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Liu D, Li ZA, Li Y, Molloy DP, Huang C. The DYW domain of RARE1 plays an indispensable role in regulating accD-C794 RNA editing in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 334:111751. [PMID: 37263527 DOI: 10.1016/j.plantsci.2023.111751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/03/2023]
Abstract
The Arabidopsis pentatricopeptide repeat (PPR) proteins, required for accD RNA editing 1 (RARE1) and early chloroplast biogenesis 2 (AtECB2), each contain a DYW domain deemed essential for cytosine deamination at the accD-C794 RNA editing site in chloroplasts. Complementation assays using the rare1 mutant investigate the correlation between these PPRs and their respective DYW domain functions in RNA editing of accD-C794. The results demonstrate that the coding sequence of AtECB2 cannot replace that of RARE1. Moreover, rare1 mutants complemented with DYW-deleted RARE1 failed to recover the RNA editing of accD-C794 even in the presence of the highly similar DYW domain of the AtECB2 protein. These findings indicate that RARE1 and AtECB2 possess divergent roles in RNA editing, with specificity for accD-C794 directly attributable to DYW domain within RARE1. Structural modeling data suggest this functioning pertains to a local α-helical motif that residues slightly N-terminal to the consensus glutamate and CXXCH motif in the DYW domain for cytidine deamination during C-to-U editing by RARE1 that is absent within AtECB2.
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Affiliation(s)
- Dan Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Zi-Ang Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Yi Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - David P Molloy
- Department of Biochemistry and Molecular Biology, Basic Medical College, Chongqing Medical University, Chongqing 400016, China; Center for Molecular Medicine and Cancer Research, Basic Medical College, Chongqing Medical University, Chongqing 400016, China.
| | - Chao Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
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2
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Yang H, Wang Y, Tian Y, Teng X, Lv Z, Lei J, Duan E, Dong H, Yang X, Zhang Y, Sun Y, Chen X, Bao X, Chen R, Gu C, Zhang Y, Jiang X, Ma W, Zhang P, Ji Y, Zhang Y, Wang Y, Wan J. Rice FLOURY ENDOSPERM22, encoding a pentatricopeptide repeat protein, is involved in both mitochondrial RNA splicing and editing and is crucial for endosperm development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:755-771. [PMID: 36333887 DOI: 10.1111/jipb.13402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Most of the reported P-type pentatricopeptide repeat (PPR) proteins play roles in organelle RNA stabilization and splicing. However, P-type PPRs involved in both RNA splicing and editing have rarely been reported, and their underlying mechanism remains largely unknown. Here, we report a rice floury endosperm22 (flo22) mutant with delayed amyloplast development in endosperm cells. Map-based cloning and complementation tests demonstrated that FLO22 encodes a mitochondrion-localized P-type PPR protein. Mutation of FLO22 resulting in defective trans-splicing of mitochondrial nad1 intron 1 and perhaps causing instability of mature transcripts affected assembly and activity of complex Ⅰ, and mitochondrial morphology and function. RNA-seq analysis showed that expression levels of many genes involved in starch and sucrose metabolism were significantly down-regulated in the flo22 mutant compared with the wild type, whereas genes related to oxidative phosphorylation and the tricarboxylic acid cycle were significantly up-regulated. In addition to involvement in splicing as a P-type PPR protein, we found that FLO22 interacted with DYW3, a DYW-type PPR protein, and they may function synergistically in mitochondrial RNA editing. The present work indicated that FLO22 plays an important role in endosperm development and plant growth by participating in nad1 maturation and multi-site editing of mitochondrial messager RNA.
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Affiliation(s)
- Hang Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunlong Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuan Teng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zehui Lv
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jie Lei
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Erchao Duan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Dong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xue Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanyan Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yinglun Sun
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoli Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiuhao Bao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongbo Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chuanwei Gu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yipeng Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaokang Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenyu Ma
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pengcheng Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi Ji
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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3
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Liu L, Wang Y, Tian Y, Song S, Wu Z, Ding X, Zheng H, Huang Y, Liu S, Dong X, Wan J, Liu L. Isolation and Characterization of SPOTTED LEAF42 Encoding a Porphobilinogen Deaminase in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:403. [PMID: 36679117 PMCID: PMC9866984 DOI: 10.3390/plants12020403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
The formation and development of chloroplasts play a vital role in the breeding of high-yield rice (Oryza sativa L.). Porphobilinogen deaminases (PBGDs) act in the early stage of chlorophyll and heme biosynthesis. However, the role of PBGDs in chloroplast development and chlorophyll production remains elusive in rice. Here, we identified the spotted leaf 42 (spl42) mutant, which exhibited a reddish-brown spotted leaf phenotype. The mutant showed a significantly lower chlorophyll content, abnormal thylakoid morphology, and elevated activities of reactive oxygen species (ROS)-scavenging enzymes. Consistently, multiple genes related to chloroplast development and chlorophyll biosynthesis were significantly down-regulated, whereas many genes involved in leaf senescence, ROS production, and defense responses were upregulated in the spl42 mutant. Map-based cloning revealed that SPL42 encodes a PBGD. A C-to-T base substitution occurred in spl42, resulting in an amino acid change and significantly reduced PBGD enzyme activity. SPL42 targets to the chloroplast and interacts with the multiple organelle RNA editing factors (MORFs) OsMORF8-1 and OsMORF8-2 to affect RNA editing. The identification and characterization of spl42 helps in elucidating the molecular mechanisms associated with chlorophyll synthesis and RNA editing in rice.
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Affiliation(s)
- Lin Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunpeng Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuang Song
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Zewan Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Ding
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai Zheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunshuai Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoou Dong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Linglong Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
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4
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Huang C, Liu D, Li ZA, Molloy DP, Luo ZF, Su Y, Li HO, Liu Q, Wang RZ, Xiao LT. The PPR protein RARE1-mediated editing of chloroplast accD transcripts is required for fatty acid biosynthesis and heat tolerance in Arabidopsis. PLANT COMMUNICATIONS 2023; 4:100461. [PMID: 36221851 PMCID: PMC9860180 DOI: 10.1016/j.xplc.2022.100461] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/12/2022] [Accepted: 10/10/2022] [Indexed: 06/01/2023]
Abstract
It has been reported that Arabidopsis chloroplast accD transcripts undergo RNA editing and that loss of accD-C794 RNA editing does not affect plant growth under normal conditions. To date, the exact biological role of accD-C794 editing has remained elusive. Here, we reveal an unexpected role for accD-C794 editing in response to heat stress. Loss of accD-C794 editing results in a yellow and dwarf phenotype with decreased chloroplast gene expression under heat stress, and artificial improvement of C794-edited accD gene expression enhances heat tolerance in Arabidopsis. These data suggest that accD-C794 editing confers heat tolerance in planta. We also found that treatment with the product of acetyl coenzyme A carboxylase (ACCase) could allay mutant phenotypic characteristics and showed that a mutation in the CAC3 gene for the α-subunit of ACCase was associated with dwarfism under heat stress. These observations indicate that defective accD-C794 editing may be intrinsic to reduced ACCase activity, thereby contributing to heat sensitivity. ACCase catalyzes the committed step of de novo fatty acid (FA) biosynthesis. FA content analysis revealed that unsaturated oleic (C18:1) and linoleic acids (C18:2) were low in the accD-C794 editing-defective mutant but high in the C794-edited accD-overexpressing plants compared with the wild type. Supplying exogenous C18:1 and C18:2 could rescue the mutant phenotype, suggesting that these FAs play an essential role in tolerance to heat stress. Transmission electron microscopy observations showed that heat stress seriously affected the membrane architecture in accD editing-defective mutants but not in accD-overexpressing plants. These results provide the first evidence that accD-C794 editing regulates FA biosynthesis for maintenance of membrane structural homeostasis under heat stress.
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Affiliation(s)
- Chao Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Dan Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Zi-Ang Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - David P Molloy
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China
| | - Zhou-Fei Luo
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Yi Su
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Hai-Ou Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Qing Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Ruo-Zhong Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Lang-Tao Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
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5
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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: 7] [Impact Index Per Article: 3.5] [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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6
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Gipson AB, Hanson MR, Bentolila S. The RanBP2 zinc finger domains of chloroplast RNA editing factor OZ1 are required for protein-protein interactions and conversion of C to U. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:215-226. [PMID: 34743362 DOI: 10.1111/tpj.15569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/26/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
In the chloroplast, organelle zinc finger 1 (OZ1) is a RanBP2-type zinc finger (Znf) protein required for many RNA editing events, a process by which specific cytosines are enzymatically converted to uracils as a correction mechanism for missense mutations in the organelle genomes. RNA editing is carried out by a large multi-protein complex called the 'editosome' that contains members of the pentatricopeptide repeat (PPR) protein family, the RNA editing factor interacting protein (also known as MORF) family and the organelle RNA-recognition motif (ORRM) family, in addition to OZ1. OZ1 is an 82-kDa protein with distinct domains, including a pair of Znf domains and a unique C-terminal region. To elucidate the functions of these domains, we have generated truncations of OZ1 for use in protein-protein interaction assays that identified the C-terminal region of OZ1, as well as the Znf domains as the primary interactors with PPR proteins, which are factors required for site-specificity and enzymatic editing. Expression of these OZ1 truncations in vivo showed that the Znf domains were required to restore chloroplast RNA editing in oz1 knockout plants. Mutation of key structural residues in the Znf domains showed that they are necessary for editing and required for interaction with ORRM1, a general editing factor with an RNA-binding domain. These functional characterizations of the Znfs and novel C-terminal domain contribute to our understanding of the model for the chloroplast plant editosome.
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Affiliation(s)
- Andrew B Gipson
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY, 14853, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY, 14853, USA
| | - Stéphane Bentolila
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY, 14853, USA
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7
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Wang Y, Wang Y, Ren Y, Duan E, Zhu X, Hao Y, Zhu J, Chen R, Lei J, Teng X, Zhang Y, Wang D, Zhang X, Guo X, Jiang L, Liu S, Tian Y, Liu X, Chen L, Wang H, Wan J. white panicle2 encoding thioredoxin z, regulates plastid RNA editing by interacting with multiple organellar RNA editing factors in rice. THE NEW PHYTOLOGIST 2021; 229:2693-2706. [PMID: 33119889 PMCID: PMC8027827 DOI: 10.1111/nph.17047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/16/2020] [Indexed: 05/11/2023]
Abstract
Thioredoxins (TRXs) occur in plant chloroplasts as complex disulphide oxidoreductases. Although many biological processes are regulated by thioredoxins, the regulatory mechanism of chloroplast TRXs are largely unknown. Here we report a rice white panicle2 mutant caused by a mutation in the thioredoxin z gene, an orthologue of AtTRX z in Arabidopsis. white panicle2 (wp2) seedlings exhibited a high-temperature-sensitive albinic phenotype. We found that plastid multiple organellar RNA editing factors (MORFs) were the regulatory targets of thioredoxin z. We showed that OsTRX z protein physically interacts with OsMORFs in a redox-dependent manner and that the redox state of a conserved cysteine in the MORF box is essential for MORF-MORF interactions. wp2 and OsTRX z knockout lines show reduced editing efficiencies in many plastidial-encoded genes especially under high-temperature conditions. An Arabidopsis trx z mutant also exhibited significantly reduced chloroplast RNA editing. Our combined results suggest that thioredoxin z regulates chloroplast RNA editing in plants by controlling the redox state of MORFs.
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Affiliation(s)
- Yunlong Wang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Yulong Ren
- National Key Facility for Crop Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Erchao Duan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Xiaopin Zhu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Yuanyuan Hao
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Jianping Zhu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Rongbo Chen
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Jie Lei
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Xuan Teng
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Yuanyan Zhang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Di Wang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Xin Zhang
- National Key Facility for Crop Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Xiuping Guo
- National Key Facility for Crop Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Liangming Chen
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Haiyang Wang
- National Key Facility for Crop Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
- National Key Facility for Crop Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
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8
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Huang W, Zhang Y, Shen L, Fang Q, Liu Q, Gong C, Zhang C, Zhou Y, Mao C, Zhu Y, Zhang J, Chen H, Zhang Y, Lin Y, Bock R, Zhou F. Accumulation of the RNA polymerase subunit RpoB depends on RNA editing by OsPPR16 and affects chloroplast development during early leaf development in rice. THE NEW PHYTOLOGIST 2020; 228:1401-1416. [PMID: 32583432 PMCID: PMC7689822 DOI: 10.1111/nph.16769] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/11/2020] [Indexed: 05/02/2023]
Abstract
Plastid-encoded genes are coordinately transcribed by the nucleus-encoded RNA polymerase (NEP) and the plastid-encoded RNA polymerase (PEP). Resulting primary transcripts are frequently subject to RNA editing by cytidine-to-uridine conversions at specific sites. The physiological role of many editing events is largely unknown. Here, we have used the CRISPR/Cas9 technique in rice to knock out a member of the PLS-DYW subfamily of pentatricopeptide repeat (PPR) proteins. We found that OsPPR16 is responsible for a single editing event at position 545 in the chloroplast rpoB messenger RNA (mRNA), resulting in an amino acid change from serine to leucine in the β-subunit of the PEP. In striking contrast to loss-of-function mutations of the putative orthologue in Arabidopsis, which were reported to have no visible phenotype, knockout of OsPPR16 leads to impaired accumulation of RpoB, reduced expression of PEP-dependent genes, and a pale phenotype during early plant development. Thus, by editing the rpoB mRNA, OsPPR16 is required for faithful plastid transcription, which in turn is required for Chl synthesis and efficient chloroplast development. Our results provide new insights into the interconnection of the finely tuned regulatory mechanisms that operate at the transcriptional and post-transcriptional levels of plastid gene expression.
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Affiliation(s)
- Weifeng Huang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Yang Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Liqiang Shen
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
- University of Chinese Academy of SciencesBeijing100049China
| | - Qian Fang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Qun Liu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Chenbo Gong
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Chen Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Yong Zhou
- College of Bioscience and BioengineeringJiangxi Agricultural UniversityNanchan330045China
| | - Cui Mao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Yongli Zhu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Jinghong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Hongping Chen
- Nanchang Subcenter of Rice National Engineering LaboratoryKey Laboratory of Rice Physiology and Genetics of Jiangxi ProvinceRice Research InstituteJiangxi Academy of Agricultural SciencesNanchang330200China
| | - Yu Zhang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Ralph Bock
- Max‐Planck‐Institut für Molekulare PflanzenphysiologieAm Mühlenberg 1Potsdam‐GolmD‐14476Germany
| | - Fei Zhou
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
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9
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Searing AM, Satyanarayan MB, O′Donnell JP, Lu Y. Two organelle RNA recognition motif proteins affect distinct sets of RNA editing sites in the Arabidopsis thaliana plastid. PLANT DIRECT 2020; 4:e00213. [PMID: 32259001 PMCID: PMC7132558 DOI: 10.1002/pld3.213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/12/2019] [Accepted: 03/13/2020] [Indexed: 06/01/2023]
Abstract
Plastid and mitochondrial RNAs in vascular plants are subjected to cytidine-to-uridine editing. The model plant species Arabidopsis thaliana (Arabidopsis) has two nuclear-encoded plastid-targeted organelle RNA recognition motif (ORRM) proteins: ORRM1 and ORRM6. In the orrm1 mutant, 21 plastid RNA editing sites were affected but none are essential to photosynthesis. In the orrm6 mutants, two plastid RNA editing sites were affected: psbF-C77 and accD-C794. Because psbF encodes the β subunit of cytochrome b 559 in photosystem II, which is essential to photosynthesis, the orrm6 mutants were much smaller than the wild type. In addition, the orrm6 mutants had pale green leaves and reduced photosynthetic efficiency. To investigate the functional relationship between ORRM1 and ORRM6, we generated orrm1 orrm6 double homozygous mutants. Morphological and physiological analyses showed that the orrm1 orrm6 double mutants had a smaller plant size, reduced chlorophyll contents, and decreased photosynthetic efficiency, similar to the orrm6 single mutants. Although the orrm1 orrm6 double mutants adopted the phenotype of the orrm6 single mutants, the total number of plastid RNA editing sites affected in the orrm1 orrm6 double mutants was the sum of the sites affected in the orrm1 and orrm6 single mutants. These data suggest that ORRM1 and ORRM6 are in charge of distinct sets of plastid RNA editing sites and that simultaneous mutations in ORRM1 and ORRM6 genes do not cause additional reduction in editing extent at other plastid RNA editing sites.
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Affiliation(s)
- Audrey M. Searing
- Department of Biological SciencesWestern Michigan UniversityKalamazooMIUSA
| | | | - James P. O′Donnell
- Department of Biological SciencesWestern Michigan UniversityKalamazooMIUSA
| | - Yan Lu
- Department of Biological SciencesWestern Michigan UniversityKalamazooMIUSA
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10
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Shivaiah KK, Ding G, Upton B, Nikolau BJ. Non-Catalytic Subunits Facilitate Quaternary Organization of Plastidic Acetyl-CoA Carboxylase. PLANT PHYSIOLOGY 2020; 182:756-775. [PMID: 31792149 PMCID: PMC6997691 DOI: 10.1104/pp.19.01246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 11/19/2019] [Indexed: 05/18/2023]
Abstract
Arabidopsis (Arabidopsis thaliana), like most dicotyledonous plants, expresses a multicomponent, heteromeric acetyl-CoA carboxylase (htACCase), which catalyzes the generation of the malonyl-CoA precursor of de novo fatty acid biosynthesis. This enzyme consists of four catalytic subunits: biotin carboxylase (BC), carboxyltransferase (CT)-α, CT-β, and biotin carboxyl carrier protein (BCCP1 or BCCP2). By coexpressing combinations of components in a bacterial expression system, we demonstrate noncatalytic BADCs facilitate the assembly and activation of BCCP-BADC-BC subcomplexes catalyzing the bicarbonate-dependent hydrolysis of ATP, which is the first half-reaction catalyzed by the htACCase enzyme. Although BADC proteins do not directly impact formation of the CT-αβ subcomplex, the BADC-facilitated BCCP-BADC-BC subcomplex can more readily interact with the CT-αβ subcomplex to facilitate the generation of malonyl-CoA. The Arabidopsis genome encodes three BADC isoforms (BADC1, BADC2, and BADC3), and BADC2 and BADC3 (rather than BADC1), in combination with BCCP1, best support this quaternary-structural organization and catalytic activation of the htACCase enzyme. Physiological genetic studies validate these attributes as Arabidopsis double mutants singularly expressing BADC2, BADC3, or BADC1 present increasingly greater deleterious impacts on morphological and biochemical phenotypes. Specifically, plants expressing only BADC2 develop normally, plants only expressing BADC3 suffer a stunted root-growth phenotype, and plants expressing only BADC1 are embryo-lethal. The latter phenotype may also be associated with the distinct suborganelle localization of BADC1 in plastids as compared to the localization of the other two BADC homologs. These finding can inspire novel strategies to improve the biological sources of fats and oils for dietary and industrial applications.
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Affiliation(s)
- Kiran-Kumar Shivaiah
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
| | - Geng Ding
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
| | - Bryon Upton
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
| | - Basil J Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
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11
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Hayes ML, Santibanez PI. A plant pentatricopeptide repeat protein with a DYW-deaminase domain is sufficient for catalyzing C-to-U RNA editing in vitro. J Biol Chem 2020; 295:3497-3505. [PMID: 31996373 DOI: 10.1074/jbc.ra119.011790] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/23/2020] [Indexed: 12/27/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins with C-terminal DYW domains are present in organisms that undergo C-to-U editing of organelle RNA transcripts. PPR domains act as specificity factors through electrostatic interactions between a pair of polar residues and the nitrogenous bases of an RNA target. DYW-deaminase domains act as the editing enzyme. Two moss (Physcomitrella patens) PPR proteins containing DYW-deaminase domains, PPR65 and PPR56, can convert Cs to Us in cognate, exogenous RNA targets co-expressed in Escherichia coli We show here that purified, recombinant PPR65 exhibits robust editase activity on synthetic RNAs containing cognate, mitochondrial PpccmFC sequences in vitro, indicating that a PPR protein with a DYW domain is solely sufficient for catalyzing C-to-U RNA editing in vitro Monomeric fractions possessed the highest conversion efficiency, and oligomeric fractions had reduced activity. Inductively coupled plasma (ICP)-MS analysis indicated a stoichiometry of two zinc ions per highly active PPR65 monomer. Editing activity was sensitive to addition of zinc acetate or the zinc chelators 1,10-o-phenanthroline and EDTA. Addition of ATP or nonhydrolyzable nucleotide analogs stimulated PPR65-catalyzed RNA-editing activity on PpccmFC substrates, indicating potential allosteric regulation of PPR65 by ATP. Unlike for bacterial cytidine deaminase, addition of two putative transition-state analogs, zebularine and tetrahydrouridine, failed to disrupt RNA-editing activity. RNA oligonucleotides with a single incorporated zebularine also did not disrupt editing in vitro, suggesting that PPR65 cannot bind modified bases due to differences in the structure of the active site compared with other zinc-dependent nucleotide deaminases.
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Affiliation(s)
- Michael L Hayes
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California 90032.
| | - Paola I Santibanez
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California 90032
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12
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Sandoval R, Boyd RD, Kiszter AN, Mirzakhanyan Y, Santibańez P, Gershon PD, Hayes ML. Stable native RIP9 complexes associate with C-to-U RNA editing activity, PPRs, RIPs, OZ1, ORRM1 and ISE2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1116-1126. [PMID: 31077462 PMCID: PMC6744336 DOI: 10.1111/tpj.14384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/23/2019] [Accepted: 04/30/2019] [Indexed: 05/02/2023]
Abstract
The mitochondrial and chloroplast mRNAs of the majority of land plants are modified through cytidine to uridine (C-to-U) RNA editing. Previously, forward and reverse genetic screens demonstrated a requirement for pentatricopeptide repeat (PPR) proteins for RNA editing. Moreover, chloroplast editing factors OZ1, RIP2, RIP9 and ORRM1 were identified in co-immunoprecipitation (co-IP) experiments, albeit the minimal complex sufficient for editing activity was never deduced. The current study focuses on isolated, intact complexes that are capable of editing distinct sites. Peak editing activity for four sites was discovered in size-exclusion chromatography (SEC) fractions ≥ 670 kDa, while fractions estimated to be approximately 413 kDa exhibited the greatest ability to convert a substrate containing the editing site rps14 C80. RNA content peaked in the ≥ 670 kDa fraction. Treatment of active chloroplast extracts with RNase A abolished the relationship of editing activity with high-MW fractions, suggesting a structural RNA component in native complexes. By immunoblotting, RIP9, OTP86, OZ1 and ORRM1 were shown to be present in active gel filtration fractions, though OZ1 and ORRM1 were mainly found in low-MW inactive fractions. Active editing factor complexes were affinity-purified using anti-RIP9 antibodies, and orthologs to putative Arabidopsis thaliana RNA editing factor PPR proteins, RIP2, RIP9, RIP1, OZ1, ORRM1 and ISE2 were identified via mass spectrometry. Western blots from co-IP studies revealed the mutual association of OTP86 and OZ1 with native RIP9 complexes. Thus, RIP9 complexes were discovered to be highly associated with C-to-U RNA editing activity and other editing factors indicative of their critical role in vascular plant editosomes.
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Affiliation(s)
- Rafael Sandoval
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Robert D. Boyd
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California, 90032, USA
| | - Alena N. Kiszter
- Department of Chemistry, Graz University of Technology, Graz, Austria
| | - Yeva Mirzakhanyan
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California 92697, USA
| | - Paola Santibańez
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California, 90032, USA
| | - Paul D. Gershon
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California 92697, USA
| | - Michael L. Hayes
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California, 90032, USA
- To whom correspondence should be addressed. Michael L. Hayes: Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, CA 90032; ; Tel.(323) 343-2144
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13
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Rovira AG, Smith AG. PPR proteins - orchestrators of organelle RNA metabolism. PHYSIOLOGIA PLANTARUM 2019; 166:451-459. [PMID: 30809817 DOI: 10.1111/ppl.12950] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 05/21/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are important RNA regulators in chloroplasts and mitochondria, aiding in RNA editing, maturation, stabilisation or intron splicing, and in transcription and translation of organellar genes. In this review, we summarise all PPR proteins documented so far in plants and the green alga Chlamydomonas. By further analysis of the known target RNAs from Arabidopsis thaliana PPR proteins, we find that all organellar-encoded complexes are regulated by these proteins, although to differing extents. In particular, the orthologous complexes of NADH dehydrogenase (Complex I) in the mitochondria and NADH dehydrogenase-like (NDH) complex in the chloroplast were the most regulated, with respectively 60 and 28% of all characterised A. thaliana PPR proteins targeting their genes.
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Affiliation(s)
- Aleix Gorchs Rovira
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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14
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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: 13] [Impact Index Per Article: 2.2] [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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15
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Sun YK, Gutmann B, Yap A, Kindgren P, Small I. Editing of Chloroplast rps14 by PPR Editing Factor EMB2261 Is Essential for Arabidopsis Development. FRONTIERS IN PLANT SCIENCE 2018; 9:841. [PMID: 29973946 PMCID: PMC6019781 DOI: 10.3389/fpls.2018.00841] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 05/30/2018] [Indexed: 05/04/2023]
Abstract
RNA editing in plastids is known to be required for embryogenesis, but no single editing event had been shown to be essential. We show that the emb2261-2 mutation is lethal through a failure to express an editing factor that specifically recognizes the rps14-2 site. EMB2261 was predicted to bind the cis-element upstream of the rps14-2 site and genetic complementation with promoters of different strength followed by RNA-seq analysis was conducted to test the correlation between rps14-2 editing and EMB2261 expression. Rps14-2 is the only editing event in Arabidopsis chloroplasts that correlates with EMB2261 expression. Sequence divergence between the cis-element and the EMB2261 protein sequence in plants where rps14-2 editing is not required adds support to the association between them. We conclude that EMB2261 is the specificity factor for rps14-2 editing. This editing event converts P51 in Rps14 to L51, which is conserved among species lacking RNA editing, implying the importance of the editing event to Rps14 function. Rps14 is an essential ribosomal subunit for plastid translation, which, in turn, is essential for Arabidopsis embryogenesis.
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16
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Bayer-Császár E, Haag S, Jörg A, Glass F, Härtel B, Obata T, Meyer EH, Brennicke A, Takenaka M. The conserved domain in MORF proteins has distinct affinities to the PPR and E elements in PPR RNA editing factors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:813-828. [PMID: 28549935 DOI: 10.1016/j.bbagrm.2017.05.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/11/2017] [Accepted: 05/14/2017] [Indexed: 11/15/2022]
Abstract
In plant organelles specific nucleotide motifs at C to U RNA editing sites are recognized by the PLS-class of pentatricopeptide repeat (PPR) proteins, which are additionally characterized by a C-terminal E domain. The PPR elements bind the nucleotides in the target RNA, while the function of the E domain has remained unknown. At most sites RNA editing also requires multiple organellar RNA editing factor (MORF) proteins. To understand how these two types of proteins are involved in RNA editing complexes, we systematically analyzed their protein-protein interactions. In vivo pull-down and yeast two-hybrid assays show that MORF proteins connect with selected PPR proteins. In a loss of function mutant of MORF1, a single amino acid alteration in the conserved MORF domain abrogates interactions with many PLS-class PPR proteins, implying the requirement of direct interaction to PPR proteins for the RNA editing function of MORF1. Subfragment analyses show that predominantly the N-terminal/central regions of the MORF domain in MORF1 and MORF3 bind the PPR proteins. Within the PPR proteins, the E domains in addition to PPR elements contact MORF proteins. In chimeric PPR proteins, different E domains alter the specificity of the interaction with MORF proteins. The selective interactions between E domain containing PPR and MORF proteins suggest that the E domains and MORF proteins play a key role for specific protein complexes to assemble at different RNA editing sites.
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Affiliation(s)
| | - Sascha Haag
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
| | - Anja Jörg
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
| | | | | | - Toshihiro Obata
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam, Golm, Germany
| | - Etienne H Meyer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam, Golm, Germany
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17
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Xiao-Ming Z, Junrui W, Li F, Sha L, Hongbo P, Lan Q, Jing L, Yan S, Weihua Q, Lifang Z, Yunlian C, Qingwen Y. Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants. Sci Rep 2017; 7:1555. [PMID: 28484234 PMCID: PMC5431534 DOI: 10.1038/s41598-017-01518-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 03/29/2017] [Indexed: 01/08/2023] Open
Abstract
The chloroplast genome originated from photosynthetic organisms and has retained the core genes that mainly encode components of photosynthesis. However, the causes of variations in chloroplast genome size in seed plants have only been thoroughly analyzed within small subsets of spermatophytes. In this study, we conducted the first comparative analysis on a large scale to examine the relationship between sequence characteristics and genome size in 272 seed plants based on cross-species and phylogenetic signal analysis. Our results showed that inverted repeat regions, large or small single copies, intergenic regions, and gene number can be attributed to the variations in chloroplast genome size among closely related species. However, chloroplast gene length underwent evolution affecting chloroplast genome size in seed plants irrespective of whether phylogenetic information was incorporated. Among chloroplast genes, atpA, accD and ycf1 account for 13% of the variation in genome size, and the average Ka/Ks values of homologous pairs of the three genes are larger than 1. The relationship between chloroplast genome size and gene length might be affected by selection during the evolution of spermatophytes. The variation in chloroplast genome size may influence energy generation and ecological strategy in seed plants.
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Affiliation(s)
- Zheng Xiao-Ming
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wang Junrui
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Feng Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liu Sha
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pang Hongbo
- College of Chemistry and Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Qi Lan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sun Yan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiao Weihua
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhang Lifang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cheng Yunlian
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Qingwen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Hackett JB, Lu Y. Whole-transcriptome RNA-seq, gene set enrichment pathway analysis, and exon coverage analysis of two plastid RNA editing mutants. PLANT SIGNALING & BEHAVIOR 2017; 12:e1312242. [PMID: 28387567 PMCID: PMC5501230 DOI: 10.1080/15592324.2017.1312242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 03/18/2017] [Accepted: 03/23/2017] [Indexed: 06/02/2023]
Abstract
In land plants, plastid and mitochondrial RNAs are subject to post-transcriptional C-to-U RNA editing. T-DNA insertions in the ORGANELLE RNA RECOGNITION MOTIF PROTEIN6 gene resulted in reduced photosystem II (PSII) activity and smaller plant and leaf sizes. Exon coverage analysis of the ORRM6 gene showed that orrm6-1 and orrm6-2 are loss-of-function mutants. Compared to other ORRM proteins, ORRM6 affects a relative small number of RNA editing sites. Sanger sequencing of reverse transcription-PCR products of plastid transcripts revealed 2 plastid RNA editing sites that are substantially affected in the orrm6 mutants: psbF-C77 and accD-C794. The psbF gene encodes the β subunit of cytochrome b559, an essential component of PSII. The accD gene encodes the β subunit of acetyl-CoA carboxylase, a protein required in plastid fatty acid biosynthesis. Whole-transcriptome RNA-seq demonstrated that editing at psbF-C77 is nearly absent and the editing extent at accD-C794 was significantly reduced. Gene set enrichment pathway analysis showed that expression of multiple gene sets involved in photosynthesis, especially photosynthetic electron transport, is significantly upregulated in both orrm6 mutants. The upregulation could be a mechanism to compensate for the reduced PSII electron transport rate in the orrm6 mutants. These results further demonstrated that Organelle RNA Recognition Motif protein ORRM6 is required in editing of specific RNAs in the Arabidopsis (Arabidopsis thaliana) plastid.
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Affiliation(s)
- Justin B. Hackett
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - Yan Lu
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
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19
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Hackett JB, Shi X, Kobylarz AT, Lucas MK, Wessendorf RL, Hines KM, Bentolila S, Hanson MR, Lu Y. An Organelle RNA Recognition Motif Protein Is Required for Photosystem II Subunit psbF Transcript Editing. PLANT PHYSIOLOGY 2017; 173:2278-2293. [PMID: 28213559 PMCID: PMC5373051 DOI: 10.1104/pp.16.01623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/13/2017] [Indexed: 05/02/2023]
Abstract
Loss-of-function mutations in ORGANELLE RNA RECOGNITION MOTIF PROTEIN6 (ORRM6) result in the near absence of RNA editing of psbF-C77 and the reduction in accD-C794 editing in Arabidopsis (Arabidopsis thaliana). The orrm6 mutants have decreased levels of photosystem II (PSII) proteins, especially PsbF, lower PSII activity, pale green pigmentation, smaller leaf and plant sizes, and retarded growth. Stable expression of ORRM6 rescues the orrm6 editing defects and mutant phenotype. Unlike ORRM1, the other known ORRM plastid editing factor, ORRM6, does not contain RNA editing interacting protein/multiple organellar RNA editing factor (RIP/MORF) boxes, which are required for ORRM1 to interact with site-specific pentatricopeptide repeat protein editing factors. ORRM6 interacts with RIP1/MORF8, RIP2/MORF2, and RIP9/MORF9, known components of RNA editosomes. While some plastid RRM proteins are involved in other forms of RNA processing and translation, the primary function of ORRM6 is evidently to mediate psbF-C77 editing, like the essential site-specific pentatricopeptide repeat protein LOW PSII ACCUMULATION66. Stable expression in the orrm6 mutants of a nucleus-encoded, plastid-targeted PsbF protein from a psbF gene carrying a T at nucleotide 77 significantly increases leaf and plant sizes, chlorophyll content, and PSII activity. These transformants demonstrate that plastid RNA editing can be bypassed through the expression of nucleus-encoded, edited forms of plastid genes.
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Affiliation(s)
- Justin B Hackett
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Xiaowen Shi
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Amy T Kobylarz
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Meriah K Lucas
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Ryan L Wessendorf
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Kevin M Hines
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Stephane Bentolila
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Maureen R Hanson
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Yan Lu
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
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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: 5] [Impact Index Per Article: 0.7] [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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Sun T, Bentolila S, Hanson MR. The Unexpected Diversity of Plant Organelle RNA Editosomes. TRENDS IN PLANT SCIENCE 2016; 21:962-973. [PMID: 27491516 DOI: 10.1016/j.tplants.2016.07.005] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/04/2016] [Accepted: 07/05/2016] [Indexed: 05/02/2023]
Abstract
Flowering plants convert many hundreds of organelle cytidines (Cs) to uridines (Us) during post-transcriptional RNA editing. Pentatricopeptide repeat (PPR) proteins dictate specificity by recognizing RNA sequences near C targets. However, the complete mechanism of the editing machinery is not yet understood. Recently, non-PPR editing factors [RNA editing factor interacting proteins (RIPs)/multiple organellar RNA editing factors (MORFs), organelle RNA recognition motif (ORRM) proteins, organelle zinc-finger (OZ) proteins, and protoporphyrinogen oxidase 1 (PPO1)] have been identified as components of the plant RNA editosome, which is a small RNA-protein complex. Surprisingly, plant editosomes are highly diverse not only with regard to the PPR proteins they contain but also in the non-PPR components that are present. Here we review the most recent progress in the field and discuss the implications of the diversity of plant editosomes for the evolution of RNA editing and for possible future applications.
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Affiliation(s)
- Tao Sun
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Stephane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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23
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Shi X, Bentolila S, Hanson MR. Organelle RNA recognition motif-containing (ORRM) proteins are plastid and mitochondrial editing factors in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2016; 11:e1167299. [PMID: 27082488 PMCID: PMC4977459 DOI: 10.1080/15592324.2016.1167299] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Post-transcriptional C-to-U RNA editing occurs at specific sites in plastid and plant mitochondrial transcripts. Members of the Arabidopsis pentatricopeptide repeat (PPR) motif-containing protein family and RNA-editing factor Interacting Protein (RIP, also known as MORF) family have been characterized as essential components of the RNA editing apparatus. Recent studies reveal that several organelle-targeted RNA recognition motif (RRM)-containing proteins are involved in either plastid or mitochondrial RNA editing. ORRM1 (Organelle RRM protein 1) is essential for plastid editing, whereas ORRM2, ORRM3 and ORRM4 are involved in mitochondrial RNA editing. The RRM domain of ORRM1, ORRM3 and ORRM4 is required for editing activity, whereas the auxiliary RIP and Glycine-Rich (GR) domains mediate the ORRM proteins' interactions with other editing factors. The identification of the ORRM proteins as RNA editing factors further expands our knowledge of the composition of the editosome.
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Affiliation(s)
- Xiaowen Shi
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY, USA
| | - Stephane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY, USA
| | - Maureen R. Hanson
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY, USA
- Maureen R Hanson
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24
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Salie MJ, Thelen JJ. Regulation and structure of the heteromeric acetyl-CoA carboxylase. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1207-1213. [PMID: 27091637 DOI: 10.1016/j.bbalip.2016.04.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 11/16/2022]
Abstract
The enzyme acetyl-CoA carboxylase (ACCase) catalyzes the committed step of the de novo fatty acid biosynthesis (FAS) pathway by converting acetyl-CoA to malonyl-CoA. Two forms of ACCase exist in nature, a homomeric and heteromic form. The heteromeric form of this enzyme requires four different subunits for activity: biotin carboxylase; biotin carboxyl carrier protein; and α- and β-carboxyltransferases. Heteromeric ACCases (htACCase) can be found in prokaryotes and the plastids of most plants. The plant htACCase is regulated by diverse mechanisms reflected by the biochemical and genetic complexity of this multienzyme complex and the plastid stroma where it resides. In this review we summarize the regulation of the plant htACCase and also describe the structural characteristics of this complex from both prokaryotes and plants. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.
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Affiliation(s)
- Matthew J Salie
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, 1201 E. Rollins, Columbia, MO 65201, USA.
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, 1201 E. Rollins, Columbia, MO 65201, USA.
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25
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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: 41] [Impact Index Per Article: 5.1] [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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Shi X, Germain A, Hanson MR, Bentolila S. RNA Recognition Motif-Containing Protein ORRM4 Broadly Affects Mitochondrial RNA Editing and Impacts Plant Development and Flowering. PLANT PHYSIOLOGY 2016; 170:294-309. [PMID: 26578708 PMCID: PMC4704580 DOI: 10.1104/pp.15.01280] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/13/2015] [Indexed: 05/02/2023]
Abstract
Plant RNA editosomes modify cytidines (C) to uridines (U) at specific sites in plastid and mitochondrial transcripts. Members of the RNA-editing factor interacting protein (RIP) family and Organelle RNA Recognition Motif-containing (ORRM) family are essential components of the Arabidopsis (Arabidopsis thaliana) editosome. ORRM2 and ORRM3 have been recently identified as minor mitochondrial editing factors whose silencing reduces editing efficiency at ∼6% of the mitochondrial C targets. Here we report the identification of ORRM4 (for organelle RRM protein 4) as a novel, major mitochondrial editing factor that controls ∼44% of the mitochondrial editing sites. C-to-U conversion is reduced, but not eliminated completely, at the affected sites. The orrm4 mutant exhibits slower growth and delayed flowering time. ORRM4 affects editing in a site-specific way, though orrm4 mutation affects editing of the entire transcript of certain genes. ORRM4 contains an RRM domain at the N terminus and a Gly-rich domain at the C terminus. The RRM domain provides the editing activity of ORRM4, whereas the Gly-rich domain is required for its interaction with ORRM3 and with itself. The presence of ORRM4 in the editosome is further supported by its interaction with RIP1 in a bimolecular fluorescence complementation assay. The identification of ORRM4 as a major mitochondrial editing factor further expands our knowledge of the composition of the RNA editosome and reveals that adequate mitochondrial editing is necessary for normal plant development.
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Affiliation(s)
- Xiaowen Shi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 (X.S., A.G., M.R.H., S.B.)
| | - Arnaud Germain
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 (X.S., A.G., M.R.H., S.B.)
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 (X.S., A.G., M.R.H., S.B.)
| | - Stéphane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 (X.S., A.G., M.R.H., S.B.)
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Zhang HD, Cui YL, Huang C, Yin QQ, Qin XM, Xu T, He XF, Zhang Y, Li ZR, Yang ZN. PPR protein PDM1/SEL1 is involved in RNA editing and splicing of plastid genes in Arabidopsis thaliana. PHOTOSYNTHESIS RESEARCH 2015; 126:311-21. [PMID: 26123918 DOI: 10.1007/s11120-015-0171-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 06/22/2015] [Indexed: 05/10/2023]
Abstract
After transcription, most chloroplast precursor RNAs undergo further post-transcriptional processing including cleavage, editing, and splicing. Previous investigation has shown that the cleavage of the rpoA transcript and most editing sites, including accD-1, are defective in the knockout mutant of PDM1/SEL1, a PLS-type PPR protein, and that PDM1 is associated with the rpoA transcript. In this work, we found that the splicing of group II introns in trnK and ndhA is also affected in pdm1. Co-immunoprecipitation mass spectrometry experiments were performed to identify proteins that are associated with PDM1. We obtained 126 non-redundant proteins, of which MORF9 was reported to be involved in RNA editing in chloroplast. Yeast two-hybrid assays showed that PDM1 interacts directly with MORF9, MORF2, and MORF8. RNA immunoprecipitation showed that PDM1 associates with the transcripts of trnK and ndhA, as well as accD-1, suggesting that PDM1 is involved in RNA editing and splicing. Therefore, PDM1 is an important protein for post-transcriptional regulation in chloroplast.
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Affiliation(s)
- Hong-Dao Zhang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yong-Lan Cui
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Chao Huang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Qian-Qian Yin
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xue-Mei Qin
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Te Xu
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xiao-Fang He
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yi Zhang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zi-Ran Li
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhong-Nan Yang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China.
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Pentatricopeptide-repeat family protein RF6 functions with hexokinase 6 to rescue rice cytoplasmic male sterility. Proc Natl Acad Sci U S A 2015; 112:14984-9. [PMID: 26578814 DOI: 10.1073/pnas.1511748112] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytoplasmic male sterility (CMS) has been extensively used for hybrid seed production in many major crops. Honglian CMS (HL-CMS) is one of the three major types of CMS in rice and has contributed greatly to food security worldwide. The HL-CMS trait is associated with an aberrant chimeric mitochondrial transcript, atp6-orfH79, which causes pollen sterility and can be rescued by two nonallelic restorer-of-fertility (Rf) genes, Rf5 or Rf6. Here, we report the identification of Rf6, which encodes a novel pentatricopeptide repeat (PPR) family protein with a characteristic duplication of PPR motifs 3-5. RF6 is targeted to mitochondria, where it physically associates with hexokinase 6 (OsHXK6) and promotes the processing of the aberrant CMS-associated transcript atp6-orfH79 at nucleotide 1238, which ensures normal pollen development and restores fertility. The duplicated motif 3 of RF6 is essential for RF6-OsHXK6 interactions, processing of the aberrant transcript, and restoration of fertility. Furthermore, reductions in the level of OsHXK6 result in atp6-orfH79 transcript accumulation and male sterility. Together these results reveal a novel mechanism for CMS restoration by which RF6 functions with OsHXK6 to restore HL-CMS fertility. The present study also provides insight into the function of hexokinase 6 in regulating mitochondrial RNA metabolism and may facilitate further exploitation of heterosis in rice.
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29
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Brehme N, Bayer-Császár E, Glass F, Takenaka M. The DYW Subgroup PPR Protein MEF35 Targets RNA Editing Sites in the Mitochondrial rpl16, nad4 and cob mRNAs in Arabidopsis thaliana. PLoS One 2015; 10:e0140680. [PMID: 26470017 PMCID: PMC4607164 DOI: 10.1371/journal.pone.0140680] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 09/29/2015] [Indexed: 11/30/2022] Open
Abstract
RNA editing in plant mitochondria and plastids alters specific nucleotides from cytidine (C) to uridine (U) mostly in mRNAs. A number of PLS-class PPR proteins have been characterized as RNA recognition factors for specific RNA editing sites, all containing a C-terminal extension, the E domain, and some an additional DYW domain, named after the characteristic C-terminal amino acid triplet of this domain. Presently the recognition factors for more than 300 mitochondrial editing sites are still unidentified. In order to characterize these missing factors, the recently proposed computational prediction tool could be of use to assign target RNA editing sites to PPR proteins of yet unknown function. Using this target prediction approach we identified the nuclear gene MEF35 (Mitochondrial Editing Factor 35) to be required for RNA editing at three sites in mitochondria of Arabidopsis thaliana. The MEF35 protein contains eleven PPR repeats and E and DYW extensions at the C-terminus. Two T-DNA insertion mutants, one inserted just upstream and the other inside the reading frame encoding the DYW domain, show loss of editing at a site in each of the mRNAs for protein 16 in the large ribosomal subunit (site rpl16-209), for cytochrome b (cob-286) and for subunit 4 of complex I (nad4-1373), respectively. Editing is restored upon introduction of the wild type MEF35 gene in the reading frame mutant. The MEF35 protein interacts in Y2H assays with the mitochondrial MORF1 and MORF8 proteins, mutation of the latter also influences editing at two of the three MEF35 target sites. Homozygous mutant plants develop indistinguishably from wild type plants, although the RPL16 and COB/CYTB proteins are essential and the amino acids encoded after the editing events are conserved in most plant species. These results demonstrate the feasibility of the computational target prediction to screen for target RNA editing sites of E domain containing PLS-class PPR proteins.
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Affiliation(s)
- Nadja Brehme
- Molekulare Botanik, Universität Ulm, Ulm, Germany
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Glass F, Härtel B, Zehrmann A, Verbitskiy D, Takenaka M. MEF13 Requires MORF3 and MORF8 for RNA Editing at Eight Targets in Mitochondrial mRNAs in Arabidopsis thaliana. MOLECULAR PLANT 2015; 8:1466-77. [PMID: 26048647 DOI: 10.1016/j.molp.2015.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 05/07/2015] [Accepted: 05/17/2015] [Indexed: 05/02/2023]
Abstract
RNA editing sites in plant mitochondria and plastids are addressed by pentatricopeptide repeat (PPR) proteins with E or E and DYW domains, which recognize a specific nucleotide motif upstream of the edited nucleotide. In addition, some sites require MORF proteins for efficient RNA editing. Here, we assign the novel E domain-containing PPR protein, MEF13, as being required for editing at eight sites in Arabidopsis thaliana. A SNP in ecotype C24 altering the editing level at only one of the eight target sites was located by genomic mapping. An EMS mutant allele of the gene for MEF13 was identified in a SNaPshot screen of a mutated plant population. At all eight target sites of MEF13, editing levels are reduced in both morf3 and morf8 mutants, but at only one site in morf1 mutants, suggesting that specific MEF13-MORF interactions are required. Yeast two-hybrid analyses detect solid connections of MEF13 with MORF1 and weak contact with MORF3 proteins. Yeast three-hybrid (Y3H) analysis shows that the presence of MORF8 enhances the connection between MEF13 and MORF3, suggesting that a MORF3-MORF8 heteromer may form stably or transiently to establish interaction with MEF13.
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Affiliation(s)
| | | | - Anja Zehrmann
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
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31
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Germain A, Hanson MR, Bentolila S. High-throughput quantification of chloroplast RNA editing extent using multiplex RT-PCR mass spectrometry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:546-554. [PMID: 26032222 DOI: 10.1111/tpj.12892] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/14/2015] [Accepted: 05/26/2015] [Indexed: 06/04/2023]
Abstract
RNA editing in plants, animals, and humans modifies genomically encoded cytidine or adenosine nucleotides to uridine or inosine, respectively, in mRNAs. We customized the MassARRAY System (Sequenom Inc., San Diego, CA, USA, www.sequenom.com) to assay multiplex PCR-amplified single-stranded cDNAs and easily analyse and display the captured data. By using appropriate oligonucleotide probes, the method can be tailored to any organism and gene where RNA editing occurs. Editing extent of up to 40 different nucleotides in each of either 94 or 382 different samples (3760 or 15 280 editing targets, respectively) can be examined by assaying a single plate and by performing one repetition. We have established this mass spectrometric method as a dependable, cost-effective and time-saving technique to examine the RNA editing efficiency at 37 Arabidopsis thaliana chloroplast editing sites at a high level of multiplexing. The high-throughput editing assay, named Multiplex RT-PCR Mass Spectrometry (MRMS), is ideal for large-scale experiments such as identifying population variation, examining tissue-specific changes in editing extent, or screening a mutant or transgenic collection. Moreover, the required amount of starting material is so low that RNA from fewer than 50 cells can be examined without amplification. We demonstrate the use of the method to identify natural variation in editing extent of chloroplast C targets in a collection of Arabidopsis accessions.
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Affiliation(s)
- Arnaud Germain
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY, 14853, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY, 14853, USA
| | - Stéphane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY, 14853, USA
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32
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Shi X, Hanson MR, Bentolila S. Two RNA recognition motif-containing proteins are plant mitochondrial editing factors. Nucleic Acids Res 2015; 43:3814-25. [PMID: 25800738 PMCID: PMC4402546 DOI: 10.1093/nar/gkv245] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/10/2015] [Indexed: 12/17/2022] Open
Abstract
Post-transcriptional C-to-U RNA editing occurs in plant plastid and mitochondrial transcripts. Members of the Arabidopsis RNA-editing factor interacting protein (RIP) family and ORRM1 (Organelle RNA Recognition Motif-containing protein 1) have been recently characterized as essential components of the chloroplast RNA editing apparatus. ORRM1 belongs to a distinct clade of RNA Recognition Motif (RRM)-containing proteins, most of which are predicted to be organelle-targeted. Here we report the identification of two proteins, ORRM2 (organelle RRM protein 2) and ORRM3 (organelle RRM protein 3), as the first members of the ORRM clade to be identified as mitochondrial editing factors. Transient silencing of ORRM2 and ORRM3 resulted in reduced editing efficiency at ∼6% of the mitochondrial C targets. In addition to an RRM domain at the N terminus, ORRM3 carries a glycine-rich domain at the C terminus. The N-terminal RRM domain by itself provides the editing activity of ORRM3. In yeast-two hybrid assays, ORRM3 interacts with RIP1, ORRM2 and with itself. Transient silencing of ORRM2 in the orrm3 mutant further impairs the editing activity at sites controlled by both ORRM2 and ORRM3. Identification of the effect of ORRM2 and ORRM3 on RNA editing reveals a previously undescribed role of RRM-containing proteins as mitochondrial RNA editing factors.
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Affiliation(s)
- Xiaowen Shi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Stéphane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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33
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A zinc finger motif-containing protein is essential for chloroplast RNA editing. PLoS Genet 2015; 11:e1005028. [PMID: 25768119 PMCID: PMC4359148 DOI: 10.1371/journal.pgen.1005028] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/27/2015] [Indexed: 01/07/2023] Open
Abstract
C-to-U editing of transcripts in plant organelles is carried out by small (<400 kD) protein complexes called editosomes. Recognition of the proper C target for editing is mediated by pentatricopeptide repeat (PPR) containing proteins that recognize cis-elements. Members of two additional gene families, the RIP/MORF and ORRM families, have each been found to be required for editing of particular sets of Cs in mitochondria and/or chloroplasts. By co-immunoprecipitation of the chloroplast editing factor ORRM1, followed by mass spectrometry, we have now identified a member of the RanBP2 type zinc fingers (pFAM00641) protein family that is required for editing of 14 sites in chloroplasts and affects editing efficiency of another 16 chloroplast C targets. In yeast two-hybrid assays, OZ1 (Organelle Zinc finger 1) interacts with PPR site recognition factors whose cognate sites are affected when OZ1 is mutated. No interaction of OZ1 with the chloroplast editing factors RIP2 and RIP9 was detected; however, OZ1 interacts with ORRM1, which binds to RIP proteins, allowing us to build a model for the chloroplast RNA editosome. The RNA editosomes that act upon most chloroplast C targets are likely to contain a PPR protein recognition factor, either RIP2 or RIP9, ORRM1, and OZ1. The organelle zinc finger editing factor family (OZ) contains 4 members in Arabidopsis, three that are predicted to be targeted to chloroplasts and one to mitochondria. With the identification of OZ1, there are now 4 nuclear-encoded protein families known to be essential for plant organelle RNA editing. Transcripts encoding chloroplast and mitochondrial proteins of flowering plants are profoundly affected by RNA editing. In Arabidopsis, over 600 genomically-encoded Cs are modified to Us in organelle transcripts, altering the encoded amino acids and creating stop and start codons. Pentatricopeptide proteins are known to bind to cis-elements near C targets of editing and chloroplast RNA editing also requires members of two additional protein families. Nevertheless, not all protein components of the editosome have been identified. We now report the discovery of a member of fourth gene family essential for chloroplast RNA editing: OZ1, member of a family of Arabidopsis RanBP2-type zinc finger proteins. Identifying all of the proteins in the RNA editosome is critical for understanding the mechanism behind the remarkable specificity of C-to-U editing.
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34
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Hayes ML, Dang KN, Diaz MF, Mulligan RM. A conserved glutamate residue in the C-terminal deaminase domain of pentatricopeptide repeat proteins is required for RNA editing activity. J Biol Chem 2015; 290:10136-42. [PMID: 25739442 DOI: 10.1074/jbc.m114.631630] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Indexed: 11/06/2022] Open
Abstract
Many transcripts expressed from plant organelle genomes are modified by C-to-U RNA editing. Nuclear encoded pentatricopeptide repeat (PPR) proteins include an RNA binding domain that provides site specificity. In addition, many PPR proteins include a C-terminal DYW deaminase domain with characteristic zinc binding motifs (CXXC, HXE) and has recently been shown to bind zinc ions. The glutamate residue of the HXE motif is catalytically required in the reaction catalyzed by cytidine deaminase. In this work, we examine the activity of the DYW deaminase domain through truncation or mutagenesis of the HXE motif. OTP84 is required for editing three chloroplast sites, and transgenes expressing OTP84 with C-terminal truncations were capable of editing only one of the three cognate sites at high efficiency. These results suggest that the deaminase domain of OTP84 is required for editing two of the sites, but another deaminase is able to supply the deamination activity for the third site. OTP84 and CREF7 transgenes were mutagenized to replace the glutamate residue of the HXE motif, and transgenic plants expressing OTP84-E824A and CREF7-E554A were unable to efficiently edit the cognate editing sites for these genes. In addition, plants expressing CREF7-E554A exhibited substantially reduced capacity to edit a non-cognate site, rpoA C200. These results indicate that the DYW deaminase domains of PPR proteins are involved in editing their cognate editing sites, and in some cases may participate in editing additional sites in the chloroplast.
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Affiliation(s)
- Michael L Hayes
- From the Developmental and Cell Biology, University of California, Irvine, California 92697
| | - Kim N Dang
- From the Developmental and Cell Biology, University of California, Irvine, California 92697
| | - Michael F Diaz
- From the Developmental and Cell Biology, University of California, Irvine, California 92697
| | - R Michael Mulligan
- From the Developmental and Cell Biology, University of California, Irvine, California 92697
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Yap A, Kindgren P, Colas des Francs-Small C, Kazama T, Tanz SK, Toriyama K, Small I. AEF1/MPR25 is implicated in RNA editing of plastid atpF and mitochondrial nad5, and also promotes atpF splicing in Arabidopsis and rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:661-9. [PMID: 25585673 DOI: 10.1111/tpj.12756] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/15/2014] [Accepted: 12/18/2014] [Indexed: 05/20/2023]
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.
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Affiliation(s)
- Aaron Yap
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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36
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Wagoner JA, Sun T, Lin L, Hanson MR. Cytidine deaminase motifs within the DYW domain of two pentatricopeptide repeat-containing proteins are required for site-specific chloroplast RNA editing. J Biol Chem 2014; 290:2957-68. [PMID: 25512379 DOI: 10.1074/jbc.m114.622084] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In angiosperm organelles, cytidines are converted to uridines by a deamination reaction in the process termed RNA editing. The C targets of editing are recognized by members of the pentatricopeptide repeat (PPR) protein family. Although other members of the editosome have begun to be identified, the enzyme that catalyzes the C-U conversion is still unknown. The DYW motif at the C terminus of many PPR editing factors contains residues conserved with known cytidine deaminase active sites; however, some PPR editing factors lack a DYW motif. Furthermore, in many PPR-DYW editing factors, the truncation of the DYW motif does not affect editing efficiency, so the role of the DYW motif in RNA editing is unclear. Here, a chloroplast PPR-DYW editing factor, quintuple editing factor 1 (QED1), was shown to affect five different plastid editing sites, the greatest number of chloroplast C targets known to be affected by a single PPR protein. Loss of editing at the five sites resulted in stunted growth and accumulation of apparent photodamage. Adding a C-terminal protein tag to QED1 was found to severely inhibit editing function. QED1 and RARE1, another plastid PPR-DYW editing factor, were discovered to require their DYW motifs for efficient editing. To identify specific residues critical for editing, conserved deaminase residues in each PPR protein were mutagenized. The mutant PPR proteins, when expressed in qed1 or rare1 mutant protoplasts, could not complement the editing defect. Therefore, the DYW motif, and specifically, the deaminase residues, of QED1 and RARE1 are required for editing efficiency.
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Affiliation(s)
- Jessica A Wagoner
- From the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Tao Sun
- From the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Lin Lin
- From the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Maureen R Hanson
- From the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
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37
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Chi W, He B, Manavski N, Mao J, Ji D, Lu C, Rochaix JD, Meurer J, Zhang L. RHON1 mediates a Rho-like activity for transcription termination in plastids of Arabidopsis thaliana. THE PLANT CELL 2014; 26:4918-32. [PMID: 25480370 PMCID: PMC4311204 DOI: 10.1105/tpc.114.132118] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/02/2014] [Accepted: 11/15/2014] [Indexed: 05/20/2023]
Abstract
Although transcription termination is essential to generate functional RNAs, its underlying molecular mechanisms are still poorly understood in plastids of vascular plants. Here, we show that the RNA binding protein RHON1 participates in transcriptional termination of rbcL (encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase) in Arabidopsis thaliana. Inactivation of RHON1 leads to enhanced rbcL read-through transcription and to aberrant accD (encoding β-subunit of the acetyl-CoA carboxylase) transcriptional initiation, which may result from inefficient transcription termination of rbcL. RHON1 can bind to the mRNA as well as to single-stranded DNA of rbcL, displays an RNA-dependent ATPase activity, and terminates transcription of rbcL in vitro. These results suggest that RHON1 terminates rbcL transcription using an ATP-driven mechanism similar to that of Rho of Escherichia coli. This RHON1-dependent transcription termination occurs in Arabidopsis but not in rice (Oryza sativa) and appears to reflect a fundamental difference between plastomes of dicotyledonous and monocotyledonous plants. Our results point to the importance and significance of plastid transcription termination and provide insights into its machinery in an evolutionary context.
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Affiliation(s)
- Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Baoye He
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nikolay Manavski
- Biozentrum der Ludwig-Maximilians-Universität, Plant Molecular Biology/Botany, 82152 Planegg-Martinsried, Germany
| | - Juan Mao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Daili Ji
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Congming Lu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jean David Rochaix
- Departments of Molecular Biology and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Jörg Meurer
- Biozentrum der Ludwig-Maximilians-Universität, Plant Molecular Biology/Botany, 82152 Planegg-Martinsried, Germany
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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38
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Arenas-M A, Zehrmann A, Moreno S, Takenaka M, Jordana X. The pentatricopeptide repeat protein MEF26 participates in RNA editing in mitochondrial cox3 and nad4 transcripts. Mitochondrion 2014; 19 Pt B:126-34. [PMID: 25173472 DOI: 10.1016/j.mito.2014.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/16/2014] [Accepted: 08/20/2014] [Indexed: 11/15/2022]
Abstract
In angiosperms most members of the large nuclear-encoded family of pentatricopeptide repeat (PPR) proteins are predicted to play relevant roles in the maturation of organellar RNAs. Here we report the novel Mitochondrial Editing Factor 26, a DYW-PPR protein involved in RNA editing at two sites. While at one site, cox3-311, editing is abolished in the absence of MEF26, the other site, nad4-166, is still partially edited. These sites share similar cis-elements and application of the recently proposed amino acid code for RNA recognition by PPR proteins ranks them at first and second positions of the most probable targets.
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Affiliation(s)
- Anita Arenas-M
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile.
| | - Anja Zehrmann
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany.
| | - Sebastian Moreno
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile.
| | | | - Xavier Jordana
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile.
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39
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Neuman H, Galpaz N, Cunningham FX, Zamir D, Hirschberg J. The tomato mutation nxd1 reveals a gene necessary for neoxanthin biosynthesis and demonstrates that violaxanthin is a sufficient precursor for abscisic acid biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:80-93. [PMID: 24506237 DOI: 10.1111/tpj.12451] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/13/2014] [Accepted: 01/17/2014] [Indexed: 05/20/2023]
Abstract
Carotenoid pigments are indispensable for plant life. They are synthesized within plastids where they provide essential functions in photosynthesis. Carotenoids serve as precursors for the synthesis of the strigolactone phytohormones, which are made from β-carotene, and of abscisic acid (ABA), which is produced from certain xanthophylls. Despite the significant progress that has been made in our understanding of the carotenoid biosynthesis pathway, the synthesis of the xanthophyll neoxanthin has remained unknown. We report here on the isolation of a tomato (Solanum lycopersicum) mutant, neoxanthin-deficient 1 (nxd1), which lacks neoxanthin, and on the cloning of a gene that is necessary for neoxanthin synthesis in both tomato and Arabidopsis. The locus nxd1 encodes a gene of unknown function that is conserved in all higher plants. The activity of NXD1 is essential but cannot solely support neoxanthin synthesis. Lack of neoxanthin does not significantly reduce the fitness of tomato plants in cultivated field conditions and does not impair the synthesis of ABA, suggesting that in tomato violaxanthin is a sufficient precursor for ABA production in vivo.
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Affiliation(s)
- Hadar Neuman
- Department of Genetics, Alexander Silberman Institute of Life Sciences, Jerusalem, 91904, Israel
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40
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Zhang J, Ruhlman TA, Mower JP, Jansen RK. Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing. BMC PLANT BIOLOGY 2013; 13:228. [PMID: 24373163 PMCID: PMC3880972 DOI: 10.1186/1471-2229-13-228] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 12/20/2013] [Indexed: 05/24/2023]
Abstract
BACKGROUND Organelle genomes of Geraniaceae exhibit several unusual evolutionary phenomena compared to other angiosperm families including accelerated nucleotide substitution rates, widespread gene loss, reduced RNA editing, and extensive genomic rearrangements. Since most organelle-encoded proteins function in multi-subunit complexes that also contain nuclear-encoded proteins, it is likely that the atypical organellar phenomena affect the evolution of nuclear genes encoding organellar proteins. To begin to unravel the complex co-evolutionary interplay between organellar and nuclear genomes in this family, we sequenced nuclear transcriptomes of two species, Geranium maderense and Pelargonium x hortorum. RESULTS Normalized cDNA libraries of G. maderense and P. x hortorum were used for transcriptome sequencing. Five assemblers (MIRA, Newbler, SOAPdenovo, SOAPdenovo-trans [SOAPtrans], Trinity) and two next-generation technologies (454 and Illumina) were compared to determine the optimal transcriptome sequencing approach. Trinity provided the highest quality assembly of Illumina data with the deepest transcriptome coverage. An analysis to determine the amount of sequencing needed for de novo assembly revealed diminishing returns of coverage and quality with data sets larger than sixty million Illumina paired end reads for both species. The G. maderense and P. x hortorum transcriptomes contained fewer transcripts encoding the PLS subclass of PPR proteins relative to other angiosperms, consistent with reduced mitochondrial RNA editing activity in Geraniaceae. In addition, transcripts for all six plastid targeted sigma factors were identified in both transcriptomes, suggesting that one of the highly divergent rpoA-like ORFs in the P. x hortorum plastid genome is functional. CONCLUSIONS The findings support the use of the Illumina platform and assemblers optimized for transcriptome assembly, such as Trinity or SOAPtrans, to generate high-quality de novo transcriptomes with broad coverage. In addition, results indicated no major improvements in breadth of coverage with data sets larger than six billion nucleotides or when sampling RNA from four tissue types rather than from a single tissue. Finally, this work demonstrates the power of cross-compartmental genomic analyses to deepen our understanding of the correlated evolution of the nuclear, plastid, and mitochondrial genomes in plants.
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Affiliation(s)
- Jin Zhang
- Department of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, 205 W. 24th St. Stop C0930, Austin, TX 78712, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, 205 W. 24th St. Stop C0930, Austin, TX 78712, USA
| | - Jeffrey P Mower
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Robert K Jansen
- Department of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, 205 W. 24th St. Stop C0930, Austin, TX 78712, USA
- Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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41
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Pyo YJ, Kwon KC, Kim A, Cho MH. Seedling Lethal1, a pentatricopeptide repeat protein lacking an E/E+ or DYW domain in Arabidopsis, is involved in plastid gene expression and early chloroplast development. PLANT PHYSIOLOGY 2013; 163:1844-58. [PMID: 24144791 PMCID: PMC3850184 DOI: 10.1104/pp.113.227199] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Chloroplasts are the site of photosynthesis and the biosynthesis of essential metabolites, including amino acids, fatty acids, and secondary metabolites. It is known that many seedling-lethal mutants are impaired in chloroplast function or development, indicating the development of functional chloroplast is essential for plant growth and development. Here, we isolated a novel transfer DNA insertion mutant, dubbed sel1 (for seedling lethal1), that exhibited a pigment-defective and seedling-lethal phenotype with a disrupted pentatricopeptide repeat (PPR) gene. Sequence analysis revealed that SEL1 is a member of the PLS subgroup, which is lacking known E/E(+) or DYW domains at the C terminus, in the PLS subfamily of the PPR protein family containing a putative N-terminal transit peptide and 14 putative PPR or PPR-like motifs. Confocal microscopic analysis showed that the SEL1-green fluorescent protein fusion protein is localized in chloroplasts. Transmission electron microscopic analysis revealed that the sel1 mutant is impaired in the etioplast, as well as in chloroplast development. In sel1 mutants, plastid-encoded proteins involved in photosynthesis were rarely detected due to the lack of the corresponding transcripts. Furthermore, transcript profiles of plastid genes revealed that, in sel1 mutants, the transcript levels of plastid-encoded RNA polymerase-dependent genes were greatly reduced, but those of nuclear-encoded RNA polymerase-dependent genes were increased or not changed. Additionally, the RNA editing of two editing sites of the acetyl-CoA carboxylase beta subunit gene transcripts in the sel1 mutant was compromised, though it is not directly connected with the sel1 mutant phenotype. Our results demonstrate that SEL1 is involved in the regulation of plastid gene expression required for normal chloroplast development.
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MESH Headings
- Amino Acid Sequence
- Arabidopsis/genetics
- Arabidopsis/growth & development
- Arabidopsis/ultrastructure
- Arabidopsis Proteins/chemistry
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Base Sequence
- Blotting, Northern
- Chloroplast Proteins/chemistry
- Chloroplast Proteins/genetics
- Chloroplast Proteins/metabolism
- Chloroplasts/genetics
- Chloroplasts/ultrastructure
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Genes, Plant
- Molecular Sequence Data
- Molecular Weight
- Multiprotein Complexes/metabolism
- Mutation/genetics
- Photosynthesis
- Protein Structure, Tertiary
- RNA Editing/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Transfer/metabolism
- Repetitive Sequences, Amino Acid
- Ribosomes/metabolism
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42
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Hayes ML, Giang K, Berhane B, Mulligan RM. Identification of two pentatricopeptide repeat genes required for RNA editing and zinc binding by C-terminal cytidine deaminase-like domains. J Biol Chem 2013; 288:36519-29. [PMID: 24194514 DOI: 10.1074/jbc.m113.485755] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Many transcripts expressed from plant organelle genomes are modified by C-to-U RNA editing. Nuclear encoded pentatricopeptide repeat (PPR) proteins are required as RNA binding specificity determinants in the RNA editing mechanism. Bioinformatic analysis has shown that most of the Arabidopsis PPR proteins necessary for RNA editing events include a C-terminal portion that shares structural characteristics with a superfamily of deaminases. The DYW deaminase domain includes a highly conserved zinc binding motif that shares characteristics with cytidine deaminases. The Arabidopsis PPR genes, ELI1 and DOT4, both have DYW deaminase domains and are required for single RNA editing events in chloroplasts. The ELI1 DYW deaminase domain was expressed as a recombinant protein in Escherichia coli and was shown to bind two zinc atoms per polypeptide. Thus, the DYW deaminase domain binds a zinc metal ion, as expected for a cytidine deaminase, and is potentially the catalytic component of an editing complex. Genetic complementation experiments demonstrate that large portions of the DYW deaminase domain of ELI1 may be eliminated, but the truncated genes retain the ability to restore editing site conversion in a mutant plant. These results suggest that the catalytic activity can be supplied in trans by uncharacterized protein(s) of the editosome.
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Ichinose M, Sugita C, Yagi Y, Nakamura T, Sugita M. Two DYW Subclass PPR Proteins are Involved in RNA Editing of ccmFc and atp9 Transcripts in the Moss Physcomitrella patens: First Complete Set of PPR Editing Factors in Plant Mitochondria. ACTA ACUST UNITED AC 2013; 54:1907-16. [DOI: 10.1093/pcp/pct132] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Tseng CC, Lee CJ, Chung YT, Sung TY, Hsieh MH. Differential regulation of Arabidopsis plastid gene expression and RNA editing in non-photosynthetic tissues. PLANT MOLECULAR BIOLOGY 2013; 82:375-92. [PMID: 23645360 DOI: 10.1007/s11103-013-0069-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 04/27/2013] [Indexed: 05/17/2023]
Abstract
RNA editing is one of the post-transcriptional processes that commonly occur in plant plastids and mitochondria. In Arabidopsis, 34 C-to-U RNA editing events, affecting transcripts of 18 plastid genes, have been identified. Here, we examined the editing and expression of these transcripts in different organs, and in green and non-green seedlings (etiolated, cia5-2, ispF and ispG albino mutants, lincomycin-, and norflurazon-treated). The editing efficiency of Arabidopsis plastid transcripts varies from site to site, and may be specifically regulated in different tissues. Steady state levels of plastid transcripts are low or undetectable in etiolated seedlings, but most editing sites are edited with efficiencies similar to those observed in green seedlings. By contrast, the editing of some sites is completely lost or significantly reduced in other non-green tissues; for instance, the editing of ndhB-149, ndhB-1255, and ndhD-2 is completely lost in roots and in lincomycin-treated seedlings. The editing of ndhD-2 is also completely lost in albino mutants and norflurazon-treated seedlings. However, matK-640 is completely edited, and accD-794, atpF-92, psbE-214, psbF-77, psbZ-50, and rps14-50 are completely or highly edited in both green and non-green tissues. In addition, the expression of nucleus-encoded RNA polymerase dependent transcripts is specifically induced by lincomycin, and the splicing of ndhB transcripts is significantly reduced in the albino mutants and inhibitor-treated seedlings. Our results indicate that plastid gene expression, and the splicing and editing of plastid transcripts are specifically and differentially regulated in various types of non-green tissues.
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Affiliation(s)
- Ching-Chih Tseng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Bentolila S, Oh J, Hanson MR, Bukowski R. Comprehensive high-resolution analysis of the role of an Arabidopsis gene family in RNA editing. PLoS Genet 2013; 9:e1003584. [PMID: 23818871 PMCID: PMC3688494 DOI: 10.1371/journal.pgen.1003584] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 05/01/2013] [Indexed: 11/19/2022] Open
Abstract
In flowering plants, mitochondrial and chloroplast mRNAs are edited by C-to-U base modification. In plant organelles, RNA editing appears to be generally a correcting mechanism that restores the proper function of the encoded product. Members of the Arabidopsis RNA editing-Interacting Protein (RIP) family have been recently shown to be essential components of the plant editing machinery. We report the use of a strand- and transcript-specific RNA-seq method (STS-PCRseq) to explore the effect of mutation or silencing of every RIP gene on plant organelle editing. We confirm RIP1 to be a major editing factor that controls the editing extent of 75% of the mitochondrial sites and 20% of the plastid C targets of editing. The quantitative nature of RNA sequencing allows the precise determination of overlapping effects of RIP factors on RNA editing. Over 85% of the sites under the influence of RIP3 and RIP8, two moderately important mitochondrial factors, are also controlled by RIP1. Previously uncharacterized RIP family members were found to have only a slight effect on RNA editing. The preferential location of editing sites controlled by RIP7 on some transcripts suggests an RNA metabolism function for this factor other than editing. In addition to a complete characterization of the RIP factors for their effect on RNA editing, our study highlights the potential of RNA-seq for studying plant organelle editing. Unlike previous attempts to use RNA-seq to analyze RNA editing extent, our methodology focuses on sequencing of organelle cDNAs corresponding to known transcripts. As a result, the depth of coverage of each editing site reaches unprecedented values, assuring a reliable measurement of editing extent and the detection of numerous new sites. This strategy can be applied to the study of RNA editing in any organism. RNA editing is a co- or post-transcriptional RNA processing reaction that changes the nucleotide sequence of the RNA substrate. In flowering plants, mRNA editing is confined to organelle transcripts, altering cytidine to uridine. Recently, some members of a small Arabidopsis gene family were found to be important for editing of chloroplast and mitochondrial transcripts. Several methods have been developed to measure the amount of edited transcripts at specific Cs, but most of these methods either lack sensitivity or are unable to determine the number and location of edited Cs in a particular transcript. While sensitive assays have been previously developed, they are costly and labor-intensive precluding their use on a large-scale. In order to characterize the role of an entire gene family in RNA editing, we have successfully adapted RNA sequencing technology to characterize the effect of mutation and silencing of family members on organelle RNA editing. Our method to measure editing extent is sensitive, reliable, and cost-effective. As well as detecting additional family members that play a role in RNA editing, we have detected numerous new editing sites. Our strategy should benefit the investigation of RNA editing in any organism.
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Affiliation(s)
- Stéphane Bentolila
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, New York, USA.
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Bentolila S, Babina AM, Germain A, Hanson MR. Quantitative trait locus mapping identifies REME2, a PPR-DYW protein required for editing of specific C targets in Arabidopsis mitochondria. RNA Biol 2013; 10:1520-5. [PMID: 23807026 DOI: 10.4161/rna.25297] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Targeted RNA editing by C-to-U alteration occurs at hundreds of sites in the mitochondrial transcriptome of flowering plants. By using natural variation and positional cloning on a population of Arabidopsis recombinant inbred lines between the ecotypes Col and Ler, we found that two of these occurrences involve the Arabidopsis PPR-DYW protein REME2 (Required for Efficiency of Mitochondrial Editing2). The analysis of a knockdown mutant along with silenced tissues confirms the specificity of REME2 for both sites located in mitochondrial ribosomal protein genes (rps3-1534 and rps4-175). The conservation level of both cis elements is relatively high, as is the amino acid conservation among flowering plants for both genes in that location, underlining the importance of these editing events and REME2.
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Affiliation(s)
- Stéphane Bentolila
- Department of Molecular Biology and Genetics; Cornell University; Ithaca, NY USA
| | - Arianne M Babina
- Department of Molecular Biology and Genetics; Cornell University; Ithaca, NY USA
| | - Arnaud Germain
- Department of Molecular Biology and Genetics; Cornell University; Ithaca, NY USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics; Cornell University; Ithaca, NY USA
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Yagi Y, Tachikawa M, Noguchi H, Satoh S, Obokata J, Nakamura T. Pentatricopeptide repeat proteins involved in plant organellar RNA editing. RNA Biol 2013; 10:1419-25. [PMID: 23669716 PMCID: PMC3858424 DOI: 10.4161/rna.24908] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
C-to-U RNA editing has been widely observed in organellar RNAs in terrestrial plants. Recent research has revealed the significance of a large, plant-specific family of pentatricopeptide repeat (PPR) proteins for RNA editing and other RNA processing events in plant mitochondria and chloroplasts. PPR protein is a sequence-specific RNA-binding protein that identifies specific C residues for editing. Discovery of the RNA recognition code for PPR motifs, including verification and prediction of the individual RNA editing site and its corresponding PPR protein, expanded our understanding of the molecular function of PPR proteins in plant organellar RNA editing. Using this knowledge and the co-expression database, we have identified two new PPR proteins that mediate chloroplast RNA editing. Further, computational target assignment using the PPR RNA recognition codes suggests a distinct, unknown mode-of-action, by which PPR proteins serve a function beyond site recognition in RNA editing.
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Affiliation(s)
- Yusuke Yagi
- Faculty of Agriculture; Kyushu University; Fukuoka, Japan
| | - Makoto Tachikawa
- Graduate School of Life and Environmental Sciences; Kyoto Prefectural University; Kyoto, Japan
| | - Hisayo Noguchi
- Faculty of Agriculture; Kyushu University; Fukuoka, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environmental Sciences; Kyoto Prefectural University; Kyoto, Japan
| | - Junichi Obokata
- Graduate School of Life and Environmental Sciences; Kyoto Prefectural University; Kyoto, Japan
| | - Takahiro Nakamura
- Faculty of Agriculture; Kyushu University; Fukuoka, Japan; Biotron Application Center; Kyushu University; Fukuoka, Japan
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Germain A, Hotto AM, Barkan A, Stern DB. RNA processing and decay in plastids. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:295-316. [PMID: 23536311 DOI: 10.1002/wrna.1161] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Plastids were derived through endosymbiosis from a cyanobacterial ancestor, whose uptake was followed by massive gene transfer to the nucleus, resulting in the compact size and modest coding capacity of the extant plastid genome. Plastid gene expression is essential for plant development, but depends on nucleus-encoded proteins recruited from cyanobacterial or host-cell origins. The plastid genome is heavily transcribed from numerous promoters, giving posttranscriptional events a critical role in determining the quantity and sizes of accumulating RNA species. The major events reviewed here are RNA editing, which restores protein conservation or creates correct open reading frames by converting C residues to U, RNA splicing, which occurs both in cis and trans, and RNA cleavage, which relies on a variety of exoribonucleases and endoribonucleases. Because the RNases have little sequence specificity, they are collectively able to remove extraneous RNAs whose ends are not protected by RNA secondary structures or sequence-specific RNA-binding proteins (RBPs). Other plastid RBPs, largely members of the helical-repeat superfamily, confer specificity to editing and splicing reactions. The enzymes that catalyze RNA processing are also the main actors in RNA decay, implying that these antagonistic roles are optimally balanced. We place the actions of RBPs and RNases in the context of a recent proteomic analysis that identifies components of the plastid nucleoid, a protein-DNA complex with multiple roles in gene expression. These results suggest that sublocalization and/or concentration gradients of plastid proteins could underpin the regulation of RNA maturation and degradation.
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An RNA recognition motif-containing protein is required for plastid RNA editing in Arabidopsis and maize. Proc Natl Acad Sci U S A 2013; 110:E1169-78. [PMID: 23487777 DOI: 10.1073/pnas.1220162110] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plant RNA editing modifies cytidines (C) to uridines (U) at specific sites in the transcripts of both mitochondria and plastids. Specific targeting of particular Cs is achieved by pentatricopeptide proteins that recognize cis elements upstream of the C that is edited. Members of the RNA-editing factor interacting protein (RIP) family in Arabidopsis have recently been shown to be essential components of the plant editosome. We have identified a gene that contains a pair of truncated RIP domains (RIP-RIP). Unlike any previously described RIP family member, the encoded protein carries an RNA recognition motif (RRM) at its C terminus and has therefore been named Organelle RRM protein 1 (ORRM1). ORRM1 is an essential plastid editing factor; in Arabidopsis and maize mutants, RNA editing is impaired at particular sites, with an almost complete loss of editing for 12 sites in Arabidopsis and 9 sites in maize. Transfection of Arabidopsis orrm1 mutant protoplasts with constructs encoding a region encompassing the RIP-RIP domain or a region spanning the RRM domain of ORRM1 demonstrated that the RRM domain is sufficient for the editing function of ORRM1 in vitro. According to a yeast two-hybrid assay, ORRM1 interacts selectively with pentatricopeptide transfactors via its RIP-RIP domain. Phylogenetic analysis reveals that the RRM in ORRM1 clusters with a clade of RRM proteins that are targeted to organelles. Taken together, these results suggest that other members of the ORRM family may likewise function in RNA editing.
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Verbitskiy D, Zehrmann A, Härtel B, Brennicke A, Takenaka M. Two related RNA-editing proteins target the same sites in mitochondria of Arabidopsis thaliana. J Biol Chem 2012; 287:38064-72. [PMID: 22977245 DOI: 10.1074/jbc.m112.397992] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The facilitators for specific cytosine-to-uridine RNA-editing events in plant mitochondria and plastids are pentatricopeptide repeat (PPR)-containing proteins with specific additional C-terminal domains. Here we report the related PPR proteins mitochondrial editing factor 8 (MEF8) and MEF8S with only five such repeats each to be both involved in RNA editing at the same two sites in mitochondria of Arabidopsis thaliana. Mutants of MEF8 show diminished editing in leaves but not in pollen, whereas mutants of the related protein MEF8S show reduced RNA editing in pollen but not in leaves. Overexpressed MEF8 or MEF8S both increase editing at the two target sites in a mef8 mutant. Double mutants of MEF8 and MEF8S are not viable although both identified target sites are in mRNAs for nonessential proteins. This suggests that MEF8 and MEF8S may have other essential functions beyond these two editing sites in complex I mRNAs.
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