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Jeon Y, Ahn HK, Kang YW, Pai HS. Functional characterization of chloroplast-targeted RbgA GTPase in higher plants. PLANT MOLECULAR BIOLOGY 2017; 95:463-479. [PMID: 29038916 DOI: 10.1007/s11103-017-0664-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 10/01/2017] [Indexed: 06/07/2023]
Abstract
KEY MESSAGE Plant RbgA GTPase is targeted to chloroplasts and co-fractionated with chloroplast ribosomes, and plays a role in chloroplast rRNA processing and/or ribosome biogenesis. Ribosome Biogenesis GTPase A (RbgA) homologs are evolutionarily conserved GTPases that are widely distributed in both prokaryotes and eukaryotes. In this study, we investigated functions of chloroplast-targeted RbgA. Nicotiana benthamiana RbgA (NbRbgA) and Arabidopsis thaliana RbgA (AtRbgA) contained a conserved GTP-binding domain and a plant-specific C-terminal domain. NbRbgA and AtRbgA were mainly localized in chloroplasts, and possessed GTPase activity. Since Arabidopsis rbgA null mutants exhibited an embryonic lethal phenotype, virus-induced gene silencing (VIGS) of NbRbgA was performed in N. benthamiana. NbRbgA VIGS resulted in a leaf-yellowing phenotype caused by disrupted chloroplast development. NbRbgA was mainly co-fractionated with 50S/70S ribosomes and interacted with the chloroplast ribosomal proteins cpRPL6 and cpRPL35. NbRbgA deficiency lowered the levels of mature 23S and 16S rRNAs in chloroplasts and caused processing defects. Sucrose density gradient sedimentation revealed that NbRbgA-deficient chloroplasts contained reduced levels of mature 23S and 16S rRNAs and diverse plastid-encoded mRNAs in the polysomal fractions, suggesting decreased protein translation activity in the chloroplasts. Interestingly, NbRbgA protein was highly unstable under high light stress, suggesting its possible involvement in the control of chloroplast ribosome biogenesis under environmental stresses. Collectively, these results suggest a role for RbgA GTPase in chloroplast rRNA processing/ribosome biogenesis, affecting chloroplast protein translation in higher plants.
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Affiliation(s)
- Young Jeon
- Department of Systems Biology, Yonsei University, Seoul, 03722, South Korea
| | - Hee-Kyung Ahn
- Department of Systems Biology, Yonsei University, Seoul, 03722, South Korea
| | - Yong Won Kang
- R&D Center, Morechem Co., Ltd., Yongin, Gyeonggi-do, 16954, South Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul, 03722, South Korea.
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102
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Meurer J, Schmid LM, Stoppel R, Leister D, Brachmann A, Manavski N. PALE CRESS binds to plastid RNAs and facilitates the biogenesis of the 50S ribosomal subunit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:400-413. [PMID: 28805278 DOI: 10.1111/tpj.13662] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/04/2017] [Accepted: 08/08/2017] [Indexed: 05/11/2023]
Abstract
The plant-specific PALE CRESS (PAC) protein has previously been shown to be essential for photoautotrophic growth. Here we further investigated the molecular function of the PAC protein. PAC localizes to plastid nucleoids and forms large proteinaceous and RNA-containing megadalton complexes. It co-immunoprecipitates with a specific subset of chloroplast RNAs including psbK-psbI, ndhF, ndhD, and 23S ribosomal RNA (rRNA), as demonstrated by RNA immunoprecipitation in combination with high throughput RNA sequencing (RIP-seq) analyses. Furthermore, it co-migrates with premature 50S ribosomal particles and specifically binds to 23S rRNA in vitro. This coincides with severely reduced levels of 23S rRNA in pac leading to translational deficiencies and related alterations of plastid transcript patterns and abundance similar to plants treated with the translation inhibitor lincomycin. Thus, we conclude that deficiency in plastid ribosomes accounts for the pac phenotype. Moreover, the absence or reduction of PAC levels in the corresponding mutants induces structural changes of the 23S rRNA, as demonstrated by in vivo RNA structure probing. Our results indicate that PAC binds to the 23S rRNA to promote the biogenesis of the 50S subunit.
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Affiliation(s)
- Jörg Meurer
- Plant Sciences, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Lisa-Marie Schmid
- Plant Sciences, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Rhea Stoppel
- Plant Sciences, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Sciences, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Andreas Brachmann
- Genetics, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Nikolay Manavski
- Plant Sciences, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
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103
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Ahmed T, Shi J, Bhushan S. Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation. Nucleic Acids Res 2017; 45:8581-8595. [PMID: 28582576 PMCID: PMC5737520 DOI: 10.1093/nar/gkx499] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 05/26/2017] [Indexed: 12/30/2022] Open
Abstract
Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, cS23, bTHXc, cL37 and cL38) which have been suggested to play important regulatory roles in translation. However, their exact locations on the chloroplast ribosome remain elusive due to lack of a high-resolution structure, hindering our progress to understand their possible roles. Here we present a cryo-EM structure of the 70S chloroplast ribosome from spinach resolved to 3.4 Å and focus our discussion mainly on the architecture of the 30S small subunit (SSU) which is resolved to 3.7 Å. cS22 localizes at the SSU foot where it seems to compensate for the deletions in 16S rRNA. The mRNA exit site is highly remodeled due to the presence of cS23 suggesting an alternative mode of translation initiation. bTHXc is positioned at the SSU head and appears to stabilize the intersubunit bridge B1b during thermal fluctuations. The translation factor plastid pY binds to the SSU on the intersubunit side and interacts with the conserved nucleotide bases involved in decoding. Most of the intersubunit bridges are conserved compared to the bacteria, except for a new bridge involving uL2c and bS6c.
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Affiliation(s)
- Tofayel Ahmed
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Jian Shi
- Center for BioImaging Sciences, National University of Singapore, 117546, Singapore
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 639798, Singapore
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104
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Lu S, Li C, Zhang Y, Zheng Z, Liu D. Functional Disruption of a Chloroplast Pseudouridine Synthase Desensitizes Arabidopsis Plants to Phosphate Starvation. FRONTIERS IN PLANT SCIENCE 2017; 8:1421. [PMID: 28861101 PMCID: PMC5559850 DOI: 10.3389/fpls.2017.01421] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 07/31/2017] [Indexed: 05/29/2023]
Abstract
Phosphate (Pi) deficiency is a common nutritional stress of plants in both agricultural and natural ecosystems. Plants respond to Pi starvation in the environment by triggering a suite of biochemical, physiological, and developmental changes that increase survival and growth. The key factors that determine plant sensitivity to Pi starvation, however, are unclear. In this research, we identified an Arabidopsis mutant, dps1, with greatly reduced sensitivity to Pi starvation. The dps1 phenotypes are caused by a mutation in the previously characterized SVR1 (SUPPRESSION OF VARIAGATION 1) gene, which encodes a chloroplast-localized pseudouridine synthase. The mutation of SVR1 results in defects in chloroplast rRNA biogenesis, which subsequently reduces chloroplast translation. Another mutant, rps5, which contains a mutation in the chloroplast ribosomal protein RPS5 and has reduced chloroplast translation, also displayed decreased sensitivity to Pi starvation. Furthermore, wild type plants treated with lincomycin, a chemical inhibitor of chloroplast translation, showed similar growth phenotypes and Pi starvation responses as dps1 and rps5. These results suggest that impaired chloroplast translation desensitizes plants to Pi starvation. Combined with previously published results showing that enhanced leaf photosynthesis augments plant responses to Pi starvation, we propose that the decrease in responses to Pi starvation in dps1, rps5, and lincomycin-treated plants is due to their reduced demand for Pi input from the environment.
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Affiliation(s)
| | | | | | | | - Dong Liu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua UniversityBeijing, China
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105
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Graf M, Arenz S, Huter P, Dönhöfer A, Novácek J, Wilson DN. Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions. Nucleic Acids Res 2017; 45:2887-2896. [PMID: 27986857 PMCID: PMC5389730 DOI: 10.1093/nar/gkw1272] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/06/2016] [Indexed: 11/30/2022] Open
Abstract
Ribosomes are the protein synthesizing machines of the cell. Recent advances in cryo-EM have led to the determination of structures from a variety of species, including bacterial 70S and eukaryotic 80S ribosomes as well as mitoribosomes from eukaryotic mitochondria, however, to date high resolution structures of plastid 70S ribosomes have been lacking. Here we present a cryo-EM structure of the spinach chloroplast 70S ribosome, with an average resolution of 5.4 Å for the small 30S subunit and 3.6 Å for the large 50S ribosomal subunit. The structure reveals the location of the plastid-specific ribosomal proteins (RPs) PSRP1, PSRP4, PSRP5 and PSRP6 as well as the numerous plastid-specific extensions of the RPs. We discover many features by which the plastid-specific extensions stabilize the ribosome via establishing additional interactions with surrounding ribosomal RNA and RPs. Moreover, we identify a large conglomerate of plastid-specific protein mass adjacent to the tunnel exit site that could facilitate interaction of the chloroplast ribosome with the thylakoid membrane and the protein-targeting machinery. Comparing the Escherichia coli 70S ribosome with that of the spinach chloroplast ribosome provides detailed insight into the co-evolution of RP and rRNA.
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Affiliation(s)
- Michael Graf
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany
| | - Stefan Arenz
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany
| | - Paul Huter
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany
| | - Alexandra Dönhöfer
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany
| | - Jirí Novácek
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Daniel N Wilson
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany.,Department of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
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106
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Bobik K, McCray TN, Ernest B, Fernandez JC, Howell KA, Lane T, Staton M, Burch-Smith TM. The chloroplast RNA helicase ISE2 is required for multiple chloroplast RNA processing steps in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:114-131. [PMID: 28346704 DOI: 10.1111/tpj.13550] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 03/14/2017] [Accepted: 03/21/2017] [Indexed: 05/06/2023]
Abstract
INCREASED SIZE EXCLUSION LIMIT2 (ISE2) is a chloroplast-localized RNA helicase that is indispensable for proper plant development. Chloroplasts in leaves with reduced ISE2 expression have previously been shown to exhibit reduced thylakoid contents and increased stromal volume, indicative of defective development. It has recently been reported that ISE2 is required for the splicing of group II introns from chloroplast transcripts. The current study extends these findings, and presents evidence for ISE2's role in multiple aspects of chloroplast RNA processing beyond group II intron splicing. Loss of ISE2 from Arabidopsis thaliana leaves resulted in defects in C-to-U RNA editing, altered accumulation of chloroplast transcripts and chloroplast-encoded proteins, and defective processing of chloroplast ribosomal RNAs. Potential ISE2 substrates were identified by RNA immunoprecipitation followed by next-generation sequencing (RIP-seq), and the diversity of RNA species identified supports ISE2's involvement in multiple aspects of chloroplast RNA metabolism. Comprehensive phylogenetic analyses revealed that ISE2 is a non-canonical Ski2-like RNA helicase that represents a separate sub-clade unique to green photosynthetic organisms, consistent with its function as an essential protein. Thus ISE2's evolutionary conservation may be explained by its numerous roles in regulating chloroplast gene expression.
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Affiliation(s)
- Krzysztof Bobik
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tyra N McCray
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Ben Ernest
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jessica C Fernandez
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Katharine A Howell
- Plant Energy Biology, ARC Center of Excellence, University of Western Australia, Perth, Australia
| | - Thomas Lane
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA
| | - Margaret Staton
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA
| | - Tessa M Burch-Smith
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
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107
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Yurina NP, Sharapova LS, Odintsova MS. Structure of Plastid Genomes of Photosynthetic Eukaryotes. BIOCHEMISTRY (MOSCOW) 2017; 82:678-691. [PMID: 28601077 DOI: 10.1134/s0006297917060049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This review presents current views on the plastid genomes of higher plants and summarizes data on the size, structural organization, gene content, and other features of plastid DNAs. Special emphasis is placed on the properties of organization of land plant plastid genomes (nucleoids) that distinguish them from bacterial genomes. The prospects of genetic engineering of chloroplast genomes are discussed.
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Affiliation(s)
- N P Yurina
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
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108
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Wang WJ, Zheng KL, Gong XD, Xu JL, Huang JR, Lin DZ, Dong YJ. The rice TCD11 encoding plastid ribosomal protein S6 is essential for chloroplast development at low temperature. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 259:1-11. [PMID: 28483049 DOI: 10.1016/j.plantsci.2017.02.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 02/18/2017] [Accepted: 02/20/2017] [Indexed: 05/20/2023]
Abstract
Plastid ribosome proteins (PRPs) are important components for chloroplast biogenesis and early chloroplast development. Although it has been known that chloroplast ribosomes are similar to bacterial ones, the precise molecular function of ribosomal proteins remains to be elucidated in rice. Here, we identified a novel rice mutant, designated tcd11 (thermo-sensitive chlorophyll-deficient mutant 11), characterized by the albino phenotype until it died at 20°C, while displaying normal phenotype at 32°C. The alteration of leaf color in tcd11 mutants was aligned with chlorophyll (Chl) content and chloroplast development. The map-based cloning and molecular complementation showed that TCD11 encodes the ribosomal small subunit protein S6 in chloroplasts (RPS6). TCD11 was abundantly expressed in leaves, suggesting its different expressions in tissues. In addition, the disruption of TCD11 greatly reduced the transcript levels of certain chloroplasts-associated genes and prevented the assembly of ribosome in chloroplasts at low temperature (20°C), whereas they recovered to nearly normal levels at high temperature (32°C). Thus, our data indicate that TCD11 plays an important role in chloroplast development at low temperature. Upon our knowledge, the observations from this study provide a first glimpse into the importance of RPS6 function in rice chloroplast development.
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Affiliation(s)
- Wen-Juan Wang
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Kai-Lun Zheng
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiao-Di Gong
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China; Institute of Genetics and Developmental Biology Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 10010, China
| | - Jian-Long Xu
- The Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan Cun Street, Beijing 100081, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ji-Rong Huang
- Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Dong-Zhi Lin
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Yan-Jun Dong
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
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109
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Lin CS, Chen JJW, Chiu CC, Hsiao HCW, Yang CJ, Jin XH, Leebens-Mack J, de Pamphilis CW, Huang YT, Yang LH, Chang WJ, Kui L, Wong GKS, Hu JM, Wang W, Shih MC. Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:994-1006. [PMID: 28258650 DOI: 10.1111/tpj.13525] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 05/23/2023]
Abstract
The chloroplast NAD(P)H dehydrogenase-like (NDH) complex consists of about 30 subunits from both the nuclear and chloroplast genomes and is ubiquitous across most land plants. In some orchids, such as Phalaenopsis equestris, Dendrobium officinale and Dendrobium catenatum, most of the 11 chloroplast genome-encoded ndh genes (cp-ndh) have been lost. Here we investigated whether functional cp-ndh genes have been completely lost in these orchids or whether they have been transferred and retained in the nuclear genome. Further, we assessed whether both cp-ndh genes and nucleus-encoded NDH-related genes can be lost, resulting in the absence of the NDH complex. Comparative analyses of the genome of Apostasia odorata, an orchid species with a complete complement of cp-ndh genes which represents the sister lineage to all other orchids, and three published orchid genome sequences for P. equestris, D. officinale and D. catenatum, which are all missing cp-ndh genes, indicated that copies of cp-ndh genes are not present in any of these four nuclear genomes. This observation suggests that the NDH complex is not necessary for some plants. Comparative genomic/transcriptomic analyses of currently available plastid genome sequences and nuclear transcriptome data showed that 47 out of 660 photoautotrophic plants and all the heterotrophic plants are missing plastid-encoded cp-ndh genes and exhibit no evidence for maintenance of a functional NDH complex. Our data indicate that the NDH complex can be lost in photoautotrophic plant species. Further, the loss of the NDH complex may increase the probability of transition from a photoautotrophic to a heterotrophic life history.
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Affiliation(s)
- Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Jeremy J W Chen
- Institute of Biomedical Sciences, National Chung-Hsing University, Taichung, Taiwan
| | - Chi-Chou Chiu
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Han C W Hsiao
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung City, Taiwan
| | - Chen-Jui Yang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Xiao-Hua Jin
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | | | | | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Ling-Hung Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ling Kui
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Jer-Ming Hu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Wen Wang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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110
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Wittenberg G, Järvi S, Hojka M, Tóth SZ, Meyer EH, Aro EM, Schöttler MA, Bock R. Identification and characterization of a stable intermediate in photosystem I assembly in tobacco. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:478-490. [PMID: 28161893 DOI: 10.1111/tpj.13505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/29/2017] [Accepted: 01/31/2017] [Indexed: 05/06/2023]
Abstract
Photosystem I (PSI) is the most efficient bioenergetic nanomachine in nature and one of the largest membrane protein complexes known. It is composed of 18 protein subunits that bind more than 200 co-factors and prosthetic groups. While the structure and function of PSI have been studied in great detail, very little is known about the PSI assembly process. In this work, we have characterized a PSI assembly intermediate in tobacco plants, which we named PSI*. We found PSI* to contain only a specific subset of the core subunits of PSI. PSI* is particularly abundant in young leaves where active thylakoid biogenesis takes place. Moreover, PSI* was found to overaccumulate in PsaF-deficient mutant plants, and we show that re-initiation of PsaF synthesis promotes the maturation of PSI* into PSI. The attachment of antenna proteins to PSI also requires the transition from PSI* to mature PSI. Our data could provide a biochemical entry point into the challenging investigation of PSI biogenesis and allow us to improve the model for the assembly pathway of PSI in thylakoid membranes of vascular plants.
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Affiliation(s)
- Gal Wittenberg
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Sari Järvi
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014, Turku, Finland
| | - Marta Hojka
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Szilvia Z Tóth
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Etienne H Meyer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Eva-Mari Aro
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014, Turku, Finland
| | - Mark A Schöttler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
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111
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Moreno JC, Tiller N, Diez M, Karcher D, Tillich M, Schöttler MA, Bock R. Generation and characterization of a collection of knock-down lines for the chloroplast Clp protease complex in tobacco. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2199-2218. [PMID: 28369470 PMCID: PMC5447895 DOI: 10.1093/jxb/erx066] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Protein degradation in chloroplasts is carried out by a set of proteases that eliminate misfolded, damaged, or superfluous proteins. The ATP-dependent caseinolytic protease (Clp) is the most complex protease in plastids and has been implicated mainly in stromal protein degradation. In contrast, FtsH, a thylakoid membrane-associated metalloprotease, is believed to participate mainly in the degradation of thylakoidal proteins. To determine the role of specific Clp and FtsH subunits in plant growth and development, RNAi lines targeting at least one subunit of each Clp ring and FtsH were generated in tobacco. In addition, mutation of the translation initiation codon was employed to down-regulate expression of the plastid-encoded ClpP1 subunit. These protease lines cover a broad range of reductions at the transcript and protein levels of the targeted genes. A wide spectrum of phenotypes was obtained, including pigment deficiency, alterations in leaf development, leaf variegations, and impaired photosynthesis. When knock-down lines for the different protease subunits were compared, both common and specific phenotypes were observed, suggesting distinct functions of at least some subunits. Our work provides a well-characterized collection of knock-down lines for plastid proteases in tobacco and reveals the importance of the Clp protease in physiology and plant development.
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Affiliation(s)
- Juan C Moreno
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Nadine Tiller
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mercedes Diez
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniel Karcher
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Michael Tillich
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mark A Schöttler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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112
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Tamburino R, Vitale M, Ruggiero A, Sassi M, Sannino L, Arena S, Costa A, Batelli G, Zambrano N, Scaloni A, Grillo S, Scotti N. Chloroplast proteome response to drought stress and recovery in tomato (Solanum lycopersicum L.). BMC PLANT BIOLOGY 2017; 17:40. [PMID: 28183294 PMCID: PMC5301458 DOI: 10.1186/s12870-017-0971-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 01/04/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Drought is a major constraint for plant growth and crop productivity that is receiving an increased attention due to global climate changes. Chloroplasts act as environmental sensors, however, only partial information is available on stress-induced mechanisms within plastids. Here, we investigated the chloroplast response to a severe drought treatment and a subsequent recovery cycle in tomato through physiological, metabolite and proteomic analyses. RESULTS Under stress conditions, tomato plants showed stunted growth, and elevated levels of proline, abscisic acid (ABA) and late embryogenesis abundant gene transcript. Proteomics revealed that water deficit deeply affects chloroplast protein repertoire (31 differentially represented components), mainly involving energy-related functional species. Following the rewatering cycle, physiological parameters and metabolite levels indicated a recovery of tomato plant functions, while proteomics revealed a still ongoing adjustment of the chloroplast protein repertoire, which was even wider than during the drought phase (54 components differentially represented). Changes in gene expression of candidate genes and accumulation of ABA suggested the activation under stress of a specific chloroplast-to-nucleus (retrograde) signaling pathway and interconnection with the ABA-dependent network. CONCLUSIONS Our results give an original overview on the role of chloroplast as enviromental sensor by both coordinating the expression of nuclear-encoded plastid-localised proteins and mediating plant stress response. Although our data suggest the activation of a specific retrograde signaling pathway and interconnection with ABA signaling network in tomato, the involvement and fine regulation of such pathway need to be further investigated through the development and characterization of ad hoc designed plant mutants.
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Affiliation(s)
- Rachele Tamburino
- Institute of Biosciences and BioResources, National Research Council of Italy (CNR-IBBR), via Università 133, 80055, Portici, NA, Italy
| | - Monica Vitale
- Institute for the Animal Production System in the Mediterranean Environment, National Research Council of Italy (CNR-ISPAAM), via Argine 1085, 80147, Napoli, Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Pansini, 80100, Napoli, Italy
| | - Alessandra Ruggiero
- Institute of Biosciences and BioResources, National Research Council of Italy (CNR-IBBR), via Università 133, 80055, Portici, NA, Italy
| | - Mauro Sassi
- Institute for the Animal Production System in the Mediterranean Environment, National Research Council of Italy (CNR-ISPAAM), via Argine 1085, 80147, Napoli, Italy
| | - Lorenza Sannino
- Institute of Biosciences and BioResources, National Research Council of Italy (CNR-IBBR), via Università 133, 80055, Portici, NA, Italy
| | - Simona Arena
- Institute for the Animal Production System in the Mediterranean Environment, National Research Council of Italy (CNR-ISPAAM), via Argine 1085, 80147, Napoli, Italy
| | - Antonello Costa
- Institute of Biosciences and BioResources, National Research Council of Italy (CNR-IBBR), via Università 133, 80055, Portici, NA, Italy
| | - Giorgia Batelli
- Institute of Biosciences and BioResources, National Research Council of Italy (CNR-IBBR), via Università 133, 80055, Portici, NA, Italy
| | - Nicola Zambrano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Pansini, 80100, Napoli, Italy
- Center of Genetics Engineering (CEINGE) Biotecnologie Avanzate S.c. a R.l, via Pansini, 80100, Napoli, Italy
| | - Andrea Scaloni
- Institute for the Animal Production System in the Mediterranean Environment, National Research Council of Italy (CNR-ISPAAM), via Argine 1085, 80147, Napoli, Italy
| | - Stefania Grillo
- Institute of Biosciences and BioResources, National Research Council of Italy (CNR-IBBR), via Università 133, 80055, Portici, NA, Italy
| | - Nunzia Scotti
- Institute of Biosciences and BioResources, National Research Council of Italy (CNR-IBBR), via Università 133, 80055, Portici, NA, Italy.
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113
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Tabatabaei I, Ruf S, Bock R. A bifunctional aminoglycoside acetyltransferase/phosphotransferase conferring tobramycin resistance provides an efficient selectable marker for plastid transformation. PLANT MOLECULAR BIOLOGY 2017; 93:269-281. [PMID: 27858324 PMCID: PMC5306187 DOI: 10.1007/s11103-016-0560-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/10/2016] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE A new selectable marker gene for stable transformation of the plastid genome was developed that is similarly efficient as the aadA, and produces no background of spontaneous resistance mutants. More than 25 years after its development for Chlamydomonas and tobacco, the transformation of the chloroplast genome still represents a challenging technology that is available only in a handful of species. The vast majority of chloroplast transformation experiments conducted thus far have relied on a single selectable marker gene, the spectinomycin resistance gene aadA. Although a few alternative markers have been reported, the aadA has remained unrivalled in efficiency and is, therefore, nearly exclusively used. The development of new marker genes for plastid transformation is of crucial importance to all efforts towards extending the species range of the technology as well as to those applications in basic research, biotechnology and synthetic biology that involve the multistep engineering of plastid genomes. Here, we have tested a bifunctional resistance gene for its suitability as a selectable marker for chloroplast transformation. The bacterial enzyme aminoglycoside acetyltransferase(6')-Ie/aminoglycoside phosphotransferase(2″)-Ia possesses an N-terminal acetyltransferase domain and a C-terminal phosphotransferase domain that can act synergistically and detoxify aminoglycoside antibiotics highly efficiently. We report that, in combination with selection for resistance to the aminoglycoside tobramycin, the aac(6')-Ie/aph(2″)-Ia gene represents an efficient marker for plastid transformation in that it produces similar numbers of transplastomic lines as the spectinomycin resistance gene aadA. Importantly, no spontaneous antibiotic resistance mutants appear under tobramycin selection.
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Affiliation(s)
- Iman Tabatabaei
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Stephanie Ruf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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114
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Aryamanesh N, Ruwe H, Sanglard LVP, Eshraghi L, Bussell JD, Howell KA, Small I, des Francs-Small CC. The Pentatricopeptide Repeat Protein EMB2654 Is Essential for Trans-Splicing of a Chloroplast Small Ribosomal Subunit Transcript. PLANT PHYSIOLOGY 2017; 173:1164-1176. [PMID: 28011633 PMCID: PMC5291019 DOI: 10.1104/pp.16.01840] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 12/20/2016] [Indexed: 05/04/2023]
Abstract
We report the partial complementation and subsequent comparative molecular analysis of two nonviable mutants impaired in chloroplast translation, one (emb2394) lacking the RPL6 protein, and the other (emb2654) carrying a mutation in a gene encoding a P-class pentatricopeptide repeat protein. We show that EMB2654 is required for the trans-splicing of the plastid rps12 transcript and that therefore the emb2654 mutant lacks Rps12 protein and fails to assemble the small subunit of the plastid ribosome, explaining the loss of plastid translation and consequent embryo-lethal phenotype. Predictions of the EMB2654 binding site match a small RNA "footprint" located on the 5' half of the trans-spliced intron that is almost absent in the partially complemented mutant. EMB2654 binds sequence specifically to this target sequence in vitro. Altered patterns in nuclease-protected small RNA fragments in emb2654 show that EMB2654 binding must be an early step in, or prior to, the formation of a large protein-RNA complex covering the free ends of the two rps12 intron halves.
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Affiliation(s)
- Nader Aryamanesh
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009 Western Australia, Australia (N.A., H.R., L.V.P.S., L.E., J.D.B., K.A.H., I.S., C.C.d.F.-S.); and
- Institute of Biology, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R.)
| | - Hannes Ruwe
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009 Western Australia, Australia (N.A., H.R., L.V.P.S., L.E., J.D.B., K.A.H., I.S., C.C.d.F.-S.); and
- Institute of Biology, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R.)
| | - Lilian Vincis Pereira Sanglard
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009 Western Australia, Australia (N.A., H.R., L.V.P.S., L.E., J.D.B., K.A.H., I.S., C.C.d.F.-S.); and
- Institute of Biology, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R.)
| | - Leila Eshraghi
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009 Western Australia, Australia (N.A., H.R., L.V.P.S., L.E., J.D.B., K.A.H., I.S., C.C.d.F.-S.); and
- Institute of Biology, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R.)
| | - John D Bussell
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009 Western Australia, Australia (N.A., H.R., L.V.P.S., L.E., J.D.B., K.A.H., I.S., C.C.d.F.-S.); and
- Institute of Biology, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R.)
| | - Katharine A Howell
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009 Western Australia, Australia (N.A., H.R., L.V.P.S., L.E., J.D.B., K.A.H., I.S., C.C.d.F.-S.); and
- Institute of Biology, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R.)
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009 Western Australia, Australia (N.A., H.R., L.V.P.S., L.E., J.D.B., K.A.H., I.S., C.C.d.F.-S.); and
- Institute of Biology, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R.)
| | - Catherine Colas des Francs-Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009 Western Australia, Australia (N.A., H.R., L.V.P.S., L.E., J.D.B., K.A.H., I.S., C.C.d.F.-S.); and
- Institute of Biology, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R.)
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115
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Ivanova Z, Sablok G, Daskalova E, Zahmanova G, Apostolova E, Yahubyan G, Baev V. Chloroplast Genome Analysis of Resurrection Tertiary Relict Haberlea rhodopensis Highlights Genes Important for Desiccation Stress Response. FRONTIERS IN PLANT SCIENCE 2017; 8:204. [PMID: 28265281 PMCID: PMC5316520 DOI: 10.3389/fpls.2017.00204] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/03/2017] [Indexed: 05/20/2023]
Abstract
Haberlea rhodopensis is a paleolithic tertiary relict species, best known as a resurrection plant with remarkable tolerance to desiccation. When exposed to severe drought stress, H. rhodopensis shows an ability to maintain the structural integrity of its photosynthetic apparatus, which re-activates easily upon rehydration. We present here the results from the assembly and annotation of the chloroplast (cp) genome of H. rhodopensis, which was further subjected to comparative analysis with the cp genomes of closely related species. H. rhodopensis showed a cp genome size of 153,099 bp, harboring a pair of inverted repeats (IR) of 25,415 bp separated by small and large copy regions (SSC and LSC) of 17,826 and 84,443 bp. The genome structure, gene order, GC content and codon usage are similar to those of the typical angiosperm cp genomes. The genome hosts 137 genes representing 70.66% of the plastome, which includes 86 protein-coding genes, 36 tRNAs, and 4 rRNAs. A comparative plastome analysis with other closely related Lamiales members revealed conserved gene order in the IR and LSC/SSC regions. A phylogenetic analysis based on protein-coding genes from 33 species defines this species as belonging to the Gesneriaceae family. From an evolutionary point of view, a site-specific selection analysis detected positively selected sites in 17 genes, most of which are involved in photosynthesis (e.g., rbcL, ndhF, accD, atpE, etc.). The observed codon substitutions may be interpreted as being a consequence of molecular adaptation to drought stress, which ensures an evolutionary advantage to H. rhodopensis.
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Affiliation(s)
- Zdravka Ivanova
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
| | - Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster, University of Technology at Sydney, SydneyNSW, Australia
| | - Evelina Daskalova
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
| | - Gergana Zahmanova
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
| | - Elena Apostolova
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
| | - Galina Yahubyan
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
| | - Vesselin Baev
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
- *Correspondence: Vesselin Baev,
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116
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Leister D, Wang L, Kleine T. Organellar Gene Expression and Acclimation of Plants to Environmental Stress. FRONTIERS IN PLANT SCIENCE 2017; 8:387. [PMID: 28377785 PMCID: PMC5359298 DOI: 10.3389/fpls.2017.00387] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/07/2017] [Indexed: 05/03/2023]
Abstract
Organelles produce ATP and a variety of vital metabolites, and are indispensable for plant development. While most of their original gene complements have been transferred to the nucleus in the course of evolution, they retain their own genomes and gene-expression machineries. Hence, organellar function requires tight coordination between organellar gene expression (OGE) and nuclear gene expression (NGE). OGE requires various nucleus-encoded proteins that regulate transcription, splicing, trimming, editing, and translation of organellar RNAs, which necessitates nucleus-to-organelle (anterograde) communication. Conversely, changes in OGE trigger retrograde signaling that modulates NGE in accordance with the current status of the organelle. Changes in OGE occur naturally in response to developmental and environmental changes, and can be artificially induced by inhibitors such as lincomycin or mutations that perturb OGE. Focusing on the model plant Arabidopsis thaliana and its plastids, we review here recent findings which suggest that perturbations of OGE homeostasis regularly result in the activation of acclimation and tolerance responses, presumably via retrograde signaling.
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117
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Xu D, Leister D, Kleine T. Arabidopsis thaliana mTERF10 and mTERF11, but Not mTERF12, Are Involved in the Response to Salt Stress. FRONTIERS IN PLANT SCIENCE 2017; 8:1213. [PMID: 28769941 PMCID: PMC5509804 DOI: 10.3389/fpls.2017.01213] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/27/2017] [Indexed: 05/10/2023]
Abstract
Plastid gene expression (PGE) is crucial for plant development and acclimation to various environmental stress conditions. Members of the "mitochondrial transcription termination factor" (mTERF) family, which are present in both metazoans and plants, are involved in organellar gene expression. Arabidopsis thaliana contains 35 mTERF proteins, of which mTERF10, mTERF11, and mTERF12 were previously assigned to the "chloroplast-associated" group. Here, we show that all three are localized to chloroplast nucleoids, which are associated with PGE. Knock-down of MTERF10, MTERF11, or MTERF12 has no overt phenotypic effect under normal growth conditions. However, in silico analysis of MTERF10, -11, and -12 expression levels points to a possible involvement of mTERF10 and mTERF11 in responses to abiotic stress. Exposing mutant lines for 7 days to moderate heat (30°C) or light stress (400 μmol photons m-2 s-1) fails to induce a phenotype in mterf mutant lines. However, growth on MS medium supplemented with NaCl reveals that overexpression of MTERF11 results in higher salt tolerance. Conversely, mterf10 mutants are hypersensitive to salt stress, while plants that modestly overexpress MTERF10 are markedly less susceptible. Furthermore, MTERF10 overexpression leads to enhanced germination and growth on MS medium supplemented with ABA. These findings point to an involvement of mTERF10 in salt tolerance, possibly through an ABA-mediated mechanism. Thus, characterization of an increasing number of plant mTERF proteins reveals their roles in the response, tolerance and acclimation to different abiotic stresses.
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118
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Bieri P, Leibundgut M, Saurer M, Boehringer D, Ban N. The complete structure of the chloroplast 70S ribosome in complex with translation factor pY. EMBO J 2016; 36:475-486. [PMID: 28007896 PMCID: PMC5694952 DOI: 10.15252/embj.201695959] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/24/2016] [Accepted: 11/28/2016] [Indexed: 01/21/2023] Open
Abstract
Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo‐EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid‐specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid‐specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light‐ and temperature‐dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A‐site and P‐site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non‐rotated state, in which the intersubunit bridges to the large subunit are stabilized.
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Affiliation(s)
- Philipp Bieri
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Martin Saurer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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119
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Köhler D, Helm S, Agne B, Baginsky S. Importance of Translocon Subunit Tic56 for rRNA Processing and Chloroplast Ribosome Assembly. PLANT PHYSIOLOGY 2016; 172:2429-2444. [PMID: 27733515 PMCID: PMC5129725 DOI: 10.1104/pp.16.01393] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/11/2016] [Indexed: 05/20/2023]
Abstract
Toc159-containing complexes at the outer chloroplast envelope membrane form stable supercomplexes with a 1-MD translocon at the inner chloroplast envelope membrane of which Tic56 is one essential subunit. While the single mutants tic56-1 and ppi2 (toc159) have an albino phenotype and are able to grow heterotrophically, we find the double mutant to be embryo lethal. Comprehensive quantitative proteome profiling with both single mutants in combination with GeneChip analyses identified a posttranscriptional defect in the accumulation of plastid ribosomal proteins and diminished expression of plastid encoded proteins. In the tic56-1 mutant, the assembly of functional ribosomes is furthermore hampered by a processing defect of the plastid 23S rRNA. Spectinomycin-treatment of wild-type plants phenocopies the molecular phenotype of plastid proteome accumulation in tic56-1 and to a smaller degree also ppi2 plastids, suggesting that a defect in plastid translation is largely responsible for the phenotype of both import mutants. Import experiments with the tic56-3 mutant revealed no significant defect in the import of small ribosomal protein 16 in the absence of full-length Tic56, suggesting that the defect in ribosome assembly in tic56-1 may be independent of a function of Tic56 in protein import. Our data establish a previously unknown link between plastid protein import, the processing of plastid rRNAs, and the assembly of plastid ribosomes and provide further knowledge on the function of the translocon components and the molecular basis for their albino phenotype.
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Affiliation(s)
- Daniel Köhler
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
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120
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Isolation of Plastid Ribosomes. Methods Mol Biol 2016. [PMID: 27730617 DOI: 10.1007/978-1-4939-6533-5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Plastid ribosomes are responsible for a large part of the protein synthesis in plant leaves, green algal cells, and the vast majority in the thalli of red algae. Plastid translation is necessary not only for photosynthesis but also for development/differentiation of plants and algae. While some isolated plastid ribosomes from a few green lineages have been characterized by biochemical and proteomic approaches, in-depth proteomics including analyses of posttranslational modifications and processing, comparative proteomics of plastid ribosomes isolated from the cells grown under different conditions, and those from different taxa are still to be carried out. Establishment of isolation methods for pure plastid ribosomes from a wider range of species would be beneficial to study the relationship between structure, function, and evolution of plastid ribosomes. Here I describe methodologies and provide example protocols for extraction and isolation of plastid ribosomes from a unicellular green alga (Chlamydomonas reinhardtii), a land plant (Arabidopsis thaliana), and a marine red macroalga (Pyropia yezoensis).
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121
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Zheng M, Liu X, Liang S, Fu S, Qi Y, Zhao J, Shao J, An L, Yu F. Chloroplast Translation Initiation Factors Regulate Leaf Variegation and Development. PLANT PHYSIOLOGY 2016; 172:1117-1130. [PMID: 27535792 PMCID: PMC5047069 DOI: 10.1104/pp.15.02040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 08/15/2016] [Indexed: 05/18/2023]
Abstract
Chloroplast development requires the coordinated expressions of nuclear and chloroplast genomes, and both anterograde and retrograde signals exist and work together to facilitate this coordination. We have utilized the Arabidopsis yellow variegated (var2) mutant as a tool to dissect the genetic regulatory network of chloroplast development. Here, we report the isolation of a new (to our knowledge) var2 genetic suppressor locus, SUPPRESSOR OF VARIEGATION9 (SVR9). SVR9 encodes a chloroplast-localized prokaryotic type translation initiation factor 3 (IF3). svr9-1 mutant can be fully rescued by the Escherichia coli IF3 infC, suggesting that SVR9 functions as a bona fide IF3 in the chloroplast. Genetic and molecular evidence indicate that SVR9 and its close homolog SVR9-LIKE1 (SVR9L1) are functionally interchangeable and their combined activities are essential for chloroplast development and plant survival. Interestingly, we found that SVR9 and SVR9L1 are also involved in normal leaf development. Abnormalities in leaf anatomy, cotyledon venation patterns, and leaf margin development were identified in svr9-1 and mutants that are homozygous for svr9-1 and heterozygous for svr9l1-1 (svr9-1 svr9l1-1/+). Meanwhile, as indicated by the auxin response reporter DR5:GUS, auxin homeostasis was disturbed in svr9-1, svr9-1 svr9l1-1/+, and plants treated with inhibitors of chloroplast translation. Genetic analysis established that SVR9/SVR9L1-mediated leaf margin development is dependent on CUP-SHAPED COTYLEDON2 activities and is independent of their roles in chloroplast development. Together, our findings provide direct evidence that chloroplast IF3s are essential for chloroplast development and can also regulate leaf development.
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Affiliation(s)
- Mengdi Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China (M.Z., X.L., S.L., S.F., Y.Q., J.Z., J.S., L.A., F.Y.)
| | - Xiayan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China (M.Z., X.L., S.L., S.F., Y.Q., J.Z., J.S., L.A., F.Y.)
| | - Shuang Liang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China (M.Z., X.L., S.L., S.F., Y.Q., J.Z., J.S., L.A., F.Y.)
| | - Shiying Fu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China (M.Z., X.L., S.L., S.F., Y.Q., J.Z., J.S., L.A., F.Y.)
| | - Yafei Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China (M.Z., X.L., S.L., S.F., Y.Q., J.Z., J.S., L.A., F.Y.)
| | - Jun Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China (M.Z., X.L., S.L., S.F., Y.Q., J.Z., J.S., L.A., F.Y.)
| | - Jingxia Shao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China (M.Z., X.L., S.L., S.F., Y.Q., J.Z., J.S., L.A., F.Y.)
| | - Lijun An
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China (M.Z., X.L., S.L., S.F., Y.Q., J.Z., J.S., L.A., F.Y.)
| | - Fei Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China (M.Z., X.L., S.L., S.F., Y.Q., J.Z., J.S., L.A., F.Y.)
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Olejniczak SA, Łojewska E, Kowalczyk T, Sakowicz T. Chloroplasts: state of research and practical applications of plastome sequencing. PLANTA 2016; 244:517-27. [PMID: 27259501 PMCID: PMC4983300 DOI: 10.1007/s00425-016-2551-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/29/2016] [Indexed: 05/07/2023]
Abstract
This review presents origins, structure and expression of chloroplast genomes. It also describes their sequencing, analysis and modification, focusing on potential practical uses and biggest challenges of chloroplast genome modification. During the evolution of eukaryotes, cyanobacteria are believed to have merged with host heterotrophic cell. Afterward, most of cyanobacterial genes from cyanobacteria were transferred to cell nucleus or lost in the process of endosymbiosis. As a result of these changes, a primary plastid was established. Nowadays, plastid genome (plastome) is almost always circular, has a size of 100-200 kbp (120-160 in land plants), and harbors 100-120 highly conserved unique genes. Plastids have their own gene expression system, which is similar to one of their cyanobacterial ancestors. Two different polymerases, plastid-derived PEP and nucleus-derived NEP, participate in transcription. Translation is similar to the one observed in cyanobacteria, but it also utilizes protein translation factors and positive regulatory mRNA elements absent from bacteria. Plastoms play an important role in genetic transformation. Transgenes are introduced into them either via gene gun (in undamaged tissues) or polyethylene glycol treatment (when protoplasts are targeted). Antibiotic resistance markers are the most common tool used for selection of transformed plants. In recent years, plastome transformation emerged as a promising alternative to nuclear transformation because of (1) high yield of target protein, (2) removing the risk of outcrossing with weeds, (3) lack of silencing mechanisms, and (4) ability to engineer the entire metabolic pathways rather than single gene traits. Currently, the main directions of such research regard: developing efficient enzyme, vaccine antigen, and biopharmaceutical protein production methods in plant cells and improving crops by increasing their resistance to a wide array of biotic and abiotic stresses. Because of that, the detailed knowledge of plastome structure and mechanism of functioning started to play a major role.
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Affiliation(s)
- Szymon Adam Olejniczak
- Department of Genetics and Plant Molecular Biology and Biotechnology, The University of Lodz, Banacha Street 12/16, 90-237, Lodz, Poland.
| | - Ewelina Łojewska
- Department of Genetics and Plant Molecular Biology and Biotechnology, The University of Lodz, Banacha Street 12/16, 90-237, Lodz, Poland
| | - Tomasz Kowalczyk
- Department of Genetics and Plant Molecular Biology and Biotechnology, The University of Lodz, Banacha Street 12/16, 90-237, Lodz, Poland
| | - Tomasz Sakowicz
- Department of Genetics and Plant Molecular Biology and Biotechnology, The University of Lodz, Banacha Street 12/16, 90-237, Lodz, Poland
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Siniauskaya MG, Danilenko NG, Lukhanina NV, Shymkevich AM, Davydenko OG. Expression of the chloroplast genome: Modern concepts and experimental approaches. ACTA ACUST UNITED AC 2016. [DOI: 10.1134/s2079059716050117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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124
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Logacheva MD, Schelkunov MI, Shtratnikova VY, Matveeva MV, Penin AA. Comparative analysis of plastid genomes of non-photosynthetic Ericaceae and their photosynthetic relatives. Sci Rep 2016; 6:30042. [PMID: 27452401 PMCID: PMC4958920 DOI: 10.1038/srep30042] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/27/2016] [Indexed: 12/24/2022] Open
Abstract
Although plastid genomes of flowering plants are typically highly conserved regarding their size, gene content and order, there are some exceptions. Ericaceae, a large and diverse family of flowering plants, warrants special attention within the context of plastid genome evolution because it includes both non-photosynthetic and photosynthetic species with rearranged plastomes and putative losses of "essential" genes. We characterized plastid genomes of three species of Ericaceae, non-photosynthetic Monotropa uniflora and Hypopitys monotropa and photosynthetic Pyrola rotundifolia, using high-throughput sequencing. As expected for non-photosynthetic plants, M. uniflora and H. monotropa have small plastid genomes (46 kb and 35 kb, respectively) lacking genes related to photosynthesis, whereas P. rotundifolia has a larger genome (169 kb) with a gene set similar to other photosynthetic plants. The examined genomes contain an unusually high number of repeats and translocations. Comparative analysis of the expanded set of Ericaceae plastomes suggests that the genes clpP and accD that are present in the plastid genomes of almost all plants have not been lost in this family (as was previously thought) but rather persist in these genomes in unusual forms. Also we found a new gene in P. rotundifolia that emerged as a result of duplication of rps4 gene.
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Affiliation(s)
- Maria D. Logacheva
- Lomonosov Moscow State University, A.N Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Kazan Federal University, Institute of Fundamental Biology and Medicine, Kazan, Russia
| | - Mikhail I. Schelkunov
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Victoria Y. Shtratnikova
- Lomonosov Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, Russia
| | - Maria V. Matveeva
- Kazan Federal University, Institute of Fundamental Biology and Medicine, Kazan, Russia
| | - Aleksey A. Penin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Lomonosov Moscow State University, Department of Genetics, Moscow, Russia
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125
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Gimpel JA, Nour-Eldin HH, Scranton MA, Li D, Mayfield SP. Refactoring the Six-Gene Photosystem II Core in the Chloroplast of the Green Algae Chlamydomonas reinhardtii. ACS Synth Biol 2016. [PMID: 26214707 DOI: 10.1021/acssynbio.5b00076] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Oxygenic photosynthesis provides the energy to produce all food and most of the fuel on this planet. Photosystem II (PSII) is an essential and rate-limiting component of this process. Understanding and modifying PSII function could provide an opportunity for optimizing photosynthetic biomass production, particularly under specific environmental conditions. PSII is a complex multisubunit enzyme with strong interdependence among its components. In this work, we have deleted the six core genes of PSII in the eukaryotic alga Chlamydomonas reinhardtii and refactored them in a single DNA construct. Complementation of the knockout strain with the core PSII synthetic module from three different green algae resulted in reconstitution of photosynthetic activity to 85, 55, and 53% of that of the wild-type, demonstrating that the PSII core can be exchanged between algae species and retain function. The strains, synthetic cassettes, and refactoring strategy developed for this study demonstrate the potential of synthetic biology approaches for tailoring oxygenic photosynthesis and provide a powerful tool for unraveling PSII structure-function relationships.
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Affiliation(s)
- Javier A. Gimpel
- California Center for Algae
Biotechnology Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0368, United States
| | - Hussam H. Nour-Eldin
- California Center for Algae
Biotechnology Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0368, United States
| | - Melissa A. Scranton
- California Center for Algae
Biotechnology Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0368, United States
| | - Daphne Li
- California Center for Algae
Biotechnology Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0368, United States
| | - Stephen P. Mayfield
- California Center for Algae
Biotechnology Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0368, United States
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126
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Daniell H, Lin CS, Yu M, Chang WJ. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 2016; 17:134. [PMID: 27339192 PMCID: PMC4918201 DOI: 10.1186/s13059-016-1004-2] [Citation(s) in RCA: 738] [Impact Index Per Article: 92.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.
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Affiliation(s)
- Henry Daniell
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA, 19104-6030, USA.
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming Yu
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA, 19104-6030, USA
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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Van Dingenen J, De Milde L, Vermeersch M, Maleux K, De Rycke R, De Bruyne M, Storme V, Gonzalez N, Dhondt S, Inzé D. Chloroplasts Are Central Players in Sugar-Induced Leaf Growth. PLANT PHYSIOLOGY 2016; 171:590-605. [PMID: 26932234 PMCID: PMC4854676 DOI: 10.1104/pp.15.01669] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/29/2016] [Indexed: 05/18/2023]
Abstract
Leaves are the plant's powerhouses, providing energy for all organs through sugar production during photosynthesis. However, sugars serve not only as a metabolic energy source for sink tissues but also as signaling molecules, affecting gene expression through conserved signaling pathways to regulate plant growth and development. Here, we describe an in vitro experimental assay, allowing one to alter the sucrose (Suc) availability during early Arabidopsis (Arabidopsis thaliana) leaf development, with the aim to identify the affected cellular and molecular processes. The transfer of seedlings to Suc-containing medium showed a profound effect on leaf growth by stimulating cell proliferation and postponing the transition to cell expansion. Furthermore, rapidly after transfer to Suc, mesophyll cells contained fewer and smaller plastids, which are irregular in shape and contain fewer starch granules compared with control mesophyll cells. Short-term transcriptional responses after transfer to Suc revealed the repression of well-known sugar-responsive genes and multiple genes encoded by the plastid, on the one hand, and up-regulation of a GLUCOSE-6-PHOSPHATE TRANSPORTER (GPT2), on the other hand. Mutant gpt2 seedlings showed no stimulation of cell proliferation and no repression of chloroplast-encoded transcripts when transferred to Suc, suggesting that GPT2 plays a critical role in the Suc-mediated effects on early leaf growth. Our findings, therefore, suggest that induction of GPT2 expression by Suc increases the import of glucose-6-phosphate into the plastids that would repress chloroplast-encoded transcripts, restricting chloroplast differentiation. Retrograde signaling from the plastids would then delay the transition to cell expansion and stimulate cell proliferation.
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Affiliation(s)
- Judith Van Dingenen
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.)
| | - Liesbeth De Milde
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.)
| | - Mattias Vermeersch
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.)
| | - Katrien Maleux
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.)
| | - Riet De Rycke
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.)
| | - Michiel De Bruyne
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.)
| | - Véronique Storme
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.)
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.)
| | - Stijn Dhondt
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.)
| | - Dirk Inzé
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.V.D., L.D.M., M.V., K.M., R.D.R., M.D.B., V.S., N.G., S.D., D.I.)
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128
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Zhao DS, Zhang CQ, Li QF, Yang QQ, Gu MH, Liu QQ. A residue substitution in the plastid ribosomal protein L12/AL1 produces defective plastid ribosome and causes early seedling lethality in rice. PLANT MOLECULAR BIOLOGY 2016; 91:161-77. [PMID: 26873698 DOI: 10.1007/s11103-016-0453-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 02/08/2016] [Indexed: 05/25/2023]
Abstract
The plastid ribosome is essential for chloroplast biogenesis as well as seedling formation. As the plastid ribosome closely resembles the prokaryotic 70S ribosome, many plastid ribosomal proteins (PRPs) have been identified in higher plants. However, their assembly in the chloroplast ribosome in rice remains unclear. In the present study, we identified a novel rice mutant, albino lethal 1 (al1), from a chromosome segment substitution line population. The al1 mutant displayed an albino phenotype at the seedling stage and did not survive past the three-leaf stage. No other apparent differences in plant morphology were observed in the al1 mutant. The albino phenotype of the al1 mutant was associated with decreased chlorophyll content and abnormal chloroplast morphology. Using fine mapping, AL1 was shown to encode the PRPL12, a protein localized in the chloroplasts of rice, and a spontaneous single-nucleotide mutation (C/T), resulting in a residue substitution from leucine in AL1 to phenylalanine in al1, was found to be responsible for the early seedling lethality. This point mutation is located at the L10 interface feature of the L12/AL1 protein. Yeast two-hybrid analysis showed that there was no physical interaction between al1 and PRPL10. In addition, the mutation had little effect on the transcript abundance of al1, but had a remarkable effect on the protein abundance of al1 and transcript abundance of chloroplast biogenesis-related and photosynthesis-related genes. These results provide a first glimpse into the molecular details of L12's function in rice.
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Affiliation(s)
- Dong-Sheng Zhao
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Chang-Quan Zhang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Qian-Feng Li
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Qing-Qing Yang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Ming-Hong Gu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Qiao-Quan Liu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, 225009, People's Republic of China.
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129
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Hammani K, Takenaka M, Miranda R, Barkan A. A PPR protein in the PLS subfamily stabilizes the 5'-end of processed rpl16 mRNAs in maize chloroplasts. Nucleic Acids Res 2016; 44:4278-88. [PMID: 27095196 PMCID: PMC4872118 DOI: 10.1093/nar/gkw270] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are a large family of helical-repeat proteins that bind RNA in mitochondria and chloroplasts. Precise RNA targets and functions have been assigned to only a small fraction of the >400 members of the PPR family in plants. We used the amino acid code governing the specificity of RNA binding by PPR repeats to infer candidate-binding sites for the maize protein PPR103 and its ortholog Arabidopsis EMB175. Genetic and biochemical data confirmed a predicted binding site in the chloroplast rpl16 5′UTR to be a site of PPR103 action. This site maps to the 5′ end of transcripts that fail to accumulate in ppr103 mutants. A small RNA corresponding to the predicted PPR103 binding site accumulates in a PPR103-dependent fashion, as expected of PPR103's in vivo footprint. Recombinant PPR103 bound specifically to this sequence in vitro. These observations imply that PPR103 stabilizes rpl16 mRNA by impeding 5′→3′ RNA degradation. Previously described PPR proteins with this type of function consist of canonical PPR motifs. By contrast, PPR103 is a PLS-type protein, an architecture typically associated with proteins that specify sites of RNA editing. However, PPR103 is not required to specify editing sites in chloroplasts.
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Affiliation(s)
- Kamel Hammani
- Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Moléculaire des Plantes, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | | | - Rafael Miranda
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
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130
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Massouh A, Schubert J, Yaneva-Roder L, Ulbricht-Jones ES, Zupok A, Johnson MTJ, Wright SI, Pellizzer T, Sobanski J, Bock R, Greiner S. Spontaneous Chloroplast Mutants Mostly Occur by Replication Slippage and Show a Biased Pattern in the Plastome of Oenothera. THE PLANT CELL 2016; 28:911-29. [PMID: 27053421 PMCID: PMC4863383 DOI: 10.1105/tpc.15.00879] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 03/23/2016] [Accepted: 03/31/2016] [Indexed: 05/08/2023]
Abstract
Spontaneous plastome mutants have been used as a research tool since the beginning of genetics. However, technical restrictions have severely limited their contributions to research in physiology and molecular biology. Here, we used full plastome sequencing to systematically characterize a collection of 51 spontaneous chloroplast mutants in Oenothera (evening primrose). Most mutants carry only a single mutation. Unexpectedly, the vast majority of mutations do not represent single nucleotide polymorphisms but are insertions/deletions originating from DNA replication slippage events. Only very few mutations appear to be caused by imprecise double-strand break repair, nucleotide misincorporation during replication, or incorrect nucleotide excision repair following oxidative damage. U-turn inversions were not detected. Replication slippage is induced at repetitive sequences that can be very small and tend to have high A/T content. Interestingly, the mutations are not distributed randomly in the genome. The underrepresentation of mutations caused by faulty double-strand break repair might explain the high structural conservation of seed plant plastomes throughout evolution. In addition to providing a fully characterized mutant collection for future research on plastid genetics, gene expression, and photosynthesis, our work identified the spectrum of spontaneous mutations in plastids and reveals that this spectrum is very different from that in the nucleus.
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Affiliation(s)
- Amid Massouh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Julia Schubert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Liliya Yaneva-Roder
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | | | - Arkadiusz Zupok
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Marc T J Johnson
- Department of Biology, University of Toronto-Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Tommaso Pellizzer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Johanna Sobanski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Stephan Greiner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
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131
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Zhang J, Yuan H, Yang Y, Fish T, Lyi SM, Thannhauser TW, Zhang L, Li L. Plastid ribosomal protein S5 is involved in photosynthesis, plant development, and cold stress tolerance in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2731-44. [PMID: 27006483 PMCID: PMC4861020 DOI: 10.1093/jxb/erw106] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plastid ribosomal proteins are essential components of protein synthesis machinery and have diverse roles in plant growth and development. Mutations in plastid ribosomal proteins lead to a range of developmental phenotypes in plants. However, how they regulate these processes is not fully understood, and the functions of some individual plastid ribosomal proteins remain unknown. To identify genes responsible for chloroplast development, we isolated and characterized a mutant that exhibited pale yellow inner leaves with a reduced growth rate in Arabidopsis. The mutant (rps5) contained a missense mutation of plastid ribosomal protein S5 (RPS5), which caused a dramatically reduced abundance of chloroplast 16S rRNA and seriously impaired 16S rRNA processing to affect ribosome function and plastid translation. Comparative proteomic analysis revealed that the rps5 mutation suppressed the expression of a large number of core components involved in photosystems I and II as well as many plastid ribosomal proteins. Unexpectedly, a number of proteins associated with cold stress responses were greatly decreased in rps5, and overexpression of the plastid RPS5 improved plant cold stress tolerance. Our results indicate that RPS5 is an important constituent of the plastid 30S subunit and affects proteins involved in photosynthesis and cold stress responses to mediate plant growth and development.
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Affiliation(s)
- Junxiang Zhang
- College of Horticulture, State Key Laboratory of Crop Stress Biology for Arid Area, Northwest A&F University, Yangling, 712100, China Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Hui Yuan
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Yong Yang
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Tara Fish
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Sangbom M Lyi
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Theodore W Thannhauser
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Lugang Zhang
- College of Horticulture, State Key Laboratory of Crop Stress Biology for Arid Area, Northwest A&F University, Yangling, 712100, China
| | - Li Li
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
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132
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Sugliani M, Abdelkefi H, Ke H, Bouveret E, Robaglia C, Caffarri S, Field B. An Ancient Bacterial Signaling Pathway Regulates Chloroplast Function to Influence Growth and Development in Arabidopsis. THE PLANT CELL 2016; 28:661-79. [PMID: 26908759 PMCID: PMC4826016 DOI: 10.1105/tpc.16.00045] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 02/19/2016] [Indexed: 05/06/2023]
Abstract
The chloroplast originated from the endosymbiosis of an ancient photosynthetic bacterium by a eukaryotic cell. Remarkably, the chloroplast has retained elements of a bacterial stress response pathway that is mediated by the signaling nucleotides guanosine penta- and tetraphosphate (ppGpp). However, an understanding of the mechanism and outcomes of ppGpp signaling in the photosynthetic eukaryotes has remained elusive. Using the model plant Arabidopsis thaliana, we show that ppGpp is a potent regulator of chloroplast gene expression in vivo that directly reduces the quantity of chloroplast transcripts and chloroplast-encoded proteins. We then go on to demonstrate that the antagonistic functions of different plant RelA SpoT homologs together modulate ppGpp levels to regulate chloroplast function and show that they are required for optimal plant growth, chloroplast volume, and chloroplast breakdown during dark-induced and developmental senescence. Therefore, our results show that ppGpp signaling is not only linked to stress responses in plants but is also an important mediator of cooperation between the chloroplast and the nucleocytoplasmic compartment during plant growth and development.
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Affiliation(s)
- Matteo Sugliani
- Aix Marseille University, Biologie Végétale et Microbiologie Environnementales UMR 7265, Laboratoire de Génétique et Biophysique des Plantes, Marseille F-13009, France CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Marseille F-13009, France CEA, Bioscience and Biotechnology Institute of Aix-Marseille, Marseille F-13009, France
| | - Hela Abdelkefi
- Aix Marseille University, Biologie Végétale et Microbiologie Environnementales UMR 7265, Laboratoire de Génétique et Biophysique des Plantes, Marseille F-13009, France CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Marseille F-13009, France CEA, Bioscience and Biotechnology Institute of Aix-Marseille, Marseille F-13009, France University of Tunis El Manar, Faculté des Sciences de Tunis, Laboratory of Molecular Genetics, Immunology, and Biotechnology, 2092 El Manar Tunis, Tunisia
| | - Hang Ke
- Aix Marseille University, Biologie Végétale et Microbiologie Environnementales UMR 7265, Laboratoire de Génétique et Biophysique des Plantes, Marseille F-13009, France CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Marseille F-13009, France CEA, Bioscience and Biotechnology Institute of Aix-Marseille, Marseille F-13009, France
| | - Emmanuelle Bouveret
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS/Aix-Marseille University, Marseille F-13009, France
| | - Christophe Robaglia
- Aix Marseille University, Biologie Végétale et Microbiologie Environnementales UMR 7265, Laboratoire de Génétique et Biophysique des Plantes, Marseille F-13009, France CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Marseille F-13009, France CEA, Bioscience and Biotechnology Institute of Aix-Marseille, Marseille F-13009, France
| | - Stefano Caffarri
- Aix Marseille University, Biologie Végétale et Microbiologie Environnementales UMR 7265, Laboratoire de Génétique et Biophysique des Plantes, Marseille F-13009, France CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Marseille F-13009, France CEA, Bioscience and Biotechnology Institute of Aix-Marseille, Marseille F-13009, France
| | - Ben Field
- Aix Marseille University, Biologie Végétale et Microbiologie Environnementales UMR 7265, Laboratoire de Génétique et Biophysique des Plantes, Marseille F-13009, France CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Marseille F-13009, France CEA, Bioscience and Biotechnology Institute of Aix-Marseille, Marseille F-13009, France
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133
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Wu W, Liu S, Ruwe H, Zhang D, Melonek J, Zhu Y, Hu X, Gusewski S, Yin P, Small ID, Howell KA, Huang J. SOT1, a pentatricopeptide repeat protein with a small MutS-related domain, is required for correct processing of plastid 23S-4.5S rRNA precursors in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:607-21. [PMID: 26800847 DOI: 10.1111/tpj.13126] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 01/12/2016] [Indexed: 05/22/2023]
Abstract
Ribosomal RNA processing is essential for plastid ribosome biogenesis, but is still poorly understood in higher plants. Here, we show that SUPPRESSOR OF THYLAKOID FORMATION1 (SOT1), a plastid-localized pentatricopeptide repeat (PPR) protein with a small MutS-related domain, is required for maturation of the 23S-4.5S rRNA dicistron. Loss of SOT1 function leads to slower chloroplast development, suppression of leaf variegation, and abnormal 23S and 4.5S processing. Predictions based on the PPR motif sequences identified the 5' end of the 23S-4.5S rRNA dicistronic precursor as a putative SOT1 binding site. This was confirmed by electrophoretic mobility shift assay, and by loss of the abundant small RNA 'footprint' associated with this site in sot1 mutants. We found that more than half of the 23S-4.5S rRNA dicistrons in sot1 mutants contain eroded and/or unprocessed 5' and 3' ends, and that the endonucleolytic cleavage product normally released from the 5' end of the precursor is absent in a sot1 null mutant. We postulate that SOT1 binding protects the 5' extremity of the 23S-4.5S rRNA dicistron from exonucleolytic attack, and favours formation of the RNA structure that allows endonucleolytic processing of its 5' and 3' ends.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Base Sequence
- Binding Sites/genetics
- Blotting, Western
- Gene Expression Regulation, Plant
- Mutation
- Plants, Genetically Modified
- Plastids/genetics
- Plastids/metabolism
- Protein Binding
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Wenjuan Wu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sheng Liu
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Hannes Ruwe
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Joanna Melonek
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Yajuan Zhu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xupeng Hu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sandra Gusewski
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ian D Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, 6009, Australia
- Centre of Excellence in Computational Systems Biology, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Katharine A Howell
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Jirong Huang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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134
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Baute J, Herman D, Coppens F, De Block J, Slabbinck B, Dell'Acqua M, Pè ME, Maere S, Nelissen H, Inzé D. Combined Large-Scale Phenotyping and Transcriptomics in Maize Reveals a Robust Growth Regulatory Network. PLANT PHYSIOLOGY 2016; 170:1848-67. [PMID: 26754667 PMCID: PMC4775144 DOI: 10.1104/pp.15.01883] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/07/2016] [Indexed: 05/20/2023]
Abstract
Leaves are vital organs for biomass and seed production because of their role in the generation of metabolic energy and organic compounds. A better understanding of the molecular networks underlying leaf development is crucial to sustain global requirements for food and renewable energy. Here, we combined transcriptome profiling of proliferative leaf tissue with in-depth phenotyping of the fourth leaf at later stages of development in 197 recombinant inbred lines of two different maize (Zea mays) populations. Previously, correlation analysis in a classical biparental mapping population identified 1,740 genes correlated with at least one of 14 traits. Here, we extended these results with data from a multiparent advanced generation intercross population. As expected, the phenotypic variability was found to be larger in the latter population than in the biparental population, although general conclusions on the correlations among the traits are comparable. Data integration from the two diverse populations allowed us to identify a set of 226 genes that are robustly associated with diverse leaf traits. This set of genes is enriched for transcriptional regulators and genes involved in protein synthesis and cell wall metabolism. In order to investigate the molecular network context of the candidate gene set, we integrated our data with publicly available functional genomics data and identified a growth regulatory network of 185 genes. Our results illustrate the power of combining in-depth phenotyping with transcriptomics in mapping populations to dissect the genetic control of complex traits and present a set of candidate genes for use in biomass improvement.
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Affiliation(s)
- Joke Baute
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Dorota Herman
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Frederik Coppens
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Jolien De Block
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Bram Slabbinck
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Matteo Dell'Acqua
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Mario Enrico Pè
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Steven Maere
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Hilde Nelissen
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Dirk Inzé
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
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135
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De Marchis F, Bellucci M, Pompa A. Phaseolin expression in tobacco chloroplast reveals an autoregulatory mechanism in heterologous protein translation. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:603-14. [PMID: 26031839 DOI: 10.1111/pbi.12405] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/20/2015] [Accepted: 04/25/2015] [Indexed: 06/04/2023]
Abstract
Plastid DNA engineering is a well-established research area of plant biotechnology, and plastid transgenes often give high expression levels. However, it is still almost impossible to predict the accumulation rate of heterologous protein in transplastomic plants, and there are many cases of unsuccessful transgene expression. Chloroplasts regulate their proteome at the post-transcriptional level, mainly through translation control. One of the mechanisms to modulate the translation has been described in plant chloroplasts for the chloroplast-encoded subunits of multiprotein complexes, and the autoregulation of the translation initiation of these subunits depends on the availability of their assembly partners [control by epistasy of synthesis (CES)]. In Chlamydomonas reinhardtii, autoregulation of endogenous proteins recruited in the assembly of functional complexes has also been reported. In this study, we revealed a self-regulation mechanism triggered by the accumulation of a soluble recombinant protein, phaseolin, in the stroma of chloroplast-transformed tobacco plants. Immunoblotting experiments showed that phaseolin could avoid this self-regulation mechanism when targeted to the thylakoids in transplastomic plants. To inhibit the thylakoid-targeted phaseolin translation as well, this protein was expressed in the presence of a nuclear version of the phaseolin gene with a transit peptide. Pulse-chase and polysome analysis revealed that phaseolin mRNA translation on plastid ribosomes was repressed due to the accumulation in the stroma of the same soluble polypeptide imported from the cytosol. We suggest that translation autoregulation in chloroplast is not limited to heteromeric protein subunits but also involves at least some of the foreign soluble recombinant proteins, leading to the inhibition of plastome-encoded transgene expression in chloroplast.
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Affiliation(s)
- Francesca De Marchis
- Research Division of Perugia, Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | - Michele Bellucci
- Research Division of Perugia, Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | - Andrea Pompa
- Research Division of Perugia, Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
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136
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Dobrenel T, Mancera-Martínez E, Forzani C, Azzopardi M, Davanture M, Moreau M, Schepetilnikov M, Chicher J, Langella O, Zivy M, Robaglia C, Ryabova LA, Hanson J, Meyer C. The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S6. FRONTIERS IN PLANT SCIENCE 2016; 7:1611. [PMID: 27877176 PMCID: PMC5100631 DOI: 10.3389/fpls.2016.01611] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/12/2016] [Indexed: 05/05/2023]
Abstract
Protein translation is an energy consuming process that has to be fine-tuned at both the cell and organism levels to match the availability of resources. The target of rapamycin kinase (TOR) is a key regulator of a large range of biological processes in response to environmental cues. In this study, we have investigated the effects of TOR inactivation on the expression and regulation of Arabidopsis ribosomal proteins at different levels of analysis, namely from transcriptomic to phosphoproteomic. TOR inactivation resulted in a coordinated down-regulation of the transcription and translation of nuclear-encoded mRNAs coding for plastidic ribosomal proteins, which could explain the chlorotic phenotype of the TOR silenced plants. We have identified in the 5' untranslated regions (UTRs) of this set of genes a conserved sequence related to the 5' terminal oligopyrimidine motif, which is known to confer translational regulation by the TOR kinase in other eukaryotes. Furthermore, the phosphoproteomic analysis of the ribosomal fraction following TOR inactivation revealed a lower phosphorylation of the conserved Ser240 residue in the C-terminal region of the 40S ribosomal protein S6 (RPS6). These results were confirmed by Western blot analysis using an antibody that specifically recognizes phosphorylated Ser240 in RPS6. Finally, this antibody was used to follow TOR activity in plants. Our results thus uncover a multi-level regulation of plant ribosomal genes and proteins by the TOR kinase.
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Affiliation(s)
- Thomas Dobrenel
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
- Université Paris-Sud–Université Paris-SaclayOrsay, France
- Umeå Plant Science Center, Department of Plant Physiology, Umeå UniversityUmeå, Sweden
| | - Eder Mancera-Martínez
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, Université de StrasbourgStrasbourg, France
| | - Céline Forzani
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
| | - Marianne Azzopardi
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
| | | | - Manon Moreau
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
- Laboratoire de Génétique et Biophysique des Plantes, UMR 7265, DSV, IBEB, SBVME, CEA, CNRS, Aix-Marseille Université, Faculté des Sciences de LuminyMarseille, France
| | - Mikhail Schepetilnikov
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, Université de StrasbourgStrasbourg, France
| | - Johana Chicher
- Plateforme Protéomique Strasbourg-Esplanade, CNRS FRC1589, Institut de Biologie Moléculaire et CellulaireStrasbourg, France
| | | | - Michel Zivy
- Plateforme PAPPSO, UMR GQE-Le MoulonGif sur Yvette, France
| | - Christophe Robaglia
- Laboratoire de Génétique et Biophysique des Plantes, UMR 7265, DSV, IBEB, SBVME, CEA, CNRS, Aix-Marseille Université, Faculté des Sciences de LuminyMarseille, France
| | - Lyubov A. Ryabova
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, Université de StrasbourgStrasbourg, France
| | - Johannes Hanson
- Umeå Plant Science Center, Department of Plant Physiology, Umeå UniversityUmeå, Sweden
| | - Christian Meyer
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
- *Correspondence: Christian Meyer,
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137
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Colombo M, Tadini L, Peracchio C, Ferrari R, Pesaresi P. GUN1, a Jack-Of-All-Trades in Chloroplast Protein Homeostasis and Signaling. FRONTIERS IN PLANT SCIENCE 2016; 7:1427. [PMID: 27713755 PMCID: PMC5032792 DOI: 10.3389/fpls.2016.01427] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/07/2016] [Indexed: 05/04/2023]
Abstract
The GENOMES UNCOUPLED 1 (GUN1) gene has been reported to encode a chloroplast-localized pentatricopeptide-repeat protein, which acts to integrate multiple indicators of plastid developmental stage and altered plastid function, as part of chloroplast-to-nucleus retrograde communication. However, the molecular mechanisms underlying signal integration by GUN1 have remained elusive, up until the recent identification of a set of GUN1-interacting proteins, by co-immunoprecipitation and mass-spectrometric analyses, as well as protein-protein interaction assays. Here, we review the molecular functions of the different GUN1 partners and propose a major role for GUN1 as coordinator of chloroplast translation, protein import, and protein degradation. This regulatory role is implemented through proteins that, in most cases, are part of multimeric protein complexes and whose precise functions vary depending on their association states. Within this framework, GUN1 may act as a platform to promote specific functions by bringing the interacting enzymes into close proximity with their substrates, or may inhibit processes by sequestering particular pools of specific interactors. Furthermore, the interactions of GUN1 with enzymes of the tetrapyrrole biosynthesis (TPB) pathway support the involvement of tetrapyrroles as signaling molecules in retrograde communication.
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Affiliation(s)
- Monica Colombo
- Centro Ricerca e Innovazione, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Luca Tadini
- Dipartimento di Bioscienze, Università degli Studi di MilanoMilan, Italy
| | - Carlotta Peracchio
- Dipartimento di Bioscienze, Università degli Studi di MilanoMilan, Italy
| | - Roberto Ferrari
- Dipartimento di Bioscienze, Università degli Studi di MilanoMilan, Italy
| | - Paolo Pesaresi
- Dipartimento di Bioscienze, Università degli Studi di MilanoMilan, Italy
- *Correspondence: Paolo Pesaresi
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138
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Yang Z, Shang Z, Wang L, Lu Q, Wen X, Chi W, Zhang L, Lu C. Purine biosynthetic enzyme ATase2 is involved in the regulation of early chloroplast development and chloroplast gene expression in Arabidopsis. PHOTOSYNTHESIS RESEARCH 2015; 126:285-300. [PMID: 25837856 DOI: 10.1007/s11120-015-0131-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/24/2015] [Indexed: 05/14/2023]
Abstract
To investigate the molecular mechanism of chloroplast biogenesis and development, we characterized an Arabidopsis mutant (dg169, delayed greening 169) which showed growth retardation and delayed greening phenotype in leaves. Newly emerged chlorotic leaves recovered gradually with leaf development in the mutant, and the mature leaves showed similar phenotype to those of wild-typewild-type plants. Compared with wild-type, the chloroplasts were oval-shaped and smaller and the thylakoid membranes were less abundant in yellow section of young leaves of dg169. In addition, the functions of photosystem II (PSII) and photosystem I (PSI) were also impaired. Furthermore, the amount of core subunits of PSII and PSI, as well as PSII and PSI complexes reduced in yellow section of young leaves of dg169. Map-based positional cloning identified that phenotype of dg169 was attributed to a point mutation of ATase2 which converts the conserved Ile-155 residue to Asn. ATase2 catalyzes the first step of de novo purine biosynthesis. This mutation resulted in impaired purine synthesis and a significant decrease in ATP, ADP, GTP and GDP contents. The analysis of ATase2-GFP protein fusion showed that ATase2 was localized to nucleoid of chloroplasts. Our results further demonstrated that the levels of PEP-dependent transcripts in yellow section of young leaves of dg169 were decreased while NEP-dependent and both PEP- and NEP-dependent transcripts and chloroplast DNA replications were increased. The results in this study suggest that ATase2 plays an essential role in early chloroplast development through maintaining PEP function.
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Affiliation(s)
- Zhipan Yang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zengzhen Shang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingtao Lu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaogang Wen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Congming Lu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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139
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Mateo-Bonmatí E, Casanova-Sáez R, Quesada V, Hricová A, Candela H, Micol JL. Plastid control of abaxial-adaxial patterning. Sci Rep 2015; 5:15975. [PMID: 26522839 PMCID: PMC4629159 DOI: 10.1038/srep15975] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/07/2015] [Indexed: 01/31/2023] Open
Abstract
Translational regulation, exerted by the cytosolic ribosome, has been shown to participate in the establishment of abaxial-adaxial polarity in Arabidopsis thaliana: many hypomorphic and null alleles of genes encoding proteins of the cytosolic ribosome enhance the leaf polarity defects of asymmetric leaves1 (as1) and as2 mutants. Here, we report the identification of the SCABRA1 (SCA1) nuclear gene, whose loss-of-function mutations also enhance the polarity defects of the as2 mutants. In striking contrast to other previously known enhancers of the phenotypes caused by the as1 and as2 mutations, we found that SCA1 encodes a plastid-type ribosomal protein that functions as a structural component of the 70S plastid ribosome and, therefore, its role in abaxial-adaxial patterning was not expected.
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Affiliation(s)
- Eduardo Mateo-Bonmatí
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Rubén Casanova-Sáez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Víctor Quesada
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Andrea Hricová
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
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140
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Gu L, Jung HJ, Kim BM, Xu T, Lee K, Kim YO, Kang H. A chloroplast-localized S1 domain-containing protein SRRP1 plays a role in Arabidopsis seedling growth in the presence of ABA. JOURNAL OF PLANT PHYSIOLOGY 2015; 189:34-41. [PMID: 26513458 DOI: 10.1016/j.jplph.2015.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 10/07/2015] [Accepted: 10/07/2015] [Indexed: 05/07/2023]
Abstract
Although the roles of S1 domain-containing proteins have been characterized in diverse cellular processes in the cytoplasm, the functional roles of a majority of S1 domain-containing proteins targeted to the chloroplast are largely unknown. Here, we characterized the function of a nuclear-encoded chloroplast-targeted protein harboring two S1 domains, designated SRRP1 (for S1 RNA-binding ribosomal protein 1), in Arabidopsis thaliana. Subcellular localization analysis of SRRP1-GFP fusion proteins revealed that SRRP1 is localized to the chloroplast. The T-DNA tagged loss-of-function srrp1 mutants displayed poorer seedling growth and less cotyledon greening than the wild-type plants on MS medium supplemented with abscisic acid (ABA), suggesting that SRRP1 plays a role in seedling growth in the presence of ABA. Splicing of the trnL intron and processing of 5S rRNA in chloroplasts were altered in the mutant plants. Importantly, SRRP1 complemented the growth-defective phenotypes of an RNA chaperone-deficient Escherichia coli mutant at low temperatures and had nucleic acid-melting ability, indicating that SRRP1 possesses RNA chaperone activity. Taken together, these results suggest that SRRP1, the chloroplast-localized S1 domain-containing protein, harboring RNA chaperone activity affects the splicing and processing of chloroplast transcripts and plays a role in Arabidopsis seedling growth in the presence of ABA.
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Affiliation(s)
- Lili Gu
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Hyun Ju Jung
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Bo Mi Kim
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Tao Xu
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea; College of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, PR China
| | - Kwanuk Lee
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Yeon-Ok Kim
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea.
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141
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Romani I, Manavski N, Morosetti A, Tadini L, Maier S, Kühn K, Ruwe H, Schmitz-Linneweber C, Wanner G, Leister D, Kleine T. A Member of the Arabidopsis Mitochondrial Transcription Termination Factor Family Is Required for Maturation of Chloroplast Transfer RNAIle(GAU). PLANT PHYSIOLOGY 2015; 169:627-46. [PMID: 26152711 PMCID: PMC4577433 DOI: 10.1104/pp.15.00964] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/07/2015] [Indexed: 05/20/2023]
Abstract
Plastid gene expression is crucial for organelle function, but the factors that control it are still largely unclear. Members of the so-called mitochondrial transcription termination factor (mTERF) family are found in metazoans and plants and regulate organellar gene expression at different levels. Arabidopsis (Arabidopsis thaliana) mTERF6 is localized in chloroplasts and mitochondria, and its knockout perturbs plastid development and results in seedling lethality. In the leaky mterf6-1 mutant, a defect in photosynthesis is associated with reduced levels of photosystem subunits, although corresponding messenger RNA levels are unaffected, whereas translational capacity and maturation of chloroplast ribosomal RNAs (rRNAs) are perturbed in mterf6-1 mutants. Bacterial one-hybrid screening, electrophoretic mobility shift assays, and coimmunoprecipitation experiments reveal a specific interaction between mTERF6 and an RNA sequence in the chloroplast isoleucine transfer RNA gene (trnI.2) located in the rRNA operon. In vitro, recombinant mTERF6 bound to its plastid DNA target site can terminate transcription. At present, it is unclear whether disturbed rRNA maturation is a primary or secondary defect. However, it is clear that mTERF6 is required for the maturation of trnI.2. This points to an additional function of mTERFs.
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MESH Headings
- 5' Untranslated Regions/genetics
- Aminoacylation
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Base Sequence
- Basic-Leucine Zipper Transcription Factors/genetics
- Basic-Leucine Zipper Transcription Factors/metabolism
- Chloroplasts/metabolism
- DNA, Bacterial/genetics
- Gene Expression Regulation, Plant
- Genetic Loci
- Mitochondria/metabolism
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Molecular Sequence Data
- Mutagenesis, Insertional/genetics
- Mutation
- Phenotype
- Photosynthesis
- Protein Binding
- Protein Transport
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/genetics
- RNA, Transfer, Ile/chemistry
- RNA, Transfer, Ile/genetics
- RNA, Transfer, Ile/metabolism
- Ribosomes/metabolism
- Seedlings/metabolism
- Seeds/ultrastructure
- Transcription Termination, Genetic
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Affiliation(s)
- Isidora Romani
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Nikolay Manavski
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Arianna Morosetti
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Luca Tadini
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Swetlana Maier
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Kristina Kühn
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Hannes Ruwe
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Christian Schmitz-Linneweber
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Gerhard Wanner
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Dario Leister
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
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142
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Chi W, Feng P, Ma J, Zhang L. Metabolites and chloroplast retrograde signaling. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:32-8. [PMID: 25912815 DOI: 10.1016/j.pbi.2015.04.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 05/23/2023]
Abstract
Intracellular signaling from chloroplast to nucleus followed by a subsequent response in the chloroplast is called retrograde signaling. It not only coordinates the expression of nuclear and chloroplast genes, which is essential for chloroplast biogenesis, but also maintains chloroplast function at optimal levels in response to fluxes in metabolites and changes in environmental conditions. In recent years several putative retrograde signals have been identified and signaling pathways have been proposed. Here we review retrograde signals derived from tetrapyrroles, carotenoids, nucleotides and isoprene precursors in response to abiotic stresses, including oxidative stress. We discuss the responses that these signals elicit and show that they not only modify chloroplast function but also influence other aspects of plant development and adaptation.
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Affiliation(s)
- Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Peiqiang Feng
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jinfang Ma
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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143
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Wuyts N, Dhondt S, Inzé D. Measurement of plant growth in view of an integrative analysis of regulatory networks. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:90-97. [PMID: 26002069 DOI: 10.1016/j.pbi.2015.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/17/2015] [Accepted: 05/01/2015] [Indexed: 05/29/2023]
Abstract
As the regulatory networks of growth at the cellular level are elucidated at a fast pace, their complexity is not reduced; on the contrary, the tissue, organ and even whole-plant level affect cell proliferation and expansion by means of development-induced and environment-induced signaling events in growth regulatory processes. Measurement of growth across different levels aids in gaining a mechanistic understanding of growth, and in defining the spatial and temporal resolution of sampling strategies for molecular analyses in the model Arabidopsis thaliana and increasingly also in crop species. The latter claim their place at the forefront of plant research, since global issues and future needs drive the translation from laboratory model-acquired knowledge of growth processes to improvements in crop productivity in field conditions.
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Affiliation(s)
- Nathalie Wuyts
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Stijn Dhondt
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium.
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144
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Sun Y, Zerges W. Translational regulation in chloroplasts for development and homeostasis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:809-20. [PMID: 25988717 DOI: 10.1016/j.bbabio.2015.05.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 04/13/2015] [Accepted: 05/10/2015] [Indexed: 11/16/2022]
Abstract
Chloroplast genomes encode 100-200 proteins which function in photosynthesis, the organellar genetic system, and other pathways and processes. These proteins are synthesized by a complete translation system within the chloroplast, with bacterial-type ribosomes and translation factors. Here, we review translational regulation in chloroplasts, focusing on changes in translation rates which occur in response to requirements for proteins encoded by the chloroplast genome for development and homeostasis. In addition, we delineate the developmental and physiological contexts and model organisms in which translational regulation in chloroplasts has been studied. This article is part of a Special Issue entitled: Chloroplast biogenesis.
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Affiliation(s)
- Yi Sun
- Biology Department and Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke W., Montreal, Quebec H4B 1R6, Canada
| | - William Zerges
- Biology Department and Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke W., Montreal, Quebec H4B 1R6, Canada.
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145
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Browning KS, Bailey-Serres J. Mechanism of cytoplasmic mRNA translation. THE ARABIDOPSIS BOOK 2015; 13:e0176. [PMID: 26019692 PMCID: PMC4441251 DOI: 10.1199/tab.0176] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein synthesis is a fundamental process in gene expression that depends upon the abundance and accessibility of the mRNA transcript as well as the activity of many protein and RNA-protein complexes. Here we focus on the intricate mechanics of mRNA translation in the cytoplasm of higher plants. This chapter includes an inventory of the plant translational apparatus and a detailed review of the translational processes of initiation, elongation, and termination. The majority of mechanistic studies of cytoplasmic translation have been carried out in yeast and mammalian systems. The factors and mechanisms of translation are for the most part conserved across eukaryotes; however, some distinctions are known to exist in plants. A comprehensive understanding of the complex translational apparatus and its regulation in plants is warranted, as the modulation of protein production is critical to development, environmental plasticity and biomass yield in diverse ecosystems and agricultural settings.
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Affiliation(s)
- Karen S. Browning
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas at Austin, Austin TX 78712-0165
- Both authors contributed equally to this work
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California, Riverside, CA, 92521 USA
- Both authors contributed equally to this work
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146
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Chloroplast RNA polymerases: Role in chloroplast biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:761-9. [PMID: 25680513 DOI: 10.1016/j.bbabio.2015.02.004] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/26/2015] [Accepted: 02/02/2015] [Indexed: 12/18/2022]
Abstract
Plastid genes are transcribed by two types of RNA polymerase in angiosperms: the bacterial type plastid-encoded RNA polymerase (PEP) and one (RPOTp in monocots) or two (RPOTp and RPOTmp in dicots) nuclear-encoded RNA polymerase(s) (NEP). PEP is a bacterial-type multisubunit enzyme composed of core subunits (coded for by the plastid rpoA, rpoB, rpoC1 and rpoC2 genes) and additional protein factors (sigma factors and polymerase associated protein, PAPs) encoded in the nuclear genome. Sigma factors are required by PEP for promoter recognition. Six different sigma factors are used by PEP in Arabidopsis plastids. NEP activity is represented by phage-type RNA polymerases. Only one NEP subunit has been identified, which bears the catalytic activity. NEP and PEP use different promoters. Many plastid genes have both PEP and NEP promoters. PEP dominates in the transcription of photosynthesis genes. Intriguingly, rpoB belongs to the few genes transcribed exclusively by NEP. Both NEP and PEP are active in non-green plastids and in chloroplasts at all stages of development. The transcriptional activity of NEP and PEP is affected by endogenous and exogenous factors. This article is part of a Special Issue entitled: Chloroplast Biogenesis.
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147
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Schelkunov MI, Shtratnikova VY, Nuraliev MS, Selosse MA, Penin AA, Logacheva MD. Exploring the limits for reduction of plastid genomes: a case study of the mycoheterotrophic orchids Epipogium aphyllum and Epipogium roseum. Genome Biol Evol 2015; 7:1179-91. [PMID: 25635040 PMCID: PMC4419786 DOI: 10.1093/gbe/evv019] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The question on the patterns and limits of reduction of plastid genomes in nonphotosynthetic plants and the reasons of their conservation is one of the intriguing topics in plant genome evolution. Here, we report sequencing and analysis of plastid genome in nonphotosynthetic orchids Epipogium aphyllum and Epipogium roseum, which, with sizes of 31 and 19 kbp, respectively, represent the smallest plastid genomes characterized by now. Besides drastic reduction, which is expected, we found several unusual features of these “minimal” plastomes: Multiple rearrangements, highly biased nucleotide composition, and unprecedentedly high substitution rate. Only 27 and 29 genes remained intact in the plastomes of E. aphyllum and E. roseum—those encoding ribosomal components, transfer RNAs, and three additional housekeeping genes (infA, clpP, and accD). We found no signs of relaxed selection acting on these genes. We hypothesize that the main reason for retention of plastid genomes in Epipogium is the necessity to translate messenger RNAs (mRNAs) of accD and/or clpP proteins which are essential for cell metabolism. However, these genes are absent in plastomes of several plant species; their absence is compensated by the presence of a functional copy arisen by gene transfer from plastid to the nuclear genome. This suggests that there is no single set of plastid-encoded essential genes, but rather different sets for different species and that the retention of a gene in the plastome depends on the interaction between the nucleus and plastids.
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Affiliation(s)
| | | | - Maxim S Nuraliev
- M. V. Lomonosov Moscow State University, Moscow, Russia Joint Russian-Vietnamese Tropical Scientific and Technological Center, Cau Giay, Hanoi, Vietnam
| | - Marc-Andre Selosse
- Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Paris, France
| | | | - Maria D Logacheva
- M. V. Lomonosov Moscow State University, Moscow, Russia Kazan Federal University, Kazan, Russia
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148
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Bobik K, Burch-Smith TM. Chloroplast signaling within, between and beyond cells. FRONTIERS IN PLANT SCIENCE 2015; 6:781. [PMID: 26500659 PMCID: PMC4593955 DOI: 10.3389/fpls.2015.00781] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/10/2015] [Indexed: 05/18/2023]
Abstract
The most conspicuous function of plastids is the oxygenic photosynthesis of chloroplasts, yet plastids are super-factories that produce a plethora of compounds that are indispensable for proper plant physiology and development. Given their origins as free-living prokaryotes, it is not surprising that plastids possess their own genomes whose expression is essential to plastid function. This semi-autonomous character of plastids requires the existence of sophisticated regulatory mechanisms that provide reliable communication between them and other cellular compartments. Such intracellular signaling is necessary for coordinating whole-cell responses to constantly varying environmental cues and cellular metabolic needs. This is achieved by plastids acting as receivers and transmitters of specific signals that coordinate expression of the nuclear and plastid genomes according to particular needs. In this review we will consider the so-called retrograde signaling occurring between plastids and nuclei, and between plastids and other organelles. Another important role of the plastid we will discuss is the involvement of plastid signaling in biotic and abiotic stress that, in addition to influencing retrograde signaling, has direct effects on several cellular compartments including the cell wall. We will also review recent evidence pointing to an intriguing function of chloroplasts in regulating intercellular symplasmic transport. Finally, we consider an intriguing yet less widely known aspect of plant biology, chloroplast signaling from the perspective of the entire plant. Thus, accumulating evidence highlights that chloroplasts, with their complex signaling pathways, provide a mechanism for exquisite regulation of plant development, metabolism and responses to the environment. As chloroplast processes are targeted for engineering for improved productivity the effect of such modifications on chloroplast signaling will have to be carefully considered in order to avoid unintended consequences on plant growth and development.
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Affiliation(s)
| | - Tessa M. Burch-Smith
- *Correspondence: Tessa M. Burch-Smith, Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, 1414 Cumberland Avenue, M407 Walters Life Science, Knoxville, TN 37932, USA,
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Rogalski M, do Nascimento Vieira L, Fraga HP, Guerra MP. Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology. FRONTIERS IN PLANT SCIENCE 2015; 6:586. [PMID: 26284102 PMCID: PMC4520007 DOI: 10.3389/fpls.2015.00586] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/15/2015] [Indexed: 05/20/2023]
Abstract
During the evolution of the eukaryotic cell, plastids, and mitochondria arose from an endosymbiotic process, which determined the presence of three genetic compartments into the incipient plant cell. After that, these three genetic materials from host and symbiont suffered several rearrangements, bringing on a complex interaction between nuclear and organellar gene products. Nowadays, plastids harbor a small genome with ∼130 genes in a 100-220 kb sequence in higher plants. Plastid genes are mostly highly conserved between plant species, being useful for phylogenetic analysis in higher taxa. However, intergenic spacers have a relatively higher mutation rate and are important markers to phylogeographical and plant population genetics analyses. The predominant uniparental inheritance of plastids is like a highly desirable feature for phylogeny studies. Moreover, the gene content and genome rearrangements are efficient tools to capture and understand evolutionary events between different plant species. Currently, genetic engineering of the plastid genome (plastome) offers a number of attractive advantages as high-level of foreign protein expression, marker gene excision, gene expression in operon and transgene containment because of maternal inheritance of plastid genome in most crops. Therefore, plastid genome can be used for adding new characteristics related to synthesis of metabolic compounds, biopharmaceutical, and tolerance to biotic and abiotic stresses. Here, we describe the importance and applications of plastid genome as tools for genetic and evolutionary studies, and plastid transformation focusing on increasing the performance of horticultural species in the field.
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Affiliation(s)
- Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de ViçosaViçosa, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Centro de Ciências Agrárias, Universidade Federal de Santa CatarinaFlorianópolis, Brazil
| | - Hugo P. Fraga
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Centro de Ciências Agrárias, Universidade Federal de Santa CatarinaFlorianópolis, Brazil
| | - Miguel P. Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Centro de Ciências Agrárias, Universidade Federal de Santa CatarinaFlorianópolis, Brazil
- *Correspondence: Miguel P. Guerra, Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Rod. Admar Gonzaga, 1346 Florianópolis, SC 88034-000, Brazil,
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150
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Parker N, Wang Y, Meinke D. Natural variation in sensitivity to a loss of chloroplast translation in Arabidopsis. PLANT PHYSIOLOGY 2014; 166:2013-27. [PMID: 25336520 PMCID: PMC4256881 DOI: 10.1104/pp.114.249052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Mutations that eliminate chloroplast translation in Arabidopsis (Arabidopsis thaliana) result in embryo lethality. The stage of embryo arrest, however, can be influenced by genetic background. To identify genes responsible for improved growth in the absence of chloroplast translation, we examined seedling responses of different Arabidopsis accessions on spectinomycin, an inhibitor of chloroplast translation, and crossed the most tolerant accessions with embryo-defective mutants disrupted in chloroplast ribosomal proteins generated in a sensitive background. The results indicate that tolerance is mediated by ACC2, a duplicated nuclear gene that targets homomeric acetyl-coenzyme A carboxylase to plastids, where the multidomain protein can participate in fatty acid biosynthesis. In the presence of functional ACC2, tolerance is enhanced by a second locus that maps to chromosome 5 and heightened by additional genetic modifiers present in the most tolerant accessions. Notably, some of the most sensitive accessions contain nonsense mutations in ACC2, including the "Nossen" line used to generate several of the mutants studied here. Functional ACC2 protein is therefore not required for survival in natural environments, where heteromeric acetyl-coenzyme A carboxylase encoded in part by the chloroplast genome can function instead. This work highlights an interesting example of a tandem gene duplication in Arabidopsis, helps to explain the range of embryo phenotypes found in Arabidopsis mutants disrupted in essential chloroplast functions, addresses the nature of essential proteins encoded by the chloroplast genome, and underscores the value of using natural variation to study the relationship between chloroplast translation, plant metabolism, protein import, and plant development.
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Affiliation(s)
- Nicole Parker
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Yixing Wang
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078
| | - David Meinke
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078
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