1
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Bentolila S, Gipson AB, Kehl AJ, Hamm LN, Hayes ML, Mulligan RM, Hanson MR. A RanBP2-type zinc finger protein functions in intron splicing in Arabidopsis mitochondria and is involved in the biogenesis of respiratory complex I. Nucleic Acids Res 2021; 49:3490-3506. [PMID: 33660772 PMCID: PMC8034646 DOI: 10.1093/nar/gkab066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/22/2021] [Accepted: 02/25/2021] [Indexed: 11/14/2022] Open
Abstract
The RanBP2 zinc finger (Znf) domain is a prevalent domain that mediates protein interaction and RNA binding. In Arabidopsis, a clade of four RanBP2 Znf-containing proteins, named the Organelle Zinc (OZ) finger family, are known or predicted to be targeted to either the mitochondria or the plastids. Previously we reported that OZ1 is absolutely required for the editing of 14 sites in chloroplasts. We now have investigated the function of OZ2, whose null mutation is embryo lethal. We rescued the null mutant by expressing wild-type OZ2 under the control of the seed-specific ABSCISIC ACID-INSENSITIVE3 (ABI3) promoter. Rescued mutant plants exhibit severely delayed development and a distinctive morphological phenotype. Genetic and biochemical analyses demonstrated that OZ2 promotes the splicing of transcripts of several mitochondrial nad genes and rps3. The splicing defect of nad transcripts results in the destabilization of complex I, which in turn affects the respiratory ability of oz2 mutants, turning on the alternative respiratory pathway, and impacting the plant development. Protein-protein interaction assays demonstrated binding of OZ2 to several known mitochondrial splicing factors targeting the same splicing events. These findings extend the known functional repertoire of the RanBP2 zinc finger domain in nuclear splicing to include plant organelle splicing.
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Affiliation(s)
- Stéphane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Andrew B Gipson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Alexander J Kehl
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Lauren N Hamm
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Michael L Hayes
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - R Michael Mulligan
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 90032, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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2
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Yang Y, Liu X, Wang K, Li J, Zhu G, Ren S, Deng Z, Zhu B, Fu D, Qu G, Luo Y, Zhu H. Molecular and functional diversity of organelle RNA editing mediated by RNA recognition motif-containing protein ORRM4 in tomato. THE NEW PHYTOLOGIST 2020; 228:570-585. [PMID: 32473605 DOI: 10.1111/nph.16714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Plant organellar RNA editing is a distinct type of post-transcriptional RNA modification that is critical for plant development. We showed previously that the RNA editing factor SlORRM4 is required for mitochondrial function and fruit ripening in tomato (Solanum lycopersicum). However, a comprehensive atlas of the RNA editing mediated by SlORRM4 is lacking. We observed that SlORRM4 is targeted to both chloroplasts and mitochondria, and its knockout results in pale-green leaves and delayed fruit ripening. Using high-throughput sequencing, we identified 12 chloroplast editing sites and 336 mitochondrial editing sites controlled by SlORRM4, accounting for 23% of chloroplast sites in leaves and 61% of mitochondrial sites in fruits, respectively. Analysis of native RNA immunoprecipitation sequencing revealed that SlORRM4 binds to 31 RNA targets; 19 of these targets contain SlORRM4-dependent editing sites. Large-scale analysis of putative SlORRM4-interacting proteins identified SlRIP1b, a RIP/MORF protein. Moreover, functional characterization demonstrated that SlRIP1b is involved in tomato fruit ripening. Our results indicate that SlORRM4 binds to RNA targets and interacts with SlRIP1b to broadly affect RNA editing in tomato organelles. These results provide insights into the molecular and functional diversity of RNA editing factors in higher plants.
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Affiliation(s)
- Yongfang Yang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xiuying Liu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Keru Wang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Guoning Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Shuang Ren
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Zhiping Deng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, China
| | - Benzhong Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Daqi Fu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Guiqin Qu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yunbo Luo
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
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3
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Wang Y, Liu XY, Yang YZ, Huang J, Sun F, Lin J, Gu ZQ, Sayyed A, Xu C, Tan BC. Empty Pericarp21 encodes a novel PPR-DYW protein that is required for mitochondrial RNA editing at multiple sites, complexes I and V biogenesis, and seed development in maize. PLoS Genet 2019; 15:e1008305. [PMID: 31374076 PMCID: PMC6693784 DOI: 10.1371/journal.pgen.1008305] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 08/14/2019] [Accepted: 07/11/2019] [Indexed: 01/08/2023] Open
Abstract
C-to-U editing is an important event in post-transcriptional RNA processing, which converts a specific cytidine (C)-to-uridine (U) in transcripts of mitochondria and plastids. Typically, the pentatricopeptide repeat (PPR) protein, which specifies the target C residue by binding to its upstream sequence, is involved in the editing of one or a few sites. Here we report a novel PPR-DYW protein EMP21 that is associated with editing of 81 sites in maize. EMP21 is localized in mitochondria and loss of the EMP21 function severely inhibits the embryogenesis and endosperm development in maize. From a scan of 35 mitochondrial transcripts produced by the Emp21 loss-of-function mutant, the C-to-U editing was found to be abolished at five sites (nad7-77, atp1-1292, atp8-437, nad3-275 and rps4-870), while reduced at 76 sites in 21 transcripts. In most cases, the failure to editing resulted in the translation of an incorrect residue. In consequence, the mutant became deficient with respect to the assembly and activity of mitochondrial complexes I and V. As six of the decreased editing sites in emp21 overlap with the affected editing sites in emp5-1, and the editing efficiency at rpl16-458 showed a substantial reduction in the emp21-1 emp5-4 double mutant compared with the emp21-1 and emp5-4 single mutants, we explored their interaction. A yeast two hybrid assay suggested that EMP21 does not interact with EMP5, but both EMP21 and EMP5 interact with ZmMORF8. Together, these results indicate that EMP21 is a novel PPR-DYW protein required for the editing of ~17% of mitochondrial target Cs, and the editing process may involve an interaction between EMP21 and ZmMORF8 (and probably other proteins).
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Affiliation(s)
- Yong Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Xin-Yuan Liu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Yan-Zhuo Yang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Jin Huang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Feng Sun
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Jishan Lin
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhi-Qun Gu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Aqib Sayyed
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Chunhui Xu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
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4
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Takenaka M, Jörg A, Burger M, Haag S. RNA editing mutants as surrogates for mitochondrial SNP mutants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 135:310-321. [PMID: 30599308 DOI: 10.1016/j.plaphy.2018.12.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/13/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
In terrestrial plants, RNA editing converts specific cytidines to uridines in mitochondrial and plastidic transcripts. Most of these events appear to be important for proper function of organellar encoded genes, since translated proteins from edited mRNAs show higher similarity with evolutionary conserved polypeptide sequences. So far about 100 nuclear encoded proteins have been characterized as RNA editing factors in plant organelles. Respective RNA editing mutants reduce or lose editing activity at different sites and display various macroscopic phenotypes from pale or albino in the case of chloroplasts to growth retardation or even embryonic lethality. Therefore, RNA editing mutants can be a useful resource of surrogate mutants for organellar encoded genes, especially for mitochondrially encoded genes that it is so far unfeasible to manipulate. However, connections between RNA editing defects and observed phenotypes in the mutants are often hard to elucidate, since RNA editing factors often target multiple RNA sites in different genes simultaneously. In this review article, we summarize the physiological aspects of respective RNA editing mutants and discuss them as surrogate mutants for functional analysis of mitochondrially encoded genes.
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Affiliation(s)
- Mizuki Takenaka
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.
| | - Anja Jörg
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | - Matthias Burger
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | - Sascha Haag
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
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Sun Y, Huang J, Zhong S, Gu H, He S, Qu LJ. Novel DYW-type pentatricopeptide repeat (PPR) protein BLX controls mitochondrial RNA editing and splicing essential for early seed development of Arabidopsis. J Genet Genomics 2018; 45:155-168. [PMID: 29580769 DOI: 10.1016/j.jgg.2018.01.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 01/20/2018] [Indexed: 01/01/2023]
Abstract
In plants, RNA editing is a post-transcriptional process that changes specific cytidine to uridine in both mitochondria and plastids. Most pentatricopeptide repeat (PPR) proteins are involved in organelle RNA editing by recognizing specific RNA sequences. We here report the functional characterization of a PPR protein from the DYW subclass, Baili Xi (BLX), which contains five PPR motifs and a DYW domain. BLX is essential for early seed development, as plants lacking the BLX gene was embryo lethal and the endosperm failed to initiate cellularization. BLX was highly expressed in the embryo and endosperm, and the BLX protein was specifically localized in mitochondria, which is essential for BLX function. We found that BLX was required for the efficient editing of 36 editing sites in mitochondria. Moreover, BLX was involved in the splicing regulation of the fourth intron of nad1 and the first intron of nad2. The loss of BLX function impaired the mitochondrial function and increased the reactive oxygen species (ROS) level. Genetic complementation with truncated variants of BLX revealed that, in addition to the DYW domain, only the fifth PPR motif was essential for BLX function. The upstream sequences of the BLX-targeted editing sites are not conserved, suggesting that BLX serves as a novel and major mitochondrial editing factor (MEF) via a new non-RNA-interacting manner. This finding provides new insights into how a DYW-type PPR protein with fewer PPR motifs regulates RNA editing in plants.
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Affiliation(s)
- Yan Sun
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
| | - Jiaying Huang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
| | - Sheng Zhong
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
| | - Hongya Gu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China; The National Plant Gene Research Center (Beijing), Beijing 100101, China
| | - Shan He
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China.
| | - Li-Jia Qu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China; The National Plant Gene Research Center (Beijing), Beijing 100101, China.
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6
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Arenas-M A, González-Durán E, Gómez I, Burger M, Brennicke A, Takenaka M, Jordana X. The Pentatricopeptide Repeat Protein MEF31 is Required for Editing at Site 581 of the Mitochondrial tatC Transcript and Indirectly Influences Editing at Site 586 of the Same Transcript. PLANT & CELL PHYSIOLOGY 2018; 59:355-365. [PMID: 29216369 DOI: 10.1093/pcp/pcx190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/25/2017] [Indexed: 06/07/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins constitute the largest family of proteins in angiosperms, and most members are predicted to play roles in the maturation of organellar RNAs. Here we describe the novel mitochondrial editing factor 31 (MEF31), an E-PPR protein involved in editing at two close sites in the same transcript encoding subunit C of the twin-arginine translocation (tat) pathway. MEF31 is essential for editing at site tatC-581 and application of the recently proposed amino acid code for RNA recognition by PPR proteins supports the view that MEF31 directly targets this site by recognizing its cis sequence. In contrast, editing at site tatC-586 five nucleotides downstream is only partially affected in plants lacking MEF31, being restored to wild-type levels in complemented plants. Application of the amino acid code and analysis of individual RNA molecules for editing at sites 581 and 586 suggest that MEF31 does not directly target site tatC-586, and only indirectly influences editing at this site. It is likely that editing at site tatC-581 improves recognition of the site tatC-586 cis sequence by a second unknown PPR protein.
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Affiliation(s)
- Anita Arenas-M
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile
| | - Enrique González-Durán
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile
| | - Isabel Gómez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile
| | | | - Axel Brennicke
- Molekulare Botanik, Universität Ulm, D-89069 Ulm, Germany
| | | | - Xavier Jordana
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile
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7
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Hassani D, Khalid M, Bilal M, Zhang YD, Huang D. Pentatricopeptide Repeat-directed RNA Editing and Their Biomedical Applications. INT J PHARMACOL 2017. [DOI: 10.3923/ijp.2017.762.772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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8
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Multiple PPR protein interactions are involved in the RNA editing system in Arabidopsis mitochondria and plastids. Proc Natl Acad Sci U S A 2017; 114:8883-8888. [PMID: 28761003 DOI: 10.1073/pnas.1705815114] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Recent identification of several different types of RNA editing factors in plant organelles suggests complex RNA editosomes within which each factor has a different task. However, the precise protein interactions between the different editing factors are still poorly understood. In this paper, we show that the E+-type pentatricopeptide repeat (PPR) protein SLO2, which lacks a C-terminal cytidine deaminase-like DYW domain, interacts in vivo with the DYW-type PPR protein DYW2 and the P-type PPR protein NUWA in mitochondria, and that the latter enhances the interaction of the former ones. These results may reflect a protein scaffold or complex stabilization role of NUWA between E+-type PPR and DYW2 proteins. Interestingly, DYW2 and NUWA also interact in chloroplasts, and DYW2-GFP overexpressing lines show broad editing defects in both organelles, with predominant specificity for sites edited by E+-type PPR proteins. The latter suggests a coordinated regulation of organellar multiple site editing through DYW2, which probably provides the deaminase activity to E+ editosomes.
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9
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Chen X, Feng F, Qi W, Xu L, Yao D, Wang Q, Song R. Dek35 Encodes a PPR Protein that Affects cis-Splicing of Mitochondrial nad4 Intron 1 and Seed Development in Maize. MOLECULAR PLANT 2017; 10:427-441. [PMID: 27596292 DOI: 10.1016/j.molp.2016.08.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/19/2016] [Accepted: 08/26/2016] [Indexed: 05/20/2023]
Abstract
In higher plants, the splicing of organelle-encoded mRNA involves a complex collaboration with nuclear-encoded proteins. Pentatricopeptide repeat (PPR) proteins have been implicated in these RNA-protein interactions. In this study, we performed the cloning and functional characterization of maize Defective kernel 35 (Dek35). The dek35-ref mutant is a lethal-seed mutant with developmental deficiency. Dek35 was cloned through Mutator tag isolation and further confirmed by four additional independent mutant alleles. Dek35 encodes an P-type PPR protein that targets the mitochondria. The dek35 mutation causes significant reduction in the accumulation of DEK35 proteins and reduced splicing efficiency of mitochondrial nad4 intron 1. Analysis of mitochondrial complex in dek35 immature seeds indicated severe deficiency in the complex I assembly and NADH dehydrogenase activity. Transcriptome analysis of dek35 endosperm revealed enhanced expression of genes involved in the alternative respiratory pathway and extensive differentially expressed genes related to mitochondrial function and activity. Collectively, these results indicate that Dek35 encodes an PPR protein that affects the cis-splicing of mitochondrial nad4 intron 1 and is required for mitochondrial function and seed development.
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Affiliation(s)
- Xinze Chen
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Fan Feng
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Weiwei Qi
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China; Coordinated Crop Biology Research Center (CBRC), Beijing 100193, China
| | - Liming Xu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Dongsheng Yao
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Qun Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Rentao Song
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China; National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China; Coordinated Crop Biology Research Center (CBRC), Beijing 100193, China.
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10
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Hu Z, Vanderhaeghen R, Cools T, Wang Y, De Clercq I, Leroux O, Nguyen L, Belt K, Millar AH, Audenaert D, Hilson P, Small I, Mouille G, Vernhettes S, Van Breusegem F, Whelan J, Höfte H, De Veylder L. Mitochondrial Defects Confer Tolerance against Cellulose Deficiency. THE PLANT CELL 2016; 28:2276-2290. [PMID: 27543091 PMCID: PMC5059812 DOI: 10.1105/tpc.16.00540] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/08/2016] [Accepted: 08/19/2016] [Indexed: 05/03/2023]
Abstract
Because the plant cell wall provides the first line of defense against biotic and abiotic assaults, its functional integrity needs to be maintained under stress conditions. Through a phenotype-based compound screening approach, we identified a novel cellulose synthase inhibitor, designated C17. C17 administration depletes cellulose synthase complexes from the plasma membrane in Arabidopsis thaliana, resulting in anisotropic cell elongation and a weak cell wall. Surprisingly, in addition to mutations in CELLULOSE SYNTHASE1 (CESA1) and CESA3, a forward genetic screen identified two independent defective genes encoding pentatricopeptide repeat (PPR)-like proteins (CELL WALL MAINTAINER1 [CWM1] and CWM2) as conferring tolerance to C17. Functional analysis revealed that mutations in these PPR proteins resulted in defective cytochrome c maturation and activation of mitochondrial retrograde signaling, as evidenced by the induction of an alternative oxidase. These mitochondrial perturbations increased tolerance to cell wall damage induced by cellulose deficiency. Likewise, administration of antimycin A, an inhibitor of mitochondrial complex III, resulted in tolerance toward C17. The C17 tolerance of cwm2 was partially lost upon depletion of the mitochondrial retrograde regulator ANAC017, demonstrating that ANAC017 links mitochondrial dysfunction with the cell wall. In view of mitochondria being a major target of a variety of stresses, our data indicate that plant cells might modulate mitochondrial activity to maintain a functional cell wall when subjected to stresses.
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Affiliation(s)
- Zhubing Hu
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
- College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Rudy Vanderhaeghen
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Toon Cools
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Yan Wang
- Department of Botany, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora 3086, Victoria, Australia
| | - Inge De Clercq
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Olivier Leroux
- Department of Biology, Ghent University, B-9000 Gent, Belgium
| | - Long Nguyen
- Compound Screening Facility, VIB, B-9052 Gent, Belgium
| | - Katharina Belt
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Australia
| | - A Harvey Millar
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Australia
| | | | - Pierre Hilson
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
- Institut Jean-Pierre Bourgin, INRA, Centre National pour la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Australia
| | - Grégory Mouille
- Institut Jean-Pierre Bourgin, INRA, Centre National pour la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Samantha Vernhettes
- Institut Jean-Pierre Bourgin, INRA, Centre National pour la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - James Whelan
- Department of Botany, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora 3086, Victoria, Australia
| | - Herman Höfte
- Institut Jean-Pierre Bourgin, INRA, Centre National pour la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Lieven De Veylder
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
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11
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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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12
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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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13
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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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14
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Hammani K, Giegé P. RNA metabolism in plant mitochondria. TRENDS IN PLANT SCIENCE 2014; 19:380-9. [PMID: 24462302 DOI: 10.1016/j.tplants.2013.12.008] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 12/11/2013] [Accepted: 12/19/2013] [Indexed: 05/02/2023]
Abstract
Mitochondria are essential for the eukaryotic cell and are derived from the endosymbiosis of an α-proteobacterial ancestor. Compared to other eukaryotes, RNA metabolism in plant mitochondria is complex and combines bacterial-like traits with novel features that evolved in the host cell. These complex RNA processes are regulated by families of nucleus-encoded RNA-binding proteins. Transcription is particularly relaxed and is initiated from multiple promoters covering the entire genome. The variety of RNA precursors accumulating in mitochondria highlights the importance of post-transcriptional processes to determine the size and abundance of transcripts. Here we review RNA metabolism in plant mitochondria, from RNA transcription to translation, with a special focus on their unique features that are controlled by trans-factors.
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Affiliation(s)
- Kamel Hammani
- Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Philippe Giegé
- Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
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15
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Gabotti D, Caporali E, Manzotti P, Persico M, Vigani G, Consonni G. The maize pentatricopeptide repeat gene empty pericarp4 (emp4) is required for proper cellular development in vegetative tissues. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 223:25-35. [PMID: 24767112 DOI: 10.1016/j.plantsci.2014.02.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 02/21/2014] [Accepted: 02/24/2014] [Indexed: 06/03/2023]
Abstract
The empty pericarp4 (emp4) gene encodes a mitochondrion-targeted pentatricopeptide repeat (ppr) protein that is involved in the regulation of mitochondrial gene expression and is required for seed development. In homozygous mutant emp4-1 kernels the endosperm is drastically reduced and the embryo is retarded in its development and unable to germinate. With the aim of investigating the role of emp4 during post-germinative development, homozygous mutant seedlings were obtained by cultivation of excised immature embryos on a synthetic medium. In the mutants both germination frequency as well as the proportion of seedlings reaching the first and second leaf stages were reduced. The anatomy of the leaf blades and the root cortex was not affected by the mutation, however severe alterations such as the presence of empty cells or cells containing poorly organized organelles, were observed. Moreover both mitochondria and chloroplast functionality was impaired in the mutants. Our hypothesis is that mitochondrial impairment, the primary effect of the mutation, causes secondary effects on the development of other cellular organelles. Ultra-structural features of mutant leaf blade mesophyll cells are reminiscent of cells undergoing senescence. Interestingly, both structural and functional damage was less severe in seedlings grown in total darkness compared with those exposed to light, thus suggesting that the effects of the mutation are enhanced by the presence of light.
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Affiliation(s)
- Damiano Gabotti
- DISAA - Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia Università degli Studi di Milano - Via Celoria 2, 20133 Milano, Italy
| | - Elisabetta Caporali
- Dipartimento di Bioscienze, Università degli Studi di Milano - Via Celoria 26, 20133 Milano, Italy
| | - Priscilla Manzotti
- DISAA - Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia Università degli Studi di Milano - Via Celoria 2, 20133 Milano, Italy
| | - Martina Persico
- DISAA - Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia Università degli Studi di Milano - Via Celoria 2, 20133 Milano, Italy
| | - Gianpiero Vigani
- DISAA - Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia Università degli Studi di Milano - Via Celoria 2, 20133 Milano, Italy
| | - Gabriella Consonni
- DISAA - Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia Università degli Studi di Milano - Via Celoria 2, 20133 Milano, Italy.
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16
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Abstract
Plant regulatory circuits coordinating nuclear and plastid gene expression have evolved in response to external stimuli. RNA editing is one of such control mechanisms. We determined the Arabidopsis nuclear-encoded homeodomain-containing protein OCP3 is incorporated into the chloroplast, and contributes to control over the extent of ndhB transcript editing. ndhB encodes the B subunit of the chloroplast NADH dehydrogenase-like complex (NDH) involved in cyclic electron flow (CEF) around photosystem I. In ocp3 mutant strains, ndhB editing efficiency decays, CEF is impaired and disease resistance to fungal pathogens substantially enhanced, a process recapitulated in plants defective in editing plastid RNAs encoding NDH complex subunits due to mutations in previously described nuclear-encoded pentatricopeptide-related proteins (i.e. CRR21, CRR2). Furthermore, we observed that following a pathogenic challenge, wild type plants respond with editing inhibition of ndhB transcript. In parallel, rapid destabilization of the plastidial NDH complex is also observed in the plant following perception of a pathogenic cue. Therefore, NDH complex activity and plant immunity appear as interlinked processes.
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17
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Surrogate mutants for studying mitochondrially encoded functions. Biochimie 2013; 100:234-42. [PMID: 23994752 DOI: 10.1016/j.biochi.2013.08.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 08/18/2013] [Indexed: 11/24/2022]
Abstract
Although chloroplast transformation is possible in some plant species, it is extremely difficult to create or select mutations in plant mitochondrial genomes, explaining why few genetic studies of mitochondrially encoded functions exist. In recent years it has become clear that many nuclear genes encode factors with key functions in organelle gene expression, and that often their action is restricted to a single organelle gene or transcript. Mutations in one of these nuclear genes thus leads to a specific primary defect in expression of a single organelle gene, and the nuclear mutation can be used as a surrogate for a phenotypically equivalent mutation in the organelle genome. These surrogate mutations often result in defective assembly of respiratory complexes, and lead to severe phenotypes including reduced growth and fertility, or even embryo-lethality. A wide collection of such mutants is now available, and this review summarises the progress in basic knowledge of mitochondrial biogenesis they have contributed to and points out areas where this resource has not been exploited yet.
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18
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Fujii S, Sato N, Shikanai T. Mutagenesis of individual pentatricopeptide repeat motifs affects RNA binding activity and reveals functional partitioning of Arabidopsis PROTON gradient regulation3. THE PLANT CELL 2013; 25:3079-88. [PMID: 23975900 PMCID: PMC3784600 DOI: 10.1105/tpc.113.112193] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins bind RNA and act in multiple eukaryotic processes, including RNA editing, RNA stability, and translation. Here, we investigated the mechanism underlying the functional versatility of Arabidopsis thaliana proton gradient regulation3 (PGR3), a chloroplast protein harboring 27 PPR motifs. Previous studies suggested that PGR3 acts in (1) stabilization of photosynthetic electron transport L (petL) operon RNA, (2) translation of petL, and (3) translation of ndhA. We showed here that replacement of the 4th amino acid of the 12th PPR with nonpolar or charged amino acids abolished functions (1) and (2) but not (3) of PGR3 by compromising the function of this specific PPR. This discovery enabled us to knock out the RNA binding ability of individual PPR motifs. Consequently, we showed that the 16 N-terminal PPRs were sufficient for function (1) via sequence-specific RNA binding, whereas the 11 C-terminal motifs were essential for functions (2) and (3) by activating translation. We also clarified that the 14th amino acid of the 12th PPR should be positively charged to make the PPR functionally active. Our finding opens up the possibility of selectively manipulating the functions of PPR proteins.
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Affiliation(s)
- Sota Fujii
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Nozomi Sato
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0076, Japan
- Address correspondence to
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19
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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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20
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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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21
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Liu YJ, Xiu ZH, Meeley R, Tan BC. Empty pericarp5 encodes a pentatricopeptide repeat protein that is required for mitochondrial RNA editing and seed development in maize. THE PLANT CELL 2013; 25:868-83. [PMID: 23463776 PMCID: PMC3634694 DOI: 10.1105/tpc.112.106781] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Revised: 12/28/2012] [Accepted: 02/15/2013] [Indexed: 05/18/2023]
Abstract
In flowering plants, RNA editing is a posttranscriptional mechanism that converts specific cytidines to uridines in both mitochondrial and plastidial transcripts, altering the information encoded by these genes. Here, we report the molecular characterization of the empty pericarp5 (emp5) mutants in maize (Zea mays). Null mutation of Emp5 results in abortion of embryo and endosperm development at early stages. Emp5 encodes a mitochondrion-targeted DYW subgroup pentatricopeptide repeat (PPR) protein. Analysis of the mitochondrial transcripts revealed that loss of the EMP5 function abolishes the C-to-U editing of ribosomal protein L16 at the rpl16-458 site (100% edited in the wild type), decreases the editing at nine sites in NADH dehydrogenase9 (nad9), cytochrome c oxidase3 (cox3), and ribosomal protein S12 (rps12), and surprisingly increases the editing at five sites of ATP synthase F0 subunit a (atp6), apocytochrome b (cob), nad1, and rpl16. Mutant EMP5-4 lacking the E+ and DYW domains still retains the substrate specificity and editing function, only at reduced efficiency. This suggests that the E+ and DYW domains of EMP5 are not essential to the EMP5 editing function but are necessary for efficiency. Analysis of the ortholog in rice (Oryza sativa) indicates that rice EMP5 has a conserved function in C-to-U editing of the rice mitochondrial rpl16-458 site. EMP5 knockdown expression in transgenics resulted in slow growth and defective seeds. These results demonstrate that Emp5 encodes a PPR-DYW protein that is required for the editing of multiple transcripts in mitochondria, and the editing events, particularly the C-to-U editing at the rpl16-458 site, are critical to the mitochondrial functions and, hence, to seed development in maize.
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Affiliation(s)
- Yu-Jun Liu
- State Key Lab of Agrobiotechnology, Institute of Plant Molecular Biology and Agrobiotechnology, School of Life Science, Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Zhi-Hui Xiu
- State Key Lab of Agrobiotechnology, Institute of Plant Molecular Biology and Agrobiotechnology, School of Life Science, Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | | | - Bao-Cai Tan
- State Key Lab of Agrobiotechnology, Institute of Plant Molecular Biology and Agrobiotechnology, School of Life Science, Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- Address correspondence to
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22
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Stoll B, Stoll K, Steinhilber J, Jonietz C, Binder S. Mitochondrial transcript length polymorphisms are a widespread phenomenon in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2013; 81:221-233. [PMID: 23225154 DOI: 10.1007/s11103-012-9993-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 11/27/2012] [Indexed: 05/27/2023]
Abstract
Natural genetic variation affects development, physiology, biochemical properties as well as mitochondrial transcripts of the model species Arabidopsis thaliana (Arabidopsis). In a previous study, we identified mitochondrial transcript end polymorphisms in Arabidopsis accessions Columbia, C24 and Landsberg erecta. The polymorphic transcript species could either be assigned to differences in the mitochondrial DNA or to natural genetic variation in the nucleus. To analyze the distribution and to identify additional 5' end polymorphisms we now analyzed 19 mitochondrial transcription units in 26 different accessions. We found additional 5' end polymorphisms indicating that such transcript length differences are a widespread phenomenon in Arabidopsis. The new polymorphisms affect cox1, cox2, nad2 as well nad3-rps12 transcript species. While the cox2 polymorphism can be attributed to a recombination event in the mitochondrial DNA, the nad2 transcript polymorphism is linked to differences in the nuclear DNA. A complex pattern is found for nad3-rps12 mRNA whose 5' ends differ between several accessions. These new polymorphisms provide an important basis for a more detailed characterization of mitochondrial 5' end processing.
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MESH Headings
- 5' Untranslated Regions/genetics
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Cell Nucleus/genetics
- Cells, Cultured
- DNA, Mitochondrial/genetics
- DNA, Plant/genetics
- Gene Expression Regulation, Plant
- Genetic Variation
- Genotype
- Mitochondria/genetics
- Mitochondria/metabolism
- Polymorphism, Genetic
- RNA Processing, Post-Transcriptional
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Mitochondrial
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Recombination, Genetic
- Seedlings/genetics
- Seedlings/metabolism
- Sequence Analysis, DNA
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Affiliation(s)
- Birgit Stoll
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069 Ulm, Germany
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23
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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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24
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Zhu Q, Dugardeyn J, Zhang C, Takenaka M, Kühn K, Craddock C, Smalle J, Karampelias M, Denecke J, Peters J, Gerats T, Brennicke A, Eastmond P, Meyer EH, Van Der Straeten D. SLO2, a mitochondrial pentatricopeptide repeat protein affecting several RNA editing sites, is required for energy metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:836-49. [PMID: 22540321 DOI: 10.1111/j.1365-313x.2012.05036.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins belong to a family of approximately 450 members in Arabidopsis, of which few have been characterized. We identified loss of function alleles of SLO2, defective in a PPR protein belonging to the E+ subclass of the P-L-S subfamily. slo2 mutants are characterized by retarded leaf emergence, restricted root growth, and late flowering. This phenotype is enhanced in the absence of sucrose, suggesting a defect in energy metabolism. The slo2 growth retardation phenotypes are largely suppressed by supplying sugars or increasing light dosage or the concentration of CO₂. The SLO2 protein is localized in mitochondria. We identified four RNA editing defects and reduced editing at three sites in slo2 mutants. The resulting amino acid changes occur in four mitochondrial proteins belonging to complex I of the electron transport chain. Both the abundance and activity of complex I are highly reduced in the slo2 mutants, as well as the abundance of complexes III and IV. Moreover, ATP, NAD+, and sugar contents were much lower in the mutants. In contrast, the abundance of alternative oxidase was significantly enhanced. We propose that SLO2 is required for carbon energy balance in Arabidopsis by maintaining the abundance and/or activity of complexes I, III, and IV of the mitochondrial electron transport chain.
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Affiliation(s)
- Qiang Zhu
- Laboratory of Functional Plant Biology, Department of Physiology, Ghent University, K L Ledeganckstraat 35, B-9000 Ghent, Belgium
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25
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Manavski N, Guyon V, Meurer J, Wienand U, Brettschneider R. An essential pentatricopeptide repeat protein facilitates 5' maturation and translation initiation of rps3 mRNA in maize mitochondria. THE PLANT CELL 2012; 24:3087-105. [PMID: 22773745 PMCID: PMC3426134 DOI: 10.1105/tpc.112.099051] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are members of one of the largest nucleus-encoded protein families in plants. Here, we describe the previously uncharacterized maize (Zea mays) PPR gene, MPPR6, which was isolated from a Mutator-induced collection of maize kernel mutants by a cDNA-based forward genetic approach. Identification of a second mutant allele and cosegregation analysis confirmed correlation with the mutant phenotype. Histological investigations revealed that the mutation coincides with abnormities in the transfer cell layer, retardation of embryo development, and a considerable reduction of starch level. The function of MPPR6 is conserved across a wide phylogenetic distance as revealed by heterologous complementation of the Arabidopsis thaliana mutant in the orthologous APPR6 gene. MPPR6 appeared to be exclusively present in mitochondria. RNA coimmunoprecipitation and in vitro binding studies revealed a specific physical interaction of MPPR6 with the 5' untranslated region of ribosomal protein S3 (rps3) mRNA. Mapping of transcript termini showed specifically extended rps3 5' ends in the mppr6 mutant. Considerable reduction of mitochondrial translation was observed, indicating loss of RPS3 function. This is consistent with the appearance of truncated RPS3 protein lacking the N terminus in mppr6. Our results suggest that MPPR6 is directly involved in 5' maturation and translation initiation of rps3 mRNA.
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Affiliation(s)
- Nikolay Manavski
- Biozentrum Klein Flottbek und Botanischer Garten, Universität Hamburg, 22609 Hamburg, Germany
- Biozentrum der Ludwig-Maximillians-Universität München, Plant Molecular Biology/Botany, 82152 Planegg-Martinsried, Germany
| | - Virginie Guyon
- Cereal Genetics and Genomics, Biogemma Société par Actions Simplifiées, 63720 Chappes, France
| | - Jörg Meurer
- Biozentrum der Ludwig-Maximillians-Universität München, Plant Molecular Biology/Botany, 82152 Planegg-Martinsried, Germany
| | - Udo Wienand
- Biozentrum Klein Flottbek und Botanischer Garten, Universität Hamburg, 22609 Hamburg, Germany
| | - Reinhold Brettschneider
- Biozentrum Klein Flottbek und Botanischer Garten, Universität Hamburg, 22609 Hamburg, Germany
- Address correspondence to
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RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing. Proc Natl Acad Sci U S A 2012; 109:E1453-61. [PMID: 22566615 DOI: 10.1073/pnas.1121465109] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Transcripts of plant organelle genes are modified by cytidine-to-uridine (C-to-U) RNA editing, often changing the encoded amino acid predicted from the DNA sequence. Members of the PLS subclass of the pentatricopeptide repeat (PPR) motif-containing family are site-specific recognition factors for either chloroplast or mitochondrial C targets of editing. However, other than PPR proteins and the cis-elements on the organelle transcripts, no other components of the editing machinery in either organelle have previously been identified. The Arabidopsis chloroplast PPR protein Required for AccD RNA Editing 1 (RARE1) specifies editing of a C in the accD transcript. RARE1 was detected in a complex of >200 kDa. We immunoprecipitated epitope-tagged RARE1, and tandem MS/MS analysis identified a protein of unknown function lacking PPR motifs; we named it RNA-editing factor interacting protein 1 (RIP1). Yeast two-hybrid analysis confirmed RIP1 interaction with RARE1, and RIP1-GFP fusions were found in both chloroplasts and mitochondria. Editing assays for all 34 known Arabidopsis chloroplast targets in a rip1 mutant revealed altered efficiency of 14 editing events. In mitochondria, 266 editing events were found to have reduced efficiency, with major loss of editing at 108 C targets. Virus-induced gene silencing of RIP1 confirmed the altered editing efficiency. Transient introduction of a WT RIP1 allele into rip1 improved the defective RNA editing. The presence of RIP1 in a protein complex along with chloroplast editing factor RARE1 indicates that RIP1 is an important component of the RNA editing apparatus that acts on many chloroplast and mitochondrial C targets.
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Yuan H, Liu D. Functional disruption of the pentatricopeptide protein SLG1 affects mitochondrial RNA editing, plant development, and responses to abiotic stresses in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:432-44. [PMID: 22248025 DOI: 10.1111/j.1365-313x.2011.04883.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Land plants contain a large family of genes that encode for pentatricopeptide (PPR) proteins. To date, few of these PPR proteins have been functionally characterized. In this study, we have analyzed an Arabidopsis mutant, slg1, which exhibits slow growth and delayed development. In addition, slg1 shows an enhanced response to ABA and increased tolerance to drought stress. The SLG1 gene encodes a PPR protein that is localized in mitochondria. In the slg1 mutant, RNA editing in a single site of the mitochondrial transcript nad3 is abolished. nad3 is a subunit of complex I of the electron transport chain in mitochondria. As a consequence, the NADH dehydrogenase activity of complex I in slg1 is strongly impaired and production of ATP is reduced. When responding to ABA treatment, slg1 accumulates more H(2) O(2) in its guard cells than the wild type. The slg1 mutant also has an increased expression of genes involved in the alternative respiratory pathway, which may compensate for the disrupted function of complex I and help scavenge the excess accumulation of H(2) O(2). Our functional characterization of the slg1 mutant revealed a putative link between mitochondrial RNA editing and plant responses to abiotic stress.
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Affiliation(s)
- Hui Yuan
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
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Okuda K, Shikanai T. A pentatricopeptide repeat protein acts as a site-specificity factor at multiple RNA editing sites with unrelated cis-acting elements in plastids. Nucleic Acids Res 2012; 40:5052-64. [PMID: 22362750 PMCID: PMC3367199 DOI: 10.1093/nar/gks164] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In plant organelles, RNA editing alters specific cytidine residues to uridine in transcripts. All of the site-specificity factors of RNA editing identified so far are pentatricopeptide repeat (PPR) proteins. A defect in a specific PPR protein often impairs RNA editing at multiple sites, at which the cis-acting elements are not highly conserved. The molecular mechanism for sharing a single PPR protein over multiple sites is still unclear. We focused here on the PPR proteins OTP82 and CRR22, the putative target elements of which are, respectively, partially and barely conserved. Recombinant OTP82 specifically bound to the −15 to 0 regions of its target sites. Recombinant CRR22 specifically bound to the −20 to 0 regions of the ndhB-7 and ndhD-5 sites and to the −17 to 0 region of the rpoB-3 site. Taking this information together with the genetic data, we conclude that OTP82 and CRR22 act as site-specificity factors at multiple sites in plastids. In addition, the high-affinity binding of CRR22 to unrelated cis-acting elements suggests that only certain specific nucleotides in a cis-acting element are sufficient for high-affinity binding of a PPR protein. The cis-acting elements can therefore be rather divergent and still be recognized by a single PPR protein.
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Affiliation(s)
- Kenji Okuda
- Department of Life Science, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo 112-8551, Japan.
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Sosso D, Mbelo S, Vernoud V, Gendrot G, Dedieu A, Chambrier P, Dauzat M, Heurtevin L, Guyon V, Takenaka M, Rogowsky PM. PPR2263, a DYW-Subgroup Pentatricopeptide repeat protein, is required for mitochondrial nad5 and cob transcript editing, mitochondrion biogenesis, and maize growth. THE PLANT CELL 2012; 24:676-91. [PMID: 22319053 PMCID: PMC3315240 DOI: 10.1105/tpc.111.091074] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
RNA editing plays an important role in organelle gene expression in various organisms, including flowering plants, changing the nucleotide information at precise sites. Here, we present evidence that the maize (Zea mays) nuclear gene Pentatricopeptide repeat 2263 (PPR2263) encoding a DYW domain-containing PPR protein is required for RNA editing in the mitochondrial NADH dehydrogenase5 (nad5) and cytochrome b (cob) transcripts at the nad5-1550 and cob-908 sites, respectively. Its putative ortholog, MITOCHONDRIAL EDITING FACTOR29, fulfills the same role in Arabidopsis thaliana. Both the maize and the Arabidopsis proteins show preferential localization to mitochondria but are also detected in chloroplasts. In maize, the corresponding ppr2263 mutation causes growth defects in kernels and seedlings. Embryo and endosperm growth are reduced, leading to the production of small but viable kernels. Mutant plants have narrower and shorter leaves, exhibit a strong delay in flowering time, and generally do not reach sexual maturity. Whereas mutant chloroplasts do not have major defects, mutant mitochondria lack complex III and are characterized by a compromised ultrastructure, increased transcript levels, and the induction of alternative oxidase. The results suggest that mitochondrial RNA editing at the cob-908 site is necessary for mitochondrion biogenesis, cell division, and plant growth in maize.
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Affiliation(s)
- Davide Sosso
- University of Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 879 Reproduction et Développement des Plantes, F-69364 Lyon, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5667 Reproduction et Développement des Plantes, F-69364 Lyon, France
| | - Sylvie Mbelo
- University of Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 879 Reproduction et Développement des Plantes, F-69364 Lyon, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5667 Reproduction et Développement des Plantes, F-69364 Lyon, France
| | - Vanessa Vernoud
- University of Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 879 Reproduction et Développement des Plantes, F-69364 Lyon, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5667 Reproduction et Développement des Plantes, F-69364 Lyon, France
| | - Ghislaine Gendrot
- University of Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 879 Reproduction et Développement des Plantes, F-69364 Lyon, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5667 Reproduction et Développement des Plantes, F-69364 Lyon, France
| | - Annick Dedieu
- University of Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 879 Reproduction et Développement des Plantes, F-69364 Lyon, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5667 Reproduction et Développement des Plantes, F-69364 Lyon, France
| | - Pierre Chambrier
- University of Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 879 Reproduction et Développement des Plantes, F-69364 Lyon, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5667 Reproduction et Développement des Plantes, F-69364 Lyon, France
| | - Myriam Dauzat
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 759 Ecophysiologie des Plantes sous Stress Environnementaux, F-34060 Montpellier, France
| | - Laure Heurtevin
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165 Recherche en Génomique Végétale, F-91057 Evry, France
| | - Virginie Guyon
- Biogemma SAS, Cereals Genetics and Genomics, F-63720 Chappes, France
| | - Mizuki Takenaka
- Department of Molecular Botany, University of Ulm, D-89069 Ulm, Germany
| | - Peter M. Rogowsky
- University of Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 879 Reproduction et Développement des Plantes, F-69364 Lyon, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5667 Reproduction et Développement des Plantes, F-69364 Lyon, France
- Address correspondence to
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Castandet B, Araya A. RNA editing in plant organelles. Why make it easy? BIOCHEMISTRY (MOSCOW) 2011; 76:924-31. [DOI: 10.1134/s0006297911080086] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Rüdinger M, Szövényi P, Rensing SA, Knoop V. Assigning DYW-type PPR proteins to RNA editing sites in the funariid mosses Physcomitrella patens and Funaria hygrometrica. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 67:370-380. [PMID: 21466601 DOI: 10.1111/j.1365-313x.2011.04600.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The plant-specific pentatricopeptide repeat (PPR) proteins with variable PPR repeat lengths (PLS-type) and protein extensions up to the carboxyterminal DYW domain have received attention as specific recognition factors for the C-to-U type of RNA editing events in plant organelles. Here, we report a DYW-protein knockout in the model plant Physcomitrella patens specifically affecting mitochondrial RNA editing positions cox1eU755SL and rps14eU137SL. Assignment of DYW proteins and RNA editing sites might best be corroborated by data from a taxon with a slightly different, yet similarly manageable low number of editing sites and DYW proteins. To this end we investigated the mitochondrial editing status of the related funariid moss Funaria hygrometrica. We find that: (i) Funaria lacks three mitochondrial RNA editing positions present in Physcomitrella, (ii) that F. hygrometrica cDNA sequence data identify nine DYW proteins as clear orthologues of their P. patens counterparts, and (iii) that the 'missing' 10th DYW protein in F. hygrometrica is responsible for two mitochondrial editing sites in P. patens lacking in F. hygrometrica (nad3eU230SL, nad4eU272SL). Interestingly, the third site of RNA editing missing in F. hygrometrica (rps14eU137SL) is addressed by the DYW protein characterized here and the presence of its orthologue in F. hygrometrica is explained through its simultaneous action on site cox1eU755SL conserved in both mosses.
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Affiliation(s)
- Mareike Rüdinger
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, Bonn, Germany
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Abstract
The pentatricopeptide repeat (PPR) is a degenerate 35-amino-acid structural motif identified from analysis of the sequenced genome of the model plant Arabidopsis thaliana. From the wealth of sequence information now available from plant genomes, the PPR protein family is now known to be one of the largest families in angiosperm species, as most genomes encode 400-600 members. As the number of PPR genes is generally only c. 10-20 in other eukaryotic organisms, including green algae, the family has obviously greatly expanded during land plant evolution. This provides a rare opportunity to study selection pressures driving a 50-fold expansion of a single gene family. PPR proteins are sequence-specific RNA-binding proteins involved in many aspects of RNA processing in organelles. In this review, we will summarize our current knowledge about the evolution of PPR genes, and will discuss the relevance of the dramatic expansion in the family to the functional diversification of plant organelles, focusing primarily on RNA editing.
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Affiliation(s)
- Sota Fujii
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley 6009, WA, Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley 6009, WA, Australia
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Uchida M, Ohtani S, Ichinose M, Sugita C, Sugita M. The PPR-DYW proteins are required for RNA editing of rps14, cox1 and nad5 transcripts in Physcomitrella patens mitochondria. FEBS Lett 2011; 585:2367-71. [PMID: 21708151 DOI: 10.1016/j.febslet.2011.06.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 06/10/2011] [Accepted: 06/10/2011] [Indexed: 10/18/2022]
Abstract
We identified two DYW subclass pentatricopeptide repeat (PPR) proteins, PpPPR_78 and PpPPR_79, as RNA editing factors in the moss Physcomitrella patens. Disruption of each gene by homologous recombination revealed that PpPPR_78 was involved in RNA editing at the rps14 (rps14-C137) and cox1 (cox1-C755) sites and PpPPR_79 at the nad5-1 (nad5-C598) site in the mitochondrial transcripts. RNA editing defects did not affect transcript patterns of the target genes. Thus, DYW subclass PPR proteins seem to be site-specific trans-acting factors for RNA editing.
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Affiliation(s)
- Masato Uchida
- Center for Gene Research, Nagoya University, Chikusa-ku, Nagoya, Japan
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Castandet B, Araya A. The RNA editing pattern of cox2 mRNA is affected by point mutations in plant mitochondria. PLoS One 2011; 6:e20867. [PMID: 21695137 PMCID: PMC3113845 DOI: 10.1371/journal.pone.0020867] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 05/11/2011] [Indexed: 11/24/2022] Open
Abstract
The mitochondrial transcriptome from land plants undergoes hundreds of specific C-to-U changes by RNA editing. These events are important since most of them occur in the coding region of mRNAs. One challenging question is to understand the mechanism of recognition of a selected C residue (editing sites) on the transcript. It has been reported that a short region surrounding the target C forms the cis-recognition elements, but individual residues on it do not play similar roles for the different editing sites. Here, we studied the role of the −1 and +1 nucleotide in wheat cox2 editing site recognition using an in organello approach. We found that four different recognition patterns can be distinguished: (a) +1 dependency, (b) −1 dependency, (c) +1/−1 dependency, and (d) no dependency on nearest neighbor residues. A striking observation was that whereas a 23 nt cis region is necessary for editing, some mutants affect the editing efficiency of unmodified distant sites. As a rule, mutations or pre-edited variants of the transcript have an impact on the complete set of editing targets. When some Cs were changed into Us, the remaining editing sites presented a higher efficiency of C-to-U conversion than in wild type mRNA. Our data suggest that the complex response observed for cox2 mRNA may be a consequence of the fate of the transcript during mitochondrial gene expression.
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Affiliation(s)
- Benoît Castandet
- Laboratoire de Microbiologie Cellulaire et Moléculaire et Pathogénicité, MCMP- UMR5234, Centre National de la Recherche Scientifique and Université Bordeaux Segalen. Bordeaux, France
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Hammani K, des Francs-Small CC, Takenaka M, Tanz SK, Okuda K, Shikanai T, Brennicke A, Small I. The pentatricopeptide repeat protein OTP87 is essential for RNA editing of nad7 and atp1 transcripts in Arabidopsis mitochondria. J Biol Chem 2011; 286:21361-71. [PMID: 21504904 DOI: 10.1074/jbc.m111.230516] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In plant organelles, RNA editing is a post-transcriptional mechanism that converts specific cytidines to uridines in RNA of both mitochondria and plastids, altering the information encoded by the gene. The cytidine to be edited is determined by a cis-element surrounding the editing site that is specifically recognized and bound by a trans-acting factor. All the trans-acting editing factors identified so far in plant organelles are members of a large protein family, the pentatricopeptide repeat (PPR) proteins. We have identified the Organelle Transcript Processing 87 (OTP87) gene, which is required for RNA editing of the nad7-C24 and atp1-C1178 sites in Arabidopsis mitochondria. OTP87 encodes an E-subclass PPR protein with an unusually short E-domain. The recombinant protein expressed in Escherichia coli specifically binds to RNAs comprising 30 nucleotides upstream and 10 nucleotides downstream of the nad7-C24 and atp1-C1178 editing sites. The loss-of-function of OTP87 results in small plants with growth and developmental delays. In the otp87 mutant, the amount of assembled respiratory complex V (ATP synthase) is highly reduced compared with the wild type suggesting that the amino acid alteration in ATP1 caused by loss of editing at the atp1-C1178 site affects complex V assembly in mitochondria.
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Affiliation(s)
- Kamel Hammani
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009 Western Australia, Australia.
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Verbitskiy D, Härtel B, Zehrmann A, Brennicke A, Takenaka M. The DYW-E-PPR protein MEF14 is required for RNA editing at site matR-1895 in mitochondria of Arabidopsis thaliana. FEBS Lett 2011; 585:700-4. [PMID: 21281638 DOI: 10.1016/j.febslet.2011.01.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 01/25/2011] [Accepted: 01/25/2011] [Indexed: 11/17/2022]
Abstract
We here identify the PPR protein MEF14 of the DYW subclass as a specific trans-factor required for C to U editing of site matR-1895 by genetic mapping of an EMS induced editing mutant in Arabidopsis thaliana. The wild type Col MEF14 gene complements mutant protoplasts. A T-DNA insertion in the MEF14 gene abolishes detectable editing at the matR-1895 site. Lack of RNA editing at the matR-1895 site does not alter the level of mature and precursor nad1 mRNA molecules. Such RNA editing mutants can be used to analyse the function of genes like this maturase related reading frame in plant mitochondria.
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