1
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Thielen M, Gärtner B, Knoop V, Schallenberg-Rüdinger M, Lesch E. Conquering new grounds: plant organellar C-to-U RNA editing factors can be functional in the plant cytosol. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:895-915. [PMID: 38753873 DOI: 10.1111/tpj.16804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/17/2024] [Accepted: 04/30/2024] [Indexed: 05/18/2024]
Abstract
Plant mitochondrial and chloroplast transcripts are subject to numerous events of specific cytidine-to-uridine (C-to-U) RNA editing to correct genetic information. Key protein factors for this process are specific RNA-binding pentatricopeptide repeat (PPR) proteins, which are encoded in the nucleus and post-translationally imported into the two endosymbiotic organelles. Despite hundreds of C-to-U editing sites in the plant organelles, no comparable editing has been found for nucleo-cytosolic mRNAs raising the question why plant RNA editing is restricted to chloroplasts and mitochondria. Here, we addressed this issue in the model moss Physcomitrium patens, where all PPR-type RNA editing factors comprise specific RNA-binding and cytidine deamination functionalities in single proteins. To explore whether organelle-type RNA editing can principally also take place in the plant cytosol, we expressed PPR56, PPR65 and PPR78, three editing factors recently shown to also function in a bacterial setup, together with cytosolic co-transcribed native targets in Physcomitrium. While we obtained unsatisfying results upon their constitutive expression, we found strong cytosolic RNA editing under hormone-inducible expression. Moreover, RNA-Seq analyses revealed varying numbers of up to more than 900 off-targets in other cytosolic transcripts. We conclude that PPR-mediated C-to-U RNA editing is not per se incompatible with the plant cytosol but that its limited target specificity has restricted its occurrence to the much less complex transcriptomes of mitochondria and chloroplast in the course of evolution.
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Affiliation(s)
- Mirjam Thielen
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Béla Gärtner
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Mareike Schallenberg-Rüdinger
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Elena Lesch
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
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2
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Kwok van der Giezen FM, Viljoen A, Campbell-Clause L, Dao NT, Colas des Francs-Small C, Small I. Insights into U-to-C RNA editing from the lycophyte Phylloglossum drummondii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:445-459. [PMID: 38652016 DOI: 10.1111/tpj.16775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/15/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024]
Abstract
The lycophyte Phylloglossum drummondii is the sole inhabitant of its genus in the Huperzioideae group and one of a small minority of plants which perform uridine to cytidine RNA editing. We assembled the P. drummondii chloroplast and mitochondrial genomes and used RNA sequence data to build a comprehensive profile of organellar RNA editing events. In addition to many C-to-U editing events in both organelles, we found just four U-to-C editing events in the mitochondrial transcripts cob, nad1, nad5 and rpl2. These events are conserved in related lycophytes in the genera Huperzia and Phlegmariurus. De novo transcriptomes for three of these lycophytes were assembled to search for putative U-to-C RNA editing enzymes. Four putative U-to-C editing factors could be matched to the four mitochondrial U-to-C editing sites. Due to the unusually few numbers of U-to-C RNA editing sites, P. drummondii and related lycophytes are useful models for studying this poorly understood mechanism.
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Affiliation(s)
- Farley M Kwok van der Giezen
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Amy Viljoen
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Leni Campbell-Clause
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Nhan Trong Dao
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Catherine Colas des Francs-Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
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3
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Shen C, Xu H, Huang WZ, Zhao Q, Zhu RL. Is RNA editing truly absent in the complex thalloid liverworts (Marchantiopsida)? Evidence of extensive RNA editing from Cyathodium cavernarum. THE NEW PHYTOLOGIST 2024; 242:2817-2831. [PMID: 38587065 DOI: 10.1111/nph.19750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/20/2024] [Indexed: 04/09/2024]
Abstract
RNA editing is a crucial modification in plants' organellar transcripts that converts cytidine to uridine (C-to-U; and sometimes uridine to cytidine) in RNA molecules. This post-transcriptional process is controlled by the PLS-class protein with a DYW domain, which belongs to the pentatricopeptide repeat (PPR) protein family. RNA editing is widespread in land plants; however, complex thalloid liverworts (Marchantiopsida) are the only group reported to lack both RNA editing and DYW-PPR protein. The liverwort Cyathodium cavernarum (Marchantiopsida, Cyathodiaceae), typically found in cave habitats, was newly found to have 129 C-to-U RNA editing sites in its chloroplast and 172 sites in its mitochondria. The Cyathodium genus, specifically C. cavernarum, has a large number of PPR editing factor genes, including 251 DYW-type PPR proteins. These DYW-type PPR proteins may be responsible for C-to-U RNA editing in C. cavernarum. Cyathodium cavernarum possesses both PPR DYW proteins and RNA editing. Our analysis suggests that the remarkable RNA editing capability of C. cavernarum may have been acquired alongside the emergence of DYW-type PPR editing factors. These findings provide insight into the evolutionary pattern of RNA editing in land plants.
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Affiliation(s)
- Chao Shen
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Hao Xu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Wen-Zhuan Huang
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Qiong Zhao
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Rui-Liang Zhu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
- Tiantong National Station of Forest Ecosystem, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai, 200241, China
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4
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Lesch E, Stempel MS, Dressnandt V, Oldenkott B, Knoop V, Schallenberg-Rüdinger M. Conservation of the moss RNA editing factor PPR78 despite the loss of its known cytidine-to-uridine editing sites is explained by a hidden extra target. THE PLANT CELL 2024; 36:727-745. [PMID: 38000897 PMCID: PMC10896298 DOI: 10.1093/plcell/koad292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/27/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023]
Abstract
Cytidine (C)-to-uridine (U) RNA editing in plant organelles relies on specific RNA-binding pentatricopeptide repeat (PPR) proteins. In the moss Physcomitrium patens, all such RNA editing factors feature a C-terminal DYW domain that acts as the cytidine deaminase for C-to-U conversion. PPR78 of Physcomitrium targets 2 mitochondrial editing sites, cox1eU755SL and rps14eU137SL. Remarkably, the latter is edited to highly variable degrees in different mosses. Here, we aimed to unravel the coevolution of PPR78 and its 2 target sites in mosses. Heterologous complementation in a Physcomitrium knockout line revealed that the variable editing of rps14eU137SL depends on the PPR arrays of different PPR78 orthologues but not their C-terminal domains. Intriguingly, PPR78 has remained conserved despite the simultaneous loss of editing at both known targets among Hypnales (feather mosses), suggesting it serves an additional function. Using a recently established RNA editing assay in Escherichia coli, we confirmed site-specific RNA editing by PPR78 in the bacterium and identified 4 additional off-targets in the bacterial transcriptome. Based on conservation profiles, we predicted ccmFNeU1465RC as a candidate editing target of PPR78 in moss mitochondrial transcriptomes. We confirmed editing at this site in several mosses and verified that PPR78 targets ccmFNeU1465RC in the bacterial editing system, explaining the conservation and functional adaptation of PPR78 during moss evolution.
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Affiliation(s)
- Elena Lesch
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Maike Simone Stempel
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Vanessa Dressnandt
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Bastian Oldenkott
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Volker Knoop
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Mareike Schallenberg-Rüdinger
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
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5
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Yang Y, Oldenkott B, Ramanathan S, Lesch E, Takenaka M, Schallenberg-Rüdinger M, Knoop V. DYW cytidine deaminase domains have a long-range impact on RNA recognition by the PPR array of chimeric plant C-to-U RNA editing factors and strongly affect target selection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:840-854. [PMID: 37565789 DOI: 10.1111/tpj.16412] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 08/12/2023]
Abstract
The protein factors for the specific C-to-U RNA editing events in plant mitochondria and chloroplasts possess unique arrays of RNA-binding pentatricopeptide repeats (PPRs) linked to carboxy-terminal cytidine deaminase DYW domains via the extension motifs E1 and E2. The E1 and E2 motifs have distant similarities to tetratricopeptide repeats known to mediate protein-protein interactions but their precise function is unclear. Here, we investigate the tolerance of PPR56 and PPR65, two functionally characterized RNA editing factors of the moss Physcomitrium patens, for the creation of chimeras by variably replacing their C-terminal protein regions. Making use of a heterologous RNA editing assay system in Escherichia coli we find that heterologous DYW domains can strongly restrict or widen the spectrum of off-targets in the bacterial transcriptome for PPR56. Surprisingly, our data suggest that these changes are not only caused by the preference of a given heterologous DYW domain for the immediate sequence environment of the cytidine to be edited but also by a long-range impact on the nucleotide selectivity of the upstream PPRs.
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Affiliation(s)
- Yingying Yang
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Bastian Oldenkott
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Shyam Ramanathan
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Elena Lesch
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Mizuki Takenaka
- Department of Botany Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Mareike Schallenberg-Rüdinger
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
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6
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Lesch E, Schilling MT, Brenner S, Yang Y, Gruss O, Knoop V, Schallenberg-Rüdinger M. Plant mitochondrial RNA editing factors can perform targeted C-to-U editing of nuclear transcripts in human cells. Nucleic Acids Res 2022; 50:9966-9983. [PMID: 36107771 PMCID: PMC9508816 DOI: 10.1093/nar/gkac752] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/10/2022] [Accepted: 08/29/2022] [Indexed: 11/12/2022] Open
Abstract
RNA editing processes are strikingly different in animals and plants. Up to thousands of specific cytidines are converted into uridines in plant chloroplasts and mitochondria whereas up to millions of adenosines are converted into inosines in animal nucleo-cytosolic RNAs. It is unknown whether these two different RNA editing machineries are mutually incompatible. RNA-binding pentatricopeptide repeat (PPR) proteins are the key factors of plant organelle cytidine-to-uridine RNA editing. The complete absence of PPR mediated editing of cytosolic RNAs might be due to a yet unknown barrier that prevents its activity in the cytosol. Here, we transferred two plant mitochondrial PPR-type editing factors into human cell lines to explore whether they could operate in the nucleo-cytosolic environment. PPR56 and PPR65 not only faithfully edited their native, co-transcribed targets but also different sets of off-targets in the human background transcriptome. More than 900 of such off-targets with editing efficiencies up to 91%, largely explained by known PPR-RNA binding properties, were identified for PPR56. Engineering two crucial amino acid positions in its PPR array led to predictable shifts in target recognition. We conclude that plant PPR editing factors can operate in the entirely different genetic environment of the human nucleo-cytosol and can be intentionally re-engineered towards new targets.
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Affiliation(s)
- Elena Lesch
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn , Kirschallee 1 , D-53115 Bonn , Germany
| | - Maximilian T Schilling
- Institut für Genetik, Abteilung Zellteilung, Universität Bonn , Karlrobert-Kreiten-Str. 13 , D-53115 Bonn , Germany
| | - Sarah Brenner
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn , Kirschallee 1 , D-53115 Bonn , Germany
| | - Yingying Yang
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn , Kirschallee 1 , D-53115 Bonn , Germany
| | - Oliver J Gruss
- Institut für Genetik, Abteilung Zellteilung, Universität Bonn , Karlrobert-Kreiten-Str. 13 , D-53115 Bonn , Germany
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn , Kirschallee 1 , D-53115 Bonn , Germany
| | - Mareike Schallenberg-Rüdinger
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn , Kirschallee 1 , D-53115 Bonn , Germany
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7
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Sugita M. An Overview of Pentatricopeptide Repeat (PPR) Proteins in the Moss Physcomitrium patens and Their Role in Organellar Gene Expression. PLANTS 2022; 11:plants11172279. [PMID: 36079663 PMCID: PMC9459714 DOI: 10.3390/plants11172279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022]
Abstract
Pentatricopeptide repeat (PPR) proteins are one type of helical repeat protein that are widespread in eukaryotes. In particular, there are several hundred PPR members in flowering plants. The majority of PPR proteins are localized in the plastids and mitochondria, where they play a crucial role in various aspects of RNA metabolism at the post-transcriptional and translational steps during gene expression. Among the early land plants, the moss Physcomitrium (formerly Physcomitrella) patens has at least 107 PPR protein-encoding genes, but most of their functions remain unclear. To elucidate the functions of PPR proteins, a reverse-genetics approach has been applied to P. patens. To date, the molecular functions of 22 PPR proteins were identified as essential factors required for either mRNA processing and stabilization, RNA splicing, or RNA editing. This review examines the P. patens PPR gene family and their current functional characterization. Similarities and a diversity of functions of PPR proteins between P. patens and flowering plants and their roles in the post-transcriptional regulation of organellar gene expression are discussed.
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Affiliation(s)
- Mamoru Sugita
- Graduate School of Informatics, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
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8
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Rodrigues NF, Nogueira FCS, Domont GB, Margis R. Identification of soybean trans-factors associated with plastid RNA editing sites. Genet Mol Biol 2020; 43:e20190067. [PMID: 32459826 PMCID: PMC7231544 DOI: 10.1590/1678-4685-gmb-2019-0067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/09/2019] [Indexed: 12/05/2022] Open
Abstract
RNA editing is a posttranscriptional process that changes nucleotide sequences, among which cytosine-to-uracil by a deamination reaction can revert non-neutral codon mutations. Pentatricopeptide repeat (PPR) proteins comprise a family of RNA-binding proteins, with members acting as editing trans-factors that recognize specific RNA cis-elements and perform the deamination reaction. PPR proteins are classified into P and PLS subfamilies. In this work, we have designed RNA biotinylated probes based in soybean plastid RNA editing sites to perform trans-factor specific protein isolation. Soybean cis-elements from these three different RNA probes show differences in respect to other species. Pulldown samples were submitted to mass spectrometry for protein identification. Among detected proteins, five corresponded to PPR proteins. More than one PPR protein, with distinct functional domains, was pulled down with each one of the RNA probes. Comparison of the soybean PPR proteins to Arabidopsis allowed identification of the closest homologous. Differential gene expression analysis demonstrated that the PPR locus Glyma.02G174500 doubled its expression under salt stress, which correlates with the increase of its potential rps14 editing. The present study represents the first identification of RNA editing trans-factors in soybean. Data also indicated that potential multiple trans-factors should interact with RNA cis-elements to perform the RNA editing.
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Affiliation(s)
- Nureyev F. Rodrigues
- Universidade Federal do Rio Grande do Sul (UFRGS), Centro de Biotecnologia,
Programa de Pós-Graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre,
RS, Brazil
| | - Fábio C. S. Nogueira
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Departamento de Bioquímica, Programa de Pós-Graduação em Bioquímica (PPGBq), Unidade
Proteômica, Rio de Janeiro, RJ, Brazil
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Laboratório de Apoio ao Desenvolvimento Tecnológico (LADETEC), Rio de Janeiro, RJ,
Brazil
| | - Gilberto B. Domont
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Departamento de Bioquímica, Programa de Pós-Graduação em Bioquímica (PPGBq), Unidade
Proteômica, Rio de Janeiro, RJ, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul (UFRGS), Centro de Biotecnologia,
Programa de Pós-Graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre,
RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Departamento de
Biofísica, Porto Alegre, RS, Brazil
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9
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Small ID, Schallenberg-Rüdinger M, Takenaka M, Mireau H, Ostersetzer-Biran O. Plant organellar RNA editing: what 30 years of research has revealed. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1040-1056. [PMID: 31630458 DOI: 10.1111/tpj.14578] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/25/2019] [Accepted: 10/08/2019] [Indexed: 05/21/2023]
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.
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Affiliation(s)
- Ian D Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Mareike Schallenberg-Rüdinger
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abt. Molekulare Evolution, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Mizuki Takenaka
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hakim Mireau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
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10
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Gerke P, Szövényi P, Neubauer A, Lenz H, Gutmann B, McDowell R, Small I, Schallenberg-Rüdinger M, Knoop V. 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. THE NEW PHYTOLOGIST 2020; 225:1974-1992. [PMID: 31667843 DOI: 10.1111/nph.16297] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/20/2019] [Indexed: 06/10/2023]
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.
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Affiliation(s)
- Philipp Gerke
- Institut für Zelluläre und Molekulare Botanik (IZMB), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstr. 107, 8008, Zürich, Switzerland
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstr. 107, 8008, Zürich, Switzerland
| | - Henning Lenz
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Bernard Gutmann
- EditForce Inc., West Zone #429, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka, 819-0395, Japan
| | - Rose McDowell
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia at Crawley, Perth, WA, 6009, Australia
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia at Crawley, Perth, WA, 6009, Australia
| | | | - Volker Knoop
- Institut für Zelluläre und Molekulare Botanik (IZMB), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
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Plant-type pentatricopeptide repeat proteins with a DYW domain drive C-to-U RNA editing in Escherichia coli. Commun Biol 2019; 2:85. [PMID: 30854477 PMCID: PMC6397227 DOI: 10.1038/s42003-019-0328-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/18/2019] [Indexed: 11/09/2022] Open
Abstract
RNA editing converting cytidines into uridines is a hallmark of gene expression in land plant chloroplasts and mitochondria. Pentatricopeptide repeat (PPR) proteins have a key role in target recognition, but the functional editosome in the plant organelles has remained elusive. Here we show that individual Physcomitrella patens DYW-type PPR proteins alone can perform efficient C-to-U editing in Escherichia coli reproducing the moss mitochondrial editing. Single amino acid exchanges in the DYW domain abolish RNA editing, confirming it as the functional cytidine deaminase. The modification of RNA targets and the identification of numerous off-targets in the E. coli transcriptome reveal nucleotide identities critical for RNA recognition and cytidine conversion. The straightforward amenability of the new E. coli setup will accelerate future studies on RNA target recognition through PPRs, on the C-to-U editing deamination machinery and towards future establishment of transcript editing in other genetic systems. Bastian Oldenkott et al. show that single moss pentatricopeptide repeat proteins with a DYW domain are sufficient to drive efficient C-to-U RNA editing in Escherichia coli. They demonstrate that the E.coli system is an easy to manipulate platform for future studies on RNA target recognition and C-to-U RNA editing.
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Lenz H, Hein A, Knoop V. Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0. BMC Bioinformatics 2018; 19:255. [PMID: 29970001 PMCID: PMC6029061 DOI: 10.1186/s12859-018-2244-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/13/2018] [Indexed: 01/20/2023] Open
Abstract
Background Gene expression in plant chloroplasts and mitochondria is affected by RNA editing. Numerous C-to-U conversions, accompanied by reverse U-to-C exchanges in some plant clades, alter the genetic information encoded in the organelle genomes. Predicting and analyzing RNA editing, which ranges from only few sites in some species to thousands in other taxa, is bioinformatically demanding. Results Here, we present major enhancements and extensions of PREPACT, a WWW-based service for analysing, predicting and cataloguing plant-type RNA editing. New features in PREPACT’s core include direct GenBank accession query input and options to restrict searches to candidate U-to-C editing or to sites where editing has been documented previously in the references. The reference database has been extended by 20 new organelle editomes. PREPACT 3.0 features new modules “EdiFacts” and “TargetScan”. EdiFacts integrates information on pentatricopeptide repeat (PPR) proteins characterized as site-specific RNA editing factors. PREPACT’s editome references connect into EdiFacts, linking editing events to specific co-factors where known. TargetScan allows position-weighted querying for sequence motifs in the organelle references, optionally restricted to coding regions or sequences around editing sites, or in queries uploaded by the user. TargetScan is mainly intended to evaluate and further refine the proposed PPR-RNA recognition code but may be handy for other tasks as well. We present an analysis for the immediate sequence environment of more than 15,000 documented editing sites finding strong and different bias in the editome data sets. Conclusions We exemplarily present the novel features of PREPACT 3.0 aimed to enhance the analyses of plant-type RNA editing, including its new modules EdiFacts integrating information on characterized editing factors and TargetScan aimed to analyse RNA editing site recognition specificities. Electronic supplementary material The online version of this article (10.1186/s12859-018-2244-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Henning Lenz
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany.,IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Anke Hein
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany.
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Hein A, Knoop V. Expected and unexpected evolution of plant RNA editing factors CLB19, CRR28 and RARE1: retention of CLB19 despite a phylogenetically deep loss of its two known editing targets in Poaceae. BMC Evol Biol 2018; 18:85. [PMID: 29879897 PMCID: PMC5992886 DOI: 10.1186/s12862-018-1203-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/24/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND C-to-U RNA editing in mitochondria and chloroplasts and the nuclear-encoded, RNA-binding PPR proteins acting as editing factors present a wide field of co-evolution between the different genetic systems in a plant cell. Recent studies on chloroplast editing factors RARE1 and CRR28 addressing one or two chloroplast editing sites, respectively, found them strictly conserved among 65 flowering plants as long as one of their RNA editing targets remained present. RESULTS Extending the earlier sampling to 117 angiosperms with high-quality genome or transcriptome data, we find more evidence confirming previous conclusions but now also identify cases for expected evolutionary transition states such as retention of RARE1 despite loss of its editing target or the degeneration of CRR28 truncating its carboxyterminal DYW domain. The extended angiosperm set was now used to explore CLB19, an "E+"-type PPR editing factor targeting two chloroplast editing sites, rpoAeU200SF and clpPeU559HY, in Arabidopsis thaliana. We found CLB19 consistently conserved if one of the two targets was retained and three independent losses of CLB19 after elimination of both targets. The Ericales show independent regains of the ancestrally lost clpPeU559HY editing, further explaining why multiple-target editing factors are lost much more rarely than single target factors like RARE1. The retention of CLB19 despite loss of both editing targets in some Ericaceae, Apocynaceae and in Camptotheca (Nyssaceae) likely represents evolutionary transitions. However, the retention of CLB19 after a phylogenetic deep loss in the Poaceae rather suggests a yet unrecognized further editing target, for which we suggest editing event ndhAeU473SL. CONCLUSION Extending the scope of studies on plant organelle RNA editing to further taxa and additional nuclear cofactors reveals expected evolutionary transitions, strikingly different evolutionary dynamics for multiple-target editing factors like CLB19 and CRR28 and suggests additional functions for editing factor CLB19 among the Poaceae.
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Affiliation(s)
- Anke Hein
- IZMB – Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | - Volker Knoop
- IZMB – Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115 Bonn, Germany
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Jiang T, Zhang J, Rong L, Feng Y, Wang Q, Song Q, Zhang L, Ouyang M. ECD1 functions as an RNA-editing trans-factor of rps14-149 in plastids and is required for early chloroplast development in seedlings. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3037-3051. [PMID: 29648606 PMCID: PMC5972661 DOI: 10.1093/jxb/ery139] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/29/2018] [Indexed: 05/18/2023]
Abstract
Chloroplast development is a highly complex process and the regulatory mechanisms have not yet been fully characterized. In this study, we identified Early Chloroplast Development 1 (ECD1), a chloroplast-localized pentatricopeptide repeat protein (PPR) belonging to the PLS subfamily. Inactivation of ECD1 in Arabidopsis led to embryo lethality, and abnormal embryogenesis occurred in ecd1/+ heterozygous plants. A decrease in ECD1 expression induced by RNAi resulted in seedlings with albino cotyledons but normal true leaves. The aberrant morphology and under-developed thylakoid membrane system in cotyledons of RNAi seedlings suggests a role of ECD1 specifically in chloroplast development in seedlings. In cotyledons of ECD1-RNAi plants, RNA-editing of rps14-149 (encoding ribosomal protein S14) was seriously impaired. In addition, dramatically decreased plastid-encoded RNA polymerase-dependent gene expression and abnormal chloroplast rRNA processing were also observed. Taken together, our results indicate that ECD1 is indispensable for chloroplast development at the seedling stage in Arabidopsis.
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Affiliation(s)
- Tian Jiang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liwei Rong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanjiang Feng
- Cultivation and Crop Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qi Wang
- Cultivation and Crop Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qiulai Song
- Cultivation and Crop Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Ouyang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Correspondence:
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Schallenberg-Rüdinger M, Oldenkott B, Hiss M, Trinh PL, Knoop V, Rensing SA. A Single-Target Mitochondrial RNA Editing Factor of Funaria hygrometrica Can Fully Reconstitute RNA Editing at Two Sites in Physcomitrella patens. PLANT & CELL PHYSIOLOGY 2017; 58:496-507. [PMID: 28394399 DOI: 10.1093/pcp/pcw229] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 12/21/2016] [Indexed: 05/26/2023]
Abstract
Nuclear-encoded pentatricopeptide repeat (PPR) proteins are key factors for site-specific RNA editing, converting cytidines into uridines in plant mitochondria and chloroplasts. All editing factors in the model moss Physcomitrella patens have a C-terminal DYW domain with similarity to cytidine deaminase. However, numerous editing factors in flowering plants lack such a terminal DYW domain, questioning its immediate role in the pyrimidine base conversion process. Here we further investigate the Physcomitrella DYW-type PPR protein PPR_78, responsible for mitochondrial editing sites cox1eU755SL and rps14eU137SL. Complementation assays with truncated proteins demonstrate that the DYW domain is essential for full PPR_78 editing functionality. The DYW domain can be replaced, however, with its counterpart from another editing factor, PPR_79. The PPR_78 ortholog of the related moss Funaria hygrometrica fully complements the Physcomitrella mutant for editing at both sites, although the editing site in rps14 is lacking in Funaria. Editing factor orthologs in different taxa may thus retain editing capacity for multiple sites despite the absence of editing requirement.
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Affiliation(s)
- Mareike Schallenberg-Rüdinger
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee, Bonn, Germany
| | - Bastian Oldenkott
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee, Bonn, Germany
| | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Phuong Le Trinh
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee, Bonn, Germany
- Key Laboratory of Enzyme and Protein Technology (KLEPT), VNU University of Science, Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Volker Knoop
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee, Bonn, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
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Ichinose M, Sugita M. RNA Editing and Its Molecular Mechanism in Plant Organelles. Genes (Basel) 2016; 8:genes8010005. [PMID: 28025543 PMCID: PMC5295000 DOI: 10.3390/genes8010005] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/23/2016] [Accepted: 12/20/2016] [Indexed: 12/03/2022] Open
Abstract
RNA editing by cytidine (C) to uridine (U) conversions is widespread in plant mitochondria and chloroplasts. In some plant taxa, “reverse” U-to-C editing also occurs. However, to date, no instance of RNA editing has yet been reported in green algae and the complex thalloid liverworts. RNA editing may have evolved in early land plants 450 million years ago. However, in some plant species, including the liverwort, Marchantia polymorpha, editing may have been lost during evolution. Most RNA editing events can restore the evolutionarily conserved amino acid residues in mRNAs or create translation start and stop codons. Therefore, RNA editing is an essential process to maintain genetic information at the RNA level. Individual RNA editing sites are recognized by plant-specific pentatricopeptide repeat (PPR) proteins that are encoded in the nuclear genome. These PPR proteins are characterized by repeat elements that bind specifically to RNA sequences upstream of target editing sites. In flowering plants, non-PPR proteins also participate in multiple RNA editing events as auxiliary factors. C-to-U editing can be explained by cytidine deamination. The proteins discovered to date are important factors for RNA editing but a bona fide RNA editing enzyme has yet to be identified.
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Affiliation(s)
- Mizuho Ichinose
- Center for Gene Research, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan.
- Institute of Transformative Bio-Molecules, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan.
| | - Mamoru Sugita
- Center for Gene Research, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan.
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Goto S, Kawaguchi Y, Sugita C, Ichinose M, Sugita M. P-class pentatricopeptide repeat protein PTSF1 is required for splicing of the plastid pre-tRNA(I) (le) in Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:493-503. [PMID: 27117879 DOI: 10.1111/tpj.13184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/31/2016] [Accepted: 04/05/2016] [Indexed: 06/05/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are widely distributed in eukaryotes and are mostly localized in mitochondria or plastids. PPR proteins play essential roles in various RNA processing steps in organelles; however, the function of the majority of PPR proteins remains unknown. To examine the function of plastid PPR proteins, PpPPR_4 gene knock-out mutants were characterized in Physcomitrella patens. The knock-out mosses displayed severe growth retardation and reduced effective quantum yield of photosystem II. Immunoblot analysis showed that knock-out of PpPPR_4 resulted in a strongly reduced level of plastid-encoded proteins, such as photosystem II reaction center protein D1, the β subunit of ATP synthase, and the stromal enzyme, Rubisco. To further investigate whether knock-out of the PpPPR_4 gene affects plastid gene expression, we analyzed steady-state transcript levels of protein- and rRNA-coding genes by quantitative RT-PCR. This analysis showed that the level of many protein-coding transcripts increased in the mutants. In contrast, splicing of a spacer tRNA(I) (le) precursor encoded by the rrn operon was specifically impaired in the mutants, whereas the accumulation of other plastid tRNAs and rRNAs was not largely affected. Thus, the defect in tRNA(I) (le) splicing leads to a considerable reduction of mature tRNA(I) (le) , which may be accountable for the reduced protein level. An RNA mobility shift assay showed that the recombinant PpPPR_4 bound preferentially to domain III of the tRNA(I) (le) group-II intron. These results provide evidence that PpPPR_4 functions in RNA splicing of the tRNA(I) (le) intron, and hence PpPPR_4 was named plastid tRNA splicing factor 1 (PTSF1).
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Affiliation(s)
- Seiya Goto
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
| | | | - Chieko Sugita
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
| | - Mizuho Ichinose
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya, 464-8602, Japan
| | - Mamoru Sugita
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
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18
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Cheng S, Gutmann B, Zhong X, Ye Y, Fisher MF, Bai F, Castleden I, Song Y, Song B, Huang J, Liu X, Xu X, Lim BL, Bond CS, Yiu SM, Small I. Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:532-47. [PMID: 26764122 DOI: 10.1111/tpj.13121] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 01/05/2016] [Indexed: 05/02/2023]
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 (http://www.plantppr.com) that provides open access to these resources for the community.
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Affiliation(s)
- Shifeng Cheng
- HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, The University of Hong Kong, Hong Kong, China
- BGI-Shenzhen, Shenzhen, 518083, China
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Bernard Gutmann
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, 6009, Australia
| | | | - Yongtao Ye
- HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Mark F Fisher
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | | | - Ian Castleden
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, 6009, Australia
| | - Yue Song
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Bo Song
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xin Liu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Boon L Lim
- HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, The University of Hong Kong, Hong Kong, China
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Siu-Ming Yiu
- HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, 6009, Australia
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Hein A, Polsakiewicz M, Knoop V. Frequent chloroplast RNA editing in early-branching flowering plants: pilot studies on angiosperm-wide coexistence of editing sites and their nuclear specificity factors. BMC Evol Biol 2016; 16:23. [PMID: 26809609 PMCID: PMC4727281 DOI: 10.1186/s12862-016-0589-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 01/12/2016] [Indexed: 11/11/2022] Open
Abstract
Background RNA editing by cytidine-to-uridine conversions is an essential step of RNA maturation in plant organelles. Some 30–50 sites of C-to-U RNA editing exist in chloroplasts of flowering plant models like Arabidopsis, rice or tobacco. We now predicted significantly more RNA editing in chloroplasts of early-branching angiosperm genera like Amborella, Calycanthus, Ceratophyllum, Chloranthus, Illicium, Liriodendron, Magnolia, Nuphar and Zingiber. Nuclear-encoded RNA-binding pentatricopeptide repeat (PPR) proteins are key editing factors expected to coevolve with their cognate RNA editing sites in the organelles. Results With an extensive chloroplast transcriptome study we identified 138 sites of RNA editing in Amborella trichopoda, approximately the 3- to 4-fold of cp editing in Arabidopsis thaliana or Oryza sativa. Selected cDNA studies in the other early-branching flowering plant taxa furthermore reveal a high diversity of early angiosperm RNA editomes. Many of the now identified editing sites in Amborella have orthologues in ferns, lycophytes or hornworts. We investigated the evolution of CRR28 and RARE1, two known Arabidopsis RNA editing factors responsible for cp editing events ndhBeU467PL, ndhDeU878SL and accDeU794SL, respectively, all of which we now found conserved in Amborella. In a phylogenetically wide sampling of 65 angiosperm genomes we find evidence for only one single loss of CRR28 in chickpea but several independent losses of RARE1, perfectly congruent with the presence of their cognate editing sites in the respective cpDNAs. Conclusion Chloroplast RNA editing is much more abundant in early-branching than in widely investigated model flowering plants. RNA editing specificity factors can be traced back for more than 120 million years of angiosperm evolution and show highly divergent patterns of evolutionary losses, matching the presence of their target editing events. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0589-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anke Hein
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany.
| | - Monika Polsakiewicz
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany.
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany.
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