ORCID Profile
0000-0003-2004-5217
Current Organisation
University of Western Australia
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Plant Biology | Crop and pasture production | Analytical Chemistry | Biochemistry and cell biology | Synthetic biology | Colloid And Surface Chemistry | Electrochemistry | Botany Not Elsewhere Classified | Animal reproduction and breeding | Sensor Technology (Chemical aspects) | Horticultural crop improvement (incl. selection and breeding) | Crop and pasture improvement (incl. selection and breeding) | Immunological and Bioassay Methods | Crop and Pasture Production | Physical Chemistry (Incl. Structural) | Plant Biochemistry And Physiology | Environmental biotechnology not elsewhere classified | Plant Growth And Development | Plant Cell and Molecular Biology | Plant Physiology | Analytical Biochemistry | Cell Metabolism | Population And Ecological Genetics | Plant Physiology | Nanobiotechnology
ANZSRC Socio-Economic Objective (SEO)
Oilseeds | Expanding Knowledge in the Biological Sciences | Climate Change Adaptation Measures | Primary products from plants | Field crops | Rice | Immune system and allergy | Higher education | Biological sciences | Expanding Knowledge in Technology | Primary plant products not elsewhere classified | Expanding Knowledge in the Information and Computing Sciences |
Related Links
Publications
Insights into female sperm storage from the spermathecal fluid proteome of the honeybee Apis mellifera
Publisher: Springer Science and Business Media LLC
Date: 2009
Distinct changes in mature root and growing root tip proteomes underlie physiological responses of bread wheat to salinity stress
Publisher: Cold Spring Harbor Laboratory
Date: 25-05-2021
DOI: 10.1101/2021.05.24.445367
Abstract: The impact of salinity on wheat plants is often studied by analysis of shoot responses, even though the main mechanism of tolerance is shoot Na + exclusion. There is a need to understand the molecular responses of root tissues that directly experience rising NaCl concentrations. We have combined analysis of root growth, ion content and respiration with proteome responses in wheat root tip and mature root tissues under saline conditions. We find significant changes in translation and protein synthesis, energy metabolism and amino acid metabolism in a root tissue specific manner. Translation and protein synthesis related proteins showed significant decreases in abundance only in root tips, as did most of the glycolytic enzymes and selected TCA cycle enzymes and ATP synthase subunits. This selective root tip proteome response indicates protein synthesis capacity and energy production were impaired under salt stress, correlating with the anatomical response of roots and reduced root tip respiration rate. Wheat roots respond directly to soil salinity, therefore shoot responses such as reduction in shoot growth and photosynthetic capacity need to be considered in light of these effects.
Metabolic adaptations leading to lignification in wheat roots under salinity stress
Publisher: Cold Spring Harbor Laboratory
Date: 08-06-2023
DOI: 10.1101/2023.06.08.544172
Abstract: Analysis of salinity tolerance processes in wheat has focused on salt exclusion from shoots while root phenotypes have received limited attention. Here we consider the varying phenotypic response of four bread wheat varieties that differ in their type and degree of salt tolerance and consider in detail their molecular responses to salinity and changes in root cell wall lignification. These varieties were Westonia introgressed with Nax1 and Nax2 root sodium transporters ( HKT1 -A ) that reduce Na + accumulation in leaves, as well as the ‘tissue tolerant’ Portugese landrace Mocho de Espiga Branca that has a mutation in the homologous gene HKT1 -D and has high Na + concentration in leaves. These three varieties were compared with the more salt-sensitive cultivar Gladius. Through the use of root structural analysis, ion concentrations, as well as differential proteomics and targeted metabolomics we provide an integrated view of the wheat root response to salinity. We show different metabolic re-arrangements in energy conversion, primary metabolic machinery and phenylpropanoid pathway leading to monolignol production in a genotype and genotype by treatment dependent manner that alters the extent and localisation of root lignification which correlated with an improved capacity of wheat roots to cope better under salinity stress.
Cold sensitivity of mitochondrial ATP synthase restricts oxidative phosphorylation in Arabidopsis thaliana
Publisher: Wiley
Date: 08-11-2018
DOI: 10.1111/NPH.15509
Abstract: The combined action of the electron transport chain (ETC) and ATP synthase is essential in determining energy efficiency in plants, and so is important for cellular biosynthesis, growth and development. Owing to the sessile nature of plants, mitochondria must operate over a wide temperature range in the environment, necessitating a broad temperature tolerance of their biochemical reactions. We investigated the temperature response of mitochondrial respiratory processes in isolated mitochondria and intact plants of Arabidopsis thaliana and considered the effect of instantaneous responses to temperature and acclimation responses to low temperatures. We show that at 4°C the plant mitochondrial ATP synthase is differentially inhibited compared with other elements of the respiratory pathway, leading to decreased ADP : oxygen ratios and a limitation to the rate of ATP synthesis. This effect persists in vivo and cannot be overcome by cold-temperature acclimation of plants. This mechanism adds a new element to the respiratory acclimation model and provides a direct means of temperature perception by plant mitochondria. This also provides an alternative explanation for non-phosphorylating ETC bypass mechanisms, like the alternative oxidase to maintain respiratory rates, albeit at lower ATP synthesis efficiency, in response to the sensitivity of ATP synthase to the prevailing temperature.
Isolation of Mitochondria from Model and Crop Plants
Publisher: Springer New York
Date: 2017
DOI: 10.1007/978-1-4939-7292-0_12
Abstract: The ability to isolate intact and functional mitochondria has greatly deepened our understanding of mitochondrial structure and function. With the advancement of molecular biology techniques and progression into omics-based research over recent decades, mitochondrial research has shifted from crop species such as wheat, pea, and potato to genetically sequenced models such as Arabidopsis thaliana and rice. Although there are many attributes that make model species particularly appealing for plant research, they are often less than ideal for conducting biochemical investigations and as such, considerable modification to mitochondrial isolation methods has been made.As the cost of genome sequencing continues to decrease however, an increasing number of crop species are now being sequenced and with these new resources it appears that the research community is turning back toward crop research. In this chapter we present mitochondrial isolation methods using density gradient centrifugation for both model species such as Arabidopsis thaliana, rice, and Medicago and crop species including wheat, potato, and pea. In addition, we present a number of marker enzyme assays to confirm mitochondrial purity as well as respiratory assays to determine outer membrane integrity and respiratory function of isolated mitochondria.
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.
Assessment of respiration in isolated plant mitochondria using Clark-type electrodes
Publisher: Springer New York
Date: 2015
DOI: 10.1007/978-1-4939-2639-8_12
Abstract: Mitochondrial respiration involves two key gas exchanges, the consumption of oxygen and the release of carbon dioxide. The ability to measure the consumption of oxygen via Clark-type electrodes has been one of the key techniques for advancing our knowledge of mitochondrial function in whole organisms, tissue s les, cells, and isolated subcellular fractions. In plants, oxygen electrode analyses provided the first evidence for some of the unique respiratory properties of plant mitochondria. This chapter briefs the principles of respiration and oxidative phosphorylation, how oxygen consumption measurements can be used to assess the quality of isolated mitochondrial preparations, and how these measurements can answer important questions in plant biochemistry and physiology. Finally, it presents instructions on assembling the oxygen electrode apparatus and how to conduct various assays.
The role of mitochondrial respiration in salinity tolerance
Publisher: Elsevier BV
Date: 11-2011
DOI: 10.1016/J.TPLANTS.2011.08.002
Abstract: NaCl is the most abundant salt in salinity-affected land. The ability of plants to sift the water table, limit NaCl uptake, compartmentalise Na⁺/Cl⁻ ions and prevent negative ionic and osmotic effects on cell function, are the foundations of salinity tolerance mechanisms. In this review, we show that although the quantitative response of respiratory rate to changes in salt concentration is complex, the properties of respiratory processes are crucial for tolerance during ion exclusion and tissue tolerance. We consider whole-plant gas exchange and carbon balance analysis alongside the salt responses of mitochondrial properties and genetic studies manipulating respiratory processes. We showcase the importance of efficient ATP generation, d ened reactive oxygen species and mitochondrial osmolytes for salinity tolerance in plants.
The Pentatricopeptide Repeat Gene OTP43 Is Required for trans-Splicing of the Mitochondrial nad1 Intron 1 in Arabidopsis thaliana
Publisher: Oxford University Press (OUP)
Date: 10-2007
Abstract: The mitochondrial NADH:ubiquinone oxidoreductase complex (Complex I) is a large protein complex formed from both nuclearly and mitochondrially encoded subunits. Subunit ND1 is encoded by a mitochondrial gene comprising five exons, and the mature transcript requires four RNA splicing events, two of which involve trans-splicing independently transcribed RNAs. We have identified a nuclear gene (OTP43) absolutely required for trans-splicing of intron 1 (and only intron 1) of Arabidopsis thaliana nad1 transcripts. This gene encodes a previously uncharacterized pentatricopeptide repeat protein. Mutant Arabidopsis plants with a disrupted OTP43 gene do not present detectable mitochondrial Complex I activity and show severe defects in seed development, germination, and to a lesser extent in plant growth. The alternative respiratory pathway involving alternative oxidase is significantly induced in the mutant.
Disruption of ptLPD1 or ptLPD2, Genes That Encode Isoforms of the Plastidial Lipoamide Dehydrogenase, Confers Arsenate Hypersensitivity in Arabidopsis
Publisher: Oxford University Press (OUP)
Date: 20-05-2010
Abstract: Arsenic is a ubiquitous environmental poison that inhibits root elongation and seed germination to a variable extent depending on the plant species. To understand the molecular mechanisms of arsenic resistance, a genetic screen was developed to isolate arsenate overly sensitive (aos) mutants from an activation-tagged Arabidopsis (Arabidopsis thaliana) population. Three aos mutants were isolated, and the phenotype of each was demonstrated to be due to an identical disruption of plastidial LIPOAMIDE DEHYDROGENASE1 (ptLPD1), a gene that encodes one of the two E3 isoforms found in the plastidial pyruvate dehydrogenase complex. In the presence of arsenate, ptlpd1-1 plants exhibited reduced root and shoot growth and enhanced anthocyanin accumulation compared with wild-type plants. The ptlpd1-1 plants accumulated the same amount of arsenic as wild-type plants, indicating that the aos phenotype was not due to increased arsenate in the tissues but to an increase in the innate sensitivity to the poison. Interestingly, a ptlpd1-4 knockdown allele produced a partial aos phenotype. Two loss-of-function alleles of ptLPD2 in Arabidopsis also caused elevated arsenate sensitivity, but the sensitivity was less pronounced than for the ptlpd1 mutants. Moreover, both the ptlpd1 and ptlpd2 mutants were more sensitive to arsenite than wild-type plants, and the LPD activity in isolated chloroplasts from wild-type plants was sensitive to arsenite but not arsenate. These findings show that the ptLPD isoforms are critical in vivo determinants of arsenite-mediated arsenic sensitivity in Arabidopsis and possible strategic targets for increasing arsenic tolerance.
Proteomic profiling of mature leaves from oil palm (Elaeis guineensis Jacq.)
Publisher: Wiley
Date: 02-03-2017
Abstract: Oil palm is one of the most productive oil bearing crops grown in Southeast Asia. Due to the dwindling availability of agricultural land and increasing demand for high yielding oil palm seedlings, clonal propagation is vital to the oil palm industry. Most commonly, leaf explants are used for in vitro micropropagation of oil palm and to optimize this process it is important to unravel the physiological and molecular mechanisms underlying somatic embryo production from leaves. In this study, a proteomic approach was used to determine protein abundance of mature oil palm leaves. To do this, leaf proteins were extracted using TCA/acetone precipitation protocol and separated by 2DE. A total of 191 protein spots were observed on the 2D gels and 67 of the most abundant protein spots that were consistently observed were selected for further analysis with 35 successfully identified using MALDI TOF/TOF MS. The majority of proteins were classified as being involved in photosynthesis, metabolism, cellular biogenesis, stress response, and transport. This study provides the first proteomic assessment of oil palm leaves in this important oil crop and demonstrates the successful identification of selected proteins spots using the Malaysian Palm Oil Board (MPOB) Elaeis guineensis EST and NCBI-protein databases. The MS data have been deposited in the ProteomeXchange Consortium database with the data set identifier PXD001307.
The cytotoxic lipid peroxidation product 4-hydroxy-2-nonenal covalently modifies a selective range of proteins linked to respiratory function in plant mitochondria
Publisher: Elsevier BV
Date: 12-2007
Mitochondrial Complex I activity is inhibited by changes in the abundance of phosphatidylinositol and phosphatidylserine in wheat plants exposed to high temperatures
Publisher: Cold Spring Harbor Laboratory
Date: 06-02-2023
DOI: 10.1101/2023.02.05.527222
Abstract: Identifying the molecular basis of thermotolerance in crops is becoming increasingly important with the changing climatic conditions that challenge future food security. Sustaining cellular energy production under heat stress is vital in maintaining an uninterrupted growth cycle, and thus the mitochondria is instrumental in facilitating the overall heat-tolerance of a crop plant. Using targeted mass spectrometry, the changes in abundance of the lipo-protein network in mitochondrial membranes following a short episode of extremely high temperature were analysed in two wheat cultivars of differing thermotolerance. The results indicated that membrane lipids remodel in favour of shorter fatty acyl tails, and an increase in the abundance of phosphatidylinositol, while specific to the heat-tolerant cultivar was an increase in the abundance of phosphatidylserine. The differences between the lipid profiles of the two cultivars is a likely explanation for the decrease in Complex I NADH dehydrogenase activity in the heat-sensitive cultivar. Further metabolite analysis by LC-MS revealed malate accumulation, indicating that the disruption in Complex I activity impacts the catabolism of reducing equivalents. The measured increase in the total amount of phosphatidylserine in the heat-tolerant cultivar suggests a potential role in conveying thermotolerance for this minor membrane constituent, and highlights that a focus on membrane lipid composition during thermal stress will be essential for the breeding of future heat tolerant crops. We evaluated changes to the lipo-protein network of wheat mitochondria of differing heat tolerance in response to heat shock. Using targeted mass spectrometry, candidate transitions were selected to quantify changes in membrane lipids and the embedded protein components of the electron transport chain, which play a vital role in maintaining respiration. A significant increase in phosphatidylserine was exclusive to the mitochondria of the heat-tolerant wheat cultivar. In the absence of this, the heat-sensitive cultivar displayed a reduced Complex I activity. The minor membrane constituent phosphatidylserine plays a role in conveying thermotolerance, making this membrane lipid a focal point for the breeding of future heat tolerant crops.
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
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.
Multiplex micro-respiratory measurements of Arabidopsis tissues
Publisher: Wiley
Date: 08-07-2013
DOI: 10.1111/NPH.12394
Abstract: Researchers often want to study the respiratory properties of in idual parts of plants in response to a range of treatments. A rabidopsis is an obvious model for this work however, because of its size, it represents a challenge for gas exchange measurements of respiration. The combination of micro‐respiratory technologies with multiplex assays has the potential to bridge this gap, and make measurements possible in this model plant species. We show the adaptation of the commercial technology used for mammalian cell respiration analysis to study three critical tissues of interest: leaf sections, root tips and seeds. The measurement of respiration in single leaf discs has allowed the age dependence of the respiration rate in A rabidopsis leaves across the rosette to be observed. The oxygen consumption of single root tips from plate‐grown seedlings shows the enhanced respiration of root tips and their time‐dependent susceptibility to salinity. The monitoring of single A rabidopsis seeds shows the kinetics of respiration over 48 h post‐imbibition, and the effect of the phytohormones gibberellic acid ( GA 3 ) and abscisic acid ( ABA ) on respiration during seed germination. These studies highlight the potential for multiplexed micro‐respiratory assays to study oxygen consumption in A rabidopsis tissues, and open up new possibilities to screen and study mutants and to identify differences in ecotypes or populations of different plant species.
Energy costs of salt tolerance in crop plants
Publisher: Wiley
Date: 11-07-2019
DOI: 10.1111/NPH.15864
Abstract: Agriculture is expanding into regions that are affected by salinity. This review considers the energetic costs of salinity tolerance in crop plants and provides a framework for a quantitative assessment of costs. Different sources of energy, and modifications of root system architecture that would maximize water vs ion uptake are addressed. Energy requirements for transport of salt (NaCl) to leaf vacuoles for osmotic adjustment could be small if there are no substantial leaks back across plasma membrane and tonoplast in root and leaf. The coupling ratio of the H
Diverse cyclic seed peptides in the Mexican zinnia (Zinnia haageana)
Publisher: Wiley
Date: 11-2016
DOI: 10.1002/BIP.22901
Abstract: A new family of small plant peptides was recently described and found to be widespread throughout the Millereae and Heliantheae tribes of the sunflower family Asteraceae. These peptides originate from the post-translational processing of unusual seed-storage albumin genes, and have been termed PawS-derived peptides (PDPs). The prototypic family member is a 14-residue cyclic peptide with potent trypsin inhibitory activity named SunFlower Trypsin Inhibitor (SFTI-1). In this study we present the features of three new PDPs discovered in the seeds of the sunflower species Zinnia haageana by a combination of de novo transcriptomics and liquid chromatography-mass spectrometry. Two-dimensional solution NMR spectroscopy was used to elucidate their structural characteristics. All three Z. haageana peptides have well-defined folds with a head-to-tail cyclized peptide backbone and a single disulfide bond. Although two possess an anti-parallel β-sheet structure, like SFTI-1, the Z. haageana peptide PDP-21 has a more irregular backbone structure. Despite structural similarities with SFTI-1, PDP-20 was not able to inhibit trypsin, thus the functional roles of these peptides is yet to be discovered. Defining the structural features of the small cyclic peptides found in the sunflower family will be useful for guiding the exploitation of these peptides as scaffolds for grafting and protein engineering applications.
Matrix-assisted laser desorption/ionisation mass spectrometry imaging and its development for plant protein imaging
Publisher: Springer Science and Business Media LLC
Date: 05-07-2011
Abstract: M atrix- A ssisted L aser D esorption/ I onisation (MALDI) mass spectrometry imaging (MSI) uses the power of high mass resolution time of flight (ToF) mass spectrometry coupled to the raster of lasers shots across the cut surface of tissues to provide new insights into the spatial distribution of biomolecules within biological tissues. The history of this technique in animals and plants is considered and the potential for analysis of proteins by this technique in plants is discussed. Protein biomarker identification from MALDI-MSI is a challenge and a number of different approaches to address this bottleneck are discussed. The technical considerations needed for MALDI-MSI are reviewed and these are presented alongside ex les from our own work and a protocol for MALDI-MSI of proteins in plant s les.
Abiotic environmental stress induced changes in the Arabidopsis thaliana chloroplast, mitochondria and peroxisome proteomes
Publisher: Elsevier BV
Date: 04-2009
DOI: 10.1016/J.JPROT.2008.11.006
Abstract: Exposure to adverse abiotic environmental conditions causes oxidative stress in plants, leading to debilitation and death or to response and tolerance. The subcellular energy organelles (chloroplast, mitochondria and peroxisomes) in plants are responsible for major metabolic processes including photosynthesis, photorespiration, oxidative phosphorylation, beta-oxidation and the tricarboxylic acid cycle. Here we analyze data and review a collection of both whole tissue and organellar proteomic studies that have investigated the effects of environmental stress in the model plant Arabidopsis thaliana. We assess these data from an organellar perspective to begin to build an understanding of the changes in protein abundance within these organelles during environmental stresses. We found 279 claims of proteins that change in abundance that could be assigned to protein components of the energy organelles. These could be placed into eight different functional categories and nearly 80% of the specific protein isoforms detected were only reported to change in a single environmental stress. We propose primary and secondary mechanisms in organelles by which the protein changes observed could be mediated in order to begin developing an integrated and mechanistic understanding of environmental stress response.
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
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.
The isolation of plant organelles and structures in the post-genomic era
Publisher: Springer New York
Date: 12-10-2017
DOI: 10.1007/978-1-4939-6533-5_1
Abstract: In this chapter, we provide an overview of the techniques and approaches used in the isolation of plant organelles and structures. This overview shows there is a great ersity of methods currently used for the initial physical disruption of plant tissue before the downstream isolation of a target cellular component. These include hand grinding, high-speed mechanical disruption, and enzymatic digestion of cell walls by a variety of methods. Coupled to these disruption techniques is a wide array of additives included as ingredients in extraction solutions to minimize chemical or physical damage that may occur to target components. These additives are collated into a table outlining their function. We also provide an introduction to some of the history of common approaches used for the isolation plant organelles and structures and a synopsis of the methods used by researchers for assessment of the purity of their isolated structures. This chapter therefore provides an introduction to the following chapters that document the methodology for the isolation of in idual plant organelles or structures.
Could mitochondrial dysfunction play a role in manganese toxicity?
Publisher: Elsevier BV
Date: 03-1999
DOI: 10.1016/S1382-6689(98)00054-4
Abstract: In iduals suffering from manganese toxicity exhibit several symptoms, including mitochondrial dysfunction, which are similar to those frequently observed in cases of Parkinson's disease. We review the literature concerning manganese toxicity and mitochondrial function, and propose a simple conceptual model of the aetiology of manganese toxicity which involves an interaction between inhibition of mitochondrial energy transduction, generation of free radicals and mutations of the mitochondrial genome. This conceptual model prompts a number of relatively simple experiments which would provide a test of the model.
Early Events in Plastid Protein Degradation in stay-greenArabidopsis Reveal Differential Regulation beyond the Retention of LHCII and Chlorophyll
Publisher: American Chemical Society (ACS)
Date: 22-10-2012
DOI: 10.1021/PR300691K
Abstract: An in idually darkened leaf model was used to study protein changes in the Arabidopsis mutant stay-green1 (sgr1) to partially mimic the process of leaf covering senescence that occurs naturally in the shaded rosettes of Arabidopsis plants. Utilizing this controlled and predictable induced senescence model has allowed the direct comparison of sgr1 with Col-0 during the developmental period preceding the retention of chlorophyll and light harvesting complex II (LHCII) in sgr1 and the induction of senescence in Col-0. Quantitative proteomic analysis of soluble leaf proteins from sgr1 and Col-0 before the initiation of senescence has revealed a range of differences in plastid soluble protein abundance in sgr1 when compared to Col-0. Changes were also observed in membrane located machinery for photosystem II (PSII), in Calvin cycle components, proteins involved in redox control of the stromal compartment and ammonia assimilation that differentiated sgr1 during the early stages of the senescence process. The changes in PSII abundance were accompanied with a lower capacity of photosynthetic CO(2) assimilation in sgr1 than Col-0 after return of plants to lighted conditions following 3 and 5 days of darkness. A light-harvesting chlorophyll-a/b binding protein (LHCB2) was retained during the later stages of senescence in sgr1 but this was accompanied by an enhanced loss of oxygen evolving complex (OEC) subunits from PSII, which was confirmed by Western blotting, and an enhanced stability of PSII repair proteins in sgr1, compared to Col-0. Together these data provide insights into the significant differences in the steady-state proteome in sgr1 and its response to senescence, showing this cosmetic stay-green mutant is in fact significantly different to wild-type plants both before and during leaf senescence.
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
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 advances in the composition and heterogeneity of the Arabidopsis mitochondrial proteome
Publisher: Frontiers Media SA
Date: 2013
Response of mitochondria to light intensity in the leaves of sun and shade species
Publisher: Wiley
Date: 09-03-2005
We Are Not Alone: The iMOP Initiative and Its Roles in a Biology- and Disease-Driven Human Proteome Project
Publisher: American Chemical Society (ACS)
Date: 31-10-2017
DOI: 10.1021/ACS.JPROTEOME.7B00408
Abstract: Mapping of the human proteome has advanced significantly in recent years and will provide a knowledge base to accelerate our understanding of how proteins and protein networks can affect human health and disease. However, providing solutions to human health challenges will likely fail if insights are exclusively based on studies of human s les and human proteomes. In recent years, it has become evident that human health depends on an integrated understanding of the many species that make human life possible. These include the commensal microorganisms that are essential to human life, pathogens, and food species as well as the classic model organisms that enable studies of biological mechanisms. The Human Proteome Organization (HUPO) initiative on multiorganism proteomes (iMOP) works to support proteome research undertaken on nonhuman species that remain widely under-studied compared with the progress in human proteome research. This perspective argues the need for further research on multiple species that impact human life. We also present an update on recent progress in model organisms, microbiota, and food species, address the emerging problem of antibiotics resistance, and outline how iMOP activities could lead to a more inclusive approach for the human proteome project (HPP) to better support proteome research aimed at improving human health and furthering knowledge on human biology.
Isolation of Mitochondria, Their Sub-Organellar Compartments, and Membranes
Publisher: Springer New York
Date: 12-10-2016
DOI: 10.1007/978-1-4939-6533-5_7
Abstract: Mitochondria are the sites of a erse set of essential biochemical processes in plants. In order to facilitate the analysis of these functions, this chapter presents protocols for the isolation of intact mitochondria from a range of plant tissues as well two workflows for fractionation into their four subcompartments the inner and outer membranes and the two aqueous compartments, the inter membrane space and matrix. Protocols for the assessment of mitochondrial integrity and purity through enzymatic function and suggestions of commercially available compartment marker antibodies are provided.
The seminal fluid proteome of the honeybee Apis mellifera
Publisher: Wiley
Date: 04-2009
Abstract: Ejaculates contain sperm but also seminal fluid, which is increasingly recognized to be of central importance for reproductive success. However, a detailed biochemical composition and physiological understanding of seminal fluid is still elusive. We have used MS to identify the 57 most abundant proteins within the ejaculated seminal fluid of the honeybee Apis mellifera. Their amino acid sequences revealed the presence of erse functional categories of enzymes, regulators and structural proteins. A number have known or predicted roles in maintaining sperm viability, protecting sperm from microbial infections or interacting with the physiology of the female. A range of putative glycoproteins or glycosylation enzymes were detected among the 57, subsequent fluorescent staining of glycolysation revealed several prominent glycoproteins in seminal fluid, while no glycoproteins were detected in sperm s les. Many of the abundant proteins that accumulate in the seminal fluid did not contain predictable tags for secretion for the cell. Comparison of the honeybee seminal fluid proteins with Drosophila seminal fluid proteins (including secreted accessory gland proteins known as ACPs), and with the human seminal fluid proteome revealed the bee protein set contains a range of newly identified seminal fluid proteins and we noted more similarity of the bee protein set with the current human seminal fluid protein set than with the known Drosophila seminal fluid proteins. The honeybee seminal fluid proteome thus represents an important addition to available data for comparative studies of seminal fluid proteomes in insects.
Mitochondrial uncoupling protein is required for efficient photosynthesis
Publisher: Proceedings of the National Academy of Sciences
Date: 19-12-2006
Abstract: Uncoupling proteins (UCPs) occur in the inner mitochondrial membrane and dissipate the proton gradient across this membrane that is normally used for ATP synthesis. Although the catalytic function and regulation of plant UCPs have been described, the physiological purpose of UCP in plants has not been established. Here, biochemical and physiological analyses of an insertional knockout of one of the Arabidopsis UCP genes ( AtUCP1 ) are presented that resolve this issue. Absence of UCP1 results in localized oxidative stress but does not impair the ability of the plant to withstand a wide range of abiotic stresses. However, absence of UCP1 results in a photosynthetic phenotype. Specifically there is a restriction in photorespiration with a decrease in the rate of oxidation of photorespiratory glycine in the mitochondrion. This change leads to an associated reduced photosynthetic carbon assimilation rate. Collectively, these results suggest that the main physiological role of UCP1 in Arabidopsis leaves is related to maintaining the redox poise of the mitochondrial electron transport chain to facilitate photosynthetic metabolism.
Connecting salt stress signalling pathways with salinity‐induced changes in mitochondrial metabolic processes in C3 plants
Publisher: Wiley
Date: 06-10-2017
DOI: 10.1111/PCE.13034
Abstract: Salinity exerts a severe detrimental effect on crop yields globally. Growth of plants in saline soils results in physiological stress, which disrupts the essential biochemical processes of respiration, photosynthesis, and transpiration. Understanding the molecular responses of plants exposed to salinity stress can inform future strategies to reduce agricultural losses due to salinity however, it is imperative that signalling and functional response processes are connected to tailor these strategies. Previous research has revealed the important role that plant mitochondria play in the salinity response of plants. Review of this literature shows that 2 biochemical processes required for respiratory function are affected under salinity stress: the tricarboxylic acid cycle and the transport of metabolites across the inner mitochondrial membrane. However, the mechanisms by which components of these processes are affected or react to salinity stress are still far from understood. Here, we examine recent findings on the signal transduction pathways that lead to adaptive responses of plants to salinity and discuss how they can be involved in and be affected by modulation of the machinery of energy metabolism with attention to the role of the tricarboxylic acid cycle enzymes and mitochondrial membrane transporters in this process.
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
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.
Plant mitochondrial proteomics
Publisher: Humana Press
Date: 22-08-2014
DOI: 10.1007/978-1-62703-631-3_34
Abstract: Mitochondria are responsible for a number of major biochemical processes in plant cells including oxidative phosphorylation and photorespiration. Traditionally their primary role has been viewed as the oxidation of organic acids via the tricarboxylic acid cycle and the synthesis of ATP coupled to the transfer of electrons to O2. More recently its role in the synthesis of many metabolites such as amino acids, lipids, and vitamins has been revealed. They also contain large number of transporters including members of the mitochondrial carrier substrate family (MCSF) that allow the exchange of metabolites with the cytosol. Mitochondria also contain their own genome and actively transcribe and translate a set of proteins that are coordinated with proteins encoded by the nuclear genome to produce large multisubunit enzymes. To reveal the full ersity of metabolism carried out by mitochondria significant efforts have sought to uncover the protein profile of mitochondria from both crops and model plants. Successful proteomic analysis depends on the preparation of high-quality isolated mitochondria, coupled to high-resolution proteomic techniques for identification, quantitation, and assessment of the degree of contamination by other organelles and cellular compartments. Here we outline a mitochondrial isolation protocol that can be applied to a range of plant tissues, and detail methods of assessing the quality and purity of the resultant s le, including calculations of respiratory control ratio, marker enzyme assays, differential in-gel electrophoresis, and quantitative gel-free mass spectrometry.
The metabolic acclimation of Arabidopsis thaliana to arsenate is sensitized by the loss of mitochondrial LIPOAMIDE DEHYDROGENASE2, a key enzyme in oxidative metabolism
Publisher: Wiley
Date: 11-11-2014
DOI: 10.1111/PCE.12187
Abstract: Mitochondrial lipoamide dehydrogenase is essential for the activity of four mitochondrial enzyme complexes central to oxidative metabolism. The reduction in protein amount and enzyme activity caused by disruption of mitochondrial LIPOAMIDE DEHYDROGENASE2 enhanced the arsenic sensitivity of Arabidopsis thaliana. Both arsenate and arsenite inhibited root elongation, decreased seedling size and increased anthocyanin production more profoundly in knockout mutants than in wild-type seedlings. Arsenate also stimulated lateral root formation in the mutants. The activity of lipoamide dehydrogenase in isolated mitochondria was sensitive to arsenite, but not arsenate, indicating that arsenite could be the mediator of the observed phenotypes. Steady-state metabolite abundances were only mildly affected by mutation of mitochondrial LIPOAMIDE DEHYDROGENASE2. In contrast, arsenate induced the remodelling of metabolite pools associated with oxidative metabolism in wild-type seedlings, an effect that was enhanced in the mutant, especially around the enzyme complexes containing mitochondrial lipoamide dehydrogenase. These results indicate that mitochondrial lipoamide dehydrogenase is an important protein for determining the sensitivity of oxidative metabolism to arsenate in Arabidopsis.
Arabidopsis organelle isolation and characterization
Publisher: Humana Press
Date: 30-08-2014
DOI: 10.1007/978-1-62703-580-4_29
Abstract: The subcellular energy organelles (chloroplast, mitochondria, and peroxisome) in plants are responsible for major metabolic processes including photosynthesis, photorespiration, oxidative phosphorylation, β-oxidation, and the tricarboxylic acid cycle. Arabidopsis thaliana provides a considerable challenge to organellar researchers that have traditionally focused their methods on the use of larger plants and storage organs from which organelles are relatively easy to isolate. In contrast, the small size and lack of abundant heterotrophic organs in Arabidopsis thaliana means that many traditional techniques have required significant modification to yield enough isolated organelles for experimentation. However, these challenges are balanced by the advantages of working in an organism that has such a wide array of publically available genetic resources. Here we present methods for the isolation of chloroplasts, mitochondria and peroxisomes from Arabidopsis thaliana plants and heterotrophic cell cultures as well as a number of commonly used assays to assess their functional integrity and purity.
Protein corona formation moderates the release kinetics of ion channel antagonists from transferrin-functionalized polymeric nanoparticles
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/C9RA09523C
Abstract: Transferrin (Tf)-functionalized p(HEMA- ran -GMA) nanoparticles were designed to incorporate and release a water-soluble combination of three ion channel antagonists, identified as a promising therapy for secondary degeneration following neurotrauma.
INTERMEDIATE CLEAVAGE PEPTIDASE55 Modifies Enzyme Amino Termini and Alters Protein Stability in Arabidopsis Mitochondria
Publisher: Oxford University Press (OUP)
Date: 10-04-2015
DOI: 10.1104/PP.15.00300
Effects of water stress on respiration in soybean leaves
Publisher: Oxford University Press (OUP)
Date: 26-08-2005
Abstract: The effect of water stress on respiration and mitochondrial electron transport has been studied in soybean (Glycine max) leaves, using the oxygen-isotope-fractionation technique. Treatments with three levels of water stress were applied by irrigation to replace 100%, 50%, and 0% of daily water use by transpiration. The levels of water stress were characterized in terms of light-saturated stomatal conductance (gs): well irrigated (gs & 0.2 mol H2O m−2 s−1), mildly water stressed (gs between 0.1 and 0.2 mol H2O m−2 s−1), and severely water stressed (gs & 0.1 mol H2O m−2 s−1). Although net photosynthesis decreased by 40% and 70% under mild and severe water stress, respectively, the total respiratory oxygen uptake (Vt) was not significantly different at any water-stress level. However, severe water stress caused a significant shift of electrons from the cytochrome to the alternative pathway. The electron partitioning through the alternative pathway increased from 10% to 12% under well-watered or mild water-stress conditions to near 40% under severe water stress. Consequently, the calculated rate of mitochondrial ATP synthesis decreased by 32% under severe water stress. Unlike many other stresses, water stress did not affect the levels of mitochondrial alternative oxidase protein. This suggests a biochemical regulation (other than protein synthesis) that causes this mitochondrial electron shift.
Wheat mitochondrial respiration shifts from the tricarboxylic acid cycle to the GABA shunt under salt stress
Publisher: Wiley
Date: 03-2020
DOI: 10.1111/NPH.15713
Abstract: Mitochondrial respiration and tricarboxylic acid (TCA) cycle activity are required during salt stress in plants to provide ATP and reductants for adaptive processes such as ion exclusion, compatible solute synthesis and reactive oxygen species (ROS) detoxification. However, there is a poor mechanistic understanding of how salinity affects mitochondrial metabolism, particularly respiratory substrate source. To determine the mechanism of respiratory changes under salt stress in wheat leaves, we conducted an integrated analysis of metabolite content, respiratory rate and targeted protein abundance measurements. Also, we investigated the direct effect of salt on mitochondrial enzyme activities. Salt-treated wheat leaves exhibit higher respiration rate and extensive metabolite changes. The activity of the TCA cycle enzymes pyruvate dehydrogenase complex and the 2-oxoglutarate dehydrogenase complex were shown to be directly salt-sensitive. Multiple lines of evidence showed that the γ-aminobutyric acid (GABA) shunt was activated under salt treatment. During salt exposure, key metabolic enzymes required for the cyclic operation of the TCA cycle are physiochemically inhibited by salt. This inhibition is overcome by increased GABA shunt activity, which provides an alternative carbon source for mitochondria that bypasses salt-sensitive enzymes, to facilitate the increased respiration of wheat leaves.
Components of Mitochondrial Oxidative Phosphorylation Vary in Abundance Following Exposure to Cold and Chemical Stresses
Publisher: American Chemical Society (ACS)
Date: 31-05-2012
DOI: 10.1021/PR3003535
Abstract: Plant mitochondria are highly responsive organelles that vary their metabolism in response to a wide range of chemical and environmental conditions. Quantitative proteomics studies have begun to allow the analysis of these large-scale protein changes in mitochondria. However studies of the integral membrane proteome of plant mitochondria, arguably the site responsible for the most fundamental mitochondrial processes of oxidative phosphorylation, protein import and metabolite transport, remain a technical challenge. Here we have investigated the changes in protein abundance in response to a number of chemical stresses and cold. In addition to refining the subcellular localization of 66 proteins, we have been able to characterize 596 protein × treatment combinations following a range of stresses. To date it has been assumed that the main mitochondrial response to stress involved the induction of alternative respiratory proteins such as AOX, UCPs, and alternative NAD(P)H dehydrogenases we now provide evidence for a number of very specific protein abundance changes that have not been highlighted previously by transcript studies. This includes both previously characterized stress responsive proteins as well as major components of oxidative phosphorylation, protein import/export, and metabolite transport.
The pentatricopeptide repeat gene OTP51 with two LAGLIDADG motifs is required for the cis-splicing of plastid ycf3 intron 2 in Arabidopsis thaliana
Publisher: Wiley
Date: 10-2008
Energy costs of salinity tolerance in crop plants
Publisher: Wiley
Date: 29-11-2019
DOI: 10.1111/NPH.15555
Enhancing crop yields through improvements in the efficiency of photosynthesis and respiration
Publisher: Wiley
Date: 17-11-2023
DOI: 10.1111/NPH.18545
Abstract: The rate with which crop yields per hectare increase each year is plateauing at the same time that human population growth and other factors increase food demand. Increasing yield potential () of crops is vital to address these challenges. In this review, we explore a component of that has yet to be optimised – that being improvements in the efficiency with which light energy is converted into biomass () via modifications to CO 2 fixed per unit quantum of light ( α ), efficiency of respiratory ATP production () and efficiency of ATP use (). For α , targets include changes in photoprotective machinery, ribulose bisphosphate carboxylase/oxygenase kinetics and photorespiratory pathways. There is also potential for to be increased via targeted changes to the expression of the alternative oxidase and mitochondrial uncoupling pathways. Similarly, there are possibilities to improve via changes to the ATP costs of phloem loading, nutrient uptake, futile cycles and/or protein/membrane turnover. Recently developed high‐throughput measurements of respiration can serve as a proxy for the cumulative energy cost of these processes. There are thus exciting opportunities to use our growing knowledge of factors influencing the efficiency of photosynthesis and respiration to create a step‐change in yield potential of globally important crops.
Plant mitochondrial proteomics.
Publisher: Springer New York
Date: 2015
DOI: 10.1007/978-1-4939-2639-8_6
Abstract: Mitochondrial proteomics has significantly developed since the first plant mitochondrial proteomes were published in 2001. Many studies have added to our knowledge of the protein components that make up plant mitochondria in a wide range of species. Here we present two common and one emerging quantitative proteomic techniques that can be used to study the abundance of mitochondrial proteins. For this publication, we have described the methods as an approach to determine the amount of contamination in a mitochondrial isolation to contrast historical approaches that involved the use of use of antibodies to specific marker proteins or the measurement of activity of marker enzymes. However, these approaches could easily be adapted to carry out control versus treatment studies.
The Protein Corona of PEGylated PGMA-Based Nanoparticles is Preferentially Enriched with Specific Serum Proteins of Varied Biological Function
Publisher: American Chemical Society (ACS)
Date: 30-10-2017
DOI: 10.1021/ACS.LANGMUIR.7B02568
Abstract: The composition of the protein corona formed on poly(ethylene glycol)-functionalized (PEGylated) poly(glycidyl methacrylate) (PGMA) nanoparticles (NPs) was qualitatively and quantitatively compared to the protein corona on non-PEGylated PGMA NPs. Despite the reputation of PEGylated NPs for stealth functionality, we demonstrate the preferential enrichment of specific serum proteins of varied biological function in the protein corona on PEGylated NPs when compared to non-PEGylated NPs. Additionally, we suggest that the base material of polymeric NPs plays a role in the preferential enrichment of select serum proteins to the hard corona.
The rice mitochondria proteome and its response during development and to the environment
Publisher: Frontiers Media SA
Date: 2013
Analysis of the sodium chloride-dependent respiratory kinetics of wheat mitochondria reveals differential effects on phosphorylating and non-phosphorylating electron transport pathways
Publisher: Wiley
Date: 11-12-2016
DOI: 10.1111/PCE.12653
Abstract: A number of previous studies have documented the gross response of mitochondrial respiration to salinity treatment, but it is unclear how NaCl directly affects the kinetics of plant phosphorylating and non-phosphorylating electron transport pathways. This study investigates the direct effects of NaCl upon different respiratory pathways in wheat, by measuring rates of isolated mitochondrial oxygen consumption across different substrate oxidation pathways in saline media. We also profile the abundance of respiratory proteins by using targeted selected reaction monitoring (SRM) mass spectrometry of mitochondria isolated from control and salt-treated wheat plants. We show that all pathways of electron transport were inhibited by NaCl concentrations above 400 mM however electron transfer chains showed ergent responses to NaCl concentrations between 0 and 200 mM. Stimulation of oxygen consumption was measured in response to NaCl in scenarios where exogenous NADH was provided as substrate and electron flow was coupled to the generation of a proton gradient across the inner membrane. Protein abundance measurements show that several enzymes with activities less affected by NaCl are induced by salinity, whereas enzymes with activities inhibited by NaCl are depleted. These data deepen our understanding of how plant respiration responds to NaCl, offering new mechanistic explanations for the ergent salinity responses of whole-plant respiratory rate in the literature.
Targets of stress-induced oxidative damage in plant mitochondria and their impact on cell carbon/nitrogen metabolism
Publisher: Oxford University Press (OUP)
Date: 28-11-2004
DOI: 10.1093/JXB/ERH001
Free-flow electrophoresis for purification of plant mitochondria by surface charge
Publisher: Wiley
Date: 28-08-2007
A survey of the Arabidopsis thaliana mitochondrial phosphoproteome
Publisher: Wiley
Date: 31-08-2009
Abstract: Plant mitochondria play central roles in cellular energy production, metabolism and stress responses. Recent phosphoproteomic studies in mammalian and yeast mitochondria have presented evidence indicating that protein phosphorylation is a likely regulatory mechanism across a broad range of important mitochondrial processes. This study investigated protein phosphorylation in purified mitochondria from cell suspensions of the model plant Arabidopsis thaliana using affinity enrichment and proteomic tools. Eighteen putative phosphoproteins consisting of mitochondrial metabolic enzymes, HSPs, a protease and several proteins of unknown function were detected on 2-DE separations of Arabidopsis mitochondrial proteins and affinity-enriched phosphoproteins using the Pro-Q Diamond phospho-specific in-gel dye. Comparisons with mitochondrial phosphoproteomes of yeast and mouse indicate that these three species share few validated phosphoproteins. Phosphorylation sites for seven of the eighteen mitochondrial proteins were characterized by titanium dioxide enrichment and MS/MS. In the process, 71 phosphopeptides from Arabidopsis proteins which are not present in mitochondria but found as contaminants in various types of mitochondrial preparations were also identified, indicating the low level of phosphorylation of mitochondrial components compared with other cellular components in Arabidopsis. Information gained from this study provides a better understanding of protein phosphorylation at both the subcellular and the cellular level in Arabidopsis.
Succinate dehydrogenase assembly factor 2 is needed for assembly and activity of mitochondrial complex II and for normal root elongation in Arabidopsis
Publisher: Wiley
Date: 29-11-2013
DOI: 10.1111/TPJ.12041
Abstract: Mitochondria complex II (succinate dehydrogenase, SDH) plays a central role in respiratory metabolism as a component of both the electron transport chain and the tricarboxylic acid cycle. We report the identification of an SDH assembly factor by analysis of T-DNA insertions in At5g51040, a protein with unknown function that was identified by mass spectrometry analysis as a low abundance mitochondrial protein. This gene is co-expressed with a number of genes encoding mitochondrial proteins, including SDH1-1, and has low partial sequence similarity to human SDHAF2, a protein required for flavin-adenine dinucleotide (FAD) insertion into SDH. In contrast to observations of other SDH deficient lines in Arabidopsis, the sdhaf2 line did not affect photosynthetic rate or stomatal conductance, but instead showed inhibition of primary root elongation with early lateral root emergence, presumably due to the low SDH activity caused by the reduced abundance of SDHAF2. Both roots and leaves showed succinate accumulation but different responses in the abundance of other organic acids and amino acids assayed. Isolated mitochondria showed lowered SDH1 protein abundance, lowered maximal SDH activity and less protein-bound flavin-adenine dinucleotide (FAD) at the molecular mass of SDH1 in the gel separation. The short root phenotype and SDH function of sdhaf2 was fully complemented by transformation with SDHAF2. Application of the SDH inhibitor, malonate, phenocopied the sdhaf2 root architecture in WT. Whole root respiratory assays showed no difference between WT and sdhaf2, but micro-respirometry of the tips of roots clearly showed low oxygen consumption in sdhaf2 which could explain a metabolic deficit responsible for root tip growth.
Wheat mitochondrial proteomes provide new links between antioxidant defense and plant salinity tolerance
Publisher: American Chemical Society (ACS)
Date: 15-11-2010
DOI: 10.1021/PR1007834
Abstract: The mitochondrial proteome and differences associated with salt tolerance have been investigated in Australian commercial varieties of wheat. Mitochondria isolated from shoots were used to generate a wheat mitochondrial reference map 68 unique wheat mitochondrial proteins were identified from 192 gel spots using 2D PAGE and LC-MS/MS. This analysis also provided MS/MS spectra for 199 proteotypic peptides as a foundation for the development of targeted proteomics to study the respiratory apparatus in wheat. Using this reference map and 2D DIGE, we have found quantitative differences in the shoot mitochondrial proteomes of v. Wyalkatchem and v. Janz, two commercially important wheat varieties that are known from a range of experiments to differ in salinity tolerance. These proteins included Mn-superoxide dismutase (Mn-SOD), cysteine synthase, nucleotide diphosphate kinase, and the voltage dependent anion channel (VDAC). Antibodies to the mitochondrial alternative oxidase (AOX), previously linked to reduced ROS formation from the electron transport chain and salt tolerance in Arabidopsis, also showed a commensurate higher abundance in v. Wyakatchem in both control and salt-treated conditions. Together, the data presented here suggest that differences in mitochondrial ROS defense pathways in the mitochondrial proteomes of key Australian wheat varieties correlate with whole-plant salinity tolerance.
The Arabidopsis thaliana 2-D gel mitochondrial proteome: Refining the value of reference maps for assessing protein abundance, contaminants and post-translational modifications
Publisher: Wiley
Date: 07-04-2011
Abstract: Mitochondria undertake the process of oxidative phosphorylation yielding ATP for plant cell maintenance and growth. The principles of isolation and fractionation of plant mitochondrial proteins have been improved over decades, and surveys of the mitochondrial proteome in a number of plants species have been performed. Over time, many quantitative analyses of changes in the plant mitochondrial proteome have been performed by 2-D gel analyses revealing the induction, degradation and modification of mitochondrial proteins in responses to mutation, stress and development. Here, we present a saturating MS analysis of 2-D gel separable protein spots from a typical purification of Arabidopsis mitochondria identifying 264 proteins, alongside an LC-MS/MS survey by non-gel methods identifying 220 proteins. This allowed us to characterise the major mitochondrial proteins that are not observed on 2-D gels, the common contaminants and the abundance of the protein machinery of key mitochondrial biochemical pathways, and consider the impact of N-terminal pre-sequence cleavage and phosphorylation as explanations of multiple protein spots and the co-ordinates of proteins on 2-D gels.
A family of small, cyclic peptides buried in preproalbumin since the Eocene epoch
Publisher: Wiley
Date: 02-2018
DOI: 10.1002/PLD3.42
Opportunities for wheat proteomics to discover the biomarkers for respiration-dependent biomass production, stress tolerance and cytoplasmic male sterility
Publisher: Elsevier BV
Date: 06-2016
DOI: 10.1016/J.JPROT.2016.02.014
Abstract: Wheat has served as a key species for characterising fundamental aspects of mitochondrial biochemistry and respiratory physiology. Respiratory traits are linked to many important agronomic properties, so identifying the proteins that carry out these molecular processes would define a new set of targets for wheat breeding. To date, systematic proteomic investigations into wheat mitochondria have lagged behind other species, due to the size and complexity of the wheat genome. However this situation is changing with new sequence data increasing the power of proteomics applied to wheat. In this review, we argue that the impact of wheat mitochondrial proteomics on wheat respiratory traits can be improved through integrating data from current proteomics approaches with knowledge from the wheat respiration literature. We present a historical overview of biochemical and physiological studies of mitochondrial respiration in wheat, highlighting respiratory properties linked to agronomically important traits, such as biomass production, stress tolerance and cytoplasmic male sterility. Also, we summarise the current status of the wheat mitochondrial proteome and present a predicted set of 2000 probable mitochondrial proteins from Triticum urartu. Finally, we present a set of strategies outlining how future proteomics experiments can be applied to wheat mitochondria, by targeting studies to build on pre-existing knowledge.
Arabidopsis tRNA Adenosine Deaminase Arginine Edits the Wobble Nucleotide of Chloroplast tRNA(Arg)(ACG) and Is Essential for Efficient Chloroplast Translation
Publisher: Oxford University Press (OUP)
Date: 07-2009
Abstract: RNA editing changes the coding/decoding information relayed by transcripts via nucleotide insertion, deletion, or conversion. Editing of tRNA anticodons by deamination of adenine to inosine is used both by eukaryotes and prokaryotes to expand the decoding capacity of in idual tRNAs. This limits the number of tRNA species required for codon-anticodon recognition. We have identified the Arabidopsis thaliana gene that codes for tRNA adenosine deaminase arginine (TADA), a chloroplast tRNA editing protein specifically required for deamination of chloroplast (cp)-tRNAArg(ACG) to cp-tRNAArg(ICG). Land plant TADAs have a C-terminal domain similar in sequence and predicted structure to prokaryotic tRNA deaminases and also have very long N-terminal extensions of unknown origin and function. Biochemical and mutant complementation studies showed that the C-terminal domain is sufficient for cognate tRNA deamination both in vitro and in planta. Disruption of TADA has profound effects on chloroplast translation efficiency, leading to reduced yields of chloroplast-encoded proteins and impaired photosynthetic function. By contrast, chloroplast transcripts accumulate to levels significantly above those of wild-type plants. Nevertheless, absence of cp-tRNAArg(ICG) is compatible with plant survival, implying that two out of three CGN codon recognition occurs in chloroplasts, though this mechanism is less efficient than wobble pairing.
Application of selected reaction monitoring mass spectrometry to field-grown crop plants to allow dissection of the molecular mechanisms of abiotic stress tolerance
Publisher: Frontiers Media SA
Date: 2013
Mitochondrial biochemistry
Publisher: John Wiley & Sons, Ltd
Date: 08-12-2017
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.
Environmental stress causes oxidative damage to plant mitochondria leading to inhibition of glycine decarboxylase
Publisher: Elsevier BV
Date: 11-2002
Development and Governance of FAIR Thresholds for a Data Federation
Publisher: Ubiquity Press, Ltd.
Date: 2022
DOI: 10.5334/DSJ-2022-013
Selected reaction monitoring to determine protein abundance in Arabidopsis using the Arabidopsis proteotypic predictor
Publisher: Oxford University Press (OUP)
Date: 02-12-2014
Addressing Research Bottlenecks to Crop Productivity
Publisher: Elsevier BV
Date: 06-2021
Lipoic Acid-Dependent Oxidative Catabolism of α-Keto Acids in Mitochondria Provides Evidence for Branched-Chain Amino Acid Catabolism in Arabidopsis
Publisher: Oxford University Press (OUP)
Date: 02-2004
Abstract: Lipoic acid-dependent pathways of α-keto acid oxidation by mitochondria were investigated in pea (Pisum sativum), rice (Oryza sativa), and Arabidopsis. Proteins containing covalently bound lipoic acid were identified on isoelectric focusing/sodium dodecyl sulfate-polyacrylamide gel electrophoresis separations of mitochondrial proteins by the use of antibodies raised to this cofactor. All these proteins were identified by tandem mass spectrometry. Lipoic acid-containing acyltransferases from pyruvate dehydrogenase complex and α-ketoglutarate dehydrogenase complex were identified from all three species. In addition, acyltransferases from the branched-chain dehydrogenase complex were identified in both Arabidopsis and rice mitochondria. The substrate-dependent reduction of NAD+ was analyzed by spectrophotometry using specific α-keto acids. Pyruvate- and α-ketoglutarate-dependent reactions were measured in all three species. Activity of the branched-chain dehydrogenase complex was only measurable in Arabidopsis mitochondria using substrates that represented the α-keto acids derived by deamination of branched-chain amino acids (Val [valine], leucine, and isoleucine). The rate of branched-chain amino acid- and α-keto acid-dependent oxygen consumption by intact Arabidopsis mitochondria was highest with Val and the Val-derived α-keto acid, α-ketoisovaleric acid. Sequencing of peptides derived from trypsination of Arabidopsis mitochondrial proteins revealed the presence of many of the enzymes required for the oxidation of all three branched-chain amino acids. The potential role of branched-chain amino acid catabolism as an oxidative phosphorylation energy source or as a detoxification pathway during plant stress is discussed.
Editorial for Special Issue “Plant Mitochondria”
Publisher: MDPI AG
Date: 03-12-2018
DOI: 10.3390/IJMS19123849
Abstract: The primary function of mitochondria is respiration, where catabolism of substrates is coupled to adenosine triphosphate (ATP) synthesis via oxidative phosphorylation (OxPhos). [...]
Pursuing the identification of O 2 deprivation survival mechanisms in plants related to selective mRNA translation, hormone-independent cellular elongation and preparation for the arrival of oxygen
Publisher: Informa UK Limited
Date: 10-2011
Investigating the Role of Respiration in Plant Salinity Tolerance by Analyzing Mitochondrial Proteomes from Wheat and a Salinity-Tolerant Amphiploid (Wheat x Lophopyrum elongatum)
Publisher: American Chemical Society (ACS)
Date: 16-08-2013
DOI: 10.1021/PR400504A
Abstract: The effect of salinity on mitochondrial properties was investigated by comparing the reference wheat variety Chinese Spring (CS) to a salt-tolerant hiploid (AMP). The octoploid AMP genotype was previously generated by combining hexaploid bread wheat (CS) with the diploid wild wheatgrass adapted to salt marshes, Lophopyrum elongatum. Here we used a combination of physiological, biochemical, and proteomic analyses to explore the mitochondrial and respiratory response to salinity in these two genotypes. The AMP showed greater growth tolerance to salinity treatments and altered respiration rate in both roots and shoots. A proteomic workflow of 2D-DIGE and MALDI TOF/TOF mass spectrometry was used to compare the protein composition of isolated mitochondrial s les from roots and shoots of both genotypes, following control or salt treatment. A large set of mitochondrial proteins were identified as responsive to salinity in both genotypes, notably enzymes involved in detoxification of reactive oxygen species. Genotypic differences in mitochondrial composition were also identified, with AMP exhibiting a higher abundance of manganese superoxide dismutase, serine hydroxymethyltransferase, aconitase, malate dehydrogenase, and β-cyanoalanine synthase compared to CS. We present peptide fragmentation spectra derived from some of these AMP-specific protein spots, which could serve as biomarkers to track superior protein variants.
Subcellular proteomics-where cell biology meets protein chemistry
Publisher: Frontiers Media SA
Date: 2014
Resource: Mapping the Triticum aestivum proteome
Publisher: Wiley
Date: 02-2017
DOI: 10.1111/TPJ.13402
Abstract: Yield and quality improvement of bread wheat (Triticum aestivum) is a focus in efforts to meet new demands from population growth and changing human diets. As the complexity of the wheat genome is unravelled, determining how it is used to build the protein machinery of wheat plants is a key next step in explaining detailed aspects of wheat growth and development. The specific functions of wheat organs during vegetative development and the role of metabolism, protein degradation and remobilisation in driving grain production are the foundations of crop performance and have recently become accessible through studies of the wheat proteome. We present a large scale, publicly accessible proteome mapping of wheat consisting of 24 organ and developmental s les. Tissue specific sub-proteomes and ubiquitously expressed markers of the wheat proteome are identified, alongside hierarchical assessment of protein functional classes, their presence in different tissues and correlations between the abundance of functional classes of proteins. Gene-specific identifications and protein family relationships are accounted for in the organisation of the data and 202 new protein-coding transcripts identified by proteogenomic mapping. The interactive database will serve as a vehicle to build, refine and deposit confirmed targeted proteomic assays for wheat proteins and protein families to assess function (www.wheatproteome.org).
Responses of the Mitochondrial Respiratory System to Low Temperature in Plants
Publisher: Informa UK Limited
Date: 04-07-2017
Identification of intra- and intermolecular disulphide bonding in the plant mitochondrial proteome by diagonal gel electrophoresis
Publisher: Wiley
Date: 11-2007
Abstract: Redox active proteins in plant mitochondria were examined using 2-D oxidant/reductant diagonal-SDS-PAGE to separate and identify proteins with intermolecular or intramolecular disulphide bonds using diamide in the first dimension and DTT in the second dimension. Eighteen proteins spots were resolved either above or below the diagonal and these were in-gel digested and identified by MS/MS. This analysis revealed intermolecular disulphide bonds in alternative oxidase, O-acetylserine (thiol) lyase, citrate synthase and between subunits of the ATP synthase. Intramolecular disulphide bonds were observed in a range of mitochondrial dehydrogenases, elongation factor Tu, adenylate kinase and the phosphate translocator. Many of the soluble proteins found were known glutaredoxin/thioredoxin targets in other plants, but the membrane proteins were not found by these methods nor were the nature of the disulphides able to be investigated. The accessibility of thiols involved in disulphide bonds to modification by a lipid derived aldehyde gave an insight into the potential impact of Cys modification on redox-functions in mitochondria during lipid peroxidation. Comparison of the protein sequences of the identified proteins with homologs from other species has identified specific Cys residues that may be responsible for plant-specific redox modulations of mitochondrial proteins.
Elucidating the Inability of Functionalized Nanoparticles to Cross the Blood–Brain Barrier and Target Specific Cells in Vivo
Publisher: American Chemical Society (ACS)
Date: 31-05-2019
Abstract: The adsorption of serum proteins on the surface of nanoparticles (NPs) delivered into a biological environment has been known to alter NP surface properties and consequently their targeting efficiency. In this paper, we use random copolymer (p(HEMA- ran-GMA))-based NPs synthesized using 2-hydroxyethyl methacrylate (HEMA) and glycidyl methacrylate (GMA). We show that serum proteins bind to the NP and that functionalization with antibodies and peptides designed to facilitate NP passage across the blood-brain barrier (BBB) to bind specific cell types is ineffective. In particular, we use systematic in vitro and in vivo analyses to demonstrate that p(HEMA- ran-GMA) NPs functionalized with HIV-1 trans-activating transcriptor peptide (known to cross the BBB) and α neural/glial antigen 2 (NG2) (known for targeting oligodendrocyte precursor cells (OPCs)), in idually and in combination, do not specifically target OPCs and are unable to cross the BBB, likely due to the serum protein binding to the NPs.
Differential impact of environmental stresses on the pea mitochondrial proteome
Publisher: Elsevier BV
Date: 08-2005
Long bugs to short plants - The Lon protease in protein stability and thermotolerance
Publisher: Wiley
Date: 15-01-2009
Resolving and identifying protein components of plant mitochondrial respiratory complexes using three dimensions of gel electrophoresis
Publisher: American Chemical Society (ACS)
Date: 12-01-2008
DOI: 10.1021/PR700595P
Abstract: Analyzing highly hydrophobic proteins is a challenge for identification protocols based on gel separation and mass spectrometry. We combined Blue Native and 2D tricine gel electrophoresis to allow separation and identification of respiratory complex subunits from Arabidopsis mitochondria. We identified many of the highly hydrophobic mitochondrion-encoded subunits (GRAVY scores between +0.6 to +1.4) and also found a number of nucleus-encoded proteins associated with complex I for the first time in plants.
Novel Proteins, Putative Membrane Transporters, and an Integrated Metabolic Network Are Revealed by Quantitative Proteomic Analysis of Arabidopsis Cell Culture Peroxisomes
Publisher: Oxford University Press (OUP)
Date: 17-10-2008
Abstract: Peroxisomes play key roles in energy metabolism, cell signaling, and plant development. A better understanding of these important functions will be achieved with a more complete definition of the peroxisome proteome. The isolation of peroxisomes and their separation from mitochondria and other major membrane systems have been significant challenges in the Arabidopsis (Arabidopsis thaliana) model system. In this study, we present new data on the Arabidopsis peroxisome proteome obtained using two new technical advances that have not previously been applied to studies of plant peroxisomes. First, we followed density gradient centrifugation with free-flow electrophoresis to improve the separation of peroxisomes from mitochondria. Second, we used quantitative proteomics to identify proteins enriched in the peroxisome fractions relative to mitochondrial fractions. We provide evidence for peroxisomal localization of 89 proteins, 36 of which have not previously been identified in other analyses of Arabidopsis peroxisomes. Chimeric green fluorescent protein constructs of 35 proteins have been used to confirm their localization in peroxisomes or to identify endoplasmic reticulum contaminants. The distribution of many of these peroxisomal proteins between soluble, membrane-associated, and integral membrane locations has also been determined. This core peroxisomal proteome from nonphotosynthetic cultured cells contains a proportion of proteins that cannot be predicted to be peroxisomal due to the lack of recognizable peroxisomal targeting sequence 1 (PTS1) or PTS2 signals. Proteins identified are likely to be components in peroxisome biogenesis, β-oxidation for fatty acid degradation and hormone biosynthesis, photorespiration, and metabolite transport. A considerable number of the proteins found in peroxisomes have no known function, and potential roles of these proteins in peroxisomal metabolism are discussed. This is aided by a metabolic network analysis that reveals a tight integration of functions and highlights specific metabolite nodes that most probably represent entry and exit metabolites that could require transport across the peroxisomal membrane.
Mitochondrial Composition, Function and Stress Response in Plants
Publisher: Wiley
Date: 10-2012
DOI: 10.1111/J.1744-7909.2012.01177.X
Abstract: The primary function of mitochondria is respiration, where catabolism of substrates is coupled to ATP synthesis via oxidative phosphorylation. In plants, mitochondrial composition is relatively complex and flexible and has specific pathways to support photosynthetic processes in illuminated leaves. This review begins with outlining current models of mitochondrial composition in plant cells, with an emphasis upon the assembly of the complexes of the classical electron transport chain (ETC). Next, we focus upon the comparative analysis of mitochondrial function from different tissue types. A prominent theme in the plant mitochondrial literature involves linking mitochondrial composition to environmental stress responses, and this review then gives a detailed outline of how oxidative stress impacts upon the plant mitochondrial proteome with particular attention to the role of transition metals. This is followed by an analysis of the signaling capacity of mitochondrial reactive oxygen species, which studies the transcriptional changes of stress responsive genes as a framework to define specific signals emanating from the mitochondrion. Finally, specific mitochondrial roles during exposure to harsh environments are outlined, with attention paid to mitochondrial delivery of energy and intermediates, mitochondrial support for photosynthesis, and mitochondrial processes operating within root cells that mediate tolerance to anoxia and unfavorable soil chemistries. [Formula: see text] [ A. Harvey Millar (Corresponding author)].
Diel‐ and temperature‐driven variation of leaf dark respiration rates and metabolite levels in rice
Publisher: Wiley
Date: 07-06-2020
DOI: 10.1111/NPH.16661
An Ancient Peptide Family Buried within Vicilin Precursors
Publisher: American Chemical Society (ACS)
Date: 11-04-2019
DOI: 10.1021/ACSCHEMBIO.9B00167
Abstract: New proteins can evolve by duplication and ergence or de novo, from previously noncoding DNA. A recently observed mechanism is for peptides to evolve within a "host" protein and emerge by proteolytic processing. The first ex les of such interstitial peptides were ones hosted by precursors for seed storage albumin. Interstitial peptides have also been observed in precursors for seed vicilins, but current evidence for vicilin-buried peptides (VBPs) is limited to seeds of the broadleaf plants pumpkin and macadamia. Here, an extensive sequence analysis of vicilin precursors suggested that peptides buried within the N-terminal region of preprovicilins are widespread and truly ancient. Gene sequences indicative of interstitial peptides were found in species from Amborellales to eudicots and include important grass and legume crop species. We show the first protein evidence for a monocot VBP in date palm seeds as well as protein evidence from other crops including the common tomato, sesame and pumpkin relatives, cucumber, and the sponge loofah ( Luffa aegyptiaca). Their excision was consistent with asparaginyl endopeptidase-mediated maturation, and sequences were confirmed by tandem mass spectrometry. Our findings suggest that the family is large and ancient and that based on the NMR solution structures for loofah Luffin P1 and tomato VBP-8, VBPs adopt a helical hairpin fold stapled by two internal disulfide bonds. The first VBPs characterized were a protease inhibitor, antimicrobials, and a ribosome inactivator. The age and evolutionary retention of this peptide family suggest its members play important roles in plant biology.
Differential Molecular Responses of Rice and Wheat Coleoptiles to Anoxia Reveal Novel Metabolic Adaptations in Amino Acid Metabolism for Tissue Tolerance
Publisher: Oxford University Press (OUP)
Date: 08-2011
Abstract: Rice (Oryza sativa) and wheat (Triticum aestivum) are the most important starch crops in world agriculture. While both germinate with an anatomically similar coleoptile, this tissue defines the early anoxia tolerance of rice and the anoxia intolerance of wheat seedlings. We combined protein and metabolite profiling analysis to compare the differences in response to anoxia between the rice and wheat coleoptiles. Rice coleoptiles responded to anoxia dramatically, not only at the level of protein synthesis but also at the level of altered metabolite pools, while the wheat response to anoxia was slight in comparison. We found significant increases in the abundance of proteins in rice coleoptiles related to protein translation and antioxidant defense and an accumulation of a set of enzymes involved in serine, glycine, and alanine biosynthesis from glyceraldehyde-3-phosphate or pyruvate, which correlates with an observed accumulation of these amino acids in anoxic rice. We show a positive effect on wheat root anoxia tolerance by exogenous addition of these amino acids, indicating that their synthesis could be linked to rice anoxia tolerance. The potential role of amino acid biosynthesis contributing to anoxia tolerance in cells is discussed.
Divalent Metal Ions in Plant Mitochondria and Their Role in Interactions with Proteins and Oxidative Stress-Induced Damage to Respiratory Function
Publisher: Oxford University Press (OUP)
Date: 14-12-2009
Abstract: Understanding the metal ion content of plant mitochondria and metal ion interactions with the proteome are vital for insights into both normal respiratory function and the process of protein damage during oxidative stress. We have analyzed the metal content of isolated Arabidopsis (Arabidopsis thaliana) mitochondria, revealing a 26:8:6:1 molar ratio for iron:zinc:copper:manganese and trace amounts of cobalt and molybdenum. We show that selective changes occur in mitochondrial copper and iron content following in vivo and in vitro oxidative stresses. Immobilized metal affinity chromatography charged with Cu2+, Zn2+, and Co2+ was used to identify over 100 mitochondrial proteins with metal-binding properties. There were strong correlations between the sets of immobilized metal affinity chromatography-interacting proteins, proteins predicted to contain metal-binding motifs, and protein sets known to be oxidized or degraded during abiotic stress. Mitochondrial respiratory chain pathways and matrix enzymes varied widely in their susceptibility to metal-induced loss of function, showing the selectivity of the process. A detailed study of oxidized residues and predicted metal interaction sites in the tricarboxylic acid cycle enzyme aconitase identified selective oxidation of residues in the active site and showed an approach for broader screening of functionally significant oxidation events in the mitochondrial proteome.
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