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Aguirre-Bottger C, Zolla G. The best of both worlds: photosynthesis and Solanaceae biodiversity seeking a sustainable food and cosmetic industry. FRONTIERS IN PLANT SCIENCE 2024; 15:1362814. [PMID: 38434437 PMCID: PMC10904534 DOI: 10.3389/fpls.2024.1362814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/05/2024] [Indexed: 03/05/2024]
Affiliation(s)
| | - Gaston Zolla
- Grupo de Investigation en Fisiología Molecular de Plantas, Facultad de Agronomia, Universidad Nacional Agraria La Molina, Lima, Peru
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2
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Su J, Jiao Q, Jia T, Hu X. The photosystem-II repair cycle: updates and open questions. PLANTA 2023; 259:20. [PMID: 38091081 DOI: 10.1007/s00425-023-04295-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023]
Abstract
MAIN CONCLUSION The photosystem-II (PSII) repair cycle is essential for the maintenance of photosynthesis in plants. A number of novel findings have illuminated the regulatory mechanisms of the PSII repair cycle. Photosystem II (PSII) is a large pigment-protein complex embedded in the thylakoid membrane. It plays a vital role in photosynthesis by absorbing light energy, splitting water, releasing molecular oxygen, and transferring electrons for plastoquinone reduction. However, PSII, especially the PsbA (D1) core subunit, is highly susceptible to oxidative damage. To prevent irreversible damage, plants have developed a repair cycle. The main objective of the PSII repair cycle is the degradation of photodamaged D1 and insertion of newly synthesized D1 into the PSII complex. While many factors are known to be involved in PSII repair, the exact mechanism is still under investigation. In this review, we discuss the primary steps of PSII repair, focusing on the proteolytic degradation of photodamaged D1 and the factors involved.
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Affiliation(s)
- Jinling Su
- International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
- Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Qingsong Jiao
- International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
- Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Ting Jia
- International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
- Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
| | - Xueyun Hu
- International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
- Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China.
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3
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Kafri M, Patena W, Martin L, Wang L, Gomer G, Ergun SL, Sirkejyan AK, Goh A, Wilson AT, Gavrilenko SE, Breker M, Roichman A, McWhite CD, Rabinowitz JD, Cross FR, Wühr M, Jonikas MC. Systematic identification and characterization of genes in the regulation and biogenesis of photosynthetic machinery. Cell 2023; 186:5638-5655.e25. [PMID: 38065083 PMCID: PMC10760936 DOI: 10.1016/j.cell.2023.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 08/03/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
Photosynthesis is central to food production and the Earth's biogeochemistry, yet the molecular basis for its regulation remains poorly understood. Here, using high-throughput genetics in the model eukaryotic alga Chlamydomonas reinhardtii, we identify with high confidence (false discovery rate [FDR] < 0.11) 70 poorly characterized genes required for photosynthesis. We then enable the functional characterization of these genes by providing a resource of proteomes of mutant strains, each lacking one of these genes. The data allow assignment of 34 genes to the biogenesis or regulation of one or more specific photosynthetic complexes. Further analysis uncovers biogenesis/regulatory roles for at least seven proteins, including five photosystem I mRNA maturation factors, the chloroplast translation factor MTF1, and the master regulator PMR1, which regulates chloroplast genes via nuclear-expressed factors. Our work provides a rich resource identifying regulatory and functional genes and placing them into pathways, thereby opening the door to a system-level understanding of photosynthesis.
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Affiliation(s)
- Moshe Kafri
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Lance Martin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Gillian Gomer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sabrina L Ergun
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
| | - Arthur K Sirkejyan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Audrey Goh
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alexandra T Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sophia E Gavrilenko
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Michal Breker
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10021, USA
| | - Asael Roichman
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Claire D McWhite
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Frederick R Cross
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10021, USA
| | - Martin Wühr
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.
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4
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Wang F, Dischinger K, Westrich LD, Meindl I, Egidi F, Trösch R, Sommer F, Johnson X, Schroda M, Nickelsen J, Willmund F, Vallon O, Bohne AV. One-helix protein 2 is not required for the synthesis of photosystem II subunit D1 in Chlamydomonas. PLANT PHYSIOLOGY 2023; 191:1612-1633. [PMID: 36649171 PMCID: PMC10022639 DOI: 10.1093/plphys/kiad015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
In land plants and cyanobacteria, co-translational association of chlorophyll (Chl) to the nascent D1 polypeptide, a reaction center protein of photosystem II (PSII), requires a Chl binding complex consisting of a short-chain dehydrogenase (high chlorophyll fluorescence 244 [HCF244]/uncharacterized protein 39 [Ycf39]) and one-helix proteins (OHP1 and OHP2 in chloroplasts) of the light-harvesting antenna complex superfamily. Here, we show that an ohp2 mutant of the green alga Chlamydomonas (Chlamydomonas reinhardtii) fails to accumulate core PSII subunits, in particular D1 (encoded by the psbA mRNA). Extragenic suppressors arose at high frequency, suggesting the existence of another route for Chl association to PSII. The ohp2 mutant was complemented by the Arabidopsis (Arabidopsis thaliana) ortholog. In contrast to land plants, where psbA translation is prevented in the absence of OHP2, ribosome profiling experiments showed that the Chlamydomonas mutant translates the psbA transcript over its full length. Pulse labeling suggested that D1 is degraded during or immediately after translation. The translation of other PSII subunits was affected by assembly-controlled translational regulation. Proteomics showed that HCF244, a translation factor which associates with and is stabilized by OHP2 in land plants, still partly accumulates in the Chlamydomonas ohp2 mutant, explaining the persistence of psbA translation. Several Chl biosynthesis enzymes overaccumulate in the mutant membranes. Partial inactivation of a D1-degrading protease restored a low level of PSII activity in an ohp2 background, but not photoautotrophy. Taken together, our data suggest that OHP2 is not required for psbA translation in Chlamydomonas, but is necessary for D1 stabilization.
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Affiliation(s)
- Fei Wang
- Molecular Plant Sciences, LMU Munich, Planegg-Martinsried 82152, Germany
- UMR 7141, Centre National de la Recherche Scientifique/Sorbonne Université, Institut de Biologie Physico-Chimique, Paris 75005, France
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | | | - Lisa Désirée Westrich
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Irene Meindl
- Molecular Plant Sciences, LMU Munich, Planegg-Martinsried 82152, Germany
| | - Felix Egidi
- Molecular Plant Sciences, LMU Munich, Planegg-Martinsried 82152, Germany
| | - Raphael Trösch
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Xenie Johnson
- UMR 7141, Centre National de la Recherche Scientifique/Sorbonne Université, Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Joerg Nickelsen
- Molecular Plant Sciences, LMU Munich, Planegg-Martinsried 82152, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Olivier Vallon
- UMR 7141, Centre National de la Recherche Scientifique/Sorbonne Université, Institut de Biologie Physico-Chimique, Paris 75005, France
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5
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Gao LL, Hong ZH, Wang Y, Wu GZ. Chloroplast proteostasis: A story of birth, life, and death. PLANT COMMUNICATIONS 2023; 4:100424. [PMID: 35964157 PMCID: PMC9860172 DOI: 10.1016/j.xplc.2022.100424] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/02/2022] [Accepted: 08/10/2022] [Indexed: 06/02/2023]
Abstract
Protein homeostasis (proteostasis) is a dynamic balance of protein synthesis and degradation. Because of the endosymbiotic origin of chloroplasts and the massive transfer of their genetic information to the nucleus of the host cell, many protein complexes in the chloroplasts are constituted from subunits encoded by both genomes. Hence, the proper function of chloroplasts relies on the coordinated expression of chloroplast- and nucleus-encoded genes. The biogenesis and maintenance of chloroplast proteostasis are dependent on synthesis of chloroplast-encoded proteins, import of nucleus-encoded chloroplast proteins from the cytosol, and clearance of damaged or otherwise undesired "old" proteins. This review focuses on the regulation of chloroplast proteostasis, its interaction with proteostasis of the cytosol, and its retrograde control over nuclear gene expression. We also discuss significant issues and perspectives for future studies and potential applications for improving the photosynthetic performance and stress tolerance of crops.
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Affiliation(s)
- Lin-Lin Gao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zheng-Hui Hong
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yinsong Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Guo-Zhang Wu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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6
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Zhang M, Zeng Y, Peng R, Dong J, Lan Y, Duan S, Chang Z, Ren J, Luo G, Liu B, Růžička K, Zhao K, Wang HB, Jin HL. N 6-methyladenosine RNA modification regulates photosynthesis during photodamage in plants. Nat Commun 2022; 13:7441. [PMID: 36460653 PMCID: PMC9718803 DOI: 10.1038/s41467-022-35146-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 11/18/2022] [Indexed: 12/04/2022] Open
Abstract
N6-methyladenosine (m6A) modification of mRNAs affects many biological processes. However, the function of m6A in plant photosynthesis remains unknown. Here, we demonstrate that m6A modification is crucial for photosynthesis during photodamage caused by high light stress in plants. The m6A modification levels of numerous photosynthesis-related transcripts are changed after high light stress. We determine that the Arabidopsis m6A writer VIRILIZER (VIR) positively regulates photosynthesis, as its genetic inactivation drastically lowers photosynthetic activity and photosystem protein abundance under high light conditions. The m6A levels of numerous photosynthesis-related transcripts decrease in vir mutants, extensively reducing their transcript and translation levels, as revealed by multi-omics analyses. We demonstrate that VIR associates with the transcripts of genes encoding proteins with functions related to photoprotection (such as HHL1, MPH1, and STN8) and their regulatory proteins (such as regulators of transcript stability and translation), promoting their m6A modification and maintaining their stability and translation efficiency. This study thus reveals an important mechanism for m6A-dependent maintenance of photosynthetic efficiency in plants under high light stress conditions.
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Affiliation(s)
- Man Zhang
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China ,grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China ,grid.484195.5Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, 510640 Guangzhou, People’s Republic of China
| | - Yunping Zeng
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China
| | - Rong Peng
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China
| | - Jie Dong
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Yelin Lan
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Sujuan Duan
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China
| | - Zhenyi Chang
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China
| | - Jian Ren
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Guanzheng Luo
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Bing Liu
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Kamil Růžička
- grid.418095.10000 0001 1015 3316Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Prague 6, Czech Republic
| | - Kewei Zhao
- grid.411866.c0000 0000 8848 7685Guangzhou Key Laboratory of Chinese Medicine Research on Prevention and Treatment of Osteoporosis, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, No.263, Longxi Avenue, Guangzhou, People’s Republic of China
| | - Hong-Bin Wang
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China ,grid.419897.a0000 0004 0369 313XKey Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, People’s Republic of China ,grid.411866.c0000 0000 8848 7685State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Hong-Lei Jin
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China ,grid.411866.c0000 0000 8848 7685Guangzhou Key Laboratory of Chinese Medicine Research on Prevention and Treatment of Osteoporosis, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, No.263, Longxi Avenue, Guangzhou, People’s Republic of China
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Zhang S, Wu Z, Ma D, Zhai J, Han X, Jiang Z, Liu S, Xu J, Jiao P, Li Z. Chromosome-scale assemblies of the male and female Populus euphratica genomes reveal the molecular basis of sex determination and sexual dimorphism. Commun Biol 2022; 5:1186. [PMCID: PMC9636151 DOI: 10.1038/s42003-022-04145-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Reference-quality genomes of both sexes are essential for studying sex determination and sex-chromosome evolution, as their gene contents and expression profiles differ. Here, we present independent chromosome-level genome assemblies for the female (XX) and male (XY) genomes of desert poplar (Populus euphratica), resolving a 22.7-Mb X and 24.8-Mb Y chromosome. We also identified a relatively complete 761-kb sex-linked region (SLR) in the peritelomeric region on chromosome 14 (Y). Within the SLR, recombination around the partial repeats for the feminizing factor ARR17 (ARABIDOPSIS RESPONSE REGULATOR 17) was potentially suppressed by flanking palindromic arms and the dense accumulation of retrotransposons. The inverted small segments S1 and S2 of ARR17 exhibited relaxed selective pressure and triggered sex determination by generating 24-nt small interfering RNAs that induce male-specific hyper-methylation at the promoter of the autosomal targeted ARR17. We also detected two male-specific fusion genes encoding proteins with NB-ARC domains at the breakpoint region of an inversion in the SLR that may be responsible for the observed sexual dimorphism in immune responses. Our results show that the SLR appears to follow proposed evolutionary dynamics for sex chromosomes and advance our understanding of sex determination and the evolution of sex chromosomes in Populus. Reference-quality genomes of both sexes of the dioecious tree species, Populus euphratica, provide further insight into the evolution of Populus sex chromosomes and highlight male-specific fusion genes that may contribute to sexual dimorphism.
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Affiliation(s)
- Shanhe Zhang
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Zhihua Wu
- grid.453534.00000 0001 2219 2654College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004 China
| | - De Ma
- grid.410753.4Novogene Bioinformatics Institute, Beijing, 100083 China
| | - Juntuan Zhai
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Xiaoli Han
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Zhenbo Jiang
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Shuo Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430074 China
| | - Jingdong Xu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430074 China
| | - Peipei Jiao
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Zhijun Li
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
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8
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Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii. Nat Genet 2022; 54:705-714. [PMID: 35513725 PMCID: PMC9110296 DOI: 10.1038/s41588-022-01052-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 03/15/2022] [Indexed: 12/12/2022]
Abstract
Most genes in photosynthetic organisms remain functionally uncharacterized. Here, using a barcoded mutant library of the model eukaryotic alga Chlamydomonas reinhardtii, we determined the phenotypes of more than 58,000 mutants under more than 121 different environmental growth conditions and chemical treatments. A total of 59% of genes are represented by at least one mutant that showed a phenotype, providing clues to the functions of thousands of genes. Mutant phenotypic profiles place uncharacterized genes into functional pathways such as DNA repair, photosynthesis, the CO2-concentrating mechanism and ciliogenesis. We illustrate the value of this resource by validating phenotypes and gene functions, including three new components of an actin cytoskeleton defense pathway. The data also inform phenotype discovery in land plants; mutants in Arabidopsis thaliana genes exhibit phenotypes similar to those we observed in their Chlamydomonas homologs. We anticipate that this resource will guide the functional characterization of genes across the tree of life. Systematic phenotyping of 58,101 mutants of the model eukaryotic alga Chlamydomonas reinhardtii under 121 environmental and chemical stress conditions provides a large resource for characterizing gene function.
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9
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Maeda H, Takahashi K, Ueno Y, Sakata K, Yokoyama A, Yarimizu K, Myouga F, Shinozaki K, Ozawa SI, Takahashi Y, Tanaka A, Ito H, Akimoto S, Takabayashi A, Tanaka R. Characterization of photosystem II assembly complexes containing ONE-HELIX PROTEIN1 in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2022; 135:361-376. [PMID: 35146632 DOI: 10.1007/s10265-022-01376-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
The assembly process of photosystem II (PSII) requires several auxiliary proteins to form assembly intermediates. In plants, early assembly intermediates comprise D1 and D2 subunits of PSII together with a few auxiliary proteins including at least ONE-HELIX PROTEIN1 (OHP1), OHP2, and HIGH-CHLOROPHYLL FLUORESCENCE 244 (HCF244) proteins. Herein, we report the basic characterization of the assembling intermediates, which we purified from Arabidopsis transgenic plants overexpressing a tagged OHP1 protein and named the OHP1 complexes. We analyzed two major forms of OHP1 complexes by mass spectrometry, which revealed that the complexes consist of OHP1, OHP2, and HCF244 in addition to the PSII subunits D1, D2, and cytochrome b559. Analysis of chlorophyll fluorescence showed that a major form of the complex binds chlorophyll a and carotenoids and performs quenching with a time constant of 420 ps. To identify the localization of the auxiliary proteins, we solubilized thylakoid membranes using a digitonin derivative, glycodiosgenin, and separated them into three fractions by ultracentrifugation, and detected these proteins in the loose pellet containing the stroma lamellae and the grana margins together with two chlorophyll biosynthesis enzymes. The results indicated that chlorophyll biosynthesis and assembly may take place in the same compartments of thylakoid membranes. Inducible suppression of the OHP2 mRNA substantially decreased the OHP2 protein in mature Arabidopsis leaves without a significant reduction in the maximum quantum yield of PSII under low-light conditions, but it compromised the yields under high-light conditions. This implies that the auxiliary protein is required for acclimation to high-light conditions.
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Affiliation(s)
- Hanaki Maeda
- Institute of Low Temperature Science, N19W8 Kita-ku, Sapporo, 060-0819, Japan
| | - Koharu Takahashi
- Institute of Low Temperature Science, N19W8 Kita-ku, Sapporo, 060-0819, Japan
| | - Yoshifumi Ueno
- Graduate School of Science, Kobe University, Kobe, 657‑8501, Japan
| | - Kei Sakata
- Institute of Low Temperature Science, N19W8 Kita-ku, Sapporo, 060-0819, Japan
| | - Akari Yokoyama
- Institute of Low Temperature Science, N19W8 Kita-ku, Sapporo, 060-0819, Japan
| | - Kozue Yarimizu
- Institute of Low Temperature Science, N19W8 Kita-ku, Sapporo, 060-0819, Japan
| | - Fumiyoshi Myouga
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Shin-Ichiro Ozawa
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Yuichiro Takahashi
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, N19W8 Kita-ku, Sapporo, 060-0819, Japan
| | - Hisashi Ito
- Institute of Low Temperature Science, N19W8 Kita-ku, Sapporo, 060-0819, Japan
| | - Seiji Akimoto
- Graduate School of Science, Kobe University, Kobe, 657‑8501, Japan
| | - Atsushi Takabayashi
- Institute of Low Temperature Science, N19W8 Kita-ku, Sapporo, 060-0819, Japan
| | - Ryouichi Tanaka
- Institute of Low Temperature Science, N19W8 Kita-ku, Sapporo, 060-0819, Japan.
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10
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Lamelas L, Valledor L, López-Hidalgo C, Cañal MJ, Meijón M. Nucleus and chloroplast: A necessary understanding to overcome heat stress in Pinus radiata. PLANT, CELL & ENVIRONMENT 2022; 45:446-458. [PMID: 34855991 DOI: 10.1111/pce.14238] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
The recovery and maintenance of plant homeostasis under stressful environments are complex processes involving organelle crosstalk for a coordinated cellular response. Here, we revealed through nuclear and chloroplast subcellular proteomics, biochemical cell profiles and targeted transcriptomics how chloroplasts and nuclei developed their responses under increased temperatures in a long-lived species (Pinus radiata). Parallel to photosynthetic impairment and reactive oxygen species production in the chloroplast, a DNA damage response was triggered in the nucleus followed by an altered chromatin conformation. In addition, in the nuclei, we found several proteins, such as HEMERA or WHIRLY, which change their locations from the chloroplasts to the nuclei carrying the stress message. Additionally, our data showed a deep rearrangement of RNA metabolism in both organelles, revealing microRNAs and AGO1 as potential regulators of the acclimation mechanisms. Altogether, our study highlights the synchronisation among the different stages required for thermotolerance acquisition in P. radiata, pointing out the role of chromatin conformation and posttranscriptional gene regulation in overcoming heat stress and assuring plant survival for the following years.
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Affiliation(s)
- Laura Lamelas
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - Cristina López-Hidalgo
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - María Jesús Cañal
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
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11
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Che L, Meng H, Ruan J, Peng L, Zhang L. Rubredoxin 1 Is Required for Formation of the Functional Photosystem II Core Complex in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:824358. [PMID: 35283894 PMCID: PMC8905225 DOI: 10.3389/fpls.2022.824358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/13/2022] [Indexed: 05/03/2023]
Abstract
Chloroplast thylakoid protein rubredoxin 1 (RBD1) in Chlamydomonas and its cyanobacterial homolog RubA contain a rubredoxin domain. These proteins have been proposed to participate in the assembly of photosystem II (PSII) at early stages. However, the effects of inactivation of RBD1 on PSII assembly in higher plants are largely unclear. Here, we characterized an Arabidopsis rbd1 mutant in detail. A drastic reduction of intact PSII complex but relatively higher levels of assembly intermediates including PSII RC, pre-CP47, and pre-CP43 were found in rbd1. Polysome association and ribosome profiling revealed that ribosome recruitment of psbA mRNA is specifically reduced. Consistently, in vivo protein pulse-chase labeling showed that the rate of D1/pD1 synthesis is significantly reduced in rbd1 compared with WT. Moreover, newly synthesized mature D1 and pD1/D2 can assemble into the PSII reaction center (RC) complex but further formation of larger PSII complexes is nearly totally blocked in rbd1. Our data imply that RBD1 is not only required for the formation of a functional PSII core complex during the early stages of PSII assembly but may also be involved in the translation of D1 in higher plants.
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Affiliation(s)
- Liping Che
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, China
| | - Han Meng
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Junxiang Ruan
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, China
| | - Lianwei Peng
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Lin Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- *Correspondence: Lin Zhang,
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12
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Chotewutmontri P, Barkan A. Ribosome profiling elucidates differential gene expression in bundle sheath and mesophyll cells in maize. PLANT PHYSIOLOGY 2021; 187:59-72. [PMID: 34618144 PMCID: PMC8418429 DOI: 10.1093/plphys/kiab272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/10/2021] [Indexed: 05/20/2023]
Abstract
The efficiencies offered by C4 photosynthesis have motivated efforts to understand its biochemical, genetic, and developmental basis. Reactions underlying C4 traits in most C4 plants are partitioned between two cell types, bundle sheath (BS), and mesophyll (M) cells. RNA-seq has been used to catalog differential gene expression in BS and M cells in maize (Zea mays) and several other C4 species. However, the contribution of translational control to maintaining the distinct proteomes of BS and M cells has not been addressed. In this study, we used ribosome profiling and RNA-seq to describe translatomes, translational efficiencies, and microRNA abundance in BS- and M-enriched fractions of maize seedling leaves. A conservative interpretation of our data revealed 182 genes exhibiting cell type-dependent differences in translational efficiency, 31 of which encode proteins with core roles in C4 photosynthesis. Our results suggest that non-AUG start codons are used preferentially in upstream open reading frames of BS cells, revealed mRNA sequence motifs that correlate with cell type-dependent translation, and identified potential translational regulators that are differentially expressed. In addition, our data expand the set of genes known to be differentially expressed in BS and M cells, including genes encoding transcription factors and microRNAs. These data add to the resources for understanding the evolutionary and developmental basis of C4 photosynthesis and for its engineering into C3 crops.
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Affiliation(s)
- Prakitchai Chotewutmontri
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403 USA
- Author for communication:
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403 USA
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13
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Nakazato I, Okuno M, Yamamoto H, Tamura Y, Itoh T, Shikanai T, Takanashi H, Tsutsumi N, Arimura SI. Targeted base editing in the plastid genome of Arabidopsis thaliana. NATURE PLANTS 2021; 7:906-913. [PMID: 34211131 PMCID: PMC8289735 DOI: 10.1038/s41477-021-00954-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/26/2021] [Indexed: 05/17/2023]
Abstract
Bacterial cytidine deaminase fused to the DNA binding domains of transcription activator-like effector nucleases was recently reported to transiently substitute a targeted C to a T in mitochondrial DNA of mammalian cultured cells1. We applied this system to targeted base editing in the Arabidopsis thaliana plastid genome. The targeted Cs were homoplasmically substituted to Ts in some plantlets of the T1 generation and the mutations were inherited by their offspring independently of their nuclear-introduced vectors.
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Affiliation(s)
- Issei Nakazato
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Miki Okuno
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Hiroshi Yamamoto
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yoshiko Tamura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hideki Takanashi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Nobuhiro Tsutsumi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shin-Ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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14
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Gawroński P, Enroth C, Kindgren P, Marquardt S, Karpiński S, Leister D, Jensen PE, Vinther J, Scharff LB. Light-Dependent Translation Change of Arabidopsis psbA Correlates with RNA Structure Alterations at the Translation Initiation Region. Cells 2021; 10:322. [PMID: 33557293 PMCID: PMC7914831 DOI: 10.3390/cells10020322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 01/21/2023] Open
Abstract
mRNA secondary structure influences translation. Proteins that modulate the mRNA secondary structure around the translation initiation region may regulate translation in plastids. To test this hypothesis, we exposed Arabidopsis thaliana to high light, which induces translation of psbA mRNA encoding the D1 subunit of photosystem II. We assayed translation by ribosome profiling and applied two complementary methods to analyze in vivo RNA secondary structure: DMS-MaPseq and SHAPE-seq. We detected increased accessibility of the translation initiation region of psbA after high light treatment, likely contributing to the observed increase in translation by facilitating translation initiation. Furthermore, we identified the footprint of a putative regulatory protein in the 5' UTR of psbA at a position where occlusion of the nucleotide sequence would cause the structure of the translation initiation region to open up, thereby facilitating ribosome access. Moreover, we show that other plastid genes with weak Shine-Dalgarno sequences (SD) are likely to exhibit psbA-like regulation, while those with strong SDs do not. This supports the idea that changes in mRNA secondary structure might represent a general mechanism for translational regulation of psbA and other plastid genes.
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Affiliation(s)
- Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (P.G.); (S.K.)
| | - Christel Enroth
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N, Denmark; (C.E.); (J.V.)
| | - Peter Kindgren
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; (P.K.); (S.M.)
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; (P.K.); (S.M.)
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (P.G.); (S.K.)
| | - Dario Leister
- Plant Molecular Biology, Department Biology I, Ludwig-Maximilians-University Munich, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany;
| | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark;
| | - Jeppe Vinther
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N, Denmark; (C.E.); (J.V.)
| | - Lars B. Scharff
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; (P.K.); (S.M.)
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15
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He Y, Shi Y, Zhang X, Xu X, Wang H, Li L, Zhang Z, Shang H, Wang Z, Wu JL. The OsABCI7 Transporter Interacts with OsHCF222 to Stabilize the Thylakoid Membrane in Rice. PLANT PHYSIOLOGY 2020; 184:283-299. [PMID: 32661060 PMCID: PMC7479889 DOI: 10.1104/pp.20.00445] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/23/2020] [Indexed: 05/05/2023]
Abstract
The thylakoid membrane is a highly complex membrane system in plants and plays crucial roles in the biogenesis of the photosynthetic apparatus and plant development. However, the genetic factors involved in chloroplast development and its relationship with intracellular metabolites are largely unknown. Here, a rice (Oryza sativa) chlorotic and necrotic leaf1 (cnl1) mutant was identified and map-based cloning revealed that a single base substitution followed by a 6-bp deletion in the ATP-binding cassette transporter I family member7 (OsABCI7) resulted in chlorotic and necrotic leaves with thylakoid membrane degradation, chlorophyll breakdown, photosynthesis impairment, and cell death in cnl1 Furthermore, the expression of OsABCI7 was inducible under lower temperatures, which severely affected cnl1 chloroplast development, and etiolated cnl1 seedlings were unable to recover to a normal green state under light conditions. Functional complementation and overexpression showed that OsABCI7 could rescue the cnl1 chlorotic and necrotic phenotype. OsABCI7 interacted with HIGH CHLOROPHYLL FLUORESCENCE222 (OsHCF222) to regulate cellular reactive oxygen species (ROS) homeostasis for thylakoid membrane stability. OsABCI7 localized to thylakoid membranes, while OsHCF222 targeted to endoplasmic reticulum and chloroplasts. Exogenous application of ascorbic acid eased the yellowish leaf phenotype by increasing chlorophyll content and alleviating ROS stress in cnl1 Unlike cnl1, the CRISPR/Cas9-mediated OsHCF222 knockout lines showed chlorotic leaves but were seedling lethal. Our results provide insight into the functions of ABC transporters in rice, especially within the relationship between ROS homeostasis and stability of thylakoid membranes.
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Affiliation(s)
- Yan He
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yongfeng Shi
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Xiaobo Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Xia Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Huimei Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Liangjian Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Zhihong Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Huihui Shang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Zhonghao Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Jian-Li Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
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16
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Light-induced psbA translation in plants is triggered by photosystem II damage via an assembly-linked autoregulatory circuit. Proc Natl Acad Sci U S A 2020; 117:21775-21784. [PMID: 32817480 DOI: 10.1073/pnas.2007833117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The D1 reaction center protein of photosystem II (PSII) is subject to light-induced damage. Degradation of damaged D1 and its replacement by nascent D1 are at the heart of a PSII repair cycle, without which photosynthesis is inhibited. In mature plant chloroplasts, light stimulates the recruitment of ribosomes specifically to psbA mRNA to provide nascent D1 for PSII repair and also triggers a global increase in translation elongation rate. The light-induced signals that initiate these responses are unclear. We present action spectrum and genetic data indicating that the light-induced recruitment of ribosomes to psbA mRNA is triggered by D1 photodamage, whereas the global stimulation of translation elongation is triggered by photosynthetic electron transport. Furthermore, mutants lacking HCF136, which mediates an early step in D1 assembly, exhibit constitutively high psbA ribosome occupancy in the dark and differ in this way from mutants lacking PSII for other reasons. These results, together with the recent elucidation of a thylakoid membrane complex that functions in PSII assembly, PSII repair, and psbA translation, suggest an autoregulatory mechanism in which the light-induced degradation of D1 relieves repressive interactions between D1 and translational activators in the complex. We suggest that the presence of D1 in this complex coordinates D1 synthesis with the need for nascent D1 during both PSII biogenesis and PSII repair in plant chloroplasts.
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17
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Li X, Wang HB, Jin HL. Light Signaling-Dependent Regulation of PSII Biogenesis and Functional Maintenance. PLANT PHYSIOLOGY 2020; 183:1855-1868. [PMID: 32439719 PMCID: PMC7401124 DOI: 10.1104/pp.20.00200] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/04/2020] [Indexed: 05/16/2023]
Abstract
Light is a key environmental cue regulating photomorphogenesis and photosynthesis in plants. However, the molecular mechanisms underlying the interaction between light signaling pathways and photosystem function are unknown. Here, we show that various monochromatic wavelengths of light cooperate to regulate PSII function in Arabidopsis (Arabidopsis thaliana). The photoreceptors cryptochromes and phytochromes modulate the expression of HIGH CHLOROPHYLL FLUORESCENCE173 (HCF173), which is required for PSII biogenesis by regulating PSII core protein D1 synthesis mediated by the transcription factor ELONGATED HYPOCOTYL5 (HY5). HY5 directly binds to the ACGT-containing element ACE motif and G-box cis-element present in the HCF173 promoter and regulates its activity. PSII activity was decreased significantly in hy5 mutants under various monochromatic wavelengths of light. Interestingly, we demonstrate that HY5 also directly regulates the expression of the genes associated with PSII assembly and repair, including ALBINO3, HCF136, HYPERSENSITIVE TO HIGH LIGHT1, etc., which is required for the functional maintenance of PSII under photodamaging conditions. Moreover, deficiency of HY5 broadly decreases the accumulation of other photosystem proteins besides PSII proteins. Thus, our study reveals an important role of light signaling in both biogenesis and functional regulation of the photosystem and provides insight into the link between light signaling and photosynthesis in land plants.
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Affiliation(s)
- Xue Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China
| | - Hong-Bin Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People's Republic of China
| | - Hong-Lei Jin
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People's Republic of China
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18
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Zou M, Mu Y, Chai X, Ouyang M, Yu LJ, Zhang L, Meurer J, Chi W. The critical function of the plastid rRNA methyltransferase, CMAL, in ribosome biogenesis and plant development. Nucleic Acids Res 2020; 48:3195-3210. [PMID: 32095829 PMCID: PMC7102989 DOI: 10.1093/nar/gkaa129] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 12/12/2022] Open
Abstract
Methylation of nucleotides in ribosomal RNAs (rRNAs) is a ubiquitous feature that occurs in all living organisms. The formation of methylated nucleotides is performed by a variety of RNA-methyltransferases. Chloroplasts of plant cells result from an endosymbiotic event and possess their own genome and ribosomes. However, enzymes responsible for rRNA methylation and the function of modified nucleotides in chloroplasts remain to be determined. Here, we identified an rRNA methyltransferase, CMAL (Chloroplast MraW-Like), in the Arabidopsis chloroplast and investigated its function. CMAL is the Arabidopsis ortholog of bacterial MraW/ RsmH proteins and accounts to the N4-methylation of C1352 in chloroplast 16S rRNA, indicating that CMAL orthologs and this methyl-modification nucleotide is conserved between bacteria and the endosymbiont-derived eukaryotic organelle. The knockout of CMAL in Arabidopsis impairs the chloroplast ribosome accumulation and accordingly reduced the efficiency of mRNA translation. Interestingly, the loss of CMAL leads not only to defects in chloroplast function, but also to abnormal leaf and root development and overall plant morphology. Further investigation showed that CMAL is involved in the plant development probably by modulating auxin derived signaling pathways. This study uncovered the important role of 16S rRNA methylation mediated by CMAL in chloroplast ribosome biogenesis and plant development.
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Affiliation(s)
- Meijuan Zou
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ying Mu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xin Chai
- 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
| | - Min Ouyang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Long-Jiang Yu
- 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.,Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University, Munich, D-82152 Planegg-Martinsried, Germany
| | - Wei Chi
- 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
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19
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Watkins KP, Williams-Carrier R, Chotewutmontri P, Friso G, Teubner M, Belcher S, Ruwe H, Schmitz-Linneweber C, van Wijk KJ, Barkan A. Exploring the proteome associated with the mRNA encoding the D1 reaction center protein of Photosystem II in plant chloroplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:369-382. [PMID: 31793101 DOI: 10.1111/tpj.14629] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/14/2019] [Accepted: 11/20/2019] [Indexed: 05/13/2023]
Abstract
Synthesis of the D1 reaction center protein of Photosystem II is dynamically regulated in response to environmental and developmental cues. In chloroplasts, much of this regulation occurs at the post-transcriptional level, but the proteins responsible are largely unknown. To discover proteins that impact psbA expression, we identified proteins that associate with maize psbA mRNA by: (i) formaldehyde cross-linking of leaf tissue followed by antisense oligonucleotide affinity capture of psbA mRNA; and (ii) co-immunoprecipitation with HCF173, a psbA translational activator that is known to bind psbA mRNA. The S1 domain protein SRRP1 and two RNA Recognition Motif (RRM) domain proteins, CP33C and CP33B, were enriched with both approaches. Orthologous proteins were also among the enriched protein set in a previous study in Arabidopsis that employed a designer RNA-binding protein as a psbA RNA affinity tag. We show here that CP33B is bound to psbA mRNA in vivo, as was shown previously for CP33C and SRRP1. Immunoblot, pulse labeling, and ribosome profiling analyses of mutants lacking CP33B and/or CP33C detected some decreases in D1 protein levels under some conditions, but no change in psbA RNA abundance or translation. However, analogous experiments showed that SRRP1 represses psbA ribosome association in the dark, represses ycf1 ribosome association, and promotes accumulation of ndhC mRNA. As SRRP1 is known to harbor RNA chaperone activity, we postulate that SRRP1 mediates these effects by modulating RNA structures. The uncharacterized proteins that emerged from our analyses provide a resource for the discovery of proteins that impact the expression of psbA and other chloroplast genes.
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Affiliation(s)
- Kenneth P Watkins
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | | | | | - Giulia Friso
- Section of Plant Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Marlene Teubner
- Institute of Biology, Department of Life Sciences, Humboldt University Berlin, 10115, Berlin, Germany
| | - Susan Belcher
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | - Hannes Ruwe
- Institute of Biology, Department of Life Sciences, Humboldt University Berlin, 10115, Berlin, Germany
| | | | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
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20
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Teubner M, Lenzen B, Espenberger LB, Fuss J, Nickelsen J, Krause K, Ruwe H, Schmitz-Linneweber C. The Chloroplast Ribonucleoprotein CP33B Quantitatively Binds the psbA mRNA. PLANTS 2020; 9:plants9030367. [PMID: 32192026 PMCID: PMC7154868 DOI: 10.3390/plants9030367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 01/25/2023]
Abstract
Chloroplast RNAs are stabilized and processed by a multitude of nuclear-encoded RNA-binding proteins, often in response to external stimuli like light and temperature. A particularly interesting RNA-based regulation occurs with the psbA mRNA, which shows light-dependent translation. Recently, the chloroplast ribonucleoprotein CP33B was identified as a ligand of the psbA mRNA. We here characterized the interaction of CP33B with chloroplast RNAs in greater detail using a combination of RIP-chip, quantitative dot-blot, and RNA-Bind-n-Seq experiments. We demonstrate that CP33B prefers psbA over all other chloroplast RNAs and associates with the vast majority of the psbA transcript pool. The RNA sequence target motif, determined in vitro, does not fully explain CP33B's preference for psbA, suggesting that there are other determinants of specificity in vivo.
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Affiliation(s)
- Marlene Teubner
- Institute of Biology, Department of Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany; (M.T.); (B.L.); (L.B.E.); (H.R.)
| | - Benjamin Lenzen
- Institute of Biology, Department of Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany; (M.T.); (B.L.); (L.B.E.); (H.R.)
| | - Lucas Bernal Espenberger
- Institute of Biology, Department of Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany; (M.T.); (B.L.); (L.B.E.); (H.R.)
| | - Janina Fuss
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway; (J.F.); (K.K.)
| | - Jörg Nickelsen
- Department Biologie I, Botanik, Ludwig-Maximilians-Universität, 82152 Planegg-Martinsried, Germany;
| | - Kirsten Krause
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway; (J.F.); (K.K.)
| | - Hannes Ruwe
- Institute of Biology, Department of Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany; (M.T.); (B.L.); (L.B.E.); (H.R.)
| | - Christian Schmitz-Linneweber
- Institute of Biology, Department of Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany; (M.T.); (B.L.); (L.B.E.); (H.R.)
- Correspondence: ; Tel.: ++49-30-2093-49700
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21
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Exploring the Link between Photosystem II Assembly and Translation of the Chloroplast psbA mRNA. PLANTS 2020; 9:plants9020152. [PMID: 31991763 PMCID: PMC7076361 DOI: 10.3390/plants9020152] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/16/2020] [Accepted: 01/21/2020] [Indexed: 12/12/2022]
Abstract
Photosystem II (PSII) in chloroplasts and cyanobacteria contains approximately fifteen core proteins, which organize numerous pigments and prosthetic groups that mediate the light-driven water-splitting activity that drives oxygenic photosynthesis. The PSII reaction center protein D1 is subject to photodamage, whose repair requires degradation of damaged D1 and its replacement with nascent D1. Mechanisms that couple D1 synthesis with PSII assembly and repair are poorly understood. We address this question by using ribosome profiling to analyze the translation of chloroplast mRNAs in maize and Arabidopsis mutants with defects in PSII assembly. We found that OHP1, OHP2, and HCF244, which comprise a recently elucidated complex involved in PSII assembly and repair, are each required for the recruitment of ribosomes to psbA mRNA, which encodes D1. By contrast, HCF136, which acts upstream of the OHP1/OHP2/HCF244 complex during PSII assembly, does not have this effect. The fact that the OHP1/OHP2/HCF244 complex brings D1 into proximity with three proteins with dual roles in PSII assembly and psbA ribosome recruitment suggests that this complex is the hub of a translational autoregulatory mechanism that coordinates D1 synthesis with need for nascent D1 during PSII biogenesis and repair.
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22
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Zhang N, Zhao B, Fan Z, Yang D, Guo X, Wu Q, Yu B, Zhou S, Wang H. Systematic identification of genes associated with plant growth-defense tradeoffs under JA signaling in Arabidopsis. PLANTA 2020; 251:43. [PMID: 31907627 DOI: 10.1007/s00425-019-03335-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/21/2019] [Indexed: 05/27/2023]
Abstract
Co-expression and regulatory networks yield important insights into the growth-defense tradeoffs mechanism under jasmonic acid (JA) signals in Arabidopsis. Elevated defense is commonly associated with growth inhibition. However, a comprehensive atlas of the genes associated with the plant growth-defense tradeoffs under JA signaling is lacking. To gain an insight into the dynamic architecture of growth-defense tradeoffs, a coexpression network analysis was employed on publicly available high-resolution transcriptomes of Arabidopsis treated with coronatine (COR), a mimic of jasmonoyl-l-isoleucine. The genes involved in JA-mediated growth-defense tradeoffs were systematically revealed. Promoter enrichment analysis revealed the core regulatory module in which the genes underwent rapid activation, sustained upregulation after COR treatment, and mediated the growth-defense tradeoffs. Several transcription factors (TFs), including RAP2.6L, MYB44, WRKY40, and WRKY18, were identified as instantly activated components associated with pathogen and insect resistance. JA might rapidly activate RAV1 and KAN1 to repress brassinosteroid (BR) response genes, upregulate KAN1, the C2H2 TF families ZF2, ZF3, ZAT6, and STZ/ZAT10 to repress the biosynthesis, transport, and signaling of auxin to arrest growth. Independent datasets and preserved analyses validated the reproducibility of the results. Our study provided a comprehensive snapshot of genes that respond to JA signals and provided valuable resources for functional studies on the genetic modification of breeding population that exhibit robust growth and defense simultaneously.
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Affiliation(s)
- Nailou Zhang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No. 94 Weijin Road, Tianjin, 300071, People's Republic of China
| | - Bin Zhao
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No. 94 Weijin Road, Tianjin, 300071, People's Republic of China
| | - Zhijin Fan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No. 94 Weijin Road, Tianjin, 300071, People's Republic of China.
| | - Dongyan Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No. 94 Weijin Road, Tianjin, 300071, People's Republic of China
| | - Xiaofeng Guo
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No. 94 Weijin Road, Tianjin, 300071, People's Republic of China
| | - Qifan Wu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No. 94 Weijin Road, Tianjin, 300071, People's Republic of China
| | - Bin Yu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No. 94 Weijin Road, Tianjin, 300071, People's Republic of China
| | - Shuang Zhou
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No. 94 Weijin Road, Tianjin, 300071, People's Republic of China
| | - Haiying Wang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No. 94 Weijin Road, Tianjin, 300071, People's Republic of China
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23
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Wang Y, Li G, Guo X, Sun R, Dong T, Yang Q, Wang Q, Li C. Dissecting the genetic architecture of seed-cotton and lint yields in Upland cotton using genome-wide association mapping. BREEDING SCIENCE 2019; 69:611-620. [PMID: 31988625 PMCID: PMC6977443 DOI: 10.1270/jsbbs.19057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/23/2019] [Indexed: 05/18/2023]
Abstract
Seed-cotton yield (SY) and lint yield (LY) are the most important yield traits of cotton. Thus, it is critical to dissect their genetic architecture. Upland cotton (Gossypium hirsutum) is widely grown worldwide. In this study, a genome-wide association mapping was performed based on the CottonSNP80K array to dissect the genetic architecture of SY and LY in Upland cotton. Twenty-three significant associations were detected within four environments, including 11 associated with SY and 12 associated with LY. Seven single nucleotide polymorphisms (SNPs), TM234, TM237, TM247, TM255, TM256, TM263, and TM264, were co-associated with the two traits, which may indicate pleiotropy or intergenic tight linkages. Five SNPs, TM13332, TM39771, TM57119, TM81653, and TM81660, were coincided with those of previous reports and could be used in marker-assisted selection. Combining functional annotations with expression analyses of the genes identified within 400 kb of the significantly associated SNPs, we hypothesize that the three genes, Gh_D05G1077 and Gh_D13G1571 for SY, and Gh_A11G0775 for LY, may have the potential to increase cotton yield. The results would provide useful information for understanding the genetic basis of yield traits in Upland cotton and for facilitating its high-yield breeding through molecular design.
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Affiliation(s)
- Yuanyuan Wang
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology,
Xinxiang 453003,
China
| | - Guirong Li
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology,
Xinxiang 453003,
China
| | - Xinlei Guo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics,
Beijing 100081,
China
| | - Runrun Sun
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology,
Xinxiang 453003,
China
| | - Tao Dong
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology,
Xinxiang 453003,
China
| | - Qiuyue Yang
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology,
Xinxiang 453003,
China
| | - Qinglian Wang
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology,
Xinxiang 453003,
China
| | - Chengqi Li
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology,
Xinxiang 453003,
China
- Corresponding author (e-mail: )
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24
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McDermott JJ, Watkins KP, Williams-Carrier R, Barkan A. Ribonucleoprotein Capture by in Vivo Expression of a Designer Pentatricopeptide Repeat Protein in Arabidopsis. THE PLANT CELL 2019; 31:1723-1733. [PMID: 31123048 PMCID: PMC6713294 DOI: 10.1105/tpc.19.00177] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/01/2019] [Accepted: 05/14/2019] [Indexed: 05/15/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins bind RNA via a mechanism that facilitates the customization of sequence specificity. However, natural PPR proteins have irregular features that limit the degree to which their specificity can be predicted and customized. We demonstrate here that artificial PPR proteins built from consensus PPR motifs selectively bind the intended RNA in vivo, and we use this property to develop a new tool for ribonucleoprotein characterization. We show by RNA coimmunoprecipitation sequencing (RIP-seq) that artificial PPR proteins designed to bind the Arabidopsis (Arabidopsis thaliana) chloroplast psbA mRNA bind with high specificity to psbA mRNA in vivo. Analysis of coimmunoprecipitating proteins by mass spectrometry showed the psbA translational activator HCF173 and two RNA binding proteins of unknown function (CP33C and SRRP1) to be highly enriched. RIP-seq revealed that these proteins are bound primarily to psbA RNA in vivo, and precise mapping of the HCF173 and CP33C binding sites placed them in different locations on psbA mRNA. These results demonstrate that artificial PPR proteins can be tailored to bind specific endogenous RNAs in vivo, add to the toolkit for characterizing native ribonucleoproteins, and open the door to other applications that rely on the ability to target a protein to a specified RNA sequence.
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Affiliation(s)
- James J McDermott
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Kenneth P Watkins
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | | | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
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25
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Williams-Carrier R, Brewster C, Belcher SE, Rojas M, Chotewutmontri P, Ljungdahl S, Barkan A. The Arabidopsis pentatricopeptide repeat protein LPE1 and its maize ortholog are required for translation of the chloroplast psbJ RNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:56-66. [PMID: 30844105 DOI: 10.1111/tpj.14308] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 02/04/2019] [Accepted: 02/28/2019] [Indexed: 05/21/2023]
Abstract
The expression of chloroplast genes relies on a host of nucleus-encoded proteins. Identification of such proteins and elucidation of their functions are ongoing challenges. We used ribosome profiling to revisit the function of the pentatricopeptide repeat protein LPE1, reported to stimulate translation of the chloroplast psbA mRNA in Arabidopsis. Mutation of the maize LPE1 ortholog causes a photosystem II (PSII) deficiency and a defect in translation of the chloroplast psbJ open reading frame (ORF) but has no effect on psbA expression. To reflect this function, we named the maize LPE1 ortholog Translation of psbJ 1 (TPJ1). Arabidopsis lpe1 mutants likewise exhibit a loss of psbJ translation, and have, in addition, a decrease in psbN translation. We detected a small decrease in ribosome occupancy on the psbA mRNA in Arabidopsis lpe1 mutants, but ribosome profiling analyses of other PSII mutants (hcf107 and hcf173) in conjunction with in vitro RNA binding data strongly suggest that this is a secondary effect of their PSII deficiency. We conclude that maize TPJ1 promotes PSII synthesis by activating translation of the psbJ ORF, that this function is conserved in Arabidopsis LPE1, and that an additional role for LPE1 in psbN translation contributes to the PSII deficiency in lpe1 mutants.
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Affiliation(s)
| | - Carolyn Brewster
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | - Susan E Belcher
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | - Margarita Rojas
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | | | - Sonja Ljungdahl
- 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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26
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Grossman A, Sanz-Luque E, Yi H, Yang W. Building the GreenCut2 suite of proteins to unmask photosynthetic function and regulation. Microbiology (Reading) 2019; 165:697-718. [DOI: 10.1099/mic.0.000788] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Arthur Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Emanuel Sanz-Luque
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Heng Yi
- Key Laboratory of Photobiology, Institute of Botany (CAS), Beijing, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Wenqiang Yang
- Key Laboratory of Photobiology, Institute of Botany (CAS), Beijing, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
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27
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Li X, Patena W, Fauser F, Jinkerson RE, Saroussi S, Meyer MT, Ivanova N, Robertson JM, Yue R, Zhang R, Vilarrasa-Blasi J, Wittkopp TM, Ramundo S, Blum SR, Goh A, Laudon M, Srikumar T, Lefebvre PA, Grossman AR, Jonikas MC. A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis. Nat Genet 2019. [PMID: 30886426 DOI: 10.1038/s41588-019-0370-376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Photosynthetic organisms provide food and energy for nearly all life on Earth, yet half of their protein-coding genes remain uncharacterized1,2. Characterization of these genes could be greatly accelerated by new genetic resources for unicellular organisms. Here we generated a genome-wide, indexed library of mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii. The 62,389 mutants in the library, covering 83% of nuclear protein-coding genes, are available to the community. Each mutant contains unique DNA barcodes, allowing the collection to be screened as a pool. We performed a genome-wide survey of genes required for photosynthesis, which identified 303 candidate genes. Characterization of one of these genes, the conserved predicted phosphatase-encoding gene CPL3, showed that it is important for accumulation of multiple photosynthetic protein complexes. Notably, 21 of the 43 higher-confidence genes are novel, opening new opportunities for advances in understanding of this biogeochemically fundamental process. This library will accelerate the characterization of thousands of genes in algae, plants, and animals.
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Affiliation(s)
- Xiaobo Li
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- School of Life Sciences, Westlake Institute for Advanced Study, Westlake University, Hangzhou, China
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Friedrich Fauser
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Robert E Jinkerson
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Shai Saroussi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Moritz T Meyer
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Nina Ivanova
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Jacob M Robertson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Rebecca Yue
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Ru Zhang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Tyler M Wittkopp
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Silvia Ramundo
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Sean R Blum
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Audrey Goh
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Matthew Laudon
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Tharan Srikumar
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Paul A Lefebvre
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA.
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28
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A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis. Nat Genet 2019; 51:627-635. [PMID: 30886426 PMCID: PMC6636631 DOI: 10.1038/s41588-019-0370-6] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 02/08/2019] [Indexed: 12/22/2022]
Abstract
Photosynthetic organisms provide food and energy for nearly all life on Earth, yet half of their protein-coding genes remain uncharacterized1,2. Characterization of these genes could be greatly accelerated by new genetic resources for unicellular organisms. Here, we generated a genome-wide, indexed library of mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii. The 62,389 mutants in the library, covering 83% of nuclear, protein-coding genes, are available to the community. Each mutant contains unique DNA barcodes, allowing the collection to be screened as a pool. We performed a genome-wide survey of genes required for photosynthesis, which identified 303 candidate genes. Characterization of one of these genes, the conserved predicted phosphatase-encoding gene CPL3, showed it is important for accumulation of multiple photosynthetic protein complexes. Notably, 21 of the 43 highest-confidence genes are novel, opening new opportunities for advances in our understanding of this biogeochemically fundamental process. This library will accelerate the characterization of thousands of genes in algae, plants and animals. Generation of a library of 62,389 mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii enables screening for genes required for photosynthesis and the identification of 303 candidate genes.
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29
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Li Y, Liu B, Zhang J, Kong F, Zhang L, Meng H, Li W, Rochaix JD, Li D, Peng L. OHP1, OHP2, and HCF244 Form a Transient Functional Complex with the Photosystem II Reaction Center. PLANT PHYSIOLOGY 2019; 179:195-208. [PMID: 30397023 PMCID: PMC6324237 DOI: 10.1104/pp.18.01231] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 10/29/2018] [Indexed: 05/19/2023]
Abstract
The reaction center (RC) of photosystem II (PSII), which is composed of D1, D2, PsbI, and cytochrome b559 subunits, forms at an early stage of PSII biogenesis. However, it is largely unclear how these components assemble to form a functional unit. In this work, we show that synthesis of the PSII core proteins D1/D2 and formation of the PSII RC is blocked specifically in the absence of ONE-HELIX PROTEIN1 (OHP1) and OHP2 proteins in Arabidopsis (Arabidopsis thaliana), indicating that OHP1 and OHP2 are essential for the formation of the PSII RC. Mutagenesis of the chlorophyll-binding residues in OHP proteins impairs their function and/or stability, suggesting that they may function in the binding of chlorophyll in vivo. We further show that OHP1, OHP2, and HIGH CHLOROPHYLL FLUORESCENCE244 (HCF244), together with D1, D2, PsbI, and cytochrome b559, form a complex. We designated this complex the PSII RC-like complex to distinguish it from the RC subcomplex in the intact PSII complex. Our data imply that OHP1, OHP2, and HCF244 are present in this PSII RC-like complex for a limited time at an early stage of PSII de novo assembly and of PSII repair under high-light conditions. In a subsequent stage of PSII biogenesis, OHP1, OHP2, and HCF244 are released from the PSII RC-like complex and replaced by the other PSII subunits. Together with previous reports on the cyanobacterium Synechocystis, our results demonstrate that the process of PSII RC assembly is highly conserved among photosynthetic species.
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Affiliation(s)
- Yonghong Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Bei Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jiao Zhang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Fanna Kong
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lin Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Han Meng
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Wenjing Li
- College of Life Sciences, Langfang Teachers University, Langfang Hebei 065000, China
| | - Jean-David Rochaix
- Departments of Molecular Biology and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Dan Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lianwei Peng
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
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30
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Nassrallah A, Rougée M, Bourbousse C, Drevensek S, Fonseca S, Iniesto E, Ait-Mohamed O, Deton-Cabanillas AF, Zabulon G, Ahmed I, Stroebel D, Masson V, Lombard B, Eeckhout D, Gevaert K, Loew D, Genovesio A, Breyton C, De Jaeger G, Bowler C, Rubio V, Barneche F. DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis. eLife 2018; 7:37892. [PMID: 30192741 PMCID: PMC6128693 DOI: 10.7554/elife.37892] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/22/2018] [Indexed: 12/11/2022] Open
Abstract
DE-ETIOLATED 1 (DET1) is an evolutionarily conserved component of the ubiquitination machinery that mediates the destabilization of key regulators of cell differentiation and proliferation in multicellular organisms. In this study, we provide evidence from Arabidopsis that DET1 is essential for the regulation of histone H2B monoubiquitination (H2Bub) over most genes by controlling the stability of a deubiquitination module (DUBm). In contrast with yeast and metazoan DUB modules that are associated with the large SAGA complex, the Arabidopsis DUBm only comprises three proteins (hereafter named SGF11, ENY2 and UBP22) and appears to act independently as a major H2Bub deubiquitinase activity. Our study further unveils that DET1-DDB1-Associated-1 (DDA1) protein interacts with SGF11 in vivo, linking the DET1 complex to light-dependent ubiquitin-mediated proteolytic degradation of the DUBm. Collectively, these findings uncover a signaling path controlling DUBm availability, potentially adjusting H2Bub turnover capacity to the cell transcriptional status.
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Affiliation(s)
- Amr Nassrallah
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Martin Rougée
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Université Paris-Sud, Orsay, France
| | - Clara Bourbousse
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Université Paris-Sud, Orsay, France
| | - Stephanie Drevensek
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Sandra Fonseca
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Elisa Iniesto
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Ouardia Ait-Mohamed
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Anne-Flore Deton-Cabanillas
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Gerald Zabulon
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Ikhlak Ahmed
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - David Stroebel
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Vanessa Masson
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie PSL Research University, 75005 Paris, France
| | - Berangere Lombard
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie PSL Research University, 75005 Paris, France
| | - Dominique Eeckhout
- Department of Plant Systems Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium.,VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Damarys Loew
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie PSL Research University, 75005 Paris, France
| | - Auguste Genovesio
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Cecile Breyton
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
| | - Geert De Jaeger
- Department of Plant Systems Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Chris Bowler
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Vicente Rubio
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Fredy Barneche
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
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Chotewutmontri P, Barkan A. Multilevel effects of light on ribosome dynamics in chloroplasts program genome-wide and psbA-specific changes in translation. PLoS Genet 2018; 14:e1007555. [PMID: 30080854 PMCID: PMC6095610 DOI: 10.1371/journal.pgen.1007555] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/16/2018] [Accepted: 07/11/2018] [Indexed: 11/22/2022] Open
Abstract
Plants and algae adapt to fluctuating light conditions to optimize photosynthesis, minimize photodamage, and prioritize energy investments. Changes in the translation of chloroplast mRNAs are known to contribute to these adaptations, but the scope and magnitude of these responses are unclear. To clarify the phenomenology, we used ribosome profiling to analyze chloroplast translation in maize seedlings following dark-to-light and light-to-dark shifts. The results resolved several layers of regulation. (i) The psbA mRNA exhibits a dramatic gain of ribosomes within minutes after shifting plants to the light and reverts to low ribosome occupancy within one hour in the dark, correlating with the need to replace damaged PsbA in Photosystem II. (ii) Ribosome occupancy on all other chloroplast mRNAs remains similar to that at midday even after 12 hours in the dark. (iii) Analysis of ribosome dynamics in the presence of lincomycin revealed a global decrease in the translation elongation rate shortly after shifting plants to the dark. The pausing of chloroplast ribosomes at specific sites changed very little during these light-shift regimes. A similar but less comprehensive analysis in Arabidopsis gave similar results excepting a trend toward reduced ribosome occupancy at the end of the night. Our results show that all chloroplast mRNAs except psbA maintain similar ribosome occupancy following short-term light shifts, but are nonetheless translated at higher rates in the light due to a plastome-wide increase in elongation rate. A light-induced recruitment of ribosomes to psbA mRNA is superimposed on this global response, producing a rapid and massive increase in PsbA synthesis. These findings highlight the unique translational response of psbA in mature chloroplasts, clarify which steps in psbA translation are light-regulated in the context of Photosystem II repair, and provide a foundation on which to explore mechanisms underlying the psbA-specific and global effects of light on chloroplast translation.
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Affiliation(s)
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR, United States of America
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Hey D, Grimm B. ONE-HELIX PROTEIN2 (OHP2) Is Required for the Stability of OHP1 and Assembly Factor HCF244 and Is Functionally Linked to PSII Biogenesis. PLANT PHYSIOLOGY 2018; 177:1453-1472. [PMID: 29930106 PMCID: PMC6084673 DOI: 10.1104/pp.18.00540] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 06/13/2018] [Indexed: 05/07/2023]
Abstract
The members of the light-harvesting complex protein family, which include the one-helix proteins (OHPs), are characterized by one to four membrane-spanning helices. These proteins function in light absorption and energy dissipation, sensing light intensity, and triggering photomorphogenesis or the binding of chlorophyll and intermediates of chlorophyll biosynthesis. Arabidopsis (Arabidopsis thaliana) contains two OHPs, while four homologs (named high-light-induced proteins) exist in Synechocystis PCC6803. Various functions have been assigned to high-light-induced proteins, ranging from photoprotection and the assembly of photosystem I (PSI) and PSII to regulation of the early steps of chlorophyll biosynthesis, but little is known about the function of the two plant OHPs. Here, we show that the two Arabidopsis OHPs form heterodimers and that the stromal part of OHP2 interacts with the plastid-localized PSII assembly factor HIGH CHLOROPHYLL FLUORESCENCE244 (HCF244). Moreover, concurrent accumulation of the two OHPs and HCF244 is critical for the stability of all three proteins. In particular, the absence of OHP2 leads to the complete loss of OHP1 and HCF244. We used a virus-induced gene silencing approach to minimize the expression of OHP1 or OHP2 in adult Arabidopsis plants and revealed that OHP2 is essential for the accumulation of the PSII core subunits, while the other photosynthetic complexes and the major light-harvesting complex proteins remained unaffected. We examined the potential functions of the OHP1-OHP2-HCF244 complex in the assembly and/or repair of PSII and propose a role for this heterotrimeric complex in thylakoid membrane biogenesis.
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Affiliation(s)
- Daniel Hey
- Humboldt-Universität zu Berlin, Lebenswissenschaftliche Fakultät, Institut für Biologie, AG Pflanzenphysiologie, 10115 Berlin, Germany
| | - Bernhard Grimm
- Humboldt-Universität zu Berlin, Lebenswissenschaftliche Fakultät, Institut für Biologie, AG Pflanzenphysiologie, 10115 Berlin, Germany
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LOW PHOTOSYNTHETIC EFFICIENCY 1 is required for light-regulated photosystem II biogenesis in Arabidopsis. Proc Natl Acad Sci U S A 2018; 115:E6075-E6084. [PMID: 29891689 PMCID: PMC6042084 DOI: 10.1073/pnas.1807364115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Photosystem II (PSII) reaction center protein D1 is encoded by chloroplast gene psbA and is crucial to the biogenesis and functional maintenance of PSII. D1 proteins are highly dynamic under varying light conditions and thus require efficient synthesis, but the mechanism remains poorly understood. We reported that Arabidopsis LPE1 directly binds to the 5′ UTR of psbA mRNA in a light-dependent manner through a redox-based mechanism and facilitates the association of HCF173 with psbA mRNA to regulate D1 translation. These findings fill a major gap in our understanding of the mechanism of light-regulated D1 synthesis in higher plants and imply that higher plants and primitive photosynthetic organisms share conserved mechanisms but use distinct regulators to regulate biogenesis of PSII subunits. Photosystem II (PSII), a multisubunit protein complex of the photosynthetic electron transport chain, functions as a water-plastoquinone oxidoreductase, which is vital to the initiation of photosynthesis and electron transport. Although the structure, composition, and function of PSII are well understood, the mechanism of PSII biogenesis remains largely elusive. Here, we identified a nuclear-encoded pentatricopeptide repeat (PPR) protein LOW PHOTOSYNTHETIC EFFICIENCY 1 (LPE1; encoded by At3g46610) in Arabidopsis, which plays a crucial role in PSII biogenesis. LPE1 is exclusively targeted to chloroplasts and directly binds to the 5′ UTR of psbA mRNA which encodes the PSII reaction center protein D1. The loss of LPE1 results in less efficient loading of ribosome on the psbA mRNA and great synthesis defects in D1 protein. We further found that LPE1 interacts with a known regulator of psbA mRNA translation HIGH CHLOROPHYLL FLUORESCENCE 173 (HCF173) and facilitates the association of HCF173 with psbA mRNA. More interestingly, our results indicate that LPE1 associates with psbA mRNA in a light-dependent manner through a redox-based mechanism. This study enhances our understanding of the mechanism of light-regulated D1 synthesis, providing important insight into PSII biogenesis and the functional maintenance of efficient photosynthesis in higher plants.
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Wittkopp TM, Saroussi S, Yang W, Johnson X, Kim RG, Heinnickel ML, Russell JJ, Phuthong W, Dent RM, Broeckling CD, Peers G, Lohr M, Wollman FA, Niyogi KK, Grossman AR. GreenCut protein CPLD49 of Chlamydomonas reinhardtii associates with thylakoid membranes and is required for cytochrome b 6 f complex accumulation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:1023-1037. [PMID: 29602195 DOI: 10.1111/tpj.13915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/23/2018] [Accepted: 03/06/2018] [Indexed: 06/08/2023]
Abstract
The GreenCut encompasses a suite of nucleus-encoded proteins with orthologs among green lineage organisms (plants, green algae), but that are absent or poorly conserved in non-photosynthetic/heterotrophic organisms. In Chlamydomonas reinhardtii, CPLD49 (Conserved in Plant Lineage and Diatoms49) is an uncharacterized GreenCut protein that is critical for maintaining normal photosynthetic function. We demonstrate that a cpld49 mutant has impaired photoautotrophic growth under high-light conditions. The mutant exhibits a nearly 90% reduction in the level of the cytochrome b6 f complex (Cytb6 f), which impacts linear and cyclic electron transport, but does not compromise the ability of the strain to perform state transitions. Furthermore, CPLD49 strongly associates with thylakoid membranes where it may be part of a membrane protein complex with another GreenCut protein, CPLD38; a mutant null for CPLD38 also impacts Cytb6 f complex accumulation. We investigated several potential functions of CPLD49, with some suggested by protein homology. Our findings are congruent with the hypothesis that CPLD38 and CPLD49 are part of a novel thylakoid membrane complex that primarily modulates accumulation, but also impacts the activity of the Cytb6 f complex. Based on motifs of CPLD49 and the activities of other CPLD49-like proteins, we suggest a role for this putative dehydrogenase in the synthesis of a lipophilic thylakoid membrane molecule or cofactor that influences the assembly and activity of Cytb6 f.
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Affiliation(s)
- Tyler M Wittkopp
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Shai Saroussi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Wenqiang Yang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Xenie Johnson
- Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, CEA Cadarache, Saint Paul lez Durance, France
| | - Rick G Kim
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Mark L Heinnickel
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - James J Russell
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Witchukorn Phuthong
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Rachel M Dent
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, 80523, USA
| | - Graham Peers
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Martin Lohr
- Institut für Molekulare Physiologie - Pflanzenbiochemie, Johannes Gutenberg-Universität, 55099, Mainz, Germany
| | | | - Krishna K Niyogi
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
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Zoschke R, Bock R. Chloroplast Translation: Structural and Functional Organization, Operational Control, and Regulation. THE PLANT CELL 2018; 30:745-770. [PMID: 29610211 PMCID: PMC5969280 DOI: 10.1105/tpc.18.00016] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/26/2018] [Accepted: 04/01/2018] [Indexed: 05/20/2023]
Abstract
Chloroplast translation is essential for cellular viability and plant development. Its positioning at the intersection of organellar RNA and protein metabolism makes it a unique point for the regulation of gene expression in response to internal and external cues. Recently obtained high-resolution structures of plastid ribosomes, the development of approaches allowing genome-wide analyses of chloroplast translation (i.e., ribosome profiling), and the discovery of RNA binding proteins involved in the control of translational activity have greatly increased our understanding of the chloroplast translation process and its regulation. In this review, we provide an overview of the current knowledge of the chloroplast translation machinery, its structure, organization, and function. In addition, we summarize the techniques that are currently available to study chloroplast translation and describe how translational activity is controlled and which cis-elements and trans-factors are involved. Finally, we discuss how translational control contributes to the regulation of chloroplast gene expression in response to developmental, environmental, and physiological cues. We also illustrate the commonalities and the differences between the chloroplast and bacterial translation machineries and the mechanisms of protein biosynthesis in these two prokaryotic systems.
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Affiliation(s)
- Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
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36
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Myouga F, Takahashi K, Tanaka R, Nagata N, Kiss AZ, Funk C, Nomura Y, Nakagami H, Jansson S, Shinozaki K. Stable Accumulation of Photosystem II Requires ONE-HELIX PROTEIN1 (OHP1) of the Light Harvesting-Like Family. PLANT PHYSIOLOGY 2018; 176:2277-2291. [PMID: 29438089 PMCID: PMC5841713 DOI: 10.1104/pp.17.01782] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/25/2018] [Indexed: 05/19/2023]
Abstract
The cellular functions of two Arabidopsis (Arabidopsis thaliana) one-helix proteins, OHP1 and OHP2 (also named LIGHT-HARVESTING-LIKE2 [LIL2] and LIL6, respectively, because they have sequence similarity to light-harvesting chlorophyll a/b-binding proteins), remain unclear. Tagged null mutants of OHP1 and OHP2 (ohp1 and ohp2) showed stunted growth with pale-green leaves on agar plates, and these mutants were unable to grow on soil. Leaf chlorophyll fluorescence and the composition of thylakoid membrane proteins revealed that ohp1 deletion substantially affected photosystem II (PSII) core protein function and led to reduced levels of photosystem I core proteins; however, it did not affect LHC accumulation. Transgenic ohp1 plants rescued with OHP1-HA or OHP1-Myc proteins developed a normal phenotype. Using these tagged OHP1 proteins in transgenic plants, we localized OHP1 to thylakoid membranes, where it formed protein complexes with both OHP2 and High Chlorophyll Fluorescence244 (HCF244). We also found PSII core proteins D1/D2, HCF136, and HCF173 and a few other plant-specific proteins associated with the OHP1/OHP2-HCF244 complex, suggesting that these complexes are early intermediates in PSII assembly. OHP1 interacted directly with HCF244 in the complex. Therefore, OHP1 and HCF244 play important roles in the stable accumulation of PSII.
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Affiliation(s)
- Fumiyoshi Myouga
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Kaori Takahashi
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Ryoichi Tanaka
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Noriko Nagata
- Department of Chemical Biological Sciences, Japan Women's University, Bunkyo-ku, Tokyo 112-8681, Japan
| | - Anett Z Kiss
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umea, Sweden
- Department of Chemistry, Umeå University, SE-901 87 Umea, Sweden
| | - Christiane Funk
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umea, Sweden
- Department of Chemistry, Umeå University, SE-901 87 Umea, Sweden
| | - Yuko Nomura
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Hirofumi Nakagami
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Stefan Jansson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umea, Sweden
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
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37
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Chotewutmontri P, Barkan A. Dynamics of Chloroplast Translation during Chloroplast Differentiation in Maize. PLoS Genet 2016; 12:e1006106. [PMID: 27414025 PMCID: PMC4945096 DOI: 10.1371/journal.pgen.1006106] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/13/2016] [Indexed: 11/18/2022] Open
Abstract
Chloroplast genomes in land plants contain approximately 100 genes, the majority of which reside in polycistronic transcription units derived from cyanobacterial operons. The expression of chloroplast genes is integrated into developmental programs underlying the differentiation of photosynthetic cells from non-photosynthetic progenitors. In C4 plants, the partitioning of photosynthesis between two cell types, bundle sheath and mesophyll, adds an additional layer of complexity. We used ribosome profiling and RNA-seq to generate a comprehensive description of chloroplast gene expression at four stages of chloroplast differentiation, as displayed along the maize seedling leaf blade. The rate of protein output of most genes increases early in development and declines once the photosynthetic apparatus is mature. The developmental dynamics of protein output fall into several patterns. Programmed changes in mRNA abundance make a strong contribution to the developmental shifts in protein output, but output is further adjusted by changes in translational efficiency. RNAs with prioritized translation early in development are largely involved in chloroplast gene expression, whereas those with prioritized translation in photosynthetic tissues are generally involved in photosynthesis. Differential gene expression in bundle sheath and mesophyll chloroplasts results primarily from differences in mRNA abundance, but differences in translational efficiency amplify mRNA-level effects in some instances. In most cases, rates of protein output approximate steady-state protein stoichiometries, implying a limited role for proteolysis in eliminating unassembled or damaged proteins under non-stress conditions. Tuned protein output results from gene-specific trade-offs between translational efficiency and mRNA abundance, both of which span a large dynamic range. Analysis of ribosome footprints at sites of RNA editing showed that the chloroplast translation machinery does not generally discriminate between edited and unedited RNAs. However, editing of ACG to AUG at the rpl2 start codon is essential for translation initiation, demonstrating that ACG does not serve as a start codon in maize chloroplasts.
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Affiliation(s)
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
- * E-mail:
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38
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Herritt M, Dhanapal AP, Fritschi FB. Identification of Genomic Loci Associated with the Photochemical Reflectance Index by Genome-Wide Association Study in Soybean. THE PLANT GENOME 2016; 9. [PMID: 27898827 DOI: 10.3835/plantgenome2015.08.0072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 02/24/2016] [Indexed: 05/10/2023]
Abstract
The photochemical reflectance index (PRI) is determined from canopy spectral reflectance measurements and can provide important information about photosynthesis. The PRI can be used to assess the epoxidation state of xanthophyll pigments, which provides information on nonphotochemical quenching (NPQ) and the amount of energy used for photosynthesis. Genome-wide association analyses were conducted to identify single-nucleotide polymorphisms (SNPs) and genomic loci associated with PRI using data from a soybean [ (L.) Merr.] diversity panel grown under field conditions over 2 yr. Based on a mixed linear model (MLM), 31 unique candidate SNPs that identify 15 putative loci on 11 chromosomes were identified. Several candidate genes known to be associated with NPQ, photosynthesis, and sugar transport processes were identified in the proximity of 10 putative loci. Violaxanthin de-epoxidase, one of the identified genes, is directly involved in the xanthophyll cycle, which plays a major role in NPQ. This study is the first to identify genomic loci for PRI and illustrates the potential of canopy spectral reflectance measurements for high-throughput phenotyping of a photosynthesis related trait. Significant SNPs, candidate genes, and genotypes contrasting for PRI identified in this study may prove useful for crop improvement efforts.
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39
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Nakamura M, Hibi Y, Okamoto T, Sugiura M. Cooperation between the chloroplast psbA 5'-untranslated region and coding region is important for translational initiation: the chloroplast translation machinery cannot read a human viral gene coding region. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:772-80. [PMID: 26931095 DOI: 10.1111/tpj.13150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 06/05/2023]
Abstract
Chloroplast mRNA translation is regulated by the 5'-untranslated region (5'-UTR). Chloroplast 5'-UTRs also support translation of the coding regions of heterologous genes. Using an in vitro translation system from tobacco chloroplasts, we detected no translation from a human immunodeficiency virus tat coding region fused directly to the tobacco chloroplast psbA 5'-UTR. This lack of apparent translation could have been due to rapid degradation of mRNA templates or synthesized protein products. Replacing the psbA 5'-UTR with the E. coli phage T7 gene 10 5'-UTR, a highly active 5'-UTR, and substituting synonymous codons led to some translation of the tat coding region. The Tat protein thus synthesized was stable during translation reactions. No significant degradation of the added tat mRNAs was observed after translation reactions. These results excluded the above two possibilities and confirmed that the tat coding region prevented its own translation. The tat coding region was then fused to the psbA 5'-UTR with a cognate 5'-coding segment. Significant translation was detected from the tat coding region when fused after 10 or more codons. That is, translation could be initiated from the tat coding region once translation had started, indicating that the tat coding region inhibits translational initiation but not elongation. Hence, cooperation/compatibility between the 5'-UTR and its coding region is important for translational initiation.
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Affiliation(s)
- Masayuki Nakamura
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho-ku, Nagoya, 467-8501, Japan
| | - Yurina Hibi
- Department of Molecular and Cellular Biology, Graduate School of Medical Sciences, Nagoya City University, Kawasumi, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Graduate School of Medical Sciences, Nagoya City University, Kawasumi, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Masahiro Sugiura
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho-ku, Nagoya, 467-8501, Japan
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40
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Lu Y. Identification and Roles of Photosystem II Assembly, Stability, and Repair Factors in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2016; 7:168. [PMID: 26909098 PMCID: PMC4754418 DOI: 10.3389/fpls.2016.00168] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/31/2016] [Indexed: 05/18/2023]
Abstract
Photosystem II (PSII) is a multi-component pigment-protein complex that is responsible for water splitting, oxygen evolution, and plastoquinone reduction. Components of PSII can be classified into core proteins, low-molecular-mass proteins, extrinsic oxygen-evolving complex (OEC) proteins, and light-harvesting complex II proteins. In addition to these PSII subunits, more than 60 auxiliary proteins, enzymes, or components of thylakoid protein trafficking/targeting systems have been discovered to be directly or indirectly involved in de novo assembly and/or the repair and reassembly cycle of PSII. For example, components of thylakoid-protein-targeting complexes and the chloroplast-vesicle-transport system were found to deliver PSII subunits to thylakoid membranes. Various auxiliary proteins, such as PsbP-like (Psb stands for PSII) and light-harvesting complex-like proteins, atypical short-chain dehydrogenase/reductase family proteins, and tetratricopeptide repeat proteins, were discovered to assist the de novo assembly and stability of PSII and the repair and reassembly cycle of PSII. Furthermore, a series of enzymes were discovered to catalyze important enzymatic steps, such as C-terminal processing of the D1 protein, thiol/disulfide-modulation, peptidylprolyl isomerization, phosphorylation and dephosphorylation of PSII core and antenna proteins, and degradation of photodamaged PSII proteins. This review focuses on the current knowledge of the identities and molecular functions of different types of proteins that influence the assembly, stability, and repair of PSII in the higher plant Arabidopsis thaliana.
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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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42
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He B, Mu Y, Chi W. Effects of inefficient transcription termination of rbcL on the expression of accD in plastids of Arabidopsis thaliana. PHOTOSYNTHESIS RESEARCH 2015; 126:323-330. [PMID: 26003009 DOI: 10.1007/s11120-015-0159-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/16/2015] [Indexed: 06/04/2023]
Abstract
The plastid accD gene encodes one subunit of a multimeric acetyl-CoA carboxylase that is required for fatty acid biosynthesis. In Arabidopsis thaliana, the accD gene is transcribed by the nuclear-encoded phage-type RNA polymerase, and the accumulation of accD transcripts is subjected to a dynamic pattern during chloroplast development. However, the mechanisms underlying the regulation of accD expression remain unknown. Here, we showed that the inefficient transcription termination of rbcL due to the absence of RHON1 impaired the developmental profile of accD, resulting in the constitutive expression of accD during chloroplast development. Moreover, the accumulation of accD transcripts accordingly resulted in an increase in accD protein levels, suggesting that transcript abundance is critical for accD gene production. Our study demonstrates that the interplay between accD and upstream rbcL regulates the expression of accD and highlights the significance of transcriptional regulation in plastid gene expression in higher plants.
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Affiliation(s)
- Baoye He
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Mu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China.
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Steffens A, Bräutigam A, Jakoby M, Hülskamp M. The BEACH Domain Protein SPIRRIG Is Essential for Arabidopsis Salt Stress Tolerance and Functions as a Regulator of Transcript Stabilization and Localization. PLoS Biol 2015; 13:e1002188. [PMID: 26133670 PMCID: PMC4489804 DOI: 10.1371/journal.pbio.1002188] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 05/26/2015] [Indexed: 12/22/2022] Open
Abstract
Members of the highly conserved class of BEACH domain containing proteins (BDCPs) have been established as broad facilitators of protein-protein interactions and membrane dynamics in the context of human diseases like albinism, bleeding diathesis, impaired cellular immunity, cancer predisposition, and neurological dysfunctions. Also, the Arabidopsis thaliana BDCP SPIRRIG (SPI) is important for membrane integrity, as spi mutants exhibit split vacuoles. In this work, we report a novel molecular function of the BDCP SPI in ribonucleoprotein particle formation. We show that SPI interacts with the P-body core component DECAPPING PROTEIN 1 (DCP1), associates to mRNA processing bodies (P-bodies), and regulates their assembly upon salt stress. The finding that spi mutants exhibit salt hypersensitivity suggests that the local function of SPI at P-bodies is of biological relevance. Transcriptome-wide analysis revealed qualitative differences in the salt stress-regulated transcriptional response of Col-0 and spi. We show that SPI regulates the salt stress-dependent post-transcriptional stabilization, cytoplasmic agglomeration, and localization to P-bodies of a subset of salt stress-regulated mRNAs. Finally, we show that the PH-BEACH domains of SPI and its human homolog FAN (Factor Associated with Neutral sphingomyelinase activation) interact with DCP1 isoforms from plants, mammals, and yeast, suggesting the evolutionary conservation of an association of BDCPs and P-bodies.
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Affiliation(s)
| | - Andrea Bräutigam
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
- Plant Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Marc Jakoby
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Martin Hülskamp
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
- * E-mail:
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Walter B, Pieta T, Schünemann D. Arabidopsis thaliana mutants lacking cpFtsY or cpSRP54 exhibit different defects in photosystem II repair. FRONTIERS IN PLANT SCIENCE 2015; 6:250. [PMID: 25918516 PMCID: PMC4394663 DOI: 10.3389/fpls.2015.00250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/27/2015] [Indexed: 05/24/2023]
Abstract
Photosystem II (PS II) is a multi subunit protein complex embedded in the thylakoid membrane of cyanobacteria and chloroplasts. As the PS II reaction center protein D1 is prone to a light induced damage that inhibits PS II function especially at elevated light intensities, a highly ordered repair process including synthesis, targeting and insertion of D1 has evolved. To elucidate the function of the chloroplast signal recognition particle subunits, cpSRP43 and cpSRP54, and the cpSRP-receptor cpFtsY in D1 biogenesis we investigated the efficiency of the PS II repair cycle in the corresponding mutants of Arabidopsis thaliana. Immunological analyses, PAM measurements and in vivo labeling experiments demonstrate an impaired replacement of damaged D1 in the cpftsy mutant, while the chaos and the ffc mutant lacking cpSRP43 and cpSRP54, respectively, were not or hardly affected. The defect in cpftsy was neither caused by an impaired psbA transcript accumulation, D1 translation initiation nor by an enhanced D1 degradation. Further experiments revealed a decreased amount of salt stable, thylakoid membrane-associated translating ribosomes in the cpftsy mutant, while the amount of membrane-associated translating ribosomes is unaltered in the chaos and the ffc mutants. Therefore, our data indicate that the lack of cpFtsY leads to an inefficient PS II repair cycle caused by an impaired binding of translating ribosomes to the thylakoid membrane.
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Affiliation(s)
- Björn Walter
- Molecular Biology of Plant Organelles, Ruhr-University BochumBochum, Germany
| | - Thomas Pieta
- Plant Cell Physiology and Molecular Biology, Ruhr-University BochumBochum, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Ruhr-University BochumBochum, Germany
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Endo T, Uebayashi N, Ishida S, Ikeuchi M, Sato F. Light energy allocation at PSII under field light conditions: how much energy is lost in NPQ-associated dissipation? PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 81:115-120. [PMID: 24726274 DOI: 10.1016/j.plaphy.2014.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 03/18/2014] [Indexed: 06/03/2023]
Abstract
In the field, plants are exposed to fluctuating light, where photosynthesis occurs under conditions far from a steady state. Excess energy dissipation associated with energy quenching of chlorophyll fluorescence (qE) functions as an efficient photo-protection mechanism in photosystem II. PsbS is an important regulator of qE, especially for the induction phase of qE. Beside the regulatory energy dissipation, some part of energy is lost through relaxation of excited chlorophyll molecules. To date, several models to quantify energy loss through these dissipative pathways in PSII have been proposed. In this short review, we compare and evaluate these models for PSII energy allocation when they are applied to non-steady state photosynthesis. As a case study, an investigation on energy allocation to qE-associated dissipation at PSII under non-steady state photosynthesis using PsbS-deficient rice transformants is introduced. Diurnal and seasonal changes in PSII energy allocation in rice under natural light are also presented. Future perspective of studies on PSII energy allocation is discussed.
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Affiliation(s)
- Tsuyoshi Endo
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
| | - Nozomu Uebayashi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Satoshi Ishida
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Masahiro Ikeuchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Fumihiko Sato
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
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Rühle T, Razeghi JA, Vamvaka E, Viola S, Gandini C, Kleine T, Schünemann D, Barbato R, Jahns P, Leister D. The Arabidopsis protein CONSERVED ONLY IN THE GREEN LINEAGE160 promotes the assembly of the membranous part of the chloroplast ATP synthase. PLANT PHYSIOLOGY 2014; 165:207-26. [PMID: 24664203 PMCID: PMC4012581 DOI: 10.1104/pp.114.237883] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 03/23/2014] [Indexed: 05/18/2023]
Abstract
The chloroplast F1Fo-ATP synthase/ATPase (cpATPase) couples ATP synthesis to the light-driven electrochemical proton gradient. The cpATPase is a multiprotein complex and consists of a membrane-spanning protein channel (comprising subunit types a, b, b', and c) and a peripheral domain (subunits α, β, γ, δ, and ε). We report the characterization of the Arabidopsis (Arabidopsis thaliana) CONSERVED ONLY IN THE GREEN LINEAGE160 (AtCGL160) protein (AtCGL160), conserved in green algae and plants. AtCGL160 is an integral thylakoid protein, and its carboxyl-terminal portion is distantly related to prokaryotic ATP SYNTHASE PROTEIN1 (Atp1/UncI) proteins that are thought to function in ATP synthase assembly. Plants without AtCGL160 display an increase in xanthophyll cycle activity and energy-dependent nonphotochemical quenching. These photosynthetic perturbations can be attributed to a severe reduction in cpATPase levels that result in increased acidification of the thylakoid lumen. AtCGL160 is not an integral cpATPase component but is specifically required for the efficient incorporation of the c-subunit into the cpATPase. AtCGL160, as well as a chimeric protein containing the amino-terminal part of AtCGL160 and Synechocystis sp. PCC6803 Atp1, physically interact with the c-subunit. We conclude that AtCGL160 and Atp1 facilitate the assembly of the membranous part of the cpATPase in their hosts, but loss of their functions provokes a unique compensatory response in each organism.
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Abstract
Overall translational machinery in plastids is similar to that of E. coli. Initiation is the crucial step for translation and this step in plastids is somewhat different from that of E. coli. Unlike the Shine-Dalgarno sequence in E. coli, cis-elements for translation initiation are not well conserved in plastid mRNAs. Specific trans-acting factors are generally required for translation initiation and its regulation in plastids. During translation elongation, ribosomes pause sometimes on photosynthesis-related mRNAs due probably to proper insertion of nascent polypeptides into membrane complexes. Codon usage of plastid mRNAs is different from that of E. coli and mammalian cells. Plastid mRNAs do not have the so-called rare codons. Translation efficiencies of several synonymous codons are not always correlated with codon usage in plastid mRNAs.
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Krokida A, Delis C, Geisler K, Garagounis C, Tsikou D, Peña-Rodríguez LM, Katsarou D, Field B, Osbourn AE, Papadopoulou KK. A metabolic gene cluster in Lotus japonicus discloses novel enzyme functions and products in triterpene biosynthesis. THE NEW PHYTOLOGIST 2013; 200:675-690. [PMID: 23909862 DOI: 10.1111/nph.12414] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/20/2013] [Indexed: 05/03/2023]
Abstract
Genes for triterpene biosynthetic pathways exist as metabolic gene clusters in oat and Arabidopsis thaliana plants. We characterized the presence of an analogous gene cluster in the model legume Lotus japonicus. In the genomic regions flanking the oxidosqualene cyclase AMY2 gene, genes for two different classes of cytochrome P450 and a gene predicted to encode a reductase were identified. Functional characterization of the cluster genes was pursued by heterologous expression in Nicotiana benthamiana. The gene expression pattern was studied under different developmental and environmental conditions. The physiological role of the gene cluster in nodulation and plant development was studied in knockdown experiments. A novel triterpene structure, dihydrolupeol, was produced by AMY2. A new plant cytochrome P450, CYP71D353, which catalyses the formation of 20-hydroxybetulinic acid in a sequential three-step oxidation of 20-hydroxylupeol was characterized. The genes within the cluster are highly co-expressed during root and nodule development, in hormone-treated plants and under various environmental stresses. A transcriptional gene silencing mechanism that appears to be involved in the regulation of the cluster genes was also revealed. A tightly co-regulated cluster of functionally related genes is involved in legume triterpene biosynthesis, with a possible role in plant development.
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Affiliation(s)
- Afrodite Krokida
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Costas Delis
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Katrin Geisler
- Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Constantine Garagounis
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Daniela Tsikou
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Luis M Peña-Rodríguez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Dimitra Katsarou
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Ben Field
- Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Anne E Osbourn
- Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Kalliope K Papadopoulou
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
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Berry JO, Yerramsetty P, Zielinski AM, Mure CM. Photosynthetic gene expression in higher plants. PHOTOSYNTHESIS RESEARCH 2013; 117:91-120. [PMID: 23839301 DOI: 10.1007/s11120-013-9880-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/26/2013] [Indexed: 05/08/2023]
Abstract
Within the chloroplasts of higher plants and algae, photosynthesis converts light into biological energy, fueling the assimilation of atmospheric carbon dioxide into biologically useful molecules. Two major steps, photosynthetic electron transport and the Calvin-Benson cycle, require many gene products encoded from chloroplast as well as nuclear genomes. The expression of genes in both cellular compartments is highly dynamic and influenced by a diverse range of factors. Light is the primary environmental determinant of photosynthetic gene expression. Working through photoreceptors such as phytochrome, light regulates photosynthetic genes at transcriptional and posttranscriptional levels. Other processes that affect photosynthetic gene expression include photosynthetic activity, development, and biotic and abiotic stress. Anterograde (from nucleus to chloroplast) and retrograde (from chloroplast to nucleus) signaling insures the highly coordinated expression of the many photosynthetic genes between these different compartments. Anterograde signaling incorporates nuclear-encoded transcriptional and posttranscriptional regulators, such as sigma factors and RNA-binding proteins, respectively. Retrograde signaling utilizes photosynthetic processes such as photosynthetic electron transport and redox signaling to influence the expression of photosynthetic genes in the nucleus. The basic C3 photosynthetic pathway serves as the default form used by most of the plant species on earth. High temperature and water stress associated with arid environments have led to the development of specialized C4 and CAM photosynthesis, which evolved as modifications of the basic default expression program. The goal of this article is to explain and summarize the many gene expression and regulatory processes that work together to support photosynthetic function in plants.
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Affiliation(s)
- James O Berry
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA,
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Xia S, Cheng YT, Huang S, Win J, Soards A, Jinn TL, Jones JD, Kamoun S, Chen S, Zhang Y, Li X. Regulation of transcription of nucleotide-binding leucine-rich repeat-encoding genes SNC1 and RPP4 via H3K4 trimethylation. PLANT PHYSIOLOGY 2013; 162:1694-705. [PMID: 23690534 PMCID: PMC3707539 DOI: 10.1104/pp.113.214551] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Plant nucleotide-binding leucine-rich repeat (NB-LRR) proteins serve as intracellular sensors to detect pathogen effectors and trigger immune responses. Transcription of the NB-LRR-encoding Resistance (R) genes needs to be tightly controlled to avoid inappropriate defense activation. How the expression of the NB-LRR R genes is regulated is poorly understood. The Arabidopsis (Arabidopsis thaliana) suppressor of npr1-1, constitutive 1 (snc1) mutant carries a gain-of-function mutation in a Toll/Interleukin1 receptor-like (TIR)-NB-LRR-encoding gene, resulting in the constitutive activation of plant defense responses. A snc1 suppressor screen identified modifier of snc1,9 (mos9), which partially suppresses the autoimmune phenotypes of snc1. Positional cloning revealed that MOS9 encodes a plant-specific protein of unknown function. Expression analysis showed that MOS9 is required for the full expression of TIR-NB-LRR protein-encoding RECOGNITION OF PERONOSPORA PARASITICA 4 (RPP4) and SNC1, both of which reside in the RPP4 cluster. Coimmunoprecipitation and mass spectrometry analyses revealed that MOS9 associates with the Set1 class lysine 4 of histone 3 (H3K4) methyltransferase Arabidopsis Trithorax-Related7 (ATXR7). Like MOS9, ATXR7 is also required for the full expression of SNC1 and the autoimmune phenotypes in the snc1 mutant. In atxr7 mutant plants, the expression of RPP4 is similarly reduced, and resistance against Hyaloperonospora arabidopsidis Emwa1 is compromised. Consistent with the attenuated expression of SNC1 and RPP4, trimethylated H3K4 marks are reduced around the promoters of SNC1 and RPP4 in mos9 plants. Our data suggest that MOS9 functions together with ATXR7 to regulate the expression of SNC1 and RPP4 through H3K4 methylation, which plays an important role in fine-tuning their transcription levels and functions in plant defense.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Xin Li
- Corresponding author; e-mail
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