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Legen J, Lenzen B, Kachariya N, Feltgen S, Gao Y, Mergenthal S, Weber W, Klotzsch E, Zoschke R, Sattler M, Schmitz-Linneweber C. A prion-like domain is required for phase separation and chloroplast RNA processing during cold acclimation in Arabidopsis. THE PLANT CELL 2024; 36:2851-2872. [PMID: 38723165 PMCID: PMC11289645 DOI: 10.1093/plcell/koae145] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/06/2024] [Indexed: 08/02/2024]
Abstract
Arabidopsis (Arabidopsis thaliana) plants can produce photosynthetic tissue with active chloroplasts at temperatures as low as 4°C, and this process depends on the presence of the nuclear-encoded, chloroplast-localized RNA-binding protein CP29A. In this study, we demonstrate that CP29A undergoes phase separation in vitro and in vivo in a temperature-dependent manner, which is mediated by a prion-like domain (PLD) located between the two RNA recognition motif domains of CP29A. The resulting droplets display liquid-like properties and are found near chloroplast nucleoids. The PLD is required to support chloroplast RNA splicing and translation in cold-treated tissue. Together, our findings suggest that plant chloroplast gene expression is compartmentalized by inducible condensation of CP29A at low temperatures, a mechanism that could play a crucial role in plant cold resistance.
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Affiliation(s)
- Julia Legen
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstrasse 13, Berlin 10115, Germany
| | - Benjamin Lenzen
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstrasse 13, Berlin 10115, Germany
| | - Nitin Kachariya
- Helmholtz Munich, Institute of Structural Biology, Ingolstädter Landstrasse 1, Munich 85764, Germany
- Department of Bioscience, Bavarian NMR Center, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, Garching 85747, Germany
| | - Stephanie Feltgen
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstrasse 13, Berlin 10115, Germany
| | - Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Simon Mergenthal
- Institute for Biology, Experimental Biophysics/Mechanobiology, Humboldt-Universität zu Berlin, Invalidenstrasse 42, Berlin 10115, Germany
| | - Willi Weber
- Institute for Biology, Experimental Biophysics/Mechanobiology, Humboldt-Universität zu Berlin, Invalidenstrasse 42, Berlin 10115, Germany
| | - Enrico Klotzsch
- Institute for Biology, Experimental Biophysics/Mechanobiology, Humboldt-Universität zu Berlin, Invalidenstrasse 42, Berlin 10115, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Michael Sattler
- Helmholtz Munich, Institute of Structural Biology, Ingolstädter Landstrasse 1, Munich 85764, Germany
- Department of Bioscience, Bavarian NMR Center, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, Garching 85747, Germany
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2
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Réthoré E, Pelletier S, Balliau T, Zivy M, Avelange-Macherel MH, Macherel D. Multi-scale analysis of heat stress acclimation in Arabidopsis seedlings highlights the primordial contribution of energy-transducing organelles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:300-331. [PMID: 38613336 DOI: 10.1111/tpj.16763] [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: 10/09/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Much progress has been made in understanding the molecular mechanisms of plant adaptation to heat stress. However, the great diversity of models and stress conditions, and the fact that analyses are often limited to a small number of approaches, complicate the picture. We took advantage of a liquid culture system in which Arabidopsis seedlings are arrested in their development, thus avoiding interference with development and drought stress responses, to investigate through an integrative approach seedlings' global response to heat stress and acclimation. Seedlings perfectly tolerate a noxious heat shock (43°C) when subjected to a heat priming treatment at a lower temperature (38°C) the day before, displaying a thermotolerance comparable to that previously observed for Arabidopsis. A major effect of the pre-treatment was to partially protect energy metabolism under heat shock and favor its subsequent rapid recovery, which was correlated with the survival of seedlings. Rapid recovery of actin cytoskeleton and mitochondrial dynamics were another landmark of heat shock tolerance. The omics confirmed the role of the ubiquitous heat shock response actors but also revealed specific or overlapping responses to priming, heat shock, and their combination. Since only a few components or functions of chloroplast and mitochondria were highlighted in these analyses, the preservation and rapid recovery of their bioenergetic roles upon acute heat stress do not require extensive remodeling of the organelles. Protection of these organelles is rather integrated into the overall heat shock response, thus allowing them to provide the energy required to elaborate other cellular responses toward acclimation.
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Affiliation(s)
- Elise Réthoré
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
| | - Sandra Pelletier
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
| | - Thierry Balliau
- INRAE, PAPPSO, UMR/UMR Génétique Végétale, Gif sur Yvette, France
| | - Michel Zivy
- INRAE, PAPPSO, UMR/UMR Génétique Végétale, Gif sur Yvette, France
| | | | - David Macherel
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
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3
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Sanita Lima M, Silva Domingues D, Rossi Paschoal A, Smith DR. Long-read RNA-Seq for the discovery of long noncoding and antisense RNAs in plant organelles. PHYSIOLOGIA PLANTARUM 2024; 176:e14418. [PMID: 39004808 DOI: 10.1111/ppl.14418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 05/28/2024] [Indexed: 07/16/2024]
Abstract
Plant organelle transcription has been studied for decades. As techniques advanced, so did the fields of mitochondrial and plastid transcriptomics. The current view is that organelle genomes are pervasively transcribed, irrespective of their size, content, structure, and taxonomic origin. However, little is known about the nature of organelle noncoding transcriptomes, including pervasively transcribed noncoding RNAs (ncRNAs). Next-generation sequencing data have uncovered small ncRNAs in the organelles of plants and other organisms, but long ncRNAs remain poorly understood. Here, we argue that publicly available third-generation long-read RNA sequencing data from plants can provide a fine-tuned picture of long ncRNAs within organelles. Indeed, given their bloated architectures, plant mitochondrial genomes are well suited for studying pervasive transcription of ncRNAs. Ultimately, we hope to showcase this new avenue of plant research while also underlining the limitations of the proposed approach.
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Affiliation(s)
| | - Douglas Silva Domingues
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science, Bioinformatics and Pattern Recognition Group (BIOINFO-CP), Federal University of Technology-Paraná-UTFPR, Cornélio Procópio, PR, Brazil
| | - David Roy Smith
- Department of Biology, Western University, London, ON, Canada
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4
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Sanita Lima M, Silva Domingues D, Rossi Paschoal A, Smith DR. Long-read RNA sequencing can probe organelle genome pervasive transcription. Brief Funct Genomics 2024:elae026. [PMID: 38880995 DOI: 10.1093/bfgp/elae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/20/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024] Open
Abstract
40 years ago, organelle genomes were assumed to be streamlined and, perhaps, unexciting remnants of their prokaryotic past. However, the field of organelle genomics has exposed an unparallel diversity in genome architecture (i.e. genome size, structure, and content). The transcription of these eccentric genomes can be just as elaborate - organelle genomes are pervasively transcribed into a plethora of RNA types. However, while organelle protein-coding genes are known to produce polycistronic transcripts that undergo heavy posttranscriptional processing, the nature of organelle noncoding transcriptomes is still poorly resolved. Here, we review how wet-lab experiments and second-generation sequencing data (i.e. short reads) have been useful to determine certain types of organelle RNAs, particularly noncoding RNAs. We then explain how third-generation (long-read) RNA-Seq data represent the new frontier in organelle transcriptomics. We show that public repositories (e.g. NCBI SRA) already contain enough data for inter-phyla comparative studies and argue that organelle biologists can benefit from such data. We discuss the prospects of using publicly available sequencing data for organelle-focused studies and examine the challenges of such an approach. We highlight that the lack of a comprehensive database dedicated to organelle genomics/transcriptomics is a major impediment to the development of a field with implications in basic and applied science.
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Affiliation(s)
- Matheus Sanita Lima
- Department of Biology, Western University, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Douglas Silva Domingues
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Avenida Padua Dias 11, Piracicaba, SP 13418-900, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science, Bioinformatics and Pattern Recognition Group (BIOINFO-CP), Federal University of Technology - Paraná - UTFPR, Avenida Alberto Carazzai 1640, Cornélio Procópio, PR 86300000, Brazil
| | - David Roy Smith
- Department of Biology, Western University, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
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Zhang A, Tian L, Zhu T, Li M, Sun M, Fang Y, Zhang Y, Lu C. Uncovering the photosystem I assembly pathway in land plants. NATURE PLANTS 2024; 10:645-660. [PMID: 38503963 DOI: 10.1038/s41477-024-01658-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 02/29/2024] [Indexed: 03/21/2024]
Abstract
Photosystem I (PSI) is one of two large pigment-protein complexes responsible for converting solar energy into chemical energy in all oxygenic photosynthetic organisms. The PSI supercomplex consists of the PSI core complex and peripheral light-harvesting complex I (LHCI) in eukaryotic photosynthetic organisms. However, how the PSI complex assembles in land plants is unknown. Here we describe PHOTOSYSTEM I BIOGENESIS FACTOR 8 (PBF8), a thylakoid-anchored protein in Arabidopsis thaliana that is required for PSI assembly. PBF8 regulates two key consecutive steps in this process, the building of two assembly intermediates comprising eight or nine subunits, by interacting with PSI core subunits. We identified putative PBF8 orthologues in charophytic algae and land plants but not in Cyanobacteria or Chlorophyta. Our data reveal the major PSI assembly pathway in land plants. Our findings suggest that novel assembly mechanisms evolved during plant terrestrialization to regulate PSI assembly, perhaps as a means to cope with terrestrial environments.
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Affiliation(s)
- Aihong Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Lin Tian
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Tong Zhu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Mengyu Li
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Mengwei Sun
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Ying Fang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Yi Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China.
| | - Congming Lu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China.
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Delannoy E, Liehrmann A, Castandet B. The Use of Nanopore Sequencing to Analyze the Chloroplast Transcriptome Part II: Bioinformatic Analyzes and Virtual RNA Blots. Methods Mol Biol 2024; 2776:259-267. [PMID: 38502510 DOI: 10.1007/978-1-0716-3726-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Nanopore sequencing of full-length cDNAs offers unprecedented details of the plastid RNA metabolism. After the generation of the nanopore reads, several bioinformatic steps are required to analyze the data. In this chapter, we describe in a few simple command lines the processing and mapping of the reads as well as the generation of virtual Northern blots as a simple and familiar way to visualize Nanopore sequencing data.
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Affiliation(s)
- Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France.
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, France.
| | - Arnaud Liehrmann
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, France
- Laboratoire de Mathématiques et de Modélisation d'Evry (LaMME), Université d'Evry-Val-d'Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, Evry, France
| | - Benoît Castandet
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, France
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7
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Skiada S, Launay-Avon A, Liehrmann A, Delannoy E, Castandet B. The Use of Nanopore Sequencing to Analyze the Chloroplast Transcriptome Part I: Library Preparation. Methods Mol Biol 2024; 2776:243-257. [PMID: 38502509 DOI: 10.1007/978-1-0716-3726-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Global understanding of plastid gene expression has always been impaired by its complexity. RNA splicing, editing, and intercistronic processing create multiple transcripts isoforms that can hardly be resolved using traditional molecular biology techniques. During the last decade, the wide adoption of RNA-seq-based techniques has, however, allowed an unprecedented understanding of all the different steps of chloroplast gene expression, from transcription to translation. Current strategies are nonetheless unable to identify and quantify full length transcripts isoforms, a limitation that can now be overcome using Nanopore Sequencing. We here provide a complete protocol to produce, from total leaf RNA, cDNA libraries ready for Nanopore sequencing. While most Nanopore protocols take advantage of the mRNA polyA tail we here first ligate an RNA adapter to the 3' ends of the RNAs and use it to initiate the template switching reverse transcription. The cDNA is then prepared and indexed for use with the regular Oxford Nanopore v14 chemistry. This protocol is of particular interest to researchers willing to simultaneously study the multiple post-transcriptional processes prevalent in the chloroplast.
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Affiliation(s)
- Sébastien Skiada
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France
| | - Alexandra Launay-Avon
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France
- Laboratoire de Mathématiques et de Modélisation d'Evry (LaMME), Université d'Evry-Val-d'Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, Evry, France
| | - Arnaud Liehrmann
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France
- Laboratoire de Mathématiques et de Modélisation d'Evry (LaMME), Université d'Evry-Val-d'Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, Evry, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France
| | - Benoît Castandet
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France.
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Xu D, Tang Q, Xu P, Schäffner AR, Leister D, Kleine T. Response of the organellar and nuclear (post)transcriptomes of Arabidopsis to drought. FRONTIERS IN PLANT SCIENCE 2023; 14:1220928. [PMID: 37528975 PMCID: PMC10387551 DOI: 10.3389/fpls.2023.1220928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 06/28/2023] [Indexed: 08/03/2023]
Abstract
Plants have evolved sophisticated mechanisms to cope with drought, which involve massive changes in nuclear gene expression. However, little is known about the roles of post-transcriptional processing of nuclear or organellar transcripts and how meaningful these changes are. To address these issues, we used RNA-sequencing after ribosomal RNA depletion to monitor (post)transcriptional changes during different times of drought exposure in Arabidopsis Col-0. Concerning the changes detected in the organellar transcriptomes, chloroplast transcript levels were globally reduced, editing efficiency dropped, but splicing was not affected. Mitochondrial transcripts were slightly elevated, while editing and splicing were unchanged. Conversely, alternative splicing (AS) affected nearly 1,500 genes (9% of expressed nuclear genes). Of these, 42% were regulated solely at the level of AS, representing transcripts that would have gone unnoticed in a microarray-based approach. Moreover, we identified 927 isoform switching events. We provide a table of the most interesting candidates, and as proof of principle, increased drought tolerance of the carbonic anhydrase ca1 and ca2 mutants is shown. In addition, altering the relative contributions of the spliced isoforms could increase drought resistance. For example, our data suggest that the accumulation of a nonfunctional FLM (FLOWERING LOCUS M) isoform and not the ratio of FLM-ß and -δ isoforms may be responsible for the phenotype of early flowering under long-day drought conditions. In sum, our data show that AS enhances proteome diversity to counteract drought stress and represent a valuable resource that will facilitate the development of new strategies to improve plant performance under drought.
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Affiliation(s)
- Duorong Xu
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Qian Tang
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Ping Xu
- Department of Environmental Sciences, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, München, Germany
| | - Anton R. Schäffner
- Department of Environmental Sciences, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, München, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
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Mohammed T, Firoz A, Ramadan AM. RNA Editing in Chloroplast: Advancements and Opportunities. Curr Issues Mol Biol 2022; 44:5593-5604. [PMID: 36421663 PMCID: PMC9688838 DOI: 10.3390/cimb44110379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/05/2022] [Accepted: 11/10/2022] [Indexed: 07/25/2023] Open
Abstract
Many eukaryotic and prokaryotic organisms employ RNA editing (insertion, deletion, or conversion) as a post-transcriptional modification mechanism. RNA editing events are common in these organelles of plants and have gained particular attention due to their role in the development and growth of plants, as well as their ability to cope with abiotic stress. Owing to rapid developments in sequencing technologies and data analysis methods, such editing sites are being accurately predicted, and many factors that influence RNA editing are being discovered. The mechanism and role of the pentatricopeptide repeat protein family of proteins in RNA editing are being uncovered with the growing realization of accessory proteins that might help these proteins. This review will discuss the role and type of RNA editing events in plants with an emphasis on chloroplast RNA editing, involved factors, gaps in knowledge, and future outlooks.
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Affiliation(s)
- Taimyiah Mohammed
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia
| | - Ahmad Firoz
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed M. Ramadan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza 12619, Egypt
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Wang ZX, Wang DJ, Yi TS. Does IR-loss promote plastome structural variation and sequence evolution? FRONTIERS IN PLANT SCIENCE 2022; 13:888049. [PMID: 36247567 PMCID: PMC9560873 DOI: 10.3389/fpls.2022.888049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Plastids are one of the main distinguishing characteristics of the plant cell. The plastid genome (plastome) of most autotrophic seed plants possesses a highly conserved quadripartite structure containing a large single-copy (LSC) and a small single-copy (SSC) region separated by two copies of the inverted repeat (termed as IRA and IRB). The IRs have been inferred to stabilize the plastid genome via homologous recombination-induced repair mechanisms. IR loss has been documented in seven autotrophic flowering plant lineages and two autotrophic gymnosperm lineages, and the plastomes of these species (with a few exceptions) are rearranged to a great extent. However, some plastomes containing normal IRs also show high structural variation. Therefore, the role of IRs in maintaining plastome stability is still controversial. In this study, we first integrated and compared genome structure and sequence evolution of representative plastomes of all nine reported IR-lacking lineages and those of their closest relative(s) with canonical inverted repeats (CRCIRs for short) to explore the role of the IR in maintaining plastome structural stability and sequence evolution. We found the plastomes of most IR-lacking lineages have experienced significant structural rearrangement, gene loss and duplication, accumulation of novel small repeats, and acceleration of synonymous substitution compared with those of their CRCIRs. However, the IR-lacking plastomes show similar structural variation and sequence evolution rate, and even less rearrangement distance, dispersed repeat number, tandem repeat number, indels frequency and GC3 content than those of IR-present plastomes with variation in Geraniaceae. We argue that IR loss is not a driver of these changes but is instead itself a consequence of other processes that more broadly shape both structural and sequence-level plastome evolution.
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Affiliation(s)
- Zi-Xun Wang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Ding-Jie Wang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
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Forsythe ES, Grover CE, Miller ER, Conover JL, Arick MA, Chavarro MCF, Leal-Bertioli SCM, Peterson DG, Sharbrough J, Wendel JF, Sloan DB. Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels. Proc Natl Acad Sci U S A 2022; 119:e2204187119. [PMID: 35858449 PMCID: PMC9335225 DOI: 10.1073/pnas.2204187119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/14/2022] [Indexed: 01/21/2023] Open
Abstract
Mitochondrial and plastid functions depend on coordinated expression of proteins encoded by genomic compartments that have radical differences in copy number of organellar and nuclear genomes. In polyploids, doubling of the nuclear genome may add challenges to maintaining balanced expression of proteins involved in cytonuclear interactions. Here, we use ribo-depleted RNA sequencing (RNA-seq) to analyze transcript abundance for nuclear and organellar genomes in leaf tissue from four different polyploid angiosperms and their close diploid relatives. We find that even though plastid genomes contain <1% of the number of genes in the nuclear genome, they generate the majority (69.9 to 82.3%) of messenger RNA (mRNA) transcripts in the cell. Mitochondrial genes are responsible for a much smaller percentage (1.3 to 3.7%) of the leaf mRNA pool but still produce much higher transcript abundances per gene compared to nuclear genome. Nuclear genes encoding proteins that functionally interact with mitochondrial or plastid gene products exhibit mRNA expression levels that are consistently more than 10-fold lower than their organellar counterparts, indicating an extreme cytonuclear imbalance at the RNA level despite the predominance of equimolar interactions at the protein level. Nevertheless, interacting nuclear and organellar genes show strongly correlated transcript abundances across functional categories, suggesting that the observed mRNA stoichiometric imbalance does not preclude coordination of cytonuclear expression. Finally, we show that nuclear genome doubling does not alter the cytonuclear expression ratios observed in diploid relatives in consistent or systematic ways, indicating that successful polyploid plants are able to compensate for cytonuclear perturbations associated with nuclear genome doubling.
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Affiliation(s)
- Evan S. Forsythe
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010
| | - Emma R. Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010
| | - Justin L. Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010
| | - Mark A. Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762
| | - M. Carolina F. Chavarro
- Institute of Plant Breeding, Genetics and Genomics, Athens, GA 30602
- Bayer Crop Science, Chesterfield, MO 63017
| | | | - Daniel G. Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762
| | - Joel Sharbrough
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM 87801
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523
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12
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Morton BR. Context-Dependent Mutation Dynamics, Not Selection, Explains the Codon Usage Bias of Most Angiosperm Chloroplast Genes. J Mol Evol 2022; 90:17-29. [PMID: 34932159 PMCID: PMC8821512 DOI: 10.1007/s00239-021-10038-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 11/17/2021] [Indexed: 01/12/2023]
Abstract
Two competing proposals about the degree to which selection affects codon usage of angiosperm chloroplast genes are examined. The first, based on observations that codon usage does not match expectations under the naïve assumption that base composition will be identical at all neutral sites, is that selection plays a significant role. The second is that codon usage is determined almost solely by mutation bias and drift, with selection influencing only one or two highly expressed genes, in particular psbA. First it is shown that, as a result of an influence of neighboring base composition on mutation dynamics, compositional biases are expected to be widely divergent at different sites in the absence of selection. The observed mutation properties are then used to predict expected neutral codon usage biases and to show that observed deviations from the naïve expectations are in fact expected given the context-dependent mutational dynamics. It is also shown that there is a match between the observed and expected codon usage when context effects are taken into consideration, with psbA being a notable exception. Overall, the data support the model that selection is not a widespread factor affecting the codon usage of angiosperm chloroplast genes and highlight the need to have an accurate model of mutational dynamics.
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Affiliation(s)
- Brian R Morton
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA.
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13
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CAF Proteins Help SOT1 Regulate the Stability of Chloroplast ndhA Transcripts. Int J Mol Sci 2021; 22:ijms222312639. [PMID: 34884441 PMCID: PMC8657633 DOI: 10.3390/ijms222312639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/20/2021] [Accepted: 11/20/2021] [Indexed: 12/26/2022] Open
Abstract
Protein-mediated RNA stabilization plays profound roles in chloroplast gene expression. Genetic studies have indicated that chloroplast ndhA transcripts, encoding a key subunit of the NADH dehydrogenase-like complex that mediates photosystem I cyclic electron transport and facilitates chlororespiration, are stabilized by PPR53 and its orthologs, but the underlying mechanisms are unclear. Here, we report that CHLOROPLAST RNA SPLICING 2 (CRS2)-ASSOCIATED FACTOR (CAF) proteins activate SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), an ortholog of PPR53 in Arabidopsis thaliana, enhancing their affinity for the 5' ends of ndhA transcripts to stabilize these molecules while inhibiting the RNA endonuclease activity of the SOT1 C-terminal SMR domain. In addition, we established that SOT1 improves the splicing efficiency of ndhA by facilitating the association of CAF2 with the ndhA intron, which may be due to the SOT1-mediated stability of the ndhA transcripts. Our findings shed light on the importance of PPR protein interaction partners in moderating RNA metabolism.
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14
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Ling Y, Mahfouz MM, Zhou S. Pre-mRNA alternative splicing as a modulator for heat stress response in plants. TRENDS IN PLANT SCIENCE 2021; 26:1153-1170. [PMID: 34334317 DOI: 10.1016/j.tplants.2021.07.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 05/11/2023]
Abstract
The molecular responses of plants to the important abiotic stress, heat stress (HS), have been extensively studied at the transcriptional level. Alternative splicing (AS) is a post-transcriptional regulatory process in which an intron-containing gene can generate more than one mRNA variant. The impact of HS on the pre-mRNA splicing process has been reported in various eukaryotes but seldom discussed in-depth, especially in plants. Here, we review AS regulation in response to HS in different plant species. We discuss potential molecular mechanisms controlling heat-inducible AS regulation in plants and hypothesize that AS regulation participates in heat-priming establishment and HS memory maintenance. We propose that the pre-mRNA splicing variation is an important regulator of plant HS responses (HSRs).
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Affiliation(s)
- Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China; Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, PR China.
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Shuangxi Zhou
- New Zealand Institute for Plant and Food Research Limited, Hawke's Bay 4130, New Zealand
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15
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Guilcher M, Liehrmann A, Seyman C, Blein T, Rigaill G, Castandet B, Delannoy E. Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing. Int J Mol Sci 2021; 22:ijms222011297. [PMID: 34681956 PMCID: PMC8537030 DOI: 10.3390/ijms222011297] [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: 08/29/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Abstract
Plastid gene expression involves many post-transcriptional maturation steps resulting in a complex transcriptome composed of multiple isoforms. Although short-read RNA-Seq has considerably improved our understanding of the molecular mechanisms controlling these processes, it is unable to sequence full-length transcripts. This information is crucial, however, when it comes to understanding the interplay between the various steps of plastid gene expression. Here, we describe a protocol to study the plastid transcriptome using nanopore sequencing. In the leaf of Arabidopsis thaliana, with about 1.5 million strand-specific reads mapped to the chloroplast genome, we could recapitulate most of the complexity of the plastid transcriptome (polygenic transcripts, multiple isoforms associated with post-transcriptional processing) using virtual Northern blots. Even if the transcripts longer than about 2500 nucleotides were missing, the study of the co-occurrence of editing and splicing events identified 42 pairs of events that were not occurring independently. This study also highlighted a preferential chronology of maturation events with splicing happening after most sites were edited.
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Affiliation(s)
- Marine Guilcher
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91405 Orsay, France; (M.G.); (A.L.); (T.B.); (G.R.); (B.C.)
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
| | - Arnaud Liehrmann
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91405 Orsay, France; (M.G.); (A.L.); (T.B.); (G.R.); (B.C.)
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
- Laboratoire de Mathématiques et de Modélisation d’Evry (LaMME), Université d’Evry-Val-d’Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, 91000 Evry, France;
| | - Chloé Seyman
- Laboratoire de Mathématiques et de Modélisation d’Evry (LaMME), Université d’Evry-Val-d’Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, 91000 Evry, France;
| | - Thomas Blein
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91405 Orsay, France; (M.G.); (A.L.); (T.B.); (G.R.); (B.C.)
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
| | - Guillem Rigaill
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91405 Orsay, France; (M.G.); (A.L.); (T.B.); (G.R.); (B.C.)
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
- Laboratoire de Mathématiques et de Modélisation d’Evry (LaMME), Université d’Evry-Val-d’Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, 91000 Evry, France;
| | - Benoit Castandet
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91405 Orsay, France; (M.G.); (A.L.); (T.B.); (G.R.); (B.C.)
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91405 Orsay, France; (M.G.); (A.L.); (T.B.); (G.R.); (B.C.)
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
- Correspondence:
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16
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Gogolev YV, Ahmar S, Akpinar BA, Budak H, Kiryushkin AS, Gorshkov VY, Hensel G, Demchenko KN, Kovalchuk I, Mora-Poblete F, Muslu T, Tsers ID, Yadav NS, Korzun V. OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security. PLANTS (BASEL, SWITZERLAND) 2021; 10:1423. [PMID: 34371624 PMCID: PMC8309286 DOI: 10.3390/plants10071423] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.
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Affiliation(s)
- Yuri V. Gogolev
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | | | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT 59802, USA; (B.A.A.); (H.B.)
| | - Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Vladimir Y. Gorshkov
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, 40225 Dusseldorf, Germany;
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | - Tugdem Muslu
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey;
| | - Ivan D. Tsers
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Viktor Korzun
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
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17
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Kleine T, Nägele T, Neuhaus HE, Schmitz-Linneweber C, Fernie AR, Geigenberger P, Grimm B, Kaufmann K, Klipp E, Meurer J, Möhlmann T, Mühlhaus T, Naranjo B, Nickelsen J, Richter A, Ruwe H, Schroda M, Schwenkert S, Trentmann O, Willmund F, Zoschke R, Leister D. Acclimation in plants - the Green Hub consortium. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:23-40. [PMID: 33368770 DOI: 10.1111/tpj.15144] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 05/04/2023]
Abstract
Acclimation is the capacity to adapt to environmental changes within the lifetime of an individual. This ability allows plants to cope with the continuous variation in ambient conditions to which they are exposed as sessile organisms. Because environmental changes and extremes are becoming even more pronounced due to the current period of climate change, enhancing the efficacy of plant acclimation is a promising strategy for mitigating the consequences of global warming on crop yields. At the cellular level, the chloroplast plays a central role in many acclimation responses, acting both as a sensor of environmental change and as a target of cellular acclimation responses. In this Perspective article, we outline the activities of the Green Hub consortium funded by the German Science Foundation. The main aim of this research collaboration is to understand and strategically modify the cellular networks that mediate plant acclimation to adverse environments, employing Arabidopsis, tobacco (Nicotiana tabacum) and Chlamydomonas as model organisms. These efforts will contribute to 'smart breeding' methods designed to create crop plants with improved acclimation properties. To this end, the model oilseed crop Camelina sativa is being used to test modulators of acclimation for their potential to enhance crop yield under adverse environmental conditions. Here we highlight the current state of research on the role of gene expression, metabolism and signalling in acclimation, with a focus on chloroplast-related processes. In addition, further approaches to uncovering acclimation mechanisms derived from systems and computational biology, as well as adaptive laboratory evolution with photosynthetic microbes, are highlighted.
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Affiliation(s)
- Tatjana Kleine
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Thomas Nägele
- Plant Evolutionary Cell Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - H Ekkehard Neuhaus
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | | | - Alisdair R Fernie
- Central Metabolism, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
| | - Peter Geigenberger
- Plant Metabolism, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Bernhard Grimm
- Plant Physiology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Edda Klipp
- Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Torsten Möhlmann
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Belen Naranjo
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Jörg Nickelsen
- Molecular Plant Science, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Andreas Richter
- Physiology of Plant Organelles, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Hannes Ruwe
- Molecular Genetics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Michael Schroda
- Molecular Biotechnology & Systems Biology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Serena Schwenkert
- Plant Biochemistry and Physiology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Oliver Trentmann
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Reimo Zoschke
- Translational Regulation in Plants, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
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18
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Anand A, Pandi G. Noncoding RNA: An Insight into Chloroplast and Mitochondrial Gene Expressions. Life (Basel) 2021; 11:life11010049. [PMID: 33450961 PMCID: PMC7828403 DOI: 10.3390/life11010049] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 12/22/2022] Open
Abstract
Regulation of gene expression in any biological system is a complex process with many checkpoints at the transcriptional, post-transcriptional and translational levels. The control mechanism is mediated by various protein factors, secondary metabolites and a newly included regulatory member, i.e., noncoding RNAs (ncRNAs). It is known that ncRNAs modulate the mRNA or protein profiles of the cell depending on the degree of complementary and context of the microenvironment. In plants, ncRNAs are essential for growth and development in normal conditions by controlling various gene expressions and have emerged as a key player to guard plants during adverse conditions. In order to have smooth functioning of the plants under any environmental pressure, two very important DNA-harboring semi-autonomous organelles, namely, chloroplasts and mitochondria, are considered as main players. These organelles conduct the most crucial metabolic pathways that are required to maintain cell homeostasis. Thus, it is imperative to explore and envisage the molecular machineries responsible for gene regulation within the organelles and their coordination with nuclear transcripts. Therefore, the present review mainly focuses on ncRNAs origination and their gene regulation in chloroplasts and plant mitochondria.
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Affiliation(s)
- Asha Anand
- Correspondence: (A.A.); (G.P.); Tel.: +91-452-245-8230 (G.P.)
| | - Gopal Pandi
- Correspondence: (A.A.); (G.P.); Tel.: +91-452-245-8230 (G.P.)
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19
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Abstract
Computers are able to systematically exploit RNA-seq data allowing us to efficiently detect RNA editing sites in a genome-wide scale. This chapter introduces a very flexible computational framework for detecting RNA editing sites in plant organelles. This framework comprises three major steps: RNA-seq data processing, RNA read alignment, and RNA editing site detection. Each step is discussed in sufficient detail to be implemented by the reader. As a study case, the framework will be used with publicly available sequencing data to detect C-to-U RNA editing sites in the coding sequences of the mitochondrial genome of Nicotiana tabacum.
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Affiliation(s)
- Alejandro A Edera
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown, Argentina.
| | - M Virginia Sanchez-Puerta
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Argentina
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20
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Wang X, Yang Z, Zhang Y, Zhou W, Zhang A, Lu C. Pentatricopeptide repeat protein PHOTOSYSTEM I BIOGENESIS FACTOR2 is required for splicing of ycf3. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1741-1761. [PMID: 32250043 DOI: 10.1111/jipb.12936] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 03/27/2020] [Indexed: 05/04/2023]
Abstract
To gain a better understanding of the molecular mechanisms of photosystem I (PSI) biogenesis, we characterized the Arabidopsis thaliana photosystem I biogenesis factor 2 (pbf2) mutant, which lacks PSI complex. PBF2 encodes a P-class pentatricopeptide repeat (PPR) protein. In the pbf2 mutants, we observed a striking decrease in the transcript level of only one gene, the chloroplast gene ycf3, which is essential for PSI assembly. Further analysis of ycf3 transcripts showed that PBF2 is specifically required for the splicing of ycf3 intron 1. Computational prediction of binding sequences and electrophoretic mobility shift assays reveal that PBF2 specifically binds to a sequence in ycf3 intron 1. Moreover, we found that PBF2 interacted with two general factors for group II intron splicing CHLOROPLAST RNA SPLICING2-ASSOCIATED FACTOR1 (CAF1) and CAF2, and facilitated the association of these two factors with ycf3 intron 1. Our results suggest that PBF2 is specifically required for the splicing of ycf3 intron 1 through cooperating with CAF1 and CAF2. Our results also suggest that additional proteins are required to contribute to the specificity of CAF-dependent group II intron splicing.
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Affiliation(s)
- Xuemei Wang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhipan Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Wen Zhou
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Aihong Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Congming Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
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21
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Castandet B, Germain A, Hotto AM, Stern DB. Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures. Nucleic Acids Res 2020; 47:11889-11905. [PMID: 31732725 PMCID: PMC7145512 DOI: 10.1093/nar/gkz1059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/02/2019] [Accepted: 11/05/2019] [Indexed: 12/23/2022] Open
Abstract
Chloroplast transcription requires numerous quality control steps to generate the complex but selective mixture of accumulating RNAs. To gain insight into how this RNA diversity is achieved and regulated, we systematically mapped transcript ends by developing a protocol called Terminome-seq. Using Arabidopsis thaliana as a model, we catalogued >215 primary 5′ ends corresponding to transcription start sites (TSS), as well as 1628 processed 5′ ends and 1299 3′ ends. While most termini were found in intergenic regions, numerous abundant termini were also found within coding regions and introns, including several major TSS at unexpected locations. A consistent feature was the clustering of both 5′ and 3′ ends, contrasting with the prevailing description of discrete 5′ termini, suggesting an imprecision of the transcription and/or RNA processing machinery. Numerous termini correlated with the extremities of small RNA footprints or predicted stem-loop structures, in agreement with the model of passive RNA protection. Terminome-seq was also implemented for pnp1–1, a mutant lacking the processing enzyme polynucleotide phosphorylase. Nearly 2000 termini were altered in pnp1–1, revealing a dominant role in shaping the transcriptome. In summary, Terminome-seq permits precise delineation of the roles and regulation of the many factors involved in organellar transcriptome quality control.
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Affiliation(s)
- Benoît Castandet
- Boyce Thompson Institute, Ithaca, NY 14853, USA.,Institut des Sciences des Plantes de Paris Saclay (IPS2), UEVE, INRA, CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91192 Gif sur Yvette, France.,Université de Paris, IPS2, F-91192 Gif sur Yvette, France
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22
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Sun J, Tian Y, Lian Q, Liu JX. Mutation of DELAYED GREENING1 impairs chloroplast RNA editing at elevated ambient temperature in Arabidopsis. J Genet Genomics 2020; 47:201-212. [PMID: 32505546 DOI: 10.1016/j.jgg.2020.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/09/2020] [Accepted: 03/23/2020] [Indexed: 11/18/2022]
Abstract
Chloroplasts are important for plant growth and development. RNA editing in chloroplast converts cytidines (Cs) to uridines (Us) at specific transcript positions and provides a correction mechanism to restore conserved codons or creates start or stop codons. However, the underlined molecular mechanism is not yet fully understood. In the present study, we identified a thermo-sensitive mutant in leaf color 1 (tsl1) and found that TSL1 is allelic to DELAYED GREENING 1 (DG1). The missense mutation of DG1 in tsl1 mutant confers a high temperature sensitivity and impaired chloroplast development at an elevated ambient temperature in Arabidopsis. Subsequent analysis showed that chloroplast RNA editing at several sites including accD-1568, ndhD-2, and petL-5 is impaired in tsl1 mutant plants grown at an elevated temperature. DG1 interacts with MORF2 and other proteins such as DYW1 and DYW2 involved in chloroplast RNA editing. In vitro RNA electrophoretic mobility shift assay demonstrated that DG1 binds to RNA targets such as accD, ndhD, and petL. Thus, our results revealed that DG1 is important for maintaining chloroplast mRNA editing in Arabidopsis.
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Affiliation(s)
- Jingliang Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China; State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Yingying Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Qichao Lian
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jian-Xiang Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China; State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China.
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Armijos Carrion AD, Hinsinger DD, Strijk JS. ECuADOR-Easy Curation of Angiosperm Duplicated Organellar Regions, a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines. PeerJ 2020; 8:e8699. [PMID: 32292644 PMCID: PMC7147433 DOI: 10.7717/peerj.8699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/06/2020] [Indexed: 11/25/2022] Open
Abstract
Background With the rapid increase in availability of genomic resources offered by Next-Generation Sequencing (NGS) and the availability of free online genomic databases, efficient and standardized metadata curation approaches have become increasingly critical for the post-processing stages of biological data. Especially in organelle-based studies using circular chloroplast genome datasets, the assembly of the main structural regions in random order and orientation represents a major limitation in our ability to easily generate “ready-to-align” datasets for phylogenetic reconstruction, at both small and large taxonomic scales. In addition, current practices discard the most variable regions of the genomes to facilitate the alignment of the remaining coding regions. Nevertheless, no software is currently available to perform curation to such a degree, through simple detection, organization and positioning of the main plastome regions, making it a time-consuming and error-prone process. Here we introduce a fast and user friendly software ECuADOR, a Perl script specifically designed to automate the detection and reorganization of newly assembled plastomes obtained from any source available (NGS, sanger sequencing or assembler output). Methods ECuADOR uses a sliding-window approach to detect long repeated sequences in draft sequences, which then identifies the inverted repeat regions (IRs), even in case of artifactual breaks or sequencing errors and automates the rearrangement of the sequence to the widely used LSC–Irb–SSC–IRa order. This facilitates rapid post-editing steps such as creation of genome alignments, detection of variable regions, SNP detection and phylogenomic analyses. Results ECuADOR was successfully tested on plant families throughout the angiosperm phylogeny by curating 161 chloroplast datasets. ECuADOR first identified and reordered the central regions (LSC–Irb–SSC–IRa) for each dataset and then produced a new annotation for the chloroplast sequences. The process took less than 20 min with a maximum memory requirement of 150 MB and an accuracy of over 99%. Conclusions ECuADOR is the sole de novo one-step recognition and re-ordination tool that provides facilitation in the post-processing analysis of the extra nuclear genomes from NGS data. The program is available at https://github.com/BiodivGenomic/ECuADOR/.
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Affiliation(s)
- Angelo D Armijos Carrion
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China
| | - Damien D Hinsinger
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China.,Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
| | - Joeri S Strijk
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China.,Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi, PR China
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24
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Plant Ribonuclease J: An Essential Player in Maintaining Chloroplast RNA Quality Control for Gene Expression. PLANTS 2020; 9:plants9030334. [PMID: 32151111 PMCID: PMC7154860 DOI: 10.3390/plants9030334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/27/2022]
Abstract
RNA quality control is an indispensable but poorly understood process that enables organisms to distinguish functional RNAs from nonfunctional or inhibitory ones. In chloroplasts, whose gene expression activities are required for photosynthesis, retrograde signaling, and plant development, RNA quality control is of paramount importance, as transcription is relatively unregulated. The functional RNA population is distilled from this initial transcriptome by a combination of RNA-binding proteins and ribonucleases. One of the key enzymes is RNase J, a 5′→3′ exoribonuclease and an endoribonuclease that has been shown to trim 5′ RNA termini and eliminate deleterious antisense RNA. In the absence of RNase J, embryo development cannot be completed. Land plant RNase J contains a highly conserved C-terminal domain that is found in GT-1 DNA-binding transcription factors and is not present in its bacterial, archaeal, and algal counterparts. The GT-1 domain may confer specificity through DNA and/or RNA binding and/or protein–protein interactions and thus be an element in the mechanisms that identify target transcripts among diverse RNA populations. Further understanding of chloroplast RNA quality control relies on discovering how RNase J is regulated and how its specificity is imparted.
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25
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Methods and Tools for Plant Organelle Genome Sequencing, Assembly, and Downstream Analysis. Methods Mol Biol 2020; 2107:49-98. [PMID: 31893443 DOI: 10.1007/978-1-0716-0235-5_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Organelles play an important role in a eukaryotic cell. Among them, the two organelles, chloroplast and mitochondria, are responsible for the critical function of photosynthesis and aerobic respiration. Organellar genomes are also very important for plant systematic studies. Here we have described the methods for isolation of the mitochondrial and plastid DNA and its subsequent sequencing with the help of NGS technology. We have also discussed in detail the various tools available for assembly, annotation, and visualization of the organelle genome sequence.
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26
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Krüger M, Abeyawardana OAJ, Juříček M, Krüger C, Štorchová H. Variation in plastid genomes in the gynodioecious species Silene vulgaris. BMC PLANT BIOLOGY 2019; 19:568. [PMID: 31856730 PMCID: PMC6921581 DOI: 10.1186/s12870-019-2193-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/10/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Gynodioecious species exist in two sexes - male-sterile females and hermaphrodites. Male sterility in higher plants often results from mitonuclear interaction between the CMS (cytoplasmic male sterility) gene(s) encoded by mitochondrial genome and by nuclear-encoded restorer genes. Mitochondrial and nuclear-encoded transcriptomes in females and hermaphrodites are intensively studied, but little is known about sex-specific gene expression in plastids. We have compared plastid transcriptomes between females and hermaphrodites in two haplotypes of a gynodioecious species Silene vulgaris with known CMS candidate genes. RESULTS We generated complete plastid genome sequences from five haplotypes S. vulgaris including the haplotypes KRA and KOV, for which complete mitochondrial genome sequences were already published. We constructed a phylogenetic tree based on plastid sequences of S. vulgaris. Whereas lowland S. vulgaris haplotypes including KRA and KOV clustered together, the accessions from high European mountains diverged early in the phylogram. S. vulgaris belongs among Silene species with slowly evolving plastid genomes, but we still detected 212 substitutions and 112 indels between two accessions of this species. We estimated elevated Ka/Ks in the ndhF gene, which may reflect the adaptation of S. vulgaris to high altitudes, or relaxed selection. We compared depth of coverage and editing rates between female and hermaphrodite plastid transcriptomes and found no significant differences between the two sexes. We identified 51 unique C to U editing sites in the plastid genomes of S. vulgaris, 38 of them in protein coding regions, 2 in introns, and 11 in intergenic regions. The editing site in the psbZ gene was edited only in one of two plastid genomes under study. CONCLUSIONS We revealed no significant differences between the sexes in plastid transcriptomes of two haplotypes of S. vulgaris. It suggests that gene expression of plastid genes is not affected by CMS in flower buds of S. vulgaris, although both sexes may still differ in plastid gene expression in specific tissues. We revealed the difference between the plastid transcriptomes of two S. vulgaris haplotypes in editing rate and in the coverage of several antisense transcripts. Our results document the variation in plastid genomes and transcriptomes in S. vulgaris.
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Affiliation(s)
- Manuela Krüger
- Plant Reproduction Laboratory, Institute of Experimental Botany v.v.i, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Oushadee A. J. Abeyawardana
- Plant Reproduction Laboratory, Institute of Experimental Botany v.v.i, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Miloslav Juříček
- Plant Reproduction Laboratory, Institute of Experimental Botany v.v.i, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | | | - Helena Štorchová
- Plant Reproduction Laboratory, Institute of Experimental Botany v.v.i, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
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27
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Complete mitochondrial genomes from transcriptomes: assessing pros and cons of data mining for assembling new mitogenomes. Sci Rep 2019; 9:14806. [PMID: 31616005 PMCID: PMC6794255 DOI: 10.1038/s41598-019-51313-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 09/25/2019] [Indexed: 11/16/2022] Open
Abstract
Thousands of eukaryotes transcriptomes have been generated, mainly to investigate nuclear genes expression, and the amount of available data is constantly increasing. A neglected but promising use of this large amount of data is to assemble organelle genomes. To assess the reliability of this approach, we attempted to reconstruct complete mitochondrial genomes from RNA-Seq experiments of Reticulitermes termite species, for which transcriptomes and conspecific mitogenomes are available. We successfully assembled complete molecules, although a few gaps corresponding to tRNAs had to be filled manually. We also reconstructed, for the first time, the mitogenome of Reticulitermes banyulensis. The accuracy and completeness of mitogenomes reconstruction appeared independent from transcriptome size, read length and sequencing design (single/paired end), and using reference genomes from congeneric or intra-familial taxa did not significantly affect the assembly. Transcriptome-derived mitogenomes were found highly similar to the conspecific ones obtained from genome sequencing (nucleotide divergence ranging from 0% to 3.5%) and yielded a congruent phylogenetic tree. Reads from contaminants and nuclear transcripts, although slowing down the process, did not result in chimeric sequence reconstruction. We suggest that the described approach has the potential to increase the number of available mitogenomes by exploiting the rapidly increasing number of transcriptomes.
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28
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MORF9 Functions in Plastid RNA Editing with Tissue Specificity. Int J Mol Sci 2019; 20:ijms20184635. [PMID: 31546885 PMCID: PMC6769653 DOI: 10.3390/ijms20184635] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/11/2019] [Accepted: 09/13/2019] [Indexed: 11/17/2022] Open
Abstract
RNA editing in plant mitochondria and plastids converts specific nucleotides from cytidine (C) to uridine (U). These editing events differ among plant species and are relevant to developmental stages or are impacted by environmental conditions. Proteins of the MORF family are essential components of plant editosomes. One of the members, MORF9, is considered the core protein of the editing complex and is involved in the editing of most sites in chloroplasts. In this study, the phenotypes of a T-DNA insertion line with loss of MORF9 and of the genetic complementation line of Arabidopsis were analyzed, and the editing efficiencies of plastid RNAs in roots, rosette leaves, and flowers from the morf9 mutant and the wild-type (WT) control were compared by bulk-cDNA sequencing. The results showed that most of the known MORF9-associated plastid RNA editing events in rosette leaves and flowers were similarly reduced by morf9 mutation, with the exception that the editing rate of the sites ndhB-872 and psbF-65 declined in the leaves and that of ndhB-586 decreased only in the flowers. In the roots, however, the loss of MORF9 had a much lower effect on overall plastid RNA editing, with nine sites showing no significant editing efficiency change, including accD-794, ndhD-383, psbZ-50, ndhF-290, ndhD-878, matK-706, clpP1-559, rpoA-200, and ndhD-674, which were reduced in the other tissues. Furthermore, we found that during plant aging, MORF9 mRNA level, but not the protein level, was downregulated in senescent leaves. On the basis of these observations, we suggest that MORF9-mediated RNA editing is tissue-dependent and the resultant organelle proteomes are pertinent to the specific tissue functions.
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29
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Dorrell RG, Nisbet RER, Barbrook AC, Rowden SJL, Howe CJ. Integrated Genomic and Transcriptomic Analysis of the Peridinin Dinoflagellate Amphidinium carterae Plastid. Protist 2019; 170:358-373. [PMID: 31415953 DOI: 10.1016/j.protis.2019.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/10/2019] [Accepted: 06/14/2019] [Indexed: 01/17/2023]
Abstract
The plastid genomes of peridinin-containing dinoflagellates are highly unusual, possessing very few genes, which are located on small chromosomal elements termed "minicircles". These minicircles may contain genes, or no recognisable coding information. Transcripts produced from minicircles may undergo unusual processing events, such as the addition of a 3' poly(U) tail. To date, little is known about the genetic or transcriptional diversity of non-coding sequences in peridinin dinoflagellate plastids. These sequences include empty minicircles, and regions of non-coding DNA in coding minicircles. Here, we present an integrated plastid genome and transcriptome for the model peridinin dinoflagellate Amphidinium carterae, identifying a previously undescribed minicircle. We also profile transcripts covering non-coding regions of the psbA and petB/atpA minicircles. We present evidence that antisense transcripts are produced within the A. carterae plastid, but show that these transcripts undergo different end cleavage events from sense transcripts, and do not receive 3' poly(U) tails. The difference in processing events between sense and antisense transcripts may enable the removal of non-coding transcripts from peridinin dinoflagellate plastid transcript pools.
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Affiliation(s)
| | - R Ellen R Nisbet
- Department of Biochemistry, University of Cambridge, United Kingdom
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30
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Pérez Di Giorgio JA, Lepage É, Tremblay-Belzile S, Truche S, Loubert-Hudon A, Brisson N. Transcription is a major driving force for plastid genome instability in Arabidopsis. PLoS One 2019; 14:e0214552. [PMID: 30943245 PMCID: PMC6447228 DOI: 10.1371/journal.pone.0214552] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/15/2019] [Indexed: 12/14/2022] Open
Abstract
Though it is an essential process, transcription can be a source of genomic instability. For instance, it may generate RNA:DNA hybrids as the nascent transcript hybridizes with the complementary DNA template. These hybrids, called R-loops, act as a major cause of replication fork stalling and DNA breaks. In this study, we show that lowering transcription and R-loop levels in plastids of Arabidopsis thaliana reduces DNA rearrangements and mitigates plastid genome instability phenotypes. This effect can be observed on a genome-wide scale, as the loss of the plastid sigma transcription factor SIG6 prevents DNA rearrangements by favoring conservative repair in the presence of ciprofloxacin-induced DNA damage or in the absence of plastid genome maintenance actors such as WHY1/WHY3, RECA1 and POLIB. Additionally, resolving R-loops by the expression of a plastid-targeted exogenous RNAse H1 produces similar results. We also show that highly-transcribed genes are more susceptible to DNA rearrangements, as increased transcription of the psbD operon by SIG5 correlates with more locus-specific rearrangements. The effect of transcription is not specific to Sigma factors, as decreased global transcription levels by mutation of heat-stress-induced factor HSP21, mutation of nuclear-encoded polymerase RPOTp, or treatment with transcription-inhibitor rifampicin all prevent the formation of plastid genome rearrangements, especially under induced DNA damage conditions.
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Affiliation(s)
| | - Étienne Lepage
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Samuel Tremblay-Belzile
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Sébastien Truche
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Audrey Loubert-Hudon
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Normand Brisson
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
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Lo Giudice C, Hernández I, Ceci LR, Pesole G, Picardi E. RNA editing in plants: A comprehensive survey of bioinformatics tools and databases. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 137:53-61. [PMID: 30738217 DOI: 10.1016/j.plaphy.2019.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/30/2019] [Accepted: 02/02/2019] [Indexed: 06/09/2023]
Abstract
RNA editing is a widespread epitranscriptomic mechanism by which primary RNAs are specifically modified through insertions/deletions or nucleotide substitutions. In plants, RNA editing occurs in organelles (plastids and mitochondria), involves the cytosine to uridine modification (rarely uridine to cytosine) within protein-coding and non-protein-coding regions of RNAs and affects organelle biogenesis, adaptation to environmental changes and signal transduction. High-throughput sequencing technologies have dramatically improved the detection of RNA editing sites at genomic scale. Consequently, different bioinformatics resources have been released to discovery and/or collect novel events. Here, we review and describe the state-of-the-art bioinformatics tools devoted to the characterization of RNA editing in plant organelles with the aim to improve our knowledge about this fascinating but yet under investigated process.
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Affiliation(s)
- Claudio Lo Giudice
- IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Italy
| | - Irene Hernández
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, C/ Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Luigi R Ceci
- IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Italy
| | - Graziano Pesole
- IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Italy; Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari A. Moro, Bari, Italy
| | - Ernesto Picardi
- IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Italy; Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari A. Moro, Bari, Italy.
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32
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Hein A, Brenner S, Knoop V. Multifarious Evolutionary Pathways of a Nuclear RNA Editing Factor: Disjunctions in Coevolution of DOT4 and Its Chloroplast Target rpoC1eU488SL. Genome Biol Evol 2019; 11:798-813. [PMID: 30753430 PMCID: PMC6424221 DOI: 10.1093/gbe/evz032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2019] [Indexed: 12/25/2022] Open
Abstract
Nuclear-encoded pentatricopeptide repeat (PPR) proteins are site-specific factors for C-to-U RNA editing in plant organelles coevolving with their targets. Losing an editing target by C-to-T conversion allows for eventual loss of its editing factor, as recently confirmed for editing factors CLB19, CRR28, and RARE1 targeting ancient chloroplast editing sites in flowering plants. Here, we report on alternative evolutionary pathways for DOT4 addressing rpoC1eU488SL, a chloroplast editing site in the RNA polymerase β' subunit mRNA. Upon loss of rpoC1eU488SL by C-to-T conversion, DOT4 got lost multiple times independently in angiosperm evolution with intermediate states of DOT4 orthologs in various stages of degeneration. Surprisingly, we now also observe degeneration and loss of DOT4 despite retention of a C in the editing position (in Carica, Coffea, Vicia, and Spirodela). We find that the cytidine remains unedited, proving that DOT4 was not replaced by another editing factor. Yet another pathway of DOT4 evolution is observed among the Poaceae. Although the rpoC1eU488SL edit has been lost through C-to-T conversion, DOT4 orthologs not only remain conserved but also have their array of PPRs extended by six additional repeats. Here, the loss of the ancient target has likely allowed DOT4 to adapt for a new function. We suggest rps3 antisense transcripts as previously demonstrated in barley (Hordeum vulgare) arising from promotor sequences newly emerging in the rpl16 intron of Poaceae as a new candidate target for the extended PPR stretch of DOT4. Altogether, DOT4 and its target show more flexible pathways for evolution than the previously explored editing factors CLB19, CRR28, and RARE1. Certain plant clades (e.g., Amaranthus, Vaccinium, Carica, the Poaceae, Fabales, and Caryophyllales) show pronounced dynamics in the evolution of editing sites and corresponding factors.
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Affiliation(s)
- Anke Hein
- IZMB – Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Germany
| | - Sarah Brenner
- IZMB – Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Germany
| | - Volker Knoop
- IZMB – Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Germany
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Kawabe A, Furihata HY, Tsujino Y, Kawanabe T, Fujii S, Yoshida T. Divergence of RNA editing among Arabidopsis species. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:241-247. [PMID: 30824002 DOI: 10.1016/j.plantsci.2018.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/05/2018] [Accepted: 12/12/2018] [Indexed: 05/25/2023]
Abstract
RNA editing altered the RNA sequence by replacing the C nucleotide to U in the organellar genomes of plants. RNA editing status sometimes differed among distant species. The pattern of conservation and variation of RNA editing status made it possible to evaluate evolutionary mechanisms impacting functional aspects of RNA editing. In this study, divergence of RNA editing in the chloroplast genome among Arabidopsis species was analyzed to determine 9 losses and 1 gain in RNA editing. All changes in A. thaliana lineage resulted from changes to the chloroplast genome sequence, whereas changes in the A. lyrata / halleri lineage were possibly due to exclusive changes in the nuclear editing factors. One loss of RNA editing in A. lyrata was caused by a deficiency in the PPR gene OTP80. The changes in RNA editing occurred approximately every two million years and were not observed at functionally important sites. These results highlight the conserved nature of RNA editing status suggesting the importance of RNA editing during evolution.
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Affiliation(s)
- Akira Kawabe
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan.
| | - Hazuka Y Furihata
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Yudai Tsujino
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Takahiro Kawanabe
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Sota Fujii
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takanori Yoshida
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
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Sablok G, Amiryousefi A, He X, Hyvönen J, Poczai P. Sequencing the Plastid Genome of Giant Ragweed ( Ambrosia trifida, Asteraceae) From a Herbarium Specimen. FRONTIERS IN PLANT SCIENCE 2019; 10:218. [PMID: 30873197 PMCID: PMC6403193 DOI: 10.3389/fpls.2019.00218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/08/2019] [Indexed: 05/09/2023]
Abstract
We report the first plastome sequence of giant ragweed (Ambrosia trifida); with this new genome information, we assessed the phylogeny of Asteraceae and the transcriptional profiling against glyphosate resistance in giant ragweed. Assembly and genic features show a normal angiosperm quadripartite plastome structure with no signatures of deviation in gene directionality. Comparative analysis revealed large inversions across the plastome of giant ragweed and the previously sequenced members of the plant family. Asteraceae plastid genomes contain two inversions of 22.8 and 3.3 kb; the former is located between trnS-GCU and trnG-UCC genes, and the latter between trnE-UUC and trnT-GGU genes. The plastid genome sequences of A. trifida and the related species, Ambrosia artemisiifolia, are identical in gene content and arrangement, but they differ in length. The phylogeny is well-resolved and congruent with previous hypotheses about the phylogenetic relationship of Asteraceae. Transcriptomic analysis revealed divergence in the relative expressions at the exonic and intronic levels, providing hints toward the ecological adaptation of the genus. Giant ragweed shows various levels of glyphosate resistance, with introns displaying higher expression patterns at resistant time points after the assumed herbicide treatment.
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Affiliation(s)
- Gaurav Sablok
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Xiaolan He
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Péter Poczai
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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35
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Wang S, Yang C, Zhao X, Chen S, Qu GZ. Complete chloroplast genome sequence of Betula platyphylla: gene organization, RNA editing, and comparative and phylogenetic analyses. BMC Genomics 2018; 19:950. [PMID: 30572840 PMCID: PMC6302522 DOI: 10.1186/s12864-018-5346-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 11/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Betula platyphylla is a common tree species in northern China that has high economic and medicinal value. Our laboratory has been devoted to genome research on B. platyphylla for approximately 10 years. As primary organelle genomes, the complete genome sequences of chloroplasts are important to study the divergence of species, RNA editing and phylogeny. In this study, we sequenced and analyzed the complete chloroplast (cp) genome sequence of B. platyphylla. RESULTS The complete cp genome of B. platyphylla was 160,518 bp in length, which included a pair of inverted repeats (IRs) of 26,056 bp that separated a large single copy (LSC) region of 89,397 bp and a small single copy (SSC) region of 19,009 bp. The annotation contained a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes and 8 rRNA genes. There were 3 genes using alternative initiation codons. Comparative genomics showed that the sequence of the Fagales species cp genome was relatively conserved, but there were still some high variation regions that could be used as molecular markers. The IR expansion event of B. platyphylla resulted in larger cp genomes and rps19 pseudogene formation. The simple sequence repeat (SSR) analysis showed that there were 105 SSRs in the cp genome of B. platyphylla. RNA editing sites recognition indicated that at least 80 RNA editing events occurred in the cp genome. Most of the substitutions were C to U, while a small proportion of them were not. In particular, three editing loci on the rRNA were converted to more than two other bases that had never been reported. For synonymous conversion, most of them increased the relative synonymous codon usage (RSCU) value of the codons. The phylogenetic analysis suggested that B. platyphylla had a closer evolutionary relationship with B. pendula than B. nana. CONCLUSIONS In this study, we not only obtained and annotated the complete cp genome sequence of B. platyphylla, but we also identified new RNA editing sites and predicted the phylogenetic relationships among Fagales species. These findings will facilitate genomic, genetic engineering and phylogenetic studies of this important species.
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Affiliation(s)
- Sui Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Xiyang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Guan-Zheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
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Guan D, Yang F, Xia X, Shi Y, Yang S, Cheng W, He S. CaHSL1 Acts as a Positive Regulator of Pepper Thermotolerance Under High Humidity and Is Transcriptionally Modulated by CaWRKY40. FRONTIERS IN PLANT SCIENCE 2018; 9:1802. [PMID: 30581449 PMCID: PMC6292930 DOI: 10.3389/fpls.2018.01802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/20/2018] [Indexed: 05/27/2023]
Abstract
Pepper (Capsicum annuum) is an economically important vegetable and heat stress can severely impair pepper growth, development, and productivity. The molecular mechanisms underlying pepper thermotolerance are therefore important to understand but remain elusive. In the present study, we characterized the function of CaHSL1, encoding a HAESA-LIKE (HSL) receptor-like protein kinase (RLK), during the response of pepper to high temperature and high humidity (HTHH). CaHSL1 exhibits the typical structural features of an arginine-aspartate RLK. Transient overexpression of CaHSL1 in the mesophyll cells of Nicotiana benthamiana showed that CaHSL1 localizes throughout the cell, including the plasma membrane, cytoplasm, and the nucleus. CaHSL1 was significantly upregulated by HTHH or the exogenous application of abscisic acid but not by R. solanacearum inoculation. However, CaHSL1 was downregulated by exogenously applied salicylic acid, methyl jasmonate, or ethephon. Silencing of CaHSL1 by virus-induced gene silencing significantly was reduced tolerance to HTHH and downregulated transcript levels of an associated gene CaHSP24. In contrast, transient overexpression of CaHSL1 enhanced the transcript abundance of CaHSP24 and increased tolerance to HTHH, as manifested by enhanced optimal/maximal photochemical efficiency of photosystem II in the dark (Fv/Fm) and actual photochemical efficiency of photosystem II in the light. In addition, CaWRKY40 targeted the promoter of CaHSL1 and induced transcription during HTHH but not in response to R. solanacearum. All of these results suggest that CaHSL1 is directly modulated at the transcriptional level by CaWRKY40 and functions as a positive regulator in the response of pepper to HTHH.
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Affiliation(s)
- Deyi Guan
- Fujian Provincial Key Laboratory of Applied Genetics, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Feng Yang
- Fujian Provincial Key Laboratory of Applied Genetics, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoqin Xia
- Fujian Provincial Key Laboratory of Applied Genetics, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Shi
- Fujian Provincial Key Laboratory of Applied Genetics, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Yang
- Fujian Provincial Key Laboratory of Applied Genetics, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Cheng
- Fujian Provincial Key Laboratory of Applied Genetics, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuilin He
- Fujian Provincial Key Laboratory of Applied Genetics, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
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Smith DR, Sanitá Lima M. Unraveling chloroplast transcriptomes with ChloroSeq, an organelle RNA-Seq bioinformatics pipeline. Brief Bioinform 2018; 18:1012-1016. [PMID: 27677960 PMCID: PMC5862312 DOI: 10.1093/bib/bbw088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Indexed: 11/18/2022] Open
Abstract
Online sequence repositories are teeming with RNA sequencing (RNA-Seq) data from a wide range of eukaryotes. Although most of these data sets contain large numbers of organelle-derived reads, researchers tend to ignore these data, focusing instead on the nuclear-derived transcripts. Consequently, GenBank contains massive amounts of organelle RNA-Seq data that are just waiting to be downloaded and analyzed. Recently, a team of scientists designed an open-source bioinformatics program called ChloroSeq, which systemically analyzes an organelle transcriptome using RNA-Seq. The ChloroSeq pipeline uses RNA-Seq alignment data to deliver detailed analyses of organelle transcriptomes, which can be fed into statistical software for further analysis and for generating graphical representations of the data. In addition to providing data on expression levels via coverage statistics, ChloroSeq can examine splicing efficiency and RNA editing profiles. Ultimately, ChloroSeq provides a well-needed avenue for researchers of all stripes to start exploring organelle transcription and could be a key step toward a more thorough understanding of organelle gene expression.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, Ontario, Canada
- Corresponding author: David Roy Smith, Department of Biology, University of Western Ontario, London, Ontario N6A 5B7, Canada. Tel.: (519) 661 2111, ext; 86482; E-mail:
| | - Matheus Sanitá Lima
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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Mirzaei S, Mansouri M, Mohammadi-Nejad G, Sablok G. Comparative assessment of chloroplast transcriptional responses highlights conserved and unique patterns across Triticeae members under salt stress. PHOTOSYNTHESIS RESEARCH 2018; 136:357-369. [PMID: 29230609 DOI: 10.1007/s11120-017-0469-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/30/2017] [Indexed: 06/07/2023]
Abstract
Chloroplast functional genomics, in particular understanding the chloroplast transcriptional response is of immense importance mainly due to its role in oxygenic photosynthesis. As a photosynthetic unit, its efficiency and transcriptional activity is directly regulated by reactive oxygen species during abiotic and biotic stress and subsequently affects carbon assimilation, and plant biomass. In crops, understanding photosynthesis is crucial for crop domestication by identifying the traits that could be exploited for crop improvement. Transcriptionally and translationally active chloroplast plays a key role by regulating the PSI and PSII photo-reaction centres, which ubiquitously affects the light harvesting. Using a comparative transcriptomics mapping approach, we identified differential regulation of key chloroplast genes during salt stress across Triticeae members with potential genes involved in photosynthesis and electron transport system such as CytB6f. Apart from differentially regulated genes involved in PSI and PSII, we found widespread evidence of intron splicing events, specifically uniquely spliced petB and petD in Triticum aestivum and high proportion of RNA editing in ndh genes across the Triticeae members during salt stress. We also highlight the role and differential regulation of ATP synthase as member of CF0CF1 and also revealed the effect of salt stress on the water-splitting complex under salt stress. It is worthwhile to mention that the observed conserved down-regulation of psbJ across the Triticeae is limiting the assembly of water-splitting complexes and thus making the BEP clade Triticeae members more vulnerable to high light during the salt stress. Comparative understanding of the chloroplast transcriptional dynamics and photosynthetic regulation will improve the approaches for improved crop domestication.
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Affiliation(s)
- Saeid Mirzaei
- Department of Biotechnology, Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, 7631818356, Iran.
| | - Mehdi Mansouri
- Department of Agricultural Biotechnology, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ghasem Mohammadi-Nejad
- Research and Technology Institute of Plant Production, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Gaurav Sablok
- Finnish Museum of Natural History (Botany), PO Box 7, 00014, Helsinki, Finland
- Department of Bioscience, Viikki Plant Science Center, PO Box 7, 00014, Helsinki, Finland
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Song M, Kuo LY, Huiet L, Pryer KM, Rothfels CJ, Li FW. A novel chloroplast gene reported for flagellate plants. AMERICAN JOURNAL OF BOTANY 2018. [PMID: 29532931 DOI: 10.1002/ajb2.1010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
PREMISE OF THE STUDY Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame (ORF) in the fern lineage that is conserved across flagellate plants. METHODS We initially detected a putative uncharacterized ORF by the existence of a highly conserved region between rps16 and matK in a series of matK alignments of leptosporangiate ferns. We mined available plastid genomes for this ORF, which we now refer to as ycf94, to infer evolutionary selection pressures and assist in functional prediction. To further examine the transcription of ycf94, we assembled the plastid genome and sequenced the transcriptome of the leptosporangiate fern Adiantum shastense Huiet & A.R. Sm. KEY RESULTS The ycf94 predicted protein has a distinct transmembrane domain but with no sequence homology to other proteins with known function. The nonsynonymous/synonymous substitution rate ratio of ycf94 is on par with other fern plastid protein-encoding genes, and additional homologs can be found in a few lycophyte, moss, hornwort, and liverwort plastid genomes. Homologs of ycf94 were not found in seed plants. In addition, we report a high level of RNA editing for ycf94 transcripts-a hallmark of protein-coding genes in fern plastomes. CONCLUSIONS The degree of sequence conservation, together with the presence of a distinct transmembrane domain and RNA-editing sites, suggests that ycf94 is a protein-coding gene of functional significance in ferns and, potentially, bryophytes and lycophytes. However, the origin and exact function of this gene require further investigation.
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Affiliation(s)
- Michael Song
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California, 94720, USA
| | - Li-Yaung Kuo
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Section of Plant Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California, 94720, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Section of Plant Biology, Cornell University, Ithaca, New York, 14853, USA
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40
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Sun YK, Gutmann B, Yap A, Kindgren P, Small I. Editing of Chloroplast rps14 by PPR Editing Factor EMB2261 Is Essential for Arabidopsis Development. FRONTIERS IN PLANT SCIENCE 2018; 9:841. [PMID: 29973946 PMCID: PMC6019781 DOI: 10.3389/fpls.2018.00841] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 05/30/2018] [Indexed: 05/04/2023]
Abstract
RNA editing in plastids is known to be required for embryogenesis, but no single editing event had been shown to be essential. We show that the emb2261-2 mutation is lethal through a failure to express an editing factor that specifically recognizes the rps14-2 site. EMB2261 was predicted to bind the cis-element upstream of the rps14-2 site and genetic complementation with promoters of different strength followed by RNA-seq analysis was conducted to test the correlation between rps14-2 editing and EMB2261 expression. Rps14-2 is the only editing event in Arabidopsis chloroplasts that correlates with EMB2261 expression. Sequence divergence between the cis-element and the EMB2261 protein sequence in plants where rps14-2 editing is not required adds support to the association between them. We conclude that EMB2261 is the specificity factor for rps14-2 editing. This editing event converts P51 in Rps14 to L51, which is conserved among species lacking RNA editing, implying the importance of the editing event to Rps14 function. Rps14 is an essential ribosomal subunit for plastid translation, which, in turn, is essential for Arabidopsis embryogenesis.
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Abstract
Since its first use in plants in 2007, high-throughput RNA sequencing (RNA-Seq) has generated a vast amount of data for both model and nonmodel species. Organellar transcriptomes, however, are virtually always overlooked at the data analysis step. We therefore developed ChloroSeq, a bioinformatic pipeline aimed at facilitating the systematic analysis of chloroplast RNA metabolism, and we provide here a step-by-step user's manual. Following the alignment of quality-controlled data to the genome of interest, ChloroSeq measures genome expression level along with splicing and RNA editing efficiencies. When used in combination with the Tuxedo suite (TopHat and Cufflinks), ChloroSeq allows the simultaneous analysis of organellar and nuclear transcriptomes, opening the way to a better understanding of nucleus-organelle cross talk. We also describe the use of R commands to produce publication-quality figures based on ChloroSeq outputs. The effectiveness of the pipeline is illustrated through analysis of an RNA-Seq dataset covering the transition from growth to maturation to senescence of Arabidopsis thaliana leaves.
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Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists. G3-GENES GENOMES GENETICS 2017; 7:3789-3796. [PMID: 28935754 PMCID: PMC5677165 DOI: 10.1534/g3.117.300290] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Organelle genomes are among the most sequenced kinds of chromosome. This is largely because they are small and widely used in molecular studies, but also because next-generation sequencing technologies made sequencing easier, faster, and cheaper. However, studies of organelle RNA have not kept pace with those of DNA, despite huge amounts of freely available eukaryotic RNA-sequencing (RNA-seq) data. Little is known about organelle transcription in nonmodel species, and most of the available eukaryotic RNA-seq data have not been mined for organelle transcripts. Here, we use publicly available RNA-seq experiments to investigate organelle transcription in 30 diverse plastid-bearing protists with varying organelle genomic architectures. Mapping RNA-seq data to organelle genomes revealed pervasive, genome-wide transcription, regardless of the taxonomic grouping, gene organization, or noncoding content. For every species analyzed, transcripts covered ≥85% of the mitochondrial and/or plastid genomes (all of which were ≤105 kb), indicating that most of the organelle DNA—coding and noncoding—is transcriptionally active. These results follow earlier studies of model species showing that organellar transcription is coupled and ubiquitous across the genome, requiring significant downstream processing of polycistronic transcripts. Our findings suggest that noncoding organelle DNA can be transcriptionally active, raising questions about the underlying function of these transcripts and underscoring the utility of publicly available RNA-seq data for recovering complete genome sequences. If pervasive transcription is also found in bigger organelle genomes (>105 kb) and across a broader range of eukaryotes, this could indicate that noncoding organelle RNAs are regulating fundamental processes within eukaryotic cells.
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Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria. Proc Natl Acad Sci U S A 2017; 114:8877-8882. [PMID: 28760958 DOI: 10.1073/pnas.1705780114] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
RNA editing is converting hundreds of cytosines into uridines during organelle gene expression of land plants. The pentatricopeptide repeat (PPR) proteins are at the core of this posttranscriptional RNA modification. Even if a PPR protein defines the editing site, a DYW domain of the same or another PPR protein is believed to catalyze the deamination. To give insight into the organelle RNA editosome, we performed tandem affinity purification of the plastidial CHLOROPLAST BIOGENESIS 19 (CLB19) PPR editing factor. Two PPR proteins, dually targeted to mitochondria and chloroplasts, were identified as potential partners of CLB19. These two proteins, a P-type PPR and a member of a small PPR-DYW subfamily, were shown to interact in yeast. Insertional mutations resulted in embryo lethality that could be rescued by embryo-specific complementation. A transcriptome analysis of these complemented plants showed major editing defects in both organelles with a very high PPR type specificity, indicating that the two proteins are core members of E+-type PPR editosomes.
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Shi X, Castandet B, Germain A, Hanson MR, Bentolila S. ORRM5, an RNA recognition motif-containing protein, has a unique effect on mitochondrial RNA editing. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2833-2847. [PMID: 28549172 PMCID: PMC5853588 DOI: 10.1093/jxb/erx139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/30/2017] [Indexed: 05/02/2023]
Abstract
Plants have an RNA editing mechanism that prevents deleterious organelle mutations from resulting in impaired proteins. A typical flowering plant modifies about 40 cytidines in chloroplast transcripts and many hundreds of cytidines in mitochondrial transcripts. The plant editosome, the molecular machinery responsible for this process, contains members of several protein families, including the organelle RNA recognition motif (ORRM)-containing family. ORRM1 and ORRM6 are chloroplast editing factors, while ORRM2, ORRM3, and ORRM4 are mitochondrial editing factors. Here we report the identification of organelle RRM protein 5 (ORRM5) as a mitochondrial editing factor with a unique mode of action. Unlike other ORRM editing factors, the absence of ORRM5 in orrm5 mutant plants results in an increase of the editing extent in 14% of the mitochondrial sites surveyed. The orrm5 mutant also exhibits a reduced splicing efficiency of the first nad5 intron and slower growth and delayed flowering time. ORRM5 contains an RNA recognition motif (RRM) and a glycine-rich domain at the C terminus. The RRM provides the editing activity of ORRM5 and is able to complement the splicing but not the morphological defects.
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Affiliation(s)
- Xiaowen Shi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | | | - Arnaud Germain
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Stéphane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Correspondence:
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Havird JC, Sloan DB. The Roles of Mutation, Selection, and Expression in Determining Relative Rates of Evolution in Mitochondrial versus Nuclear Genomes. Mol Biol Evol 2016; 33:3042-3053. [PMID: 27563053 DOI: 10.1093/molbev/msw185] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Eukaryotes rely on proteins encoded by the nuclear and mitochondrial (mt) genomes, which interact within multisubunit complexes such as oxidative-phosphorylation enzymes. Although selection is thought to be less efficient on the asexual mt genome, in bilaterian animals the ratio of nonsynonymous to synonymous substitutions (ω) is lower in mt- compared with nuclear-encoded OXPHOS subunits, suggesting stronger effects of purifying selection in the mt genome. Because high levels of gene expression constrain protein sequence evolution, one proposed resolution to this paradox is that mt genes are expressed more highly than nuclear genes. To test this hypothesis, we investigated expression and sequence evolution of mt and nuclear genes from 84 diverse eukaryotes that vary in mt gene content and mutation rate. We found that the relationship between mt and nuclear ω values varied dramatically across eukaryotes. In contrast, transcript abundance is consistently higher for mt genes than nuclear genes, regardless of which genes happen to be in the mt genome. Consequently, expression levels cannot be responsible for the differences in ω Rather, 84% of the variance in the ratio of ω values between mt and nuclear genes could be explained by differences in mutation rate between the two genomes. We relate these findings to the hypothesis that high rates of mt mutation select for compensatory changes in the nuclear genome. We also propose an explanation for why mt transcripts consistently outnumber their nuclear counterparts, with implications for mitonuclear protein imbalance and aging.
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Affiliation(s)
- Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO
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