Ian Small

The gene encoding Arabidopsis thaliana mitochondrial ribosomal protein S13 is a recent duplication of the gene encoding plastid S13

Publisher: Springer Science and Business Media LLC

Date: 03-2002

DOI: 10.1007/S00294-002-0271-5

Abstract: A gene encoding mitochondrial S13 is generally present in the mitochondrial genome of higher plants, but is lacking from the Arabidopsis thaliana mitochondrial genome. Previous research has failed to identify a nuclear gene capable of encoding a mitochondrial S13 protein or the protein itself. Doubts have even been raised as to whether a mitochondrial S13 exists in Arabidopsis. Here, we show that the nuclear gene encoding the plastid S13 has been partially duplicated in A. thaliana, such that the copy has lost the exon encoding the plastid transit peptide and acquired a sequence capable of encoding a mitochondrial targeting sequence. The two S13 sequences were fused to green fluorescent protein and shown to be targeted to plastids and mitochondria respectively.

Pentatricopeptide repeat (PPR) proteins as sequence-specificity factors in post-transcriptional processes in organelles

Publisher: Portland Press Ltd.

Date: 23-11-2007

DOI: 10.1042/BST0351643

Abstract: PPR (pentatricopeptide repeat) genes form a large family particularly prevalent in higher plants and targeted to organelles. They are involved in many post-transcriptional processes such as splicing, editing, processing and translation. Current data suggest that PPR proteins are involved in targeting effectors to the correct sites on the correct transcripts but the molecular mechanisms for RNA binding and effector recruitment by PPR proteins are not understood yet.

Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit

Publisher: EMBO

Date: 2012

DOI: 10.1038/MSB.2012.39

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

DOI: 10.1105/TPC.107.054841

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.

Characterization of the nuclear gene encoding chloroplast ribosomal protein S13 from Arabidopsis thaliana

Publisher: Springer Science and Business Media LLC

Date: 09-1995

DOI: 10.1007/BF00326432

RNAi for revealing and engineering plant gene functions

Publisher: Elsevier BV

Date: 04-2007

DOI: 10.1016/J.COPBIO.2007.01.012

Abstract: RNA interference (RNAi) is now widely used in plant biotechnology, both as a useful tool for discovering or validating gene functions as well as a quick way of engineering specific reductions in expression of chosen genes. Although the amazing popularity of RNAi as a biotechnology tool is certainly justified, the underlying biology is still being worked out and the relative advantages and disadvantages of the approach are only now becoming clear. Recent breakthroughs in elucidating the multiple pathways of RNA-based post-transcriptional control and preliminary results from the first large-scale uses of RNAi in plants will make it easier to gauge the usefulness of the technique. To fully capitalize on the potential of RNAi, we need to become better at predicting and controlling its effects.

A DYW-protein knockout in Physcomitrella affects two closely spaced mitochondrial editing sites and causes a severe developmental phenotype

Publisher: Wiley

Date: 10-09-2013

DOI: 10.1111/TPJ.12304

Abstract: RNA-binding pentatricopeptide repeat (PPR) proteins carrying a carboxy-terminal DYW domain similar to cytidine deaminases have been characterized as site-specific factors for C-to-U RNA editing in plant organelles. Here we report that knockout of DYW-PPR_65 in Physcomitrella patens causes a severe developmental phenotype in the moss and specifically affects two editing sites located 18 nucleotides apart on the mitochondrial ccmFC mRNA. Intriguingly, PPR_71, another DYW-type PPR, had been identified previously as an editing factor specifically affecting only the downstream editing site, ccmFCeU122SF. The now characterized PPR_65 binds specifically only to the upstream target site, ccmFCeU103PS, in full agreement with a recent RNA-recognition code for PPR arrays. The functional interference between the two editing events may be caused by a combination of three factors: (i) the destabilization of an RNA secondary structure interfering with PPR_71 binding by prior binding of PPR_65 (ii) the resulting upstream C-U conversion or (iii) a direct interaction between the two DYW proteins. Indeed, we find the Physcomitrella DYW-PPRs to interact in yeast-two-hybrid assays. The moss DYW-PPRs also interact yet more strongly with MORF (Multiple Organellar RNA editing Factor)/RIP (RNA editing factor interacting proteins) proteins of Arabidopsis known to be general editing factors in flowering plants, although MORF homologues are entirely absent in the moss. Finally, we demonstrate binding of Physcomitrella DYW-PPR_98, for which no KO lines could be raised, to its predicted target sequence upstream of editing site atp9eU92SL. Together with the functional characterization of DYW-PPR_65, this completes the assignment of RNA editing factors to all editing sites in the Physcomitrella mitochondrial transcriptome.

Predictable alteration of sequence recognition by RNA editing factors from arabidopsis

Publisher: Oxford University Press (OUP)

Date: 02-2015

DOI: 10.1105/TPC.114.134189

A reevaluation of dual-targeting of proteins to mitochondria and chloroplasts

Publisher: Elsevier BV

Date: 02-2013

DOI: 10.1016/J.BBAMCR.2012.05.029

Abstract: Over 100 proteins are found in both mitochondria and chloroplasts, via a variety of processes known generally as 'dual-targeting'. Dual-targeting has attracted interest from many different research groups because of its profound implications concerning the mechanisms of protein import into these organelles and the evolution of both the protein import machinery and the targeting sequences within the imported proteins. Beyond these aspects, dual-targeting is also interesting for its implications concerning shared functions between mitochondria and chloroplasts, and especially the control of the activities of these two very different energy organelles. We discuss each of these points in the light of the latest relevant research findings and make some suggestions for where research might be most illuminating in the near future. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.

Purification of mitochondria and mitochondrial nucleic acids from embryogenic suspension cultures of a gymnosperm, Larix x leptoeuropaea

Publisher: Springer Science and Business Media LLC

Date: 05-1995

DOI: 10.1007/BF00232790

Mitochondrial Defects Confer Tolerance against Cellulose Deficiency

Publisher: Oxford University Press (OUP)

Date: 19-08-2016

DOI: 10.1105/TPC.16.00540

SUBA: the Arabidopsis subcellular database

Publisher: Oxford University Press (OUP)

Date: 28-10-2007

DOI: 10.1093/NAR/GKL863

Editing and import: Strategies for providing plant mitochondria with a complete set of functional transfer RNAs

Publisher: Elsevier BV

Date: 1996

DOI: 10.1016/0300-9084(96)84758-4

Abstract: The recombinations and mutations that plant mitochondrial DNA has undergone during evolution have led to the inactivation or complete loss of a number of the 'native' transfer RNA genes deriving from the genome of the ancestral endosymbiont. Following sequence ergence in their genes, some native mitochondrial tRNAs are 'rescued' by editing, a post-transcriptional process which changes the RNA primary sequence. According to in vitro studies with the native mitochondrial tRNA(Phe) from potato and tRNA(His) from larch, editing is required for efficient processing. Some of the native tRNA genes which have been inactivated or lost have been replaced by tRNA genes present in plastid DNA sequences acquired by the mitochondrial genome during evolution, which raises the problem of the transcriptional regulation of tRNA genes in plant mitochondria. Finally, tRNAs for which no gene is present in the mitochondrial genome are imported from the cytosol. This process is highly specific for certain tRNAs, and it has been suggested that the cognate aminoacyl-tRNA synthetases may be responsible for this specificity. Indeed, a mutation which blocks recognition of the cytosolic Arabidopsis thaliana tRNA(Ala) by the corresponding alanyl-tRNA synthetase also prevents mitochondrial import of this tRNA in transgenic plants. Conversely, no significant mitochondrial co-import of the normally cytosol-specific tRNA(Asp) was detected in transgenic plants expressing the yeast cytosolic aspartyl-tRNA synthetase fused to a mitochondrial targeting sequence, suggesting that, although necessary, recognition by a cognate aminoacyl-tRNA synthetase might not be sufficient to allow tRNA import into plant mitochondria.

Plant organellar RNA maturation

Publisher: Oxford University Press (OUP)

Date: 21-02-2023

DOI: 10.1093/PLCELL/KOAD049

Abstract: Plant organellar RNA metabolism is run by a multitude of nucleus-encoded RNA-binding proteins (RBPs) that control RNA stability, processing, and degradation. In chloroplasts and mitochondria, these post-transcriptional processes are vital for the production of a small number of essential components of the photosynthetic and respiratory machinery—and consequently for organellar biogenesis and plant survival. Many organellar RBPs have been functionally assigned to in idual steps in RNA maturation, often specific to selected transcripts. While the catalog of factors identified is ever-growing, our knowledge of how they achieve their functions mechanistically is far from complete. This review summarizes the current knowledge of plant organellar RNA metabolism taking an RBP-centric approach and focusing on mechanistic aspects of RBP functions and the kinetics of the processes they are involved in.

Remodeled Respiration in ndufs4 with Low Phosphorylation Efficiency Suppresses Arabidopsis Germination and Growth and Alters Control of Metabolism at Night

Publisher: Oxford University Press (OUP)

Date: 12-08-2009

DOI: 10.1104/PP.109.141770

Abstract: Respiratory oxidative phosphorylation is a cornerstone of cellular metabolism in aerobic multicellular organisms. The efficiency of this process is generally assumed to be maximized, but the presence of dynamically regulated nonphosphorylating bypasses implies that plants can alter phosphorylation efficiency and can benefit from lowered energy generation during respiration under certain conditions. We characterized an Arabidopsis (Arabidopsis thaliana) mutant, ndufs4 (for NADH dehydrogenase [ubiquinone] fragment S subunit 4), lacking complex I of the respiratory chain, which has constitutively lowered phosphorylation efficiency. Through analysis of the changes to mitochondrial function as well as whole cell transcripts and metabolites, we provide insights into how cellular metabolism flexibly adapts to reduced phosphorylation efficiency and why this state may benefit the plant by providing moderate stress tolerance. We show that removal of the single protein subunit NDUFS4 prevents assembly of complex I and removes its function from mitochondria without pleiotropic effects on other respiratory components. However, the lack of complex I promotes broad changes in the nuclear transcriptome governing growth and photosynthetic function. We observed increases in organic acid and amino acid pools in the mutant, especially at night, concomitant with alteration of the adenylate content. While germination is delayed, this can be rescued by application of gibberellic acid, and root growth assays of seedlings show enhanced tolerance to cold, mild salt, and osmotic stress. We discuss these observations in the light of recent data on the knockout of nonphosphorylating respiratory bypass enzymes that show opposite changes in metabolites and stress sensitivity. Our data suggest that the absence of complex I alters the adenylate control of cellular metabolism.

Nuclearly encoded splicing factors implicated in RNA splicing in higher plant organelles

Publisher: Elsevier BV

Date: 07-2010

DOI: 10.1093/MP/SSQ025

Abstract: Plant organelles arose from two independent endosymbiosis events. Throughout evolutionary history, tight control of chloroplasts and mitochondria has been gained by the nucleus, which regulates most steps of organelle genome expression and metabolism. In particular, RNA maturation, including RNA splicing, is highly dependent on nuclearly encoded splicing factors. Most introns in organelles are group II introns, whose catalytic mechanism closely resembles that of the nuclear spliceosome. Plant group II introns have lost the ability to self-splice in vivo and require nuclearly encoded proteins as cofactors. Since the first splicing factor was identified in chloroplasts more than 10 years ago, many other proteins have been shown to be involved in splicing of one or more introns in chloroplasts or mitochondria. These new proteins belong to a variety of different families of RNA binding proteins and provide new insights into ribonucleo-protein complexes and RNA splicing machineries in organelles. In this review, we describe how splicing factors, encoded by the nucleus and targeted to the organelles, take part in post-transcriptional steps in higher plant organelle gene expression. We go on to discuss the potential for these factors to regulate organelle gene expression.

Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences

Publisher: Wiley

Date: 25-05-2004

DOI: 10.1002/PMIC.200300776

Abstract: Probably more than 25% of the proteins encoded by the nuclear genomes of multicellular eukaryotes are targeted to membrane-bound compartments by N-terminal targeting signals. The major signals are those for the endoplasmic reticulum, the mitochondria, and in plants, plastids. The most abundant of these targeted proteins are well-known and well-studied, but a large proportion remain unknown, including most of those involved in regulation of organellar gene expression or regulation of biochemical pathways. The discovery and characterization of these proteins by biochemical means will be long and difficult. An alternative method is to identify candidate organellar proteins via their characteristic N-terminal targeting sequences. We have developed a neural network-based approach (Predotar--Prediction of Organelle Targeting sequences) for identifying genes encoding these proteins amongst eukaryotic genome sequences. The power of this approach for identifying and annotating novel gene families has been illustrated by the discovery of the pentatricopeptide repeat family.

In Silico Identification of Candidate Genes for Fertility Restoration in Cytoplasmic Male Sterile Perennial Ryegrass (Lolium perenne L.)

Publisher: Oxford University Press (OUP)

Date: 06-03-2017

DOI: 10.1093/GBE/EVW047

Mutations in an Arabidopsis Mitochondrial Transcription Termination Factor-Related Protein Enhance Thermotolerance in the Absence of the Major Molecular Chaperone HSP101

Publisher: Oxford University Press (OUP)

Date: 08-2012

DOI: 10.1105/TPC.112.101006

Identification of a pentatricopeptide repeat protein implicated in splicing of intron 1 of mitochondrial nad7 transcripts

Publisher: Elsevier BV

Date: 10-2010

DOI: 10.1074/JBC.M110.147603

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

Publisher: Oxford University Press (OUP)

Date: 16-02-2012

DOI: 10.1104/PP.111.192351

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

Role of editing in plant mitochondrial transfer RNAs

Publisher: Elsevier BV

Date: 03-2002

DOI: 10.1016/S0378-1119(01)00817-4

Abstract: Editing in plant mitochondria consists in C to U changes and mainly affects messenger RNAs, thus providing the correct genetic information for the biosynthesis of mitochondrial (mt) proteins. But editing can also affect some of the plant mt tRNAs encoded by the mt genome. In dicots, a C to U editing event corrects a C:A mismatch into a U:A base pair in the acceptor stem of mt tRNA(Phe) (GAA). In larch mitochondria, three C to U editing events restore U:A base pairs in the acceptor stem, D stem and anticodon stem, respectively, of mt tRNA(His) (GUG). For both these mt RNA(Phe) and tRNA(His), editing of the precursors is a prerequisite for their processing into mature tRNAs. In potato mt tRNA(Cys) (GCA), editing converts a C28:U42 mismatch in the anticodon stem into a U28:U42 non-canonical base pair, and reverse transcriptase minisequencing has shown that the mature mt tRNA(Cys) is fully edited. In the bryophyte Marchantia polymorpha this U residue is encoded in the mt genome and evolutionary studies suggest that restoration of a U28 residue is necessary when it is not encoded in the gene. However, in vitro studies have shown that neither processing of the precursor, nor aminoacylation of tRNA(Cys), requires C to U editing at this position. But sequencing of the purified mt tRNA(Cys) has shown that Psi is present at position 28, indicating that C to U editing is a prerequisite for the subsequent isomerization of U into Psi at position 28.

Alteration of Mitochondrial Transcript Expression in Arabidopsis thaliana Using a Custom-Made Library of Pentatricopeptide Repeat Proteins

Publisher: MDPI AG

Date: 26-08-2023

DOI: 10.3390/IJMS241713233

Abstract: Pentatricopeptide repeat (PPR) proteins are considered a potential tool for manipulating organelle gene expression in plants because they can recognise a wide range of different RNA sequences, and the molecular basis for this sequence recognition is partially known and understood. A library of redesigned PPR proteins related to restorer-of-fertility proteins was created and transformed into plants in order to target mitochondrial transcripts. Ninety different variants tested in vivo showed a wide range of phenotypes. One of these lines, which displayed slow growth and downward curled leaves, showed a clear reduction in complex V. The phenotype was due to a specific cleavage of atp1 transcripts induced by a modified PPR protein from the library, validating the use of this library as a source of mitochondrial ‘mutants’. This study is a step towards developing specific RNA targeting tools using PPR proteins that can be aimed at desired targets.

In Silico Methods for Identifying Organellar and Suborganellar Targeting Peptides in Arabidopsis Chloroplast Proteins and for Predicting the Topology of Membrane Proteins

Publisher: Humana Press

Date: 2011

DOI: 10.1007/978-1-61779-234-2_16

Abstract: Numerous experimental and in silico approaches have been developed for attempting to identify the -subcellular localisation of proteins. Approximately 2,000-4,000 proteins are thought to be targeted to plastids in plants, but a complete and unambiguous catalogue has yet to be drawn up. This article reviews the various prediction methods that identify plastid targeting sequences, and those that can help estimate location and topology within the plastid or plastid membranes. The most successful approaches are described in detail, with detailed notes to help avoid common pitfalls and advice on interpreting conflicting or ambiguous results. In most cases, it is best to try multiple approaches, and we also cover the powerful new integrated databases that provide a selected blend of experimental data and predictions.

Evolution of cox2 introns in angiosperm mitochondria and efficient splicing of an elongated cox2i691 intron

Publisher: Elsevier BV

Date: 06-2023

DOI: 10.1016/J.GENE.2023.147393

Identification of the fertility restoration locus, Rfo, in radish, as a member of the pentatricopeptide-repeat protein family

Publisher: EMBO

Date: 09-05-2003

DOI: 10.1038/SJ.EMBOR.EMBOR848

Abstract: Ogura cytoplasmic male sterility (CMS) in radish ( Raphanus sativus ) is caused by an aberrant mitochondrial gene, Orf138 , that prevents the production of functional pollen without affecting female fertility. Rfo , a nuclear gene that restores male fertility, alters the expression of Orf138 at the post‐transcriptional level. The Ogura CMS/ Rfo two‐component system is a useful model for investigating nuclear–cytoplasmic interactions, as well as the physiological basis of fertility restoration. Using a combination of positional cloning and microsynteny analysis of Arabidopsis thaliana and radish, we genetically and physically delimited the Rfo locus to a 15‐kb DNA segment. Analysis of this segment shows that Rfo is a member of the pentatricopeptide repeat (PPR) family. In Arabidopsis , this family contains more than 450 members of unknown function, although most of them are predicted to be targeted to mitochondria and chloroplasts and are thought to have roles in organellar gene expression.

A synthetic RNA editing factor edits its target site in chloroplasts and bacteria

Publisher: Springer Science and Business Media LLC

Date: 10-05-2021

DOI: 10.1038/S42003-021-02062-9

Abstract: Members of the pentatricopeptide repeat (PPR) protein family act as specificity factors in C-to-U RNA editing. The expansion of the PPR superfamily in plants provides the sequence variation required for design of consensus-based RNA-binding proteins. We used this approach to design a synthetic RNA editing factor to target one of the sites in the Arabidopsis chloroplast transcriptome recognised by the natural editing factor CHLOROPLAST BIOGENESIS 19 (CLB19). We show that our synthetic editing factor specifically recognises the target sequence in in vitro binding assays. The designed factor is equally specific for the target rpoA site when expressed in chloroplasts and in the bacterium E. coli. This study serves as a successful pilot into the design and application of programmable RNA editing factors based on plant PPR proteins.

A synthetic RNA editing factor edits its target site in chloroplasts and bacteria

Publisher: Research Square Platform LLC

Date: 12-2020

DOI: 10.21203/RS.3.RS-114803/V1

Abstract: Targeted cytidine to uridine RNA editing is a widespread phenomenon throughout the land plant lineage. Members of the pentatricopeptide repeat (PPR) protein family act as the specificity factors in this process. These proteins consist of helix-turn-helix domains, each of which recognises a single RNA nucleotide following a well-elucidated code. A cytidine deaminase-like domain (present at the C-terminus of some PPR editing factors or provided in trans via protein-protein interactions) is the catalytic domain in the process. The huge expansion of the PPR superfamily in land plants provides the sequence variation required for design of novel consensus-based RNA-binding proteins. We used this approach to construct a synthetic RNA editing factor designed to target one of the two sites in the Arabidopsis chloroplast transcriptome naturally recognised by the RNA editing factor CHLOROPLAST BIOGENESIS 19 (CLB19). We show that this designed editing factor specifically recognises the target sequence in in vitro binding assays and can partially complement a clb19 mutant. The designed factor is specific for the target rpoA site and does not recognise or edit the other site recognised by CLB19 in the clpP1 transcript. We show that the designed editing factor can function equally specifically in the bacterium E. coli, and shows some activity even in the absence of the editing cofactors that are often required for natural editing factor activity in plants. This study serves as a successful pilot into the design and application of programmable RNA editing factors based on plant PPR proteins.

Plant RNA editing

Publisher: Informa UK Limited

Date: 03-2010

DOI: 10.4161/RNA.7.2.11343

Abstract: In plants, post-transcriptional modification of transcripts includes C-to-U, U-to-C and A-to-I editing. RNA editing in plants is essential, with many mutants impaired in editing of specific sites exhibiting strong deleterious phenotypes, even lethality. The majority of editing in plants occurs in mitochondrial and plastid transcripts, however, A-to-I editing also occurs in cytosolic tRNAs. Here we review recent findings concerning the cellular machineries involved in the different types of editing, recent analysis of the proposed functions for editing, and recent models for its appearance and retention in different plant lineages.

Current status of the multinational Arabidopsis community

Publisher: Wiley

Date: 07-2020

DOI: 10.1002/PLD3.248

The potential for manipulating RNA with pentatricopeptide repeat proteins

Publisher: Wiley

Date: 29-01-2014

DOI: 10.1111/TPJ.12377

Abstract: The pentatricopeptide repeat (PPR) protein family, which is particularly prevalent in plants, includes many sequence-specific RNA-binding proteins involved in all aspects of organelle RNA metabolism, including RNA stability, processing, editing and translation. PPR proteins consist of a tandem array of 2-30 PPR motifs, each of which aligns to one nucleotide in the RNA target. The amino acid side chains at two or three specific positions in each motif confer nucleotide specificity in a predictable and programmable manner. Thus, PPR proteins appear to provide an extremely promising opportunity to create custom RNA-binding proteins with tailored specificity. We summarize recent progress in understanding RNA recognition by PPR proteins, with a particular focus on potential applications of PPR-based tools for manipulating RNA, and on the challenges that remain to be overcome before these tools may be routinely used by the scientific community.

OTP70 is a pentatricopeptide repeat protein of the E subgroup involved in splicing of the plastid transcript rpoC1

Publisher: Wiley

Date: 04-01-2011

DOI: 10.1111/J.1365-313X.2010.04441.X

Protein Complexes Implicated in RNA Editing in Plant Organelles

Publisher: Elsevier BV

Date: 10-2017

DOI: 10.1016/J.MOLP.2017.09.011

mCSF1, a nucleus-encoded CRM protein required for the processing of many mitochondrial introns, is involved in the biogenesis of respiratory complexes I and IV in Arabidopsis

Publisher: Wiley

Date: 07-05-2013

DOI: 10.1111/NPH.12282

Abstract: The coding regions of many mitochondrial genes in plants are interrupted by intervening sequences that are classified as group II introns. Their splicing is essential for the expression of the genes they interrupt and hence for respiratory function, and is facilitated by various protein cofactors. Despite the importance of these cofactors, only a few of them have been characterized. CRS 1‐ Y hb Y domain ( CRM ) is a recently recognized RNA ‐binding domain that is present in several characterized splicing factors in plant chloroplasts. The A rabidopsis genome encodes 16 CRM proteins, but these are largely uncharacterized. Here, we analyzed the intracellular location of one of these hypothetical proteins in A rabidopsis, mitochondrial CAF ‐like splicing factor 1 (m CSF 1 A t4 g31010), and analyzed the growth phenotypes and organellar activities associated with mcsf1 mutants in plants. Our data indicated that mCSF 1 resides within mitochondria and its functions are essential during embryogenesis. Mutant plants with reduced m CSF 1 displayed inhibited germination and retarded growth phenotypes that were tightly associated with reduced complex I and IV activities. Analogously to the functions of plastid‐localized CRM proteins, analysis of the RNA profiles in wildtype and mcsf1 plants showed that m CSF 1 acts in the splicing of many of the group II intron RNA s in A rabidopsis mitochondria.

The TATA motif, the CAA motif and the poly(T) transcription termination motif are all important for transcription re-initiation on plant tRNA genes

Publisher: Wiley

Date: 06-2000

DOI: 10.1046/J.1365-313X.2000.00752.X

Abstract: The effect of alteration of 5' and 3' flanking sequences on the transcription of plant tRNA genes was analysed using an RNA polymerase III-dependent in vitro transcription system derived from nuclei of cultured tobacco cells. A TATA-like sequence and the CAA motif frequently observed upstream of plant tRNA genes, and the poly(T) stretch usually present downstream, were shown to be necessary for efficient re-initiation of transcription. The CAA motif was shown to be a transcription initiation site. Introduction of the CAA and TATA-like motifs into a gene naturally lacking them greatly enhanced transcription by promoting efficient re-initiation.

Genome-scale transfer of mitochondrial DNA from legume hosts to the holoparasite Lophophytum mirabile (Balanophoraceae)

Publisher: Elsevier BV

Date: 03-2019

DOI: 10.1016/J.YMPEV.2018.12.006

Abstract: Angiosperm mitochondrial horizontal gene transfer (HGT) has been widely reported during the past decades. With a few exceptions, foreign sequences are mitochondrial genes or intronic regions from other plants, indicating that HGT has played a major role in shaping mitochondrial genome evolution. Host-parasite relationships are a valuable system to study this phenomenon due to the high frequency of HGT. In particular, the interaction between mimosoid legumes and holoparasites of the genus Lophophytum represents an outstanding opportunity to discern HGT events. The mitochondrial genome of the holoparasite L. mirabile has remarkable properties, the most extraordinary of which is the presence of 34 out of 43 mitochondrial protein genes acquired from its legume host, with the stunning replacement of up to 26 native homologs. However, the origin of the intergenic sequences that represent the majority (>90%) of the L. mirabile mtDNA remains largely unknown. The lack of mitochondrial sequences available from the donor angiosperm lineage (mimosoid legumes) precluded a large-scale evolutionary study. We sequenced and assembled the mitochondrial genome of the mimosoid Acacia ligulata and performed genome wide comparisons with L. mirabile. The A. ligulata mitochondrial genome is almost 700 kb in size, encoding 60 genes. About 60% of the L. mirabile mtDNA had greatest affinity to members of the family Fabaceae (∼49% to mimosoids in particular) with an average sequence identity of ∼96%, including genes but mostly intergenic regions. These findings strengthen the mitochondrial fusion compatibility model for angiosperm mitochondrion-to-mitochondrion HGT.

Establishment of photosynthesis through chloroplast development is controlled by two distinct regulatory phases

Publisher: Oxford University Press (OUP)

Date: 16-06-2018

DOI: 10.1104/PP.17.00435

Sequence and transcript analysis of the Nco2.5 Ogura-specific fragment correlated with cytoplasmic male sterility in Brassica cybrids

Publisher: Springer Science and Business Media LLC

Date: 11-1992

DOI: 10.1007/BF00279379

Synthetic PPR proteins as tools for sequence-specific targeting of RNA

Publisher: Elsevier BV

Date: 12-2022

DOI: 10.1016/J.YMETH.2022.10.003

Abstract: In native systems, gene expression is regulated by RNA binding proteins. Such proteins have been the target of a great deal of recent research interest, due to the potential for harnessing these regulatory effects for the construction of new biotechnological tools. In particular, focus has been targeted on building synthetic RNA binding proteins for sequence-specific targeting of new RNA transcripts. Pentatricopeptide repeat (PPR) proteins make compelling candidates as synthetic RNA binding proteins to target and bind RNA transcripts of interest, due to their defined RNA binding "code", modular structure, and native capability to deliver catalytic C-terminal domains. In this review, we present a summary of up-to-date understanding of RNA site recognition by PPR proteins, progress towards the design of synthetic PPR proteins for RNA targeting in vitro and in vivo, highlight key areas for further research around these proteins and present an outlook for future applications for synthetic PPR proteins as biotechnological tools.

Triticeae genome sequences reveal huge expansions of gene families implicated in fertility restoration

Publisher: Elsevier BV

Date: 04-2022

DOI: 10.1016/J.PBI.2021.102166

Abstract: Breakthroughs in assembly of whole-genome sequencing and targeted sequence capture data have accelerated comparative genomics analyses in cereals with big and complex genomes such as wheat. This newly acquired information has revealed unexpected expansions in two large gene families linked to restoration of fertility in species that exhibit cytoplasmic male sterility. Extreme levels of copy-number and structural variation detected within and between species illustrate the genetic ersity among the family members and reveal the evolutionary mechanisms at work. This new knowledge will greatly facilitate the development of hybrid production strategies in wheat and related species.

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

DOI: 10.1111/J.1365-313X.2008.03581.X

The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene

Publisher: Public Library of Science (PLoS)

Date: 08-05-2015

DOI: 10.1371/JOURNAL.PONE.0125768

CLB19, a pentatricopeptide repeat protein required for editing of rpoA and clpP chloroplast transcripts

Publisher: Wiley

Date: 11-2008

DOI: 10.1111/J.1365-313X.2008.03634.X

A hypothesis on the identification of the editing enzyme in plant organelles

Publisher: Wiley

Date: 10-08-2007

DOI: 10.1016/J.FEBSLET.2007.07.075

Abstract: RNA editing in plant organelles is an enigmatic process leading to conversion of cytidines into uridines. Editing specificity is determined by proteins both those known so far are pentatricopeptide repeat (PPR) proteins. The enzyme catalysing RNA editing in plants is still totally unknown. We propose that the DYW domain found in many higher plant PPR proteins is the missing catalytic domain. This hypothesis is based on two compelling observations: (i) the DYW domain contains invariant residues that match the active site of cytidine deaminases (ii) the phylogenetic distribution of the DYW domain is strictly correlated with RNA editing.

Multiple wheat genomes reveal global variation in modern breeding

Publisher: Springer Science and Business Media LLC

Date: 25-11-2020

DOI: 10.1038/S41586-020-2961-X

Abstract: Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat ( Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome 1 , and the lack of genome-assembly data for multiple wheat lines 2,3 . Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic ersity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to erse environments, grain yield and quality, and resistance to stresses 4,5 . We provide ex les outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1 6 , a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

A single base change prevents import of cytosolic tRNA^Alainto mitochondria in transgenic plants

Publisher: Wiley

Date: 11-1996

DOI: 10.1046/J.1365-313X.1996.10050913.X

Abstract: Plant mitochondria do not contain a full set of tRNA genes, and the additional tRNAs needed for protein synthesis (including tRNA(Ala) are imported from the cytosol. The import process appears to be highly specific for certain tRNAs, and it has been suggested that the cognate amino-acyl-tRNA synthetases may be responsible for this specificity. In order to test this, we have grown transgenic tobacco plants expressing Arabidopsis thaliana tRNA(Ala) carrying a U70 to C70 mutation, which we have previously shown blocks aminoacylation by the plant alanyl-tRNA synthetase. Unlike the wild-type tRNA(Ala), the mutant tRNA is not present in the mitochrondrial tRNA fraction. This is the first report of a tRNA mutation which prevents mitochondrial import and strongly supports the hypothesis that aminoacyl-tRNA synthetases are involved in this process in plants. Insertion of four bases into the anticodon loop of tRNA(Ala) does not prevent mitochondrial import, implying that the tRNA might not need to participate in translation to be imported.

A comparison of cytoplasmic revertants to fertility from different CMS-S maize sources

Publisher: Springer Science and Business Media LLC

Date: 10-1988

DOI: 10.1007/BF00260916

The coordinated action of PPR4 and EMB2654 on each intron half mediates trans‐splicing of rps12 transcripts in plant chloroplasts

Publisher: Wiley

Date: 25-09-2019

DOI: 10.1111/TPJ.14509

Abstract: The pentatricopeptide repeat proteins PPR4 and EMB2654 have been shown to be required for the trans-splicing of plastid rps12 transcripts in Zea mays (maize) and Arabidopsis, respectively, but their roles in this process are not well understood. We investigated the functions of the Arabidopsis and Oryza sativa (rice) orthologs of PPR4, designated AtPPR4 (At5g04810) and OsPPR4 (Os4g58780). Arabidopsis atppr4 and rice osppr4 mutants are embryo-lethal and seedling-lethal 3 weeks after germination, respectively, showing that PPR4 is essential in the development of both dicot and monocot plants. Artificial microRNA-mediated mutants of AtPPR4 displayed a specific defect in rps12 trans-splicing, with pale-green, yellowish or albino phenotypes, according to the degree of knock-down of AtPPR4 expression. Comparison of RNA footprints in atppr4 and emb2654 mutants showed a similar concordant loss of extensive footprints at the 3' end of intron 1a and at the 5' end of intron 1b in both cases. EMB2654 is known to bind within the footprint region in intron 1a and we show that AtPPR4 binds to the footprint region in intron 1b, via its PPR motifs. Binding of both PPR4 and EMB2654 is essential to juxtapose the two intron halves and to maintain the RNAs in a splicing-competent structure for the efficient trans-splicing of rps12 intron 1, which is crucial for chloroplast biogenesis and plant development. The similarity of EMB2654 and PPR4 orthologs and their respective binding sites across land plant phylogeny indicates that their coordinate function in rps12 trans-splicing has probably been conserved for 500 million years.

Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts

Publisher: Oxford University Press (OUP)

Date: 2009

DOI: 10.1105/TPC.108.064667

Abstract: The plant-specific DYW subclass of pentatricopeptide repeat proteins has been postulated to be involved in RNA editing of organelle transcripts. We discovered that the DYW proteins CHLORORESPIRATORY REDUCTION22 (CRR22) and CRR28 are required for editing of multiple plastid transcripts but that their DYW motifs are dispensable for editing activity in vivo. Replacement of the DYW motifs of CRR22 and CRR28 by that of CRR2, which has been shown to be capable of endonucleolytic cleavage, blocks the editing activity of both proteins. In return, the DYW motifs of neither CRR22 nor CRR28 can functionally replace that of CRR2. We propose that different DYW family members have acquired distinct functions in the ergent processes of RNA maturation, including RNA cleavage and RNA editing.

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Publisher: American Association for the Advancement of Science (AAAS)

Date: 17-08-2018

DOI: 10.1126/SCIENCE.AAR7191

Abstract: Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Ex les of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat. Science , this issue p. eaar7191 see also p. eaar6089

Fluorescent protein tagging as a tool to define the subcellular distribution of proteins in plants

Publisher: Frontiers Media SA

Date: 2013

DOI: 10.3389/FPLS.2013.00214

In Arabidopsis thaliana distinct alleles encoding mitochondrial RNA PROCESSING FACTOR 4 support the generation of additional 5′ termini of ccmB transcripts

Publisher: Springer Science and Business Media LLC

Date: 22-02-2017

DOI: 10.1007/S11103-017-0591-Y

Abstract: In plant mitochondria, the 5' ends of many transcripts are generated post-transcriptionally. We show that the pentatricopeptide repeat (PPR) protein RNA PROCESSING FACTOR 4 (RPF4) supports the generation of extra 5' ends of ccmB transcripts in Landsberg erecta (Ler) and a number of other Arabidopsis thaliana ecotypes. RPF4 was identified in Ler applying a forward genetic approach supported by complementation studies of ecotype Columbia (Col), which generates the Ler-type extra ccmB 5' termini only after the introduction of the RPF4 allele from Ler. Studies with chimeric RPF4 proteins composed of various parts of the RPF4 proteins from Ler and Col identified differences in the N-terminal and central PPR motifs that explain ecotype-specific variations in ccmB processing. These results fit well with binding site predictions in ccmB transcripts based on the known determinants of nucleotide base recognition by PPR motifs.

Quantitative analysis of motifs contributing to the interaction between PLS-subfamily members and their target RNA sequences in plastid RNA editing

Publisher: Wiley

Date: 06-11-2014

DOI: 10.1111/TPJ.12687

Abstract: In plant organelles, RNA editing alters specific cytidine residues to uridine in transcripts. Target cytidines are specifically recognized by pentatricopeptide repeat (PPR) proteins of the PLS subfamily, which have additional C-terminal E or E-DYW motifs. Recent in silico analysis proposed a model for site recognition by PLS-subfamily PPR proteins, with a correspondence of one PPR motif to one nucleotide, and with the C-terminal last S motif aligning with the nucleotide at position -4 with respect to the editing site. Here, we present quantitative biochemical data on site recognition by four PLS-subfamily proteins: CRR28 and OTP85 are DYW-class members, whereas CRR21 and OTP80 are E-class members. The minimal RNA segments required for high-affinity binding by these PPR proteins were experimentally determined. The results were generally consistent with the in silico-based model however, we clarified that several PPR motifs, including the C-terminal L2 and S motifs of CRR21 and OTP80, are dispensable for the RNA binding, suggesting distinct contributions of each PPR motif to site recognition. We also demonstrate that the DYW motif interacts with the target C and its 5' proximal region (from -3 to 0), whereas the E motif is not involved in binding.

The pentatricopeptide repeat protein OTP82 is required for RNA editing of plastid ndhB and ndhG transcripts

Publisher: Wiley

Date: 18-11-2010

DOI: 10.1111/J.1365-313X.2009.04059.X

Arabidopsis CSP41 proteins form multimeric complexes that bind and stabilize distinct plastid transcripts

Publisher: Oxford University Press (OUP)

Date: 16-11-2012

DOI: 10.1093/JXB/ERR347

The design and structural characterization of a synthetic pentatricopeptide repeat protein

Publisher: International Union of Crystallography (IUCr)

Date: 23-01-2015

DOI: 10.1107/S1399004714024869

Abstract: Proteins of the pentatricopeptide repeat (PPR) superfamily are characterized by tandem arrays of a degenerate 35-amino-acid α-hairpin motif. PPR proteins are typically single-stranded RNA-binding proteins with essential roles in organelle biogenesis, RNA editing and mRNA maturation. A modular, predictable code for sequence-specific binding of RNA by PPR proteins has recently been revealed, which opens the door to the de novo design of bespoke proteins with specific RNA targets, with widespread biotechnological potential. Here, the design and production of a synthetic PPR protein based on a consensus sequence and the determination of its crystal structure to 2.2 Å resolution are described. The crystal structure displays helical disorder, resulting in electron density representing an infinite superhelical PPR protein. A structural comparison with related tetratricopeptide repeat (TPR) proteins, and with native PPR proteins, reveals key roles for conserved residues in directing the structure and function of PPR proteins. The designed proteins have high solubility and thermal stability, and can form long tracts of PPR repeats. Thus, consensus-sequence synthetic PPR proteins could provide a suitable backbone for the design of bespoke RNA-binding proteins with the potential for high specificity.

Plant cytosolic tRNA(His) possesses an exceptional C54 in the canonical TΨC loop

Publisher: Oxford University Press (OUP)

Date: 06-1998

DOI: 10.1093/NAR/26.11.2708

Abstract: A nuclear gene coding for tRNAHis from Arabidopsis has been reported to contain C54in the TPsiC loop, although the corresponding nucleotide is an invariant U or a derivative in nearly all other tRNAs. The only previously reported plant cytosolic tRNAHis sequence, from lupin, has U54. To re-examine plant cytosolic tRNAsHis and their genes we have used DNA and RNA sequence analyses, restriction enzyme digestion of PCR- lified tRNA genes, RNA hybridization and in vivo aminoacylation assays. Our results suggest that Arabidopsis nuclear tRNAHis genes ubiquitously contain C54, as do those from tobacco, lupin and pea. The C54 nucleotide is maintained in the mature tRNAHis, which is aminoacylated in vivo , but to a relatively low level compared with other tRNAs examined. Finally, it was shown that an Arabidopsis tRNAHis gene with T54in place of C54 is over 5-fold more transcriptionally active than the wild-type gene using an in vitro system derived from plant nuclei. A possible role for this apparently sub-optimal tRNAHis sequence is suggested.

Chloroplast ribonucleoprotein CP31A is required for editing and stability of specific chloroplast mRNAs

Publisher: Proceedings of the National Academy of Sciences

Date: 07-04-2009

DOI: 10.1073/PNAS.0808529106

Abstract: Chloroplast ribonucleoproteins (cpRNPs) are nuclear-encoded, highly abundant, and light-regulated RNA binding proteins. They have been shown to be involved in chloroplast RNA processing and stabilization in vitro and are phylogenetically related to the well-described heterogeneous nuclear ribonucleoproteins (hnRNPs). cpRNPs have been found associated with mRNAs present in chloroplasts and have been regarded as nonspecific stabilizers of chloroplast transcripts. Here, we demonstrate that null mutants of the cpRNP family member CP31A exhibit highly specific and erse defects in chloroplast RNA metabolism. First, analysis of cp31a and cp31a / cp31b double mutants uncovers that these 2 paralogous genes participate nonredundantly in a combinatorial fashion in processing a subset of chloroplast editing sites in vivo. Second, a genome-wide analysis of chloroplast transcript accumulation in cp31a mutants detected a virtually complete loss of the chloroplast ndhF mRNA and lesser reductions for specific other mRNAs. Fluorescence analyses show that the activity of the NADH dehydrogenase complex, which also includes the NdhF subunit, is defective in cp31a mutants. This indicates that cpRNPs are important in vivo for calibrating the expression levels of specific chloroplast mRNAs and impact chloroplast physiology. Taken together, the specificity and combinatorial aspects of cpRNP functions uncovered suggest that these chloroplast proteins are functional equivalents of nucleocytosolic hnRNPs.

Pentatricopeptide Repeat Proteins in Plants

Publisher: Annual Reviews

Date: 29-04-2014

DOI: 10.1146/ANNUREV-ARPLANT-050213-040159

Abstract: Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in land plants, with more than 400 members in most species. Over the past decade, much has been learned about the molecular functions of these proteins, where they act in the cell, and what physiological roles they play during plant growth and development. A typical PPR protein is targeted to mitochondria or chloroplasts, binds one or several organellar transcripts, and influences their expression by altering RNA sequence, turnover, processing, or translation. Their combined action has profound effects on organelle biogenesis and function and, consequently, on photosynthesis, respiration, plant development, and environmental responses. Recent breakthroughs in understanding how PPR proteins recognize RNA sequences through modular base-specific contacts will help match proteins to potential binding sites and provide a pathway toward designing synthetic RNA-binding proteins aimed at desired targets.

The evolution of RNA editing and pentatricopeptide repeat genes

Publisher: Wiley

Date: 09-05-2011

DOI: 10.1111/J.1469-8137.2011.03746.X

Abstract: The pentatricopeptide repeat (PPR) is a degenerate 35‐amino‐acid structural motif identified from analysis of the sequenced genome of the model plant Arabidopsis thaliana . From the wealth of sequence information now available from plant genomes, the PPR protein family is now known to be one of the largest families in angiosperm species, as most genomes encode 400–600 members. As the number of PPR genes is generally only c . 10–20 in other eukaryotic organisms, including green algae, the family has obviously greatly expanded during land plant evolution. This provides a rare opportunity to study selection pressures driving a 50‐fold expansion of a single gene family. PPR proteins are sequence‐specific RNA‐binding proteins involved in many aspects of RNA processing in organelles. In this review, we will summarize our current knowledge about the evolution of PPR genes, and will discuss the relevance of the dramatic expansion in the family to the functional ersification of plant organelles, focusing primarily on RNA editing. Contents Summary 37 I. Introduction 37 II. Expansion of the PPR family 38 III. RNA editing and the evolution of PPR genes 40 IV. Sequence drift in the organelle genomes of early land plants 41 V. Loss of RNA editing in angiosperms 43 VI. Other functions besides editing 44 VII. Conclusion 44 References 44

Overlapping Destinations for Two Dual Targeted Glycyl-tRNA Synthetases in Arabidopsis thaliana and Phaseolus vulgaris

Publisher: Elsevier BV

Date: 2001

DOI: 10.1074/JBC.M011525200

Approaches to defining dual‐targeted proteins in Arabidopsis

Publisher: Wiley

Date: 03-2009

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

Towards a plant model for enigmatic U‐to‐C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis

Publisher: Wiley

Date: 14-12-2020

DOI: 10.1111/NPH.16297

Abstract: Hornworts are crucial to understand the phylogeny of early land plants. The emergence of 'reverse' U-to-C RNA editing accompanying the widespread C-to-U RNA editing in plant chloroplasts and mitochondria may be a molecular synapomorphy of a hornwort-tracheophyte clade. C-to-U RNA editing is well understood after identification of many editing factors in models like Arabidopsis thaliana and Physcomitrella patens, but there is no plant model yet to investigate U-to-C RNA editing. The hornwort Anthoceros agrestis is now emerging as such a model system. We report on the assembly and analyses of the A. agrestis chloroplast and mitochondrial genomes, their transcriptomes and editomes, and a large nuclear gene family encoding pentatricopeptide repeat (PPR) proteins likely acting as RNA editing factors. Both organelles in A. agrestis feature high amounts of RNA editing, with altogether > 1100 sites of C-to-U and 1300 sites of U-to-C editing. The nuclear genome reveals > 1400 genes for PPR proteins with variable carboxyterminal DYW domains. We observe significant variants of the 'classic' DYW domain, in the meantime confirmed as the cytidine deaminase for C-to-U editing, and discuss the first attractive candidates for reverse editing factors given their excellent matches to U-to-C editing targets according to the PPR-RNA binding code.

Transfer RNA-mediated suppression of stop codons in protoplasts and transgenic plants

Publisher: Springer Science and Business Media LLC

Date: 07-1993

DOI: 10.1007/BF00047408

What can we do with 1000 plastid genomes?

Publisher: Wiley

Date: 30-03-2017

DOI: 10.1111/TPJ.13491

Abstract: The plastid genome of plants is the smallest and most gene-rich of the three genomes in each cell and the one generally present in the highest copy number. As a result, obtaining plastid DNA sequence is a particularly cost-effective way of discovering genetic information about a plant. Until recently, the sequence information gathered in this way was generally limited to small portions of the genome lified by polymerase chain reaction, but recent advances in sequencing technology have stimulated a substantial rate of increase in the sequencing of complete plastid genomes. Within the last year, the number of complete plastid genomes accessible in public sequence repositories has exceeded 1000. This sudden flood of data raises numerous challenges in data analysis and interpretation, but also offers the keys to potential insights across large swathes of plant biology. We examine what has been learnt so far, what more could be learnt if we look at the data in the right way, and what we might gain from the tens of thousands more genome sequences that will surely arrive in the next few years. The most exciting new discoveries are likely to be made at the interdisciplinary interfaces between molecular biology and ecology.

A unique C‐terminal domain contributes to the molecular function of Restorer‐of‐fertility proteins in plant mitochondria

Publisher: Wiley

Date: 07-08-2023

DOI: 10.1111/NPH.19166

Abstract: Restorer‐of‐fertility ( Rf ) genes encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. In searching for a molecular signature unique to this class of proteins, we found that a majority of known Rf proteins have a distinct domain, which we called RfCTD ( Restorer‐of‐fertility C‐terminal domain ), and its presence correlates with the ability to induce cleavage of the mitochondrial RNA target. A screen of 219 angiosperm genomes from 123 genera using a sequence profile that can quickly and accurately identify RfCTD sequences revealed considerable variation in RFL/RfCTD gene numbers across flowering plants. We observed that plant genera with bisexual flowers have significantly higher numbers of RFL genes compared to those with unisexual flowers, consistent with a role of these proteins in restoration of male fertility. We show that removing the RfCTD from the RFL protein RNA PROCESSING FACTOR 2‐ nad6 prevented cleavage of its RNA target, the nad6 transcript, in Arabidopsis thaliana mitochondria. We provide a simple way of identifying putative Rf candidates in genome sequences, new insights into the molecular mode of action of Rf proteins and the evolution of fertility restoration in flowering plants.

Organelle transcriptomes: products of a deconstructed genome

Publisher: Elsevier BV

Date: 10-2013

DOI: 10.1016/J.MIB.2013.07.011

Abstract: Genetic drift and mutational pressure have shaped the evolution of mitochondrial and chloroplast genomes, giving rise to mechanisms that regulate their gene expression, which often differ from those in their prokaryotic ancestors. Advances in next generation sequencing technologies have enabled highly detailed characterization of organelle transcriptomes and the discovery of new transcripts and mechanisms for controlling gene expression. Here we discuss the common features of organelle transcriptomes that stem from their prokaryotic origin and some of the new innovations that are unique to organelles of multicellular organisms.

Surrogate mutants for studying mitochondrially encoded functions

Publisher: Elsevier BV

Date: 05-2014

DOI: 10.1016/J.BIOCHI.2013.08.019

Abstract: Although chloroplast transformation is possible in some plant species, it is extremely difficult to create or select mutations in plant mitochondrial genomes, explaining why few genetic studies of mitochondrially encoded functions exist. In recent years it has become clear that many nuclear genes encode factors with key functions in organelle gene expression, and that often their action is restricted to a single organelle gene or transcript. Mutations in one of these nuclear genes thus leads to a specific primary defect in expression of a single organelle gene, and the nuclear mutation can be used as a surrogate for a phenotypically equivalent mutation in the organelle genome. These surrogate mutations often result in defective assembly of respiratory complexes, and lead to severe phenotypes including reduced growth and fertility, or even embryo-lethality. A wide collection of such mutants is now available, and this review summarises the progress in basic knowledge of mitochondrial biogenesis they have contributed to and points out areas where this resource has not been exploited yet.

Rampant Gene loss in the underground orchid Rhizanthella Gardneri highlights evolutionary constraints on plastid genomes

Publisher: Oxford University Press (OUP)

Date: 02-02-2011

DOI: 10.1093/MOLBEV/MSR028

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

DOI: 10.1105/TPC.109.066654

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.

The Pentatricopeptide Repeat Protein OTP87 Is Essential for RNA Editing of nad7 and atp1 Transcripts in Arabidopsis Mitochondria

Publisher: Elsevier BV

Date: 06-2011

DOI: 10.1074/JBC.M111.230516

Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

Publisher: Springer Science and Business Media LLC

Date: 18-03-2021

DOI: 10.1038/S41588-021-00807-0

Abstract: Rye ( Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a erse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye’s incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye–wheat introgressions.

Transplastomic Arabidopsis plants at last

Publisher: Springer Science and Business Media LLC

Date: 08-03-2019

DOI: 10.1038/S41477-019-0388-X

Implication of 5'-flanking sequence elements in expression of a plant tRNA(Leu) gene

Publisher: Springer Science and Business Media LLC

Date: 1998

DOI: 10.1023/A:1005988004924

Abstract: A comparison of 5'-flanking sequences from 68 different nuclear plant tRNA genes was analyzed to find consensus sequences. Three conserved features stood out, all of which are present in the tRNA(Leu) gene used in this study: (1) a high proportion of A and T residues upstream of all tRNA genes (2) a region of low duplex stability about 30-35 bp before the coding sequence, often containing a TATA-box like motif (3) a CAA triplet in the region of the presumed transcription start. The effect of replacement of the AT-rich upstream sequences with GC-rich sequences or unrelated AT-rich sequences was tested by progressive deletions and by inserting randomly cloned sequences upstream of the tRNA gene. GC-rich 5'-flanking sequences were found to be generally incompatible with high levels of expression. The TATA-box like motifs and the CAA triplet were removed or altered by deletion or directed mutagenesis. Mutation of the CAA triplet significantly decreased expression of the tRNA(Leu) gene, suggesting that this CAA triplet is important for transcription efficiency, but mutation or elimination of the TATA-box like motifs generally had little effect. The presence or absence of each of these features in tRNA genes from other organisms is discussed there are clear and interesting differences between plant tRNA genes and those of yeast and mammals.

The plastid redox insensitive 2 mutant of Arabidopsis is impaired in PEP activity and high light-dependent plastid redox signalling to the nucleus

Publisher: Wiley

Date: 28-12-2012

DOI: 10.1111/J.1365-313X.2011.04865.X

Dual targeting to mitochondria and chloroplasts

Publisher: Elsevier BV

Date: 12-2001

DOI: 10.1016/S0167-4889(01)00146-X

Abstract: Plant cells contain two organelles originally derived from endosymbiotic bacteria: mitochondria and plastids. Their endosymbiotic origin explains why these organelles contain their own DNA, nonetheless only a few dozens of genes are actually encoded by these genomes. Many of the other genes originally present have been transferred to the nuclear genome of the host, the product of their expression being targeted back to the corresponding organelle. Although targeting of proteins to mitochondria and chloroplasts is generally highly specific, an increasing number of ex les have been discovered where the same protein is imported into both organelles. The object of this review is to compare and discuss these ex les in order to try and identify common features of dual-targeted proteins. The study helps throw some light on the factors determining organelle targeting specificity, and suggests that dual-targeted proteins may well be far more common than once thought.

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

Publisher: Oxford University Press (OUP)

Date: 25-05-2011

DOI: 10.1105/TPC.107.055046

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

Plant organellar RNA editing: what 30 years of research has revealed

Publisher: Wiley

Date: 12-12-2020

DOI: 10.1111/TPJ.14578

Abstract: The central dogma in biology defines the flow of genetic information from DNA to RNA to protein. Accordingly, RNA molecules generally accurately follow the sequences of the genes from which they are transcribed. This rule is transgressed by RNA editing, which creates RNA products that differ from their DNA templates. Analyses of the RNA landscapes of terrestrial plants have indicated that RNA editing (in the form of C-U base transitions) is highly prevalent within organelles (that is, mitochondria and chloroplasts). Numerous C→U conversions (and in some plants also U→C) alter the coding sequences of many of the organellar transcripts and can also produce translatable mRNAs by creating AUG start sites or eliminating premature stop codons, or affect the RNA structure, influence splicing and alter the stability of RNAs. RNA-binding proteins are at the heart of post-transcriptional RNA expression. The C-to-U RNA editing process in plant mitochondria involves numerous nuclear-encoded factors, many of which have been identified as pentatricopeptide repeat (PPR) proteins that target editing sites in a sequence-specific manner. In this review we report on major discoveries on RNA editing in plant organelles, since it was first documented 30 years ago.

SOT1, a pentatricopeptide repeat protein with a small MutS-related domain, is required for correct processing of plastid 23S-4.5S rRNA precursors in Arabidopsis thaliana.

Publisher: Wiley

Date: 03-2016

DOI: 10.1111/TPJ.13126

Abstract: Ribosomal RNA processing is essential for plastid ribosome biogenesis, but is still poorly understood in higher plants. Here, we show that SUPPRESSOR OF THYLAKOID FORMATION 1 ( SOT 1), a plastid‐localized pentatricopeptide repeat ( PPR ) protein with a small MutS‐related domain, is required for maturation of the 23S–4.5S rRNA dicistron. Loss of SOT 1 function leads to slower chloroplast development, suppression of leaf variegation, and abnormal 23S and 4.5S processing. Predictions based on the PPR motif sequences identified the 5′ end of the 23S–4.5S rRNA dicistronic precursor as a putative SOT 1 binding site. This was confirmed by electrophoretic mobility shift assay, and by loss of the abundant small RNA ‘footprint’ associated with this site in sot1 mutants. We found that more than half of the 23S–4.5S rRNA dicistrons in sot1 mutants contain eroded and/or unprocessed 5′ and 3′ ends, and that the endonucleolytic cleavage product normally released from the 5′ end of the precursor is absent in a sot1 null mutant. We postulate that SOT 1 binding protects the 5′ extremity of the 23S–4.5S rRNA dicistron from exonucleolytic attack, and favours formation of the RNA structure that allows endonucleolytic processing of its 5′ and 3′ ends.

The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA

Publisher: Oxford University Press (OUP)

Date: 21-01-2015

DOI: 10.1093/NAR/GKV027

The pentatricopeptide repeat protein EMB2654 is essential for trans-splicing of a chloroplast small ribosomal subunit transcript

Publisher: Oxford University Press (OUP)

Date: 23-12-2017

DOI: 10.1104/PP.16.01840

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

DOI: 10.1104/PP.108.129999

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.

Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants

Publisher: Wiley

Date: 02-2016

DOI: 10.1111/TPJ.13121

Abstract: The pentatricopeptide repeat (PPR) proteins form one of the largest protein families in land plants. They are characterised by tandem 30-40 amino acid motifs that form an extended binding surface capable of sequence-specific recognition of RNA strands. Almost all of them are post-translationally targeted to plastids and mitochondria, where they play important roles in post-transcriptional processes including splicing, RNA editing and the initiation of translation. A code describing how PPR proteins recognise their RNA targets promises to accelerate research on these proteins, but making use of this code requires accurate definition and annotation of all of the various nucleotide-binding motifs in each protein. We have used a structural modelling approach to define 10 different variants of the PPR motif found in plant proteins, in addition to the putative deaminase motif that is found at the C-terminus of many RNA-editing factors. We show that the super-helical RNA-binding surface of RNA-editing factors is potentially longer than previously recognised. We used the redefined motifs to develop accurate and consistent annotations of PPR sequences from 109 genomes. We report a high error rate in PPR gene models in many public plant proteomes, due to gene fusions and insertions of spurious introns. These consistently annotated datasets across a wide range of species are valuable resources for future comparative genomics studies, and an essential pre-requisite for accurate large-scale computational predictions of PPR targets. We have created a web portal (www.plantppr.com) that provides open access to these resources for the community.

Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution

Publisher: Proceedings of the National Academy of Sciences

Date: 10-01-2011

DOI: 10.1073/PNAS.1007667108

Abstract: Eukaryotic cells have harbored mitochondria for at least 1.5 billion years in an apparently mutually beneficial symbiosis. Studies on the agronomically important crop trait cytoplasmic male sterility (CMS) have suggested the semblance of a host–parasite relationship between the nuclear and mitochondrial genomes, but molecular evidence for this is lacking. Key players in CMS systems are the fertility restorer ( Rf ) genes required for the development of a functional male gametophyte in plants carrying a mitochondrial CMS gene. In the majority of cases, Rf genes encode pentatricopeptide repeat (PPR) proteins. We show that most angiosperms for which extensive genomic sequence data exist contain multiple PPR genes related to Rf genes. These Rf -like genes show a number of characteristic features compared with other PPR genes, including chromosomal clustering and unique patterns of evolution, notably high rates of nonsynonymous to synonymous substitutions, suggesting ersifying selection. The highest probabilities of ersifying selection were seen for amino acid residues 1, 3, and 6 within the PPR motif. PPR proteins are involved in RNA processing, and mapping the selection data to a predicted consensus structure of an array of PPR motifs suggests that these residues are likely to form base-specific contacts to the RNA ligand. We suggest that the selection patterns on Rf -like genes reveal a molecular “arms-race” between the nuclear and mitochondrial genomes that has persisted throughout most of the evolutionary history of angiosperms.

Expression of Arabidopsis thaliana mitochondrial alanyl-tRNA synthetase is not sufficient to trigger mitochondrial import of tRNA(Ala) in yeast

Publisher: Elsevier BV

Date: 05-2000

DOI: 10.1074/JBC.275.18.13291

Abstract: It has often been suggested that precursors to mitochondrial aminoacyl-tRNA synthetases are likely carriers for mitochondrial import of tRNAs in those organisms where this process occurs. In plants, it has been shown that mutation of U(70) to C(70) in Arabidopsis thaliana tRNA(Ala)(UGC) blocks aminoacylation and also prevents import of the tRNA into mitochondria. This suggests that interaction of tRNA(Ala) with alanyl-tRNA synthetase (AlaRS) is necessary for import to occur. To test whether this interaction is sufficient to drive import, we co-expressed A. thaliana tRNA(Ala)(UGC) and the precursor to the A. thaliana mitochondrial AlaRS in Saccharomyces cerevisiae. The A. thaliana enzyme and its cognate tRNA were correctly expressed in yeast in vivo. However, although the plant AlaRS was efficiently imported into mitochondria in the transformed strains, we found no evidence for import of the A. thaliana tRNA(Ala) nor of the endogenous cytosolic tRNA(Ala) isoacceptors. We conclude that at least one other factor besides the mitochondrial AlaRS precursor must be involved in mitochondrial import of tRNA(Ala) in plants.

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Publisher: Springer Science and Business Media LLC

Date: 02-07-2018

DOI: 10.1038/S41477-018-0188-8

Abstract: Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns—one at the base of ‘core leptosporangiates’ and one specific to Azolla . One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N 2 -fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla –cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

On the Expansion of the Pentatricopeptide Repeat Gene Family in Plants

Publisher: Oxford University Press (OUP)

Date: 14-01-2008

DOI: 10.1093/MOLBEV/MSN057

Abstract: Pentatricopeptide repeat (PPR) proteins form a huge family in plants (450 members in Arabidopsis and 477 in rice) defined by tandem repetitions of characteristic sequence motifs. Some of these proteins have been shown to play a role in posttranscriptional processes within organelles, and they are thought to be sequence-specific RNA-binding proteins. The origins of this family are obscure as they are lacking from almost all prokaryotes, and the spectacular expansion of the family in land plants is equally enigmatic. In this study, we investigate the growth of the family in plants by undertaking a genome-wide identification and comparison of the PPR genes of 3 organisms: the flowering plants Arabidopsis thaliana and Oryza sativa and the moss Physcomitrella patens. A large majority of the PPR genes in each of the flowering plants are intron less. In contrast, most of the 103 PPR genes in Physcomitrella are intron rich. A phylogenetic comparison of the PPR genes in all 3 species shows similarities between the intron-rich PPR genes in Physcomitrella and the few intron-rich PPR genes in higher plants. Intron-poor PPR genes in all 3 species also display a bias toward a position of their introns at their 5' ends. These results provide compelling evidence that one or more waves of retrotransposition were responsible for the expansion of the PPR gene family in flowering plants. The differing numbers of PPR proteins are highly correlated with differences in organellar RNA editing between the 3 species.

MSP1 encodes an essential RNA‐binding pentatricopeptide repeat factor required for nad1 maturation and complex I biogenesis in Arabidopsis mitochondria

Publisher: Wiley

Date: 17-04-2023

DOI: 10.1111/NPH.18880

Abstract: Mitochondrial biogenesis relies on nuclearly encoded factors, which regulate the expression of the organellar‐encoded genes. Pentatricopeptide repeat (PPR) proteins constitute a major gene family in angiosperms that are pivotal in many aspects of mitochondrial (mt)RNA metabolism (e.g. trimming, splicing, or stability). Here, we report the analysis of MITOCHONDRIA STABILITY/PROCESSING PPR FACTOR1 ( MSP1 , At4g20090), a canonical PPR protein that is necessary for mitochondrial functions and embryo development. Loss‐of‐function allele of MSP1 leads to seed abortion. Here, we employed an embryo‐rescue method for the molecular characterization of msp1 mutants. Our analyses reveal that msp1 embryogenesis fails to proceed beyond the heart/torpedo stage as a consequence of a nad1 pre‐RNA processing defect, resulting in the loss of respiratory complex I activity. Functional complementation confirmed that msp1 phenotypes result from a disruption of the MSP1 gene. In Arabidopsis, the maturation of nad1 involves the processing of three RNA fragments, nad1.1 , nad1.2 , and nad1.3 . Based on biochemical analyses and mtRNA profiles of wild‐type and msp1 plants, we concluded that MSP1 facilitates the generation of the 3′ terminus of nad1.1 transcript, a prerequisite for nad1 exons a–b splicing. Our data substantiate the importance of mtRNA metabolism for the biogenesis of the respiratory system during early plant life.

The Expansion and Diversification of Pentatricopeptide Repeat RNA-Editing Factors in Plants

Publisher: Elsevier BV

Date: 02-2020

DOI: 10.1016/J.MOLP.2019.11.002

Abstract: The RNA-binding pentatricopeptide repeat (PPR) family comprises hundreds to thousands of genes in most plants, but only a few dozen in algae, indicating massive gene expansions during land plant evolution. The nature and timing of these expansions has not been well defined due to the sparse sequence data available from early- erging land plant lineages. In this study, we exploit the comprehensive OneKP datasets of over 1000 transcriptomes from erse plants and algae toward establishing a clear picture of the evolution of this massive gene family, focusing on the proteins typically associated with RNA editing, which show the most spectacular variation in numbers and domain composition across the plant kingdom. We characterize over 2 250 000 PPR motifs in over 400 000 proteins. In lycophytes, polypod ferns, and hornworts, nearly 10% of expressed protein-coding genes encode putative PPR editing factors, whereas they are absent from algae and complex-thalloid liverworts. We show that rather than a single expansion, most land plant lineages with high numbers of editing factors have continued to generate novel sequence ersity. We identify sequence variations that imply functional differences between PPR proteins in seed plants versus non-seed plants and variations we propose to be linked to seed-plant-specific editing co-factors. Finally, using the sequence variations across the datasets, we develop a structural model of the catalytic DYW domain associated with C-to-U editing and identify a clade of unique DYW variants that are strong candidates as U-to-C RNA-editing factors, given their phylogenetic distribution and sequence characteristics.

The strange evolutionary history of plant mitochondrial tRNAs and their aminoacyl-tRNA synthetases

Publisher: Oxford University Press (OUP)

Date: 05-1999

DOI: 10.1093/JHERED/90.3.333

Plastic tRNA Genes trnC-GCA and trnN-GUU are essential for plant cell development

Publisher: Wiley

Date: 21-06-2007

DOI: 10.1111/J.1365-313X.2007.03177.X

A PPR protein involved in regulating nuclear genes encoding mitochondrial proteins?

Publisher: Informa UK Limited

Date: 05-2011

DOI: 10.4161/PSB.6.5.15148

Plastome-Wide Rearrangements and Gene Losses in Carnivorous Droseraceae

Publisher: Oxford University Press (OUP)

Date: 10-01-2019

DOI: 10.1093/GBE/EVZ005

Erratum: The complete sequence of the acacia ligulata chloroplast genome reveals a highly divergent clpp1 gene (PLoS ONE (2015) 10:5 (e0125768) DOI: 10.1371/journal.pone.0125768)

Publisher: Public Library of Science (PLoS)

Date: 14-09-2015

DOI: 10.1371/JOURNAL.PONE.0138367

The multifarious roles of PPR proteins in plant mitochondrial gene expression

Publisher: Wiley

Date: 18-09-2007

DOI: 10.1111/J.1399-3054.2006.00766.X

An Arabidopsis dual-localized pentatricopeptide repeat protein interacts with nuclear proteins involved in gene expression regulation

Publisher: Oxford University Press (OUP)

Date: 02-2011

DOI: 10.1105/TPC.110.081638

Abstract: Following the endosymbiotic acquisition of mitochondria by eukaryotic cells, most of the genes in this organelle were transferred to the nucleus. To maintain mitochondrial biogenesis and function, nuclear and mitochondrial genomes require regulated and coordinated expression. In plant organelles, nuclear-encoded proteins targeted to the organelles control posttranscriptional and posttranslational mechanisms. Pentatricopeptide repeat (PPR) proteins are good candidates to play such regulatory roles. Here, we identify PNM1 (for PPR protein localized to the nucleus and mitochondria 1), a novel PPR protein that is dual localized to mitochondria and nuclei in Arabidopsis thaliana, as observed by green fluorescent protein fusions and immunodetection on subcellular fractions and on histological sections. Genetic complementation showed that loss of PNM1 function in mitochondria, but not in nuclei, is lethal for the embryo. In mitochondria, it is associated with polysomes and may play a role in translation. A genetic screen in yeast identified protein partners of PNM1. These partners, the nucleosome assembly protein NAP1, and the transcription factor TCP8 interact with PNM1 in the nucleus in planta. Furthermore, TCP8 can bind the promoter of PNM1. This suggests that PNM1 might be involved in the regulation of its own gene expression in the nucleus and could thus play a role in gene expression adjustments between mitochondria and the nucleus.

CRISPRi-based circuits for genetic computation in plants

Publisher: Cold Spring Harbor Laboratory

Date: 07-2022

DOI: 10.1101/2022.07.01.498372

Abstract: Synthetic gene circuits can enable new cellular behaviours by integrating multiple input signals into customisable genetic programs. However, gene circuit development in plants has been limited by a lack of orthogonal and modular parts required for their construction. Here, we present a tool-kit of reversible CRISPRi-based gene circuits for use in plants. First, we created a range of engineered repressible promoters of different strengths and used them as integrators for the construction of NOT and NOR gates in Arabidopsis cells. Next, we determined the optimal processing system to express sgRNAs from RNA Pol II promoters to introduce NOR gate programmability and interface it with host regulatory sequences. Finally, we connected multiple NOR gates together in layered arrangements to create OR, NIMPLY, and AND logic functions. Our CRISPRi circuits are orthogonal, compact, reversible, programmable, and modular, providing a new platform for sophisticated and deliberate spatio-temporal control of gene expression in plants.

A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins

Publisher: Public Library of Science (PLoS)

Date: 16-08-2012

DOI: 10.1371/JOURNAL.PGEN.1002910

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

Publisher: Oxford University Press (OUP)

Date: 10-2010

DOI: 10.1105/TPC.110.074781

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

Small kernel 1 encodes a pentatricopeptide repeat protein required for mitochondrial nad7 transcript editing and seed development in maize (Zea mays) and rice (Oryza sativa)

Publisher: Wiley

Date: 28-07-2014

DOI: 10.1111/TPJ.12584

Abstract: RNA editing modifies cytidines (C) to uridines (U) at specific sites in the transcripts of mitochondria and plastids, altering the amino acid specified by the DNA sequence. Here we report the identification of a critical editing factor of mitochondrial nad7 transcript via molecular characterization of a small kernel 1 (smk1) mutant in Zea mays (maize). Mutations in Smk1 arrest both the embryo and endosperm development. Cloning of Smk1 indicates that it encodes an E-subclass pentatricopeptide repeat (PPR) protein that is targeted to mitochondria. Loss of SMK1 function abolishes the C → U editing at the nad7-836 site, leading to the retention of a proline codon that is edited to encode leucine in the wild type. The smk1 mutant showed dramatically reduced complex-I assembly and NADH dehydrogenase activity, and abnormal biogenesis of the mitochondria. Analysis of the ortholog in Oryza sativa (rice) reveals that rice SMK1 has a conserved function in C → U editing of the mitochondrial nad7-836 site. T-DNA knock-out mutants showed abnormal embryo and endosperm development, resulting in embryo or seedling lethality. The leucine at NAD7-279 is highly conserved from bacteria to flowering plants, and analysis of genome sequences from many plants revealed a molecular coevolution between the requirement for C → U editing at this site and the existence of an SMK1 homolog. These results demonstrate that Smk1 encodes a PPR-E protein that is required for nad7-836 editing, and this editing is critical to NAD7 function in complex-I assembly in mitochondria, and hence to embryo and endosperm development in maize and rice.

NMAT4, A maturase factor required for nad1 pre-mRNA processing and maturation, is essential for holocomplex I biogenesis in Arabidopsis mitochondria

Publisher: Wiley

Date: 26-03-2014

DOI: 10.1111/TPJ.12466

Abstract: Group II introns are large catalytic RNAs that are found in bacteria and organellar genomes of lower eukaryotes, but are particularly prevalent within mitochondria in plants, where they are present in many critical genes. The excision of plant mitochondrial introns is essential for respiratory functions, and is facilitated in vivo by various protein cofactors. Typical group II introns are classified as mobile genetic elements, consisting of the self-splicing ribozyme and its own intron-encoded maturase protein. A hallmark of maturases is that they are intron-specific, acting as cofactors that bind their intron-containing pre-RNAs to facilitate splicing. However, the degeneracy of the mitochondrial introns in plants and the absence of cognate intron-encoded maturase open reading frames suggest that their splicing in vivo is assisted by 'trans'-acting protein factors. Interestingly, angiosperms harbor several nuclear-encoded maturase-related (nMat) genes that contain N-terminal mitochondrial localization signals. Recently, we established the roles of two of these paralogs in Arabidopsis, nMAT1 and nMAT2, in the splicing of mitochondrial introns. Here we show that nMAT4 (At1g74350) is required for RNA processing and maturation of nad1 introns 1, 3 and 4 in Arabidopsis mitochondria. Seed germination, seedling establishment and development are strongly affected in homozygous nmat4 mutants, which also show modified respiration phenotypes that are tightly associated with complex I defects.

Emerging tools for synthetic biology in plants

Publisher: Wiley

Date: 23-05-2014

DOI: 10.1111/TPJ.12462

Pentatricopeptide repeat proteins: a socket set for organelle gene expression

Publisher: Elsevier BV

Date: 12-2008

DOI: 10.1016/J.TPLANTS.2008.10.001

Abstract: Pentatricopeptide repeat (PPR) proteins are RNA-binding proteins that are particularly prevalent in terrestrial plants. Although the PPR protein family was only recognized eight years ago, it is already clear that these proteins have a range of essential functions in post-transcriptional processes (including RNA editing, RNA splicing, RNA cleavage and translation) within mitochondria and chloroplasts. Several PPR proteins have been shown to act as fertility restorer genes in commercially important cytoplasmic male sterility systems. Here, we discuss several recent papers that cover their evolutionary history and molecular mode of action. We use these new data to propose hypotheses for their physiological roles that could explain why PPR proteins are so numerous in terrestrial plants.

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

Publisher: Oxford University Press (OUP)

Date: 09-2009

DOI: 10.1105/TPC.109.068536

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

The E domains of pentatricopeptide repeat proteins from different organelles are not functionally equivalent for RNA editing

Publisher: Wiley

Date: 25-04-2013

DOI: 10.1111/TPJ.12180

Abstract: RNA editing in plants is an essential post-transcriptional process that modifies the genetic information encoded in organelle genomes. Forward and reverse genetics approaches have revealed the prevalent role of pentatricopeptide repeat (PPR) proteins in editing in both plastids and mitochondria, confirming the shared origin of this process in both organelles. The E domain at or near the C terminus of these proteins has been shown to be essential for editing, and is presumed to recruit the enzyme that deaminates the target cytidine residue. Here, we describe two mutants, otp71 and otp72, disrupted in genes encoding mitochondrial E-type PPR proteins with single editing defects in ccmFN 2 and rpl16 transcripts, respectively. Comparisons between the E domains of these proteins and previously reported editing factors from chloroplasts suggested that there are characteristic differences in the proteins between the two organelles. To test this, we swapped E domains between two mitochondrial and two chloroplast editing factors. In all cases investigated, E domains from the same organelle (chloroplast or mitochondria) were found to be exchangeable however, swapping the E domain between organelles led to non-functional editing factors. We conclude that the E domains of mitochondrial and plastid PPR proteins are not functionally equivalent, and therefore that an important component of the putative editing complexes in the two organelles may be different.

Evolution of plant mitochondrial genomes via substoichiometric intermediates

Publisher: Elsevier BV

Date: 07-1989

DOI: 10.1016/0092-8674(89)90403-0

Abstract: Comparison of the modern fertile maize mitochondrial genome (N) with an ancestral maize mitochondrial genome (RU) reveals a 12 kb duplication (containing the atpA gene) in the modern genome that is absent from the ancestor. Cloning, mapping, and sequencing of the relevant portions of the ancestral genome shows that this duplication probably arose via a three-stage recombination process involving substoichiometric intermediates. Comparison with analogous observations on yeast mitochondrial genomes suggests that this three-stage model of genome reorganization can be generally applied to plant mitochondrial genomes to explain both deletions and the creation of novel repeats, common features of plant mitochondrial genome evolution.

SUBAcon: a consensus algorithm for unifying the subcellular localization data of the Arabidopsis proteome

Publisher: Oxford University Press (OUP)

Date: 22-08-2014

DOI: 10.1093/BIOINFORMATICS/BTU550

Abstract: Motivation: Knowing the subcellular location of proteins is critical for understanding their function and developing accurate networks representing eukaryotic biological processes. Many computational tools have been developed to predict proteome-wide subcellular location, and abundant experimental data from green fluorescent protein (GFP) tagging or mass spectrometry (MS) are available in the model plant, Arabidopsis. None of these approaches is error-free, and thus, results are often contradictory. Results: To help unify these multiple data sources, we have developed the SUBcellular Arabidopsis consensus (SUBAcon) algorithm, a naive Bayes classifier that integrates 22 computational prediction algorithms, experimental GFP and MS localizations, protein–protein interaction and co-expression data to derive a consensus call and probability. SUBAcon classifies protein location in Arabidopsis more accurately than single predictors. Availability: SUBAcon is a useful tool for recovering proteome-wide subcellular locations of Arabidopsis proteins and is displayed in the SUBA3 database (suba.plantenergy.uwa.edu.au). The source code and input data is available through the SUBA3 server (suba.plantenergy.uwa.edu.au//SUBAcon.html) and the Arabidopsis SUbproteome REference (ASURE) training set can be accessed using the ASURE web portal (suba.plantenergy.uwa.edu.au/ASURE). Contact: cornelia.hooper@uwa.edu.au or ian.castleden@uwa.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.

Complex I Dysfunction Redirects Cellular and Mitochondrial Metabolism in Arabidopsis

Publisher: Oxford University Press (OUP)

Date: 10-09-2008

DOI: 10.1104/PP.108.125880

Abstract: Mitochondrial complex I is a major avenue for reduced NAD oxidation linked to oxidative phosphorylation in plants. However, the plant enzyme has structural and functional features that set it apart from its counterparts in other organisms, raising questions about the physiological significance of this complex in plants. We have developed an experimental model in which rotenone, a classic complex I inhibitor, has been applied to Arabidopsis (Arabidopsis thaliana) cell suspension cultures in order to dissect early metabolic adjustments involved in cell acclimation to mitochondrial dysfunction. Rotenone induced a transitory decrease in cellular respiration (0–4 h after treatment). Cell respiration then progressively recovered and reached a steady state at 10 to 12 h after treatment. Complex I inhibition by rotenone did not induce obvious oxidative stress or cell death but affected longer term cell growth. Integrated analyses of gene expression, the mitochondrial proteome, and changes in primary metabolism indicated that rotenone treatment caused changes in mitochondrial function via alterations in specific components. A physical disengagement of glycolytic activities associated with the mitochondrial outer membrane was observed, and the tricarboxylic acid cycle was altered. Amino acid and organic acid pools were also modified by rotenone treatment, with a marked early decrease of 2-oxoglutarate, aspartate, and glutamine pools. These data demonstrate that, in Arabidopsis cells, complex I inhibition by rotenone induces significant remodeling of metabolic pathways involving the mitochondria and other compartments and point to early metabolic changes in response to mitochondrial dysfunction.

Knockdown of mitochondrialatp1mRNA by a custom-designed pentatricopeptide repeat protein alters F1FoATP synthase

Publisher: Cold Spring Harbor Laboratory

Date: 09-11-2022

DOI: 10.1101/2022.11.08.515711

Abstract: We show that a custom-designed RNA-binding protein binds and specifically induces cleavage of atp1 RNA in mitochondria, significantly decreasing the abundance of the Atp1 protein and the assembled F 1 F o ATP synthase in Arabidopsis thaliana . The transformed plants are characterized by delayed vegetative growth and reduced fertility. Five-fold depletion of Atp1 level was accompanied by a decrease in abundance of other ATP synthase subunits, lowered ATP synthesis rate of isolated mitochondria, but no change to mitochondrial electron transport chain complexes, adenylates or energy charge in planta . Transcripts for amino acid transport and a variety of stress response processes were differentially expressed in lines containing the PPR protein, indicating changes to achieve cellular homeostasis when ATP synthase was highly depleted. Leaves of ATP-synthase-depleted lines showed higher respiratory rates and elevated levels of most amino acids at night, most notably serine family amino acids. The results show the value of using custom-designed PPR proteins to influence expression of specific mitochondrial transcripts to carry out reverse genetics studies on mitochondrial gene functions and the consequences of ATP synthase depletion on cellular functions in Arabidopsis . Knockdown of mitochondrial atp1 mRNA by a custom-designed pentatricopeptide repeat protein alters F1Fo ATP synthase, plant growth and amino acid metabolism and ATP synthesis in Arabidopsis thaliana

Arabidopsis Chloroplast RNA Binding Proteins Cp31A and CP29A Associate with Large Transcript Pools and Confer Cold Stress Tolerance by Influencing Multiple Chloroplast RNA Processing Steps

Publisher: Oxford University Press (OUP)

Date: 10-2012

DOI: 10.1105/TPC.112.103002

The cytidine deaminase signature HxE(x)nCxxC of DYW1 binds zinc and is necessary for RNA editing of ndhD-1

Publisher: Wiley

Date: 10-07-2014

DOI: 10.1111/NPH.12928

Abstract: In flowering plants, RNA editing involves deamination of specific cytidines to uridines in both mitochondrial and chloroplast transcripts. Pentatricopeptide repeat ( PPR ) proteins and multiple organellar RNA editing factor ( MORF ) proteins have been shown to be involved in RNA editing but none have been shown to possess cytidine deaminase activity. The DYW domain of some PPR proteins contains a highly conserved signature resembling the zinc‐binding active site motif of known nucleotide deaminases. We modified these highly conserved amino acids in the DYW motif of DYW 1, an editing factor required for editing of the ndh D ‐1 site in A rabidopsis chloroplasts. We demonstrate that several amino acids of this signature motif are required for RNA editing in vivo and for zinc binding in vitro . We conclude that the DYW domain of DYW 1 has features in common with cytidine deaminases, reinforcing the hypothesis that this domain forms part of the active enzyme that carries out RNA editing in plants.

Transfer RNA import into plant mitochondria

Publisher: Elsevier

Date: 1995

DOI: 10.1016/0076-6879(95)60148-1

Abstract: Transportation infrastructure, which has always been regarded as an important element to promote regional innovation, accelerates factor flows and productivity spillovers. In February 2021, the State Council of China issued the outline of national integrated multidimensional transportation network planning (2021-2050), which proposed that during the 14th Five-Year Plan period, the Yangtze River Delta would speed up the construction of an integrated transport network to serve the dual circulation development pattern in China. However, few studies have systematically investigated the development of integrated transport in the Yangtze River Delta, especially the relationship between transport operating efficiency and regional innovation based on the theory of flow space. This study aims to calculate the integrated transport efficiency of 26 cities in the Yangtze River Delta and analyse the spillover effect of efficiency improvement on urban innovation. The results reveal that integrated transport efficiency is relatively stable at approximately 0.92. We find that the local innovation value would increase by 0.119% with every 1% increase in transport efficiency, and it would exceed 0.26% after introducing spatial factors. The spillover effect on the surrounding cities is significantly higher than that in the cities themselves, and the result is 0.292 under the economic spatial distance weight matrix. These findings will support the construction of the integrated transport network and provide useful references for government decision makers in the Yangtze River Delta.

Potential dual targeting of an Arabidopsis archaebacterial-like histidyl-tRNA synthetase to mitochondria and chloroplasts

Publisher: Wiley

Date: 10-07-1998

DOI: 10.1016/S0014-5793(98)00717-0

Abstract: A cDNA clone encoding a histidyl-tRNA synthetase (HisRS) was characterized from Arabidopsis thaliana. The deduced amino acid sequence (AtHRS1) is surprisingly more similar to HisRSs from archaebacteria than those from eukaryotes and prokaryotes. AtHRS1 has an N-terminal extension with features characteristic of mitochondrial and chloroplast transit peptides. Transient expression assays in tobacco protoplasts clearly demonstrated efficient targeting of a fusion peptide consisting of the first 71 amino acids of AtHRS1 joined to jellyfish green fluorescent protein (GFP) to both mitochondria and chloroplasts. These observations suggest that the AtHisRS1 cDNA encodes both mitochondrial and chloroplast histidyl-tRNA synthetases.

A PORR domain protein required for rpl2 and ccmF C intron splicing and for the biogenesis of c-type cytochromes in Arabidopsis mitochondria

Publisher: Wiley

Date: 28-12-2012

DOI: 10.1111/J.1365-313X.2011.04849.X

Mitochondrial genomes as living fossils

Publisher: Springer Science and Business Media LLC

Date: 15-04-2013

DOI: 10.1186/1741-7007-11-30

Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing

Publisher: Oxford University Press (OUP)

Date: 03-2019

DOI: 10.1093/AOBPLA/PLZ017

Using the SUBcellular database for Arabidopsis proteins to localize the Deg protease family.

Publisher: Frontiers Media SA

Date: 12-08-2014

DOI: 10.3389/FPLS.2014.00396

Recent surprises in protein targeting to mitochondria and plastids

Publisher: Elsevier BV

Date: 12-2006

DOI: 10.1016/J.PBI.2006.09.002

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

Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

Publisher: Cold Spring Harbor Laboratory

Date: 12-12-2019

DOI: 10.1101/2019.12.11.869693

Abstract: We present a chromosome-scale annotated assembly of the rye ( Secale cereale L. inbred line ‘Lo7’) genome, which we use to explore Triticeae genomic evolution, and rye’s superior disease and stress tolerance. The rye genome shares chromosome-level organization with other Triticeae cereals, but exhibits unique retrotransposon dynamics and structural features. Crop improvement in rye, as well as in wheat and triticale, will profit from investigations of rye gene families implicated in pathogen resistance, low temperature tolerance, and fertility control systems for hybrid breeding. We show that rye introgressions in wheat breeding panels can be characterised in high-throughput to predict the yield effects and trade-offs of rye chromatin.

High intraspecific diversity of Restorer-of-fertility-like genes in barley

Publisher: Wiley

Date: 09-11-2019

DOI: 10.1111/TPJ.14115

Dual targeting is the rule for organellar aminoacyl-tRNA synthetases in Arabidopsis thaliana

Publisher: Proceedings of the National Academy of Sciences

Date: 26-10-2005

DOI: 10.1073/PNAS.0504682102

Abstract: In plants, protein synthesis occurs in the cytosol, mitochondria, and plastids. Each compartment requires a full set of tRNAs and aminoacyl-tRNA synthetases. We have undertaken a systematic analysis of the targeting of organellar aminoacyl-tRNA synthetases in the model plant Arabidopsis thaliana . Dual targeting appeared to be a general rule. Among the 24 identified organellar aminoacyl-tRNA synthetases (aaRSs), 15 (and probably 17) are shared between mitochondria and plastids, and 5 are shared between cytosol and mitochondria (one of these aaRSs being present also in chloroplasts). Only two were shown to be uniquely chloroplastic and none to be uniquely mitochondrial. Moreover, there are no ex les where the three aaRS genes originating from the three ancestral genomes still coexist. These results indicate that extensive exchange of aaRSs has occurred during evolution and that many are now shared between two or even three compartments. The findings have important implications for studies of the translation machinery in plants and on protein targeting and gene transfer in general.

Organellar RNA editing

Publisher: Wiley

Date: 14-04-0014

DOI: 10.1002/WRNA.72

Abstract: RNA editing is a term used for a number of mechanistically different processes that alter the nucleotide sequence of RNA molecules to differ from the gene sequence. RNA editing occurs in a wide variety of organisms and is particularly frequent in organelle transcripts of eukaryotes. The discontiguous phylogenetic distribution of mRNA editing, the mechanistic differences observed in different organisms, and the nonhomologous editing machinery described in different taxonomic groups all suggest that RNA editing has appeared independently several times. This raises questions about the selection pressures acting to maintain editing that are yet to be completely resolved. Editing tends to be frequent in organisms with atypical organelle genomes and acts to correct the effect of DNA mutations that would otherwise compromise the synthesis of functional proteins. Additional functions of editing in generating protein ersity or regulating gene expression have been proposed but so far lack widespread experimental evidence, at least in organelles.

Characterization of some major identity elements in plant alanine and phenylalanine transfer RNAs

Publisher: Springer Science and Business Media LLC

Date: 12-1994

DOI: 10.1007/BF00019497

Abstract: Ageing is a risk factor for cancer. Worldwide, the number and proportion of adults aged ≥65 will increase, along with the incidence of ovarian cancer. Older adults are under-represented in randomised clinical trials (RCTs), and those who are enrolled have a good performance status and no major health issues. These patients are not representative of older patients seen in everyday clinical practice therefore, age-specific data on efficacy and toxicity of olaparib in the 'real-world' setting are lacking. This observational study was conducted in the Central Jutland Region in Denmark. Data in unselected older (≥65) patients with known BRCA mutation receiving olaparib maintenance treatment for platinum-sensitive relapsed ovarian cancer were registered between 2015 and 2019. Toxicity and progression-free survival (PFS) were registered. No geriatric assessment has been performed. In total, 20 consecutive patients ≥65 years were included with a median age of 75 years (range: 65-85). Most of the patients (18/20) had ECOG PS: 0-1. Treatment interruption and dose reduction occurred in 65% of the patients. Toxicities of any grade occurred in 18 (90%), whereas grade 3/4 toxicities occurred in 6 patients (30%). Treatment was terminated due to disease progression or unacceptable toxicity in 13 (65%) patients. The median PFS was 6 months (range: 2-31), and the median follow-up was 15 months (range: 3-30). Our 'real-world' experience shows that unselected older patients represent a significant larger proportion in real life than in RCTs furthermore, older patients in a real-world setting may experience more side effects possibly affecting the quality of life. The median PFS data suggest that older patients may not derive the same clinical benefit than their fit and younger counterparts.There is a need to enrol vulnerable/frail older patients into RCTs, ensuring that data will also be applicable in standard clinical settings. Incorporating geriatric assessment into these trials should be encouraged.

NMAT1, a nuclear-encoded maturase involved in the trans-splicing of nad1 intron 1, is essential for mitochondrial complex i assembly and function

Publisher: Wiley

Date: 22-05-2012

DOI: 10.1111/J.1365-313X.2012.04998.X

Discrete mutations in the presequence of potato formate dehydrogenase inhibit the in vivo targeting of GFP fusions into mitochondria

Publisher: Elsevier BV

Date: 11-2003

DOI: 10.1016/J.BBRC.2003.10.099

Abstract: Most mitochondrial proteins are encoded by the nucleus, translated in the cytosol, and imported. Mitochondrial precursors generally contain their targeting information in a cleavable N-terminal presequence, which is rich in hydroxylated and positively charged residues and can form hiphilic alpha-helices. We report the in vivo targeting of green fluorescent protein (GFP) by the FDH presequence, as well as several truncated or mutated variants. Some of these mutations modify the hiphilicity of the predicted alpha-helix. The removal of the first two residues abolishes import and some single amino acid mutations strongly inhibit import. Such strong effects on import had not been observed in similar studies on other plant mitochondrial presequences, suggesting that the FDH presequence is a particularly good model for functional studies.

Structure and expression of several bean (Phaseolus vulgaris) nuclear transfer RNA genes: Relevance to the process of tRNA import into plant mitochondria

Publisher: Springer Science and Business Media LLC

Date: 1998

DOI: 10.1023/A:1005972023506

Abstract: Bean nuclear genes for tRNA(Pro), tRNA(Thr) and tRNA(Leu) were isolated. Expression of the tRNA(Pro) genes was demonstrated in vivo and sequence analysis suggested lification of the tRNA(Pro) gene copy number through duplication of a gene cluster at the same locus of the bean genome. The two tRNA(Thr) genes isolated were actively transcribed and their transcripts processed in a HeLa cell system. In vivo expression tests of these genes and aminoacylation assays of the corresponding in vitro transcripts showed the presence of identity determinants in the anticodon of plant tRNA(Thr). The tRNA(Leu) gene was not expressed due to deviation from the consensus in the internal B-box promoter. The same sequence deviation also prevented aminoacylation of the corresponding in vitro transcript. This tRNA(Leu) however exists in plants and is synthesized from another gene with a consensus B-box promoter. Plant mitochondria import from the cytosol a number of nucleus-encoded tRNAs, including tRNA(Leu) and tRNA(Thr). From the available sequence data, we could not identify any conserved structural motif characteristic for the nucleus-encoded tRNAs imported into plant mitochondria, either in the tRNAs, or in the gene flanking sequences. These results suggest that recognition of tRNAs for import is idiosyncratic and likely to depend on protein/RNA interactions that are specific to each tRNA or each isoacceptor group.

Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics

Publisher: Springer Science and Business Media LLC

Date: 04-01-2020

DOI: 10.1186/S13007-019-0534-5

Abstract: Herbaria are valuable sources of extensive curated plant material that are now accessible to genetic studies because of advances in high-throughput, next-generation sequencing methods. As an applied assessment of large-scale recovery of plastid and ribosomal genome sequences from herbarium material for plant identification and phylogenomics, we sequenced 672 s les covering 21 families, 142 genera and 530 named and proposed named species. We explored the impact of parameters such as s le age, DNA concentration and quality, read depth and fragment length on plastid assembly error. We also tested the efficacy of DNA sequence information for identifying plant s les using 45 specimens recently collected in the Pilbara. Genome skimming was effective at producing genomic information at large scale. Substantial sequence information on the chloroplast genome was obtained from 96.1% of s les, and complete or near-complete sequences of the nuclear ribosomal RNA gene repeat were obtained from 93.3% of s les. We were able to extract sequences for the core DNA barcode regions rbcL and matK from 96 to 93.3% of s les, respectively. Read quality and DNA fragment length had significant effects on sequencing outcomes and error correction of reads proved essential. Assembly problems were specific to certain taxa with low GC and high repeat content ( Goodenia , Scaevola , Cyperus , Bulbostylis , Fimbristylis ) suggesting biological rather than technical explanations. The structure of related genomes was needed to guide the assembly of repeats that exceeded the read length. DNA-based matching proved highly effective and showed that the efficacy for species identification declined in the order cpDNA rDNA matK rbcL. We showed that a large-scale approach to genome sequencing using herbarium specimens produces high-quality complete cpDNA and rDNA sequences as a source of data for DNA barcoding and phylogenomics.

Resolving intergeneric relationships in the aervoid clade and the backbone of Ptilotus (Amaranthaceae): Evidence from whole plastid genomes and morphology

Publisher: Wiley

Date: 04-2019

DOI: 10.1002/TAX.12054

Complete chloroplast genome sequences of four meliaceae species and comparative analyses

Publisher: MDPI AG

Date: 03-2018

DOI: 10.3390/IJMS19030701

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

Publisher: Wiley

Date: 25-07-2012

DOI: 10.1016/J.FEBSLET.2012.07.043

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

Two Interacting Proteins Are Necessary for the Editing of the NdhD-1 Site in Arabidopsis Plastids

Publisher: Oxford University Press (OUP)

Date: 09-2012

DOI: 10.1105/TPC.112.099507

Abstract: After transcription, mRNA editing in angiosperm chloroplasts and mitochondria results in the conversion of cytidine to uridine by deamination. Analysis of Arabidopsis thaliana mutants affected in RNA editing have shown that many pentatricopeptide repeat proteins (PPRs) are required for specific cytidine deamination events. PPR proteins have been shown to be sequence-specific RNA binding proteins allowing the recognition of the C to be edited. The C-terminal DYW domain present in many editing factors has been proposed to catalyze C deamination, as it shows sequence similarities with cytidine deaminases in other organisms. However, many editing factors, such as the first to be discovered, CHLORORESPIRATORY REDUCTION4 (CRR4), lack this domain, so its importance has been unclear. Using a reverse genetic approach, we identified DYW1, an RNA editing factor acting specifically on the plastid ndhD-1 editing site recognized by CRR4. Unlike other known editing factors, DYW1 contains no identifiable PPR motifs but does contain a clear DYW domain. We were able to show interaction between CRR4 and DYW1 by bimolecular fluorescence complementation and to reconstitute a functional chimeric CRR4-DYW1 protein complementing the crr4 dyw1double mutant. We propose that CRR4 and DYW1 act together to edit the ndhD-1 site.

Plant biotechnology 2007: all three genomes make contributions to progress

Publisher: Elsevier BV

Date: 04-2007

DOI: 10.1016/J.COPBIO.2007.03.004

Plastid signalling to the nucleus and beyond

Publisher: Elsevier BV

Date: 11-2008

DOI: 10.1016/J.TPLANTS.2008.08.008

Abstract: Communication between the compartments or organelles of cells is essential for plant growth and development. There is an emerging understanding of signals generated within energy-transducing organelles, such as chloroplasts and mitochondria, and the nuclear genes that respond to them, a process known as retrograde signalling. A recent series of unconnected breakthroughs have given scientists a glimpse inside the 'black box' of organellar signalling thanks to the identification of some of the factors involved in generating and propagating signals to the nucleus and, in some instances, systemically throughout photosynthetic tissues. This review will focus on recent developments in our understanding of retrograde and systemic signals generated by organelles, with an emphasis on chloroplasts.

The Arabidopsis gene YS1 encoding a DYW protein is required for editing of rpoB transcripts and the rapid development of chloroplasts during early growth

Publisher: Wiley

Date: 26-03-2009

DOI: 10.1111/J.1365-313X.2008.03766.X

Pentatricopeptide repeat proteins in trypanosoma brucei function in mitochondrial ribosomes

Publisher: Informa UK Limited

Date: 10-2007

DOI: 10.1128/MCB.00708-07

Albinism does not correlate with biparental inheritance of plastid DNA in interspecific hybrids in Cicer species

Publisher: Elsevier BV

Date: 04-2011

DOI: 10.1016/J.PLANTSCI.2011.01.003

Abstract: Cultivated chickpea (Cicer arietinum) was crossed with its wild relatives from the genus Cicer to transfer favorable genes from the wider gene pool into the cultivar. Post-hybridization barriers led to yellowing and subsequent senescence from as early as 5 days after fertilization, however, the ovules of hybrid embryos could be rescued in vitro. Hybrids were classified as green, partially green or albino. The hybrid status of regenerated plantlets in vitro was confirmed by lification of nuclear DNA markers. To check whether chloroplast development correlated with plastid DNA inheritance in these crosses, primers were designed using conserved plastid gene sequences from wild and cultivated species. All three possible plastid inheritance patterns were observed: paternal, maternal and biparental. This is the first report of biparental inheritance of plastid DNA in Cicer. No correlation was observed between parental origin of the plastid genome and degree of albinism, indicating that chloroplast development in hybrid genotypes was mostly influenced by nuclear factors.

The GENOMES UNCOUPLED1 protein has an ancient, highly conserved role but not in retrograde signalling

Publisher: Wiley

Date: 05-07-2022

DOI: 10.1111/NPH.18318

Abstract: The pentatricopeptide repeat protein GENOMES UNCOUPLED1 (GUN1) is required for chloroplast‐to‐nucleus signalling when plastid translation becomes inhibited during chloroplast development in Arabidopsis thaliana , but its exact molecular function remains unknown. We analysed GUN1 sequences in land plants and streptophyte algae. We tested functional conservation by complementation of the Arabidopsis gun1 mutant with GUN1 genes from the streptophyte alga Coleochate orbicularis or the liverwort Marchantia polymorpha. We also analysed the transcriptomes of M. polymorpha gun1 knockout mutant lines during chloroplast development. GUN1 evolved within the streptophyte algal ancestors of land plants and is highly conserved among land plants but missing from the Rafflesiaceae that lack chloroplast genomes. GUN1 genes from C. orbicularis and M. polymorpha suppress the cold‐sensitive phenotype of the Arabidopsis gun1 mutant and restore typical retrograde responses to treatments with inhibitors of plastid translation, even though M. polymorpha responds very differently to such treatments. Our findings suggest that GUN1 is an ancient protein that evolved within the streptophyte algal ancestors of land plants before the first plants colonized land more than 470 million years ago. Its primary role is likely to be in chloroplast gene expression and its role in chloroplast retrograde signalling probably evolved more recently.

Surveillance and Cleavage of Eukaryotic tRNAs

Publisher: MDPI AG

Date: 15-01-2015

DOI: 10.3390/IJMS16011873

Deepred-Mt

Publisher: Elsevier BV

Date: 09-2021

DOI: 10.1016/J.COMPBIOMED.2021.104682

The pentatricopeptide repeat proteins TANG2 and ORGANELLE TRANSCRIPT PROCESSING439 are involved in the splicing of the multipartite nad5 transcript encoding a subunit of mitochondrial complex

Publisher: Oxford University Press (OUP)

Date: 23-06-2014

DOI: 10.1104/PP.114.244616

A unique C-terminal domain contributes to the molecular function of restorer-of-fertility proteins in plant mitochondria

Publisher: Cold Spring Harbor Laboratory

Date: 02-05-2023

DOI: 10.1101/2023.05.02.538898

Abstract: Restorer-of-fertility ( Rf ) genes have practical applications in hybrid seed production as a means to control self-pollination. They encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. In searching for a molecular signature unique to this class of proteins, we found that a majority of known Rf proteins have a unique domain, which we called RfCTD ( Restorer-of-fertility C-terminal domain ), and its presence correlates with the ability to induce cleavage of the mitochondrial RNA target. We constructed a sequence profile that can quickly and accurately identify RfCTD sequences in plant genomes or transcriptomes. We screened 219 angiosperm genomes from 123 genera and found that each diploid genome encodes, on average, 25 Rf-like (RFL) proteins, of which approximately 55% contain the C-terminal signature domain. This screen also revealed considerable variation in RFL gene numbers across flowering plants. We observed that plant genera with bisexual flowers have significantly higher numbers of RFL genes compared to those with unisexual flowers, consistent with a role of these proteins in restoration of male fertility. Finally, we show that removing the RfCTD from the RFL protein RNA PROCESSING FACTOR 2- nad6 prevented cleavage of its RNA target, the nad6 transcript, in Arabidopsis thaliana mitochondria. This research provides a simple way of identifying putative Rf candidates in genome sequences, new insights into the molecular mode of action of Rf proteins in plant mitochondria and expands our understanding of the evolution of fertility restoration in flowering plants.

Cofactor-independent RNA editing by a synthetic S-type PPR protein

Publisher: Oxford University Press (OUP)

Date: 23-12-2021

DOI: 10.1093/SYNBIO/YSAB034

Abstract: Pentatricopeptide repeat (PPR) proteins are RNA-binding proteins that are attractive tools for RNA processing in synthetic biology applications given their modular structure and ease of design. Several distinct types of motifs have been described from natural PPR proteins, but almost all work so far with synthetic PPR proteins has focused on the most widespread P-type motifs. We have investigated synthetic PPR proteins based on tandem repeats of the more compact S-type PPR motif found in plant organellar RNA editing factors and particularly prevalent in the lycophyte Selaginella. With the aid of a novel plate-based screening method, we show that synthetic S-type PPR proteins are easy to design and bind with high affinity and specificity and are functional in a wide range of pH, salt and temperature conditions. We find that they outperform a synthetic P-type PPR scaffold in many situations. We designed an S-type editing factor to edit an RNA target in E. coli and demonstrate that it edits effectively without requiring any additional cofactors to be added to the system. These qualities make S-type PPR scaffolds ideal for developing new RNA processing tools.

The Pentatricopeptide Repeat Protein MEF100 Is Required for the Editing of Four Mitochondrial Editing Sites in Arabidopsis

Publisher: MDPI AG

Date: 22-02-2021

DOI: 10.3390/CELLS10020468

Abstract: In Arabidopsis thaliana there are more than 600 C-to-U RNA editing events in the mitochondria and at least 44 in the chloroplasts. Pentatricopeptide repeat (PPR) proteins provide the specificity for these reactions. They recognize RNA sequences in a partially predictable fashion via key amino acids at the fifth and last position in each PPR motif that bind to in idual ribonucleotides. A combined approach of RNA-Seq, mutant complementation, electrophoresis of mitochondrial protein complexes and Western blotting allowed us to show that MEF100, a PPR protein identified in a genetic screen for mutants resistant to an inhibitor of γ -glutamylcysteine synthetase, is required for the editing of nad1-493, nad4-403, nad7-698 and ccmFN2-356 sites in Arabidopsis mitochondria. The absence of editing in mef100 leads to a decrease in mitochondrial Complex I activity, which probably explains the physiological phenotype. Some plants have lost the requirement for MEF100 at one or more of these sites through mutations in the mitochondrial genome. We show that loss of the requirement for MEF100 editing leads to ergence in the MEF100 binding site.

Genome-wide analysis of arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis

Publisher: Oxford University Press (OUP)

Date: 08-2004

DOI: 10.1105/TPC.104.022236

Abstract: The complete sequence of the Arabidopsis thaliana genome revealed thousands of previously unsuspected genes, many of which cannot be ascribed even putative functions. One of the largest and most enigmatic gene families discovered in this way is characterized by tandem arrays of pentatricopeptide repeats (PPRs). We describe a detailed bioinformatic analysis of 441 members of the Arabidopsis PPR family plus genomic and genetic data on the expression (microarray data), localization (green fluorescent protein and red fluorescent protein fusions), and general function (insertion mutants and RNA binding assays) of many family members. The basic picture that arises from these studies is that PPR proteins play constitutive, often essential roles in mitochondria and chloroplasts, probably via binding to organellar transcripts. These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of in idual mutants in other organisms.

The mitochondrial pentatricopeptide repeat protein PPR19 is involved in the stabilization of NADH dehydrogenase 1 transcripts and is crucial for mitochondrial function and Arabidopsis thaliana development

Publisher: Wiley

Date: 23-03-2021

DOI: 10.1111/NPH.14528

Abstract: Despite the importance of pentatricopeptide repeat ( PPR ) proteins in organellar RNA metabolism and plant development, the functions of many PPR proteins remain unknown. Here, we determined the role of a mitochondrial PPR protein (At1g52620) comprising 19 PPR motifs, thus named PPR 19, in Arabidopsis thaliana . The ppr19 mutant displayed abnormal seed development, reduced seed yield, delayed seed germination, and retarded growth, indicating that PPR 19 is indispensable for normal growth and development of Arabidopsis thaliana . Splicing pattern analysis of mitochondrial genes revealed that PPR 19 specifically binds to the specific sequence in the 3′‐terminus of the NADH dehydrogenase 1 ( nad1 ) transcript and stabilizes transcripts containing the second and third exons of nad1 . Loss of these transcripts in ppr19 leads to multiple secondary effects on accumulation and splicing of other nad1 transcripts, from which we can infer the order in which cis ‐ and trans ‐spliced nad1 transcripts are normally processed. Improper splicing of nad1 transcripts leads to the absence of mitochondrial complex I and alteration of the nuclear transcriptome, notably influencing the alternative splicing of a variety of nuclear genes. Our results indicate that the mitochondrial PPR 19 is an essential component in the splicing of nad1 transcripts, which is crucial for mitochondrial function and plant development.

Editing of chloroplast rps14 by PPR editing factor EMB2261 is essential for Arabidopsis development

Publisher: Frontiers Media SA

Date: 20-06-2018

DOI: 10.3389/FPLS.2018.00841

A Study of New Arabidopsis Chloroplast RNA Editing Mutants Reveals General Features of Editing Factors and Their Target Sites

Publisher: Oxford University Press (OUP)

Date: 11-2009

DOI: 10.1105/TPC.109.071472

Abstract: RNA editing in higher plant organelles results in the conversion of specific cytidine residues to uridine residues in RNA. The recognition of a specific target C site by the editing machinery involves trans-acting factors that bind to the RNA upstream of the C to be edited. In the last few years, analysis of mutants affected in chloroplast biogenesis has identified several pentatricopeptide repeat (PPR) proteins from the PLS subfamily that are essential for the editing of particular RNA transcripts. We selected other genes from the same subfamily and used a reverse genetics approach to identify six new chloroplast editing factors in Arabidopsis thaliana (OTP80, OTP81, OTP82, OTP84, OTP85, and OTP86). These six factors account for nine editing sites not previously assigned to an editing factor and, together with the nine PPR editing proteins previously described, explain more than half of the 34 editing events in Arabidopsis chloroplasts. OTP80, OTP81, OTP85, and OTP86 target only one editing site each, OTP82 two sites, and OTP84 three sites in different transcripts. An analysis of the target sites requiring the five editing factors involved in editing of multiple sites (CRR22, CRR28, CLB19, OTP82, and OTP84) suggests that editing factors can generally distinguish pyrimidines from purines and, at some positions, must be able to recognize specific bases.

AEF1/MPR25 is implicated in RNA editing of plastid atpF and mitochondrial nad5, and also promotes atpF splicing in Arabidopsis and rice.

Publisher: Wiley

Date: 24-02-2015

DOI: 10.1111/TPJ.12756

Abstract: RNA editing is an essential mechanism that modifies target cytidines to uridine in both mitochondrial and plastid mRNA. Target sites are recognized by pentatricopeptide repeat (PPR) proteins. Using bioinformatics predictions based on the code describing sequence recognition by PPR proteins, we have identified an Arabidopsis editing factor required for editing of atpF in plastids. A loss-of-function mutation in ATPF EDITING FACTOR 1 (AEF1, AT3G22150) results in severe variegation, presumably due to decreased plastid ATP synthase levels. Loss of editing at the atpF site is coupled with a large decrease in splicing of the atpF transcript, even though the editing site is within an exon and 53 nucleotides distant from the splice site. The rice orthologue of AEF1, MPR25, has been reported to be required for editing of a site in mitochondrial nad5 transcripts, and we confirm that editing of the same site is affected in the Arabidopsis aef1 mutant. We also show that splicing of chloroplast atpF transcripts is affected in the rice mpr25 mutant. AEF1 is thus highly unusual for an RNA editing specificity factor in that it has functions in both organelles.

The GENOMES UNCOUPLED1 protein has an ancient, highly conserved role in chloroplast gene expression but not in retrograde signalling

Publisher: Cold Spring Harbor Laboratory

Date: 26-02-2022

DOI: 10.1101/2022.02.25.481377

Abstract: The pentatricopeptide repeat protein GENOMES UNCOUPLED1 (GUN1) is required for chloroplast-to-nucleus signalling in response to plastid stress during chloroplast development in Arabidopsis thaliana but its exact molecular function remains unknown. We analysed GUN1 sequences in land plants and streptophyte algae. We tested functional conservation by complementation of the Arabidopsis gun1 mutant with GUN1 genes from the streptophyte alga Coleochate orbicularis or the liverwort Marchantia polymorpha. We also analysed the transcriptomes of M. polymorpha gun1 knock-out mutant lines during chloroplast development. GUN1 evolved within the streptophyte algal ancestors of land plants and is highly conserved among land plants but missing from the Rafflesiaceae that lack chloroplast genomes. GUN1 genes from C. orbicularis and M. polymorpha restore chloroplast retrograde signalling and suppress the cold-sensitive phenotype of the Arabidopsis gun1 mutant. However, GUN1 is not required for chloroplast retrograde signalling in the liverwort M. polymorpha . Our findings suggest that GUN1 is an ancient protein that evolved within the streptophyte algal ancestors of land plants before the first plants colonised land more than 470 million years ago. Its primary role is likely to be in chloroplast gene expression and its role in chloroplast retrograde signalling probably evolved more recently.

Albinism in plants: A major bottleneck in wide hybridization, androgenesis and doubled haploid culture

Publisher: Informa UK Limited

Date: 04-11-2009

DOI: 10.1080/07352680903133252

European consortia building integrated resources for Arabidopsis functional genomics

Publisher: Elsevier BV

Date: 10-2003

DOI: 10.1016/S1369-5266(03)00086-4

Abstract: European laboratories specializing in functional genomics technologies collaborate in several consortia to build resources that facilitate gene function discovery in Arabidopsis thaliana. These resources include CATMA (a repertoire of gene-specific sequence tags), CAGE (a compendium of transcript profiles), AGRIKOLA (which consists of plasmids and mutant lines for gene silencing), ORFEUS (a collection of open reading frames) and SAP (a collection of promoter regions).

Targeted cleavage of nad6 mRNA induced by a modified pentatricopeptide repeat protein in plant mitochondria

Publisher: Springer Science and Business Media LLC

Date: 11-10-2018

DOI: 10.1038/S42003-018-0166-8

Abstract: Mitochondrial genes encode key components of the cellular energy machinery, but their genetic analysis is difficult or impossible in most organisms (including plants) because of the lack of viable transformation approaches. We report here a method to block the expression of the mitochondrial nad6 gene encoding a subunit of respiratory complex I in Arabidopsis tha liana , via the modification of the specificity of the RNA-binding protein RNA PROCESSING FACTOR 2 (RPF2). We show that the modified RPF2 binds and specifically induces cleavage of nad6 RNA, almost eliminating expression of the Nad6 protein and consequently complex I accumulation and activity. To our knowledge, this is the first ex le of a targeted block in expression of a specific mitochondrial transcript by a custom-designed RNA-binding protein. This opens the path to reverse genetics studies on mitochondrial gene functions and leads to potential applications in agriculture.

Transactivation of a target gene using a suppressor tRNA in transgenic tobacco plants

Publisher: Wiley

Date: 03-1997

DOI: 10.1046/J.1365-313X.1997.11030597.X

Abstract: The abundance of tRNAs, together with their central role in translation, has generated considerable interest in the use of tRNA genes for biotechnological applications. One such application is the use of suppressor tRNAs to transactive target genes containing premature stop codons. Previous work has shown that such systems can work in transient expression experiments in plant protoplasts here these experiments are extended to show that suppression of stop codons can occur in whole plants. Transgenic tobacco plants homozygous for a modified tRNA(Leu) gene expressing a strong amber suppressor tRNA, and plants carrying a beta-glucuronidase (gus) gene inactivated by a premature amber stop codon have been obtained. When the two types of plants are crossed, many of the F1 hybrids show significant GUS activity. The GUS activity is dependent on the presence of both the suppressor tRNA gene and the gus gene. Tobacco plants carrying the suppressor tRNA gene are phenotypically normal, fertile and the gene shows normal Menedelian inheritance. The potential applications of such a system are discussed.

The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic

Publisher: Oxford University Press (OUP)

Date: 29-11-2016

DOI: 10.1093/NAR/GKW1122

Duplication and quadruplication of Arabidopsis thaliana cysteinyl- and asparaginyl-tRNA synthetase genes of organellar origin

Publisher: Springer Science and Business Media LLC

Date: 05-2000

DOI: 10.1007/S002390010044

Abstract: Two cysteinyl-tRNA synthetases (CysRS) and four asparaginyl-tRNA synthetases (AsnRS) from Arabidopsis thaliana were characterized from genome sequence data, EST sequences, and RACE sequences. For one CysRS and one AsnRS, sequence alignments and prediction programs suggested the presence of an N-terminal organellar targeting peptide. Transient expression of these putative targeting sequences joined to jellyfish green fluorescent protein (GFP) demonstrated that both presequences can efficiently dual-target GFP to mitochondria and plastids. The other CysRS and AsnRSs lack targeting sequences and presumably aminoacylate cytosolic tRNAs. Phylogenetic analysis suggests that the four AsnRSs evolved by repeated duplication of a gene transferred from an ancestral plastid and that the CysRSs also arose by duplication of a transferred organelle gene (possibly mitochondrial). These case histories are the best ex les to date of capture of organellar aminoacyl-tRNA synthetases by the cytosolic protein synthesis machinery.

A rapid high-throughput method for the detection and quantification of RNA editing based on high-resolution melting of amplicons

Publisher: Oxford University Press (OUP)

Date: 28-08-2007

DOI: 10.1093/NAR/GKM640

Evolutionary Model of Plastidial RNA Editing in Angiosperms Presumed from Genome-Wide Analysis of Amborella trichopoda

Publisher: Oxford University Press (OUP)

Date: 31-05-2019

DOI: 10.1093/PCP/PCZ111

Abstract: Amborella trichopoda is placed close to the base of the angiosperm lineage (basal angiosperm). By genome-wide RNA sequencing, we identified 184C-to-U RNA editing sites in the plastid genome of Amborella. This number is much higher than that observed in other angiosperms including maize (44 sites), rice (39 sites) and grape (115 sites). Despite the high frequency of RNA editing, the biased distribution of RNA editing sites in the genome, target codon preference and nucleotide preference adjacent to the edited cytidine are similar to that in other angiosperms, suggesting a common editing machinery. Consistent with this idea, the Amborella nuclear genome encodes 2–3 times more of the E- and DYW-subclass members of pentatricopeptide repeat proteins responsible for RNA editing site recognition in plant organelles. Among 165 editing sites in plastid protein coding sequences in Amborella, 100 sites were conserved at least in one out of 38 species selected to represent key branching points of the angiosperm phylogenetic tree. We assume these 100 sites represent at least a subset of the sites in the plastid editotype of ancestral angiosperms. We then mapped the loss and gain of editing sites on the phylogenetic tree of angiosperms. Our results support the idea that the evolution of angiosperms has led to the loss of RNA editing sites in plastids.

Evolutionary plasticity of restorer-of-fertility-like proteins in rice.

Publisher: Springer Science and Business Media LLC

Date: 24-10-2016

DOI: 10.1038/SREP35152

Abstract: Hybrid seed production in rice relies on cytoplasmic male sterility (CMS) induced by specific mitochondrial proteins, whose deleterious effects are suppressed by nuclear Restorer of Fertility ( RF ) genes. The majority of RF proteins belong to a specific clade of the RNA-binding pentatricopeptide repeat protein family. We have characterised ‘ restorer-of-fertility-like’ (RFL) sequences from 13 Oryza genomes and the Brachypodium distachyon genome. The majority of the RFL sequences are found in genomic clusters located at two or three chromosomal loci with only a minor proportion being present as isolated genes. The RFL genomic cluster located on Oryza chromosome 10, the location of almost all known active rice RF genes, shows extreme variation in structure and gene content between species. We show evidence for homologous recombination events as an efficient mechanism for generating the huge repertoire of RNA sequence recognition motifs within RFL proteins and a major driver of RFL sequence evolution. The RFL sequences identified here will improve our understanding of the molecular basis of CMS and fertility restoration in plants and will accelerate the development of new breeding strategies.

Simulation of heterosis in a genome-scale metabolic network provides mechanistic explanations for increased biomass production rates in hybrid plants

Publisher: Springer Science and Business Media LLC

Date: 18-07-2019

DOI: 10.1038/S41540-019-0101-8

Abstract: Heterosis, or hybrid vigour, is said to occur when F1 in iduals exhibit increased performance for a number of traits compared to their parental lines. Improved traits can include increased size, better yield, faster development and a higher tolerance to pathogens or adverse conditions. The molecular basis for the phenomenon remains disputed, despite many decades of theorising and experimentation. In this study, we add a genetics layer to a constraint-based model of plant ( Arabidopsis ) primary metabolism and show that we can realistically reproduce and quantify heterosis in a highly complex trait (the rate of biomass production). The results demonstrate that additive effects coupled to the complex patterns of epistasis generated by a large metabolic network are sufficient to explain most or all the heterosis seen in typical F1 hybrids. Such models provide a simple approach to exploring and understanding heterosis and should assist in designing breeding strategies to exploit this phenomenon in the future.

The E domain of CRR2 participates in sequence-specific recognition of RNA in plastids

Publisher: Wiley

Date: 06-12-2019

DOI: 10.1111/NPH.15578

Abstract: Pentatricopeptide repeat (PPR) proteins are modular RNA-binding proteins involved in different aspects of RNA metabolism in organelles. PPR proteins of the PLS subclass often contain C-terminal domains that are important for their function, but the role of one of these domains, the E domain, is far from resolved. Here, we elucidate the role of the E domain in CRR2 in plastids. We identified a surprisingly large number of small RNAs that represent in vivo footprints of the Arabidopsis PLS-class PPR protein CRR2. An unexpectedly strong base conservation was found in the nucleotides aligned to the E domain. We used both in vitro and in vivo experiments to reveal the role of the E domain of CRR2. The E domain of CRR2 can be predictably altered to prefer different nucleotides in its RNA ligand, and position 5 of the E1-motif is biologically important for the PPR-RNA interaction. The 'code' of the E domain PPR motifs is different from that of P- and S-motifs. The findings presented here show that the E domain of CRR2 is involved in sequence-specific interaction with its RNA ligand and have implications for our ability to predict RNA targets for PLS-PPRs and their use as biotechnological tools to manipulate specific RNAs in vivo.

The genetic basis of cytoplasmic male sterility and fertility restoration in wheat

Publisher: Springer Science and Business Media LLC

Date: 15-02-2021

DOI: 10.1038/S41467-021-21225-0

Abstract: Hybrid wheat varieties give higher yields than conventional lines but are difficult to produce due to a lack of effective control of male fertility in breeding lines. One promising system involves the Rf1 and Rf3 genes that restore fertility of wheat plants carrying Triticum timopheevii -type cytoplasmic male sterility (T-CMS). Here, by genetic mapping and comparative sequence analyses, we identify Rf1 and Rf3 candidates that can restore normal pollen production in transgenic wheat plants carrying T-CMS. We show that Rf1 and Rf3 bind to the mitochondrial orf279 transcript and induce cleavage, preventing expression of the CMS trait. The identification of restorer genes in wheat is an important step towards the development of hybrid wheat varieties based on a CMS- Rf system. The characterisation of their mode of action brings insights into the molecular basis of CMS and fertility restoration in plants.

University Of Western Australia

Location: Australia

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Discovery Projects - Grant ID: DP200102981

Start Date: 02-2020

End Date: 12-2024

Amount: $610,871.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP150102692

Start Date: 2015

End Date: 12-2019

Amount: $524,500.00

Funder: Australian Research Council

Linkage - International - Grant ID: LX0776042

Start Date: 04-2007

End Date: 12-2008

Amount: $59,608.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0989071

Start Date: 01-2009

End Date: 07-2012

Amount: $600,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE140100096

Start Date: 03-2014

End Date: 03-2015

Amount: $180,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP200100547

Start Date: 03-2021

End Date: 12-2024

Amount: $661,039.00

Funder: Australian Research Council

Australian Laureate Fellowships - Grant ID: FL140100179

Start Date: 12-2014

End Date: 12-2019

Amount: $2,800,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE110100188

Start Date: 03-2011

End Date: 12-2012

Amount: $550,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE130100081

Start Date: 04-2013

End Date: 12-2014

Amount: $500,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP210103629

Start Date: 11-2021

End Date: 10-2024

Amount: $489,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE130100073

Start Date: 06-2013

End Date: 06-2014

Amount: $280,000.00

Funder: Australian Research Council

ARC Centres Of Excellence - Grant ID: CE230100015

Start Date: 2023

End Date: 12-2029

Amount: $35,000,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP120200699

Start Date: 07-2012

End Date: 06-2016

Amount: $282,500.00

Funder: Australian Research Council

Super Science Fellowships - Grant ID: FS100100022

Start Date: 02-2011

End Date: 06-2014

Amount: $835,200.00

Funder: Australian Research Council

ARC Centres Of Excellence - Grant ID: CE140100008

Start Date: 2014

End Date: 05-2021

Amount: $26,000,000.00

Funder: Australian Research Council

ARC Centres Of Excellence - Grant ID: CE0561495

Start Date: 12-2005

End Date: 06-2014

Amount: $22,300,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE170100225

Start Date: 2017

End Date: 12-2017

Amount: $410,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE160100086

Start Date: 05-2016

End Date: 12-2016

Amount: $850,000.00

Funder: Australian Research Council