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Nellaepalli S, Lau AS, Jarvis RP. Chloroplast protein translocation pathways and ubiquitin-dependent regulation at a glance. J Cell Sci 2023; 136:jcs241125. [PMID: 37732520 PMCID: PMC10546890 DOI: 10.1242/jcs.241125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023] Open
Abstract
Chloroplasts conduct photosynthesis and numerous metabolic and signalling processes that enable plant growth and development. Most of the ∼3000 proteins in chloroplasts are nucleus encoded and must be imported from the cytosol. Thus, the protein import machinery of the organelle (the TOC-TIC apparatus) is of fundamental importance for chloroplast biogenesis and operation. Cytosolic factors target chloroplast precursor proteins to the TOC-TIC apparatus, which drives protein import across the envelope membranes into the organelle, before various internal systems mediate downstream routing to different suborganellar compartments. The protein import system is proteolytically regulated by the ubiquitin-proteasome system (UPS), enabling centralized control over the organellar proteome. In addition, the UPS targets a range of chloroplast proteins directly. In this Cell Science at a Glance article and the accompanying poster, we present mechanistic details of these different chloroplast protein targeting and translocation events, and of the UPS systems that regulate chloroplast proteins.
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Affiliation(s)
- Sreedhar Nellaepalli
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Anne Sophie Lau
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
- Department of Plant Physiology, Faculty of Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - R. Paul Jarvis
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
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2
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Wan C, Zhang H, Cheng H, Sowden RG, Cai W, Jarvis RP, Ling Q. Selective autophagy regulates chloroplast protein import and promotes plant stress tolerance. EMBO J 2023; 42:e112534. [PMID: 37248861 PMCID: PMC10350842 DOI: 10.15252/embj.2022112534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 03/26/2023] [Accepted: 05/09/2023] [Indexed: 05/31/2023] Open
Abstract
Chloroplasts are plant organelles responsible for photosynthesis and environmental sensing. Most chloroplast proteins are imported from the cytosol through the translocon at the outer envelope membrane of chloroplasts (TOC). Previous work has shown that TOC components are regulated by the ubiquitin-proteasome system (UPS) to control the chloroplast proteome, which is crucial for the organelle's function and plant development. Here, we demonstrate that the TOC apparatus is also subject to K63-linked polyubiquitination and regulation by selective autophagy, potentially promoting plant stress tolerance. We identify NBR1 as a selective autophagy adaptor targeting TOC components, and mediating their relocation into vacuoles for autophagic degradation. Such selective autophagy is shown to control TOC protein levels and chloroplast protein import and to influence photosynthetic activity as well as tolerance to UV-B irradiation and heat stress in Arabidopsis plants. These findings uncover the vital role of selective autophagy in the proteolytic regulation of specific chloroplast proteins, and how dynamic control of chloroplast protein import is critically important for plants to cope with challenging environments.
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Affiliation(s)
- Chen Wan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hui Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
| | - Hongying Cheng
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Robert G Sowden
- Department of Plant Sciences and Section of Molecular Plant Biology (Department of Biology)University of OxfordOxfordUK
| | - Wenjuan Cai
- Core Facility Center, CAS Centre for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - R Paul Jarvis
- Department of Plant Sciences and Section of Molecular Plant Biology (Department of Biology)University of OxfordOxfordUK
| | - Qihua Ling
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- CAS‐JIC Center of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
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3
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UPL5 modulates WHY2 protein distribution in a Kub-site dependent ubiquitination in response to [Ca2+]cyt-induced leaf senescence. iScience 2023; 26:106216. [PMID: 36994183 PMCID: PMC10040967 DOI: 10.1016/j.isci.2023.106216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/08/2023] [Accepted: 02/13/2023] [Indexed: 03/08/2023] Open
Abstract
The translocation of proteins between various compartments of cells is the simplest and most direct way of an/retrograde communication. However, the mechanism of protein trafficking is far understood. In this study, we showed that the alteration of WHY2 protein abundance in various compartments of cells was dependent on a HECT-type ubiquitin E3 ligase UPL5 interacting with WHY2 in the cytoplasm, plastid, and nucleus, as well as mitochondrion to selectively ubiquitinate various Kub-sites (Kub 45 and Kub 227) of WHY2. Plastid genome stability can be maintained by the UPL5-WHY2 module, accompany by the alteration of photosystem activity and senescence-associated gene expression. In addition, the specificity of UPL5 ubiquitinating various Kub-sites of WHY2 was responded to cold or CaCl2 stress, in a dose [Ca2+]cyt-dependent manner. This demonstrates the integration of the UPL5 ubiquitination with the regulation of WHY2 distribution and retrograde communication between organelle and nuclear events of leaf senescence.
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Sun Y, Li J, Zhang L, Lin R. Regulation of chloroplast protein degradation. J Genet Genomics 2023:S1673-8527(23)00049-8. [PMID: 36863685 DOI: 10.1016/j.jgg.2023.02.010] [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: 12/24/2022] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 03/04/2023]
Abstract
Chloroplasts are unique organelles that not only provide sites for photosynthesis and many metabolic processes, but also are sensitive to various environmental stresses. Chloroplast proteins are encoded by genes from both nuclear and chloroplast genomes. During chloroplast development and responses to stresses, the robust protein quality control systems are essential for regulation of protein homeostasis and the integrity of chloroplast proteome. In this review, we summarize the regulatory mechanisms of chloroplast protein degradation refer to protease system, ubiquitin-proteasome system, and the chloroplast autophagy. These mechanisms symbiotically play a vital role in chloroplast development and photosynthesis under both normal or stress conditions.
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Affiliation(s)
- Yang Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan 475001, China
| | - Jialong Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lixin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan 475001, China.
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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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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Sun Y, Yao Z, Ye Y, Fang J, Chen H, Lyu Y, Broad W, Fournier M, Chen G, Hu Y, Mohammed S, Ling Q, Jarvis RP. Ubiquitin-based pathway acts inside chloroplasts to regulate photosynthesis. SCIENCE ADVANCES 2022; 8:eabq7352. [PMID: 36383657 PMCID: PMC9668298 DOI: 10.1126/sciadv.abq7352] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Photosynthesis is the energetic basis for most life on Earth, and in plants it operates inside double membrane-bound organelles called chloroplasts. The photosynthetic apparatus comprises numerous proteins encoded by the nuclear and organellar genomes. Maintenance of this apparatus requires the action of internal chloroplast proteases, but a role for the nucleocytosolic ubiquitin-proteasome system (UPS) was not expected, owing to the barrier presented by the double-membrane envelope. Here, we show that photosynthesis proteins (including those encoded internally by chloroplast genes) are ubiquitinated and processed via the CHLORAD pathway: They are degraded by the 26S proteasome following CDC48-dependent retrotranslocation to the cytosol. This demonstrates that the reach of the UPS extends to the interior of endosymbiotically derived chloroplasts, where it acts to regulate photosynthesis, arguably the most fundamental process of life.
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Affiliation(s)
- Yi Sun
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Zujie Yao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yiting Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Fang
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Honglin Chen
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Yuping Lyu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - William Broad
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Marjorie Fournier
- Advanced Proteomics Facility, University of Oxford, Oxford OX1 3QU, UK
| | - Genyun Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yonghong Hu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
- Rosalind Franklin Institute, Oxfordshire OX11 0FA, UK
| | - Qihua Ling
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS-JIC Center of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Corresponding author. (Q.L.); (R.P.J.)
| | - R. Paul Jarvis
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
- Corresponding author. (Q.L.); (R.P.J.)
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7
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Chloroplasts Protein Quality Control and Turnover: A Multitude of Mechanisms. Int J Mol Sci 2022; 23:ijms23147760. [PMID: 35887108 PMCID: PMC9319218 DOI: 10.3390/ijms23147760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
As the organelle of photosynthesis and other important metabolic pathways, chloroplasts contain up to 70% of leaf proteins with uniquely complex processes in synthesis, import, assembly, and turnover. Maintaining functional protein homeostasis in chloroplasts is vitally important for the fitness and survival of plants. Research over the past several decades has revealed a multitude of mechanisms that play important roles in chloroplast protein quality control and turnover under normal and stress conditions. These mechanisms include: (i) endosymbiotically-derived proteases and associated proteins that play a vital role in maintaining protein homeostasis inside the chloroplasts, (ii) the ubiquitin-dependent turnover of unimported chloroplast precursor proteins to prevent their accumulation in the cytosol, (iii) chloroplast-associated degradation of the chloroplast outer-membrane translocon proteins for the regulation of chloroplast protein import, (iv) chloroplast unfolded protein response triggered by accumulated unfolded and misfolded proteins inside the chloroplasts, and (v) vesicle-mediated degradation of chloroplast components in the vacuole. Here, we provide a comprehensive review of these diverse mechanisms of chloroplast protein quality control and turnover and discuss important questions that remain to be addressed in order to better understand and improve important chloroplast functions.
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A proteostasis network safeguards the chloroplast proteome. Essays Biochem 2022; 66:219-228. [PMID: 35670042 PMCID: PMC9400067 DOI: 10.1042/ebc20210058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 12/12/2022]
Abstract
Several protein homeostasis (proteostasis) pathways safeguard the integrity of thousands of proteins that localize in plant chloroplasts, the indispensable organelles that perform photosynthesis, produce metabolites, and sense environmental stimuli. In this review, we discuss the latest efforts directed to define the molecular process by which proteins are imported and sorted into the chloroplast. Moreover, we describe the recently elucidated protein folding and degradation pathways that modulate the levels and activities of chloroplast proteins. We also discuss the links between the accumulation of misfolded proteins and the activation of signalling pathways that cope with folding stress within the organelle. Finally, we propose new research directions that would help to elucidate novel molecular mechanisms to maintain chloroplast proteostasis.
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9
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Barth MA, Soll J, Akbaş Ş. Prokaryotic and eukaryotic traits support the biological role of the chloroplast outer envelope. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119224. [PMID: 35120999 DOI: 10.1016/j.bbamcr.2022.119224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/22/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
The plastid outer envelope (OE) is a mixture of components inherited from their prokaryotic ancestor like galactolipids, carotenoids and porin type ion channels supplemented with eukaryotic inventions to make the endosymbiotic process successful as well as to control plastid biogenesis and differentiation. In this review we wanted to highlight the importance of the OE proteins and its evolutionary origin. For a long time, the OE was thought to be a diffusion barrier only, but with the recent discoveries of all kinds of different proteins in the OE it has been shown that the OE can modulate various functions within the cell. The phenotypic changes show that channels like the outer envelope proteins OEP40, OEP16 or JASSY have a pronounced ion selectivity that cannot be replaced by other ion channels present in the OE. Eukaryotic additions, like the GTPase receptors Toc33 and Toc159 or the ubiquitin proteasome system for chloroplast protein quality control, round up the profile of the OE.
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Affiliation(s)
- Melanie Anette Barth
- Department Biologie 1, Botanik, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Jürgen Soll
- Department Biologie 1, Botanik, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany.
| | - Şebnem Akbaş
- Department Biologie 1, Botanik, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
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10
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Watson SJ, Li N, Ye Y, Wu F, Ling Q, Jarvis RP. Crosstalk between the chloroplast protein import and SUMO systems revealed through genetic and molecular investigation in Arabidopsis. eLife 2021; 10:60960. [PMID: 34473053 PMCID: PMC8497055 DOI: 10.7554/elife.60960] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/01/2021] [Indexed: 11/19/2022] Open
Abstract
The chloroplast proteome contains thousands of different proteins that are encoded by the nuclear genome. These proteins are imported into the chloroplast via the action of the TOC translocase and associated downstream systems. Our recent work has revealed that the stability of the TOC complex is dynamically regulated by the ubiquitin-dependent chloroplast-associated protein degradation pathway. Here, we demonstrate that the TOC complex is also regulated by the small ubiquitin-like modifier (SUMO) system. Arabidopsis mutants representing almost the entire SUMO conjugation pathway can partially suppress the phenotype of ppi1, a pale-yellow mutant lacking the Toc33 protein. This suppression is linked to increased abundance of TOC proteins and improvements in chloroplast development. Moreover, data from molecular and biochemical experiments support a model in which the SUMO system directly regulates TOC protein stability. Thus, we have identified a regulatory link between the SUMO system and the chloroplast protein import machinery. All green plants grow by converting light energy into chemical energy. They do this using a process called photosynthesis, which happens inside compartments in plant cells called chloroplasts. Chloroplasts use thousands of different proteins to make chemical energy. Some of these proteins allow the chloroplasts to absorb light energy using chlorophyll, the pigment that makes leaves green. The vast majority of these proteins are transported into the chloroplasts through a protein machine called the TOC complex. When plants lack parts of the TOC complex, their chloroplasts develop abnormally, and their leaves turn yellow. Photosynthesis can make toxic by-products, so cells need a way to turn it off when they are under stress; for example, by lowering the number of TOC complexes on the chloroplasts. This is achieved by tagging TOC complexes with a molecule called ubiquitin, which will lead to their removal from chloroplasts, slowing photosynthesis down. It is unknown whether another, similar, molecular tag called SUMO aids in this destruction process. To find out, Watson et al. examined a mutant of the plant Arabidopsis thaliana. This mutant had low levels of the TOC complex, turning its leaves pale yellow. A combination of genetic, molecular, and biochemical experiments showed that SUMO molecular tags control the levels of TOC complex on chloroplasts. Increasing the amount of SUMO in the mutant plants made their leaves turn yellower, while interfering with the genes responsible for depositing SUMO tags turned the leaves green. This implies that in plants with less SUMO tags, cells stopped destroying their TOC complexes, allowing the chloroplasts to develop better, and changing the colour of the leaves. The SUMO tagging of TOC complexes shares a lot of genetic similarities with the ubiquitin tag system. It is possible that SUMO tags may help to control the CHLORAD pathway, which destroys TOC complexes marked with ubiquitin. Understanding this relationship, and how to influence it, could help to improve the performance of crops. The next step is to understand exactly how SUMO tags promote the destruction of the TOC complex.
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Affiliation(s)
| | - Na Li
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Yiting Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Feijie Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Department of Biology, University of Leicester, Leicester, United Kingdom
| | - Qihua Ling
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom.,National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Department of Biology, University of Leicester, Leicester, United Kingdom
| | - R Paul Jarvis
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom.,Department of Biology, University of Leicester, Leicester, United Kingdom
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11
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Ivanova A, Ghifari AS, Berkowitz O, Whelan J, Murcha MW. The mitochondrial AAA protease FTSH3 regulates Complex I abundance by promoting its disassembly. PLANT PHYSIOLOGY 2021; 186:599-610. [PMID: 33616659 PMCID: PMC8154063 DOI: 10.1093/plphys/kiab074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/28/2021] [Indexed: 06/02/2023]
Abstract
ATP is generated in mitochondria by oxidative phosphorylation. Complex I (NADH:ubiquinone oxidoreductase or NADH dehydrogenase) is the first multisubunit protein complex of this pathway, oxidizing NADH and transferring electrons to the ubiquinone pool. Typically, Complex I mutants display a slow growth rate compared to wild-type plants. Here, using a forward genetic screen approach for restored growth of a Complex I mutant, we have identified the mitochondrial ATP-dependent metalloprotease, Filamentous Temperature Sensitive H 3 (FTSH3), as a factor that is required for the disassembly of Complex I. An ethyl methanesulfonate-induced mutation in FTSH3, named as rmb1 (restoration of mitochondrial biogenesis 1), restored Complex I abundance and plant growth. Complementation could be achieved with FTSH3 lacking proteolytic activity, suggesting the unfoldase function of FTSH3 has a role in Complex I disassembly. The introduction of the rmb1 to an additional, independent, and extensively characterized Complex I mutant, ndufs4, resulted in similar increases to Complex I abundance and a partial restoration of growth. These results show that disassembly or degradation of Complex I plays a role in determining its steady-state abundance and thus turnover may vary under different conditions.
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Affiliation(s)
- Aneta Ivanova
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Abi S Ghifari
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, School of Life Science, The ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora 3086, Vic, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, School of Life Science, The ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora 3086, Vic, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
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12
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Mielke K, Wagner R, Mishra LS, Demir F, Perrar A, Huesgen PF, Funk C. Abundance of metalloprotease FtsH12 modulates chloroplast development in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3455-3473. [PMID: 33216923 PMCID: PMC8042743 DOI: 10.1093/jxb/eraa550] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/19/2020] [Indexed: 05/11/2023]
Abstract
The ATP-dependent metalloprotease FtsH12 (filamentation temperature sensitive protein H 12) has been suggested to participate in a heteromeric motor complex, driving protein translocation into the chloroplast. FtsH12 was immuno-detected in proplastids, seedlings, leaves, and roots. Expression of Myc-tagged FtsH12 under its native promotor allowed identification of FtsHi1, 2, 4, and 5, and plastidic NAD-malate dehydrogenase, five of the six interaction partners in the suggested import motor complex. Arabidopsis thaliana mutant seedlings with reduced FTSH12 abundance exhibited pale cotyledons and small, deformed chloroplasts with altered thylakoid structure. Mature plants retained these chloroplast defects, resulting in slightly variegated leaves and lower chlorophyll content. Label-free proteomics revealed strong changes in the proteome composition of FTSH12 knock-down seedlings, reflecting impaired plastid development. The composition of the translocon on the inner chloroplast membrane (TIC) protein import complex was altered, with coordinated reduction of the FtsH12-FtsHi complex subunits and accumulation of the 1 MDa TIC complex subunits TIC56, TIC214 and TIC22-III. FTSH12 overexpressor lines showed no obvious phenotype, but still displayed distinct differences in their proteome. N-terminome analyses further demonstrated normal proteolytic maturation of plastid-imported proteins irrespective of FTSH12 abundance. Together, our data suggest that FtsH12 has highest impact during seedling development; its abundance alters the plastid import machinery and impairs chloroplast development.
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Affiliation(s)
- Kati Mielke
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Raik Wagner
- Department of Chemistry, Umeå University, Umeå, Sweden
| | | | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, Jülich, Germany
| | - Andreas Perrar
- Central Institute for Engineering, Electronics and Analytics, Jülich, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, Jülich, Germany
- CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
- Institute of Biochemistry, University of Cologne, Cologne, Germany
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13
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Rödiger A, Agne B, Dobritzsch D, Helm S, Müller F, Pötzsch N, Baginsky S. Chromoplast differentiation in bell pepper (Capsicum annuum) fruits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1431-1442. [PMID: 33258209 DOI: 10.1111/tpj.15104] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 05/21/2023]
Abstract
We report here a detailed analysis of the proteome adjustments that accompany chromoplast differentiation from chloroplasts during bell pepper (Capsicum annuum) fruit ripening. While the two photosystems are disassembled and their constituents degraded, the cytochrome b6 f complex, the ATPase complex, and Calvin cycle enzymes are maintained at high levels up to fully mature chromoplasts. This is also true for ferredoxin (Fd) and Fd-dependent NADP reductase, suggesting that ferredoxin retains a central role in the chromoplasts' redox metabolism. There is a significant increase in the amount of enzymes of the typical metabolism of heterotrophic plastids, such as the oxidative pentose phosphate pathway (OPPP) and amino acid and fatty acid biosynthesis. Enzymes of chlorophyll catabolism and carotenoid biosynthesis increase in abundance, supporting the pigment reorganization that goes together with chromoplast differentiation. The majority of plastid encoded proteins decline but constituents of the plastid ribosome and AccD increase in abundance. Furthermore, the amount of plastid terminal oxidase (PTOX) remains unchanged despite a significant increase in phytoene desaturase (PDS) levels, suggesting that the electrons from phytoene desaturation are consumed by another oxidase. This may be a particularity of non-climacteric fruits such as bell pepper that lack a respiratory burst at the onset of fruit ripening.
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Affiliation(s)
- Anja Rödiger
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
- Biochemistry of Plants, Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Birgit Agne
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
- Biochemistry of Plants, Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Dirk Dobritzsch
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Stefan Helm
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Fränze Müller
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
- Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Nina Pötzsch
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Sacha Baginsky
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
- Biochemistry of Plants, Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
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14
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The Arabidopsis NOT4A E3 ligase promotes PGR3 expression and regulates chloroplast translation. Nat Commun 2021; 12:251. [PMID: 33431870 PMCID: PMC7801604 DOI: 10.1038/s41467-020-20506-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022] Open
Abstract
Chloroplast function requires the coordinated action of nuclear- and chloroplast-derived proteins, including several hundred nuclear-encoded pentatricopeptide repeat (PPR) proteins that regulate plastid mRNA metabolism. Despite their large number and importance, regulatory mechanisms controlling PPR expression are poorly understood. Here we show that the Arabidopsis NOT4A ubiquitin-ligase positively regulates the expression of PROTON GRADIENT REGULATION 3 (PGR3), a PPR protein required for translating several thylakoid-localised photosynthetic components and ribosome subunits within chloroplasts. Loss of NOT4A function leads to a strong depletion of cytochrome b6f and NAD(P)H dehydrogenase (NDH) complexes, as well as plastid 30 S ribosomes, which reduces mRNA translation and photosynthetic capacity, causing pale-yellow and slow-growth phenotypes. Quantitative transcriptome and proteome analysis of the not4a mutant reveal it lacks PGR3 expression, and that its molecular defects resemble those of a pgr3 mutant. Furthermore, we show that normal plastid function is restored to not4a through transgenic PGR3 expression. Our work identifies NOT4A as crucial for ensuring robust photosynthetic function during development and stress-response, through promoting PGR3 production and chloroplast translation.
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15
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Ubiquitination of phytoene synthase 1 precursor modulates carotenoid biosynthesis in tomato. Commun Biol 2020; 3:730. [PMID: 33273697 PMCID: PMC7713427 DOI: 10.1038/s42003-020-01474-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/10/2020] [Indexed: 12/31/2022] Open
Abstract
Carotenoids are natural pigments that are indispensable to plants and humans, whereas the regulation of carotenoid biosynthesis by post-translational modification remains elusive. Here, we show that a tomato E3 ubiquitin ligase, Plastid Protein Sensing RING E3 ligase 1 (PPSR1), is responsible for the regulation of carotenoid biosynthesis. PPSR1 exhibits self-ubiquitination activity and loss of PPSR1 function leads to an increase in carotenoids in tomato fruit. PPSR1 affects the abundance of 288 proteins, including phytoene synthase 1 (PSY1), the key rate-limiting enzyme in the carotenoid biosynthetic pathway. PSY1 contains two ubiquitinated lysine residues (Lys380 and Lys406) as revealed by the global analysis and characterization of protein ubiquitination. We provide evidence that PPSR1 interacts with PSY1 precursor protein and mediates its degradation via ubiquitination, thereby affecting the steady-state level of PSY1 protein. Our findings not only uncover a regulatory mechanism for controlling carotenoid biosynthesis, but also provide a strategy for developing carotenoid-enriched horticultural crops. Wang et al. report on the role of a novel E3 ubiquitin ligase, Plastid Protein Sensing RING E3 ligase 1 (PPSR1), during tomato fruit ripening and find that it interacts with phytoene synthase 1 (PSY1) precursor protein and mediates its degradation via ubiquitination. This affects the steady-state level of PSY1 protein, the key rate-limiting enzyme in the carotenoid biosynthetic pathway. This study may provide a strategy for developing carotenoid-enriched horticultural crops.
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16
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Hristou A, Grimmer J, Baginsky S. The Secret Life of Chloroplast Precursor Proteins in the Cytosol. MOLECULAR PLANT 2020; 13:1111-1113. [PMID: 32679264 DOI: 10.1016/j.molp.2020.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 05/11/2023]
Affiliation(s)
- Athina Hristou
- Biochemistry of Plants, Faculty of Biochemistry and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Julia Grimmer
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Charles Tanford Proteinzentrum, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Sacha Baginsky
- Biochemistry of Plants, Faculty of Biochemistry and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801 Bochum, Germany; Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Charles Tanford Proteinzentrum, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany.
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