nitrite as an alternative electron acceptor as well as their links to respiratory chain components is discussed. By making intra-kingdom as well as cross-kingdom comparisons, conserved mechanisms of anoxia tolerance are highlighted as well as tolerance mechanisms that are specific to anoxia-tolerant rice during germination and in coleoptiles. We discuss reoxygenation as an often overlooked, yet essential stage of this environmental stress and consider the possibility that changes occurring during low oxygen may also provide benefits upon re-aeration. Finally, we consider what it takes to be low-oxygen tolerant and argue that alternative mechanisms of ATP production, glucose signalling, starch/sucrose signalling as well as reverse metabolism of fermentation end products promote the survival of rice after this debilitating stress.

Ordered Assembly of Mitochondria During Rice Germination Begins with Promitochondrial Structures Rich in Components of the Protein Import Apparatus

Publisher: Springer Science and Business Media LLC

Date: 2006

DOI: 10.1007/S11103-005-3688-7

Abstract: Mitochondrial maturation during imbibition of rice embryos follows the transition of unstructured double membrane bound pro-mitochondria to the typical cristae-rich mitochondrial structures observed in mature plant cells. During the first 48 h following imbibition, an ordered increase in the abundance of transcripts encoding mitochondrial proteins was observed. Co-incident with these changes in transcript levels was dynamic and rapid changes in mitochondrial protein content and mitochondrial function. Proteins representing components of the mitochondrial protein import apparatus are strikingly abundant in dry seeds, and a functional import apparatus was shown to operate 2 h after imbibition. Interestingly, this import process was best driven by the oxidation of NADH from outside the mitochondrial inner membrane. In later developmental stages the capacity for matrix organic acid metabolism was evident, accompanied by the appearance of proteins for TCA cycle components, and coordination of electron transport chain assembly through components encoded in both mitochondrial and nuclear genomes. Together these events provide new insights into the understanding of mitochondrial maturation and the nature of pro-mitochondrial structures in plant cells.

Analysis of the Rice Mitochondrial Carrier Family Reveals Anaerobic Accumulation of a Basic Amino Acid Carrier Involved in Arginine Metabolism during Seed Germination    

Publisher: Oxford University Press (OUP)

Date: 18-08-2010

DOI: 10.1104/PP.110.162214

Abstract: Given the substantial changes in mitochondrial gene expression, the mitochondrial proteome, and respiratory function during rice (Oryza sativa) germination under anaerobic and aerobic conditions, we have attempted to identify changes in mitochondrial membrane transport capacity during these processes. We have assembled a preliminary rice mitochondrial carrier gene family of 50 members, defined its orthology to carriers of known function, and observed significant changes in microarray expression data for these rice genes during germination under aerobic and anaerobic conditions and across rice development. To determine if these transcript changes reflect alteration of the carrier profile itself and to determine which members of the family encode the major mitochondrial carrier proteins, we analyzed mitochondrial integral membrane protein preparations using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and peptide mass spectrometry, identifying seven distinct carrier proteins. We have used mass spectrometry-based quantitative approaches to compare the abundance of these carriers between mitochondria from dry seeds and those from aerobic- or anaerobic-germinated seeds. We highlight an anaerobic-enhanced basic amino acid carrier and show concomitant increases in mitochondrial arginase and the abundance of arginine and ornithine in anaerobic-germinated seeds, consistent with an anaerobic role of this mitochondria carrier. The potential role of this carrier in facilitating mitochondrial involvement in arginine metabolism and the plant urea cycle during the growth of rice coleoptiles and early seed nitrate assimilation under anaerobic conditions are discussed.

Pentatricopeptide repeat domain protein 1 lowers the levels of mitochondrial leucine tRNAs in cells

Publisher: Oxford University Press (OUP)

Date: 03-08-2009

DOI: 10.1093/NAR/GKP627

Phage-Type RNA Polymerase RPOTmp Performs Gene-Specific Transcription in Mitochondria of Arabidopsis thaliana    

Publisher: Oxford University Press (OUP)

Date: 09-2009

DOI: 10.1105/TPC.109.068536

Abstract: Transcription of mitochondrial genes in animals, fungi, and plants relies on the activity of T3/T7 phage-type RNA polymerases. Two such enzymes, RPOTm and RPOTmp, are present in the mitochondria of eudicotyledonous plants RPOTmp is additionally found in plastids. We have characterized the transcriptional role of the dual-targeted RNA polymerase in mitochondria of Arabidopsis thaliana. Examination of mitochondrial transcripts in rpoTmp mutants revealed major differences in transcript abundances between wild-type and rpoTmp plants. Decreased levels of specific transcripts were correlated with reduced abundances of the respiratory chain complexes I and IV. Altered transcript levels in rpoTmp were found to result from gene-specific transcriptional changes, establishing that RPOTmp functions in distinct transcriptional processes within mitochondria. Decreased transcription of specific genes in rpoTmp was not associated with changes in promoter utilization therefore, RPOTmp function is not promoter specific but gene specific. This implies that additional gene-specific elements direct the transcription of a subset of mitochondrial genes by RPOTmp.

Identification, Expression, and Import of Components 17 and 23 of the Inner Mitochondrial Membrane Translocase from Arabidopsis,

Publisher: Oxford University Press (OUP)

Date: 04-2003

DOI: 10.1104/PP.102.016808

Abstract: Characterization of components 17 and 23 of the inner mitochondrial membrane translocase (TIM17:23) from Arabidopsis indicated that there were three genes present for TIM17 andTIM23 and two for TIM44.AtTIM17 differed from the yeast (Saccharomyces cerevisiae) and mammalian homologs in that two genes encoded proteins that were longer and one gene encoded a shorter protein. All Arabidopsis TIM23 predicted proteins appeared to lack the first 34 amino acids compared with yeast TIM23. All AtTIM17 andAtTIM23 genes were expressed but displayed different tissue and developmental profiles. Complementation of deletion mutants in yeast indicated that for AtTIM17, the extension at the C terminus not present in yeast had to be removed to achieve complementation, whereas for TIM23, a preprotein and amino acid transporter domain had to be present for complementation. Import assays with AtTIM17 and AtTIM23 indicated that they both contained internal signals for integration into the inner mitochondrial membrane in a membrane potential-dependent manner. The C terminus of imported AtTIM17-2 was susceptible to degradation by externally added protease with intact mitochondria. Removal of the 85 C-terminal amino acids resulted in import and full protection of the truncated protein. This suggests that the novel extension at the C terminus of AtTIM17-2 links the outer and inner membrane in a manner analogous to yeast TIM23.

Systemic and Intracellular Responses to Photooxidative Stress in Arabidopsis

Publisher: Oxford University Press (OUP)

Date: 12-2007

DOI: 10.1105/TPC.106.045898

Abstract: As the sun tracks daily through the sky from east to west, different parts of the canopy are exposed to high light (HL). The extent of and mechanisms by which a systemic acquired acclimation (SAA) response might preacclimate shaded leaves that will be subsequently exposed to full sunlight is largely undefined. We investigated the role of an Arabidopsis thaliana zinc finger transcription factor, ZAT10, in SAA. ZAT10 overexpression resulted in enhanced tolerance to photoinhibitory light and exogenous H2O2, increased expression of antioxidative genes whose products are targeted to multiple subcellular compartments. Partial HL exposure of a leaf or leaves rapidly induced ZAT10 mRNA in distal, shaded photosynthetic tissues, including the floral stem, cauline leaves, and rosette, but not in roots. Fully 86% of fivefold HL-upregulated and 71% of HL-downregulated genes were induced and repressed, respectively, in distal, shaded leaves. Between 15 and 23% of genes whose expression changed in the HL and/or distal tissues were coexpressed in the ZAT10 overexpression plants, implicating ZAT10 in modulating the expression of SAA-regulated genes. The SAA response was detectable in plants with mutations in abscisic acid, methyl jasmonate, or salicylic acid synthesis or perception, and systemic H2O2 diffusion was not detected. Hence, SAA is distinct from pathogen-stimulated systemic acquired resistance and apparently involves a novel signal or combination of signals that preacclimate photosynthetic tissues to HL.

FTSH PROTEASE 3 facilitates Complex I degradation through a direct interaction with the Complex I subunit PSST

Publisher: Oxford University Press (OUP)

Date: 13-05-2023

DOI: 10.1093/PLCELL/KOAD128

Abstract: Complex I (CI) (NADH dehydrogenase), the largest complex involved in mitochondrial oxidative phosphorylation, is composed of nuclear- and mitochondrial-encoded subunits. CI assembly occurs via the sequential addition of subdomains and modules. As CI is prone to oxidative damage, its subunits continually undergo proteolysis and turnover. We describe the mechanism by which CI abundance is regulated in a CI-deficient Arabidopsis thaliana mutant. Using a forward genetic approach, we determined that the CI Q-module domain subunit PSST interacts with FTSH PROTEASE 3 (FTSH3) to mediate the disassembly of the matrix arm domain for proteolysis and turnover as a means of protein quality control. We demonstrated the direct interaction of FTSH3 with PSST and identified the amino acid residues required for this interaction. The ATPase function of FTSH3, rather than its proteolytic activity, is required for this interaction, as its mutation was compensated for by a proteolytically inactive form of FTSH3. This study reveals the mechanistic process by which FTSH3 recognizes CI for degradation at amino acid resolution.

The Design and Structure of Outer Membrane Receptors from Peroxisomes, Mitochondria, and Chloroplasts

Publisher: Elsevier BV

Date: 10-2015

DOI: 10.1016/J.STR.2015.08.005

Abstract: The eukaryotic cell is defined by compartments that allow specialization of function. This compartmental structure generates a new concept in cell biology compared with the simpler prokaryotic cell structure, namely the specific targeting of proteins to intracellular compartments. Protein targeting is achieved by the action of specialized signals on proteins destined for organelles that are recognized by cognate receptors. An understanding of the specificity of targeting signal recognition leading to import requires an understanding of the receptor structures. Here, we focus on the structures of receptors of different import machineries located on the outer membrane of three organelles: peroxisomes, mitochondria, and chloroplasts. This review provides an overview of the structural features of outer membrane import receptors that recognize targeting signals. Finally, we briefly discuss combinatorial approaches that might aid in understanding the structural factors mediating receptor targeting signal recognition.

Studies on the import and processing of the alternative oxidase precursor by isolated soybean mitochondria

Publisher: Springer Science and Business Media LLC

Date: 02-1995

DOI: 10.1007/BF00020229

Analysis of the Alternative Oxidase Promoters from Soybean

Publisher: Oxford University Press (OUP)

Date: 11-2003

DOI: 10.1104/PP.103.028183

Abstract: Alternative oxidase (Aox) is a nuclear-encoded mitochondrial protein. In soybean (Glycine max), the three members of the gene family have been shown to be differentially expressed during normal plant development and in response to stresses. To examine the function of the Aox promoters, genomic fragments were obtained for all three soybean genes: Aox1, Aox2a, and Aox2b. The regions of these fragments immediately upstream of the coding regions were used to drive β-glucuronidase (GUS) expression during transient transformation of soybean suspension culture cells and stable transformation of Arabidopsis. The expression patterns of the GUS reporter genes in soybean cells were in agreement with the presence or absence of the various endogenous Aox proteins, determined by immunoblotting. Deletion of different portions of the upstream regions identified sequences responsible for both positive and negative regulation of Aox gene expression in soybean cells. Reporter gene analysis in Arabidopsis plants showed differential tissue expression patterns driven by the three upstream regions, similar to those reported for the endogenous proteins in soybean. The expression profiles of all five members of the Arabidopsis Aox gene family were examined also, to compare with GUS expression driven by the soybean upstream fragments. Even though the promoter activity of the upstream fragments from soybean Aox2a and Aox2b displayed the same tissue specificity in Arabidopsis as they do in soybean, the most prominently expressed endogenous genes in all tissues of Arabidopsis were of the Aox1 type. Thus although regulation of Aox expression generally appears to involve the same signals in different species, different orthologs of Aox may respond variously to these signals. A comparison of upstream sequences between soybean Aox genes and similarly expressed Arabidopsis Aox genes identified common motifs.

Single Cell App: An App for Single Cell RNA-sequencing Data Visualization, Comparison and Discovery

Publisher: Cold Spring Harbor Laboratory

Date: 10-10-2021

DOI: 10.1101/2021.10.09.463793

Abstract: The Single Cell App is a cloud-based application that allows visualisation and comparison of scRNA-seq data and is scalable according to use. Users upload their own or publicly available scRNA-seq datasets after pre-processing to be visualised using a web browser. The data can be viewed in two colour modes, Cluster - representing cell identity, and Values – level of expression, and data queried using keyword or gene identification number(s). Using the app to compare four different studies we determined that some genes frequently used as cell-type markers are in fact study specific. Phosphate transporter and hormone response genes were exemplary investigated with the app. This showed that the apparent cell specific expression of PHO1 H3 differed between GFP-tagging and scRNA-seq studies. Some phosphate transporter genes were induced by protoplasting, they retained cell specificity, indicating that cell specific stress responses (i.e. protoplasting). Examination of the cell specificity of hormone response genes revealed that 132 hormone responsive genes display restricted expression and that the jasmonate response gene TIFY8 is expressed in endodermal cells which differs from previous reports. It also appears that JAZ repressors have cell-type specific functions. These differences, identified using the Single Cell App, highlight the need for resources to enable researchers to find common and different patterns of cell specific gene expression. Thus, the Single Cell App enables researchers to form new hypothesis, perform comparative studies, allows for easy re-use of data for this emerging technology to provide novel avenues to crop improvement.

Recent advances in Cannabis sativa genomics research

Publisher: Wiley

Date: 08-01-2021

DOI: 10.1111/NPH.17140

Arabidopsis thaliana ferrochelatase‐I and ‐II are not imported into Arabidopsis mitochondria

Publisher: Wiley

Date: 27-09-2001

DOI: 10.1016/S0014-5793(01)02925-8

Abstract: Using in vitro import assays into purified mitochondria and chloroplasts we found that Arabidopsis ferrochelatase-I and ferrochelatase-II were not imported into mitochondria purified from Arabidopsis (or several other plants) but were imported into pea leaf chloroplasts. Other dual targeted proteins could be imported into purified mitochondria from Arabidopsis. As only two ferrochelatase genes are present in the completed Arabidopsis genome, the presence of ferrochelatase activity in plant mitochondria needs to be re-evaluated. Previous reports of Arabidopsis ferrochelatase-I import into pea mitochondria are due to the fact that pea leaf (and root) mitochondria appear to import a variety, but not all chloroplast proteins. Thus pea mitochondria are not a suitable system to either study dual targeting, or to distinguish between isozymes present in mitochondria and chloroplasts.

RNA-Seq analysis identifies key genes associated with haustorial development in the root hemiparasite Santalum album

Publisher: Frontiers Media SA

Date: 09-2015

DOI: 10.3389/FPLS.2015.00661

Refining the Definition of Plant Mitochondrial Presequences through Analysis of Sorting Signals, N-Terminal Modifications, and Cleavage Motifs    

Publisher: Oxford University Press (OUP)

Date: 27-05-2009

DOI: 10.1104/PP.109.137885

Abstract: Mitochondrial protein import is a complex multistep process from synthesis of proteins in the cytosol, recognition by receptors on the organelle surface, to translocation across one or both mitochondrial membranes and assembly after removal of the targeting signal, referred to as a presequence. In plants, import has to further discriminate between mitochondria and chloroplasts. In this study, we determined the precise cleavage sites in the presequences for Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) mitochondrial proteins using mass spectrometry by comparing the precursor sequences with experimental evidence of the amino-terminal peptide from mature proteins. We validated this method by assessments of false-positive rates and comparisons with previous available data using Edman degradation. In total, the cleavable presequences of 62 proteins from Arabidopsis and 52 proteins from rice mitochondria were determined. None of these proteins contained amino-terminal acetylation, in contrast to recent findings for chloroplast stromal proteins. Furthermore, the classical matrix glutamate dehydrogenase was detected with intact and amino-terminal acetylated sequences, indicating that it is imported into mitochondria without a cleavable targeting signal. Arabidopsis and rice mitochondrial presequences had similar isoelectric points, hydrophobicity, and the predicted ability to form an hiphilic α-helix at the amino-terminal region of the presequence, but variations in length, amino acid composition, and cleavage motifs for mitochondrial processing peptidase were observed. A combination of lower hydrophobicity and start point of the amino-terminal α-helix in mitochondrial presequences in both Arabidopsis and rice distinguished them (98%) from Arabidopsis chloroplast stroma transit peptides. Both Arabidopsis and rice mitochondrial cleavage sites could be grouped into three classes, with conserved −3R (class II) and −2R (class I) or without any conserved (class III) arginines. Class II was dominant in both Arabidopsis and rice (55%–58%), but in rice sequences there was much less frequently a phenylalanine (F) in the −1 position of the cleavage site than in Arabidopsis sequences. Our data also suggest a novel cleavage motif of (F/Y)↓(S/A) in plant class III sequences.

Glutaredoxin S15 Is Involved in Fe-S Cluster Transfer in Mitochondria Influencing Lipoic Acid-Dependent Enzymes, Plant Growth, and Arsenic Tolerance in Arabidopsis

Publisher: Oxford University Press (OUP)

Date: 15-12-2015

DOI: 10.1104/PP.15.01308

Ligand Recognition by the TPR Domain of the Import Factor Toc64 from Arabidopsis thaliana

Publisher: Public Library of Science (PLoS)

Date: 31-12-2013

DOI: 10.1371/JOURNAL.PONE.0083461

scCloudMine: A cloud-based app for visualization, comparison, and exploration of single-cell transcriptomic data

Publisher: Elsevier BV

Date: 07-2022

DOI: 10.1016/J.XPLC.2022.100302

Import of precursor proteins into mitochondria from soybean tissues during development

Publisher: Wiley

Date: 20-12-1999

DOI: 10.1016/S0014-5793(99)01674-9

Abstract: Characterisation of the amount of protein import of the alternative oxidase (AOX) and the F(A)d precursor proteins (previously shown to use different import pathways) into mitochondria from developing soybean tissues indicated that they displayed different patterns. Import of the AOX declined in both cotyledon and root mitochondria with increasing age, whereas the import of the F(A)d into cotyledon mitochondria remained high throughout the same period. Using primary leaf mitochondria, it was evident that import of AOX remained high while it declined in cotyledon and root mitochondria. The amount of import of the AOX into mitochondria from different tissues closely matched the amount of the Tom 20 receptor.

Organization and Regulation of Mitochondrial Respiration in Plants

Publisher: Annual Reviews

Date: 02-06-2011

DOI: 10.1146/ANNUREV-ARPLANT-042110-103857

Abstract: Mitochondrial respiration in plants provides energy for biosynthesis, and its balance with photosynthesis determines the rate of plant biomass accumulation. We describe recent advances in our understanding of the mitochondrial respiratory machinery of cells, including the presence of a classical oxidative phosphorylation system linked to the cytosol by transporters, discussed alongside nonphosphorylating (and, therefore, non-energy conserving) bypasses that alter the efficiency of ATP synthesis and play a role in oxidative stress responses in plants. We consider respiratory regulation in the context of the contrasting roles mitochondria play in different tissues, from photosynthetic leaves to nutrient-acquiring roots. We focus on the molecular nature of this regulation at transcriptional and post-transcriptional levels that allow the respiratory apparatus of plants to help shape organ development and the response of plants to environmental stress. We highlight the challenges for future research considering spatial and temporal changes of respiration in response to changing climatic conditions.

How Do Plant Mitochondria Avoid Importing Chloroplast Proteins? Components of the Import Apparatus Tom20 and Tom22 from Arabidopsis Differ from Their Fungal Counterparts

Publisher: Oxford University Press (OUP)

Date: 07-2000

DOI: 10.1104/PP.123.3.811

MRPS27 is a pentatricopeptide repeat domain protein required for the translation of mitochondrially encoded proteins

Publisher: Wiley

Date: 25-07-2012

DOI: 10.1016/J.FEBSLET.2012.07.043

Abstract: Mammalian pentatricopeptide repeat domain (PPR) proteins are involved in regulation of mitochondrial RNA metabolism and translation and are required for mitochondrial function. We investigated an uncharacterised PPR protein, the supernumerary mitochondrial ribosomal protein of the small subunit 27 (MRPS27), and show that it associates with the 12S rRNA and tRNA(Glu), however it does not affect their abundance. We found that MRPS27 is not required for mitochondrial RNA processing or the stability of the small ribosomal subunit. However, MRPS27 is required for mitochondrial protein synthesis and its knockdown causes decreased abundance in respiratory complexes and cytochrome c oxidase activity.

Exploring ligand recognition, selectivity and dynamics of TPR domains of chloroplast Toc64 and mitochondria Om64 fromArabidopsis thaliana

Publisher: Wiley

Date: 20-03-2014

DOI: 10.1002/JMR.2360

Abstract: The study aims to gain insight into the mode of ligand recognition by tetratricopeptide repeat (TPR) domains of chloroplast translocon at the outer envelope of chloroplast (Toc64) and mitochondrial Om64, two paralogous proteins that mediate import of proteins into chloroplast and mitochondria, respectively. Chaperone proteins associate with precursor proteins in the cytosol to maintain them in a translocation competent conformation and are recognized by Toc64 and Om64 that are located on the outer membrane of the target organelle. Heat shock proteins (Hsp70) and Hsp90 are two chaperones, which are known to play import roles in protein import. The C-termini of these chaperones are known to interact with the TPR domain of chloroplast Toc64 and mitochondrial Om64 in Arabidopsis thaliana (At). Using a molecular dynamics approach and binding energy calculations, we identify important residues involved in the interactions. Our findings suggest that the TPR domain from AtToc64 has higher affinity towards C-terminal residues of Hsp70. The interaction occurs as the terminal helices move towards each other enclosing the cradle on interaction of AtHsp70 with the TPR domain. In contrast, the TPR domain from AtOm64 does not discriminate between the C-termini of Hsp70 and Hsp90. These binding affinities are discussed with respect to our knowledge of protein targeting and specificity of protein import into endosymbiotic organelles in plant cells.

The N-terminal Cleavable Extension of Plant Carrier Proteins is Responsible for Efficient Insertion into the Inner Mitochondrial Membrane

Publisher: Elsevier BV

Date: 08-2005

DOI: 10.1016/J.JMB.2005.06.004

Abstract: A subset of mitochondrial carrier proteins from plants contain a cleavable N-terminal extension. We have used a reconstituted protein import assay system into intermembrane space-depleted mitochondria to study the role of the cleavable extension in the carrier import pathway. Insertion of carrier proteins into the inner membrane can be stimulated by the addition of a soluble intermembrane space fraction isolated from plant mitochondria. Greater stimulation of import of the adenine nucleotide carrier (ANT) and phosphate carrier (Pic), which contain N-terminal cleavable extensions, was observed compared to the import of the oxoglutarate malate carrier (OMT), which does not contain a cleavable extension. Removal of the N-terminal cleavable extension from ANT and Pic resulted in loss of stimulation of insertion into the inner membrane. Conversely, addition of the N-terminal extension from ANT or Pic to OMT resulted in significantly enhanced insertion into the inner membrane. The polytopic inner membrane proteins TIM17 and TIM23 that are imported via the carrier import pathway contain no cleavable extension, displayed high-level stimulation of insertion into the inner membrane by addition of the intermembrane space fraction. Addition of the N-terminal cleavable extension from carrier proteins to TIM23 enhanced insertion of TIM23 into the inner membrane even in the absence of the soluble intermembrane space fraction. Together, these results demonstrate that the cleavable N-terminal extensions present on carrier proteins from plants are required for efficient insertion into the inner mitochondrial membrane, and that they can stimulate insertion of any carrier-like protein into the inner membrane.

Community recommendations on terminology and procedures used in flooding and low oxygen stress research

Publisher: Wiley

Date: 09-03-2017

DOI: 10.1111/NPH.14519

Evidence for a link between translocation and processing during protein import into soybean mitochondria

Publisher: Elsevier BV

Date: 06-1996

DOI: 10.1016/0167-4889(96)00014-6

Abstract: The effect of metal chelators on protein import was investigated using isolated soybean mitochondria and soybean precursor proteins. Adding 1,10-phenanthroline, a metal chelator that can cross both mitochondrial membranes abolished import of both the alternative oxidase, and the F(A)d subunit of the ATP synthase, a matrix located protein. Other metal chelators such as EDTA, 1,7-phenanthroline and 4,7-phenanthroline, which cannot cross the mitochondrial membranes, had no effect on import. When processing, a known metal-dependent step inside mitochondria, was inhibited using a mutagenesis approach (changing a -2 arginine to a -2 glycine in the pre-piece of the precursor), so was import. Thus it would appear that in soybean, at least, translocation of proteins across the mitochondrial membrane, as well as processing, relies on a metal dependent step. Taken together, the data suggest the two processes may be directly connected in these mitochondria.

Identification of a Dual-Targeted Protein Belonging to the Mitochondrial Carrier Family That Is Required for Early Leaf Development in Rice      

Publisher: Oxford University Press (OUP)

Date: 14-02-2013

DOI: 10.1104/PP.112.210831

Abstract: A dual-targeted protein belonging to the mitochondrial carrier family was characterized in rice (Oryza sativa) and designated 3′-Phosphoadenosine 5′-Phosphosulfate Transporter1 (PAPST1). The papst1 mutant plants showed a defect in thylakoid development, resulting in leaf chlorosis at an early leaf developmental stage, while normal leaf development was restored 4 to 6 d after leaf emergence. OsPAPST1 is highly expressed in young leaves and roots, while the expression is reduced in mature leaves, in line with the recovery of chloroplast development seen in the older leaves of papst1 mutant plants. OsPAPST1 is located on the outer mitochondrial membrane and chloroplast envelope. Whole-genome transcriptomic analysis reveals reduced expression of genes encoding photosynthetic components (light reactions) in papst1 mutant plants. In addition, sulfur metabolism is also perturbed in papst1 plants, and it was seen that PAPST1 can act as a nucleotide transporter when expressed in Escherichia coli that can be inhibited significantly by 3′-phosphoadenosine 5′-phosphosulfate. Given these findings, together with the altered phenotype seen only when leaves are first exposed to light, it is proposed that PAPST1 may act as a 3′-phosphoadenosine 5′-phosphosulfate carrier that has been shown to act as a retrograde signal between chloroplasts and the nucleus.

Spatially resolved transcriptomic analysis of the germinating barley grain

Publisher: Oxford University Press (OUP)

Date: 23-06-2023

DOI: 10.1093/NAR/GKAD521

Abstract: Seeds are a vital source of calories for humans and a unique stage in the life cycle of flowering plants. During seed germination, the embryo undergoes major developmental transitions to become a seedling. Studying gene expression in in idual seed cell types has been challenging due to the lack of spatial information or low throughput of existing methods. To overcome these limitations, a spatial transcriptomics workflow was developed for germinating barley grain. This approach enabled high-throughput analysis of spatial gene expression, revealing specific spatial expression patterns of various functional gene categories at a sub-tissue level. This study revealed over 14 000 genes differentially regulated during the first 24 h after imbibition. In idual genes, such as the aquaporin gene family, starch degradation, cell wall modification, transport processes, ribosomal proteins and transcription factors, were found to have specific spatial expression patterns over time. Using spatial autocorrelation algorithms, we identified auxin transport genes that had increasingly focused expression within subdomains of the embryo over time, suggesting their role in establishing the embryo axis. Overall, our study provides an unprecedented spatially resolved cellular map for barley germination and identifies specific functional genomics targets to better understand cellular restricted processes during germination. The data can be viewed at spatial.latrobe.edu.au/.

Isolation of a Novel Soybean Gene Encoding a Mitochondrial ATP Synthase Subunit

Publisher: Elsevier BV

Date: 09-1994

DOI: 10.1006/ABBI.1994.1382

Abstract: A novel ATP synthase gene from soybean has been cloned and characterized. A subunit from the FA portion of the complex is encoded by two nuclear genes. The genomic clone(s) contain five exons encoding a protein of 179 amino acids. The amino terminal end contains many properties of a mitochondrial targeting sequence and preliminary in vitro import studies indicate that there is a cleavable precursor of approximately 30 amino acids. The predicted protein sequence shows high homology with the N-terminal sequence from an isolated subunit of ATP synthase complex from spinach (Hamsaur and Glaser (1992) Eur. J. Biochem. 205, 409-416). The subunit was tentatively identified as the equivalent of subunit d in bovine and P18 in yeast based on structural identity.

The retrograde signaling regulator ANAC017 recruits the MKK9–MPK3/6, ethylene, and auxin signaling pathways to balance mitochondrial dysfunction with growth

Publisher: Oxford University Press (OUP)

Date: 16-06-2022

DOI: 10.1093/PLCELL/KOAC177

Abstract: In plant cells, mitochondria are ideally positioned to sense and balance changes in energy metabolism in response to changing environmental conditions. Retrograde signaling from mitochondria to the nucleus is crucial for adjusting the required transcriptional responses. We show that ANAC017, the master regulator of mitochondrial stress, directly recruits a signaling cascade involving the plant hormones ethylene and auxin as well as the MAP KINASE KINASE (MKK) 9–MAP KINASE (MPK) 3/6 pathway in Arabidopsis thaliana. Chromatin immunoprecipitation followed by sequencing and overexpression demonstrated that ANAC017 directly regulates several genes of the ethylene and auxin pathways, including MKK9, 1-AMINO-CYCLOPROPANE-1-CARBOXYLATE SYNTHASE 2, and YUCCA 5, in addition to genes encoding transcription factors regulating plant growth and stress responses such as BASIC REGION/LEUCINE ZIPPER MOTIF (bZIP) 60, bZIP53, ANAC081/ATAF2, and RADICAL-INDUCED CELL DEATH1. A time-resolved RNA-seq experiment established that ethylene signaling precedes the stimulation of auxin signaling in the mitochondrial stress response, with a large part of the transcriptional regulation dependent on ETHYLENE-INSENSITIVE 3. These results were confirmed by mutant analyses. Our findings identify the molecular components controlled by ANAC017, which integrates the primary stress responses to mitochondrial dysfunction with whole plant growth via the activation of regulatory and partly antagonistic feedback loops.

Nine 3-ketoacyl-CoA thiolases (KATs) and acetoacetyl-CoA thiolases (ACATs) encoded by five genes in Arabidopsis thaliana are targeted either to peroxisomes or cytosol but not to mitochondria

Publisher: Springer Science and Business Media LLC

Date: 21-11-2007

DOI: 10.1007/S11103-006-9075-1

Abstract: The sub-cellular location of enzymes of fatty acid beta-oxidation in plants is controversial. In the current debate the role and location of particular thiolases in fatty acid degradation, fatty acid synthesis and isoleucine degradation are important. The aim of this research was to determine the sub-cellular location and hence provide information about possible functions of all the putative 3-ketoacyl-CoA thiolases (KAT) and acetoacetyl-CoA thiolases (ACAT) in Arabidopsis. Arabidopsis has three genes predicted to encode KATs, one of which encodes two polypeptides that differ at the N-terminal end. Expression in Arabidopsis cells of cDNAs encoding each of these KATs fused to green fluorescent protein (GFP) at their C-termini showed that three are targeted to peroxisomes while the fourth is apparently cytosolic. The four KATs are also predicted to have mitochondrial targeting sequences, but purified mitochondria were unable to import any of the proteins in vitro. Arabidopsis also has two genes encoding a total of five different putative ACATs. One isoform is targeted to peroxisomes as a fusion with GFP, while the others display no targeting in vivo as GFP fusions, or import into isolated mitochondria. Analysis of gene co-expression clusters in Arabidopsis suggests a role for peroxisomal KAT2 in beta-oxidation, while KAT5 co-expresses with genes of the flavonoid biosynthesis pathway and cytosolic ACAT2 clearly co-expresses with genes of the cytosolic mevalonate biosynthesis pathway. We conclude that KATs and ACATs are present in the cytosol and peroxisome, but are not found in mitochondria. The implications for fatty acid beta-oxidation and for isoleucine degradation in mitochondria are discussed.

Characterization of the Regulatory and Expression Context of an Alternative Oxidase Gene Provides Insights into Cyanide-Insensitive Respiration during Growth and Development

Publisher: Oxford University Press (OUP)

Date: 23-02-2007

DOI: 10.1104/PP.106.091819

Abstract: Alternative oxidase (AOX) is encoded in small multigene families in plants. Functional analysis of the Arabidopsis (Arabidopsis thaliana) alternative oxidase 1c (AtAOX1c) promoter, an AOX gene not induced by oxidative stress, indicated that regulation of expression was complex, with the upstream promoter region containing positive and negative response regions. Comparison to the promoter region of soybean (Glycine max) alternative oxidase 2b (GmAOX2b), another AOX gene not induced by oxidative stress, revealed that they contained seven sequence elements in common. All elements were active in the promoter region of AtAOX1c in suspension cells and in leaf tissue from Columbia and mutant plants, where a mitochondrial protein import receptor was inactivated. Analysis of coexpressed and putatively coregulated genes, the latter defined as containing five or more sequence elements functional in AtAOX1c, indicated that AtAOX1c was coregulated with components involved with cell ision and growth. Consistent with this analysis, we demonstrated that site II elements, previously shown to regulate the proliferating cell nuclear antigen, are present in the upstream promoter region of AtAOX1c and were strong negative regulators of AtAOX1c expression. It was demonstrated that NDB4, a gene encoding an external NAD(P)H dehydrogenase, displayed strong coexpression with AtAOX1c. Overall, these results indicate that AtAOX1c is regulated by growth and developmental signals.

ANAC017 Coordinates Organellar Functions and Stress Responses by Reprogramming Retrograde Signaling

Publisher: Oxford University Press (OUP)

Date: 14-03-2019

DOI: 10.1104/PP.18.01603

Enhanced reactive oxygen detoxification occurs in salt‐stressed soybean roots expressing GmSALT3

Publisher: Wiley

Date: 05-2022

DOI: 10.1111/PPL.13709

Abstract: Soybean ( Glycine max ) is an important crop globally for food and edible oil production. Soybean plants are sensitive to salinity (NaCl), with significant yield decreases reported under saline conditions. GmSALT3 is the dominant gene underlying a major QTL for salt tolerance in soybean. GmSALT3 encodes a transmembrane protein belonging to the plant cation roton exchanger (CHX) family, and is predominately expressed in root phloem and xylem associated cells under both saline and non‐saline conditions. It is currently unknown through which molecular mechanism(s) the ER‐localised GmSALT3 contributes to salinity tolerance, as its localisation excludes direct involvement in ion exclusion. In order to gain insights into potential molecular mechanism(s), we used RNA‐seq analysis of roots from two soybean NILs (near isogenic lines) NIL‐S (salt‐sensitive, Gmsalt3 ), and NIL‐T (salt‐tolerant, GmSALT3 ), grown under control and saline conditions (200 mM NaCl) at three time points (0 h, 6 h, and 3 days). Gene ontology (GO) analysis showed that NIL‐T has greater responses aligned to oxidation reduction. ROS were less abundant and scavenging enzyme activity was greater in NIL‐T, consistent with the RNA‐seq data. Further analysis indicated that genes related to calcium signalling, vesicle trafficking and Casparian strip (CS) development were upregulated in NIL‐T following salt treatment. We propose that GmSALT3 improves the ability of NIL‐T to cope with saline stress through preventing ROS overaccumulation in roots, and potentially modulating Ca 2+ signalling, vesicle trafficking and formation of diffusion barriers.

LETM Proteins Play a Role in the Accumulation of Mitochondrially Encoded Proteins in Arabidopsis thaliana and AtLETM2 Displays Parent of Origin Effects

Publisher: Elsevier BV

Date: 12-2012

DOI: 10.1074/JBC.M112.383836

Inactivation of Mitochondrial Complex I Induces the Expression of a Twin Cysteine Protein that Targets and Affects Cytosolic, Chloroplastidic and Mitochondrial Function

Publisher: Elsevier BV

Date: 05-2016

DOI: 10.1016/J.MOLP.2016.01.009

Abstract: At12Cys-1 (At5g64400) and At12Cys-2 (At5g09570) are two closely related isogenes that encode small, twin cysteine proteins, typically located in mitochondria. At12Cys-2 transcript is induced in a variety of mutants with disrupted mitochondrial proteins, but an increase in At12Cys protein is only detected in mutants with reduced mitochondrial complex I abundance. Induction of At12Cys protein in mutants that lack mitochondrial complex I is accompanied by At12Cys protein located in mitochondria, chloroplasts, and the cytosol. Biochemical analyses revealed that even single gene deletions, i.e., At12cys-1 or At12cys-2, have an effect on mitochondrial and chloroplast functions. However, only double mutants, i.e., At12cys-1:At12cys-2, affect the abundance of protein and mRNA transcripts encoding translation elongation factors as well as rRNA abundance. Blue native PAGE showed that At12Cys co-migrated with mitochondrial supercomplex I + III. Likewise, deletion of both At12cys-1 and At12cys-2 genes, but not single gene deletions, results in enhanced tolerance to drought and light stress and increased anti-oxidant capacity. The induction and multiple localization of At12Cys upon a reduction in complex I abundance provides a mechanism to specifically signal mitochondrial dysfunction to the cytosol and then beyond to other organelles in the cell.

Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabi

Publisher: Wiley

Date: 29-11-2013

DOI: 10.1111/TPJ.12357

Tissue-Specific Expression of the Alternative Oxidase in Soybean and Siratro

Publisher: Oxford University Press (OUP)

Date: 06-1992

DOI: 10.1104/PP.99.2.712

Oxygen Initiation of Respiration and Mitochondrial Biogenesis in Rice

Publisher: Elsevier BV

Date: 05-2007

DOI: 10.1074/JBC.M609866200

Differential Expression of Alternative Oxidase Genes in Soybean Cotyledons during Postgerminative Development

Publisher: Oxford University Press (OUP)

Date: 10-1998

DOI: 10.1104/PP.118.2.675

Abstract: The expression of the alternative oxidase (AOX) was investigated during cotyledon development in soybean (Glycine max [L.] Merr.) seedlings. The total amount of AOX protein increased throughout development, not just in earlier stages as previously thought, and was correlated with the increase in capacity of the alternative pathway. Each AOX isoform (AOX1, AOX2, and AOX3) showed a different developmental trend in mRNA abundance, such that the increase in AOX protein and capacity appears to involve a shift in gene expression fromAOX2 to AOX3. As the cotyledons aged, the size of the mitochondrial ubiquinone pool decreased. We discuss how this and other factors may affect the alternative pathway activity that results from the developmental regulation of AOX expression.

Two h-Type Thioredoxins Interact with the E2 Ubiquitin Conjugase PHO2 to Fine-Tune Phosphate Homeostasis in Rice

Publisher: Oxford University Press (OUP)

Date: 28-11-2016

DOI: 10.1104/PP.16.01639

Protein phosphorylation stimulates the rate of malate uptake across the peribacteroid membrane of soybean nodules

Publisher: Wiley

Date: 11-1991

DOI: 10.1016/0014-5793(91)81183-9

Abstract: Incubation of intact isolated symbiosomes with [gamma-32P]ATP, followed by isolation of the peribacteroid membrane and polypeptide analysis, showed that a single major polypeptide at 26 kDa was labelled. Antibodies raised against nodulin 26 reacted with a similar sized polypeptide. Incubation of the symbiosomes with alkaline phosphatase removed the label from this polypeptide. Pre-incubation with ATP stimulated malate accumulation by isolated symbiosomes, but only slightly (10-30%). Pre-treatment of symbiosomes with alkaline phosphatase inhibited malate uptake substantially and this inhibition was completely relieved by addition of ATP. The ATP stimulation of malate uptake was not affected by ATPase inhibitors. It is suggested that the rate of malate uptake across the peribacteroid membrane is controlled by phosphorylation of nodulin 26.

ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants

Publisher: Springer Science and Business Media LLC

Date: 11-04-2006

DOI: 10.1186/1746-4811-2-8

Abstract: Uncovering the key sequence elements in gene promoters that regulate the expression of plant genomes is a huge task that will require a series of complementary methods for prediction, substantial innovations in experimental validation and a much greater understanding of the role of combinatorial control in the regulation of plant gene expression. To add to this larger process and to provide alternatives to existing prediction methods, we have developed several tools in the statistical package R. ModuleFinder identifies sets of genes and treatments that we have found to form valuable sets for analysis of the mechanisms underlying gene co-expression. CoReg then links the hierarchical clustering of these co-expressed sets with frequency tables of promoter elements. These promoter elements can be drawn from known elements or all possible combinations of nucleotides in an element of various lengths. These sets of promoter elements represent putative cis -acting regulatory elements common to sets of co-expressed genes and can be prioritised for experimental testing. We have used these new tools to analyze the response of transcripts for nuclear genes encoding mitochondrial proteins in Arabidopsis to a range of chemical stresses. ModuleFinder provided a subset of co-expressed gene modules that are more logically related to biological functions than did subsets derived from traditional hierarchical clustering techniques. Importantly ModuleFinder linked responses in transcripts for electron transport chain components, carbon metabolism enzymes and solute transporter proteins. CoReg identified several promoter motifs that helped to explain the patterns of expression observed. ModuleFinder identifies sets of genes and treatments that form useful sets for analysis of the mechanisms behind co-expression. CoReg links the clustering tree of expression-based relationships in these sets with frequency tables of promoter elements. These sets of promoter elements represent putative cis -acting regulatory elements for sets of genes, and can then be tested experimentally. We consider these tools, both built on an open source software product to provide valuable, alternative tools for the prioritisation of promoter elements for experimental analysis.

The mitochondrial AAA protease FTSH3 regulates Complex I abundance by promoting its disassembly

Publisher: Oxford University Press (OUP)

Date: 22-02-2021

DOI: 10.1093/PLPHYS/KIAB074

Abstract: ATP is generated in mitochondria by oxidative phosphorylation. Complex I (NADH:ubiquinone oxidoreductase or NADH dehydrogenase) is the first multisubunit protein complex of this pathway, oxidizing NADH and transferring electrons to the ubiquinone pool. Typically, Complex I mutants display a slow growth rate compared to wild-type plants. Here, using a forward genetic screen approach for restored growth of a Complex I mutant, we have identified the mitochondrial ATP-dependent metalloprotease, Filamentous Temperature Sensitive H 3 (FTSH3), as a factor that is required for the disassembly of Complex I. An ethyl methanesulfonate-induced mutation in FTSH3, named as rmb1 (restoration of mitochondrial biogenesis 1), restored Complex I abundance and plant growth. Complementation could be achieved with FTSH3 lacking proteolytic activity, suggesting the unfoldase function of FTSH3 has a role in Complex I disassembly. The introduction of the rmb1 to an additional, independent, and extensively characterized Complex I mutant, ndufs4, resulted in similar increases to Complex I abundance and a partial restoration of growth. These results show that disassembly or degradation of Complex I plays a role in determining its steady-state abundance and thus turnover may vary under different conditions.

Noninvasive imaging technologies in plant phenotyping

Publisher: Elsevier BV

Date: 03-2022

DOI: 10.1016/J.TPLANTS.2021.06.009

Stress responsive mitochondrial proteins in Arabidopsis thaliana

Publisher: Elsevier BV

Date: 07-2018

DOI: 10.1016/J.FREERADBIOMED.2018.03.031

Abstract: In the last decade plant mitochondria have emerged as a target, sensor and initiator of signalling cascades to a variety of stress and adverse growth conditions. A combination of various 'omic profiling approaches combined with forward and reverse genetic studies have defined how mitochondria respond to stress and the signalling pathways and regulators of these responses. Reactive oxygen species (ROS)-dependent and -independent pathways, specific metabolites, complex I dysfunction, and the mitochondrial unfolded protein response (UPR) pathway have been proposed to date. These pathways are regulated by kinases (sucrose non-fermenting response like kinase cyclin dependent protein kinase E 1) and transcription factors from the abscisic acid-related, WRKY and NAC families. A number of independent studies have revealed that these mitochondrial signalling pathways interact with a variety of phytohormone signalling pathways. While this represents significant progress in the last decade there are more pathways to be uncovered. Post-transcriptional/translational regulation is also a likely determinant of the mitochondrial stress response. Unbiased analyses of the expression of genes encoding mitochondrial proteins in a variety of stress conditions reveal a modular network exerting a high degree of anterograde control. As abiotic and biotic stresses have significant impact on the yield of important crops such as rice, wheat and barley we will give an outlook of how knowledge gained in Arabidopsis may help to increase crop production and how emerging technologies may contribute.

Organic acid activation of the alterNatlve oxidase of plant mitochondria

Publisher: Wiley

Date: 30-08-1993

DOI: 10.1016/0014-5793(93)80233-K

Abstract: Alternative oxidase activity (oxygen uptake in the presence of KCN, antimycin or myxothiazol) in mitochondria isolated from the roots of soybean seedlings was very slow, even with succinate as substrate. This activity was stimulated substantially (100-400%) by the addition of pyruvate, with half maximal stimulation occurring at 0.1 mM pyruvate. Mitochondria from soybean shoots displayed high alternative oxidase activity with succinate and malate as substrates but lower activity with exogenous NADH addition of pyruvate stimulated the activity with NADH up to that seen with succinate. This stimulation of cyanide-insensitive NADH oxidation was seen also with mitochondria from other species. Hydroxypyruvate and oxoglutarate could substitute for pyruvate, although higher concentrations were required to achieve maximum stimulation. Pyruvate stimulation of cyanide-insensitive oxygen uptake was observed with exogenous quinols as substrates, with sub-mitochondrial particles, and in the presence of the pyruvate transport inhibitor, cyanohydroxycinnamic acid, but was not observed with detergent-solubilised mitochondria. It is suggested that pyruvate acts allosterically on the alternative oxidase to stimulate its activity. The implications of these findings for respiration in vivo are discussed.

MPIC: A Mitochondrial Protein Import Components Database for Plant and Non-Plant Species

Publisher: Oxford University Press (OUP)

Date: 29-11-2014

DOI: 10.1093/PCP/PCU186

Abstract: In the 2 billion years since the endosymbiotic event that gave rise to mitochondria, variations in mitochondrial protein import have evolved across different species. With the genomes of an increasing number of plant species sequenced, it is possible to gain novel insights into mitochondrial protein import pathways. We have generated the Mitochondrial Protein Import Components (MPIC) Database (DB www.plantenergy.uwa.edu.au/applications/mpic) providing searchable information on the protein import apparatus of plant and non-plant mitochondria. An in silico analysis was carried out, comparing the mitochondrial protein import apparatus from 24 species representing various lineages from Saccharomyces cerevisiae (yeast) and algae to Homo sapiens (human) and higher plants, including Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice) and other more recently sequenced plant species. Each of these species was extensively searched and manually assembled for analysis in the MPIC DB. The database presents an interactive diagram in a user-friendly manner, allowing users to select their import component of interest. The MPIC DB presents an extensive resource facilitating detailed investigation of the mitochondrial protein import machinery and allowing patterns of conservation and ergence to be recognized that would otherwise have been missed. To demonstrate the usefulness of the MPIC DB, we present a comparative analysis of the mitochondrial protein import machinery in plants and non-plant species, revealing plant-specific features that have evolved.

Adaptations Required for Mitochondrial Import following Mitochondrial to Nucleus Gene Transfer of Ribosomal Protein S10

Publisher: Oxford University Press (OUP)

Date: 22-07-2005

DOI: 10.1104/PP.105.062745

Abstract: The minimal requirements to support protein import into mitochondria were investigated in the context of the phenomenon of ongoing gene transfer from the mitochondrion to the nucleus in plants. Ribosomal protein 10 of the small subunit is encoded in the mitochondrion in soybean and many other angiosperms, whereas in several other species it is nuclear encoded and thus must be imported into the mitochondrial matrix to function. When encoded by the nuclear genome, it has adopted different strategies for mitochondrial targeting and import. In lettuce (Lactuca sativa) and carrot (Daucus carota), Rps10 independently gained different N-terminal extensions from other genes, following transfer to the nucleus. (The designation of Rps10 follows the following convention. The gene is indicated in italics. If encoded in the mitochondrion, it is rps10 if encoded in the nucleus, it is Rps10.) Here, we show that the N-terminal extensions of Rps10 in lettuce and carrot are both essential for mitochondrial import. In maize (Zea mays), Rps10 has not acquired an extension upon transfer but can be readily imported into mitochondria. Deletion analysis located the mitochondrial targeting region to the first 20 amino acids. Using site directed mutagenesis, we changed residues in the first 20 amino acids of the mitochondrial encoded soybean (Glycine max) rps10 to the corresponding amino acids in the nuclear encoded maize Rps10 until import was achieved. Changes were required that altered charge, hydrophobicity, predicted ability to form an hiphatic α-helix, and generation of a binding motif for the outer mitochondrial membrane receptor, translocase of the outer membrane 20. In addition to defining the changes required to achieve mitochondrial localization, the results demonstrate that even proteins that do not present barriers to import can require substantial changes to acquire a mitochondrial targeting signal.

Conserved and Novel Functions for Arabidopsis thaliana MIA40 in Assembly of Proteins in Mitochondria and Peroxisomes

Publisher: Elsevier BV

Date: 11-2010

DOI: 10.1074/JBC.M110.121202

Towards an Analysis of the Rice Mitochondrial Proteome

Publisher: Oxford University Press (OUP)

Date: 05-2003

DOI: 10.1104/PP.102.018986

Abstract: Purified rice (Oryza sativa) mitochondrial proteins have been arrayed by isoelectric focusing olyacrylamide gel electrophoresis (PAGE), by blue-native (BN) PAGE, and by reverse-phase high-performance liquid chromatography (LC) separation (LC-mass spectrometry [MS]). From these protein arrays, we have identified a range of rice mitochondrial proteins, including hydrophilic/hydrophobic proteins (grand average of hydropathicity = −1.27 to +0.84), highly basic and acid proteins (isoelectric point = 4.0–12.5), and proteins over a large molecular mass range (6.7–252 kD), using proteomic approaches. BN PAGE provided a detailed picture of electron transport chain protein complexes. A total of 232 protein spots from isoelectric focusing/PAGE and BN PAGE separations were excised, trypsin digested, and analyzed by tandem MS (MS/MS). Using this dataset, 149 of the protein spots (the products of 91 nonredundant genes) were identified by searching translated rice open reading frames from genomic sequence and six-frame translated rice expressed sequence tags. Sequence comparison allowed us to assign functions to a subset of 85 proteins, including many of the major function categories expected for this organelle. A further six spots were matched to rice sequences for which no specific function has yet been determined. Complete digestion of mitochondrial proteins with trypsin yielded a peptide mixture that was analyzed directly by reverse-phase LC via organic solvent elution from a C-18 column (LC-MS). These data yielded 170 MS/MS spectra that matched 72 sequence entries from open reading frame and expressed sequence tag databases. Forty-five of these were obtained using LC-MS alone, whereas 28 proteins were identified by both LC-MS and gel-based separations. In total, 136 nonredundant rice proteins were identified, including a new set of 23 proteins of unknown function located in plant mitochondria. We also report the first direct identification, to our knowledge, of PPR (pentatricopeptide repeat) proteins in the plant mitochondrial proteome. This dataset provides the first extensive picture, to our knowledge, of mitochondrial functions in a model monocot plant.

Arabidopsis ammonium transporters, atAMT1;1 and atAMT1;2, have different biochemical properties and functional roles

Publisher: Springer Science and Business Media LLC

Date: 2001

DOI: 10.1023/A:1010303813181

A multi-step peptidolytic cascade for amino acid recovery in chloroplasts

Publisher: Springer Science and Business Media LLC

Date: 31-10-2016

DOI: 10.1038/NCHEMBIO.2227

Abstract: Plastids (including chloroplasts) are subcellular sites for a plethora of proteolytic reactions, required in functions ranging from protein biogenesis to quality control. Here we show that peptides generated from pre-protein maturation within chloroplasts of Arabidopsis thaliana are degraded to amino acids by a multi-step peptidolytic cascade consisting of oligopeptidases and aminopeptidases, effectively allowing the recovery of single amino acids within these organelles.

Applications of hyperspectral imaging in plant phenotyping

Publisher: Elsevier BV

Date: 03-2022

DOI: 10.1016/J.TPLANTS.2021.12.003

Abstract: Our ability to interrogate and manipulate the genome far exceeds our capacity to measure the effects of genetic changes on plant traits. Much effort has been made recently by the plant science research community to address this imbalance. The responses of plants to environmental conditions can now be defined using a variety of imaging approaches. Hyperspectral imaging (HSI) has emerged as a promising approach to measure traits using a wide range of wavebands simultaneously in 3D to capture information in lab, glasshouse, or field settings. HSI has been applied to define abiotic, biotic, and quality traits for optimisation of crop management.

OsNLA1, a RING‐type ubiquitin ligase, maintains phosphate homeostasis in Oryza sativa via degradation of phosphate transporters

Publisher: Wiley

Date: 29-04-2017

DOI: 10.1111/TPJ.13516

Abstract: Inorganic phosphate (Pi) transporters (PTs) play vital roles in Pi uptake and translocation in plants. Under Pi sufficient conditions, PTs are degraded to prevent excess Pi accumulation. The mechanisms targeting PTs for degradation are not fully elucidated. In this study, we found that the Oryza sativa (rice) ortholog of Arabidopsis thaliana nitrogen limitation adaptation (NLA), OsNLA1 protein, a RING-type E3 ubiquitin-ligase, was predominantly localized in the plasma membrane, and could interact with rice phosphate transporters OsPT2 and OsPT8. Mutation of the 265th cysteine residue in OsNLA1 that was required for ubiquitination prevented breakdown of OsPT2/PT8, suggesting OsNLA1 targeted OsPT2/PT8 for degradation. Mutation in OsNLA1 (osnla1) led to a significant increase of Pi concentration in leaves in a nitrate-independent manner. Overexpression of OsNLA1 or repression of OsPT2/PT8 restored the high leaf Pi concentration in osnla1 mutants to a level similar to that of wild-type plants. In contrast to what has been observed in Arabidopsis, the transcript abundance of OsNLA1 did not decrease under Pi limited conditions or in OsmiR827 (microRNA827)- or OsPHR2 (PHOSPHATE STARVATION RESPONSE 2)-overexpressing transgenic lines. Moreover, there was no interaction of OsNLA1 and OsPHO2, an E2 ubiquitin-conjugase, suggesting that OsPHO2 was not the partner of OsNLA1 involved in ubiquitin-mediated PT degradation. Our results show that OsNLA1 is involved in maintaining phosphate homeostasis in rice by mediating the degradation of OsPT2 and OsPT8, and OsNLA1 differs from the ortholog in Arabidopsis in several aspects.

Cross-species transcriptomic analyses reveals common and opposite responses in Arabidopsis, rice and barley following oxidative stress and hormone treatment

Publisher: Springer Science and Business Media LLC

Date: 04-02-2022

DOI: 10.1186/S12870-021-03406-7

Abstract: For translational genomics, a roadmap is needed to know the molecular similarities or differences between species, such as model species and crop species. This knowledge is invaluable for the selection of target genes and pathways to alter downstream in response to the same stimuli. Here, the transcriptomic responses to six treatments including hormones (abscisic acid - ABA and salicylic acid - SA) treatments that cause oxidative stress (3-amino-1,2,4-triazole - 3AT, methyl viologen - MV) inhibit respiration (antimycin A - AA) or induce genetic damage (ultraviolet radiation -UV) were analysed and compared between Arabidopsis ( Arabidopsis thaliana), barley ( Hordeum vulgare) and rice ( Oryza sativa) . Common and opposite responses were identified between species, with the number of differentially expressed genes (DEGs) varying greatly between treatments and species. At least 70% of DEGs overlapped with at least one other treatment within a species, indicating overlapping response networks. Remarkably, 15 to 34% of orthologous DEGs showed opposite responses between species, indicating ersity in responses, despite orthology. Orthologous DEGs with common responses to multiple treatments across the three species were correlated with experimental data showing the functional importance of these genes in biotic/abiotic stress responses. The mitochondrial dysfunction response was revealed to be highly conserved in all three species in terms of responsive genes and regulation via the mitochondrial dysfunction element. The orthologous DEGs that showed a common response between species indicate conserved transcriptomic responses of these pathways between species. However, many genes, including prominent salt-stress responsive genes, were oppositely responsive in multiple-stresses, highlighting fundamental differences in the responses and regulation of these genes between species. This work provides a resource for translation of knowledge or functions between species.

Mitochondrial signalling is critical for acclimation and adaptation to flooding in Arabidopsis thaliana

Publisher: Wiley

Date: 10-04-2020

DOI: 10.1111/TPJ.14724

The mitochondrial outer membrane AAA ATPase AtOM66 affects cell death and pathogen resistance in Arabidopsis thaliana

Publisher: Wiley

Date: 27-10-2014

DOI: 10.1111/TPJ.12665

Abstract: One of the most stress-responsive genes encoding a mitochondrial protein in Arabidopsis (At3g50930) has been annotated as AtBCS1 (cytochrome bc1 synthase 1), but was previously functionally uncharacterised. Here, we show that the protein encoded by At3g50930 is present as a homo-multimeric protein complex on the outer mitochondrial membrane and lacks the BCS1 domain present in yeast and mammalian BCS1 proteins, with the sequence similarity restricted to the AAA ATPase domain. Thus we propose to re-annotate this protein as AtOM66 (Outer Mitochondrial membrane protein of 66 kDa). While transgenic plants with reduced AtOM66 expression appear to be phenotypically normal, AtOM66 over-expression lines have a distinct phenotype, showing strong leaf curling and reduced starch content. Analysis of mitochondrial protein content demonstrated no detectable changes in mitochondrial respiratory complex protein abundance. Consistent with the stress inducible expression pattern, over-expression lines of AtOM66 are more tolerant to drought stress but undergo stress-induced senescence earlier than wild type. Genome-wide expression analysis revealed a constitutive induction of salicylic acid-related (SA) pathogen defence and cell death genes in over-expression lines. Conversely, expression of SA marker gene PR-1 was reduced in atom66 plants, while jasmonic acid response genes PDF1.2 and VSP2 have increased transcript abundance. In agreement with the expression profile, AtOM66 over-expression plants show increased SA content, accelerated cell death rates and are more tolerant to the biotrophic pathogen Pseudomonas syringae, but more susceptible to the necrotrophic fungus Botrytis cinerea. In conclusion, our results demonstrate a role for AtOM66 in cell death and lifying SA signalling.

Mechanisms of growth and patterns of gene expression in oxygen‐deprived rice coleoptiles

Publisher: Wiley

Date: 24-03-2015

DOI: 10.1111/TPJ.12786

Abstract: Coleoptiles of rice (Oryza sativa) seedlings grown under water commonly elongate by up to 1 mm h(-1) to reach the atmosphere. We initially analysed this highly specialized phenomenon by measuring epidermal cell lengths along the coleoptile axis to determine elongation rates. This revealed a cohort of cells in the basal zone that elongated rapidly following emergence from the embryo, reaching 200 μm within 12 h. After filming coleoptiles in vivo for a day, kinematic analysis was applied. Eight time-sliced 'segments' were defined by their emergence from the embryo at four-hourly intervals, revealing a mathematically simple growth model. Each segment entering the coleoptile from the embryo elongated at a constant velocity, resulting in accelerating growth for the entire organ. Consistent with the epidermal cell lengths, relative rates of elongation (mm mm(-1) h(-1)) were tenfold greater in the small, newly emerged basal segments than the older distal tip segments. This steep axial gradient defined two contrasting growth zones (bases versus tips) in which we measured ATP production and protein, RNA and DNA content, and analysed the global transcriptome under steady-state normoxia, hypoxia (3% O2) and anoxia. Determination of the transcriptome revealed tip-specific induction of genes encoding TCP [Teosinte Branched1 (Tb1) of maize, Cycloidea (Cyc), and Proliferating Cell Factor (Pcf)] transcription factors, RNA helicases, ribosomal proteins and proteins involved in protein folding, whilst expression of F-box domain-containing proteins in the ubiquitin E3-SCF complex (Skp, Cullin, F-box containing complex) was induced specifically in bases under low oxygen conditions. We ascribed the sustained elongation under hypoxia to hypoxia-specific responses such as controlled suppression of photosystem components and induction of RNA binding/splicing functions, indicating preferential allocation of energy to cell extension.

The Absence of ALTERNATIVE OXIDASE1a in Arabidopsis Results in Acute Sensitivity to Combined Light and Drought Stress  

Publisher: Oxford University Press (OUP)

Date: 18-04-2008

DOI: 10.1104/PP.107.115121

Abstract: Treatment of Arabidopsis (Arabidopsis thaliana) alternative oxidase1a (aox1a) mutant plants with moderate light under drought conditions resulted in a phenotypic difference compared with ecotype Columbia (Col-0), as evidenced by a 10-fold increase in the accumulation of anthocyanins in leaves, alterations in photosynthetic efficiency, and increased superoxide radical and reduced root growth at the early stages of seedling growth. Analysis of metabolite profiles revealed significant changes upon treatment in aox1a plants typical of combined stress treatments, and these were less pronounced or absent in Col-0 plants. These changes were accompanied by alteration in the abundance of a variety of transcripts during the stress treatment, providing a molecular fingerprint for the stress-induced phenotype of aox1a plants. Transcripts encoding proteins involved in the synthesis of anthocyanins, transcription factors, chloroplastic and mitochondrial components, cell wall synthesis, and sucrose and starch metabolism changed, indicating that effects were not confined to mitochondria, where the AOX1a protein is located. Microarray and quantitative reverse transcription-polymerase chain reaction analysis revealed that transcripts typically induced upon stress treatment or involved in antioxidant defense systems, especially chloroplast-located antioxidant defense components, had altered basal levels in untreated aox1a plants, suggesting a significant change in the basal equilibrium of signaling pathways that regulate these components. Taken together, these results indicate that aox1a plants have a greatly altered stress response even when mitochondria or the mitochondrial electron transport chain are not the primary target of the stress and that AOX1a plays a broad role in determining the normal redox balance in the cell.

The Membrane-Bound NAC Transcription Factor ANAC013 Functions in Mitochondrial Retrograde Regulation of the Oxidative Stress Response in Arabidopsis    

Publisher: Oxford University Press (OUP)

Date: 09-2013

DOI: 10.1105/TPC.113.117168

Abstract: Upon disturbance of their function by stress, mitochondria can signal to the nucleus to steer the expression of responsive genes. This mitochondria-to-nucleus communication is often referred to as mitochondrial retrograde regulation (MRR). Although reactive oxygen species and calcium are likely candidate signaling molecules for MRR, the protein signaling components in plants remain largely unknown. Through meta-analysis of transcriptome data, we detected a set of genes that are common and robust targets of MRR and used them as a bait to identify its transcriptional regulators. In the upstream regions of these mitochondrial dysfunction stimulon (MDS) genes, we found a cis-regulatory element, the mitochondrial dysfunction motif (MDM), which is necessary and sufficient for gene expression under various mitochondrial perturbation conditions. Yeast one-hybrid analysis and electrophoretic mobility shift assays revealed that the transmembrane domain–containing NO APICAL MERISTEM/ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR/CUP-SHAPED COTYLEDON transcription factors (ANAC013, ANAC016, ANAC017, ANAC053, and ANAC078) bound to the MDM cis-regulatory element. We demonstrate that ANAC013 mediates MRR-induced expression of the MDS genes by direct interaction with the MDM cis-regulatory element and triggers increased oxidative stress tolerance. In conclusion, we characterized ANAC013 as a regulator of MRR upon stress in Arabidopsis thaliana.

The Expression of Alternative Oxidase and Uncoupling Protein during Fruit Ripening in Mango

Publisher: Oxford University Press (OUP)

Date: 08-2001

DOI: 10.1104/PP.126.4.1619

Abstract: The expression of alternative oxidase (Aox) and uncoupling proteins (Ucp) was investigated during ripening in mango (Mangifera indica) and compared with the expression of peroxisomal thiolase, a previously described ripening marker in mango. The multigene family for the Aox in mango was expressed differentially during ripening. Abundance of Aox message and protein both peaked at the ripe stage. Expression of the single gene for the Ucp peaked at the turning stage and the protein abundance peaked at the ripe stage. Proteins of the cytochrome chain peaked at the mature stage of ripening. The pattern of protein accumulation suggested that increases in cytochrome chain components played an important role in facilitating the climacteric burst of respiration and that the Aox and Ucp may play a role in post-climacteric senescent processes. Because both message and protein for the Aox and Ucp increased in a similar pattern, it suggests that their expression is not controlled in a reciprocal manner but may be active simultaneously.

Diverse phosphate and auxin transport loci distinguish phosphate tolerant from sensitive Arabidopsis accessions

Publisher: Oxford University Press (OUP)

Date: 20-09-2021

DOI: 10.1093/PLPHYS/KIAB441

Abstract: Phosphorus (P) is an essential element for plant growth often limiting agroecosystems. To identify genetic determinants of performance under variable phosphate (Pi) supply, we conducted genome-wide association studies on five highly predictive Pi starvation response traits in 200 Arabidopsis (Arabidopsis thaliana) accessions. Pi concentration in Pi-limited organs had the strongest, and primary root length had the weakest genetic component. Of 70 trait-associated candidate genes, 17 responded to Pi withdrawal. The PHOSPHATE TRANSPORTER1 gene cluster on chromosome 5 comprises PHT1 , PHT1 , and PHT1 with known impact on P status. A second locus featured uncharacterized endomembrane-associated auxin efflux carrier encoding PIN-LIKES7 (PILS7) which was more strongly suppressed in Pi-limited roots of Pi-starvation sensitive accessions. In the Col-0 background, Pi uptake and organ growth were impaired in both Pi-limited pht1 and two pils7 T-DNA insertion mutants, while Pi -limited pht1 had higher biomass and pht1 was indistinguishable from wild-type. Copy number variation at the PHT1 locus with loss of the PHT1 gene and smaller scale deletions in PHT1 and PHT1 predicted to alter both protein structure and function suggest ersification of PHT1 is a key driver for adaptation to P limitation. Haplogroup analysis revealed a phosphorylation site in the protein encoded by the PILS7 allele from stress-sensitive accessions as well as additional auxin-responsive elements in the promoter of the “stress tolerant” allele. The former allele’s inability to complement the pils7-1 mutant in the Col-0 background implies the presence of a kinase signaling loop controlling PILS7 activity in accessions from P-rich environments, while survival in P-poor environments requires fine-tuning of stress-responsive root auxin signaling.

Cloning, Analysis and Inactivation of the ndhK Gene Encoding a Subunit of NADH Quinone Oxidoreductase from Anabaena PCC 7120

Publisher: Wiley

Date: 08-1996

DOI: 10.1111/J.1432-1033.1996.0173H.X

Abstract: The function of the type-1 pyridine nucleotide dehydrogenase (NDH-1) in the cyanobacterium Anabaena PCC 7120 was investigated. Immunological analysis with antibodies raised against NdhK from Synechocystis PCC 6803, a subunit of NDH-1, showed that NdhK in Anabaena PCC 7120 is only present on the plasma membrane, which confirms the results of previous studies [Howitt, C.A., Smith, G.D. & Day, D. A. (1993) Biochim. Biophys. Acta 114], 313-320]. Southern analysis with probes from the operon encoding ndhC-K-J from Synechocystis PCC 6803 showed that this operon is also conserved in Anabaena PCC 7120. Part of the operon was lified using PCR with degenerate primers designed against two sequences encoding regions of NdhC and NdhJ that are conserved between cyanobacteria and chloroplasts. The nucleotide sequence of ndhK encodes a protein of 245 amino acids with a predicted molecular mass of 27.5 kDa. The coding regions of ndhC and ndhK overlap by 7 bp, as found in the chloroplasts of liverwort, maize, and rice. This is markedly different from the case in Synechocystis PCC 6803 where a 71-bp non-coding, intergenic spacer region lies between ndhC and ndhK. The ndhK clone was interrupted by the insertion of a kanamycin-resistance gene and used to transform Anabaena PCC 7120.20 unsegregated transformants were produced, all of which died during attempts to segregate them. This indicates that under the selection conditions used, ndhK is an essential gene in Anabaena PCC 7120.

Protein import into plant mitochondria: signals, machinery, processing, and regulation

Publisher: Oxford University Press (OUP)

Date: 16-10-2014

DOI: 10.1093/JXB/ERU399

Abstract: The majority of more than 1000 proteins present in mitochondria are imported from nuclear-encoded, cytosolically synthesized precursor proteins. This impressive feat of transport and sorting is achieved by the combined action of targeting signals on mitochondrial proteins and the mitochondrial protein import apparatus. The mitochondrial protein import apparatus is composed of a number of multi-subunit protein complexes that recognize, translocate, and assemble mitochondrial proteins into functional complexes. While the core subunits involved in mitochondrial protein import are well conserved across wide phylogenetic gaps, the accessory subunits of these complexes differ in identity and/or function when plants are compared with Saccharomyces cerevisiae (yeast), the model system for mitochondrial protein import. These differences include distinct protein import receptors in plants, different mechanistic operation of the intermembrane protein import system, the location and activity of peptidases, the function of inner-membrane translocases in linking the outer and inner membrane, and the association/regulation of mitochondrial protein import complexes with components of the respiratory chain. Additionally, plant mitochondria share proteins with plastids, i.e. dual-targeted proteins. Also, the developmental and cell-specific nature of mitochondrial biogenesis is an aspect not observed in single-celled systems that is readily apparent in studies in plants. This means that plants provide a valuable model system to study the various regulatory processes associated with protein import and mitochondrial biogenesis.

Overexpression of OsPAP10a, A Root‐Associated Acid Phosphatase, Increased Extracellular Organic Phosphorus Utilization in Rice

Publisher: Wiley

Date: 09-2012

DOI: 10.1111/J.1744-7909.2012.01143.X

Abstract: Phosphorus (P) deficiency is a major limitation for plant growth and development. Among the wide set of responses to cope with low soil P, plants increase their level of intracellular and secreted acid phosphatases (APases), which helps to catalyze inorganic phosphate (Pi) hydrolysis from organo-phosphates. In this study we characterized the rice (Oryza sativa) purple acid phosphatase 10a (OsPAP10a). OsPAP10a belongs to group Ia of purple acid phosphatases (PAPs), and clusters with the principal secreted PAPs in a variety of plant species including Arabidopsis. The transcript abundance of OsPAP10a is specifically induced by Pi deficiency and is controlled by OsPHR2, the central transcription factor controlling Pi homeostasis. In gel activity assays of root and shoot protein extracts, it was revealed that OsPAP10a is a major acid phosphatase isoform induced by Pi starvation. Constitutive overexpression of OsPAP10a results in a significant increase of phosphatase activity in both shoot and root protein extracts. In vivo root 5-bromo-4-chloro-3-indolyl-phosphate (BCIP) assays and activity measurements on external media showed that OsPAP10a is a root-associated APase. Furthermore, overexpression of OsPAP10a significantly improved ATP hydrolysis and utilization compared with wild type plants. These results indicate that OsPAP10a can potentially be used for crop breeding to improve the efficiency of P use.

Zinc-dependent intermembrane space proteins stimulate import of carrier proteins into plant mitochondria

Publisher: Wiley

Date: 06-2002

DOI: 10.1046/J.1365-313X.2002.01316.X

Abstract: Mitochondrial inner membrane carrier proteins are imported into mitochondria from yeast, fungi and mammals by specific machinery, some components of which are distinct from those utilized by other proteins. Import of two different carriers into plant mitochondria showed that one contains a cleavable presequence which was processed during import, while the other imported in a valinomycin-sensitive manner without processing. Mild osmotic shock of mitochondria released intermembrane space (IMS) components and impaired carrier protein import. Adding back the released IMS proteins as a concentrate in the presence of micromolar ZnCl2 stimulated carrier import into IMS-depleted mitochondria, but did not stimulate import of a non-carrier control precursor protein, the alternative oxidase. Anion-exchange separation of IMS components before addition to IMS-depleted mitochondria revealed a correlation between several 9-10 kDa proteins and stimulation of carrier import. MS/MS sequencing of these proteins identified them as plant homologues of the yeast zinc-finger carrier import components Tim9 and Tim10. Stimulation of import was dependent on either Zn2+ or Cd2+ and inhibited by both N-ethylmalamide (NEM) and a alent cation chelator, consistent with a functional requirement for a zinc finger protein. This represents direct functional evidence for a distinct carrier import pathway in plant mitochondria, and provides a tool for determining the potential function of other IMS proteins associated with protein import.

TCP Transcription Factors Link the Regulation of Genes Encoding Mitochondrial Proteins with the Circadian Clock in Arabidopsis thaliana    

Publisher: Oxford University Press (OUP)

Date: 12-2010

DOI: 10.1105/TPC.110.074518

Abstract: Diurnal regulation of transcripts encoding proteins located in mitochondria, plastids, and peroxisomes is important for adaptation of organelle biogenesis and metabolism to meet cellular requirements. We show this regulation is related to diurnal changes in promoter activities and the presence of specific cis-acting regulatory elements in the proximal promoter region [TGGGC(C/T)], previously defined as site II elements, and leads to diurnal changes in organelle protein abundances. These site II elements can act both as activators or repressors of transcription, depending on the night/day period and on the number and arrangement of site II elements in the promoter tested. These elements bind to the TCP family of transcriptions factors in Arabidopsis thaliana, which nearly all display distinct diurnal patterns of cycling transcript abundance. TCP2, TCP3, TCP11, and TCP15 were found to interact with different components of the core circadian clock in both yeast two-hybrid and direct protein–protein interaction assays, and tcp11 and tcp15 mutant plants showed altered transcript profiles for a number of core clock components, including LATE ELONGATED HYPOCOTYL1 and PSEUDO RESPONSE REGULATOR5. Thus, site II elements in the promoter regions of genes encoding mitochondrial, plastid, and peroxisomal proteins provide a direct mechanism for the coordination of expression for genes involved in a variety of organellar functions, including energy metabolism, with the time-of-day specific needs of the organism.

Cloning and characterization of AtNUDT13, a novel mitochondrial Arabidopsis thaliana Nudix hydrolase specific for long‐chain diadenosine polyphosphates

Publisher: Wiley

Date: 30-08-2007

DOI: 10.1111/J.1742-4658.2007.06009.X

Abstract: A cDNA corresponding to the At3g26690 gene, which encodes a Nudix protein (AtNUDT13) with predicted mitochondrial localization, was isolated from an Arabidopsis thaliana library. The 202 amino acid AtNUDT13 polypeptide was overexpressed in Escherichia coli and purified to homogeneity. The preferred substrate for this hydrolase was diadenosine hexaphosphate (Ap(6)A), with K(m) and k(cat)/K(m) values of 0.61 mm and 16.0 x 10(3) m(-)1.s(-1), respectively. Optimal activity was at alkaline pH (8.5) with Mg(2+) (5 mm) as the cofactor. MS analysis revealed that the products of diadenosine hexaphosphate hydrolysis were ADP and adenosine tetraphosphate. Diadenosine pentaphosphate and adenosine tetraphosphate were additional substrates, but diadenosine tetraphosphate and diadenosine triphosphate, adenosine nucleotides, diphosphoinositol polyphosphate and phosphoribosyl pyrophosphate were not hydrolyzed. Chemical crosslinking and size exclusion chromatography demonstrated that the protein exists as a monomer in solution. Subcellular localization studies indicated that the AtNUDT13 protein is targeted to the mitochondria. This is the first description of a plant pyrophosphatase catalyzing the hydrolysis of long-chain diadenosine polyphosphates: molecules with multiple biological activities.

The RCC1 family protein RUG3 is required for splicing of nad2 and complex I biogenesis in mitochondria of Arabidopsis thaliana

Publisher: Wiley

Date: 06-07-2011

DOI: 10.1111/J.1365-313X.2011.04658.X

Evidence for interactions between the mitochondrial import apparatus and respiratory chain complexes via Tim21-like proteins in Arabidopsis

Publisher: Frontiers Media SA

Date: 11-03-2014

DOI: 10.3389/FPLS.2014.00082

In-Depth Temporal Transcriptome Profiling Reveals a Crucial Developmental Switch with Roles for RNA Processing and Organelle Metabolism That Are Essential for Germination in Arabidopsis    

Publisher: Oxford University Press (OUP)

Date: 09-09-2011

DOI: 10.1104/PP.111.183129

Abstract: Germination represents a rapid transition from dormancy to a high level of metabolic activity. In-depth transcriptomic profiling at 10 time points in Arabidopsis (Arabidopsis thaliana), including fresh seed, ripened seed, during stratification, germination, and postgermination per se, revealed specific temporal expression patterns that to our knowledge have not previously been identified. Over 10,000 transcripts were differentially expressed during cold stratification, with subequal numbers up-regulated as down-regulated, revealing an active period in preparing seeds for germination, where transcription and RNA degradation both play important roles in regulating the molecular sequence of events. A previously unidentified transient expression pattern was observed for a group of genes, whereby a significant rise in expression was observed at the end of stratification and significantly lower expression was observed 6 h later. These genes were further defined as germination specific, as they were most highly expressed at this time in germination, in comparison with all developmental tissues in the AtGenExpress data set. Functional analysis of these genes using genetic inactivation revealed that they displayed a significant enrichment for embryo-defective or -arrested phenotype. This group was enriched in genes encoding mitochondrial and nuclear RNA-processing proteins, including more than 45% of all pentatricopeptide domain-containing proteins expressed during germination. The presence of mitochondrial DNA replication factors and RNA-processing functions in this germination-specific subset represents the earliest events in organelle biogenesis, preceding any changes associated with energy metabolism. Green fluorescent protein analysis also confirmed organellar localization for 65 proteins, largely showing germination-specific expression. These results suggest that mitochondrial biogenesis involves a two-step process to produce energetically active organelles: an initial phase at the end of stratification involving mitochondrial DNA synthesis and RNA processing, and a later phase for building the better-known energetic functions. This also suggests that signals with a mitochondrial origin and retrograde signals may be crucial for successful germination.

Evidence for Ancient Origins of Bowman-Birk Inhibitors from Selaginella moellendorffii

Publisher: Oxford University Press (OUP)

Date: 03-2017

DOI: 10.1105/TPC.16.00831

The N-terminal Extension of Plant Mitochondrial Carrier Proteins is Removed by Two-step Processing: The First Cleavage is by the Mitochondrial Processing Peptidase

Publisher: Elsevier BV

Date: 11-2004

DOI: 10.1016/J.JMB.2004.09.045

Abstract: In contrast to yeast, many plants encode mitochondrial inner membrane carrier proteins with an N-terminal extension that is removed upon organelle import. Investigations using yeast and plant mitochondria models and purified general mitochondrial processing peptidase (MPP) indicate that the extension was removed in a two-step process. The first processing was carried out by MPP, while the second processing most probably occurs in the inter-membrane space by an as yet undefined peptidase, putatively a serine protease. Purified MPP from potato processed two carrier proteins to an intermediate size, this processing was sensitive to an MPP inhibitor (1,10-phenanthroline) and further, processing could be inhibited by changing arginine residues to glycine residues at a -3 arginine consensus processing site for MPP. Interestingly, yeast mitochondria only processed plant mitochondrial carrier proteins to the same intermediate size as purified plant MPP, and this intermediary processing did not occur in a temperature sensitive yeast mutant for MPP at the restrictive temperature. Incubation of carrier proteins with intact or lysed plant mitochondria under conditions designed to slow down the rate of import revealed that the MPP processed intermediate could be observed and chased to the mature form. The second processing step is inhibited by Pefabloc, suggesting it is carried out by a serine protease. A model for the processing of the N-terminal extension of plant mitochondrial carrier proteins is presented.

A plant outer mitochondrial membrane protein with high amino acid sequence identity to a chloroplast protein import receptor

Publisher: Wiley

Date: 16-12-2003

DOI: 10.1016/S0014-5793(03)01457-1

Abstract: We have identified a novel protein on the outer membrane of Arabidopsis thaliana mitochondria. This protein displays 67% sequence identity with the 64 kDa translocase of the outer envelope membrane of chloroplasts (Toc). A mitochondrial localisation for this protein was determined by (i). its presence in the proteome of highly purified Arabidopsis mitochondria, (ii). Western blot analysis with antibodies to Toc64 from pea that indicate its presence in Arabidopsis and pea mitochondria, (iii). green fluorescent protein fusion proteins that indicate an exclusive mitochondrial localisation for this protein, and (iv). expression profiles in various tissue types and during development that are more similar to translocase of the outer mitochondrial membrane components than to chloroplastic Toc components. Thus Arabidopsis mitochondria contain a protein with high sequence identity to a plastid protein import receptor.

Protein import into plant mitochondria

Publisher: Springer Science and Business Media LLC

Date: 2001

DOI: 10.1023/A:1006456115140

Abstract: The import pathways of the alternative oxidase and the F(A)d subunit of the ATP synthase from soybean were characterised. The F(A)d precursor does not require extramitochondrial ATP for import and this was shown to be a characteristic of the mature protein. The alternative oxidase and F(A)d precursors were shown to differ in their requirement for a membrane potential. The membrane potential was modified using malonate, a competitive inhibitor to complex II. The alternative oxidase could be imported at higher malonate concentrations compared to the F(A)d. This difference could not be ascribed to the number of positive charges in each presequence as would be predicted from similar studies in fungi.

Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re‐oxygenation

Publisher: Wiley

Date: 02-2017

DOI: 10.1111/TPJ.13418

Abstract: Detailed molecular profiling of Oryza sativa (rice) was carried out to uncover the features that are essential for germination and early seedling growth under anoxic conditions. Temporal analysis of the transcriptome and methylome from germination to young seedlings under aerobic and anaerobic conditions revealed 82% similarity in the transcriptome and no differences in the epigenome up to 24 h. Following germination, significant changes in the transcriptome and DNA methylation were observed between 4-day aerobically and anaerobically grown coleoptiles. A link between the epigenomic state and cell ision versus cell elongation is suggested, as no differences in DNA methylation were observed between 24-h aerobically and anaerobically germinating embryos, when there is little cell ision. After that, epigenetic changes appear to correlate with differences between cell elongation (anaerobic conditions) versus cell ision (aerobic conditions) in the coleoptiles. Re-oxygenation of 3-day anaerobically grown seedlings resulted in rapid transcriptomic changes in DNA methylation in these coleoptiles. Unlike the transcriptome, changes in DNA methylation upon re-oxygenation did not reflect those seen in aerobic coleoptiles, but instead, reverted to a pattern similar to dry seeds. Reversion to the 'dry seed' state of DNA methylation upon re-oxygenation may act to 'reset the clock' for the rapid molecular changes and cell ision that result upon re-oxygenation.

Expression and kinetics of the mitochondrial alternative oxidase in nitrogen-fixing nodules of soybean roots

Publisher: Wiley

Date: 10-1997

DOI: 10.1046/J.1365-3040.1997.D01-25.X

The outer mitochondrial membrane in higher plants

Publisher: Elsevier BV

Date: 04-2013

DOI: 10.1016/J.TPLANTS.2012.12.004

Abstract: The acquisition and integration of intracellular organelles, such as mitochondria and plastids, were important steps in the emergence of complex multicellular life. Although the outer membranes of these organelles have lost many of the functions of their free-living bacterial ancestor, others were acquired during organellogenesis. To date, the biological roles of these proteins have not been systematically characterized. In this review, we discuss the evolutionary origins and functions of outer membrane mitochondrial (OMM) proteins in Arabidopsis thaliana. Our analysis, using phylogenetic inference, indicates that several OMM proteins either acquired novel functional roles or were recruited from other subcellular localizations during evolution in Arabidopsis. These observations suggest the existence of novel communication routes and functions between organelles within plant cells.

Dual Location of the Mitochondrial Preprotein Transporters B14.7 and Tim23-2 in Complex I and the TIM17:23 Complex in Arabidopsis Links Mitochondrial Activity and Biogenesis

Publisher: Oxford University Press (OUP)

Date: 06-2012

DOI: 10.1105/TPC.112.098731

Dynamic changes in the mitochondrial electron transport chain underpinning cold acclimation of leaf respiration

Publisher: Wiley

Date: 09-07-2008

DOI: 10.1111/J.1365-3040.2008.01830.X

Abstract: We examined the effect of short- and long-term changes in temperature on gene expression, protein abundance, and the activity of the alternative oxidase and cytochrome oxidase pathways (AOP and COP, respectively) in Arabidopsis thaliana. The AOP was more sensitive to short-term changes in temperature than the COP, with partitioning to the AOP decreasing significantly below a threshold temperature of 20 degrees C. AOP activity was increased in leaves, which had been shifted to the cold for several days, but this response was transient, with AOP activity subsiding (and COP activity increasing) following the development of leaves in the cold. The transient increase in AOP activity in 10-d cold-shifted leaves was not associated with an increase in alternative oxidase (AOX) protein or AOX1a transcript abundance. By contrast, the amount of uncoupling protein was significantly increased in cold-developed leaves. In conjunction with this, transcript levels of the uncoupling protein-encoding gene UCP1 and the external NAD(P)H dehydrogenase-encoding gene NDB2 exhibited sustained increases following growth in the cold. The data suggest a role for each of these alternative non-phosphorylating bypasses of mitochondrial electron transport at different points in time following exposure to cold, with increased AOP activity being important only in the early stages of cold treatment.

Acquisition, Conservation, and Loss of Dual-Targeted Proteins in Land Plants    

Publisher: Oxford University Press (OUP)

Date: 20-12-2012

DOI: 10.1104/PP.112.210997

Abstract: The dual-targeting ability of a variety of proteins from Physcomitrella patens, rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) was tested to determine when dual targeting arose and to what extent it was conserved in land plants. Overall, the targeting ability of over 80 different proteins from rice and P. patens, representing 42 dual-targeted proteins in Arabidopsis, was tested. We found that dual targeting arose early in land plant evolution, as it was evident in many cases with P. patens proteins that were conserved in rice and Arabidopsis. Furthermore, we found that the acquisition of dual-targeting ability is still occurring, evident in P. patens as well as rice and Arabidopsis. The loss of dual-targeting ability appears to be rare, but does occur. Ascorbate peroxidase represents such an ex le. After gene duplication in rice, in idual genes encode proteins that are targeted to a single organelle. Although we found that dual targeting was generally conserved, the ability to detect dual-targeted proteins differed depending on the cell types used. Furthermore, it appears that small changes in the targeting signal can result in a loss (or gain) of dual-targeting ability. Overall, examination of the targeting signals within this study did not reveal any clear patterns that would predict dual-targeting ability. The acquisition of dual-targeting ability also appears to be coordinated between proteins. Mitochondrial intermembrane space import and assembly protein40, a protein involved in oxidative folding in mitochondria and peroxisomes, provides an ex le where acquisition of dual targeting is accompanied by the dual targeting of substrate proteins.

Sulphur dioxide evokes a large scale reprogramming of the grape berry transcriptome associated with oxidative signalling and biotic defence responses

Publisher: Wiley

Date: 18-07-2011

DOI: 10.1111/J.1365-3040.2011.02379.X

Abstract: The grape and wine industries are heavily reliant on sulphite preservatives. However, the view that sulphites act directly on bacterial and fungal pathogens may be simplistic. Mechanisms of sulphur-enhanced defences are largely unknown many sulphur-rich compounds enhance plant defences and sulphite can also have oxidative consequences via production of H(2)O(2) or sulphitolysis. To investigate the effects of sulphur dioxide (SO(2) ) on fresh table grapes (Vitis vinifera L. 'Crimson Seedless'), transcriptome analysis was carried out on berries treated with SO(2) under commercial conditions for 21 d. We found a broad perturbation of metabolic processes, consistent with a large-scale stress response. Transcripts encoding putative sulphur-metabolizing enzymes indicated that sulphite was directed towards chelation and conjugation, and away from oxidation to sulphate. The results indicated that redox poise was altered dramatically by SO(2) treatment, evidenced by alterations in plastid and mitochondrial alternative electron transfer pathways, up-regulation of fermentation transcripts and numerous glutathione S-transferases, along with a down-regulation of components involved in redox homeostasis. Features of biotic stress were up-regulated, notably signalling via auxin, ethylene and jasmonates. Taken together, this inventory of transcriptional responses is consistent with a long-term cellular response to oxidative stress, similar to the effects of reactive oxygen species.

Alternative oxidases in Arabidopsis: A comparative analysis of differential expression in the gene family provides new insights into function of non-phosphorylating bypasses

Publisher: Elsevier BV

Date: 07-2006

DOI: 10.1016/J.BBABIO.2006.03.009

Abstract: The emergence of Arabidopsis as a model plant provides an opportunity to gain insights into the role of the alternative oxidase that cannot be as readily achieved in other plant species. The analysis of extensive mRNA expression data indicates that all five Aox genes (Aox1a, 1b, 1c, 1d and 2) are expressed, but organ and developmental regulation are evident, suggesting regulatory specialisation of Aox gene members. The stress-induced nature of the alternative pathway in a variety of plants is further supported in Arabidopsis as Aox1a and Aox1d are amongst the most stress responsive genes amongst the hundreds of known genes encoding mitochondrial proteins. Analysis of genes co-expressed with Aoxs from studies of responses to various treatments altering mitochondrial functions and/or from plants with altered Aox levels reveals that: (i) this gene set encodes more functions outside the mitochondrion than functions in mitochondria, (ii) several pathways for induction exist and there is a difference in the magnitude of the induction in each pathway, (iii) the magnitude of induction may depend on the endogenous levels of Aox, and (iv) induction of Aox can be oxidative stress-dependent or -independent depending on the gene member and the tissue analysed. An overall role for Aox in re-programming cellular metabolism in response to the ever changing environment encountered by plants is proposed.

Functional Definition of Outer Membrane Proteins Involved in Preprotein Import into Mitochondria

Publisher: Oxford University Press (OUP)

Date: 11-2007

DOI: 10.1105/TPC.107.050534

Abstract: The role of plant mitochondrial outer membrane proteins in the process of preprotein import was investigated, as some of the principal components characterized in yeast have been shown to be absent or evolutionarily distinct in plants. Three outer membrane proteins of Arabidopsis thaliana mitochondria were studied: TOM20 (translocase of the outer mitochondrial membrane), METAXIN, and mtOM64 (outer mitochondrial membrane protein of 64 kD). A single functional Arabidopsis TOM20 gene is sufficient to produce a normal multisubunit translocase of the outer membrane complex. Simultaneous inactivation of two of the three TOM20 genes changed the rate of import for some precursor proteins, revealing limited isoform subfunctionalization. Inactivation of all three TOM20 genes resulted in severely reduced rates of import for some but not all precursor proteins. The outer membrane protein METAXIN was characterized to play a role in the import of mitochondrial precursor proteins and likely plays a role in the assembly of β-barrel proteins into the outer membrane. An outer mitochondrial membrane protein of 64 kD (mtOM64) with high sequence similarity to a chloroplast import receptor was shown to interact with a variety of precursor proteins. All three proteins have domains exposed to the cytosol and interacted with a variety of precursor proteins, as determined by pull-down and yeast two-hybrid interaction assays. Furthermore, inactivation of one resulted in protein abundance changes in the others, suggesting functional redundancy. Thus, it is proposed that all three components directly interact with precursor proteins to participate in early stages of mitochondrial protein import.

A family of small, cyclic peptides buried in preproalbumin since the Eocene epoch

Publisher: Wiley

Date: 02-2018

DOI: 10.1002/PLD3.42

Cyclin-dependent Kinase E1 (CDKE1) Provides a Cellular Switch in Plants between Growth and Stress Responses

Publisher: Elsevier BV

Date: 02-2013

DOI: 10.1074/JBC.M112.416727

Exploring Multicollinearity Using a Random Matrix Theory Approach

Publisher: Walter de Gruyter GmbH

Date: 14-01-2012

DOI: 10.1515/1544-6115.1668

Abstract: Clustering of gene expression data is often done with the latent aim of dimension reduction, by finding groups of genes that have a common response to potentially unknown stimuli. However, what is poorly understood to date is the behaviour of a low dimensional signal embedded in high dimensions. This paper introduces a multicollinear model which is based on random matrix theory results, and shows potential for the characterisation of a gene cluster's correlation matrix. This model projects a one dimensional signal into many dimensions and is based on the spiked covariance model, but rather characterises the behaviour of the corresponding correlation matrix. The eigenspectrum of the correlation matrix is empirically examined by simulation, under the addition of noise to the original signal. The simulation results are then used to propose a dimension estimation procedure of clusters from data. Moreover, the simulation results warn against considering pairwise correlations in isolation, as the model provides a mechanism whereby a pair of genes with `low' correlation may simply be due to the interaction of high dimension and noise. Instead, collective information about all the variables is given by the eigenspectrum.

Subcomplexes of Ancestral Respiratory Complex I Subunits Rapidly Turn Over in Vivo as Productive Assembly Intermediates in Arabidopsis*

Publisher: Elsevier BV

Date: 02-2013

DOI: 10.1074/JBC.M112.432070

A Mitochondrial LYR Protein Is Required for Complex I Assembly

Publisher: Oxford University Press (OUP)

Date: 10-10-2019

DOI: 10.1104/PP.19.00822

Experimental Analysis of the Rice Mitochondrial Proteome, Its Biogenesis, and Heterogeneity    

Publisher: Oxford University Press (OUP)

Date: 14-11-2008

DOI: 10.1104/PP.108.131300

Abstract: Mitochondria in rice (Oryza sativa) are vital in expanding our understanding of the cellular response to reoxygenation of tissues after anaerobiosis, the crossroads of carbon and nitrogen metabolism, and the role of respiratory energy generation in cytoplasmic male sterility. We have combined density gradient and surface charge purification techniques with proteomics to provide an in-depth proteome of rice shoot mitochondria covering both soluble and integral membrane proteins. Quantitative comparisons of mitochondria purified by density gradients and after further surface charge purification have been used to ensure that the proteins identified copurify with mitochondria and to remove contaminants from the analysis. This rigorous approach to defining a subcellular proteome has yielded 322 nonredundant rice proteins and highlighted contaminants in previously reported rice mitochondrial proteomes. Comparative analysis with the Arabidopsis (Arabidopsis thaliana) mitochondrial proteome reveals conservation of a broad range of known and unknown function proteins in plant mitochondria, with only approximately 20% not having a clear homolog in the Arabidopsis mitochondrial proteome. As in Arabidopsis, only approximately 60% of the rice mitochondrial proteome is predictable using current organelle-targeting prediction tools. Use of the rice protein data set to explore rice transcript data provided insights into rice mitochondrial biogenesis during seed germination, leaf development, and heterogeneity in the expression of nucleus-encoded mitochondrial components in different rice tissues. Highlights include the identification of components involved in thiamine synthesis, evidence for coexpressed and unregulated expression of specific components of protein complexes, a selective anther-enhanced subclass of the decarboxylating segment of the tricarboxylic acid cycle, the differential expression of DNA and RNA replication components, and enhanced expression of specific metabolic components in photosynthetic tissues.

Characterization of a novel β-barrel protein (AtOM47) from the mitochondrial outer membrane ofArabidopsis thaliana

Publisher: Oxford University Press (OUP)

Date: 06-10-2016

DOI: 10.1093/JXB/ERW366

Phosphate starvation regulates cellulose synthesis to modify root growth

Publisher: Cold Spring Harbor Laboratory

Date: 17-09-2023

DOI: 10.1101/2023.09.15.557998

The plant mitochondrial protein import apparatus — The differences make it interesting

Publisher: Elsevier BV

Date: 04-2014

DOI: 10.1016/J.BBAGEN.2013.09.026

Abstract: Mitochondria play essential roles in the life and death of almost all eukaryotic cells, ranging from single-celled to multi-cellular organisms that display tissue and developmental differentiation. As mitochondria only arose once in evolution, much can be learned from studying single celled model systems such as yeast and applying this knowledge to other organisms. However, two billion years of evolution have also resulted in substantial ergence in mitochondrial function between eukaryotic organisms. Here we review our current understanding of the mechanisms of mitochondrial protein import between plants and yeast (Saccharomyces cerevisiae) and identify a high level of conservation for the essential subunits of plant mitochondrial import apparatus. Furthermore, we investigate ex les whereby ergence and acquisition of functions have arisen and highlight the emerging ex les of interactions between the import apparatus and components of the respiratory chain. After more than three decades of research into the components and mechanisms of mitochondrial protein import of plants and yeast, the differences between these systems are examined. Specifically, expansions of the small gene families that encode the mitochondrial protein import apparatus in plants are detailed, and their essential role in seed viability is revealed. These findings point to the essential role of the inner mitochondrial protein translocases in Arabidopsis, establishing their necessity for seed viability and the crucial role of mitochondrial biogenesis during germination. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research.

Mutation in xyloglucan 6-xylosytransferase results in abnormal root hair development in Oryza sativa

Publisher: Oxford University Press (OUP)

Date: 15-05-2014

DOI: 10.1093/JXB/ERU189

Identification of AtNDI1, an Internal Non-Phosphorylating NAD(P)H Dehydrogenase in Arabidopsis Mitochondria

Publisher: Oxford University Press (OUP)

Date: 12-2003

DOI: 10.1104/PP.103.029363

Abstract: Plant mitochondria contain non-phosphorylating NAD(P)H dehydrogenases (DHs) that are not found in animal mitochondria. The physiological function, substrate specificity, and location of enzymes within this family have yet to be conclusively determined. We have linked genome sequence information to protein and biochemical data to identify that At1g07180 (SwissProt Q8GWA1) from the Arabidopsis Genome Initiative database encodes AtNDI1, an internal NAD(P)H DH in Arabidopsis mitochondria. Three lines of evidence are presented: (a) The predicted protein sequence of AtNDI1 has high homology with other designated NAD(P)H DHs from microorganisms, (b) the capacity for matrix NAD(P)H oxidation via the rotenone-insensitive pathway is significantly reduced in the Atndi1 mutant plant line, and (c) the in vitro translation product of AtNDI1 is imported into isolated mitochondria and located on the inside of the inner membrane.

Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis

Publisher: Elsevier BV

Date: 11-2006

DOI: 10.1016/J.TIG.2006.09.002

Abstract: We present a statistical analysis of chromosomal clustering among nuclear genes encoding mitochondrial or chloroplast proteins in Arabidopsis. For both organelles, the clustering was significantly increased above the expectation, but the clustering effect was weak, and most clusters were small and dispersed. Clustered genes showed coexpression but not more than expected, and no substantial synteny was detected in other eukaryotic genomes. We propose that the unexpected clustering results from continuous selection favoring chromosomal proximity of genes acting in the same organelle.

Experimental Analysis of the Arabidopsis Mitochondrial Proteome Highlights Signaling and Regulatory Components, Provides Assessment of Targeting Prediction Programs, and Indicates Plant-Specific Mitoc

Publisher: Oxford University Press (OUP)

Date: 2004

DOI: 10.1105/TPC.016055

Abstract: A novel insight into Arabidopsis mitochondrial function was revealed from a large experimental proteome derived by liquid chromatography–tandem mass spectrometry. Within the experimental set of 416 identified proteins, a significant number of low-abundance proteins involved in DNA synthesis, transcriptional regulation, protein complex assembly, and cellular signaling were discovered. Nearly 20% of the experimentally identified proteins are of unknown function, suggesting a wealth of undiscovered mitochondrial functions in plants. Only approximately half of the experimental set is predicted to be mitochondrial by targeting prediction programs, allowing an assessment of the benefits and limitations of these programs in determining plant mitochondrial proteomes. Maps of putative orthology networks between yeast, human, and Arabidopsis mitochondrial proteomes and the Rickettsia prowazekii proteome provide detailed insights into the ergence of the plant mitochondrial proteome from those of other eukaryotes. These show a clear set of putative cross-species orthologs in the core metabolic functions of mitochondria, whereas considerable ersity exists in many signaling and regulatory functions.

Functional characterization of the rice SPX‐MFS family reveals a key role of OsSPX‐MFS1 in controlling phosphate homeostasis in leaves

Publisher: Wiley

Date: 17-07-2012

DOI: 10.1111/J.1469-8137.2012.04227.X

Abstract: • Proteins possessing the SPX domain are found in several proteins involved in inorganic phosphate (Pi) transport and signalling in yeast and plants. Although the functions of several SPX-domain protein subfamilies have recently been uncovered, the role of the SPX-MFS subfamily is still unclear. • Using quantitative RT-PCR analysis, we studied the regulation of SPX-MFS gene expression by the central regulator, OsPHR2 and Pi starvation. The function of OsSPX-MFS1 in Pi homeostasis was analysed using an OsSPX-MFS1 mutant (mfs1) and osa-miR827 overexpression line (miR827-Oe). Finally, heterologous complementation of a yeast mutant impaired in Pi transporter was used to assess the capacity of OsSPX-MFS1 to transport Pi. • Transcript analyses revealed that members of the SPX-MFS family were mainly expressed in the shoots, with OsSPX-MFS1 and OsSPX-MFS3 being suppressed by Pi deficiency, while OsSPX-MFS2 was induced. Mutation in OsSPX-MFS1 (mfs1) and overexpression of the upstream miR827 (miR827-Oe) plants impaired Pi homeostasis in the leaves. In addition, studies in yeast revealed that OsSPX-MFS1 may be involved in Pi transport. • The results suggest that OsSPX-MFS1 is a key player in maintaining Pi homeostasis in the leaves, potentially acting as a Pi transporter.

Unique components of the plant mitochondrial protein import apparatus

Publisher: Elsevier BV

Date: 02-2013

DOI: 10.1016/J.BBAMCR.2012.02.015

Abstract: The basic mitochondrial protein import apparatus was established in the earliest eukaryotes. Over the subsequent course of evolution and the ergence of the plant, animal and fungal lineages, this basic import apparatus has been modified and expanded in order to meet the specific needs of protein import in each kingdom. In the plant kingdom, the arrival of the plastid complicated the process of protein trafficking and is thought to have given rise to the evolution of a number of unique components that allow specific and efficient targeting of mitochondrial proteins from their site of synthesis in the cytosol, to their final location in the organelle. This includes the evolution of two unique outer membrane import receptors, plant Translocase of outer membrane 20 kDa subunit (TOM20) and Outer membrane protein of 64 kDa (OM64), the loss of a receptor domain from an ancestral import component, Translocase of outer membrane 22 kDa subunit (TOM22), evolution of unique features in the disulfide relay system of the inter membrane space, and the addition of an extra membrane spanning domain to another ancestral component of the inner membrane, Translocase of inner membrane 17 kDa subunit (TIM17). Notably, many of these components are encoded by multi-gene families and exhibit differential sub-cellular localisation and functional specialisation. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.

Anterograde and Retrograde Regulation of Nuclear Genes Encoding Mitochondrial Proteins during Growth, Development, and Stress

Publisher: Elsevier BV

Date: 07-2014

DOI: 10.1093/MP/SSU037

Abstract: Mitochondrial biogenesis and function in plants require the expression of over 1000 nuclear genes encoding mitochondrial proteins (NGEMPs). The expression of these genes is regulated by tissue-specific, developmental, internal, and external stimuli that result in a dynamic organelle involved in both metabolic and a variety of signaling processes. Although the metabolic and biosynthetic machinery of mitochondria is relatively well understood, the factors that regulate these processes and the various signaling pathways involved are only beginning to be identified at a molecular level. The molecular components of anterograde (nuclear to mitochondrial) and retrograde (mitochondrial to nuclear) signaling pathways that regulate the expression of NGEMPs interact with chloroplast-, growth-, and stress-signaling pathways in the cell at a variety of levels, with common components involved in transmission and execution of these signals. This positions mitochondria as important hubs for signaling in the cell, not only in direct signaling of mitochondrial function per se, but also in sensing and/or integrating a variety of other internal and external signals. This integrates and optimizes growth with energy metabolism and stress responses, which is required in both photosynthetic and non-photosynthetic cells.

Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

Publisher: eLife Sciences Publications, Ltd

Date: 21-07-2015

DOI: 10.7554/ELIFE.09343

Abstract: Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, and could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.

Characterization of the Import Pathway of the FAd Subunit of Mitochondrial ATP Synthase into Isolated Plant Mitochondria

Publisher: Elsevier BV

Date: 11-1996

DOI: 10.1006/ABBI.1996.0517

Abstract: The synthetic precursor of the F(A)d subunit of mitochondrial ATP synthase was imported into isolated soybean cotyledon mitochondria. Import of the F(A)d precursor was accompanied by processing to a lower molecular weight mature form. The F(A)d precursor displayed the following import characteristics not seen before with plant mitochondria: efficient import in the absence of external ATP and import of wheat germ-translated precursor. Pretreatment of the F(A)d precursor with NEM did not inhibit import. Taken together with the lack of a requirement for external ATP, this indicates that this precursor does not require extramitochondrial ATP-dependent factors for import. Binding studies indicated that the F(A)d precursor bound to a proteinaceous component of the mitochondrial outer membrane. Inhibitor studies indicated that processing was most likely via the general mitochondrial processing peptidase. The results suggest that import of this subunit occurs via a pathway different from the general import pathway described for the majority of precursor proteins.

Protein import into mitochondria: origins and functions today (Review)

Publisher: Informa UK Limited

Date: 2005

DOI: 10.1080/09687860500041247

Abstract: Mitochondria are organelles derived from alpha-proteobacteria over the course of one to two billion years. Mitochondria from the major eukaryotic lineages display some variation in functions and coding capacity but sequence analysis demonstrates them to be derived from a single common ancestral endosymbiont. The loss of assorted functions, the transfer of genes to the nucleus, and the acquisition of various 'eukaryotic' proteins have resulted in an organelle that contains approximately 1000 different proteins, with most of these proteins imported into the organelle across one or two membranes. A single translocase in the outer membrane and two translocases in the inner membrane mediate protein import. Comparative sequence analysis and functional complementation experiments suggest some components of the import pathways to be directly derived from the eubacterial endosymbiont's own proteins, and some to have arisen 'de novo' at the earliest stages of 'mitochondrification' of the endosymbiont. A third class of components appears lineage-specific, suggesting they were incorporated into the process of protein import long after mitochondria was established as an organelle and after the ergence of the various eukaryotic lineages. Protein sorting pathways inherited from the endosymbiont have been co-opted and play roles in intraorganelle protein sorting after import. The import apparatus of animals and fungi show significant similarity to one another, but vary considerably to the plant apparatus. Increasing complexity in the eukaryotic lineage, i.e., from single celled to multi-cellular life forms, has been accompanied by an expansion in genes encoding each component, resulting in small gene families encoding many components. The functional differences in these gene families remain to be elucidated, but point to a mosaic import apparatus that can be regulated by a variety of signals.

The Transcription Factor MYB29 Is a Regulator of ALTERNATIVE OXIDASE1a

Publisher: Oxford University Press (OUP)

Date: 06-02-2017

DOI: 10.1104/PP.16.01494

A Transcriptomic Signature of Mouse Liver Progenitor Cells

Publisher: Hindawi Limited

Date: 2016

DOI: 10.1155/2016/5702873

Abstract: Liver progenitor cells (LPCs) can proliferate extensively, are able to differentiate into hepatocytes and cholangiocytes, and contribute to liver regeneration. The presence of LPCs, however, often accompanies liver disease and hepatocellular carcinoma (HCC), indicating that they may be a cancer stem cell. Understanding LPC biology and establishing a sensitive, rapid, and reliable method to detect their presence in the liver will assist diagnosis and facilitate monitoring of treatment outcomes in patients with liver pathologies. A transcriptomic meta-analysis of over 400 microarrays was undertaken to compare LPC lines against datasets of muscle and embryonic stem cell lines, embryonic and developed liver (DL), and HCC. Three gene clusters distinguishing LPCs from other liver cell types were identified. Pathways overrepresented in these clusters denote the proliferative nature of LPCs and their association with HCC. Our analysis also revealed 26 novel markers, LPC markers, including Mcm2 and Ltbp3 , and eight known LPC markers, including M2pk and Ncam . These markers specified the presence of LPCs in pathological liver tissue by qPCR and correlated with LPC abundance determined using immunohistochemistry. These results showcase the value of global transcript profiling to identify pathways and markers that may be used to detect LPCs in injured or diseased liver.

Functional and composition differences between mitochondrial complex II in Arabidopsis and rice are correlated with the complex genetic history of the enzyme

Publisher: Springer Science and Business Media LLC

Date: 19-11-2009

DOI: 10.1007/S11103-009-9573-Z

Abstract: Complex II plays a central role in mitochondrial metabolism as a component of both the electron transport chain and the tricarboxylic acid cycle. However, the composition and function of the plant enzyme has been elusive and differs from the well-characterised enzymes in mammals and bacteria. Herewith, we demonstrate that mitochondrial Complex II from Arabidopsis and rice differ significantly in several aspects: (1) Stability-Rice complex II in contrast to Arabidopsis is not stable when resolved by native electrophoresis and activity staining. (2) Composition-Arabidopsis complex II contains 8 subunits, only 7 of which have homologs in the rice genome. SDH 1 and 2 subunits display high levels of amino acid identity between two species, while the remainder of the subunits are not well conserved at a sequence level, indicating significant ergence. (3) Gene expression-the pairs of orthologous SDH1 and SDH2 subunits were universally expressed in both Arabidopsis and rice. The very ergent genes for SDH3 and SDH4 were co-expressed in both species, consistent with their functional co-ordination to form the membrane anchor. The plant-specific SDH5, 6 and 7 subunits with unknown functions appeared to be differentially expressed in both species. (4) Biochemical regulation -succinate-dependent O(2) consumption and SDH activity of isolated Arabidopsis mitochondria were substantially stimulated by ATP, but a much more minor effect of ATP was observed for the rice enzyme. The ATP activation of succinate-dependent reduction of DCPIP in frozen-thawed and digitonin-solubilised mitochondrial s les, and with or without the uncoupler CCCP, indicate that the differential ATP effect on SDH is not via the protonmotive force but likely due to an allosteric effect on the plant SDH enzyme itself, in contrast to the enzyme in other organisms.

Interaction between hormonal and mitochondrial signalling during growth, development and in plant defence responses

Publisher: Wiley

Date: 20-03-2016

DOI: 10.1111/PCE.12712

Abstract: Mitochondria play a central role in plant metabolism as they are a major source of ATP through synthesis by the oxidative phosphorylation pathway and harbour key metabolic reactions such as the TCA cycle. The energy and building blocks produced by mitochondria are essential to drive plant growth and development as well as to provide fuel for responses to abiotic and biotic stresses. The majority of mitochondrial proteins are encoded in the nuclear genome and have to be imported into the organelle. For the regulation of the corresponding genes intricate signalling pathways exist to adjust their expression. Signals directly regulate nuclear gene expression (anterograde signalling) to adjust the protein composition of the mitochondria to the needs of the cell. In parallel, mitochondria communicate back their functional status to the nucleus (retrograde signalling) to prompt transcriptional regulation of responsive genes via largely unknown signalling mechanisms. Plant hormones are the major signalling components regulating all layers of plant development and cellular functions. Increasing evidence is now becoming available that plant hormones are also part of signalling networks controlling mitochondrial function and their biogenesis. This review summarizes recent advances in understanding the interaction of mitochondrial and hormonal signalling pathways.

Pentatricopeptide repeat domain protein 3 associates with the mitochondrial small ribosomal subunit and regulates translation

Publisher: Wiley

Date: 08-05-2009

DOI: 10.1016/J.FEBSLET.2009.04.048

Abstract: The basic components and mechanisms of mitochondrial transcription in mammals have been described, however, the components involved in mRNA processing, translation and stability remain largely unknown. In plants, pentatricopeptide domain RNA-binding proteins regulate the stability, expression and translation of mitochondrial transcripts. Here, we investigated the role of an uncharacterized mammalian pentatricopeptide domain protein, pentatricopeptide repeat domain protein 3 (PTCD3), and showed that it is a mitochondrial protein that associates with the small subunit of mitochondrial ribosomes. PTCD3 knockdown and over expression did not affect mitochondrial mRNA levels, suggesting that PTCD3 is not involved in RNA processing and stability. However, lowering PTCD3 in 143B osteosarcoma cells decreased mitochondrial protein synthesis, mitochondrial respiration and the activity of Complexes III and IV, suggesting that PTCD3 has a role in mitochondrial translation.

The Cytoskeleton and the Peroxisomal-Targeted SNOWY COTYLEDON3 Protein Are Required for Chloroplast Development in Arabidopsis

Publisher: Oxford University Press (OUP)

Date: 10-2010

DOI: 10.1105/TPC.110.074781

Abstract: Here, we describe the snowy cotyledon3 (sco3-1) mutation, which impairs chloroplast and etioplast development in Arabidopsis thaliana seedlings. SCO3 is a member of a largely uncharacterized protein family unique to the plant kingdom. The sco3-1 mutation alters chloroplast morphology and development, reduces chlorophyll accumulation, impairs thylakoid formation and photosynthesis in seedlings, and results in photoinhibition under extreme CO2 concentrations in mature leaves. There are no readily apparent changes to chloroplast biology, such as transcription or assembly that explain the disruption to chloroplast biogenesis. Indeed, SCO3 is actually targeted to another organelle, specifically to the periphery of peroxisomes. However, impaired chloroplast development cannot be attributed to perturbed peroxisomal metabolic processes involving germination, fatty acid β-oxidation or photorespiration, though there are so far undescribed changes in low and high CO2 sensitivity in seedlings and young true leaves. Many of the chloroplasts are bilobed, and some have persistent membranous extensions that encircle other cellular components. Significantly, there are changes to the cytoskeleton in sco3-1, and microtubule inhibitors have similar effects on chloroplast biogenesis as sco3-1 does. The localization of SCO3 to the periphery of the peroxisomes was shown to be dependent on a functional microtubule cytoskeleton. Therefore, the microtubule and peroxisome-associated SCO3 protein is required for chloroplast development, and sco3-1, along with microtubule inhibitors, demonstrates an unexpected role for the cytoskeleton and peroxisomes in chloroplast biogenesis.

Induction of alternative oxidase synthesis by herbicides inhibiting branched‐chain amino acid synthesis

Publisher: Wiley

Date: 04-1997

DOI: 10.1046/J.1365-313X.1997.11040649.X

Phosphate starvation regulates cellulose synthesis to modify root growth

Publisher: Oxford University Press (OUP)

Date: 12-10-2023

DOI: 10.1093/PLPHYS/KIAD543

A Functional Antagonistic Relationship between Auxin and Mitochondrial Retrograde Signaling Regulates Alternative Oxidase1a Expression in Arabidopsis    

Publisher: Oxford University Press (OUP)

Date: 12-05-2014

DOI: 10.1104/PP.114.237495

Abstract: The perception and integration of stress stimuli with that of mitochondrion function are important during periods of perturbed cellular homeostasis. In a continuous effort to delineate these mitochondrial/stress-interacting networks, forward genetic screens using the mitochondrial stress response marker alternative oxidase 1a (AOX1a) provide a useful molecular tool to identify and characterize regulators of mitochondrial stress signaling (referred to as regulators of alternative oxidase 1a [RAOs] components). In this study, we reveal that mutations in genes coding for proteins associated with auxin transport and distribution resulted in a greater induction of AOX1a in terms of magnitude and longevity. Three independent mutants for polarized auxin transport, rao3/big, rao4 in-formed1, and rao5/multidrug-resistance1/abcb19, as well as the Myb transcription factor rao6/asymmetric leaves1 (that displays altered auxin patterns) were identified and resulted in an acute sensitivity toward mitochondrial dysfunction. Induction of the AOX1a reporter system could be inhibited by the application of auxin analogs or reciprocally potentiated by blocking auxin transport. Promoter activation studies with AOX1a::GUS and DR5::GUS lines further confirmed a clear antagonistic relationship between the spatial distribution of mitochondrial stress and auxin response kinetics, respectively. Genome-wide transcriptome analyses revealed that mitochondrial stress stimuli, such as antimycin A, caused a transient suppression of auxin signaling and conversely, that auxin treatment repressed a part of the response to antimycin A treatment, including AOX1a induction. We conclude that mitochondrial stress signaling and auxin signaling are reciprocally regulated, balancing growth and stress response(s).

Defining Core Metabolic and Transcriptomic Responses to Oxygen Availability in Rice Embryos and Young Seedlings    

Publisher: Oxford University Press (OUP)

Date: 07-2009

DOI: 10.1104/PP.109.142026

Abstract: Analysis reveals that there is limited overlap in the sets of transcripts that show significant changes in abundance during anaerobiosis in different plant species. This may be due to the fact that a combination of primary effects, changes due to the presence or absence of oxygen, and secondary effects, responses to primary changes or tissue and developmental responses, are measured together and not differentiated from each other. In order to dissect out these responses, the effect of the presence or absence of oxygen was investigated using three different experimental designs using rice (Oryza sativa) as a model system. A total of 110 metabolites and 9,596 transcripts were found to change significantly in response to oxygen availability in at least one experiment. However, only one-quarter of these showed complementary responses to oxygen in all three experiments, allowing the core response to oxygen availability to be defined. A total of 10 metabolites and 1,136 genes could be defined as aerobic responders (up-regulated in the presence of oxygen and down-regulated in its absence), and 13 metabolites and 730 genes could be defined as anaerobic responders (up-regulated in the absence of oxygen and down-regulated in its presence). Defining core sets of transcripts that were sensitive to oxygen provided insights into alterations in metabolism, specifically carbohydrate and lipid metabolism and the putative regulatory mechanisms that allow rice to grow under anaerobic conditions. Transcript abundance of a specific set of transcription factors was sensitive to oxygen availability during all of the different experiments conducted, putatively identifying primary regulators of gene expression under anaerobic conditions. Combined with the possibility of selective transcript degradation, these transcriptional processes are involved in the core response of rice to anaerobiosis.

Molecular interaction between PHO2 and GIGANTEA reveals a new crosstalk between flowering time and phosphate homeostasis in Oryza sativa

Publisher: Wiley

Date: 19-05-2017

DOI: 10.1111/PCE.12945

Abstract: Plants are often confronted to nutrient limiting conditions, such as inorganic phosphate (Pi) deficiency, resulting in a reduction in growth and yield. PHO2, encoding a ubiquitin-conjugating E2 enzyme, is a central component of the Pi-starvation response signalling pathway. A yeast-two-hybrid screen using Oryza sativa (rice) PHO2 as bait, revealed an interaction between OsPHO2 and OsGIGANTEA, a key regulator of flowering time, which was confirmed using bimolecular fluorescence complementation (BiFC). Characterization of rice Osgi and Ospho2 mutants revealed that they displayed several similar phenotypic features supporting a physiological role for this interaction. Reduced growth, leaf tip necrosis, delayed flowering and over-accumulation of Pi in leaves compared to wild type were shared features of Osgi and Ospho2 plants. Pi analysis of in idual leaves demonstrated that Osgi, similar to Ospho2 mutants, were impaired in Pi remobilization from old to young leaves, albeit to a lesser extent. Transcriptome analyses revealed more than 55% of the genes differentially expressed in Osgi plants overlapped with the set of differentially expressed genes in Ospho2 plants. The interaction between OsPHO2 and OsGI links high-level regulators of Pi homeostasis and development in rice.

An in silico analysis of the mitochondrial protein import apparatus of plants

Publisher: Springer Science and Business Media LLC

Date: 16-11-2010

DOI: 10.1186/1471-2229-10-249

Abstract: An in silico analysis of the mitochondrial protein import apparatus from a variety of species including Chlamydomonas reinhardtii , Chlorella variabilis, Ectocarpus siliculosus , Cyanidioschyzon merolae , Physcomitrella patens , Selaginella moellendorffii, Picea glauca , Oryza sativa and Arabidopsis thaliana was undertaken to determine if components differed within and between plant and non-plant species. The channel forming subunits of the outer membrane components Tom40 and Sam50 are conserved between plant groups and other eukaryotes. In contrast, the receptor component(s) in green plants, particularly Tom20, ( C. reinhardtii, C. variabilis, P. patens, S. moellendorffii, P. glauca, O. sativa and A. thaliana ) are specific to this lineage. Red algae contain a Tom22 receptor that is orthologous to yeast Tom22. Furthermore, plant mitochondrial receptors display differences between various plant lineages. These are evidenced by distinctive motifs in all plant Metaxins, which are absent in red algae, and the presence of the outer membrane receptor OM64 in Angiosperms (rice and Arabidopsis), but not in lycophytes ( S. moellendorffii ) and gymnosperms ( P. glauca ). Furthermore, although the intermembrane space receptor Mia40 is conserved across a wide phylogenetic range, its function differs between lineages. In all plant lineages, Tim17 contains a C-terminal extension, which may act as a receptor component for the import of nucleic acids into plant mitochondria. It is proposed that the observed functional ergences are due to the selective pressure to sort proteins between mitochondria and chloroplasts, resulting in differences in protein receptor components between plant groups and other organisms. Additionally, ersity of receptor components is observed within the plant kingdom. Even when receptor components are orthologous across plant and non-plant species, it appears that the functions of these have expanded or erged in a lineage specific manner.

Alternative Oxidase Isoforms Are Differentially Activated by Tricarboxylic Acid Cycle Intermediates

Publisher: Oxford University Press (OUP)

Date: 05-12-2017

DOI: 10.1104/PP.17.01331

RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin

Publisher: Springer Science and Business Media LLC

Date: 25-03-2014

DOI: 10.1186/1471-2164-15-230

SPX4 Acts on PHR1-Dependent and -Independent Regulation of Shoot Phosphorus Status in Arabidopsis

Publisher: Oxford University Press (OUP)

Date: 07-2019

DOI: 10.1104/PP.18.00594

Multiple Lines of Evidence Localize Signaling, Morphology, and Lipid Biosynthesis Machinery to the Mitochondrial Outer Membrane of Arabidopsis  

Publisher: Oxford University Press (OUP)

Date: 06-09-2011

DOI: 10.1104/PP.111.183160

Abstract: The composition of the mitochondrial outer membrane is notoriously difficult to deduce by orthology to other organisms, and biochemical enrichments are inevitably contaminated with the closely associated inner mitochondrial membrane and endoplasmic reticulum. In order to identify novel proteins of the outer mitochondrial membrane in Arabidopsis (Arabidopsis thaliana), we integrated a quantitative mass spectrometry analysis of highly enriched and prefractionated s les with a number of confirmatory biochemical and cell biology approaches. This approach identified 42 proteins, 27 of which were novel, more than doubling the number of confirmed outer membrane proteins in plant mitochondria and suggesting novel functions for the plant outer mitochondrial membrane. The novel components identified included proteins that affected mitochondrial morphology and/or segregation, a protein that suggests the presence of bacterial type lipid A in the outer membrane, highly stress-inducible proteins, as well as proteins necessary for embryo development and several of unknown function. Additionally, proteins previously inferred via orthology to be present in other compartments, such as an NADH:cytochrome B5 reductase required for hydroxyl fatty acid accumulation in developing seeds, were shown to be located in the outer membrane. These results also revealed novel proteins, which may have evolved to fulfill plant-specific requirements of the mitochondrial outer membrane, and provide a basis for the future functional characterization of these proteins in the context of mitochondrial intracellular interaction.

Recent surprises in protein targeting to mitochondria and plastids

Publisher: Elsevier BV

Date: 12-2006

DOI: 10.1016/J.PBI.2006.09.002

Abstract: The functions of mitochondria and chloroplasts rely on thousands of proteins, mostly imported from the cytosol through specialized import channels. Neither the detailed import mechanisms nor the identities of all targeted proteins are known. Recent surprises include unexpected results concerning import receptors, unexpectedly frequent dual-targeting of proteins, and the discovery of novel routes of protein trafficking. Such findings make it more difficult to predict which proteins really are targeted to organelles. By combining experimental and bioinformatics data, we estimate the size of the mitochondrial and plastid proteomes to be approximately 2000 and 2700 proteins, respectively. Advances in cell and organelle fractionation coupled with modern proteomics techniques are probably the best route to understanding organellar protein composition.

Mitochondrial biogenesis in plants during seed germination

Publisher: Elsevier BV

Date: 11-2014

DOI: 10.1016/J.MITO.2014.04.002

Abstract: Mitochondria occupy a central role in the eukaryotic cell. In addition to being major sources of cellular energy, mitochondria are also involved in a erse range of functions including signalling, the synthesis of many essential organic compounds and a role in programmed cell death. The active proliferation and differentiation of mitochondria is termed mitochondrial biogenesis and necessitates the coordinated communication of mitochondrial status within an integrated cellular network. Two models of mitochondrial biogenesis have been defined previously, the growth and ision model and the maturation model. The former describes the growth and ision of pre-existing mature organelles through a form of binary fission, while the latter describes the propagation of mitochondria from structurally and biochemically simple promitochondrial structures that upon appropriate stimuli, mature into fully functional mitochondria. In the last decade, a number of studies have utilised seed germination in plants as a platform for the examination of the processes occurring during mitochondrial biogenesis. These studies have revealed many new aspects of the tightly regulated procession of events that define mitochondrial biogenesis during this period of rapid development. A model for mitochondrial biogenesis that supports the maturation of mitochondria from promitochondrial structures has emerged, where mitochondrial signalling plays a crucial role in the early steps of seed germination.

Isolation and Respiratory Measurements of Mitochondria from <em>Arabidopsis thaliana</em>

Publisher: MyJove Corporation

Date: 05-01-2018

DOI: 10.3791/56627

AtWRKY40 and AtWRKY63 Modulate the Expression of Stress-Responsive Nuclear Genes Encoding Mitochondrial and Chloroplast Proteins    

Publisher: Oxford University Press (OUP)

Date: 18-03-2013

DOI: 10.1104/PP.113.215996

Abstract: The expression of a variety of nuclear genes encoding mitochondrial proteins is known to adapt to changes in environmental conditions and retrograde signaling. The presence of putative WRKY transcription factor binding sites (W-boxes) in the promoters of many of these genes prompted a screen of 72 annotated WRKY factors in the Arabidopsis (Arabidopsis thaliana) genome for regulators of transcripts encoding mitochondrial proteins. A large-scale yeast one-hybrid screen was used to identify WRKY factors that bind the promoters of marker genes (Alternative oxidase1a, NADH dehydrogenaseB2, and the AAA ATPase Ubiquinol-cytochrome c reductase synthesis1), and interactions were confirmed using electromobility shift assays. Transgenic overexpression and knockout lines for 12 binding WRKY factors were generated and tested for altered expression of the marker genes during normal and stress conditions. AtWRKY40 was found to be a repressor of antimycin A-induced mitochondrial retrograde expression and high-light-induced signaling, while AtWRKY63 was identified as an activator. Genome-wide expression analysis following high-light stress in transgenic lines with perturbed AtWRKY40 and AtWRKY63 function revealed that these factors are involved in regulating stress-responsive genes encoding mitochondrial and chloroplast proteins but have little effect on more constitutively expressed genes encoding organellar proteins. Furthermore, it appears that AtWRKY40 and AtWRKY63 are particularly involved in regulating the expression of genes responding commonly to both mitochondrial and chloroplast dysfunction but not of genes responding to either mitochondrial or chloroplast perturbation. In conclusion, this study establishes the role of WRKY transcription factors in the coordination of stress-responsive genes encoding mitochondrial and chloroplast proteins.

The mitochondrial LYR protein SDHAF1 is required for succinate dehydrogenase activity in Arabidopsis

Publisher: Wiley

Date: 26-02-2022

DOI: 10.1111/TPJ.15684

Abstract: Succinate dehydrogenase (SDH, complex II), which plays an essential role in mitochondrial respiration and tricarboxylic acid metabolism, requires the assembly of eight nuclear‐encoded subunits and the insertion of various cofactors. Here, we report on the characterization of an Arabidopsis thaliana leucine‐tyrosine‐arginine (LYR) protein family member SDHAF1, (At2g39725) is a factor required for SDH activity. SDHAF1 is located in mitochondria and can fully complement the yeast SDHAF1 deletion strain. Knockdown of SDHAF1 using RNA interference resulted in a decrease in seedling hypocotyl elongation and reduced SDH activity. Proteomic analyses revealed a decreased abundance of various SDH subunits and assembly factors. Protein interaction assays revealed that SDHAF1 can interact exclusively with the Fe‐S cluster‐containing subunit SDH2 and HSCB, a cochaperone involved in Fe‐S cluster complex recruitment. Therefore, we propose that in Arabidopsis, SDHAF1 plays a role in the biogenesis of SDH2 to form the functional complex II, which is essential for mitochondrial respiration and metabolism.

Arabidopsis DGD1 SUPPRESSOR1 Is a Subunit of the Mitochondrial Contact Site and Cristae Organizing System and Affects Mitochondrial Biogenesis

Publisher: Oxford University Press (OUP)

Date: 22-05-2019

DOI: 10.1105/TPC.18.00885

Abstract: Mitochondrial and plastid biogenesis requires the biosynthesis and assembly of proteins, nucleic acids, and lipids. In Arabidopsis (Arabidopsis thaliana), the mitochondrial outer membrane protein DGD1 SUPPRESSOR1 (DGS1) is part of a large multi-subunit protein complex that contains the mitochondrial contact site and cristae organizing system 60-kD subunit, the translocase of outer mitochondrial membrane 40-kD subunit (TOM40), the TOM20s, and the Rieske FeS protein. A point mutation in DGS1, dgs1-1, altered the stability and protease accessibility of this complex. This altered mitochondrial biogenesis, mitochondrial size, lipid content and composition, protein import, and respiratory capacity. Whole plant physiology was affected in the dgs1-1 mutant as evidenced by tolerance to imposed drought stress and altered transcriptional responses of markers of mitochondrial retrograde signaling. Putative orthologs of Arabidopsis DGS1 are conserved in eukaryotes, including the Nuclear Control of ATP Synthase2 (NCA2) protein in yeast (Saccharomyces cerevisiae), but lost in Metazoa. The genes encoding DGS1 and NCA2 are part of a similar coexpression network including genes encoding proteins involved in mitochondrial fission, morphology, and lipid homeostasis. Thus, DGS1 links mitochondrial protein and lipid import with cellular lipid homeostasis and whole plant stress responses.

Regulation of Carotenoid Composition and Shoot Branching inArabidopsisby a Chromatin Modifying Histone Methyltransferase, SDG8

Publisher: Oxford University Press (OUP)

Date: 2009

DOI: 10.1105/TPC.108.063131

Abstract: Carotenoid pigments are critical for plant survival, and carotenoid composition is tuned to the developmental stage, tissue, and to environmental stimuli. We report the cloning of the CAROTENOID CHLOROPLAST REGULATORY1 (CCR1) gene. The ccr1 mutant has increased shoot branching and altered carotenoid composition, namely, reduced lutein in leaves and accumulation of cis-carotenes in dark-grown seedlings. The CCR1 gene was previously isolated as EARLY FLOWERING IN SHORT DAYS and encodes a histone methyltransferase (SET DOMAIN GROUP 8) that methylates histone H3 on Lys 4 and/or 36 (H3K4 and H3K36). ccr1 plants show reduced trimethyl-H3K4 and increased dimethyl-H3K4 surrounding the CAROTENOID ISOMERASE (CRTISO) translation start site, which correlates with low levels of CRTISO mRNA. Microarrays of ccr1 revealed the downregulation of 85 genes, including CRTISO and genes associated with signaling and development, and upregulation of just 28 genes. The reduction in CRTISO transcript abundance explains the altered carotenoid profile. The changes in shoot branching are additive with more axillary branching mutants, but the altered carotenoid profile may partially affect shoot branching, potentially by perturbed biosynthesis of the carotenoid substrates of strigolactones. These results are consistent with SDG8 regulating shoot meristem activity and carotenoid biosynthesis by modifying the chromatin surrounding key genes, including CRTISO. Thus, the level of lutein, the most abundant carotenoid in higher plants that is critical for photosynthesis and photoprotection, appears to be regulated by a chromatin modifying enzyme in Arabidopsis thaliana.

Tom22', an 8-kDa trans-Site Receptor in Plants and Protozoans, Is a Conserved Feature of the TOM Complex That Appeared Early in the Evolution of Eukaryotes

Publisher: Oxford University Press (OUP)

Date: 12-02-2004

DOI: 10.1093/MOLBEV/MSH166

Cloning of ndhK from soybean chloroplasts using antibodies raised to mitochondrial complex I

Publisher: Springer Science and Business Media LLC

Date: 12-1992

DOI: 10.1007/BF00027160

Abstract: The cardiovascular effects of adimolol, a new, potent, long acting beta-adrenoceptor blocking drug were investigated in three studies. In the first study blood pressure and heart rate were measured in five male volunteers before and at 2, 4, 6, 8, 24, 32, 48, 72 and 96 h after single oral doses of adimolol. All doses of adimolol reduced supine, standing and exercise heart rates in a dose dependent manner. The maximum effect ranged from 18% following 25 mg to 29% following 600 mg and all doses showed an effect at 96 h (range 3.5-17.2%). In the second study the effects of adimolol, 25 and 400 mg, labetalol, 200 and 800 mg, propranolol 40 mg and placebo were compared on supine and standing heart rate and blood pressure and on exercise heart rate before and at 2, 4, 6 and 8 h after single oral doses. The exercise heart rate was significantly reduced at all times following adimolol 25 and 400 mg, labetalol 800 mg and propranolol 40 mg. At 2 h all the drugs significantly reduced standing systolic blood pressure. In the third study, 4 h after single oral doses of adimolol 400 mg, labetalol 400 mg and propranolol 40 mg six subjects received serial 4 min infusions of phenylephrine. The blood pressure was measured after each infusion. Labetalol 400 mg significantly shifted the blood pressure dose-response curve to the right. There was no difference between propranolol 40 mg and adimolol 400 mg. These studies show that adimolol is a potent, long acting beta-adrenoceptor blocking drug without evidence of alpha-adrenoceptor blockade in man.

The C-terminal Region of TIM17 Links the Outer and Inner Mitochondrial Membranes in Arabidopsis and Is Essential for Protein Import

Publisher: Elsevier BV

Date: 04-2005

DOI: 10.1074/JBC.M413299200

Bioenergetic differences selectively sensitize tumorigenic liver progenitor cells to a new gold(I) compound

Publisher: Oxford University Press (OUP)

Date: 15-04-2008

DOI: 10.1093/CARCIN/BGN093

Abstract: A hallmark of cancer cells is their ability to evade apoptosis and mitochondria play a critical role in this process. Delineating mitochondrial differences between normal and cancer cells has proven challenging due to the lack of matched cell lines. Here, we compare two matched liver progenitor cell (LPC) lines, one non-tumorigenic [p53-immortalized liver (PIL) 4] and the other tumorigenic (PIL2). Analysis of these cell lines and a p53 wild-type non-tumorigenic cell line [bipotential murine oval liver (BMOL)] revealed an increase in expression of genes encoding the antiapoptotic proteins cellular inhibitor of apoptosis protein (cIAP) 1 and yes associate protein in the PIL2 cells, which resulted in an increase in the protein encoded by these genes. PIL2 cells have higher mitochondrial membrane potential (Deltapsi(m)) compared with PIL4 and BMOL and had greater levels of reactive oxygen species, despite the fact that the mitochondrial antioxidant enzyme, manganese superoxide disumutase, was elevated at transcript and protein levels. Taken together, these results may account for the observed resistance of PIL2 cells to apoptotic stimuli compared with PIL4. We tested a new gold compound to show that hyperpolarized Deltapsi(m) led to its increased accumulation in mitochondria of PIL2 cells. This compound selectively induces apoptosis in PIL2 cells but not in PIL4 or BMOL. The gold compound depolarized the Deltapsi(m), depleted the adenosine triphosphate pool and activated caspase-3 and caspase-9, suggesting that apoptosis was mediated via mitochondria. This investigation shows that the non-tumorigenic and tumorigenic LPCs are useful models to delineate the role of mitochondrial dysfunction in tumorigenesis and for the future development of mitochondria-targeted chemotherapeutics that selectively target tumor cells.

Identification of Regulatory Pathways Controlling Gene Expression of Stress-Responsive Mitochondrial Proteins in Arabidopsis    

Publisher: Oxford University Press (OUP)

Date: 20-06-2008

DOI: 10.1104/PP.108.121384

Abstract: In this study we analyzed transcript abundance and promoters of genes encoding mitochondrial proteins to identify signaling pathways that regulate stress-induced gene expression. We used Arabidopsis (Arabidopsis thaliana) alternative oxidase AOX1a, external NADP H-dehydrogenase NDB2, and two additional highly stress-responsive genes, At2g21640 and BCS1. As a starting point, the promoter region of AOX1a was analyzed and functional analysis identified 10 cis-acting regulatory elements (CAREs), which played a role in response to treatment with H2O2, rotenone, or both. Six of these elements were also functional in the NDB2 promoter. The promoter region of At2g21640, previously defined as a hallmark of oxidative stress, shared two functional CAREs with AOX1a and was responsive to treatment with H2O2 but not rotenone. Microarray analysis further supported that signaling pathways induced by H2O2 and rotenone are not identical. The promoter of BCS1 was not responsive to H2O2 or rotenone, but highly responsive to salicylic acid (SA), whereas the promoters of AOX1a and NDB2 were unresponsive to SA. Analysis of transcript abundance of these genes in a variety of defense signaling mutants confirmed that BCS1 expression is regulated in a different manner compared to AOX1a, NDB2, and At2g21640. These mutants also revealed a pathway associated with programmed cell death that regulated AOX1a in a manner distinct from the other genes. Thus, at least three distinctive pathways regulate mitochondrial stress response at a transcriptional level, an SA-dependent pathway represented by BCS1, a second pathway that represents a convergence point for signals generated by H2O2 and rotenone on multiple CAREs, some of which are shared between responsive genes, and a third pathway that acts via EDS1 and PAD4 regulating only AOX1a. Furthermore, posttranscriptional regulation accounts for changes in transcript abundance by SA treatment for some genes.

Differential Response of Gray Poplar Leaves and Roots Underpins Stress Adaptation during Hypoxia  

Publisher: Oxford University Press (OUP)

Date: 12-11-2008

DOI: 10.1104/PP.108.125989

Abstract: The molecular and physiological responses of gray poplar (Populus × canescens) following root hypoxia were studied in roots and leaves using transcript and metabolite profiling. The results indicate that there were changes in metabolite levels in both organs, but changes in transcript abundance were restricted to the roots. In roots, starch and sucrose degradation were altered under hypoxia, and concurrently, the availability of carbohydrates was enhanced, concomitant with depletion of sucrose from leaves and elevation of sucrose in the phloem. Consistent with the above, glycolytic flux and ethanolic fermentation were stimulated in roots but not in leaves. Various messenger RNAs encoding components of biosynthetic pathways such as secondary cell wall formation (i.e. cellulose and lignin biosynthesis) and other energy-demanding processes such as transport of nutrients were significantly down-regulated in roots but not in leaves. The reduction of biosynthesis was unexpected, as shoot growth was not affected by root hypoxia, suggesting that the up-regulation of glycolysis yields sufficient energy to maintain growth. Besides carbon metabolism, nitrogen metabolism was severely affected in roots, as seen from numerous changes in the transcriptome and the metabolome related to nitrogen uptake, nitrogen assimilation, and amino acid metabolism. The coordinated physiological and molecular responses in leaves and roots, coupled with the transport of metabolites, reveal important stress adaptations to ensure survival during long periods of root hypoxia.

Mitochondrial Targeting of the Arabidopsis F1-ATPase γ-Subunit via Multiple Compensatory and Synergistic Presequence Motifs

Publisher: Oxford University Press (OUP)

Date: 12-2012

DOI: 10.1105/TPC.112.105361

Abstract: The majority of mitochondrial proteins are encoded in the nuclear genome and imported into mitochondria posttranslationally from the cytosol. An N-terminal presequence functions as the signal for the import of mitochondrial proteins. However, the functional information in the presequence remains elusive. This study reports the identification of critical sequence motifs from the presequence of Arabidopsis thaliana F1-ATPase γ-subunit (pFAγ). pFAγ was ided into six 10–amino acid segments, designated P1 to P6 from the N to the C terminus, each of which was further ided into two 5–amino acid sub isions. These P segments and their sub isions were substituted with Ala residues and fused to green fluorescent protein (GFP). Protoplast targeting experiments using these GFP constructs revealed that pFAγ contains several functional sequence motifs that are dispersed throughout the presequence. The sequence motifs DQEEG (P4a) and VVRNR (P5b) were involved in translocation across the mitochondrial membranes. The sequence motifs IAARP (P2b) and IAAIR (P3a) participated in binding to mitochondria. The sequence motifs RLLPS (P2a) and SISTQ (P5a) assisted in pulling proteins into the matrix, and the sequence motif IAARP (P2b) functioned in Tom20-dependent import. In addition, these sequence motifs exhibit complex relationships, including synergistic functions. Thus, multiple sequence motifs dispersed throughout the presequence are proposed to function cooperatively during protein import into mitochondria.

Mitochondrial activity and biogenesis during resurrection of Haberlea rhodopensis

Publisher: Wiley

Date: 11-08-2022

DOI: 10.1111/NPH.18396

Abstract: Haberlea rhodopensis is a resurrection plant that can tolerate extreme and prolonged periods of desiccation with a rapid restoration of physiological function upon rehydration. Specialized mechanisms are required to minimize cellular damage during desiccation and to maintain integrity for rapid recovery following rehydration. In this study we used respiratory activity measurements, electron microscopy, transcript, protein and blue native‐PAGE analysis to investigate mitochondrial activity and biogenesis in fresh, desiccated and rehydrated detached H. rhodopensis leaves. We demonstrate that unlike photosynthesis, mitochondrial respiration was almost immediately activated to levels of fresh tissue upon rehydration. The abundance of transcripts and proteins involved in mitochondrial respiration and biogenesis were at comparable levels in fresh, desiccated and rehydrated tissues. Blue native‐PAGE analysis revealed fully assembled and equally abundant OXPHOS complexes in mitochondria isolated from fresh, desiccated and rehydrated detached leaves. We observed a high abundance of alternative respiratory components which correlates with the observed high uncoupled respiration capacity in desiccated tissue. Our study reveals that during desiccation of vascular H. rhodopensis tissue, mitochondrial composition is conserved and maintained at a functional state allowing for an almost immediate activation to full capacity upon rehydration. Mitochondria‐specific mechanisms were activated during desiccation which probably play a role in maintaining tolerance.

Environmental stresses inhibit and stimulate different protein import pathways in plant mitochondria

Publisher: Wiley

Date: 20-06-2003

DOI: 10.1016/S0014-5793(03)00691-4

Abstract: The impact of various environmental stresses (drought, chilling or herbicide treatment) on the capacity of plant mitochondria to import precursor proteins was investigated. Drought treatment stimulated import and processing of various precursor proteins via the general import pathway. The stimulatory effect of drought on the general import pathway was due to an increased rate of import, was accompanied by an increased rate of processing, and could be attributed to the presequence of the precursor protein. Interestingly, drought decreased the import of the F(A)d subunit of ATP synthase suggesting a bypass of the point of stimulation during import of this precursor. Both chilling and herbicide treatment of plants, on the other hand, caused inhibition of import with all precursors tested. No decrease in processing of imported proteins was observed by these stress treatments. Western analysis of several mitochondrial proteins indicated that the steady-state level of several mitochondrial components, including the TOM20 receptor and the core subunits of the cytochrome bc(1) complex responsible for processing, remained largely unchanged. Thus environmental stresses differentially affect import of precursor proteins in a complicated manner dependent on the import pathway utilised.

Molecular Distinction between Alternative Oxidase from Monocots and Dicots

Publisher: Oxford University Press (OUP)

Date: 07-2002

DOI: 10.1104/PP.004150

Respiratory gene expression in soybean cotyledons during post-germinative development

Publisher: Springer Science and Business Media LLC

Date: 2003

DOI: 10.1023/A:1022502501373

Abstract: Gene expression for nuclear- and mitochondrial-encoded subunits of respiratory chain components was measured in developing soybean cotyledons and compared to the abundance of the relevant proteins. Overall respiratory gene expression peaked at day 16, close to the peak in cytochrome chain and TCA cycle activities from day 10 to 15. Protein abundance followed transcript abundance for all components examined with the exception of the F1beta subunit of ATP synthase. A dramatic peak in F1beta transcript levels early in development (day 5 to 7) was not mirrored by an increase in protein suggesting translational or post-translational control. Mitochondrial-encoded transcripts were at least 10-fold more abundant than nuclear-encoded transcripts. The pattern of transcript and protein abundance for uncoupling proteins displayed a trend similar to other respiratory proteins examined, implicating similar control mechanisms. The expression of alternative oxidase differed, increasing throughout development with protein peaking at day 20, perhaps suggesting a role in senescence. Overall, this study indicated that respiratory gene expression and protein abundance is co-ordinated with respiratory activity for most components but that some components, such as the F1beta subunit may be under discrete forms of regulation.

Mitochondrial and Chloroplast Stress Responses Are Modulated in Distinct Touch and Chemical Inhibition Phases

Publisher: Oxford University Press (OUP)

Date: 09-05-2016

DOI: 10.1104/PP.16.00273

Determining Degradation and Synthesis Rates of Arabidopsis Proteins Using the Kinetics of Progressive 15N Labeling of Two-dimensional Gel-separated Protein Spots

Publisher: Elsevier BV

Date: 06-2012

DOI: 10.1074/MCP.M111.010025

Isolation of tissues and preservation of RNA from intact, germinated barley grain

Publisher: Wiley

Date: 15-06-2017

DOI: 10.1111/TPJ.13600

Abstract: Isolated barley (Hordeum vulgare L.) aleurone layers have been widely used as a model system for studying gene expression and hormonal regulation in germinating cereal grains. A serious technological limitation of this approach has been the inability to confidently extrapolate conclusions obtained from isolated tissues back to the whole grain, where the co-location of several living and non-living tissues results in complex tissue-tissue interactions and regulatory pathways coordinated across the multiple tissues. Here we have developed methods for isolating fragments of aleurone, starchy endosperm, embryo, scutellum, pericarp-testa, husk and crushed cell layers from germinated grain. An important step in the procedure involves the rapid fixation of the intact grain to freeze the transcriptional activity of in idual tissues while dissection is effected for subsequent transcriptomic analyses. The developmental profiles of 19 611 gene transcripts were precisely defined in the purified tissues and in whole grain during the first 24 h of germination by RNA sequencing. Spatial and temporal patterns of transcription were validated against well-defined data on enzyme activities in both whole grain and isolated tissues. Transcript profiles of genes involved in mitochondrial assembly and function were used to validate the very early stages of germination, while the profiles of genes involved in starch and cell wall mobilisation matched existing data on activities of corresponding enzymes. The data will be broadly applicable for the interrogation of co-expression and differential expression patterns and for the identification of transcription factors that are important in the early stages of grain and seed germination.

Influence of soiling phenomena on air-void microstructure and acoustic performance of porous asphalt pavement

Publisher: Elsevier BV

Date: 2018

DOI: 10.1016/J.CONBUILDMAT.2017.10.069

Evidence for a SAL1-PAP Chloroplast Retrograde Pathway That Functions in Drought and High Light Signaling in Arabidopsis      

Publisher: Oxford University Press (OUP)

Date: 11-2011

DOI: 10.1105/TPC.111.091033

Abstract: Compartmentation of the eukaryotic cell requires a complex set of subcellular messages, including multiple retrograde signals from the chloroplast and mitochondria to the nucleus, to regulate gene expression. Here, we propose that one such signal is a phosphonucleotide (3′-phosphoadenosine 5′-phosphate [PAP]), which accumulates in Arabidopsis thaliana in response to drought and high light (HL) stress and that the enzyme SAL1 regulates its levels by dephosphorylating PAP to AMP. SAL1 accumulates in chloroplasts and mitochondria but not in the cytosol. sal1 mutants accumulate 20-fold more PAP without a marked change in inositol phosphate levels, demonstrating that PAP is a primary in vivo substrate. Significantly, transgenic targeting of SAL1 to either the nucleus or chloroplast of sal1 mutants lowers the total PAP levels and expression of the HL-inducible ASCORBATE PEROXIDASE2 gene. This indicates that PAP must be able to move between cellular compartments. The mode of action for PAP could be inhibition of 5′ to 3′ exoribonucleases (XRNs), as SAL1 and the nuclear XRNs modulate the expression of a similar subset of HL and drought-inducible genes, sal1 mutants accumulate XRN substrates, and PAP can inhibit yeast (Saccharomyces cerevisiae) XRNs. We propose a SAL1-PAP retrograde pathway that can alter nuclear gene expression during HL and drought stress.

Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination

Publisher: Springer Science and Business Media LLC

Date: 15-09-2017

DOI: 10.1186/S13059-017-1302-3

The products of the mitochondrial orf25 and orfB genes are F_O components in the plant F₁F_O ATP synthase

Publisher: Wiley

Date: 20-03-2003

DOI: 10.1016/S0014-5793(03)00264-3

Abstract: The F(O) portion of the mitochondrial ATP synthase contains a range of different subunits in bacteria, yeast and mammals. A search of the Arabidopsis genome identified sequence orthologs for only some of these subunits. Blue native polyacrylamide gel electrophoresis separation of Arabidopsis mitochondrial respiratory chain complexes revealed intact F(1)F(O), and separated F(1) and F(O) components. The subunits of each complex were analysed by mass spectrometry and matched to Arabidopsis genes. In the F(1)F(O) complex a series of nine known subunits were identified along with two additional proteins matching the predicted products of the mitochondrial encoded orfB and orf25 genes. The F(1) complex contained the five well-characterised F(1) subunits, while four subunits in the F(O) complex were identified: subunit 9, d subunit, and the orfB and orf25 products. Previously, orfB has been suggested as the plant equivalent of subunit 8 based on structural and sequence similarity. We propose that orf25 is the plant b subunit based on structural similarity and its presence in the F(O) complex. Chimerics of orf25, orfB, subunit 9 and subunit 6 have been associated with cytoplasmic male sterility in a variety of plant species, our additional findings now place all these proteins in the same protein complex.

Zhejiang University

Location: China

View Organisation

Linkage - International - Grant ID: LX0664516

Start Date: 04-2006

End Date: 12-2007

Amount: $96,740.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP0986245

Start Date: 2009

End Date: 06-2012

Amount: $300,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP130100600

Start Date: 11-2013

End Date: 11-2016

Amount: $675,000.00

Funder: Australian Research Council

Linkage - International - Grant ID: LX0776042

Start Date: 04-2007

End Date: 12-2008

Amount: $59,608.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0989071

Start Date: 01-2009

End Date: 07-2012

Amount: $600,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP160100700

Start Date: 12-2016

End Date: 12-2019

Amount: $520,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP0343517

Start Date: 12-2003

End Date: 01-2006

Amount: $360,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP130102384

Start Date: 2013

End Date: 12-2015

Amount: $319,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP210103258

Start Date: 06-2021

End Date: 06-2024

Amount: $476,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0882866

Start Date: 12-2008

End Date: 12-2009

Amount: $470,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE110100188

Start Date: 03-2011

End Date: 12-2012

Amount: $550,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP0664692

Start Date: 01-2006

End Date: 09-2009

Amount: $620,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0561219

Start Date: 01-2005

End Date: 09-2006

Amount: $1,362,295.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0230245

Start Date: 2001

End Date: 12-2002

Amount: $600,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0560987

Start Date: 03-2005

End Date: 12-2005

Amount: $156,697.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0453722

Start Date: 2004

End Date: 12-2005

Amount: $385,240.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0347922

Start Date: 2002

End Date: 12-2002

Amount: $630,000.00

Funder: Australian Research Council

ARC Centres Of Excellence - Grant ID: CE230100015

Start Date: 2023

End Date: 12-2029

Amount: $35,000,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP140100321

Start Date: 2014

End Date: 02-2014

Amount: $414,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE110100146

Start Date: 2011

End Date: 12-2012

Amount: $500,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP200102452

Start Date: 2020

End Date: 12-2022

Amount: $435,000.00

Funder: Australian Research Council

Super Science Fellowships - Grant ID: FS100100022

Start Date: 02-2011

End Date: 06-2014

Amount: $835,200.00

Funder: Australian Research Council

ARC Centres Of Excellence - Grant ID: CE140100008

Start Date: 2014

End Date: 05-2021

Amount: $26,000,000.00

Funder: Australian Research Council

ARC Centres Of Excellence - Grant ID: CE0561495

Start Date: 12-2005

End Date: 06-2014

Amount: $22,300,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE220100185

Start Date: 2022

End Date: 12-2022

Amount: $675,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0882893

Start Date: 2008

End Date: 12-2008

Amount: $260,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE120100092

Start Date: 01-2012

End Date: 12-2012

Amount: $240,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0989782

Start Date: 10-2009

End Date: 10-2010

Amount: $524,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0990355

Start Date: 11-2009

End Date: 12-2015

Amount: $583,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0455288

Start Date: 12-2004

End Date: 12-2008

Amount: $90,168.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP130100347

Start Date: 02-2014

End Date: 06-2018

Amount: $411,582.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE200100117

Start Date: 2020

End Date: 12-2020

Amount: $1,275,000.00

Funder: Australian Research Council

Industrial Transformation Research Hubs - Grant ID: IH180100006

Start Date: 07-2019

End Date: 07-2024

Amount: $4,995,391.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE150100011

Start Date: 2015

End Date: 06-2016

Amount: $346,439.00

Funder: Australian Research Council