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

The Plant Journal, Год журнала: 2019, Номер 101(5), С. 1040 - 1056

Опубликована: Окт. 20, 2019

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

Язык: Английский

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Single organelle function and organization as estimated from Arabidopsis mitochondrial proteomics

The Plant Journal, Год журнала: 2019, Номер 101(2), С. 420 - 441

Опубликована: Сен. 14, 2019

Summary Mitochondria host vital cellular functions, including oxidative phosphorylation and co‐factor biosynthesis, which are reflected in their proteome. At the level plant mitochondria organized into hundreds of discrete functional entities, undergo dynamic fission fusion. It is individual organelle that operates living cell, yet biochemical physiological assessments have exclusively focused on characteristics large populations mitochondria. Here, we explore protein composition an average mitochondrion to deduce principles structural organisation. We perform proteomics purified from cultured heterotrophic Arabidopsis cells with intensity‐based absolute quantification scale dataset single based criteria justified by experimental evidence theoretical considerations. estimate a total 1.4 million molecules make up average. Copy numbers proteins span five orders magnitude, ranging >40 000 for Voltage‐Dependent Anion Channel 1 sub‐stoichiometric copy numbers, i.e. less than per mitochondrion, several pentatricopeptide repeat modify mitochondrial transcripts. For our analysis, consider physical chemical constraints discuss prominent features architecture, biogenesis, phosphorylation, metabolism, antioxidant defence, genome maintenance, gene expression, dynamics. While assessing limitations considerations, exemplify how understanding function organization can be connected order obtain global specific insights organelles work.

Язык: Английский

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Plant mitochondria – past, present and future

The Plant Journal, Год журнала: 2021, Номер 108(4), С. 912 - 959

Опубликована: Сен. 16, 2021

SUMMARY The study of plant mitochondria started in earnest around 1950 with the first isolations from animal and tissues. 35 years were spent establishing basic properties respiration using biochemical physiological approaches. A number unique (compared to mammalian mitochondria) observed: (i) ability oxidize malate, glycine cytosolic NAD(P)H at high rates; (ii) partial insensitivity rotenone, which turned out be due presence a second NADH dehydrogenase on inner surface mitochondrial membrane addition classical Complex I dehydrogenase; (iii) cyanide, an alternative oxidase, is also located membrane, IV, cytochrome oxidase. With appearance molecular biology methods 1985, followed by genomics, further discovered: (iv) DNA (mtDNA) 10–600 times larger than mtDNA, yet it only contains approximately 50% more genes; (v) mtDNA has kept standard genetic code, low divergence rate respect point mutations, but recombinatorial activity; (vi) mRNA maturation includes uniquely complex set activities for processing, splicing editing (at hundreds sites); (vii) recombination creates novel reading frames that can produce male sterility; (viii) have large proteome 2000–3000 different proteins containing many such as 200–300 pentatricopeptide repeat proteins. We describe present fairly detailed picture structure function how make their metabolism flexible allowing them involved diverse processes cell, photosynthesis, photorespiration, CAM C4 metabolism, heat production, temperature control, stress resistance mechanisms, programmed cell death genomic evolution. However, still challenge understand regulation expression works cellular level retrograde signaling coordinates all those processes.

Язык: Английский

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Systematic Review of Plant Ribosome Heterogeneity and Specialization

Frontiers in Plant Science, Год журнала: 2020, Номер 11

Опубликована: Июнь 25, 2020

Plants dedicate a high amount of energy and resources to the production ribosomes. Historically, these multi-protein ribosome complexes have been considered static protein synthesis machines that are not subject extensive regulation but only read mRNA produce polypeptides accordingly. New increasing evidence across various model organisms demonstrated heterogeneous nature This heterogeneity can constitute specialized ribosomes regulate translation control synthesis. A prominent example is seen in plant, Arabidopsis thaliana, which, due genome duplications, has multiple paralogs each ribosomal (RP) gene. We support notion plant evolution directing RP paralog divergence toward functional heterogeneity, underpinned part by vast resource mutants suggest specialization extends beyond pleiotropic effects single structural RPs or paralogs. Thus, highly suitable study this phenomenon. enables reverse genetics approaches could provide specialization. In review, we critically assess highlight steps along biogenesis which may arise, filling knowledge gaps science providing advanced insights from human yeast fields. propose data analysis pipeline infers deviations canonical compositions linked stress events. be extrapolated enhanced combination with other high-throughput methodologies, such as proteomics. Technologies, kinetic mass spectrometry profiling, will necessary resolve temporal spatial aspects translational while features subpopulations become clear systems biology approaches.

Язык: Английский

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Mitochondrial redox systems as central hubs in plant metabolism and signaling

PLANT PHYSIOLOGY, Год журнала: 2021, Номер 186(1), С. 36 - 52

Опубликована: Фев. 23, 2021

Abstract Plant mitochondria are indispensable for plant metabolism and tightly integrated into cellular homeostasis. This review provides an update on the latest research concerning organization operation of mitochondrial redox systems, how they affect signaling, development, stress responses. New insights energy systems such as tricarboxylic acid cycle electron transport chain (mtETC) discussed. The mtETC produces reactive oxygen nitrogen species, which can act signals or lead to damage, thus efficiently removed by antioxidant including Mn-superoxide dismutase, ascorbate–glutathione cycle, thioredoxin-dependent peroxidases. connected with photosynthesis, photorespiration, cytosolic metabolism, thereby providing redox-balancing. Mitochondrial proteins targets extensive post-translational modifications, but their functional significance added remains unclear. To operate in sync whole cell, communicate status via retrograde signaling change nuclear gene expression, several recent breakthroughs here At a organism level, play crucial roles from first minutes after seed imbibition, supporting meristem activity, growth, fertility, until senescence darkened aged tissue. Finally, organismal responses environmental challenges drought, salinity, heat, submergence, also threats posed pathogens. Both major advances outstanding questions reviewed, may help future efforts mitochondria.

Язык: Английский

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The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource

The Plant Cell, Год журнала: 2021, Номер 33(11), С. 3421 - 3453

Опубликована: Авг. 17, 2021

We developed a resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about thaliana proteome, such as significance of protein splice forms and post-translational modifications (PTMs), or simply obtain reliable information specific proteins. is based on published mass spectrometry (MS) data collected through ProteomeXchange reanalyzed uniform processing metadata annotation pipeline. All matched MS-derived peptide are linked spectral, technical, biological metadata. Nearly 40 million out ∼143 MS/MS (tandem MS) spectra were reference genome Araport11, identifying ∼0.5 unique peptides 17,858 uniquely identified proteins (only isoform per gene) at highest confidence level (false discovery rate 0.0004; 2 non-nested ≥9 amino acid each), assigned canonical proteins, 3,543 lower-confidence Physicochemical properties evaluated for targeted identification unobserved Additional isoforms currently not in Araport11 that generated from pseudogenes, alternative start, stops, and/or variants, small Open Reading Frames; these features should be considered when updating genome. Phosphorylation can inspected sophisticated PTM viewer. integrated with community resources including TAIR, tracks JBrowse, PPDB, UniProtKB. Subsequent builds will incorporate millions more data.

Язык: Английский

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C-to-U and U-to-C: RNA editing in plant organelles and beyond

Journal of Experimental Botany, Год журнала: 2022, Номер 74(7), С. 2273 - 2294

Опубликована: Дек. 17, 2022

The genomes in the two energy-converting organelles of plant cells, chloroplasts and mitochondria, contain numerous 'errors' that are corrected at level RNA transcript copies. genes encoded endosymbiotic would not function properly if their transcripts were altered by site-specific cytidine-to-uridine (C-to-U) exchanges additional reverse U-to-C hornworts, lycophytes, ferns. These peculiar processes editing, re-establishing genetic information could alternatively be present organelle genome level, has spurred much research over >30 years. Lately new studies have revealed interesting insights, notably on biochemical machinery identifying specific pyrimidine nucleobases for conversion from C to U vice versa. Here, I will summarize prominent findings lately contributed our better understanding these phenomena introducing an added layer processing cells. Some this recent progress is based successful functional expression editing factors bacteria mammalian approaches recapitulated natural horizontal gene transfer through which some protist lineages seem acquired adapted them functionally own purposes.

Язык: Английский

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Complexome Profiling—Exploring Mitochondrial Protein Complexes in Health and Disease

Frontiers in Cell and Developmental Biology, Год журнала: 2022, Номер 9

Опубликована: Янв. 12, 2022

Complexome profiling (CP) is a state-of-the-art approach that combines separation of native proteins by electrophoresis, size exclusion chromatography or density gradient centrifugation with tandem mass spectrometry identification and quantification. Resulting data are computationally clustered to visualize the inventory, abundance arrangement multiprotein complexes in biological sample. Since its formal introduction decade ago, this method has been mostly applied explore not only composition mitochondrial oxidative phosphorylation (OXPHOS) several species but also identify novel protein interactors involved their assembly, maintenance functions. Besides, complexome utilized study dynamics OXPHOS complexes, as well impact an increasing number mutations leading disorders rearrangements whole complexome. Here, we summarize major findings obtained approach; emphasize advantages current limitations; discuss multiple examples on how tool could be further investigate pathophysiological mechanisms comment latest advances opportunity areas keep developing methodology.

Язык: Английский

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Rapid Affinity Purification of Tagged Plant Mitochondria (Mito-AP) for Metabolome and Proteome Analyses

PLANT PHYSIOLOGY, Год журнала: 2020, Номер 182(3), С. 1194 - 1210

Опубликована: Янв. 7, 2020

The isolation of organelles facilitates the focused analysis subcellular protein and metabolite pools. Here we present a technique for affinity purification plant mitochondria (Mito-AP). stable ectopic expression mitochondrial outer membrane fused to GFP:Strep tag in Arabidopsis (Arabidopsis thaliana) exclusively decorates mitochondria, enabling their selective using magnetic beads coated with Strep-Tactin. With Mito-AP, intact from 0.5 g material were highly enriched 30–60 min, considerably faster than conventional gradient centrifugation. Combining centrifugation Mito-AP techniques resulted high purity >90% proteins lysate. supports proteome by shotgun proteomics. relative abundances distinct methods correlated. A cluster 619 was consistently all methods. Among these several that lack localization data or are currently assigned other compartments. is also compatible metabolome triple-quadrupole orbitrap mass spectrometry. preparations showed strong enrichment typical lipids like cardiolipins demonstrated presence ubiquinones mitochondria. Affinity powerful tool reaching higher spatial temporal resolution metabolomic proteomic dynamics within small scale, rapid, economic, potentially applicable any organelle subpopulations.

Язык: Английский

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CEDAR, an online resource for the reporting and exploration of complexome profiling data

Biochimica et Biophysica Acta (BBA) - Bioenergetics, Год журнала: 2021, Номер 1862(7), С. 148411 - 148411

Опубликована: Март 17, 2021

Complexome profiling is an emerging 'omics' approach that systematically interrogates the composition of protein complexes (the complexome) a sample, by combining biochemical separation native with mass-spectrometry based quantitation proteomics. The resulting fractionation profiles hold comprehensive information on abundance and complexome, have high potential for reuse experimental computational researchers. However, lack central resource provides access to these data, reported adequate descriptions analysis tool, has limited their reuse. Therefore, we established ComplexomE DAta Resource (CEDAR, www3.cmbi.umcn.nl/cedar/), openly accessible database depositing exploring mass spectrometry data from complexome studies. Compatibility reusability ensured standardized reporting format containing "minimum required experiment" (MIACE). can be accessed through user-friendly web interface, as well programmatically using REST API portal. Additionally, all available CEDAR inspected directly website profile viewer tool allows detection correlated inference complexes. In conclusion, unique, growing invaluable study complex dynamics across biological systems.

Язык: Английский

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