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Shen C, Xu H, Huang WZ, Zhao Q, Zhu RL. Is RNA editing truly absent in the complex thalloid liverworts (Marchantiopsida)? Evidence of extensive RNA editing from Cyathodium cavernarum. THE NEW PHYTOLOGIST 2024; 242:2817-2831. [PMID: 38587065 DOI: 10.1111/nph.19750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/20/2024] [Indexed: 04/09/2024]
Abstract
RNA editing is a crucial modification in plants' organellar transcripts that converts cytidine to uridine (C-to-U; and sometimes uridine to cytidine) in RNA molecules. This post-transcriptional process is controlled by the PLS-class protein with a DYW domain, which belongs to the pentatricopeptide repeat (PPR) protein family. RNA editing is widespread in land plants; however, complex thalloid liverworts (Marchantiopsida) are the only group reported to lack both RNA editing and DYW-PPR protein. The liverwort Cyathodium cavernarum (Marchantiopsida, Cyathodiaceae), typically found in cave habitats, was newly found to have 129 C-to-U RNA editing sites in its chloroplast and 172 sites in its mitochondria. The Cyathodium genus, specifically C. cavernarum, has a large number of PPR editing factor genes, including 251 DYW-type PPR proteins. These DYW-type PPR proteins may be responsible for C-to-U RNA editing in C. cavernarum. Cyathodium cavernarum possesses both PPR DYW proteins and RNA editing. Our analysis suggests that the remarkable RNA editing capability of C. cavernarum may have been acquired alongside the emergence of DYW-type PPR editing factors. These findings provide insight into the evolutionary pattern of RNA editing in land plants.
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Affiliation(s)
- Chao Shen
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Hao Xu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Wen-Zhuan Huang
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Qiong Zhao
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Rui-Liang Zhu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
- Tiantong National Station of Forest Ecosystem, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai, 200241, China
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2
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Bayer-Császár E, Jörg A, Härtel B, Brennicke A, Takenaka M. The Gating Domain of MEF28 Is Essential for Editing Two Contiguous Cytidines in nad2 mRNA in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2024; 65:590-601. [PMID: 37530742 DOI: 10.1093/pcp/pcad087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/21/2023] [Accepted: 08/01/2023] [Indexed: 08/03/2023]
Abstract
In plant organelles, each C-to-U RNA-editing site is specifically recognized by pentatricopeptide repeat (PPR) proteins with E1-E2, E1-E2-E+ or E1-E2-DYW domain extensions at the C-terminus. The distance between the PPR domain-binding site and the RNA-editing site is usually fixed at four bases, increasing the specificity of target-site recognition in this system. We here report, in contrast to the general case, on MEF28, which edits two adjacent mitochondrial sites, nad2-89 and nad2-90. When the sDYW domain of MEF28 was replaced with one derived from MEF11 or CRR22, the ability to edit downstream sites was lost, suggesting that the DYW domain of MEF28 provides unique target flexibility for two continuous cytidines. By contrast, substitutions of the entire E1-E2-DYW domains by MEF19E1-E2, SLO2E1-E2-E+ or CRR22E1-E2-E+ target both nad2 sites. In these cases, access to the contiguous sites in the chimeric PPR proteins is likely to be provided by the trans-associated DYW1-like proteins via the replaced E1-E2 or E1-E2-E+ domains. Furthermore, we demonstrated that the gating domain of MEF28 plays an important role in specific target-site recognition of the DYW domain. This finding suggests that the DYW domain and its internal gating domain fine-tune the specificity of the target site, which is valuable information for designing specific synthetic RNA-editing tools based on plant RNA-editing factors.
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Affiliation(s)
| | - Anja Jörg
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, Ulm 89069, Germany
| | - Barbara Härtel
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, Ulm 89069, Germany
| | - Axel Brennicke
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, Ulm 89069, Germany
| | - Mizuki Takenaka
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
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3
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Lesch E, Stempel MS, Dressnandt V, Oldenkott B, Knoop V, Schallenberg-Rüdinger M. Conservation of the moss RNA editing factor PPR78 despite the loss of its known cytidine-to-uridine editing sites is explained by a hidden extra target. THE PLANT CELL 2024; 36:727-745. [PMID: 38000897 PMCID: PMC10896298 DOI: 10.1093/plcell/koad292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/27/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023]
Abstract
Cytidine (C)-to-uridine (U) RNA editing in plant organelles relies on specific RNA-binding pentatricopeptide repeat (PPR) proteins. In the moss Physcomitrium patens, all such RNA editing factors feature a C-terminal DYW domain that acts as the cytidine deaminase for C-to-U conversion. PPR78 of Physcomitrium targets 2 mitochondrial editing sites, cox1eU755SL and rps14eU137SL. Remarkably, the latter is edited to highly variable degrees in different mosses. Here, we aimed to unravel the coevolution of PPR78 and its 2 target sites in mosses. Heterologous complementation in a Physcomitrium knockout line revealed that the variable editing of rps14eU137SL depends on the PPR arrays of different PPR78 orthologues but not their C-terminal domains. Intriguingly, PPR78 has remained conserved despite the simultaneous loss of editing at both known targets among Hypnales (feather mosses), suggesting it serves an additional function. Using a recently established RNA editing assay in Escherichia coli, we confirmed site-specific RNA editing by PPR78 in the bacterium and identified 4 additional off-targets in the bacterial transcriptome. Based on conservation profiles, we predicted ccmFNeU1465RC as a candidate editing target of PPR78 in moss mitochondrial transcriptomes. We confirmed editing at this site in several mosses and verified that PPR78 targets ccmFNeU1465RC in the bacterial editing system, explaining the conservation and functional adaptation of PPR78 during moss evolution.
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Affiliation(s)
- Elena Lesch
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Maike Simone Stempel
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Vanessa Dressnandt
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Bastian Oldenkott
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Volker Knoop
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Mareike Schallenberg-Rüdinger
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
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4
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Yang Y, Oldenkott B, Ramanathan S, Lesch E, Takenaka M, Schallenberg-Rüdinger M, Knoop V. DYW cytidine deaminase domains have a long-range impact on RNA recognition by the PPR array of chimeric plant C-to-U RNA editing factors and strongly affect target selection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:840-854. [PMID: 37565789 DOI: 10.1111/tpj.16412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 08/12/2023]
Abstract
The protein factors for the specific C-to-U RNA editing events in plant mitochondria and chloroplasts possess unique arrays of RNA-binding pentatricopeptide repeats (PPRs) linked to carboxy-terminal cytidine deaminase DYW domains via the extension motifs E1 and E2. The E1 and E2 motifs have distant similarities to tetratricopeptide repeats known to mediate protein-protein interactions but their precise function is unclear. Here, we investigate the tolerance of PPR56 and PPR65, two functionally characterized RNA editing factors of the moss Physcomitrium patens, for the creation of chimeras by variably replacing their C-terminal protein regions. Making use of a heterologous RNA editing assay system in Escherichia coli we find that heterologous DYW domains can strongly restrict or widen the spectrum of off-targets in the bacterial transcriptome for PPR56. Surprisingly, our data suggest that these changes are not only caused by the preference of a given heterologous DYW domain for the immediate sequence environment of the cytidine to be edited but also by a long-range impact on the nucleotide selectivity of the upstream PPRs.
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Affiliation(s)
- Yingying Yang
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Bastian Oldenkott
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Shyam Ramanathan
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Elena Lesch
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Mizuki Takenaka
- Department of Botany Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Mareike Schallenberg-Rüdinger
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
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5
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Dong SS, Zhou XP, Peng T, Liu Y. Mitochondrial RNA editing sites affect the phylogenetic reconstruction of gymnosperms. PLANT DIVERSITY 2023; 45:485-489. [PMID: 37601539 PMCID: PMC10435907 DOI: 10.1016/j.pld.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 08/22/2023]
Abstract
•RNA editing sites may contain homoplasious signals that cause artifactual inferences in phylogenetic analyses.•Excluding RNA editing sites from gymnosperm mitochondrial genes restored the sister relationship of gnetophytes and Pinaceae.•Phylogenetic analysis based on mitochondrial genomic data should carefully evaluate the impact of RNA editing sites.
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Affiliation(s)
- Shan-Shan Dong
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
| | - Xu-Ping Zhou
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
- School of Life Sciences, Guizhou Normal University, Guiyang 550001, Guizhou, China
| | - Tao Peng
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
- School of Life Sciences, Guizhou Normal University, Guiyang 550001, Guizhou, China
| | - Yang Liu
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, Guangdong, China
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6
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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: 3] [Impact Index Per Article: 3.0] [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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7
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Xiang YL, Jin XJ, Shen C, Cheng XF, Shu L, Zhu RL. New insights into the phylogeny of the complex thalloid liverworts (Marchantiopsida) based on chloroplast genomes. Cladistics 2022; 38:649-662. [PMID: 35779275 DOI: 10.1111/cla.12513] [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: 02/20/2022] [Revised: 05/22/2022] [Accepted: 05/25/2022] [Indexed: 01/31/2023] Open
Abstract
Marchantiopsida (complex thalloid liverworts) are one of the earliest lineages of embryophytes (land plants), and well-known for their air pores and chambers, pegged rhizoids, and absence of organellular RNA editing sites. Despite their importance to an understanding of early embryophyte evolution, many key nodes within this class remain poorly resolved, owing to the paucity of genetic loci previously available for phylogenetic analyses. Here, we sequenced 54 plastomes, representing 28 genera, nearly all families, and all orders of Marchantiopsida. Based on these plastomes, we present a hypothesis of deep relationships within the class, and make the first investigations of gene contents and synteny. Overall, the Marchantiopsida plastomes were well-conserved, with the exception of the genus Cyathodium that has plastomes with higher GC content, fewer single sequence repeats (SSRs), and more structural variations, implying that this genus might possess RNA editing sites. Abundant repetitive elements and six highly divergent regions were identified as suitable for future infrafamilial taxonomic studies. The phylogenetic topology of Sphaerocarpales, Neohodgsoniales and Blasiales within Marchantiopsida was essentially congruent with previous studies but generally we obtained higher support values. Based on molecular evidence and previous morphological studies, we include Lunulariales in Marchantiales and suggest the retention of narrowed delimitation of monotypic families. The phylogenetic relationships within Marchantiales were better resolved, and 13 monophyletic families were recovered. Our analyses confirmed that the loss of intron 2 of ycf3 is a synapomorphy of Marchantiidae. Finally, we propose a new genus, Asterellopsis (Aytoniaceae), and present an updated classification of Marchantiopsida. The highly supported phylogenetic backbone provided here establishes a framework for future comparative and evolutionary studies of the complex thalloid liverworts.
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Affiliation(s)
- You-Liang Xiang
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xin-Jie Jin
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China.,College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
| | - Chao Shen
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xia-Fang Cheng
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Lei Shu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Rui-Liang Zhu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China.,Shanghai Institute of Eco-Chongming (SIEC), Shanghai, 200062, China.,Tiantong National Station of Forest Ecosystem, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai, 200241, China
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8
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Bowman JL, Arteaga-Vazquez M, Berger F, Briginshaw LN, Carella P, Aguilar-Cruz A, Davies KM, Dierschke T, Dolan L, Dorantes-Acosta AE, Fisher TJ, Flores-Sandoval E, Futagami K, Ishizaki K, Jibran R, Kanazawa T, Kato H, Kohchi T, Levins J, Lin SS, Nakagami H, Nishihama R, Romani F, Schornack S, Tanizawa Y, Tsuzuki M, Ueda T, Watanabe Y, Yamato KT, Zachgo S. The renaissance and enlightenment of Marchantia as a model system. THE PLANT CELL 2022; 34:3512-3542. [PMID: 35976122 PMCID: PMC9516144 DOI: 10.1093/plcell/koac219] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/21/2022] [Indexed: 05/07/2023]
Abstract
The liverwort Marchantia polymorpha has been utilized as a model for biological studies since the 18th century. In the past few decades, there has been a Renaissance in its utilization in genomic and genetic approaches to investigating physiological, developmental, and evolutionary aspects of land plant biology. The reasons for its adoption are similar to those of other genetic models, e.g. simple cultivation, ready access via its worldwide distribution, ease of crossing, facile genetics, and more recently, efficient transformation, genome editing, and genomic resources. The haploid gametophyte dominant life cycle of M. polymorpha is conducive to forward genetic approaches. The lack of ancient whole-genome duplications within liverworts facilitates reverse genetic approaches, and possibly related to this genomic stability, liverworts possess sex chromosomes that evolved in the ancestral liverwort. As a representative of one of the three bryophyte lineages, its phylogenetic position allows comparative approaches to provide insights into ancestral land plants. Given the karyotype and genome stability within liverworts, the resources developed for M. polymorpha have facilitated the development of related species as models for biological processes lacking in M. polymorpha.
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Affiliation(s)
| | - Mario Arteaga-Vazquez
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Frederic Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Liam N Briginshaw
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Philip Carella
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Adolfo Aguilar-Cruz
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Kevin M Davies
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4442, New Zealand
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Liam Dolan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Ana E Dorantes-Acosta
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Tom J Fisher
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Eduardo Flores-Sandoval
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Kazutaka Futagami
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | | | - Rubina Jibran
- The New Zealand Institute for Plant & Food Research Limited, Auckland 1142, New Zealand
| | - Takehiko Kanazawa
- Division of Cellular Dynamics, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hirotaka Kato
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Jonathan Levins
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Hirofumi Nakagami
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ryuichi Nishihama
- Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | | | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Sabine Zachgo
- Division of Botany, School of Biology and Chemistry, Osnabrück University, Osnabrück 49076, Germany
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9
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Huang KY, Kan SL, Shen TT, Gong P, Feng YY, Du H, Zhao YP, Wan T, Wang XQ, Ran JH. A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms. Int J Mol Sci 2022; 23:ijms231810844. [PMID: 36142757 PMCID: PMC9505161 DOI: 10.3390/ijms231810844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 12/05/2022] Open
Abstract
Although more than 9100 plant plastomes have been sequenced, RNA editing sites of the whole plastome have been experimentally verified in only approximately 21 species, which seriously hampers the comprehensive evolutionary study of chloroplast RNA editing. We investigated the evolutionary pattern of chloroplast RNA editing sites in 19 species from all 13 families of gymnosperms based on a combination of genomic and transcriptomic data. We found that the chloroplast C-to-U RNA editing sites of gymnosperms shared many common characteristics with those of other land plants, but also exhibited many unique characteristics. In contrast to that noted in angiosperms, the density of RNA editing sites in ndh genes was not the highest in the sampled gymnosperms, and both loss and gain events at editing sites occurred frequently during the evolution of gymnosperms. In addition, GC content and plastomic size were positively correlated with the number of chloroplast RNA editing sites in gymnosperms, suggesting that the increase in GC content could provide more materials for RNA editing and facilitate the evolution of RNA editing in land plants or vice versa. Interestingly, novel G-to-A RNA editing events were commonly found in all sampled gymnosperm species, and G-to-A RNA editing exhibits many different characteristics from C-to-U RNA editing in gymnosperms. This study revealed a comprehensive evolutionary scenario for chloroplast RNA editing sites in gymnosperms, and reported that a novel type of G-to-A RNA editing is prevalent in gymnosperms.
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Affiliation(s)
- Kai-Yuan Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sheng-Long Kan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ting-Ting Shen
- School of Earth Sciences, East China University of Technology, Nanchang 330013, China
| | - Pin Gong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuan-Yuan Feng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yun-Peng Zhao
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tao Wan
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
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10
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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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11
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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: 4] [Impact Index Per Article: 2.0] [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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12
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Xiang QP, Tang JY, Yu JG, Smith DR, Zhu YM, Wang YR, Kang JS, Yang J, Zhang XC. The evolution of extremely diverged plastomes in Selaginellaceae (lycophyte) is driven by repeat patterns and the underlying DNA maintenance machinery. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:768-784. [PMID: 35648423 DOI: 10.1111/tpj.15851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Two factors are proposed to account for the unusual features of organellar genomes: the disruptions of organelle-targeted DNA replication, repair, and recombination (DNA-RRR) systems in the nuclear genome and repetitive elements in organellar genomes. Little is known about how these factors affect organellar genome evolution. The deep-branching vascular plant family Selaginellaceae is known to have a deficient DNA-RRR system and convergently evolved organellar genomes. However, we found that the plastid genome (plastome) of Selaginella sinensis has extremely accelerated substitution rates, a low GC content, pervasive repeat elements, a dynamic network structure, and it lacks direct or inverted repeats. Unexpectedly, its organelle DNA-RRR system is short of a plastid-targeted Recombinase A1 (RecA1) and a mitochondrion-targeted RecA3, in line with other explored Selaginella species. The plastome contains a large collection of short- and medium-sized repeats. Given the absence of RecA1 surveillance, we propose that these repeats trigger illegitimate recombination, accelerated mutation rates, and structural instability. The correlations between repeat quantity and architectural complexity in the Selaginella plastomes support these conclusions. We, therefore, hypothesize that the interplay of the deficient DNA-RRR system and the high repeat content has led to the extraordinary divergence of the S. sinensis plastome. Our study not only sheds new light on the mechanism of plastome divergence by emphasizing the power of cytonuclear integration, but it also reconciles the longstanding contradiction on the effects of DNA-RRR system disruption on genome structure evolution.
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Affiliation(s)
- Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jun-Yong Tang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Gao Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - David Roy Smith
- Department of Biology, University of Western Ontario, London, N6A 5B7, Ontario, Canada
| | - Yan-Mei Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Ya-Rong Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jong-Soo Kang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
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13
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Yang Y, Yu X, Wei P, Liu C, Chen Z, Li X, Liu X. Comparative chloroplast genome and transcriptome analysis on the ancient genus Isoetes from China. FRONTIERS IN PLANT SCIENCE 2022; 13:924559. [PMID: 35968088 PMCID: PMC9372280 DOI: 10.3389/fpls.2022.924559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Isoetes is a famous living fossil that plays a significant role in the evolutionary studies of the plant kingdom. To explore the adaptive evolution of the ancient genus Isoetes from China, we focused on Isoetes yunguiensis (Q.F. Wang and W.C. Taylor), I. shangrilaensis (X. Li, Y.Q. Huang, X.K. Dai & X. Liu), I. taiwanensis (DeVol), I. sinensis (T.C. Palmer), I. hypsophila_GHC (Handel-Mazzetti), and I. hypsophila_HZS in this study. We sequenced, assembled, and annotated six individuals' chloroplast genomes and transcriptomes, and performed a series of analyses to investigate their chloroplast genome structures, RNA editing events, and adaptive evolution. The six chloroplast genomes of Isoetes exhibited a typical quadripartite structure with conserved genome sequence and structure. Comparative analyses of Isoetes species demonstrated that the gene organization, genome size, and GC contents of the chloroplast genome are highly conserved across the genus. Besides, our positive selection analyses suggested that one positively selected gene was statistically supported in Isoetes chloroplast genomes using the likelihood ratio test (LRT) based on branch-site models. Moreover, we detected positive selection signals using transcriptome data, suggesting that nuclear-encoded genes involved in the adaption of Isoetes species to the extreme environment of the Qinghai-Tibetan Plateau (QTP). In addition, we identified 291-579 RNA editing sites in the chloroplast genomes of six Isoetes based on transcriptome data, well above the average of angiosperms. RNA editing in protein-coding transcripts results from amino acid changes to increase their hydrophobicity and conservation in Isoetes, which may help proteins form functional three-dimensional structure. Overall, the results of this study provide comprehensive transcriptome and chloroplast genome resources and contribute to a better understanding of adaptive evolutionary and molecular biology in Isoetes.
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Affiliation(s)
- Yujiao Yang
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaolei Yu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Pei Wei
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chenlai Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhuyifu Chen
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaoyan Li
- Biology Experimental Teaching Center, School of Life Science, Wuhan University, Wuhan, China
| | - Xing Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, China
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14
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Fernandez-Pozo N, Haas FB, Gould SB, Rensing SA. An overview of bioinformatics, genomics, and transcriptomics resources for bryophytes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4291-4305. [PMID: 35148385 DOI: 10.1093/jxb/erac052] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Bryophytes are useful models for the study of plant evolution, development, plant-fungal symbiosis, stress responses, and gametogenesis. Additionally, their dominant haploid gametophytic phase makes them great models for functional genomics research, allowing straightforward genome editing and gene knockout via CRISPR or homologous recombination. Until 2016, however, the only bryophyte genome sequence published was that of Physcomitrium patens. Throughout recent years, several other bryophyte genomes and transcriptome datasets became available, enabling better comparative genomics in evolutionary studies. The increase in the number of bryophyte genome and transcriptome resources available has yielded a plethora of annotations, databases, and bioinformatics tools to access the new data, which covers the large diversity of this clade and whose biology comprises features such as association with arbuscular mycorrhiza fungi, sex chromosomes, low gene redundancy, or loss of RNA editing genes for organellar transcripts. Here we provide a guide to resources available for bryophytes with regards to genome and transcriptome databases and bioinformatics tools.
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Affiliation(s)
- Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Subtropical and Mediterranean Fruit Crops, Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-CSIC-UMA), Málaga, Spain
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Sven B Gould
- Evolutionary Cell Biology, Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University of Marburg, Marburg, Germany
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15
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He ZS, Zhu A, Yang JB, Fan W, Li DZ. Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing. Int J Mol Sci 2021; 22:ijms22189842. [PMID: 34576004 PMCID: PMC8466565 DOI: 10.3390/ijms22189842] [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: 08/12/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Posttranscriptional modifications, including intron splicing and RNA editing, are common processes during regulation of gene expression in plant organelle genomes. However, the intermediate products of intron-splicing, and the interplay between intron-splicing and RNA-editing were not well studied. Most organelle transcriptome analyses were based on the Illumina short reads which were unable to capture the full spectrum of transcript intermediates within an organelle. To fully investigate the intermediates during intron splicing and the underlying relationships with RNA editing, we used PacBio DNA-seq and Iso-seq, together with Illumina short reads genome and transcriptome sequencing data to assemble the chloroplast and mitochondrial genomes of Nymphaea 'Joey Tomocik' and analyze their posttranscriptional features. With the direct evidence from Iso-seq, multiple intermediates partially or fully intron-spliced were observed, and we also found that both cis- and trans-splicing introns were spliced randomly. Moreover, by using rRNA-depleted and non-Oligo(dT)-enrichment strand-specific RNA-seq data and combining direct SNP-calling and transcript-mapping methods, we identified 98 and 865 RNA-editing sites in the plastome and mitogenome of N. 'Joey Tomocik', respectively. The target codon preference, the tendency of increasing protein hydrophobicity, and the bias distribution of editing sites are similar in both organelles, suggesting their common evolutionary origin and shared editing machinery. The distribution of RNA editing sites also implies that the RNA editing sites in the intron and exon regions may splice synchronously, except those exonic sites adjacent to intron which could only be edited after being intron-spliced. Our study provides solid evidence for the multiple intermediates co-existing during intron-splicing and their interplay with RNA editing in organelle genomes of a basal angiosperm.
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Affiliation(s)
- Zheng-Shan He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-S.H.); (A.Z.); (J.-B.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-S.H.); (A.Z.); (J.-B.Y.)
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-S.H.); (A.Z.); (J.-B.Y.)
| | - Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-S.H.); (A.Z.); (J.-B.Y.)
- Correspondence: (W.F.); (D.-Z.L.); Tel.: +86-871-6523-8370 (W.F.); +86-871-6522-3503 (D.-Z.L.)
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-S.H.); (A.Z.); (J.-B.Y.)
- Correspondence: (W.F.); (D.-Z.L.); Tel.: +86-871-6523-8370 (W.F.); +86-871-6522-3503 (D.-Z.L.)
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16
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Fauskee BD, Sigel EM, Pryer KM, Grusz AL. Variation in frequency of plastid RNA editing within Adiantum implies rapid evolution in fern plastomes. AMERICAN JOURNAL OF BOTANY 2021; 108:820-827. [PMID: 33969475 DOI: 10.1002/ajb2.1649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Recent studies of plant RNA editing have demonstrated that the number of editing sites can vary widely among large taxonomic groups (orders, families). Yet, very little is known about intrageneric variation in frequency of plant RNA editing, and no study has been conducted in ferns. METHODS We determined plastid RNA-editing counts for two species of Adiantum (Pteridaceae), A. shastense and A. aleuticum, by implementing a pipeline that integrated read-mapping and SNP-calling software to identify RNA-editing sites. We then compared the edits found in A. aleuticum and A. shastense with previously published edits from A. capillus-veneris by generating alignments for each plastid gene. RESULTS We found direct evidence for 505 plastid RNA-editing sites in A. aleuticum and 509 in A. shastense, compared with 350 sites in A. capillus-veneris. We observed striking variation in the number and location of the RNA-editing sites among the three species, with reverse (U-to-C) editing sites showing a higher degree of conservation than forward (C-to-U) sites. Additionally, sites involving start and stop codons were highly conserved. CONCLUSIONS Variation in the frequency of RNA editing within Adiantum implies that RNA-editing sites can be rapidly gained or lost throughout evolution. However, varying degrees of conservation between both C-to-U and U-to-C sites and sites in start or stop codons, versus other codons, hints at the likely independent origin of both types of edits and a potential selective advantage conferred by RNA editing.
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Affiliation(s)
- Blake D Fauskee
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Erin M Sigel
- Department of Biological Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | | | - Amanda L Grusz
- Department of Biology, University of Minnesota Duluth, Duluth, MN, 55812, USA
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17
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Dong S, Zhao C, Zhang S, Wu H, Mu W, Wei T, Li N, Wan T, Liu H, Cui J, Zhu R, Goffinet B, Liu Y. The Amount of RNA Editing Sites in Liverwort Organellar Genes Is Correlated with GC Content and Nuclear PPR Protein Diversity. Genome Biol Evol 2020; 11:3233-3239. [PMID: 31651960 PMCID: PMC6865856 DOI: 10.1093/gbe/evz232] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2019] [Indexed: 02/06/2023] Open
Abstract
RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here, we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded pentatricopeptide repeat (PPR) proteins in the transcriptome assemblies of these taxa. We identified 7,428 RNA editing sites in 128 organellar genes from 31 non-marchantioid liverwort species, and characterized 25,059 PPR protein sequences. The abundance of organellar RNA editing sites varies greatly among liverwort lineages, genes, and codon positions, and shows strong positive correlations with the GC content of protein-coding genes, and the diversity of the PLS class of nuclear PPR proteins.
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Affiliation(s)
- Shanshan Dong
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Chaoxian Zhao
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.,Department of Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Shouzhou Zhang
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | | | | | - Na Li
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Tao Wan
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | | | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Ruiliang Zhu
- Department of Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut
| | - Yang Liu
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
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18
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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: 171] [Impact Index Per Article: 42.8] [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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19
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Gutmann B, Royan S, Schallenberg-Rüdinger M, Lenz H, Castleden IR, McDowell R, Vacher MA, Tonti-Filippini J, Bond CS, Knoop V, Small ID. The Expansion and Diversification of Pentatricopeptide Repeat RNA-Editing Factors in Plants. MOLECULAR PLANT 2020; 13:215-230. [PMID: 31760160 DOI: 10.1016/j.molp.2019.11.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/10/2019] [Accepted: 11/11/2019] [Indexed: 05/08/2023]
Abstract
The RNA-binding pentatricopeptide repeat (PPR) family comprises hundreds to thousands of genes in most plants, but only a few dozen in algae, indicating massive gene expansions during land plant evolution. The nature and timing of these expansions has not been well defined due to the sparse sequence data available from early-diverging land plant lineages. In this study, we exploit the comprehensive OneKP datasets of over 1000 transcriptomes from diverse plants and algae toward establishing a clear picture of the evolution of this massive gene family, focusing on the proteins typically associated with RNA editing, which show the most spectacular variation in numbers and domain composition across the plant kingdom. We characterize over 2 250 000 PPR motifs in over 400 000 proteins. In lycophytes, polypod ferns, and hornworts, nearly 10% of expressed protein-coding genes encode putative PPR editing factors, whereas they are absent from algae and complex-thalloid liverworts. We show that rather than a single expansion, most land plant lineages with high numbers of editing factors have continued to generate novel sequence diversity. We identify sequence variations that imply functional differences between PPR proteins in seed plants versus non-seed plants and variations we propose to be linked to seed-plant-specific editing co-factors. Finally, using the sequence variations across the datasets, we develop a structural model of the catalytic DYW domain associated with C-to-U editing and identify a clade of unique DYW variants that are strong candidates as U-to-C RNA-editing factors, given their phylogenetic distribution and sequence characteristics.
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Affiliation(s)
- Bernard Gutmann
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia
| | - Santana Royan
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia
| | - Mareike Schallenberg-Rüdinger
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Henning Lenz
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Ian R Castleden
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia
| | - Rose McDowell
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia
| | - Michael A Vacher
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia
| | - Julian Tonti-Filippini
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Ian D Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia.
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20
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Zhang J, Fu XX, Li RQ, Zhao X, Liu Y, Li MH, Zwaenepoel A, Ma H, Goffinet B, Guan YL, Xue JY, Liao YY, Wang QF, Wang QH, Wang JY, Zhang GQ, Wang ZW, Jia Y, Wang MZ, Dong SS, Yang JF, Jiao YN, Guo YL, Kong HZ, Lu AM, Yang HM, Zhang SZ, Van de Peer Y, Liu ZJ, Chen ZD. The hornwort genome and early land plant evolution. NATURE PLANTS 2020; 6:107-118. [PMID: 32042158 PMCID: PMC7027989 DOI: 10.1038/s41477-019-0588-4] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/20/2019] [Indexed: 05/10/2023]
Abstract
Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.
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Affiliation(s)
- Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xin-Xing Fu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui-Qi Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiang Zhao
- PubBio-Tech Services Corporation, Wuhan, China
| | - Yang Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Arthur Zwaenepoel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Yan-Long Guan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jia-Yu Xue
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yi-Ying Liao
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jie-Yu Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Guo-Qiang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mei-Zhi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shan-Shan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Jian-Fen Yang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Yuan-Nian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong-Zhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - An-Ming Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | | | - Shou-Zhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Pretoria, South Africa.
- College of Horticulture, Nanjing Agricultural University, Nanjing, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
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21
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Hein A, Brenner S, Polsakiewicz M, Knoop V. The dual-targeted RNA editing factor AEF1 is universally conserved among angiosperms and reveals only minor adaptations upon loss of its chloroplast or its mitochondrial target. PLANT MOLECULAR BIOLOGY 2020; 102:185-198. [PMID: 31797248 DOI: 10.1007/s11103-019-00940-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Upon loss of either its chloroplast or mitochondrial target, a uniquely dual-targeted factor for C-to-U RNA editing in angiosperms reveals low evidence for improved molecular adaptation to its remaining target. RNA-binding pentatricopeptide repeat (PPR) proteins specifically recognize target sites for C-to-U RNA editing in the transcriptomes of plant chloroplasts and mitochondria. Among more than 80 PPR-type editing factors that have meantime been characterized, AEF1 (or MPR25) is a special case given its dual targeting to both organelles and addressing an essential mitochondrial (nad5eU1580SL) and an essential chloroplast (atpFeU92SL) RNA editing site in parallel in Arabidopsis. Here, we explored the angiosperm-wide conservation of AEF1 and its two organelle targets. Despite numerous independent losses of the chloroplast editing site by C-to-T conversion and at least four such conversions at the mitochondrial target site in other taxa, AEF1 remains consistently conserved in more than 120 sampled angiosperm genomes. Not a single case of simultaneous loss of the chloroplast and mitochondrial editing target or of AEF1 disintegration or loss could be identified, contrasting previous findings for editing factors targeted to only one organelle. Like in most RNA editing factors, the PPR array of AEF1 reveals potential for conceptually "improved fits" to its targets according to the current PPR-RNA binding code. Surprisingly, we observe only minor evidence for adaptation to the mitochondrial target also after deep losses of the chloroplast target among Asterales, Caryophyllales and Poales or, vice versa, for the remaining chloroplast target after a deep loss of the mitochondrial target among Malvales. The evolutionary observations support the notion that PPR-RNA mismatches may be essential for proper function of editing factors.
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Affiliation(s)
- Anke Hein
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Sarah Brenner
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Monika Polsakiewicz
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany.
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22
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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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23
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Myszczyński K, Ślipiko M, Sawicki J. Potential of Transcript Editing Across Mitogenomes of Early Land Plants Shows Novel and Familiar Trends. Int J Mol Sci 2019; 20:E2963. [PMID: 31216623 PMCID: PMC6627324 DOI: 10.3390/ijms20122963] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 06/15/2019] [Accepted: 06/17/2019] [Indexed: 01/04/2023] Open
Abstract
RNA editing alters the identity of nucleotides in an RNA sequence so that the mature transcript differs from the template defined in the genome. This process has been observed in chloroplasts and mitochondria of both seed and early land plants. However, the frequency of RNA editing in plant mitochondria ranges from zero to thousands of editing sites. To date, analyses of RNA editing in mitochondria of early land plants have been conducted on a small number of genes or mitochondrial genomes of a single species. This study provides an overview of the mitogenomic RNA editing potential of the main lineages of these two groups of early land plants by predicting the RNA editing sites of 33 mitochondrial genes of 37 species of liverworts and mosses. For the purpose of the research, we newly assembled seven mitochondrial genomes of liverworts. The total number of liverwort genera with known complete mitogenome sequences has doubled and, as a result, the available complete mitogenome sequences now span almost all orders of liverworts. The RNA editing site predictions revealed that C-to-U RNA editing in liverworts and mosses is group-specific. This is especially evident in the case of liverwort lineages. The average level of C-to-U RNA editing appears to be over three times higher in liverworts than in mosses, while the C-to-U editing frequency of the majority of genes seems to be consistent for each gene across bryophytes.
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Affiliation(s)
- Kamil Myszczyński
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
| | - Monika Ślipiko
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
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24
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Complete loss of RNA editing from the plastid genome and most highly expressed mitochondrial genes of Welwitschia mirabilis. SCIENCE CHINA-LIFE SCIENCES 2019; 62:498-506. [DOI: 10.1007/s11427-018-9450-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/02/2018] [Indexed: 10/27/2022]
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25
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de Santana Lopes A, Gomes Pacheco T, do Nascimento Vieira L, Guerra MP, Nodari RO, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae. Gene 2018; 671:36-49. [DOI: 10.1016/j.gene.2018.05.088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 05/20/2018] [Accepted: 05/22/2018] [Indexed: 12/18/2022]
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26
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Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, Adam C, Aki SS, Althoff F, Araki T, Arteaga-Vazquez MA, Balasubrmanian S, Barry K, Bauer D, Boehm CR, Briginshaw L, Caballero-Perez J, Catarino B, Chen F, Chiyoda S, Chovatia M, Davies KM, Delmans M, Demura T, Dierschke T, Dolan L, Dorantes-Acosta AE, Eklund DM, Florent SN, Flores-Sandoval E, Fujiyama A, Fukuzawa H, Galik B, Grimanelli D, Grimwood J, Grossniklaus U, Hamada T, Haseloff J, Hetherington AJ, Higo A, Hirakawa Y, Hundley HN, Ikeda Y, Inoue K, Inoue SI, Ishida S, Jia Q, Kakita M, Kanazawa T, Kawai Y, Kawashima T, Kennedy M, Kinose K, Kinoshita T, Kohara Y, Koide E, Komatsu K, Kopischke S, Kubo M, Kyozuka J, Lagercrantz U, Lin SS, Lindquist E, Lipzen AM, Lu CW, De Luna E, Martienssen RA, Minamino N, Mizutani M, Mizutani M, Mochizuki N, Monte I, Mosher R, Nagasaki H, Nakagami H, Naramoto S, Nishitani K, Ohtani M, Okamoto T, Okumura M, Phillips J, Pollak B, Reinders A, Rövekamp M, Sano R, Sawa S, Schmid MW, Shirakawa M, Solano R, Spunde A, Suetsugu N, Sugano S, Sugiyama A, Sun R, Suzuki Y, Takenaka M, Takezawa D, Tomogane H, Tsuzuki M, Ueda T, Umeda M, Ward JM, Watanabe Y, Yazaki K, Yokoyama R, Yoshitake Y, Yotsui I, Zachgo S, Schmutz J. Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. Cell 2017; 171:287-304.e15. [PMID: 28985561 DOI: 10.1016/j.cell.2017.09.030] [Citation(s) in RCA: 713] [Impact Index Per Article: 101.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 04/21/2017] [Accepted: 09/18/2017] [Indexed: 02/01/2023]
Abstract
The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia.
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan.
| | - Jerry Jenkins
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Catherine Adam
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Shiori Sugamata Aki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Felix Althoff
- Botany Department, University of Osnabrück, Barbarastr. 11, D-49076 Osnabrück, Germany
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Mario A Arteaga-Vazquez
- Universidad Veracruzana, INBIOTECA - Instituto de Biotecnología y Ecología Aplicada, Av. de las Culturas Veracruzanas No.101, Colonia Emiliano Zapata, 91090, Xalapa, Veracruz, México
| | | | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Diane Bauer
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Christian R Boehm
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Liam Briginshaw
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Juan Caballero-Perez
- National Laboratory of Genomics for Biodiversity, CINVESTAV-IPN, Km 9.6 Lib. Norte Carr. Irapuato-León, 36821, Irapuato, Guanajuato, México
| | - Bruno Catarino
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Shota Chiyoda
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Mansi Chovatia
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kevin M Davies
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11-600, Palmerston North, New Zealand
| | - Mihails Delmans
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia; Botany Department, University of Osnabrück, Barbarastr. 11, D-49076 Osnabrück, Germany
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ana E Dorantes-Acosta
- Universidad Veracruzana, INBIOTECA - Instituto de Biotecnología y Ecología Aplicada, Av. de las Culturas Veracruzanas No.101, Colonia Emiliano Zapata, 91090, Xalapa, Veracruz, México
| | - D Magnus Eklund
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia; Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - Stevie N Florent
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | | | - Asao Fujiyama
- National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan
| | - Hideya Fukuzawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Bence Galik
- Bioinformatics & Scientific Computing, Vienna Biocenter Core Facilities (VBCF), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Daniel Grimanelli
- Institut de Recherche pour le Développement (IRD), UMR232, Université de Montpellier, Montpellier 34394, France
| | - Jane Grimwood
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, 8008 Zürich, Switzerland
| | - Takahiro Hamada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902 Japan
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | | | - Asuka Higo
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yuki Hirakawa
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Department of Life Science, Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan
| | - Hope N Hundley
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Yoko Ikeda
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama 710-0046, Japan
| | - Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Shin-Ichiro Inoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Sakiko Ishida
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Qidong Jia
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Mitsuru Kakita
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Takehiko Kanazawa
- National Institute for Basic Biology, 38 Nishigounaka, Myodaiji, Okazaki 444-8585, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yosuke Kawai
- Department of Integrative Genomics, Tohoku Medical Bank Organization, Tohoku University, Aoba, Sendai 980-8573, Japan
| | - Tomokazu Kawashima
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Department of Plant and Soil Sciences, University of Kentucky, 321 Plant Science Building, 1405 Veterans Dr., Lexington, KY 40546, USA
| | - Megan Kennedy
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Keita Kinose
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Department of Life Science, Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan; Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Yuji Kohara
- National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan
| | - Eri Koide
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Kenji Komatsu
- Department of Bioproduction Technology, Junior College of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Sarah Kopischke
- Botany Department, University of Osnabrück, Barbarastr. 11, D-49076 Osnabrück, Germany
| | - Minoru Kubo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Ulf Lagercrantz
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Erika Lindquist
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Anna M Lipzen
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Chia-Wei Lu
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Efraín De Luna
- Instituto de Ecología, AC., Red de Biodiversidad y Sistemática, Xalapa, Veracruz, 91000, México
| | | | - Naoki Minamino
- National Institute for Basic Biology, 38 Nishigounaka, Myodaiji, Okazaki 444-8585, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masaharu Mizutani
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada, Kobe 657-8501, Japan
| | - Miya Mizutani
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Isabel Monte
- Department Genética Molecular de Plantas, Centro Nacional de Biotecnologia-CSIC, Universidad Autónoma de Madrid 28049 Madrid. Spain
| | - Rebecca Mosher
- The School of Plant Sciences, The University of Arizona, Tuscon, AZ, USA
| | - Hideki Nagasaki
- National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan; Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hirofumi Nakagami
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Satoshi Naramoto
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Kazuhiko Nishitani
- Laboratory of Plant Cell Wall Biology, Graduate School of Life Sciences, Tohoku University, Aoba, Sendai 980-8578, Japan
| | - Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Takashi Okamoto
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Masaki Okumura
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Jeremy Phillips
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Bernardo Pollak
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Anke Reinders
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Moritz Rövekamp
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, 8008 Zürich, Switzerland
| | - Ryosuke Sano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Shinichiro Sawa
- Graduate school of Science and Technology, Kumamoto University, Kurokami 2-39-1, Kumamoto 860-8555, Japan
| | - Marc W Schmid
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, 8008 Zürich, Switzerland
| | - Makoto Shirakawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Roberto Solano
- Department Genética Molecular de Plantas, Centro Nacional de Biotecnologia-CSIC, Universidad Autónoma de Madrid 28049 Madrid. Spain
| | - Alexander Spunde
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Noriyuki Suetsugu
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 Japan
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Rui Sun
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 Japan
| | | | - Daisuke Takezawa
- Graduate School of Science and Engineering and Institute for Environmental Science and Technology, Saitama University, Saitama 338-8570, Japan
| | - Hirokazu Tomogane
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902 Japan
| | - Takashi Ueda
- National Institute for Basic Biology, 38 Nishigounaka, Myodaiji, Okazaki 444-8585, Japan
| | - Masaaki Umeda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - John M Ward
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902 Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Ryusuke Yokoyama
- Laboratory of Plant Cell Wall Biology, Graduate School of Life Sciences, Tohoku University, Aoba, Sendai 980-8578, Japan
| | | | - Izumi Yotsui
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Sabine Zachgo
- Botany Department, University of Osnabrück, Barbarastr. 11, D-49076 Osnabrück, Germany
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
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27
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Functional divergence and origin of the DAG-like gene family in plants. Sci Rep 2017; 7:5688. [PMID: 28720816 PMCID: PMC5515838 DOI: 10.1038/s41598-017-05961-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/06/2017] [Indexed: 01/08/2023] Open
Abstract
The nuclear-encoded DAG-like (DAL) gene family plays critical roles in organelle C-to-U RNA editing in Arabidopsis thaliana. However, the origin, diversification and functional divergence of DAL genes remain unclear. Here, we analyzed the genomes of diverse plant species and found that: DAL genes are specific to spermatophytes, all DAL genes share a conserved gene structure and protein similarity with the inhibitor I9 domain of subtilisin genes found in ferns and mosses, suggesting that DAL genes likely arose from I9-containing proproteases via exon shuffling. Based on phylogenetic inference, DAL genes can be divided into five subfamilies, each composed of putatively orthologous and paralogous genes from different species, suggesting that all DAL genes originated from a common ancestor in early seed plants. Significant type I functional divergence was observed in 6 of 10 pairwise comparisons, indicating that shifting functional constraints have contributed to the evolution of DAL genes. This inference is supported by the finding that functionally divergent amino acids between subfamilies are predominantly located in the DAL domain, a critical part of the RNA editosome. Overall, these findings shed light on the origin of DAL genes in spermatophytes and outline functionally important residues involved in the complexity of the RNA editosome.
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28
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Cahoon AB, Nauss JA, Stanley CD, Qureshi A. Deep Transcriptome Sequencing of Two Green Algae, Chara vulgaris and Chlamydomonas reinhardtii, Provides No Evidence of Organellar RNA Editing. Genes (Basel) 2017; 8:genes8020080. [PMID: 28230734 PMCID: PMC5333069 DOI: 10.3390/genes8020080] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 02/13/2017] [Indexed: 11/16/2022] Open
Abstract
Nearly all land plants post-transcriptionally modify specific nucleotides within RNAs, a process known as RNA editing. This adaptation allows the correction of deleterious mutations within the asexually reproducing and presumably non-recombinant chloroplast and mitochondrial genomes. There are no reports of RNA editing in any of the green algae so this phenomenon is presumed to have originated in embryophytes either after the invasion of land or in the now extinct algal ancestor of all land plants. This was challenged when a recent in silico screen for RNA edit sites based on genomic sequence homology predicted edit sites in the green alga Chara vulgaris, a multicellular alga found within the Streptophyta clade and one of the closest extant algal relatives of land plants. In this study, the organelle transcriptomes of C. vulgaris and Chlamydomonas reinhardtii were deep sequenced for a comprehensive assessment of RNA editing. Initial analyses based solely on sequence comparisons suggested potential edit sites in both species, but subsequent high-resolution melt analysis, RNase H-dependent PCR (rhPCR), and Sanger sequencing of DNA and complementary DNAs (cDNAs) from each of the putative edit sites revealed them to be either single-nucleotide polymorphisms (SNPs) or spurious deep sequencing results. The lack of RNA editing in these two lineages is consistent with the current hypothesis that RNA editing evolved after embryophytes split from its ancestral algal lineage.
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Affiliation(s)
- A Bruce Cahoon
- Department of Natural Sciences, University of Virginia's College at Wise, 1 College Ave., Wise, VA 24293, USA.
| | - John A Nauss
- Department of Natural Sciences, University of Virginia's College at Wise, 1 College Ave., Wise, VA 24293, USA.
| | - Conner D Stanley
- Department of Natural Sciences, University of Virginia's College at Wise, 1 College Ave., Wise, VA 24293, USA.
| | - Ali Qureshi
- Department of Natural Sciences, University of Virginia's College at Wise, 1 College Ave., Wise, VA 24293, USA.
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Ichinose M, Sugita M. RNA Editing and Its Molecular Mechanism in Plant Organelles. Genes (Basel) 2016; 8:genes8010005. [PMID: 28025543 PMCID: PMC5295000 DOI: 10.3390/genes8010005] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/23/2016] [Accepted: 12/20/2016] [Indexed: 12/03/2022] Open
Abstract
RNA editing by cytidine (C) to uridine (U) conversions is widespread in plant mitochondria and chloroplasts. In some plant taxa, “reverse” U-to-C editing also occurs. However, to date, no instance of RNA editing has yet been reported in green algae and the complex thalloid liverworts. RNA editing may have evolved in early land plants 450 million years ago. However, in some plant species, including the liverwort, Marchantia polymorpha, editing may have been lost during evolution. Most RNA editing events can restore the evolutionarily conserved amino acid residues in mRNAs or create translation start and stop codons. Therefore, RNA editing is an essential process to maintain genetic information at the RNA level. Individual RNA editing sites are recognized by plant-specific pentatricopeptide repeat (PPR) proteins that are encoded in the nuclear genome. These PPR proteins are characterized by repeat elements that bind specifically to RNA sequences upstream of target editing sites. In flowering plants, non-PPR proteins also participate in multiple RNA editing events as auxiliary factors. C-to-U editing can be explained by cytidine deamination. The proteins discovered to date are important factors for RNA editing but a bona fide RNA editing enzyme has yet to be identified.
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Affiliation(s)
- Mizuho Ichinose
- Center for Gene Research, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan.
- Institute of Transformative Bio-Molecules, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan.
| | - Mamoru Sugita
- Center for Gene Research, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan.
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30
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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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31
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Manna S. An overview of pentatricopeptide repeat proteins and their applications. Biochimie 2015; 113:93-9. [PMID: 25882680 DOI: 10.1016/j.biochi.2015.04.004] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 04/03/2015] [Indexed: 01/24/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. These proteins facilitate processing, splicing, editing, stability and translation of RNAs. While major advances in PPR research have been achieved with plant PPR proteins, the significance of non-plant PPR proteins is becoming of increasing importance. PPR proteins are classified into different subclasses based on their domain architecture, which is often a reflection of their function. This review provides an overview of the significant findings regarding the functions, evolution and applications of PPR proteins. Horizontal gene transfer appears to have played a major role in the sporadic phylogenetic distribution of different PPR subclasses in both eukaryotes and prokaryotes. Additionally, the use of synthetic biology and protein engineering to create designer PPR proteins to control gene expression in vivo is discussed. This review also highlights some of the aspects of PPR research that require more attention particularly in non-plant organisms. This includes the lack of research into the recently discovered PPR-TGM subclass, which is not only the first PPR subclass absent from plants but present in economically and clinically-relevant pathogens. Investigation into the structure and function of PPR-TGM proteins in these pathogens presents a novel opportunity for the exploitation of PPR proteins as drug targets to prevent disease.
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Affiliation(s)
- Sam Manna
- Department of Microbiology, La Trobe University, Melbourne, Victoria, Australia.
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32
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Wagoner JA, Sun T, Lin L, Hanson MR. Cytidine deaminase motifs within the DYW domain of two pentatricopeptide repeat-containing proteins are required for site-specific chloroplast RNA editing. J Biol Chem 2014; 290:2957-68. [PMID: 25512379 DOI: 10.1074/jbc.m114.622084] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In angiosperm organelles, cytidines are converted to uridines by a deamination reaction in the process termed RNA editing. The C targets of editing are recognized by members of the pentatricopeptide repeat (PPR) protein family. Although other members of the editosome have begun to be identified, the enzyme that catalyzes the C-U conversion is still unknown. The DYW motif at the C terminus of many PPR editing factors contains residues conserved with known cytidine deaminase active sites; however, some PPR editing factors lack a DYW motif. Furthermore, in many PPR-DYW editing factors, the truncation of the DYW motif does not affect editing efficiency, so the role of the DYW motif in RNA editing is unclear. Here, a chloroplast PPR-DYW editing factor, quintuple editing factor 1 (QED1), was shown to affect five different plastid editing sites, the greatest number of chloroplast C targets known to be affected by a single PPR protein. Loss of editing at the five sites resulted in stunted growth and accumulation of apparent photodamage. Adding a C-terminal protein tag to QED1 was found to severely inhibit editing function. QED1 and RARE1, another plastid PPR-DYW editing factor, were discovered to require their DYW motifs for efficient editing. To identify specific residues critical for editing, conserved deaminase residues in each PPR protein were mutagenized. The mutant PPR proteins, when expressed in qed1 or rare1 mutant protoplasts, could not complement the editing defect. Therefore, the DYW motif, and specifically, the deaminase residues, of QED1 and RARE1 are required for editing efficiency.
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Affiliation(s)
- Jessica A Wagoner
- From the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Tao Sun
- From the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Lin Lin
- From the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Maureen R Hanson
- From the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
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33
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Oldenkott B, Yamaguchi K, Tsuji-Tsukinoki S, Knie N, Knoop V. Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata. RNA (NEW YORK, N.Y.) 2014; 20:1499-506. [PMID: 25142065 PMCID: PMC4174432 DOI: 10.1261/rna.045575.114] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
RNA editing in chloroplasts and mitochondria of land plants differs significantly in abundance. For example, some 200-500 sites of cytidine-to-uridine RNA editing exist in flowering plant mitochondria as opposed to only 30-50 such C-to-U editing events in their chloroplasts. In contrast, we predicted significantly more chloroplast RNA editing for the protein-coding genes in the available complete plastome sequences of two species of the spike moss genus Selaginella (Lycopodiophyta). To evaluate these predictions we investigated the Selaginella uncinata chloroplast transcriptome. Our exhaustive cDNA studies identified the extraordinary number of 3415 RNA-editing events, exclusively of the C-to-U type, in the 74 mRNAs encoding intact reading frames in the S. uncinata chloroplast. We find the overwhelming majority (61%) of the 428 silent editing events leaving codon meanings unaltered directly neighboring other editing events, possibly suggesting a sterically more flexible RNA-editing deaminase activity in Selaginella. No evidence of RNA editing was found for tRNAs or rRNAs but we identified a total of 74 editing sites in cDNA sequences of four group II introns (petBi6g2, petDi8g2, ycf3i124g2, and ycf3i354g2) retained in partially matured transcripts, which strongly contribute to improved base-pairing in the intron secondary structures as a likely prerequisite for their splicing.
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Affiliation(s)
- Bastian Oldenkott
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Kazuo Yamaguchi
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa 920-0934, Japan
| | - Sumika Tsuji-Tsukinoki
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa 920-0934, Japan
| | - Nils Knie
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Volker Knoop
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115 Bonn, Germany
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34
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Fu CJ, Sheikh S, Miao W, Andersson SGE, Baldauf SL. Missing genes, multiple ORFs, and C-to-U type RNA editing in Acrasis kona (Heterolobosea, Excavata) mitochondrial DNA. Genome Biol Evol 2014; 6:2240-57. [PMID: 25146648 PMCID: PMC4202320 DOI: 10.1093/gbe/evu180] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Discoba (Excavata) is an ancient group of eukaryotes with great morphological and ecological diversity. Unlike the other major divisions of Discoba (Jakobida and Euglenozoa), little is known about the mitochondrial DNAs (mtDNAs) of Heterolobosea. We have assembled a complete mtDNA genome from the aggregating heterolobosean amoeba, Acrasis kona, which consists of a single circular highly AT-rich (83.3%) molecule of 51.5 kb. Unexpectedly, A. kona mtDNA is missing roughly 40% of the protein-coding genes and nearly half of the transfer RNAs found in the only other sequenced heterolobosean mtDNAs, those of Naegleria spp. Instead, over a quarter of A. kona mtDNA consists of novel open reading frames. Eleven of the 16 protein-coding genes missing from A. kona mtDNA were identified in its nuclear DNA and polyA RNA, and phylogenetic analyses indicate that at least 10 of these 11 putative nuclear-encoded mitochondrial (NcMt) proteins arose by direct transfer from the mitochondrion. Acrasis kona mtDNA also employs C-to-U type RNA editing, and 12 homologs of DYW-type pentatricopeptide repeat (PPR) proteins implicated in plant organellar RNA editing are found in A. kona nuclear DNA. A mapping of mitochondrial gene content onto a consensus phylogeny reveals a sporadic pattern of relative stasis and rampant gene loss in Discoba. Rampant loss occurred independently in the unique common lineage leading to Heterolobosea + Tsukubamonadida and later in the unique lineage leading to Acrasis. Meanwhile, mtDNA gene content appears to be remarkably stable in the Acrasis sister lineage leading to Naegleria and in their distant relatives Jakobida.
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Affiliation(s)
- Cheng-Jie Fu
- Program in Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Sanea Sheikh
- Program in Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Siv G E Andersson
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Sweden
| | - Sandra L Baldauf
- Program in Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
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35
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Hammani K, Giegé P. RNA metabolism in plant mitochondria. TRENDS IN PLANT SCIENCE 2014; 19:380-9. [PMID: 24462302 DOI: 10.1016/j.tplants.2013.12.008] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 12/11/2013] [Accepted: 12/19/2013] [Indexed: 05/02/2023]
Abstract
Mitochondria are essential for the eukaryotic cell and are derived from the endosymbiosis of an α-proteobacterial ancestor. Compared to other eukaryotes, RNA metabolism in plant mitochondria is complex and combines bacterial-like traits with novel features that evolved in the host cell. These complex RNA processes are regulated by families of nucleus-encoded RNA-binding proteins. Transcription is particularly relaxed and is initiated from multiple promoters covering the entire genome. The variety of RNA precursors accumulating in mitochondria highlights the importance of post-transcriptional processes to determine the size and abundance of transcripts. Here we review RNA metabolism in plant mitochondria, from RNA transcription to translation, with a special focus on their unique features that are controlled by trans-factors.
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Affiliation(s)
- Kamel Hammani
- Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Philippe Giegé
- Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
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36
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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: 247] [Impact Index Per Article: 24.7] [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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37
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Schallenberg-Rüdinger M, Kindgren P, Zehrmann A, Small I, Knoop V. A DYW-protein knockout in Physcomitrella affects two closely spaced mitochondrial editing sites and causes a severe developmental phenotype. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:420-432. [PMID: 23909746 DOI: 10.1111/tpj.12304] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 07/09/2013] [Accepted: 08/01/2013] [Indexed: 06/02/2023]
Abstract
RNA-binding pentatricopeptide repeat (PPR) proteins carrying a carboxy-terminal DYW domain similar to cytidine deaminases have been characterized as site-specific factors for C-to-U RNA editing in plant organelles. Here we report that knockout of DYW-PPR_65 in Physcomitrella patens causes a severe developmental phenotype in the moss and specifically affects two editing sites located 18 nucleotides apart on the mitochondrial ccmFC mRNA. Intriguingly, PPR_71, another DYW-type PPR, had been identified previously as an editing factor specifically affecting only the downstream editing site, ccmFCeU122SF. The now characterized PPR_65 binds specifically only to the upstream target site, ccmFCeU103PS, in full agreement with a recent RNA-recognition code for PPR arrays. The functional interference between the two editing events may be caused by a combination of three factors: (i) the destabilization of an RNA secondary structure interfering with PPR_71 binding by prior binding of PPR_65; (ii) the resulting upstream C-U conversion; or (iii) a direct interaction between the two DYW proteins. Indeed, we find the Physcomitrella DYW-PPRs to interact in yeast-two-hybrid assays. The moss DYW-PPRs also interact yet more strongly with MORF (Multiple Organellar RNA editing Factor)/RIP (RNA editing factor interacting proteins) proteins of Arabidopsis known to be general editing factors in flowering plants, although MORF homologues are entirely absent in the moss. Finally, we demonstrate binding of Physcomitrella DYW-PPR_98, for which no KO lines could be raised, to its predicted target sequence upstream of editing site atp9eU92SL. Together with the functional characterization of DYW-PPR_65, this completes the assignment of RNA editing factors to all editing sites in the Physcomitrella mitochondrial transcriptome.
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Affiliation(s)
- Mareike Schallenberg-Rüdinger
- Institut für Zelluläre und Molekulare Botanik (IZMB), Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany; Faculty of Biology, Department of Cell Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany; Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA, 6009, Australia
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38
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Identification of Pentatricopeptide Repeat Proteins in the Model Organism Dictyostelium discoideum. Int J Genomics 2013; 2013:586498. [PMID: 23998118 PMCID: PMC3753752 DOI: 10.1155/2013/586498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/11/2013] [Indexed: 11/18/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are RNA binding proteins with functions in organelle RNA metabolism. They are found in all eukaryotes but have been most extensively studied in plants. We report on the identification of 12 PPR-encoding genes in the genome of the protist Dictyostelium discoideum, with potential homologs in other members of the same lineage and some predicted novel functions for the encoded gene products in protists. For one of the gene products, we show that it localizes to the mitochondria, and we also demonstrate that antisense inhibition of its expression leads to slower growth, a phenotype associated with mitochondrial dysfunction.
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39
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Grosche C, Funk HT, Maier UG, Zauner S. The chloroplast genome of Pellia endiviifolia: gene content, RNA-editing pattern, and the origin of chloroplast editing. Genome Biol Evol 2013; 4:1349-57. [PMID: 23221608 PMCID: PMC3542565 DOI: 10.1093/gbe/evs114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
RNA editing is a post-transcriptional process that can act upon transcripts from mitochondrial, nuclear, and chloroplast genomes. In chloroplasts, single-nucleotide conversions in mRNAs via RNA editing occur at different frequencies across the plant kingdom. These range from several hundred edited sites in some mosses and ferns to lower frequencies in seed plants and the complete lack of RNA editing in the liverwort Marchantia polymorpha. Here, we report the sequence and edited sites of the chloroplast genome from the liverwort Pellia endiviifolia. The type and frequency of chloroplast RNA editing display a pattern highly similar to that in seed plants. Analyses of the C to U conversions and the genomic context in which the editing sites are embedded provide evidence in favor of the hypothesis that chloroplast RNA editing evolved to compensate mutations in the first land plants.
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Affiliation(s)
- Christopher Grosche
- Philipps-University of Marburg, Laboratory for Cellular Biology, Marburg, Germany
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Sugita M, Ichinose M, Ide M, Sugita C. Architecture of the PPR gene family in the moss Physcomitrella patens. RNA Biol 2013; 10:1439-45. [PMID: 23645116 PMCID: PMC3858427 DOI: 10.4161/rna.24772] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are widespread in eukaryotes and in particular, include several hundred members in land plants. The majority of PPR proteins are localized in mitochondria and plastids, where they play a crucial role in various aspects of RNA metabolism at the post-transcriptional level in gene expression. However, many of their functions remain to be characterized. In contrast to vascular plants, the moss Physcomitrella patens has only 105 PPR genes. This number may represent a minimum set of PPR proteins required for post-transcriptional regulation in plant organelles. Here, we review the overall structure of the P. patens PPR gene family and the current status of the functional characterization of moss PPR proteins.
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Affiliation(s)
- Mamoru Sugita
- Center for Gene Research; Nagoya University; Chikusa-ku; Nagoya, Japan
| | - Mizuho Ichinose
- Center for Gene Research; Nagoya University; Chikusa-ku; Nagoya, Japan
| | - Mizuki Ide
- Center for Gene Research; Nagoya University; Chikusa-ku; Nagoya, Japan
| | - Chieko Sugita
- Center for Gene Research; Nagoya University; Chikusa-ku; Nagoya, Japan
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Verbitskiy D, Zehrmann A, Härtel B, Brennicke A, Takenaka M. Two related RNA-editing proteins target the same sites in mitochondria of Arabidopsis thaliana. J Biol Chem 2012; 287:38064-72. [PMID: 22977245 DOI: 10.1074/jbc.m112.397992] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The facilitators for specific cytosine-to-uridine RNA-editing events in plant mitochondria and plastids are pentatricopeptide repeat (PPR)-containing proteins with specific additional C-terminal domains. Here we report the related PPR proteins mitochondrial editing factor 8 (MEF8) and MEF8S with only five such repeats each to be both involved in RNA editing at the same two sites in mitochondria of Arabidopsis thaliana. Mutants of MEF8 show diminished editing in leaves but not in pollen, whereas mutants of the related protein MEF8S show reduced RNA editing in pollen but not in leaves. Overexpressed MEF8 or MEF8S both increase editing at the two target sites in a mef8 mutant. Double mutants of MEF8 and MEF8S are not viable although both identified target sites are in mRNAs for nonessential proteins. This suggests that MEF8 and MEF8S may have other essential functions beyond these two editing sites in complex I mRNAs.
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Nuclear DYW-type PPR gene families diversify with increasing RNA editing frequencies in liverwort and moss mitochondria. J Mol Evol 2012; 74:37-51. [PMID: 22302222 DOI: 10.1007/s00239-012-9486-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 01/11/2012] [Indexed: 10/14/2022]
Abstract
RNA editing in mitochondria and chloroplasts of land plants alters transcript sequences by site-specific conversions of cytidines into uridines. RNA editing frequencies vary extremely between land plant clades, ranging from zero in some liverworts to more than 2,000 sites in lycophytes. Unique pentatricopeptide repeat (PPR) proteins with variable domain extension (E/E+/DYW) have recently been identified as specific editing site recognition factors in model plants. The distinctive functions of these PPR protein domain additions have remained unclear, although deaminase function has been proposed for the DYW domain. To shed light on diversity of RNA editing and DYW proteins at the origin of land plant evolution, we investigated editing patterns of the mitochondrial nad5, nad4, and nad2 genes in a wide sampling of more than 100 liverworts and mosses using the recently developed PREPACT program (www.prepact.de) and exemplarily confirmed predicted RNA editing sites in selected taxa. Extreme variability in RNA editing frequency is seen both in liverworts and mosses. Only few editings exist in the liverwort Lejeunea cavifolia or the moss Pogonatum urnigerum whereas up to 20% of cytidines are edited in the liverwort Haplomitrium mnioides or the moss Takakia lepidozioides. Interestingly, the latter are taxa that branch very early within their respective clades. Amplicons targeting the E/E+/DYW domains and subsequent random clone sequencing show DYW domains among bryophytes to be highly conserved in comparison with their angiosperm counterparts and to correlate well with RNA editing frequencies regarding their diversities. We propose that DYW proteins are the key players of RNA editing at the origin of land plants.
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Hayes ML, Giang K, Mulligan RM. Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures. BMC Evol Biol 2012; 12:66. [PMID: 22583633 PMCID: PMC3441922 DOI: 10.1186/1471-2148-12-66] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 04/17/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pentatricopeptide repeat (PPR) proteins are required for numerous RNA processing events in plant organelles including C-to-U editing, splicing, stabilization, and cleavage. Fifteen PPR proteins are known to be required for RNA editing at 21 sites in Arabidopsis chloroplasts, and belong to the PLS class of PPR proteins. In this study, we investigate the co-evolution of four PPR genes (CRR4, CRR21, CLB19, and OTP82) and their six editing targets in Brassicaceae species. PPR genes are composed of approximately 10 to 20 tandem repeats and each repeat has two α-helical regions, helix A and helix B, that are separated by short coil regions. Each repeat and structural feature was examined to determine the selective pressures on these regions. RESULTS All of the PPR genes examined are under strong negative selection. Multiple independent losses of editing site targets are observed for both CRR21 and OTP82. In several species lacking the known editing target for CRR21, PPR genes are truncated near the 17th PPR repeat. The coding sequences of the truncated CRR21 genes are maintained under strong negative selection; however, the 3' UTR sequences beyond the truncation site have substantially diverged. Phylogenetic analyses of four PPR genes show that sequences corresponding to helix A are high compared to helix B sequences. Differential evolutionary selection of helix A versus helix B is observed in both plant and mammalian PPR genes. CONCLUSION PPR genes and their cognate editing sites are mutually constrained in evolution. Editing sites are frequently lost by replacement of an edited C with a genomic T. After the loss of an editing site, the PPR genes are observed with three outcomes: first, few changes are detected in some cases; second, the PPR gene is present as a pseudogene; and third, the PPR gene is present but truncated in the C-terminal region. The retention of truncated forms of CRR21 that are maintained under strong negative selection even in the absence of an editing site target suggests that unrecognized function(s) might exist for this PPR protein. PPR gene sequences that encode helix A are under strong selection, and could be involved in RNA substrate recognition.
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Affiliation(s)
- Michael L Hayes
- Developmental & Cell Biology, University of California, Irvine, CA 92697, USA
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Ichinose M, Tasaki E, Sugita C, Sugita M. A PPR-DYW protein is required for splicing of a group II intron of cox1 pre-mRNA in Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:271-8. [PMID: 22117821 DOI: 10.1111/j.1365-313x.2011.04869.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The pentatricopeptide repeat (PPR) protein family is involved in various steps of RNA metabolism in plastids and mitochondria. To investigate the function of a DYW sub-class PPR protein in the moss Physcomitrella patens, we constructed and characterized knockout mutants of the PpPPR_43 gene, which encodes a mitochondrial localized PPR protein with a C-terminal DYW domain. The disruptants showed poor growth of moss protonemata. To investigate whether mitochondrial transcripts were affected by disruption of PpPPR_43, we sequenced the cDNA to detect RNA editing events and performed RT-PCR analyses to measure steady-state mitochondrial transcript levels. Disruption of PpPPR_43 did not result in defective RNA editing, but a substantial reduction in the level of mature cox1 transcript was observed in the disruptants. RT-PCR analysis showed that the 3rd intron of cox1 pre-mRNA was not spliced out in the disruptants, but the 1st, 2nd and 4th introns were efficiently spliced out. This suggests that PpPPR_43 is an intron 3-specific splicing factor. The role of the C-terminal domains of PpPPR_43 in intron 3 splicing was analyzed by complementation experiments with truncated constructs lacking the DYW domain or both the E and DYW domains. Both truncated genes completely restored splicing in the PpPPR_43 knockout mutant. This indicates that the E and DYW domains of PpPPR_43 are not required for splicing, and can be deleted without loss of cox1 intron 3 splicing.
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Affiliation(s)
- Mizuho Ichinose
- Center for Gene Research, Nagoya University, Chikusa-Ku, Nagoya 468-8602, Japan
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Okuda K, Shikanai T. A pentatricopeptide repeat protein acts as a site-specificity factor at multiple RNA editing sites with unrelated cis-acting elements in plastids. Nucleic Acids Res 2012; 40:5052-64. [PMID: 22362750 PMCID: PMC3367199 DOI: 10.1093/nar/gks164] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In plant organelles, RNA editing alters specific cytidine residues to uridine in transcripts. All of the site-specificity factors of RNA editing identified so far are pentatricopeptide repeat (PPR) proteins. A defect in a specific PPR protein often impairs RNA editing at multiple sites, at which the cis-acting elements are not highly conserved. The molecular mechanism for sharing a single PPR protein over multiple sites is still unclear. We focused here on the PPR proteins OTP82 and CRR22, the putative target elements of which are, respectively, partially and barely conserved. Recombinant OTP82 specifically bound to the −15 to 0 regions of its target sites. Recombinant CRR22 specifically bound to the −20 to 0 regions of the ndhB-7 and ndhD-5 sites and to the −17 to 0 region of the rpoB-3 site. Taking this information together with the genetic data, we conclude that OTP82 and CRR22 act as site-specificity factors at multiple sites in plastids. In addition, the high-affinity binding of CRR22 to unrelated cis-acting elements suggests that only certain specific nucleotides in a cis-acting element are sufficient for high-affinity binding of a PPR protein. The cis-acting elements can therefore be rather divergent and still be recognized by a single PPR protein.
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Affiliation(s)
- Kenji Okuda
- Department of Life Science, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo 112-8551, Japan.
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Seed Plant Mitochondrial Genomes: Complexity Evolving. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2012. [DOI: 10.1007/978-94-007-2920-9_8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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48
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Rüdinger M, Fritz-Laylin L, Polsakiewicz M, Knoop V. Plant-type mitochondrial RNA editing in the protist Naegleria gruberi. RNA (NEW YORK, N.Y.) 2011; 17:2058-62. [PMID: 22025737 PMCID: PMC3222119 DOI: 10.1261/rna.02962911] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
RNA editing converts hundreds of cytidines into uridines in plant mitochondrial and chloroplast transcripts. Recognition of the RNA editing sites in the organelle transcriptomes requires numerous specific, nuclear-encoded RNA-binding pentatricopeptide repeat (PPR) proteins with characteristic carboxy-terminal protein domain extensions (E/DYW) previously thought to be unique to plants. However, a small gene family of such plant-like PPR proteins of the DYW-type was recently discovered in the genome of the protist Naegleria gruberi. This raised the possibility that plant-like RNA editing may occur in this amoeboflagellate. Accordingly, we have investigated the mitochondrial transcriptome of Naegleria gruberi and here report on identification of two sites of C-to-U RNA editing in the cox1 gene and in the cox3 gene, both of which reconstitute amino acid codon identities highly conserved in evolution. An estimated 1.5 billion years of evolution separate the heterolobosean protist Naegleria from the plant lineage. The new findings either suggest horizontal gene transfer of RNA editing factors or that plant-type RNA editing is evolutionarily much more ancestral than previously thought and yet to be discovered in many other ancient eukaryotic lineages.
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Affiliation(s)
- Mareike Rüdinger
- Department of Molecular Evolution, IZMB, University of Bonn, D-53115 Bonn, Germany
| | - Lillian Fritz-Laylin
- Department of Cellular and Molecular Pharmacology, San Francisco School of Medicine, University of California, San Francisco, California 94158, USA
| | - Monika Polsakiewicz
- Department of Molecular Evolution, IZMB, University of Bonn, D-53115 Bonn, Germany
| | - Volker Knoop
- Department of Molecular Evolution, IZMB, University of Bonn, D-53115 Bonn, Germany
- Corresponding author.E-mail .
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Castandet B, Araya A. RNA editing in plant organelles. Why make it easy? BIOCHEMISTRY (MOSCOW) 2011; 76:924-31. [DOI: 10.1134/s0006297911080086] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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50
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Rüdinger M, Szövényi P, Rensing SA, Knoop V. Assigning DYW-type PPR proteins to RNA editing sites in the funariid mosses Physcomitrella patens and Funaria hygrometrica. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 67:370-380. [PMID: 21466601 DOI: 10.1111/j.1365-313x.2011.04600.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The plant-specific pentatricopeptide repeat (PPR) proteins with variable PPR repeat lengths (PLS-type) and protein extensions up to the carboxyterminal DYW domain have received attention as specific recognition factors for the C-to-U type of RNA editing events in plant organelles. Here, we report a DYW-protein knockout in the model plant Physcomitrella patens specifically affecting mitochondrial RNA editing positions cox1eU755SL and rps14eU137SL. Assignment of DYW proteins and RNA editing sites might best be corroborated by data from a taxon with a slightly different, yet similarly manageable low number of editing sites and DYW proteins. To this end we investigated the mitochondrial editing status of the related funariid moss Funaria hygrometrica. We find that: (i) Funaria lacks three mitochondrial RNA editing positions present in Physcomitrella, (ii) that F. hygrometrica cDNA sequence data identify nine DYW proteins as clear orthologues of their P. patens counterparts, and (iii) that the 'missing' 10th DYW protein in F. hygrometrica is responsible for two mitochondrial editing sites in P. patens lacking in F. hygrometrica (nad3eU230SL, nad4eU272SL). Interestingly, the third site of RNA editing missing in F. hygrometrica (rps14eU137SL) is addressed by the DYW protein characterized here and the presence of its orthologue in F. hygrometrica is explained through its simultaneous action on site cox1eU755SL conserved in both mosses.
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Affiliation(s)
- Mareike Rüdinger
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, Bonn, Germany
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