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Hu YX, Huang A, Li Y, Molloy DP, Huang C. Emerging roles of the C-to-U RNA editing in plant stress responses. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 349:112263. [PMID: 39299521 DOI: 10.1016/j.plantsci.2024.112263] [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: 05/24/2024] [Revised: 08/08/2024] [Accepted: 09/10/2024] [Indexed: 09/22/2024]
Abstract
RNA editing is an important post-transcriptional event in all living cells. Within chloroplasts and mitochondria of higher plants, RNA editing involves the deamination of specific cytosine (C) residues in precursor RNAs to uracil (U). An increasing number of recent studies detail specificity of C-to-U RNA editing as an essential prerequisite for several plant stress-related responses. In this review, we summarize the current understanding of responses and functions of C-to-U RNA editing in plants under various stress conditions to provide theoretical reference for future research.
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Affiliation(s)
- Yu-Xuan Hu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
| | - An Huang
- College of Communication and Art Design, Swan College, Central South University of Forestry and Technology, 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.
| | - Chao Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
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2
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Park G, Shahwar D, Jang G, Shin J, Kwon G, Kim Y, Hong CO, Jin B, Kim H, Lee O, Park Y. Identification of a novel locus C2 controlling canary yellow flesh color in watermelons. Front Genet 2023; 14:1256627. [PMID: 37795242 PMCID: PMC10545963 DOI: 10.3389/fgene.2023.1256627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/29/2023] [Indexed: 10/06/2023] Open
Abstract
The flesh color of watermelon is an important trait that is determined by carotenoid composition and affects consumers' fruit desirability. Although a complete dominant control by C locus (Cllcyb) for canary yellow flesh (CY) over red flesh has been reported, red and CY colors frequently appear as a mixed pattern in the same flesh (incomplete canary yellow, ICY) in F1 and inbred lines carrying dominant C alleles. Therefore, we examined the genetic control of the mixed color pattern in ICY using whole-genome resequencing of three ICY (ICY group) and three CY inbred lines (CY group), as well as genetic linkage mapping of an F2 population. The segregation pattern in 135 F2 plants indicated that CY is controlled by a single locus (named C 2) dominant over ICY. The whole-genome resequencing of ICY and CY inbred lines revealed an ICY/CY-specific region of approximately 27.60-27.88 Mb on Chr. 2 that was polymorphic between the ICY and CY groups. Our genetic map, using nine cleaved amplified polymorphic sequence markers developed based on the single-nucleotide polymorphisms from the ICY/CY-specific region, confirmed that C 2 is located on Chr. 2 and cosegregated with the marker (M7) derived from a non-synonymous single-nucleotide polymorphism of the pentatricopeptide repeat (PPR) gene (ClPPR, Cla97C02G039880). Additionally, 27 watermelon inbred lines of ICY, CY, and red flesh were evaluated using previously reported Cllcyb (C locus)-based markers and our C 2 locus-linked ClPPR-based marker (M7). As a result, dominant alleles at the C 2 locus were required to produce CY, in addition to dominant alleles at the C locus, while a recessive homozygous genotype at the C locus gave the red flesh irrespective of the genotype at the C 2 locus. Using a ClPPR-based cleaved amplified polymorphic sequence developed in this study and Cllcyb-based markers, watermelon cultivars with CY, ICY, and red flesh could be successfully discerned, implying that the combined use of these markers will be efficient for marker-assisted selection of flesh color in watermelon breeding.
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Affiliation(s)
- Girim Park
- Department of Horticultural Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Durre Shahwar
- Department of Horticultural Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Gaeun Jang
- Department of Horticultural Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Jagyeong Shin
- Department of Horticultural Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Gibeom Kwon
- Partner Seeds Co., Ltd., Gimje, Republic of Korea
| | - Younjae Kim
- Partner Seeds Co., Ltd., Gimje, Republic of Korea
| | - Chang Oh Hong
- Department of Life Science and Environmental Biochemistry, Pusan National University, Miryang, Republic of Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Bingkui Jin
- UNELL Biotechnology Co., Ltd., Weifang, China
| | - Hoytaek Kim
- Department of Horticulture, Sunchon National University, Sunchon, Republic of Korea
| | - Oakjin Lee
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang, Republic of Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
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3
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Small I, Melonek J, Bohne AV, Nickelsen J, Schmitz-Linneweber C. Plant organellar RNA maturation. THE PLANT CELL 2023; 35:1727-1751. [PMID: 36807982 PMCID: PMC10226603 DOI: 10.1093/plcell/koad049] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/05/2023] [Accepted: 01/17/2023] [Indexed: 05/30/2023]
Abstract
Plant organellar RNA metabolism is run by a multitude of nucleus-encoded RNA-binding proteins (RBPs) that control RNA stability, processing, and degradation. In chloroplasts and mitochondria, these post-transcriptional processes are vital for the production of a small number of essential components of the photosynthetic and respiratory machinery-and consequently for organellar biogenesis and plant survival. Many organellar RBPs have been functionally assigned to individual steps in RNA maturation, often specific to selected transcripts. While the catalog of factors identified is ever-growing, our knowledge of how they achieve their functions mechanistically is far from complete. This review summarizes the current knowledge of plant organellar RNA metabolism taking an RBP-centric approach and focusing on mechanistic aspects of RBP functions and the kinetics of the processes they are involved in.
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Affiliation(s)
- Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
| | - Joanna Melonek
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
| | | | - Jörg Nickelsen
- Department of Molecular Plant Sciences, LMU Munich, 82152 Martinsried, Germany
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4
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Liu S, Liu M, Cao Y, Xu Y, Liu H, Zhu Q, Zhang X, Luan F. Identification of chromosome region and candidate genes for canary-yellow flesh (Cyf) locus in watermelon (Citrullus lanatus). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111594. [PMID: 36642105 DOI: 10.1016/j.plantsci.2023.111594] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Genetic control of fruit flesh color in watermelon is complex, and significant knowledge gaps still exist. In the present study, we investigated the genetic basis of canary-yellow flesh color in watermelon inbred line PI 635597 using a segregating population derived from a cross between PI 635597 and another inbred line, Cream of Saskatchewan (pale yellow flesh color). We showed that a single dominant gene controls the canary-yellow flesh color for the Cyf (canary-yellow flesh) trait. Bulk segregant analysis (BSA) and fine genetic mapping narrowed down the Cyf locus to a 79.62-kb region on chromosome 6, which harbors 10 predicted genes. Sequence variation analysis in the promoter and coding regions and gene expression analysis in both parental lines and selected watermelon accessions with diverse fruit flesh colors support Cla97C06G122050 (unknown protein) and Cla97C06G122120 (pentatricopeptide repeat) as predicted candidate genes for the Cyf locus. Marker-assisted selection and sequence alignment showed that the Cyf locus could differentiate canary-yellow flesh and pale-yellow flesh. Our results indicate that the Cyf locus might be responsible for canary-yellow flesh color and carotenoid accumulation levels.
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Affiliation(s)
- Shi Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Mengqiu Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Yue Cao
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Yan Xu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Hongyu Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Qianglong Zhu
- Agronomy College, Jiangxi Agricultural University, Nanchang, Jiangxi Province, China.
| | - Xian Zhang
- College of Horticulture, Northwest of A&F University, Yangling, Shaanxi Province, China.
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
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Wang Y, Li H, Huang ZQ, Ma B, Yang YZ, Xiu ZH, Wang L, Tan BC. Maize PPR-E proteins mediate RNA C-to-U editing in mitochondria by recruiting the trans deaminase PCW1. THE PLANT CELL 2023; 35:529-551. [PMID: 36200865 PMCID: PMC9806569 DOI: 10.1093/plcell/koac298] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/11/2022] [Indexed: 05/24/2023]
Abstract
RNA C-to-U editing in organelles is essential for plant growth and development; however, the underlying mechanism is not fully understood. Here, we report that pentatricopeptide repeat (PPR)-E subclass proteins carry out RNA C-to-U editing by recruiting the trans deaminase PPR motifs, coiled-coil, and DYW domain-containing protein 1 (PCW1) in maize (Zea mays) mitochondria. Loss-of-function of bZIP and coiled-coil domain-containing PPR 1 (bCCP1) or PCW1 arrests seed development in maize. bCCP1 encodes a bZIP and coiled-coil domain-containing PPR protein, and PCW1 encodes an atypical PPR-DYW protein. bCCP1 is required for editing at 66 sites in mitochondria and PCW1 is required for editing at 102 sites, including the 66 sites that require bCCP1. The PCW1-mediated editing sites are exclusively associated with PPR-E proteins. bCCP1 interacts with PCW1 and the PPR-E protein Empty pericarp7 (EMP7). Two multiple organellar RNA editing factor (MORF) proteins, ZmMORF1 and ZmMORF8, interact with PCW1, EMP7, and bCCP1. ZmMORF8 enhanced the EMP7-PCW1 interaction in a yeast three-hybrid assay. C-to-U editing at the ccmFN-1553 site in maize required EMP7, bCCP1, and PCW1. These results suggest that PPR-E proteins function in RNA editing by recruiting the trans deaminase PCW1 and bCCP1, and MORF1/8 assist this recruitment through protein-protein interactions.
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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, 266237, China
| | - Hao Li
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Zi-Qin Huang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Bing Ma
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Yan-Zhuo Yang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Zhi-Hui Xiu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Le Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
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Zhang H, Zheng Y, Zhang G, Miao Y, Liu C, Huang L. A Bibliometric Study for Plant RNA Editing Research: Trends and Future Challenges. Mol Biotechnol 2022:10.1007/s12033-022-00641-7. [PMID: 36562872 DOI: 10.1007/s12033-022-00641-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
RNA editing is a post-transcriptional process that introduces changes in RNA sequences encoded by nuclear, mitochondrial, or plastid genomes. To understand the research progress of plant RNA editing, we comprehensively analyze the articles on plant RNA editing from 2001 to 2022 through bibliometric methods. Nucleic Acids Research, Plant Journal and Plant cell are the journals that deserve attention with their high production, total local citation scores (TLCS), and h-indexes. The USA, China, and Germany are the top three countries with highly productive publications. Ulm University, Cornell University, and Chinese Acad Sci are excellent cooperative institutions with a high level of influence in the field, and KNOOP V and TAKENAKA M are good partnership. Plant RNA editing researches concentrate on the subject categories of Biochemistry & Molecular Biology, Plant Sciences, Genetics & Heredity, etc. Plant mitochondria, genome editing and messenger-RNA may be the research hotspots in the future. The main plant RNA editing research tools are JACUSA, SPRINT, and REDO, and the main databases are REDIdb, PED, and dbRES. At present, the research streams are (1) RNA editing sites; (2) Pentapeptide repeat protein (PPR) involved in RNA editing; (3) RNA editing factors. Overall, this article summarizes the research overview of plant RNA editing until 2022 and provides theoretical implications for its possible future directions.
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Affiliation(s)
- Huihui Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- Jiangxi University of Chinese Medicine, Nanchang, 330000, Jiangxi, China
| | - Yan Zheng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- Jiangxi University of Chinese Medicine, Nanchang, 330000, Jiangxi, China
| | - Guoshuai Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Yujing Miao
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Chang Liu
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
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7
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Sugita M. An Overview of Pentatricopeptide Repeat (PPR) Proteins in the Moss Physcomitrium patens and Their Role in Organellar Gene Expression. PLANTS 2022; 11:plants11172279. [PMID: 36079663 PMCID: PMC9459714 DOI: 10.3390/plants11172279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022]
Abstract
Pentatricopeptide repeat (PPR) proteins are one type of helical repeat protein that are widespread in eukaryotes. In particular, there are several hundred PPR members in flowering plants. The majority of PPR proteins are localized in the plastids and mitochondria, where they play a crucial role in various aspects of RNA metabolism at the post-transcriptional and translational steps during gene expression. Among the early land plants, the moss Physcomitrium (formerly Physcomitrella) patens has at least 107 PPR protein-encoding genes, but most of their functions remain unclear. To elucidate the functions of PPR proteins, a reverse-genetics approach has been applied to P. patens. To date, the molecular functions of 22 PPR proteins were identified as essential factors required for either mRNA processing and stabilization, RNA splicing, or RNA editing. This review examines the P. patens PPR gene family and their current functional characterization. Similarities and a diversity of functions of PPR proteins between P. patens and flowering plants and their roles in the post-transcriptional regulation of organellar gene expression are discussed.
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Affiliation(s)
- Mamoru Sugita
- Graduate School of Informatics, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
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8
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Maeda A, Takenaka S, Wang T, Frink B, Shikanai T, Takenaka M. DYW deaminase domain has a distinct preference for neighboring nucleotides of the target RNA editing sites. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:756-767. [PMID: 35652245 DOI: 10.1111/tpj.15850] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
C-to-U RNA editing sites in plant organelles show a strong bias for neighboring nucleotides. The nucleotide upstream of the target cytidine is typically C or U, whereas A and G are less common and rare, respectively. In pentatricopeptide repeat (PPR)-type RNA editing factors, the PPR domain specifically binds to the 5' sequence of target cytidines, whereas the DYW domain catalyzes the C-to-U deamination. We comprehensively analyzed the effects of neighboring nucleotides of the target cytidines using an Escherichia coli orthogonal system. Physcomitrium PPR56 efficiently edited target cytidines when the nucleotide upstream was U or C, whereas it barely edited when the position was G or the nucleotide downstream was C. This preference pattern, which corresponds well with the observed nucleotide bias for neighboring nucleotides in plant organelles, was altered when the DYW domain of OTP86 or DYW1 was adopted. The PPR56 chimeric proteins edited the target sites even when the -1 position was G. Our results suggest that the DYW domain possesses a distinct preference for the neighboring nucleotides of the target sites, thus contributing to target selection in addition to the existing selection determined by the PPR domain.
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Affiliation(s)
- Ayako Maeda
- Department of Botany Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Sachi Takenaka
- Department of Botany Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tenghua Wang
- Department of Botany Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Brody Frink
- Department of Botany Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Toshiharu Shikanai
- Department of Botany Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Mizuki Takenaka
- Department of Botany Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
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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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10
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Manavski N, Vicente A, Chi W, Meurer J. The Chloroplast Epitranscriptome: Factors, Sites, Regulation, and Detection Methods. Genes (Basel) 2021; 12:genes12081121. [PMID: 34440296 PMCID: PMC8394491 DOI: 10.3390/genes12081121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
Modifications in nucleic acids are present in all three domains of life. More than 170 distinct chemical modifications have been reported in cellular RNAs to date. Collectively termed as epitranscriptome, these RNA modifications are often dynamic and involve distinct regulatory proteins that install, remove, and interpret these marks in a site-specific manner. Covalent nucleotide modifications-such as methylations at diverse positions in the bases, polyuridylation, and pseudouridylation and many others impact various events in the lifecycle of an RNA such as folding, localization, processing, stability, ribosome assembly, and translational processes and are thus crucial regulators of the RNA metabolism. In plants, the nuclear/cytoplasmic epitranscriptome plays important roles in a wide range of biological processes, such as organ development, viral infection, and physiological means. Notably, recent transcriptome-wide analyses have also revealed novel dynamic modifications not only in plant nuclear/cytoplasmic RNAs related to photosynthesis but especially in chloroplast mRNAs, suggesting important and hitherto undefined regulatory steps in plastid functions and gene expression. Here we report on the latest findings of known plastid RNA modifications and highlight their relevance for the post-transcriptional regulation of chloroplast gene expression and their role in controlling plant development, stress reactions, and acclimation processes.
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Affiliation(s)
- Nikolay Manavski
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
| | - Alexandre Vicente
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
- Correspondence: ; Tel.: +49-89-218074556
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11
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Liu XY, Jiang RC, Wang Y, Tang JJ, Sun F, Yang YZ, Tan BC. ZmPPR26, a DYW-type pentatricopeptide repeat protein, is required for C-to-U RNA editing at atpA-1148 in maize chloroplasts. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4809-4821. [PMID: 33929512 DOI: 10.1093/jxb/erab185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are involved in the C-to-U RNA editing of organellar transcripts. The maize genome contains over 600 PPR proteins and few have been found to function in the C-to-U RNA editing in chloroplasts. Here, we report the function of ZmPPR26 in the C-to-U RNA editing and chloroplast biogenesis in maize. ZmPPR26 encodes a DYW-type PPR protein targeted to chloroplasts. The zmppr26 mutant exhibits albino seedling-lethal phenotype. Loss of function of ZmPPR26 abolishes the editing at atpA-1148 site, and decreases the editing at ndhF-62, rpl20-308, rpl2-2, rpoC2-2774, petB-668, rps8-182, and ndhA-50 sites. Overexpression of ZmPPR26 in zmppr26 restores the editing efficiency and rescues the albino seedling-lethal phenotype. Abolished editing at atpA-1148 causes a Leu to Ser change at AtpA-383 that leads to a reduction in the abundance of chloroplast ATP synthase in zmppr26. The accumulation of photosynthetic complexes are also markedly reduced in zmppr26, providing an explanation for the albino seedling-lethal phenotype. These results indicate that ZmPPR26 is required for the editing at atpA-1148 and is important for editing at the other seven sites in maize chloroplasts. The editing at atpA-1148 is critical for AtpA function, assembly of ATP synthase complex, and chloroplast biogenesis in maize.
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Affiliation(s)
- Xin-Yuan Liu
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Rui-Cheng Jiang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Yong Wang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Jiao-Jiao Tang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Feng Sun
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Yan-Zhuo Yang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Bao-Cai Tan
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
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12
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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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Piątkowski J, Golik P. Yeast pentatricopeptide protein Dmr1 (Ccm1) binds a repetitive AU-rich motif in the small subunit mitochondrial ribosomal RNA. RNA (NEW YORK, N.Y.) 2020; 26:1268-1282. [PMID: 32467310 PMCID: PMC7430664 DOI: 10.1261/rna.074880.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
PPR proteins are a diverse family of RNA binding factors found in all Eukaryotic lineages. They perform multiple functions in the expression of organellar genes, mostly on the post-transcriptional level. PPR proteins are also significant determinants of evolutionary nucleo-organellar compatibility. Plant PPR proteins recognize their RNA substrates using a simple modular code. No target sequences recognized by animal or yeast PPR proteins were identified prior to the present study, making it impossible to assess whether this plant PPR code is conserved in other organisms. Dmr1p (Ccm1p, Ygr150cp) is a S. cerevisiae PPR protein essential for mitochondrial gene expression and involved in the stability of 15S ribosomal RNA. We demonstrate that in vitro Dmr1p specifically binds a motif composed of multiple AUA repeats occurring twice in the 15S rRNA sequence as the minimal 14 nt (AUA)4AU or longer (AUA)7 variant. Short RNA fragments containing this motif are protected by Dmr1p from exoribonucleolytic activity in vitro. Presence of the identified motif in mtDNA of different yeast species correlates with the compatibility between their Dmr1p orthologs and S. cerevisiae mtDNA. RNA recognition by Dmr1p is likely based on a rudimentary form of a PPR code specifying U at every third position, and depends on other factors, like RNA structure.
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Affiliation(s)
- Jakub Piątkowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
| | - Paweł Golik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
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14
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Morales-Luna L, Hernández-Ochoa B, Ramírez-Nava EJ, Martínez-Rosas V, Ortiz-Ramírez P, Fernández-Rosario F, González-Valdez A, Cárdenas-Rodríguez N, Serrano-Posada H, Centeno-Leija S, Arreguin-Espinosa R, Cuevas-Cruz M, Ortega-Cuellar D, Pérez de la Cruz V, Rocha-Ramírez LM, Sierra-Palacios E, Castillo-Rodríguez RA, Vega-García V, Rufino-González Y, Marcial-Quino J, Gómez-Manzo S. Characterizing the Fused TvG6PD::6PGL Protein from the Protozoan Trichomonas vaginalis, and Effects of the NADP + Molecule on Enzyme Stability. Int J Mol Sci 2020; 21:E4831. [PMID: 32650494 PMCID: PMC7402283 DOI: 10.3390/ijms21144831] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 12/30/2022] Open
Abstract
This report describes a functional and structural analysis of fused glucose-6-phosphate dehydrogenase dehydrogenase-phosphogluconolactonase protein from the protozoan Trichomonas vaginalis (T. vaginalis). The glucose-6-phosphate dehydrogenase (g6pd) gene from T. vaginalis was isolated by PCR and the sequence of the product showed that is fused with 6pgl gene. The fused Tvg6pd::6pgl gene was cloned and overexpressed in a heterologous system. The recombinant protein was purified by affinity chromatography, and the oligomeric state of the TvG6PD::6PGL protein was found as tetramer, with an optimal pH of 8.0. The kinetic parameters for the G6PD domain were determined using glucose-6-phosphate (G6P) and nicotinamide adenine dinucleotide phosphate (NADP+) as substrates. Biochemical assays as the effects of temperature, susceptibility to trypsin digestion, and analysis of hydrochloride of guanidine on protein stability in the presence or absence of NADP+ were performed. These results revealed that the protein becomes more stable in the presence of the NADP+. In addition, we determined the dissociation constant for the binding (Kd) of NADP+ in the protein and suggests the possible structural site in the fused TvG6PD::6PGL protein. Finally, computational modeling studies were performed to obtain an approximation of the structure of TvG6PD::6PGL. The generated model showed differences with the GlG6PD::6PGL protein (even more so with human G6PD) despite both being fused.
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Affiliation(s)
- Laura Morales-Luna
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, 06720 Ciudad de México, Mexico;
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Ciudad de México, Mexico
| | - Edson Jiovany Ramírez-Nava
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Víctor Martínez-Rosas
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Ciudad de México, Mexico
| | - Paulina Ortiz-Ramírez
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
| | - Fabiola Fernández-Rosario
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico;
| | - Noemí Cárdenas-Rodríguez
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico;
| | - Hugo Serrano-Posada
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera los Limones-Loma de Juárez, 28629 Colima, Mexico; (H.S.-P.); (S.C.-L.)
| | - Sara Centeno-Leija
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera los Limones-Loma de Juárez, 28629 Colima, Mexico; (H.S.-P.); (S.C.-L.)
| | - Roberto Arreguin-Espinosa
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico; (R.A.-E.); (M.C.-C.)
| | - Miguel Cuevas-Cruz
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico; (R.A.-E.); (M.C.-C.)
| | - Daniel Ortega-Cuellar
- Laboratorio de Nutrición Experimental, Instituto Nacional de Pediatría, 04530 Secretaría de Salud, Mexico;
| | - Verónica Pérez de la Cruz
- Departamento de Neuroquímica, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Secretaria de Salud, 14269 Ciudad de México, Mexico;
| | - Luz María Rocha-Ramírez
- Unidad de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Dr. Márquez No. 162, Col Doctores, 06720 Delegación Cuauhtémoc, Mexico;
| | - Edgar Sierra-Palacios
- Colegio de Ciencias y Humanidades, Plantel Casa Libertad, Universidad Autónoma de la Ciudad de México, 09620 Ciudad de México, Mexico;
| | - Rosa Angélica Castillo-Rodríguez
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico;
| | - Vanesa Vega-García
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico;
| | - Yadira Rufino-González
- Laboratorio de Parasitología Experimental, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico;
| | - Jaime Marcial-Quino
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico;
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
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15
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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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16
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Small ID, Schallenberg-Rüdinger M, Takenaka M, Mireau H, Ostersetzer-Biran O. Plant organellar RNA editing: what 30 years of research has revealed. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1040-1056. [PMID: 31630458 DOI: 10.1111/tpj.14578] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/25/2019] [Accepted: 10/08/2019] [Indexed: 05/21/2023]
Abstract
The central dogma in biology defines the flow of genetic information from DNA to RNA to protein. Accordingly, RNA molecules generally accurately follow the sequences of the genes from which they are transcribed. This rule is transgressed by RNA editing, which creates RNA products that differ from their DNA templates. Analyses of the RNA landscapes of terrestrial plants have indicated that RNA editing (in the form of C-U base transitions) is highly prevalent within organelles (that is, mitochondria and chloroplasts). Numerous C→U conversions (and in some plants also U→C) alter the coding sequences of many of the organellar transcripts and can also produce translatable mRNAs by creating AUG start sites or eliminating premature stop codons, or affect the RNA structure, influence splicing and alter the stability of RNAs. RNA-binding proteins are at the heart of post-transcriptional RNA expression. The C-to-U RNA editing process in plant mitochondria involves numerous nuclear-encoded factors, many of which have been identified as pentatricopeptide repeat (PPR) proteins that target editing sites in a sequence-specific manner. In this review we report on major discoveries on RNA editing in plant organelles, since it was first documented 30 years ago.
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Affiliation(s)
- Ian D Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Mareike Schallenberg-Rüdinger
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abt. Molekulare Evolution, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Mizuki Takenaka
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hakim Mireau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
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17
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Zhang Q, Xu Y, Huang J, Zhang K, Xiao H, Qin X, Zhu L, Zhu Y, Hu J. The Rice Pentatricopeptide Repeat Protein PPR756 Is Involved in Pollen Development by Affecting Multiple RNA Editing in Mitochondria. FRONTIERS IN PLANT SCIENCE 2020; 11:749. [PMID: 32595669 PMCID: PMC7303307 DOI: 10.3389/fpls.2020.00749] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/12/2020] [Indexed: 05/21/2023]
Abstract
In land plants, the pentatricopeptide repeat (PPR) proteins form a large family involved in post-transcriptional processing of RNA in mitochondria and chloroplasts, which is critical for plant development and evolutionary adaption. Although studies showed a number of PPR proteins generally influence the editing of organellar genes, few of them were characterized in detail in rice. Here, we report a PLS-E subclass PPR protein in rice, PPR756, loss of function of which led to the abolishment of RNA editing events among three mitochondrial genes including atp6, ccmC, and nad7. Their defective C-to-U transformation then resulted in improper amino acid retention which could cause abortive pollen development. Furthermore, PPR756 could bind to the three target genes directly and interact with three OsMORFs (multiple organellar RNA editing factors): OsMORF1, OsMORF8-1, and OsMORF8-2. The knock-out plants of PPR756 exhibited retarded growth and greener leaves during the early vegetative stages, along with sterile pollen and lower seed setting at the reproductive stage. These results established a role for PPR756 in rice development, participating in RNA editing of three various transcripts and cooperating with OsMORFs via an editosome manner in rice.
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Affiliation(s)
- Qiannan Zhang
- State Key Laboratory of Hybrid Rice, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yanghong Xu
- State Key Laboratory of Hybrid Rice, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jishuai Huang
- State Key Laboratory of Hybrid Rice, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
| | - Kai Zhang
- Department of Surgery, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
- Department of Surgical Research, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
| | - Haijun Xiao
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaojian Qin
- Chongqing Key Laboratory of Molecular Biology of Plants Environmental Adaptations, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Linlin Zhu
- No.9 Middle School of Zhengzhou, Zhengzhou, China
| | - Yingguo Zhu
- State Key Laboratory of Hybrid Rice, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jun Hu
- State Key Laboratory of Hybrid Rice, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
- *Correspondence: Jun Hu,
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18
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Ishibashi K, Small I, Shikanai T. Evolutionary Model of Plastidial RNA Editing in Angiosperms Presumed from Genome-Wide Analysis of Amborella trichopoda. PLANT & CELL PHYSIOLOGY 2019; 60:2141-2151. [PMID: 31150097 DOI: 10.1093/pcp/pcz111] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 05/21/2019] [Indexed: 05/08/2023]
Abstract
Amborella trichopoda is placed close to the base of the angiosperm lineage (basal angiosperm). By genome-wide RNA sequencing, we identified 184C-to-U RNA editing sites in the plastid genome of Amborella. This number is much higher than that observed in other angiosperms including maize (44 sites), rice (39 sites) and grape (115 sites). Despite the high frequency of RNA editing, the biased distribution of RNA editing sites in the genome, target codon preference and nucleotide preference adjacent to the edited cytidine are similar to that in other angiosperms, suggesting a common editing machinery. Consistent with this idea, the Amborella nuclear genome encodes 2-3 times more of the E- and DYW-subclass members of pentatricopeptide repeat proteins responsible for RNA editing site recognition in plant organelles. Among 165 editing sites in plastid protein coding sequences in Amborella, 100 sites were conserved at least in one out of 38 species selected to represent key branching points of the angiosperm phylogenetic tree. We assume these 100 sites represent at least a subset of the sites in the plastid editotype of ancestral angiosperms. We then mapped the loss and gain of editing sites on the phylogenetic tree of angiosperms. Our results support the idea that the evolution of angiosperms has led to the loss of RNA editing sites in plastids.
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Affiliation(s)
- Kota Ishibashi
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, Japan
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, Japan
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19
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MORF9 Functions in Plastid RNA Editing with Tissue Specificity. Int J Mol Sci 2019; 20:ijms20184635. [PMID: 31546885 PMCID: PMC6769653 DOI: 10.3390/ijms20184635] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/11/2019] [Accepted: 09/13/2019] [Indexed: 11/17/2022] Open
Abstract
RNA editing in plant mitochondria and plastids converts specific nucleotides from cytidine (C) to uridine (U). These editing events differ among plant species and are relevant to developmental stages or are impacted by environmental conditions. Proteins of the MORF family are essential components of plant editosomes. One of the members, MORF9, is considered the core protein of the editing complex and is involved in the editing of most sites in chloroplasts. In this study, the phenotypes of a T-DNA insertion line with loss of MORF9 and of the genetic complementation line of Arabidopsis were analyzed, and the editing efficiencies of plastid RNAs in roots, rosette leaves, and flowers from the morf9 mutant and the wild-type (WT) control were compared by bulk-cDNA sequencing. The results showed that most of the known MORF9-associated plastid RNA editing events in rosette leaves and flowers were similarly reduced by morf9 mutation, with the exception that the editing rate of the sites ndhB-872 and psbF-65 declined in the leaves and that of ndhB-586 decreased only in the flowers. In the roots, however, the loss of MORF9 had a much lower effect on overall plastid RNA editing, with nine sites showing no significant editing efficiency change, including accD-794, ndhD-383, psbZ-50, ndhF-290, ndhD-878, matK-706, clpP1-559, rpoA-200, and ndhD-674, which were reduced in the other tissues. Furthermore, we found that during plant aging, MORF9 mRNA level, but not the protein level, was downregulated in senescent leaves. On the basis of these observations, we suggest that MORF9-mediated RNA editing is tissue-dependent and the resultant organelle proteomes are pertinent to the specific tissue functions.
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20
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Li W, Bai Q, Zhan W, Ma C, Wang S, Feng Y, Zhang M, Zhu Y, Cheng M, Xi Z. Fine mapping and candidate gene analysis of qhkw5-3, a major QTL for kernel weight in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2579-2589. [PMID: 31187154 DOI: 10.1007/s00122-019-03372-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 06/03/2019] [Indexed: 06/09/2023]
Abstract
KEY MESSAGE: qhkw5-3, a major QTL for kernel weight in maize, was mapped to an interval of 125.3 kb between the InDel markers InYM20 and InYM36, and the candidate genes were analysed. Yield, of which kernel weight is a major component, is the primary trait of interest in maize breeding programmes. In our previous study, a major QTL (named qhkw5-3), which controls hundred-kernel weight, was identified and mapped to the interval between simple sequence repeat (SSR) markers SYM033 and SYM108 on chromosome 5, using an F2:3 population derived from a cross between the maize inbred line Zheng58 and the single-segment substitution line Z22. In order to fine map qhkw5-3, a larger BC1F1 segregating population of 14,759 seeds, derived from a (Z22 × Zheng58) × Z22 cross, was screened using the SSR markers SYM036 and SYM119. Forty genotypes with donor chromosomal fragments of different lengths were obtained. Progeny testing results indicated that qhkw5-3 was mapped to an interval of 442.6 kb between the SSR markers SYM077 and SYM084. Overlap mapping results, based on seven homozygous recombinant lines, showed that qhkw5-3 was narrowed down to an interval of 125.3 kb between the InDel markers InYM20 and InYM36. Within this interval, six candidate genes were analysed using qRT-PCR. The results of this study lay the foundations for cloning and functional analysis of qhkw5-3 and will contribute to advancing our knowledge of the genetic basis of yield traits in maize.
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Affiliation(s)
- Wenliang Li
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qinghe Bai
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Weimin Zhan
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chenyu Ma
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shunyou Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yuanyuan Feng
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Mengdi Zhang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ying Zhu
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ming Cheng
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhangying Xi
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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21
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Ding S, Liu XY, Wang HC, Wang Y, Tang JJ, Yang YZ, Tan BC. SMK6 mediates the C-to-U editing at multiple sites in maize mitochondria. JOURNAL OF PLANT PHYSIOLOGY 2019; 240:152992. [PMID: 31234031 DOI: 10.1016/j.jplph.2019.152992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/01/2019] [Accepted: 06/03/2019] [Indexed: 06/09/2023]
Abstract
The recently identified PPR-E+/NVWA/DYW2 RNA editing complex provides insights into the mechanism of RNA editing in higher plant organelles. However, whether the complex works together with the previously identified editing factors RIPs/MORFs is unclear. In this paper, we identified a maize Smk6 gene, which encodes a mitochondrion-targeted PPR-E+protein with E1 and E2 domains at the C terminus. Loss of Smk6 function affects the C-to-U editing at nad1-740, nad4L-110, nad7-739, and mttB-138,139 sites, impairs mitochondrial activity and blocks embryogenesis and endosperm development. Genetic and molecular analysis indicated that SMK6 is the maize ortholog of the Arabidopsis SLO2, which is a component of the PPR-E+/NVWA/DYW2 editing complex. However, yeast two-hybrid analyses did not detect any interaction between SMK6 and any of the mitochondrion-targeted RIPs/MORFs, suggesting that RIPs/MORFs may not be a component of PPR-E+/NVWA/DYW2 RNA editing complex. Further analyses are required to provide evidence that RIP/MORFs and SMK6 do not physically interact in vivo.
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Affiliation(s)
- Shuo Ding
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Xin-Yuan Liu
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Hong-Chun Wang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yong Wang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jiao-Jiao Tang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yan-Zhuo Yang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bao-Cai Tan
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China.
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22
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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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23
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Ruwe H, Gutmann B, Schmitz-Linneweber C, Small I, Kindgren P. The E domain of CRR2 participates in sequence-specific recognition of RNA in plastids. THE NEW PHYTOLOGIST 2019; 222:218-229. [PMID: 30393849 DOI: 10.1111/nph.15578] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/28/2018] [Indexed: 06/08/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are modular RNA-binding proteins involved in different aspects of RNA metabolism in organelles. PPR proteins of the PLS subclass often contain C-terminal domains that are important for their function, but the role of one of these domains, the E domain, is far from resolved. Here, we elucidate the role of the E domain in CRR2 in plastids. We identified a surprisingly large number of small RNAs that represent in vivo footprints of the Arabidopsis PLS-class PPR protein CRR2. An unexpectedly strong base conservation was found in the nucleotides aligned to the E domain. We used both in vitro and in vivo experiments to reveal the role of the E domain of CRR2. The E domain of CRR2 can be predictably altered to prefer different nucleotides in its RNA ligand, and position 5 of the E1-motif is biologically important for the PPR-RNA interaction. The 'code' of the E domain PPR motifs is different from that of P- and S-motifs. The findings presented here show that the E domain of CRR2 is involved in sequence-specific interaction with its RNA ligand and have implications for our ability to predict RNA targets for PLS-PPRs and their use as biotechnological tools to manipulate specific RNAs in vivo.
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Affiliation(s)
- Hannes Ruwe
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany
| | - Bernard Gutmann
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
| | | | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
| | - Peter Kindgren
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
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24
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Kawabe A, Furihata HY, Tsujino Y, Kawanabe T, Fujii S, Yoshida T. Divergence of RNA editing among Arabidopsis species. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:241-247. [PMID: 30824002 DOI: 10.1016/j.plantsci.2018.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/05/2018] [Accepted: 12/12/2018] [Indexed: 05/25/2023]
Abstract
RNA editing altered the RNA sequence by replacing the C nucleotide to U in the organellar genomes of plants. RNA editing status sometimes differed among distant species. The pattern of conservation and variation of RNA editing status made it possible to evaluate evolutionary mechanisms impacting functional aspects of RNA editing. In this study, divergence of RNA editing in the chloroplast genome among Arabidopsis species was analyzed to determine 9 losses and 1 gain in RNA editing. All changes in A. thaliana lineage resulted from changes to the chloroplast genome sequence, whereas changes in the A. lyrata / halleri lineage were possibly due to exclusive changes in the nuclear editing factors. One loss of RNA editing in A. lyrata was caused by a deficiency in the PPR gene OTP80. The changes in RNA editing occurred approximately every two million years and were not observed at functionally important sites. These results highlight the conserved nature of RNA editing status suggesting the importance of RNA editing during evolution.
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Affiliation(s)
- Akira Kawabe
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan.
| | - Hazuka Y Furihata
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Yudai Tsujino
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Takahiro Kawanabe
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Sota Fujii
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takanori Yoshida
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
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25
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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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26
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Huang C, Li ZR, Yu QB, Ye LS, Cui YL, Molloy DP, Yang ZN. MORF2 tightly associates with MORF9 to regulate chloroplast RNA editing in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 278:64-69. [PMID: 30471730 DOI: 10.1016/j.plantsci.2018.10.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/12/2018] [Accepted: 10/24/2018] [Indexed: 05/21/2023]
Abstract
RNA editing in chloroplasts and mitochondria is performed by hypothetical editosomes. The MORF family proteins are essential components of these editosomes. In Arabidopsis, MORF2 and MORF9 are involved in the editing of most sites in chloroplasts. In this work, we performed immunoprecipitation and mass spectrometry assays of transgenic lines expressing MORF2-4xMYC and MORF9-4xMYC to identify interacting proteins. We found that MORF2 and MORF9 are present in the same complex. Blue-Native PAGE analysis of chloroplast protein complexes also revealed that both MORF2 and MORF9 are part of a complex of approximately 140 kDa, suggesting the existence of tight MORF2-MORF9 interaction in chloroplasts. The editing of ndhD-1 (ndhD-C2) site was reported to be blocked in both morf2 and morf9. RNA immunoprecipitation assays showed that MORF2 and MORF9 are tightly associated with the editing site of ndhD-1. However, in an RNA-EMSA assay MORF2 and MORF9 could not directly bind to transcripts harboring the editing site of ndhD-1. Taken together, these results indicate that the MORF2-MORF9 heterodimer is the core members of editosomes in chloroplasts, while they are not responsible for RNA editing site recognition.
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Affiliation(s)
- Chao Huang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China.
| | - Zi-Ran Li
- College of Life Science, Shanghai Normal University, Shanghai, 200234, China.
| | - Qing-Bo Yu
- College of Life Science, Shanghai Normal University, Shanghai, 200234, China.
| | - Lin-Shan Ye
- College of Life Science, Shanghai Normal University, Shanghai, 200234, China.
| | - Yong-Lan Cui
- College of Life Science, Shanghai Normal University, Shanghai, 200234, China.
| | - David P Molloy
- International College, Hunan University of Arts and Science, Changde, 415000, China.
| | - Zhong-Nan Yang
- College of Life Science, Shanghai Normal University, Shanghai, 200234, China.
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27
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Qulsum U, Tsukahara T. Tissue-specific alternative splicing of pentatricopeptide repeat (PPR) family genes in Arabidopsis thaliana. Biosci Trends 2018; 12:569-579. [PMID: 30555111 DOI: 10.5582/bst.2018.01178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Alternative splicing is a post- and co-transcriptional regulatory mechanism of gene expression. Pentatricopeptide repeat (PPR) family proteins were recently found to be involved in RNA editing in plants. The aim of this study was to investigate the tissue-specific expression and alternative splicing of PPR family genes and their effects on protein structure and functionality. Of the 27 PPR genes in Arabidopsis thaliana, we selected six PPR genes of the P subfamily that are likely alternatively spliced, which were confirmed by sequencing. Four of these genes show intron retention, and the two remaining genes have 3' alternative-splicing sites. Alternative-splicing events occurred in the coding regions of three genes and in the 3' UTRs of the three remaining genes. We also identified five previously unannotated alternatively spliced isoforms of these PPR genes, which were confirmed by PCR and sequencing. Among these, three contain 3' alternative-splicing sites, one contains a 5' alternative-splicing site, and the remaining gene contains a 3'-5' alternative-splicing site. The new isoforms of two genes affect protein structure, and three other alternative-splicing sites are located in 3' UTRs. These findings suggest that tissue-specific expression of different alternatively spliced transcripts occurs in Arabidopsis, even at different developmental stages.
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Affiliation(s)
- Umme Qulsum
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST)
| | - Toshifumi Tsukahara
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST).,Area of Bioscience and Biotechnology, School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST).,Division of Transdisciplinary Science, Japan Advanced Institute of Science and Technology (JAIST)
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28
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Kamba PF, Dickson DA, White NA, Ekstrom JL, Koslowsky DJ, Hoogstraten CG. The 27 kDa Trypanosoma brucei Pentatricopeptide Repeat Protein is a G-tract Specific RNA Binding Protein. Sci Rep 2018; 8:16989. [PMID: 30451852 PMCID: PMC6242908 DOI: 10.1038/s41598-018-34377-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/15/2018] [Indexed: 01/30/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins, a helical repeat family of organellar RNA binding proteins, play essential roles in post-transcriptional RNA processing. In Trypanosoma brucei, an expanded family of PPR proteins localize to the parasite’s single mitochondrion, where they are believed to perform important roles in both RNA processing and translation. We studied the RNA binding specificity of the simplest T. brucei PPR protein (KRIPP11) using electrophoretic mobility shift assays, fluorescence anisotropy, circular dichroism spectroscopy, and in vitro selection. We found KRIPP11 to be an RNA binding protein with specificity for sequences of four or more consecutive guanosine residues (G-tracts). Such G-tracts are dramatically enriched in T. brucei mitochondrial transcripts that are destined for extensive uridine insertion/deletion editing but are not present in mRNAs following editing. We further found that the quadruplex oligoguanosine RNA conformation is preferentially recognized by KRIPP11 over other conformational forms, and is bound without disruption of the quadruplex structure. In combination with prior data demonstrating association of KRIPP11 with the small ribosomal subunit, these results suggest possible roles for KRIPP11 in bridging mRNA maturation and translation or in facilitating translation of unusual dual-coded open reading frames.
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Affiliation(s)
- Pakoyo F Kamba
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Graduate Program in Cell and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Makerere University, Kampala, Uganda
| | - David A Dickson
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Sackler School of Graduate Biomedical Sciences, Tufts University, Medford, Massachusetts, USA
| | - Neil A White
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Jennifer L Ekstrom
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Department of Food Science and Human Nutrition, Michigan State University, East Lansing, Michigan, USA
| | - Donna J Koslowsky
- Graduate Program in Cell and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, 48824-1319, USA
| | - Charles G Hoogstraten
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.
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29
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Ma F, Hu Y, Ju Y, Jiang Q, Cheng Z, Zhang Q. A novel tetratricopeptide repeat protein, WHITE TO GREEN1, is required for early chloroplast development and affects RNA editing in chloroplasts. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5829-5843. [PMID: 29140512 PMCID: PMC5854136 DOI: 10.1093/jxb/erx383] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 10/05/2017] [Indexed: 05/24/2023]
Abstract
The chloroplast is essential for plant photosynthesis and production, but the regulatory mechanism of chloroplast development is still elusive. Here, a novel gene, WHITE TO GREEN1 (WTG1), was identified to have a function in chloroplast development and plastid gene expression by screening Arabidopsis leaf coloration mutants. WTG1 encodes a chloroplast-localized tetratricopeptide repeat protein that is expressed widely in Arabidopsis cells. Disruption of WTG1 suppresses plant growth, retards leaf greening and chloroplast development, and represses photosynthetic gene expression, but complemented expression of WTG1 restored a normal phenotype. Moreover, WTG1 protein is associated with the organelle RNA editing factors MORF8 and MORF9, and RNA editing of the plastid petL-5 and ndhG-50 transcripts was affected in wtg1 mutants. These results indicate that WTG1 affects both transcriptional and posttranscriptional regulation of plastid gene expression, and provide evidence for the involvement of a tetratricopeptide repeat protein in chloroplast RNA editing in Arabidopsis.
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Affiliation(s)
- Fei Ma
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
| | - Yingchun Hu
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
| | - Yan Ju
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
| | - Qianru Jiang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, China
| | - Quan Zhang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
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30
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Diaz MF, Bentolila S, Hayes ML, Hanson MR, Mulligan RM. A protein with an unusually short PPR domain, MEF8, affects editing at over 60 Arabidopsis mitochondrial C targets of RNA editing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:638-649. [PMID: 29035004 DOI: 10.1111/tpj.13709] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/27/2017] [Accepted: 08/30/2017] [Indexed: 05/15/2023]
Abstract
An RNA-seq approach was used to investigate the role of a PLS-subfamily pentatricopeptide repeat protein, Mitochondrial Editing Factor 8 (MEF8), on editing in Arabidopsis mitochondria and plastids. MEF8 has an intact DYW domain, but possesses an unusually short PLS repeat region of only five repeats. The MEF8 T-DNA insertion (mef8) line exhibited reduced editing at 38 mitochondrial editing sites and increased editing at 24 sites; therefore the absence of MEF8 affects 11% of the mitochondrial editome. Notably, 60% of the matR transcripts' sites showed a decrease of editing extent in the mef8 mutant. An E549A substitution in the MEF8 protein replaced the putatively catalytic glutamate of the HXE motif in the DYW domain. Complementation with MEF8-E549A failed to restore editing at the main target sites but was able to restore editing at the matR transcript; it also decreased the editing extent of most of the C targets exhibiting an increase of editing extent in the mef8 mutant plant. Thus, MEF8 has two antagonistic effects on mitochondrial editing: stimulatory, which requires a catalytic glutamate for most of the targets except for the matR transcript, and inhibitory, for which glutamate is dispensable.
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Affiliation(s)
- Michael F Diaz
- Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Stephane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Michael L Hayes
- Department of Chemistry and Biochemistry, California State University, Los Angeles, CA, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - R Michael Mulligan
- Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
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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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Rodrigues NF, Christoff AP, da Fonseca GC, Kulcheski FR, Margis R. Unveiling Chloroplast RNA Editing Events Using Next Generation Small RNA Sequencing Data. FRONTIERS IN PLANT SCIENCE 2017; 8:1686. [PMID: 29033962 PMCID: PMC5626879 DOI: 10.3389/fpls.2017.01686] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/13/2017] [Indexed: 05/21/2023]
Abstract
Organellar RNA editing involves the modification of nucleotide sequences to maintain conserved protein functions, mainly by reverting non-neutral codon mutations. The loss of plastid editing events, resulting from mutations in RNA editing factors or through stress interference, leads to developmental, physiological and photosynthetic alterations. Recently, next generation sequencing technology has generated the massive discovery of sRNA sequences and expanded the number of sRNA data. Here, we present a method to screen chloroplast RNA editing using public sRNA libraries from Arabidopsis, soybean and rice. We mapped the sRNAs against the nuclear, mitochondrial and plastid genomes to confirm predicted cytosine to uracil (C-to-U) editing events and identify new editing sites in plastids. Among the predicted editing sites, 40.57, 34.78, and 25.31% were confirmed using sRNAs from Arabidopsis, soybean and rice, respectively. SNP analysis revealed 58.2, 43.9, and 37.5% new C-to-U changes in the respective species and identified known and new putative adenosine to inosine (A-to-I) RNA editing in tRNAs. The present method and data reveal the potential of sRNA as a reliable source to identify new and confirm known editing sites.
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Affiliation(s)
- Nureyev F. Rodrigues
- Programa de Posgraduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana P. Christoff
- Programa de Posgraduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Guilherme C. da Fonseca
- Programa de Posgraduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Franceli R. Kulcheski
- Programa de Pósgraduação em Biologia Celular e do Desenvolvimento, Departamento de Biologia Celular, Genética e Embriologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Rogerio Margis
- Programa de Posgraduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Programa de Posgraduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- *Correspondence: Rogerio Margis
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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: 143] [Impact Index Per Article: 17.9] [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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Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods. Methods 2016; 118-119:146-162. [PMID: 27939506 DOI: 10.1016/j.ymeth.2016.12.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 01/01/2023] Open
Abstract
The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes.
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Du K, Liu Q, Wu X, Jiang J, Wu J, Fang Y, Li A, Wang Y. Morphological Structure and Transcriptome Comparison of the Cytoplasmic Male Sterility Line in Brassica napus (SaNa-1A) Derived from Somatic Hybridization and Its Maintainer Line SaNa-1B. FRONTIERS IN PLANT SCIENCE 2016; 7:1313. [PMID: 27656189 PMCID: PMC5011408 DOI: 10.3389/fpls.2016.01313] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 08/16/2016] [Indexed: 05/21/2023]
Abstract
SaNa-1A is a novel cytoplasmic male sterility (CMS) line in Brassica napus derived from progenies of somatic hybrids between B.napus and Sinapis alba, and SaNa-1B is the corresponding maintainer line. In this study, phenotypic differences of floral organs between CMS and the maintainer lines were observed. By microscope observation in different anther developmental stages of two lines, we found the anther development in SaNa-1A was abnormal since the tetrad stage, and microspore development was ceased during the uninucleate stage. Transcriptomic sequencing for floral buds of sterile and fertile plants were conducted to elucidate gene expression and regulation caused by the alien chromosome and cytoplasm from S. alba. Clean tags obtained were assembled into 195,568 unigenes, and 7811 unigenes distributed in the metabolic and protein synthesis pathways were identified with significant expression differences between two libraries. We also observed that genes participating in carbon metabolism, tricarboxylic acid cycle, oxidative phosphorylation, oxidation-reduction system, pentatricopeptide repeat, and anther development were downregulated in the sterile line. Some of them are candidates for researches on the sterility mechanism in the CMS material, fertility restoration, and improvement of economic traits in the maintainer line. Further research on the tags with expressional specificity in the fertile line would be helpful to explore desirable agronomic traits from wild species of rapeseed.
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Affiliation(s)
- Kun Du
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
| | - Qier Liu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
| | - Xinyue Wu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
| | - Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
| | - Jian Wu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
| | - Yujie Fang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
| | - Aimin Li
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Jiangsu Academy of Agricultural SciencesYangzhou, China
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
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Siniauskaya MG, Danilenko NG, Lukhanina NV, Shymkevich AM, Davydenko OG. Expression of the chloroplast genome: Modern concepts and experimental approaches. ACTA ACUST UNITED AC 2016. [DOI: 10.1134/s2079059716050117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Leu KC, Hsieh MH, Wang HJ, Hsieh HL, Jauh GY. Distinct role of Arabidopsis mitochondrial P-type pentatricopeptide repeat protein-modulating editing protein, PPME, in nad1 RNA editing. RNA Biol 2016; 13:593-604. [PMID: 27149614 PMCID: PMC4962808 DOI: 10.1080/15476286.2016.1184384] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The mitochondrion is an important power generator in most eukaryotic cells. To preserve its function, many essential nuclear-encoded factors play specific roles in mitochondrial RNA metabolic processes, including RNA editing. RNA editing consists of post-transcriptional deamination, which alters specific nucleotides in transcripts to mediate gene expression. In plant cells, many pentatricopeptide repeat proteins (PPRs) participate in diverse organellar RNA metabolic processes, but only PLS-type PPRs are involved in RNA editing. Here, we report a P-type PPR protein from Arabidopsis thaliana, P-type PPR-Modulating Editing (PPME), which has a distinct role in mitochondrial nad1 RNA editing via RNA binding activity. In the homozygous ppme mutant, cytosine (C)-to-uracil (U) conversions at both the nad1-898 and 937 sites were abolished, disrupting Arg300-to-Trp300 and Pro313-to-Ser313 amino acid changes in the mitochondrial NAD1 protein. NAD1 is a critical component of mitochondrial respiration complex I; its activity is severely reduced in the homozygous ppme mutant, resulting in significantly altered growth and development. Both abolished RNA editing and defective complex I activity were completely rescued by CaMV 35S promoter- and PPME native promoter-driven PPME genomic fragments tagged with GFP in a homozygous ppme background. Our experimental results demonstrate a distinct role of a P-type PPR protein, PPME, in RNA editing in plant organelles.
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Affiliation(s)
- Kuan-Chieh Leu
- a Institute of Plant Biology, National Taiwan University , Taipei , Taiwan.,b Institute of Plant and Microbial Biology, Academia Sinica, Nankang , Taipei , Taiwan
| | - Ming-Hsiun Hsieh
- b Institute of Plant and Microbial Biology, Academia Sinica, Nankang , Taipei , Taiwan
| | - Huei-Jing Wang
- b Institute of Plant and Microbial Biology, Academia Sinica, Nankang , Taipei , Taiwan
| | - Hsu-Liang Hsieh
- a Institute of Plant Biology, National Taiwan University , Taipei , Taiwan
| | - Guang-Yuh Jauh
- b Institute of Plant and Microbial Biology, Academia Sinica, Nankang , Taipei , Taiwan.,c Biotechnology Center, National Chung-Hsing University , Taichung , Taiwan
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38
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Zhang W, Xie Y, Xu L, Wang Y, Zhu X, Wang R, Zhang Y, Muleke EM, Liu L. Identification of microRNAs and Their Target Genes Explores miRNA-Mediated Regulatory Network of Cytoplasmic Male Sterility Occurrence during Anther Development in Radish (Raphanus sativus L.). FRONTIERS IN PLANT SCIENCE 2016; 7:1054. [PMID: 27499756 PMCID: PMC4956657 DOI: 10.3389/fpls.2016.01054] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 07/05/2016] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) are a type of endogenous non-coding small RNAs that play critical roles in plant growth and developmental processes. Cytoplasmic male sterility (CMS) is typically a maternally inherited trait and widely used in plant heterosis utilization. However, the miRNA-mediated regulatory network of CMS occurrence during anther development remains largely unknown in radish. In this study, a comparative small RNAome sequencing was conducted in floral buds of CMS line 'WA' and its maintainer line 'WB' by high-throughput sequencing. A total of 162 known miRNAs belonging to 25 conserved and 24 non-conserved miRNA families were isolated and 27 potential novel miRNA families were identified for the first time in floral buds of radish. Of these miRNAs, 28 known and 14 potential novel miRNAs were differentially expressed during anther development. Several target genes for CMS occurrence-related miRNAs encode important transcription factors and functional proteins, which might be involved in multiple biological processes including auxin signaling pathways, signal transduction, miRNA target silencing, floral organ development, and organellar gene expression. Moreover, the expression patterns of several CMS occurrence-related miRNAs and their targets during three stages of anther development were validated by qRT-PCR. In addition, a potential miRNA-mediated regulatory network of CMS occurrence during anther development was firstly proposed in radish. These findings could contribute new insights into complex miRNA-mediated genetic regulatory network of CMS occurrence and advance our understanding of the roles of miRNAs during CMS occurrence and microspore formation in radish and other crops.
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Affiliation(s)
- Wei Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Yang Xie
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
| | - Ronghua Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Yang Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Everlyne M. Muleke
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- *Correspondence: Liwang Liu
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Kobayashi T, Yagi Y, Nakamura T. Development of Genome Engineering Tools from Plant-Specific PPR Proteins Using Animal Cultured Cells. Methods Mol Biol 2016; 1469:147-55. [PMID: 27557692 DOI: 10.1007/978-1-4939-4931-1_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The pentatricopeptide repeat (PPR) motif is a sequence-specific RNA/DNA-binding module. Elucidation of the RNA/DNA recognition mechanism has enabled engineering of PPR motifs as new RNA/DNA manipulation tools in living cells, including for genome editing. However, the biochemical characteristics of PPR proteins remain unknown, mostly due to the instability and/or unfolding propensities of PPR proteins in heterologous expression systems such as bacteria and yeast. To overcome this issue, we constructed reporter systems using animal cultured cells. The cell-based system has highly attractive features for PPR engineering: robust eukaryotic gene expression; availability of various vectors, reagents, and antibodies; highly efficient DNA delivery ratio (>80 %); and rapid, high-throughput data production. In this chapter, we introduce an example of such reporter systems: a PPR-based sequence-specific translational activation system. The cell-based reporter system can be applied to characterize plant genes of interested and to PPR engineering.
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Affiliation(s)
| | - Yusuke Yagi
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan
| | - Takahiro Nakamura
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan.
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Ramos‐Vega M, Guevara‐García A, Llamas E, Sánchez‐León N, Olmedo‐Monfil V, Vielle‐Calzada JP, León P. Functional analysis of the
Arabidopsis thaliana
CHLOROPLAST BIOGENESIS
19
pentatricopeptide repeat editing protein. NEW PHYTOLOGIST 2015; 208:430-41. [PMID: 25980341 DOI: 10.1111/nph.13468] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/16/2015] [Indexed: 05/27/2023]
Affiliation(s)
- Maricela Ramos‐Vega
- Departamento de Biología Molecular de Plantas Instituto de Biotecnología Universidad Nacional Autónoma de México Av. Universidad 2001 Col. Chamilpa Cuernavaca 62210 México
| | - Arturo Guevara‐García
- Departamento de Biología Molecular de Plantas Instituto de Biotecnología Universidad Nacional Autónoma de México Av. Universidad 2001 Col. Chamilpa Cuernavaca 62210 México
| | - Ernesto Llamas
- Departamento de Biología Molecular de Plantas Instituto de Biotecnología Universidad Nacional Autónoma de México Av. Universidad 2001 Col. Chamilpa Cuernavaca 62210 México
| | - Nidia Sánchez‐León
- Grupo de Desarrollo Reproductivo y Apomixis Laboratorio Nacional de Genómica para la Biodiversidad CINVESTAV Irapuato 36821 México
| | - Vianey Olmedo‐Monfil
- Grupo de Desarrollo Reproductivo y Apomixis Laboratorio Nacional de Genómica para la Biodiversidad CINVESTAV Irapuato 36821 México
| | - Jean Philippe Vielle‐Calzada
- Grupo de Desarrollo Reproductivo y Apomixis Laboratorio Nacional de Genómica para la Biodiversidad CINVESTAV Irapuato 36821 México
| | - Patricia León
- Departamento de Biología Molecular de Plantas Instituto de Biotecnología Universidad Nacional Autónoma de México Av. Universidad 2001 Col. Chamilpa Cuernavaca 62210 México
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41
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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: 88] [Impact Index Per Article: 9.8] [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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42
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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: 58] [Impact Index Per Article: 6.4] [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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43
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Gully BS, Shah KR, Lee M, Shearston K, Smith NM, Sadowska A, Blythe AJ, Bernath-Levin K, Stanley WA, Small ID, Bond CS. The design and structural characterization of a synthetic pentatricopeptide repeat protein. ACTA ACUST UNITED AC 2015; 71:196-208. [PMID: 25664731 DOI: 10.1107/s1399004714024869] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 11/12/2014] [Indexed: 11/10/2022]
Abstract
Proteins of the pentatricopeptide repeat (PPR) superfamily are characterized by tandem arrays of a degenerate 35-amino-acid α-hairpin motif. PPR proteins are typically single-stranded RNA-binding proteins with essential roles in organelle biogenesis, RNA editing and mRNA maturation. A modular, predictable code for sequence-specific binding of RNA by PPR proteins has recently been revealed, which opens the door to the de novo design of bespoke proteins with specific RNA targets, with widespread biotechnological potential. Here, the design and production of a synthetic PPR protein based on a consensus sequence and the determination of its crystal structure to 2.2 Å resolution are described. The crystal structure displays helical disorder, resulting in electron density representing an infinite superhelical PPR protein. A structural comparison with related tetratricopeptide repeat (TPR) proteins, and with native PPR proteins, reveals key roles for conserved residues in directing the structure and function of PPR proteins. The designed proteins have high solubility and thermal stability, and can form long tracts of PPR repeats. Thus, consensus-sequence synthetic PPR proteins could provide a suitable backbone for the design of bespoke RNA-binding proteins with the potential for high specificity.
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Affiliation(s)
- Benjamin S Gully
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Kunal R Shah
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Mihwa Lee
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Kate Shearston
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Nicole M Smith
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Agata Sadowska
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Amanda J Blythe
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Kalia Bernath-Levin
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Will A Stanley
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Ian D Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
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44
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Gully BS, Cowieson N, Stanley WA, Shearston K, Small ID, Barkan A, Bond CS. The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA. Nucleic Acids Res 2015; 43:1918-26. [PMID: 25609698 PMCID: PMC4330388 DOI: 10.1093/nar/gkv027] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The pentatricopeptide repeat (PPR) protein family is a large family of RNA-binding proteins that is characterized by tandem arrays of a degenerate 35-amino-acid motif which form an α-solenoid structure. PPR proteins influence the editing, splicing, translation and stability of specific RNAs in mitochondria and chloroplasts ZEA MAYS: PPR10 is amongst the best studied PPR proteins, where sequence-specific binding to two RNA transcripts, ATPH: and PSAJ, HAS BEEN DEMONSTRATED TO FOLLOW: a recognition code where the identity of two amino acids per repeat determines the base-specificity. A recently solved ZmPPR10: PSAJ: complex crystal structure suggested a homodimeric complex with considerably fewer sequence-specific protein-RNA contacts than inferred PREVIOUSLY: Here we describe the solution structure of the ZmPPR10: ATPH: complex using size-exclusion chromatography-coupled synchrotron small-angle X-ray scattering (SEC-SY-SAXS). Our results support prior evidence that PPR10 binds RNA as a monomer, and that it does so in a manner that is commensurate with a canonical and predictable RNA-binding mode across much of the RNA-protein interface.
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Affiliation(s)
- Benjamin S Gully
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Nathan Cowieson
- SAXSWAXS beamline, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria, Australia
| | - Will A Stanley
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Kate Shearston
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Ian D Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
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45
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Shikanai T. RNA editing in plants: Machinery and flexibility of site recognition. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:779-85. [PMID: 25585161 DOI: 10.1016/j.bbabio.2014.12.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 12/23/2014] [Accepted: 12/29/2014] [Indexed: 11/20/2022]
Abstract
In plants, RNA editing is a process that deaminates specific cytidines (C) to uridines (U). PLS subfamily members of PPR proteins function in site recognition of the target C. In silico analysis has predicted the code used for PPR motif-nucleotide interaction, and the crystal structure of a protein-RNA complex supports this model. Despite progress in understanding the RNA-binding mechanism of PPR proteins, some of the flexibility of RNA recognition observed in trans-factors of RNA editing has not been fully explained. It is probably necessary to consider another unknown mechanism, and this consideration is related to the question of how PPR proteins have managed the creation of RNA editing sites during evolution. This question may be related to the mystery of the biological function of RNA editing in plants. MORF/RIP family members are required for RNA editing at multiple editing sites and are components of the RNA editosome in plants. The DYW domain has been a strong candidate for the C deaminase activity required for C-to-U conversion in RNA editing. So far, the activity of this enzyme has not been detected in recombinant DYW proteins, and several puzzling experimental results need to be explained to support the model. It is still difficult to resolve the entire image of the editosome in RNA editing in plants. This article is part of a Special Issue entitled: Chloroplast Biogenesis.
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Affiliation(s)
- Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502 Japan; CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0076, Japan.
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46
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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: 78] [Impact Index Per Article: 7.8] [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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47
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Okuda K, Shoki H, Arai M, Shikanai T, Small I, Nakamura T. Quantitative analysis of motifs contributing to the interaction between PLS-subfamily members and their target RNA sequences in plastid RNA editing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:870-82. [PMID: 25279799 DOI: 10.1111/tpj.12687] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/19/2014] [Accepted: 09/24/2014] [Indexed: 05/08/2023]
Abstract
In plant organelles, RNA editing alters specific cytidine residues to uridine in transcripts. Target cytidines are specifically recognized by pentatricopeptide repeat (PPR) proteins of the PLS subfamily, which have additional C-terminal E or E-DYW motifs. Recent in silico analysis proposed a model for site recognition by PLS-subfamily PPR proteins, with a correspondence of one PPR motif to one nucleotide, and with the C-terminal last S motif aligning with the nucleotide at position -4 with respect to the editing site. Here, we present quantitative biochemical data on site recognition by four PLS-subfamily proteins: CRR28 and OTP85 are DYW-class members, whereas CRR21 and OTP80 are E-class members. The minimal RNA segments required for high-affinity binding by these PPR proteins were experimentally determined. The results were generally consistent with the in silico-based model; however, we clarified that several PPR motifs, including the C-terminal L2 and S motifs of CRR21 and OTP80, are dispensable for the RNA binding, suggesting distinct contributions of each PPR motif to site recognition. We also demonstrate that the DYW motif interacts with the target C and its 5' proximal region (from -3 to 0), whereas the E motif is not involved in binding.
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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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48
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Zamudio-Ochoa A, Camacho-Villasana Y, García-Guerrero AE, Pérez-Martínez X. The Pet309 pentatricopeptide repeat motifs mediate efficient binding to the mitochondrial COX1 transcript in yeast. RNA Biol 2014; 11:953-67. [PMID: 25181249 PMCID: PMC4179968 DOI: 10.4161/rna.29780] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mitochondrial synthesis of Cox1, the largest subunit of the cytochrome c oxidase complex, is controlled by Mss51 and Pet309, two mRNA-specific translational activators that act via the COX1 mRNA 5′-UTR through an unknown mechanism. Pet309 belongs to the pentatricopeptide repeat (PPR) protein family, which is involved in RNA metabolism in mitochondria and chloroplasts, and its sequence predicts at least 12 PPR motifs in the central portion of the protein. Deletion of these motifs selectively disrupted translation but not accumulation of the COX1 mRNA. We used RNA coimmunoprecipitation assays to show that Pet309 interacts with the COX1 mRNA in vivo and that this association is present before processing of the COX1 mRNA from the ATP8/6 polycistronic mRNA. This association was not affected by deletion of 8 of the PPR motifs but was undetectable after deletion of the entire 12-PPR region. However, interaction of the Pet309 protein lacking 12 PPR motifs with the COX1 mRNA was detected after overexpression of the mutated form of the protein, suggesting that deletion of this region decreased the binding affinity for the COX1 mRNA without abolishing it entirely. Moreover, binding of Pet309 to the COX1 mRNA was affected by deletion of Mss51. This work demonstrates an in vivo physical interaction between a yeast mitochondrial translational activator and its target mRNA and shows the cooperativity of the PPR domains of Pet309 in interaction with the COX1 mRNA.
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Affiliation(s)
- Angélica Zamudio-Ochoa
- Departamento de Genética Molecular; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México
| | - Yolanda Camacho-Villasana
- Departamento de Genética Molecular; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México
| | - Aldo E García-Guerrero
- Departamento de Genética Molecular; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México
| | - Xochitl Pérez-Martínez
- Departamento de Genética Molecular; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México
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49
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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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50
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Takenaka M, Zehrmann A, Verbitskiy D, Härtel B, Brennicke A. RNA editing in plants and its evolution. Annu Rev Genet 2014; 47:335-52. [PMID: 24274753 DOI: 10.1146/annurev-genet-111212-133519] [Citation(s) in RCA: 249] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA editing alters the identity of nucleotides in RNA molecules such that the information for a protein in the mRNA differs from the prediction of the genomic DNA. In chloroplasts and mitochondria of flowering plants, RNA editing changes C nucleotides to U nucleotides; in ferns and mosses, it also changes U to C. The approximately 500 editing sites in mitochondria and 40 editing sites in plastids of flowering plants are individually addressed by specific proteins, genes for which are amplified in plant species with organellar RNA editing. These proteins contain repeat elements that bind to cognate RNA sequence motifs just 5' to the edited nucleotide. In flowering plants, the site-specific proteins interact selectively with individual members of a different, smaller family of proteins. These latter proteins may be connectors between the site-specific proteins and the as yet unknown deaminating enzymatic activity.
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Affiliation(s)
- Mizuki Takenaka
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany; , , , ,
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