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Cocco E, Farci D, Guadalupi G, Manconi B, Maxia A, Piano D. The elongation factor 1-alpha as storage reserve and environmental sensor in Nicotiana tabacum L. seeds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 345:112113. [PMID: 38729437 DOI: 10.1016/j.plantsci.2024.112113] [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: 11/25/2023] [Revised: 03/30/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024]
Abstract
Given their critical role in plant reproduction and survival, seeds demand meticulous regulatory mechanisms to effectively store and mobilize reserves. Within seeds, the condition of storage reserves heavily depends on environmental stimuli and hormonal activation. Unlike non-protein reserves that commonly employ dedicated regulatory proteins for signaling, proteinaceous reserves may show a unique form of 'self-regulation', amplifying efficiency and precision in this process. Proteins rely on stability to carry out their functions. However, in specific physiological contexts, particularly in seed germination, protein instability becomes essential, fulfilling roles from signaling to regulation. In this study, the elongation factor 1-alpha has been identified as a main proteinaceous reserve in Nicotiana tabacum L. seeds and showed peculiar changes in stability based on tested chemical and physical conditions. A detailed biochemical analysis followed these steps to enhance our understanding of these protein attributes. The protein varied its behavior under different conditions of pH, temperature, and salt concentration, exhibiting shifts within physiological ranges. Notably, distinct solubility transitions were observed, with the elongation factor 1-alpha becoming insoluble upon reaching specific thresholds determined by the tested chemical and physical conditions. The findings are discussed within the context of seed signaling in response to environmental conditions during the key transitions of dormancy and germination.
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Affiliation(s)
- Emma Cocco
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari, Viale S. Ignazio da Laconi 13, Cagliari 09123, Italy; Laboratory of Economic and Pharmaceutical Botany, Department of Life and Environmental Sciences, University of Cagliari, Viale S. Ignazio da Laconi 13, Cagliari 09123, Italy
| | - Domenica Farci
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari, Viale S. Ignazio da Laconi 13, Cagliari 09123, Italy; Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Nowoursynowska Str.159, Warsaw 02-776, Poland.
| | - Giulia Guadalupi
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari 09124, Italy
| | - Barbara Manconi
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari 09124, Italy
| | - Andrea Maxia
- Laboratory of Economic and Pharmaceutical Botany, Department of Life and Environmental Sciences, University of Cagliari, Viale S. Ignazio da Laconi 13, Cagliari 09123, Italy
| | - Dario Piano
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari, Viale S. Ignazio da Laconi 13, Cagliari 09123, Italy.
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2
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Sultana F, Ghosh A. Exploring the evolutionary landscape and structural resonances of ferritin with insights into functional significance in plant. Biochimie 2024:S0300-9084(24)00173-1. [PMID: 39047810 DOI: 10.1016/j.biochi.2024.07.014] [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: 04/20/2024] [Revised: 07/04/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
The mineral iron plays a crucial role in facilitating the optimal functioning of numerous biological processes within the cellular environment. These processes involve the transportation of oxygen, energy production, immune system functioning, cognitive abilities, and muscle function. However, it is crucial to note that excessive levels of iron can result in oxidative damage within cells, primarily through Fenton reactions. Iron availability and toxicity present significant challenges that have been addressed through evolution. Ferritin is an essential protein that stores iron and is divided into different subfamilies, including DNA-binding proteins under starvation (Dps), bacterioferritin, and classical ferritin. Ferritin plays a critical role in maintaining cellular balance and protecting against oxidative damage. This study delves into ferritin's evolutionary dynamics across diverse taxa, emphasizing structural features and regulatory mechanisms. Insights into ferritin's evolution and functional diversity are gained through phylogenetic and structural analysis in bacterial Dps, bacterioferritin, and classical ferritin proteins. Additionally, the involvement of ferritin in plant stress responses and development is explored. Analysis of ferritin gene expression across various developmental stages and stress conditions provides insights into its regulatory roles. This comprehensive exploration enhances our understanding of ferritin's significance in plant biology, offering insights into its evolutionary history, structural diversity, and protective mechanisms against oxidative stress.
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Affiliation(s)
- Fahmida Sultana
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh.
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3
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Zhu M, Tang Y, Xie Y, He B, Ding G, Zhou X. Research progress on differentiation and regulation of plant chromoplasts. Mol Biol Rep 2024; 51:810. [PMID: 39001942 DOI: 10.1007/s11033-024-09753-6] [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: 04/11/2024] [Accepted: 06/24/2024] [Indexed: 07/15/2024]
Abstract
Carotenoids, natural tetraterpenoids found abundantly in plants, contribute to the diverse colors of plant non-photosynthetic tissues and provide fragrance through their cleavage products, which also play crucial roles in plant growth and development. Understanding the synthesis, degradation, and storage pathways of carotenoids and identifying regulatory factors represents a significant strategy for enhancing plant quality. Chromoplasts serve as the primary plastids responsible for carotenoid accumulation, and their differentiation is linked to the levels of carotenoids, rendering them a subject of substantial research interest. The differentiation of chromoplasts involves alterations in plastid structure and protein import machinery. Additionally, this process is influenced by factors such as the ORANGE (OR) gene, Clp proteases, xanthophyll esterification, and environmental factors. This review shows the relationship between chromoplast and carotenoid accumulation by presenting recent advances in chromoplast structure, the differentiation process, and key regulatory factors, which can also provide a reference for rational exploitation of chromoplasts to enhance plant quality.
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Affiliation(s)
- Mengyao Zhu
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yunxia Tang
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yiqing Xie
- Institute of Economic Forestry, Fujian Academy of Forestry, Fuzhou, 350012, China
| | - BingBing He
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guochang Ding
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Xingwen Zhou
- College of Architecture and Planning, Fujian University of Technology, Fuzhou, 350118, China.
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4
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Inès D, Courty PE, Wendehenne D, Rosnoblet C. CDC48 in plants and its emerging function in plant immunity. TRENDS IN PLANT SCIENCE 2024; 29:786-798. [PMID: 38218650 DOI: 10.1016/j.tplants.2023.12.013] [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: 09/06/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/15/2024]
Abstract
Protein homeostasis, namely the balance between protein synthesis and degradation, must be finely controlled to ensure cell survival, notably through the ubiquitin-proteasome system (UPS). In all species, including plants, homeostasis is disrupted by biotic and abiotic stresses. A key player in the maintenance of protein balance, the protein CDC48, shows emerging functions in plants, particularly in response to biotic stress. In this review on CDC48 in plants, we detail its highly conserved structure, describe a gene expansion that is only present in Viridiplantae, discuss its various functions and regulations, and finally highlight its recruitment, still not clear, during the plant immune response.
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Affiliation(s)
- Damien Inès
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - David Wendehenne
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - Claire Rosnoblet
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France.
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5
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Jarvis RP, Li J, Lin R, Ling Q, Lyu Y, Sun Y, Yao Z. Reply: Does the polyubiquitination pathway operate inside intact chloroplasts to remove proteins? THE PLANT CELL 2024:koae105. [PMID: 38738499 DOI: 10.1093/plcell/koae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/19/2024] [Indexed: 05/14/2024]
Affiliation(s)
- R Paul Jarvis
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Jialong Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - 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, 200032, China
- CAS-JIC Center of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - 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, 200032, China
| | - Yi Sun
- Section of Molecular Plant Biology, Department of Biology, 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, 200032, China
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6
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Yang M, Chen S, Lim SL, Yang L, Zhong JY, Chan KC, Zhao Z, Wong KB, Wang J, Lim BL. A converged ubiquitin-proteasome pathway for the degradation of TOC and TOM tail-anchored receptors. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1007-1023. [PMID: 38501483 DOI: 10.1111/jipb.13645] [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: 12/06/2023] [Accepted: 02/27/2024] [Indexed: 03/20/2024]
Abstract
In plants, thousands of nucleus-encoded proteins translated in the cytosol are sorted to chloroplasts and mitochondria by binding to specific receptors of the TOC (translocon on the outer chloroplast membrane) and the TOM (translocon on the outer mitochondrial membrane) complexes for import into those organelles. The degradation pathways for these receptors are unclear. Here, we discovered a converged ubiquitin-proteasome pathway for the degradation of Arabidopsis thaliana TOC and TOM tail-anchored receptors. The receptors are ubiquitinated by E3 ligase(s) and pulled from the outer membranes by the AAA+ adenosine triphosphatase CDC48, after which a previously uncharacterized cytosolic protein, transmembrane domain (TMD)-binding protein for tail-anchored outer membrane proteins (TTOP), binds to the exposed TMDs at the C termini of the receptors and CDC48, and delivers these complexes to the 26S proteasome.
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Affiliation(s)
- Meijing Yang
- School of Biological Sciences, University of Hong Kong, Pokfulam, 999077, Hong Kong, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Shuai Chen
- School of Biomedical Engineering, Shenzhen University, Shenzhen, 518060, China
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, 999077, Hong Kong, China
| | - Shey-Li Lim
- School of Biological Sciences, University of Hong Kong, Pokfulam, 999077, Hong Kong, China
| | - Lang Yang
- School of Biological Sciences, University of Hong Kong, Pokfulam, 999077, Hong Kong, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jia Yi Zhong
- School of Biological Sciences, University of Hong Kong, Pokfulam, 999077, Hong Kong, China
| | - Koon Chuen Chan
- School of Biological Sciences, University of Hong Kong, Pokfulam, 999077, Hong Kong, China
| | - Zhizhu Zhao
- School of Biological Sciences, University of Hong Kong, Pokfulam, 999077, Hong Kong, China
| | - Kam-Bo Wong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, 999077, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, 999077, Hong Kong, China
| | - Junqi Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Boon Leong Lim
- School of Biological Sciences, University of Hong Kong, Pokfulam, 999077, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, 999077, Hong Kong, China
- HKU Shenzhen Institute of Research and Innovation, Shenzhen, 518052, China
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7
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van Wijk KJ, Adam Z. Does the polyubiquitination pathway operate inside intact chloroplasts to remove proteins? THE PLANT CELL 2024:koae104. [PMID: 38683741 DOI: 10.1093/plcell/koae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 03/19/2024] [Indexed: 05/02/2024]
Affiliation(s)
- Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14853, USA
| | - Zach Adam
- Faculty of Agriculture, Institute of Plant Sciences, The Hebrew University of Jerusalem, Rehovot 76100, Israel
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8
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Meng C, Peng X, Zhang Y, Pedro GC, Li Y, Zhang Y, Duan Y, Sun X. Transcriptomic profiling of Poa pratensis L. under treatment of various phytohormones. Sci Data 2024; 11:297. [PMID: 38491031 PMCID: PMC10942976 DOI: 10.1038/s41597-024-03119-0] [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: 09/18/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
Poa pratensis L. (Poaceae) is a valuable grass across the north hemisphere, inhabiting diverse environments with wide altitudinal span, where ubiquitous various kinds of stresses. Phytohormones would be helpful to improve tolerance to abiotic and biotic stresses, but the responses of transcriptome regulation of P. pratensis to exogenous phytohormones application remain unclear. In this study, we explored the alteration of plant physiological responses by the application of phytohormones. Aiming to achieve this knowledge, we got full-length transcriptome data 42.76 Gb, of which 74.9% of transcripts were completed. Then used 27 samples representing four treatments conducted at two time points (1 h and 6 h after application) to generate RNA-seq data. 371 and 907 common DEGs were identified in response to four phytohormones application, respectively, these DEGs were involved in "plant hormone signal transduction", "carbon metabolism" and "plant-pathogen interaction". Finally, P. pratensis basic research can gain valuable information regarding the responses to exogenous application of phytohormones in physiological indicators and transcriptional regulations in order to facilitate the development of new cultivars.
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Affiliation(s)
- Chen Meng
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education and School of Life Sciences, Shaanxi Normal University, Xi'an, 710119, PR China
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomei Peng
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Zhang
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Yumeng Li
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanni Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education and School of Life Sciences, Shaanxi Normal University, Xi'an, 710119, PR China
| | - Yuanwen Duan
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Xudong Sun
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, China.
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9
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Yang EJN, Liao PC, Pon L. Mitochondrial protein and organelle quality control-Lessons from budding yeast. IUBMB Life 2024; 76:72-87. [PMID: 37731280 PMCID: PMC10842221 DOI: 10.1002/iub.2783] [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: 06/30/2023] [Accepted: 08/11/2023] [Indexed: 09/22/2023]
Abstract
Mitochondria are essential for normal cellular function and have emerged as key aging determinants. Indeed, defects in mitochondrial function have been linked to cardiovascular, skeletal muscle and neurodegenerative diseases, premature aging, and age-linked diseases. Here, we describe mechanisms for mitochondrial protein and organelle quality control. These surveillance mechanisms mediate repair or degradation of damaged or mistargeted mitochondrial proteins, segregate mitochondria based on their functional state during asymmetric cell division, and modulate cellular fitness, the response to stress, and lifespan control in yeast and other eukaryotes.
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Affiliation(s)
- Emily Jie-Ning Yang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Pin-Chao Liao
- Institute of Molecular Medicine & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan 30013
| | - Liza Pon
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
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10
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Cadena-Ramos AI, De-la-Peña C. Picky eaters: selective autophagy in plant cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:364-384. [PMID: 37864806 DOI: 10.1111/tpj.16508] [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: 07/14/2023] [Revised: 09/21/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]
Abstract
Autophagy, a fundamental cellular process, plays a vital role in maintaining cellular homeostasis by degrading damaged or unnecessary components. While selective autophagy has been extensively studied in animal cells, its significance in plant cells has only recently gained attention. In this review, we delve into the intriguing realm selective autophagy in plants, with specific focus on its involvement in nutrient recycling, organelle turnover, and stress response. Moreover, recent studies have unveiled the interesting interplay between selective autophagy and epigenetic mechanisms in plants, elucidating the significance of epigenetic regulation in modulating autophagy-related gene expression and finely tuning the selective autophagy process in plants. By synthesizing existing knowledge, this review highlights the emerging field of selective autophagy in plant cells, emphasizing its pivotal role in maintaining nutrient homeostasis, facilitating cellular adaptation, and shedding light on the epigenetic regulation that governs these processes. Our comprehensive study provides the way for a deeper understanding of the dynamic control of cellular responses to nutrient availability and stress conditions, opening new avenues for future research in this field of autophagy in plant physiology.
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Affiliation(s)
- Alexis I Cadena-Ramos
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34 Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34 Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
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11
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Zhao Q, Wu J, Lan L, Shahid M, Qasim MU, Yu K, Zhang C, Fan C, Zhou Y. Fine mapping and candidate gene analysis of a major QTL for oil content in the seed of Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:256. [PMID: 38010528 DOI: 10.1007/s00122-023-04501-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/03/2023] [Indexed: 11/29/2023]
Abstract
KEY MESSAGE By integrating QTL fine mapping and transcriptomics, a candidate gene responsible for oil content in rapeseed was identified. The gene is anticipated to primarily function in photosynthesis and photosystem metabolism pathways. Brassica napus is one of the most important oil crops in the world, and enhancing seed oil content is an important goal in its genetic improvement. However, the underlying genetic basis for the important trait remains poorly understood in this crop. We previously identified a major locus, OILA5 responsible for seed oil content on chromosome A5 through genome-wide association study. To better understand the genetics of the QTL, we performed fine mapping of OILA5 with a double haploid population and a BC3F2 segregation population consisting of 6227 individuals. We narrowed down the QTL to an approximate 43 kb region with twelve annotated genes, flanked by markers ZDM389 and ZDM337. To unveil the potential candidate gene responsible for OILA5, we integrated fine mapping data with transcriptome profiling using high and low oil content near-isogenic lines. Among the candidate genes, BnaA05G0439400ZS was identified with high expression levels in both seed and silique tissues. This gene exhibited homology with AT3G09840 in Arabidopsis that was annotated as cell division cycle 48. We designed a site-specific marker based on resequencing data and confirmed its effectiveness in both natural and segregating populations. Our comprehensive results provide valuable genetic information not only enhancing our understanding of the genetic control of seed oil content but also novel germplasm for advancing high seed oil content breeding in B. napus and other oil crops.
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Affiliation(s)
- Qing Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jian Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China.
| | - Lei Lan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Shahid
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Uzair Qasim
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Kaidi Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
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12
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Llamas E, Koyuncu S, Lee HJ, Wehrmann M, Gutierrez-Garcia R, Dunken N, Charura N, Torres-Montilla S, Schlimgen E, Mandel AM, Theile EB, Grossbach J, Wagle P, Lackmann JW, Schermer B, Benzing T, Beyer A, Pulido P, Rodriguez-Concepcion M, Zuccaro A, Vilchez D. In planta expression of human polyQ-expanded huntingtin fragment reveals mechanisms to prevent disease-related protein aggregation. NATURE AGING 2023; 3:1345-1357. [PMID: 37783816 PMCID: PMC10645592 DOI: 10.1038/s43587-023-00502-1] [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: 02/24/2023] [Accepted: 09/01/2023] [Indexed: 10/04/2023]
Abstract
In humans, aggregation of polyglutamine repeat (polyQ) proteins causes disorders such as Huntington's disease. Although plants express hundreds of polyQ-containing proteins, no pathologies arising from polyQ aggregation have been reported. To investigate this phenomenon, we expressed an aggregation-prone fragment of human huntingtin (HTT) with an expanded polyQ stretch (Q69) in Arabidopsis thaliana plants. In contrast to animal models, we find that Arabidopsis sp. suppresses Q69 aggregation through chloroplast proteostasis. Inhibition of chloroplast proteostasis diminishes the capacity of plants to prevent cytosolic Q69 aggregation. Moreover, endogenous polyQ-containing proteins also aggregate on chloroplast dysfunction. We find that Q69 interacts with the chloroplast stromal processing peptidase (SPP). Synthetic Arabidopsis SPP prevents polyQ-expanded HTT aggregation in human cells. Likewise, ectopic SPP expression in Caenorhabditis elegans reduces neuronal Q67 aggregation and subsequent neurotoxicity. Our findings suggest that synthetic plant proteins, such as SPP, hold therapeutic potential for polyQ disorders and other age-related diseases involving protein aggregation.
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Affiliation(s)
- Ernesto Llamas
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Seda Koyuncu
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Hyun Ju Lee
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Markus Wehrmann
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Ricardo Gutierrez-Garcia
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Nick Dunken
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Nyasha Charura
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | | | - Elena Schlimgen
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Amrei M Mandel
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Erik Boelen Theile
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Jan Grossbach
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Prerana Wagle
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Jan-Wilm Lackmann
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Andreas Beyer
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Pablo Pulido
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Alga Zuccaro
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany.
- Institute for Genetics, University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.
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13
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Schwenkert S, Lo WT, Szulc B, Yip CK, Pratt AI, Cusack SA, Brandt B, Leister D, Kunz HH. Probing the physiological role of the plastid outer-envelope membrane using the oemiR plasmid collection. G3 (BETHESDA, MD.) 2023; 13:jkad187. [PMID: 37572358 PMCID: PMC10542568 DOI: 10.1093/g3journal/jkad187] [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: 07/20/2023] [Revised: 07/20/2023] [Accepted: 08/04/2023] [Indexed: 08/14/2023]
Abstract
Plastids are the site of complex biochemical pathways, most prominently photosynthesis. The organelle evolved through endosymbiosis with a cyanobacterium, which is exemplified by the outer envelope membrane that harbors more than 40 proteins in Arabidopsis. Their evolutionary conservation indicates high significance for plant cell function. While a few proteins are well-studied as part of the protein translocon complex the majority of outer envelope protein functions is unclear. Gaining a deeper functional understanding has been complicated by the lack of observable loss-of-function mutant phenotypes, which is often rooted in functional genetic redundancy. Therefore, we designed outer envelope-specific artificial micro RNAs (oemiRs) capable of downregulating transcripts from several loci simultaneously. We successfully tested oemiR function by performing a proof-of-concept screen for pale and cold-sensitive mutants. An in-depth analysis of pale mutant alleles deficient in the translocon component TOC75 using proteomics provided new insights into putative compensatory import pathways. The cold stress screen not only recapitulated 3 previously known phenotypes of cold-sensitive mutants but also identified 4 mutants of additional oemiR outer envelope loci. Altogether our study revealed a role of the outer envelope to tolerate cold conditions and showcasts the power of the oemiR collection to research the significance of outer envelope proteins.
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Affiliation(s)
- Serena Schwenkert
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Wing Tung Lo
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Beata Szulc
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Chun Kwan Yip
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Anna I Pratt
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA
| | | | - Benjamin Brandt
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Hans-Henning Kunz
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA
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14
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Lei P, Yu F, Liu X. Recent advances in cellular degradation and nuclear control of leaf senescence. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5472-5486. [PMID: 37453102 DOI: 10.1093/jxb/erad273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Senescence is the final stage of plant growth and development, and is a highly regulated process at the molecular, cellular, and organismal levels. When triggered by age, hormonal, or environmental cues, plants actively adjust their metabolism and gene expression to execute the progression of senescence. Regulation of senescence is vital for the reallocation of nutrients to sink organs, to ensure reproductive success and adaptations to stresses. Identification and characterization of hallmarks of leaf senescence are of great importance for understanding the molecular regulatory mechanisms of plant senescence, and breeding future crops with more desirable senescence traits. Tremendous progress has been made in elucidating the genetic network underpinning the metabolic and cellular changes in leaf senescence. In this review, we focus on three hallmarks of leaf senescence - chlorophyll and chloroplast degradation, loss of proteostasis, and activation of senescence-associated genes (SAGs), and discuss recent findings of the molecular players and the crosstalk of senescence pathways.
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Affiliation(s)
- Pei Lei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fei Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiayan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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15
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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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16
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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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17
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Luo Q, Wei W, Yang YY, Wu CJ, Chen JY, Lu WJ, Kuang JF, Shan W. E3 ligase MaNIP1 degradation of NON-YELLOW COLORING1 at high temperature inhibits banana degreening. PLANT PHYSIOLOGY 2023; 192:1969-1981. [PMID: 36794407 PMCID: PMC10315274 DOI: 10.1093/plphys/kiad096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/17/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Banana (Musa acuminata) fruit ripening under high temperatures (>24 °C) undergoes green ripening due to failure of chlorophyll degradation, which greatly reduces marketability. However, the mechanism underlying high temperature-repressed chlorophyll catabolism in banana fruit is not yet well understood. Here, using quantitative proteomic analysis, 375 differentially expressed proteins were identified in normal yellow and green ripening in banana. Among these, one of the key enzymes involved in chlorophyll degradation, NON-YELLOW COLORING 1 (MaNYC1), exhibited reduced protein levels when banana fruit ripened under high temperature. Transient overexpression of MaNYC1 in banana peels resulted in chlorophyll degradation under high temperature, which weakens the green ripening phenotype. Importantly, high temperature induced MaNYC1 protein degradation via the proteasome pathway. A banana RING E3 ligase, NYC1-interacting protein 1 (MaNIP1), was found to interact with and ubiquitinate MaNYC1, leading to its proteasomal degradation. Furthermore, transient overexpression of MaNIP1 attenuated MaNYC1-induced chlorophyll degradation in banana fruits, indicating that MaNIP1 negatively regulates chlorophyll catabolism by affecting MaNYC1 degradation. Taken together, the findings establish a post-translational regulatory module of MaNIP1-MaNYC1 that mediates high temperature-induced green ripening in bananas.
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Affiliation(s)
- Qi Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Ying-ying Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Chao-jie Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jian-ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wang-jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jian-fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruit and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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18
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Wang W, Wang Y, Chen T, Qin G, Tian S. Current insights into posttranscriptional regulation of fleshy fruit ripening. PLANT PHYSIOLOGY 2023; 192:1785-1798. [PMID: 36250906 PMCID: PMC10315313 DOI: 10.1093/plphys/kiac483] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/27/2022] [Indexed: 05/26/2023]
Abstract
Fruit ripening is a complicated process that is accompanied by the formation of fruit quality. It is not only regulated at the transcriptional level via transcription factors or DNA methylation but also fine-tuned after transcription occurs. Here, we review recent advances in our understanding of key regulatory mechanisms of fleshy fruit ripening after transcription. We mainly highlight the typical mechanisms by which fruit ripening is controlled, namely, alternative splicing, mRNA N6-methyladenosine RNA modification methylation, and noncoding RNAs at the posttranscriptional level; regulation of translation efficiency and upstream open reading frame-mediated translational repression at the translational level; and histone modifications, protein phosphorylation, and protein ubiquitination at the posttranslational level. Taken together, these posttranscriptional regulatory mechanisms, along with transcriptional regulation, constitute the molecular framework of fruit ripening. We also critically discuss the potential usage of some mechanisms to improve fruit traits.
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Affiliation(s)
- Weihao Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuying Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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19
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van Wijk KJ, Leppert T, Sun Z, Deutsch EW. Does the Ubiquitination Degradation Pathway Really Reach inside of the Chloroplast? A Re-Evaluation of Mass Spectrometry-Based Assignments of Ubiquitination. J Proteome Res 2023. [PMID: 37092802 DOI: 10.1021/acs.jproteome.3c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
A recent paper in Science Advances by Sun et al. claims that intra-chloroplast proteins in the model plant Arabidopsis can be polyubiquitinated and then extracted into the cytosol for subsequent degradation by the proteasome. Most of this conclusion hinges on several sets of mass spectrometry (MS) data. If the proposed results and conclusion are true, this would be a major change in the proteolysis/proteostasis field, breaking the long-standing dogma that there are no polyubiquitination mechanisms within chloroplast organelles (nor in mitochondria). Given its importance, we reanalyzed their raw MS data using both open and closed sequence database searches and encountered many issues not only with the results but also discrepancies between stated methods (e.g., use of alkylating agent iodoacetamide (IAA)) and observed mass modifications. Although there is likely enrichment of ubiquitination signatures in a subset of the data (probably from ubiquitination in the cytosol), we show that runaway alkylation with IAA caused extensive artifactual modifications of N termini and lysines to the point that a large fraction of the desired ubiquitination signatures is indistinguishable from artifactual acetamide signatures, and thus, no intra-chloroplast polyubiquitination conclusions can be drawn from these data. We provide recommendations on how to avoid such perils in future work.
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Affiliation(s)
- Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Tami Leppert
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
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20
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Winckler LI, Dissmeyer N. Molecular determinants of protein half-life in chloroplasts with focus on the Clp protease system. Biol Chem 2023; 404:499-511. [PMID: 36972025 DOI: 10.1515/hsz-2022-0320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/09/2023] [Indexed: 03/29/2023]
Abstract
Abstract
Proteolysis is an essential process to maintain cellular homeostasis. One pathway that mediates selective protein degradation and which is in principle conserved throughout the kingdoms of life is the N-degron pathway, formerly called the ‘N-end rule’. In the cytosol of eukaryotes and prokaryotes, N-terminal residues can be major determinants of protein stability. While the eukaryotic N-degron pathway depends on the ubiquitin proteasome system, the prokaryotic counterpart is driven by the Clp protease system. Plant chloroplasts also contain such a protease network, which suggests that they might harbor an organelle specific N-degron pathway similar to the prokaryotic one. Recent discoveries indicate that the N-terminal region of proteins affects their stability in chloroplasts and provides support for a Clp-mediated entry point in an N-degron pathway in plastids. This review discusses structure, function and specificity of the chloroplast Clp system, outlines experimental approaches to test for an N-degron pathway in chloroplasts, relates these aspects into general plastid proteostasis and highlights the importance of an understanding of plastid protein turnover.
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Affiliation(s)
- Lioba Inken Winckler
- Department of Plant Physiology and Protein Metabolism Laboratory, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
- Center of Cellular Nanoanalytics (CellNanOs), Barbarastrasse 11, D-49076 Osnabruck, Germany
- Faculty of Biology, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
| | - Nico Dissmeyer
- Department of Plant Physiology and Protein Metabolism Laboratory, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
- Center of Cellular Nanoanalytics (CellNanOs), Barbarastrasse 11, D-49076 Osnabruck, Germany
- Faculty of Biology, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
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21
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Christian R, Labbancz J, Usadel B, Dhingra A. Understanding protein import in diverse non-green plastids. Front Genet 2023; 14:969931. [PMID: 37007964 PMCID: PMC10063809 DOI: 10.3389/fgene.2023.969931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/24/2023] [Indexed: 03/19/2023] Open
Abstract
The spectacular diversity of plastids in non-green organs such as flowers, fruits, roots, tubers, and senescing leaves represents a Universe of metabolic processes in higher plants that remain to be completely characterized. The endosymbiosis of the plastid and the subsequent export of the ancestral cyanobacterial genome to the nuclear genome, and adaptation of the plants to all types of environments has resulted in the emergence of diverse and a highly orchestrated metabolism across the plant kingdom that is entirely reliant on a complex protein import and translocation system. The TOC and TIC translocons, critical for importing nuclear-encoded proteins into the plastid stroma, remain poorly resolved, especially in the case of TIC. From the stroma, three core pathways (cpTat, cpSec, and cpSRP) may localize imported proteins to the thylakoid. Non-canonical routes only utilizing TOC also exist for the insertion of many inner and outer membrane proteins, or in the case of some modified proteins, a vesicular import route. Understanding this complex protein import system is further compounded by the highly heterogeneous nature of transit peptides, and the varying transit peptide specificity of plastids depending on species and the developmental and trophic stage of the plant organs. Computational tools provide an increasingly sophisticated means of predicting protein import into highly diverse non-green plastids across higher plants, which need to be validated using proteomics and metabolic approaches. The myriad plastid functions enable higher plants to interact and respond to all kinds of environments. Unraveling the diversity of non-green plastid functions across the higher plants has the potential to provide knowledge that will help in developing climate resilient crops.
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Affiliation(s)
- Ryan Christian
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - June Labbancz
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | | | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
- *Correspondence: Amit Dhingra,
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22
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Li H, Wu S, Lin R, Xiao Y, Malaco Morotti AL, Wang Y, Galilee M, Qin H, Huang T, Zhao Y, Zhou X, Yang J, Zhao Q, Kanellis AK, Martin C, Tatsis EC. The genomes of medicinal skullcaps reveal the polyphyletic origins of clerodane diterpene biosynthesis in the family Lamiaceae. MOLECULAR PLANT 2023; 16:549-570. [PMID: 36639870 DOI: 10.1016/j.molp.2023.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/21/2022] [Accepted: 01/09/2023] [Indexed: 06/09/2023]
Abstract
The presence of anticancer clerodane diterpenoids is a chemotaxonomic marker for the traditional Chinese medicinal plant Scutellaria barbata, although the molecular mechanisms behind clerodane biosynthesis are unknown. Here, we report a high-quality assembly of the 414.98 Mb genome of S. barbata into 13 pseudochromosomes. Using phylogenomic and biochemical data, we mapped the plastidial metabolism of kaurene (gibberellins), abietane, and clerodane diterpenes in three species of the family Lamiaceae (Scutellaria barbata, Scutellaria baicalensis, and Salvia splendens), facilitating the identification of genes involved in the biosynthesis of the clerodanes, kolavenol, and isokolavenol. We show that clerodane biosynthesis evolved through recruitment and neofunctionalization of genes from gibberellin and abietane metabolism. Despite the assumed monophyletic origin of clerodane biosynthesis, which is widespread in species of the Lamiaceae, our data show distinct evolutionary lineages and suggest polyphyletic origins of clerodane biosynthesis in the family Lamiaceae. Our study not only provides significant insights into the evolution of clerodane biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the production of anticancer clerodanes through future metabolic engineering efforts.
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Affiliation(s)
- Haixiu Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Song Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruoxi Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yiren Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ana Luisa Malaco Morotti
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ya Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meytal Galilee
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Haowen Qin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Tao Huang
- Novogene Bioinformatics Institute, Beijing, China
| | - Yong Zhao
- Novogene Bioinformatics Institute, Beijing, China
| | - Xun Zhou
- Novogene Bioinformatics Institute, Beijing, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China
| | - Qing Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China
| | - Angelos K Kanellis
- Group of Biotechnology of Pharmaceutical Plants, Lab. of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | | | - Evangelos C Tatsis
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; CEPAMS - CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Shanghai 200032, China.
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23
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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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24
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Wang Y, Peng M, Zhong Y, Xiong W, Zhu L, Jin X. The E3 ligase RBCK1 reduces the sensitivity of ccRCC to sunitinib through the ANKRD35-MITD1-ANXA1 axis. Oncogene 2023; 42:952-966. [PMID: 36732658 DOI: 10.1038/s41388-023-02613-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023]
Abstract
Despite the promise of targeted tyrosine kinase inhibitors (TKIs), such as sunitinib, in the extension of survival time in patients with clear cell renal cell carcinoma (ccRCC) progression or metastasis, the patients eventually succumb to inevitable drug resistance. Protein degradation executed by the ubiquitin-dependent proteasome system played an important role in determining the sensitivity of ccRCC to sunitinib. Here, we applied the bioinformatic analysis to identify that E3 ligase RBCK1 was elevated in the sunitinib-resistant renal cancer cell lines or patient specimens. The subsequent in vitro or in vivo studies demonstrated that RBCK1 contributed to decreasing the sensitivity of ccRCC to sunitinib. Then, we showed that inhibition of RBCK1 inactivated the AKT and MAPK signaling pathways, which might be one of the main reasons why RBCK1 induces sunitinib resistance in ccRCC cells. Mechanistically, our results indicated that RBCK1 promotes the degradation of ANKRD35 and that ANKRD35 destabilizes MITD1 by binding with SUMO2 in ccRCC cells. In addition, we showed that the RBCK1-ANKRD35-MITD1-ANXA1 axis regulates the phosphorylation of AKT and ERK and contributes to the dysregulation of sunitinib in ccRCC cells. Therefore, we identified a novel mechanism for regulating the sensitivity of sunitinib in ccRCC. Therefore, we elucidated a novel mechanism by which RBCK1 regulates sunitinib sensitivity in ccRCC.
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Affiliation(s)
- Yapeng Wang
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Mou Peng
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Uro-Oncology Institute of Central South University, Changsha, Hunan, 410011, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yawen Zhong
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Uro-Oncology Institute of Central South University, Changsha, Hunan, 410011, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Xiong
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Uro-Oncology Institute of Central South University, Changsha, Hunan, 410011, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Liang Zhu
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
- Uro-Oncology Institute of Central South University, Changsha, Hunan, 410011, China.
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.
| | - Xin Jin
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
- Uro-Oncology Institute of Central South University, Changsha, Hunan, 410011, China.
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.
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25
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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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26
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Research progress on maintaining chloroplast homeostasis under stress conditions: a review. Acta Biochim Biophys Sin (Shanghai) 2023; 55:173-182. [PMID: 36840466 PMCID: PMC10157539 DOI: 10.3724/abbs.2023022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
On a global scale, drought, salinity, extreme temperature, and other abiotic stressors severely limit the quality and yield of crops. Therefore, it is crucial to clarify the adaptation strategies of plants to harsh environments. Chloroplasts are important environmental sensors in plant cells. For plants to thrive in different habitats, chloroplast homeostasis must be strictly regulated, which is necessary to maintain efficient plant photosynthesis and other metabolic reactions under stressful environments. To maintain normal chloroplast physiology, two important biological processes are needed: the import and degradation of chloroplast proteins. The orderly import of chloroplast proteins and the timely degradation of damaged chloroplast components play a key role in adapting plants to their environment. In this review, we briefly described the mechanism of chloroplast TOC-TIC protein transport. The importance and recent progress of chloroplast protein turnover, retrograde signaling, and chloroplast protein degradation under stress are summarized. Furthermore, the potential of targeted regulation of chloroplast homeostasis is emphasized to improve plant adaptation to environmental stresses.
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27
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Mohd Ali S, Li N, Soufi Z, Yao J, Johnson E, Ling Q, Jarvis RP. Multiple ubiquitin E3 ligase genes antagonistically regulate chloroplast-associated protein degradation. Curr Biol 2023; 33:1138-1146.e5. [PMID: 36822201 DOI: 10.1016/j.cub.2023.01.060] [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: 03/30/2021] [Revised: 12/02/2022] [Accepted: 01/26/2023] [Indexed: 02/24/2023]
Abstract
The chloroplast is the most prominent member of a diverse group of plant organelles called the plastids, and it is characterized by its vital role in photosynthesis. 1,2,3 Most of the ∼3,000 different proteins in chloroplasts are synthesized in the cytosol in precursor (preprotein) form, each with a cleavable transit peptide. 4,5,6,7,8 Preproteins are imported via translocons in the outer and inner envelope membranes of the chloroplast, termed TOC and TIC, respectively. 9,10,11,12,13 Discovery of the chloroplast-localized ubiquitin E3 ligase SUPPRESSOR OF PPI1 LOCUS1 (SP1) demonstrated that the nucleocytosolic ubiquitin-proteasome system (UPS) targets the TOC apparatus to dynamically control protein import and chloroplast biogenesis in response to developmental and environmental cues. The relevant UPS pathway is termed chloroplast-associated protein degradation (CHLORAD). 14,15,16 Two homologs of SP1 exist, SP1-like1 (SPL1) and SPL2, but their roles have remained obscure. Here, we show that SP1 is ubiquitous in the Viridiplantae and that SPL2 and SPL1 appeared early during the evolution of the Viridiplantae and land plants, respectively. Through genetic and biochemical analysis, we reveal that SPL1 functions as a negative regulator of SP1, potentially by interfering with its ability to catalyze ubiquitination. In contrast, SPL2, the more distantly related SP1 homolog, displays partial functional redundancy with SP1. Both SPL1 and SPL2 modify the extent of leaf senescence, like SP1, but do so in diametrically opposite ways. Thus, SPL1 and SPL2 are bona fide CHLORAD system components with negative and positive regulatory functions that allow for nuanced control of this vital proteolytic pathway.
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Affiliation(s)
- Sabri Mohd Ali
- Section of Molecular Plant Biology (Department of Biology) and Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Na Li
- Section of Molecular Plant Biology (Department of Biology) and Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Ziad Soufi
- Section of Molecular Plant Biology (Department of Biology) and Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Jinrong Yao
- University of Chinese Academy of Sciences, Beijing 100049, China; 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 200032, China
| | - Errin Johnson
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Qihua Ling
- Section of Molecular Plant Biology (Department of Biology) and Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; 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 200032, China
| | - R Paul Jarvis
- Section of Molecular Plant Biology (Department of Biology) and Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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28
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Kim DB, Na C, Hwang I, Lee DW. Understanding protein translocation across chloroplast membranes: Translocons and motor proteins. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:408-416. [PMID: 36223071 DOI: 10.1111/jipb.13385] [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: 08/29/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Subcellular organelles in eukaryotes are surrounded by lipid membranes. In an endomembrane system, vesicle trafficking is the primary mechanism for the delivery of organellar proteins to specific organelles. However, organellar proteins for chloroplasts, mitochondria, the nucleus, and peroxisomes that are translated in the cytosol are directly imported into their target organelles. Chloroplasts are a plant-specific organelle with outer and inner envelope membranes, a dual-membrane structure that is similar to mitochondria. Interior chloroplast proteins translated by cytosolic ribosomes are thus translocated through TOC and TIC complexes (translocons in the outer and inner envelope of chloroplasts, respectively), with stromal ATPase motor proteins playing a critical role in pulling pre-proteins through these import channels. Over the last three decades, the identity and function of TOC/TIC components and stromal motor proteins have been actively investigated, which has shed light on the action mechanisms at a molecular level. However, there remains some disagreement over the exact composition of TIC complexes and genuine stromal motor proteins. In this review, we discuss recent findings on the mechanisms by which proteins are translocated through TOC/TIC complexes and discuss future prospects for this field of research.
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Affiliation(s)
- Da Been Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Korea
| | - Changhee Na
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Korea
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Dong Wook Lee
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Korea
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 61186, Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, 61186, Korea
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29
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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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30
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Yue YL, Zhang MY, Liu JY, Fang LJ, Qu YQ. The role of autophagy in idiopathic pulmonary fibrosis: from mechanisms to therapies. Ther Adv Respir Dis 2022; 16:17534666221140972. [PMID: 36468453 PMCID: PMC9726854 DOI: 10.1177/17534666221140972] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is an interstitial pulmonary disease with an extremely poor prognosis. Autophagy is a fundamental intracellular process involved in maintaining cellular homeostasis and regulating cell survival. Autophagy deficiency has been shown to play an important role in the progression of pulmonary fibrosis. This review focused on the six steps of autophagy, as well as the interplay between autophagy and other seven pulmonary fibrosis related mechanisms, which include extracellular matrix deposition, myofibroblast differentiation, epithelial-mesenchymal transition, pulmonary epithelial cell dysfunction, apoptosis, TGF-β1 pathway, and the renin-angiotensin system. In addition, this review also summarized autophagy-related signaling pathways such as mTOR, MAPK, JAK2/STAT3 signaling, p65, and Keap1/Nrf2 signaling during the development of IPF. Furthermore, this review also illustrated the commonly used autophagy detection methods, the currently approved antifibrotic drugs pirfenidone and nintedanib, and several prospective compounds targeting autophagy for the treatment of IPF.
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Affiliation(s)
- Yue-Liang Yue
- Shandong Key Laboratory of Infectious Respiratory Diseases, Laboratory of Basic Medical Sciences, Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Meng-Yu Zhang
- Shandong Key Laboratory of Infectious Respiratory Diseases, Laboratory of Basic Medical Sciences, Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Jian-Yu Liu
- Shandong Key Laboratory of Infectious Respiratory Diseases, Laboratory of Basic Medical Sciences, Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Li-Jun Fang
- Shandong Key Laboratory of Infectious Respiratory Diseases, Laboratory of Basic Medical Sciences, Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
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31
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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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32
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Rochaix J. Chloroplast protein import machinery and quality control. FEBS J 2022; 289:6908-6918. [PMID: 35472255 PMCID: PMC9790281 DOI: 10.1111/febs.16464] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/20/2022] [Accepted: 04/25/2022] [Indexed: 01/13/2023]
Abstract
Most chloroplast proteins are nucleus-encoded, translated on cytoplasmic ribosomes as precursor proteins, and imported into chloroplasts through TOC and TIC, the translocons of the outer and inner chloroplast envelope membranes. While the composition of the TOC complex is well established, there is still some controversy about the importance of a recently identified TIC complex consisting of Tic20, Tic214, Tic100, and Tic56. TOC and TIC form a supercomplex with a protein channel at the junction of the outer and inner envelope membranes through which preproteins are pulled into the stroma by the ATP-powered Ycf2 complex consisting of several FtsH-like ATPases and/or by chloroplast Hsp proteins. Several components of the TOC/TIC system are moonlighting proteins with additional roles in chloroplast gene expression and metabolism. Chaperones and co-chaperones, associated with TOC and TIC on the cytoplasmic and stromal side of the chloroplast envelope, participate in the unfolding and folding of the precursor proteins and act together with the ubiquitin-proteasome system in protein quality control. Chloroplast protein import is also intimately linked with retrograde signaling, revealing altogether an unsuspected complexity in the regulation of this process.
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Affiliation(s)
- Jean‐David Rochaix
- Departments of Molecular Biology and Plant BiologyUniversity of GenevaSwitzerland
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33
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Zhao X, Higa T, Nakai M. Tic12, a 12-kDa essential component of the translocon at the inner envelope membrane of chloroplasts in Arabidopsis. THE PLANT CELL 2022; 34:4569-4582. [PMID: 35929083 PMCID: PMC9614449 DOI: 10.1093/plcell/koac240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
The complexes translocon at the outer envelope membrane of chloroplasts and translocon at the inner envelope membrane of chloroplasts (TIC) mediate preprotein translocation across the chloroplast outer and inner envelope membranes, respectively. Tic20, Tic56, Tic100, and Tic214 form a stable one-megadalton TIC whose function is essential for Arabidopsis thaliana and Chlamydomonas reinhardtii. Tic20 plays a central role in preprotein translocation by forming a protein-conducting channel. Tic56, Tic100, and Tic214 are also indispensable for TIC function, but whether other components are required for this process remain unclear. Here, we demonstrate that a 12-kDa protein named Tic12 is part of the TIC in A. thaliana and participates in preprotein translocation across the inner envelope membrane. Tic12 was tightly associated with the TIC but disassociated under high-salt conditions in combination with Triton X-100. Site-specific UV crosslinking experiments revealed that Tic12 and Tic20 directly interact with the transit peptide of a translocating preprotein. The tic12 null mutants are albino and seedling lethal, similar to the other tic null mutants. Tic12 and Tic20 were also involved in preprotein translocation in (Pisum sativum) pea chloroplasts. Thus, Tic12 is an essential constituent that forms the functional core together with Tic20 in the one-megadalton TIC.
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Affiliation(s)
- Xueyang Zhao
- Institute for Protein Research, Osaka University, Suita, 565-0871, Japan
| | - Takeshi Higa
- Institute for Protein Research, Osaka University, Suita, 565-0871, Japan
| | - Masato Nakai
- Institute for Protein Research, Osaka University, Suita, 565-0871, Japan
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34
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Li Y, Jian Y, Mao Y, Meng F, Shao Z, Wang T, Zheng J, Wang Q, Liu L. "Omics" insights into plastid behavior toward improved carotenoid accumulation. FRONTIERS IN PLANT SCIENCE 2022; 13:1001756. [PMID: 36275568 PMCID: PMC9583013 DOI: 10.3389/fpls.2022.1001756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Plastids are a group of diverse organelles with conserved carotenoids synthesizing and sequestering functions in plants. They optimize the carotenoid composition and content in response to developmental transitions and environmental stimuli. In this review, we describe the turbulence and reforming of transcripts, proteins, and metabolic pathways for carotenoid metabolism and storage in various plastid types upon organogenesis and external influences, which have been studied using approaches including genomics, transcriptomics, proteomics, and metabonomics. Meanwhile, the coordination of plastid signaling and carotenoid metabolism including the effects of disturbed carotenoid biosynthesis on plastid morphology and function are also discussed. The "omics" insight extends our understanding of the interaction between plastids and carotenoids and provides significant implications for designing strategies for carotenoid-biofortified crops.
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Affiliation(s)
- Yuanyuan Li
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yue Jian
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yuanyu Mao
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Fanliang Meng
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Zhiyong Shao
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Tonglin Wang
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Jirong Zheng
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Qiaomei Wang
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Lihong Liu
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
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Wan C, Ling Q. Functions of autophagy in chloroplast protein degradation and homeostasis. FRONTIERS IN PLANT SCIENCE 2022; 13:993215. [PMID: 36247630 PMCID: PMC9557084 DOI: 10.3389/fpls.2022.993215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
Chloroplasts are defining organelles in plant and algae, which carried out various critical metabolic processes, including photosynthesis. Roles of chloroplast protein homeostasis in plant development and stress adaptation were clearly demonstrated in previous studies, and its maintenance requires internal proteases originated from the prokaryotic ancestor. Recently, increasing evidence revealed that eukaryotic proteolytic pathways, ubiquitin-proteasome system (UPS) and autophagy, are also involved in the turnover of chloroplast proteins, in response to developmental and environmental cues. Notably, chloroplasts can be regulated via the selective degradation of chloroplast materials in a process called chlorophagy. Yet, understandings of the mechanism of chlorophagy are still rudimentary, particularly regarding its initiation and operation. Here we provide an updated overview of autophagy pathways for chloroplast protein degradation and discuss their importance for plant physiology. In addition, recent advance in analogous mitophagy in yeast and mammals will also be discussed, which provides clues for further elucidating the mechanism of chlorophagy.
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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 Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - 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
- University of Chinese Academy of Sciences, Beijing, China
- Chinese Academy of Sciences (CAS) and John Innes Centre, Center of Excellence for Plant and Microbial Sciences (CEPAMS), Shanghai, China
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Yu Y, Portolés S, Ren Y, Sun G, Wang XF, Zhang H, Guo S. The key clock component ZEITLUPE (ZTL) negatively regulates ABA signaling by degradation of CHLH in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:995907. [PMID: 36176682 PMCID: PMC9513469 DOI: 10.3389/fpls.2022.995907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Ubiquitination-mediated protein degradation plays important roles in ABA signal transduction and delivering responses to chloroplast stress signals in plants, but additional E3 ligases of protein ubiquitination remain to be identified to understand the complex signaling network. Here we reported that ZEITLUPE (ZTL), an F-box protein, negatively regulates abscisic acid (ABA) signaling during ABA-inhibited early seedling growth and ABA-induced stomatal closure in Arabidopsis thaliana. Using molecular biology and biochemistry approaches, we demonstrated that ZTL interacts with and ubiquitinates its substrate, CHLH/ABAR (Mg-chelatase H subunit/putative ABA receptor), to modulate CHLH stability via the 26S proteasome pathway. CHLH acts genetically downstream of ZTL in ABA and drought stress signaling. Interestingly, ABA conversely induces ZTL phosphorylation, and high levels of ABA also induce CHLH proteasomal degradation, implying that phosphorylated ZTL protein may enhance the affinity to CHLH, leading to the increased degradation of CHLH after ABA treatment. Taken together, our results revealed a possible mechanism of reciprocal regulation between ABA signaling and the circadian clock, which is thought to be essential for plant fitness and survival.
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Affiliation(s)
- Yongtao Yu
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Sergi Portolés
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yi Ren
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Guangyu Sun
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Xiao-Fang Wang
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Huihui Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Shaogui Guo
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
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37
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Hand KA, Shabek N. The Role of E3 Ubiquitin Ligases in Chloroplast Function. Int J Mol Sci 2022; 23:ijms23179613. [PMID: 36077009 PMCID: PMC9455731 DOI: 10.3390/ijms23179613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 12/14/2022] Open
Abstract
Chloroplasts are ancient organelles responsible for photosynthesis and various biosynthetic functions essential to most life on Earth. Many of these functions require tightly controlled regulatory processes to maintain homeostasis at the protein level. One such regulatory mechanism is the ubiquitin-proteasome system whose fundamental role is increasingly emerging in chloroplasts. In particular, the role of E3 ubiquitin ligases as determinants in the ubiquitination and degradation of specific intra-chloroplast proteins. Here, we highlight recent advances in understanding the roles of plant E3 ubiquitin ligases SP1, COP1, PUB4, CHIP, and TT3.1 as well as the ubiquitin-dependent segregase CDC48 in chloroplast function.
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Xing J, Pan J, Yi H, Lv K, Gan Q, Wang M, Ge H, Huang X, Huang F, Wang Y, Rochaix JD, Yang W. The plastid-encoded protein Orf2971 is required for protein translocation and chloroplast quality control. THE PLANT CELL 2022; 34:3383-3399. [PMID: 35708659 PMCID: PMC9421593 DOI: 10.1093/plcell/koac180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Photosynthesis and the biosynthesis of many important metabolites occur in chloroplasts. In these semi-autonomous organelles, the chloroplast genome encodes approximately 100 proteins. The remaining chloroplast proteins, close to 3,000, are encoded by nuclear genes whose products are translated in the cytosol and imported into chloroplasts. However, there is still no consensus on the composition of the protein import machinery including its motor proteins and on how newly imported chloroplast proteins are refolded. In this study, we have examined the function of orf2971, the largest chloroplast gene of Chlamydomonas reinhardtii. The depletion of Orf2971 causes the accumulation of protein precursors, partial proteolysis and aggregation of proteins, increased expression of chaperones and proteases, and autophagy. Orf2971 interacts with the TIC (translocon at the inner chloroplast envelope) complex, catalyzes ATP (adenosine triphosphate) hydrolysis, and associates with chaperones and chaperonins. We propose that Orf2971 is intimately connected to the protein import machinery and plays an important role in chloroplast protein quality control.
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Affiliation(s)
| | | | - Heng Yi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Kang Lv
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiuliang Gan
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Meimei Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haitao Ge
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiahe Huang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fang Huang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yingchun Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jean-David Rochaix
- Departments of Molecular Biology and Plant Biology, University of Geneva, Geneva, Switzerland
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Loudya N, Maffei DPF, Bédard J, Ali SM, Devlin PF, Jarvis RP, López-Juez E. Mutations in the chloroplast inner envelope protein TIC100 impair and repair chloroplast protein import and impact retrograde signaling. THE PLANT CELL 2022; 34:3028-3046. [PMID: 35640571 PMCID: PMC9338805 DOI: 10.1093/plcell/koac153] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/19/2022] [Indexed: 05/16/2023]
Abstract
Chloroplast biogenesis requires synthesis of proteins in the nucleocytoplasm and the chloroplast itself. Nucleus-encoded chloroplast proteins are imported via multiprotein translocons in the organelle's envelope membranes. Controversy exists around whether a 1-MDa complex comprising TIC20, TIC100, and other proteins constitutes the inner membrane TIC translocon. The Arabidopsis thaliana cue8 virescent mutant is broadly defective in plastid development. We identify CUE8 as TIC100. The tic100cue8 mutant accumulates reduced levels of 1-MDa complex components and exhibits reduced import of two nucleus-encoded chloroplast proteins of different import profiles. A search for suppressors of tic100cue8 identified a second mutation within the same gene, tic100soh1, which rescues the visible, 1 MDa complex-subunit abundance, and chloroplast protein import phenotypes. tic100soh1 retains but rapidly exits virescence and rescues the synthetic lethality of tic100cue8 when retrograde signaling is impaired by a mutation in the GENOMES UNCOUPLED 1 gene. Alongside the strong virescence, changes in RNA editing and the presence of unimported precursor proteins show that a strong signaling response is triggered when TIC100 function is altered. Our results are consistent with a role for TIC100, and by extension the 1-MDa complex, in the chloroplast import of photosynthetic and nonphotosynthetic proteins, a process which initiates retrograde signaling.
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Affiliation(s)
- Naresh Loudya
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Douglas P F Maffei
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
| | - Jocelyn Bédard
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Sabri Mohd Ali
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Paul F Devlin
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
| | - R Paul Jarvis
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Enrique López-Juez
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
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40
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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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41
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Zheng XT, Wang C, Lin W, Lin C, Han D, Xie Q, Lai J, Yang C. Importation of chloroplast proteins under heat stress is facilitated by their SUMO conjugations. THE NEW PHYTOLOGIST 2022; 235:173-187. [PMID: 35347735 DOI: 10.1111/nph.18121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Chloroplasts are hypersensitive to heat stress (HS). SUMOylation, a critical post-translational modification, is conservatively involved in HS responses. However, the functional connection between SUMOylation and chloroplasts under HS remains to be studied. The bioinformatics, biochemistry, and cell biology analyses were used to detect the SUMOylation statuses of Arabidopsis nuclear-encoded chloroplast proteins and the effect of SUMOylation on subcellular localization of these proteins under HS. PSBR, a subunit of photosystem II, was used as an example for a detailed investigation of functional mechanisms. After a global SUMOylation site prediction of nuclear-encoded chloroplast proteins, biochemical data showed that most of the selected candidates are modified by SUMO3 in the cytoplasm. The chloroplast localization of these SUMOylation targets under long-term HS is partially maintained by the SUMO ligase AtSIZ1. The HS-induced SUMOylation on PSBR contributes to the maintenance of its chloroplast localization, which is dependent on its chloroplast importation efficiency correlated to phosphorylation. The complementation analysis provided evidence that SUMOylation is essential for the physiological function of PSBR under HS. Our study illustrated a general regulatory mechanism of SUMOylation in maintaining the chloroplast protein importation during HS and provided hints for further investigation on protein modifications associated with plant organelles under stress conditions.
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Affiliation(s)
- Xiao-Ting Zheng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Caijuan Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Wenxiong Lin
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Chufang Lin
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Danlu Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Qi Xie
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
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42
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Huntington B, Zhao L, Bron P, Shahul Hameed UF, Arold ST, Qureshi BM. Thicker Ice Improves the Integrity and Angular Distribution of CDC48A Hexamers on Cryo-EM Grids. Front Mol Biosci 2022; 9:890390. [PMID: 35782862 PMCID: PMC9247313 DOI: 10.3389/fmolb.2022.890390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/26/2022] [Indexed: 11/21/2022] Open
Abstract
Many cryogenic electron microscopy (cryo-EM) single particle analyses are constrained by the sample preparation step upon which aggregation, dissociation, and/or preferential orientation of particles can be introduced. Here, we report how we solved these problems in the case of CDC48A, a hexameric AAA ATPase from Arabidopsis thaliana. CDC48A hexamers are well preserved under negative staining conditions but disassemble during grid freezing using the classical blotting method. Vitrification of grids using the blot-free Chameleon method preserved the integrity of particles but resulted in their strong preferential orientation. We then used a strategy where we improved in parallel the purification of CDC48A and the conditions for cryo-EM data acquisition. Indeed, we noted that images taken from thicker ice presented an even distribution of intact particles with random orientations, but resulted in a lower image resolution. Consequently, in our case, distribution, orientation, image resolution, and the integrity of particles were tightly correlated with ice thickness. By combining the more homogeneous and stable CDC48A hexamers resulting from our improved purification protocol with an iterative search across different ice thicknesses, we identified an intermediate thickness that retained sufficiently high-resolution structural information while maintaining a complete distribution of particle orientations. Our approach may provide a simple, fast, and generally applicable strategy to record data of sufficient quality under standard laboratory and microscope settings. This method may be of particular value when time and resources are limited.
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Affiliation(s)
- Brandon Huntington
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Biology Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Lingyun Zhao
- Imaging and Characterization Core Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Patrick Bron
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Umar F. Shahul Hameed
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Biology Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- *Correspondence: Umar F. Shahul Hameed, ; Stefan T. Arold, ; Bilal M. Qureshi,
| | - Stefan T. Arold
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Biology Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, Montpellier, France
- *Correspondence: Umar F. Shahul Hameed, ; Stefan T. Arold, ; Bilal M. Qureshi,
| | - Bilal M. Qureshi
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Biology Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Division of Structural Biology (Strubi), University of Oxford, Oxford, United Kingdom
- Scientific Center of Optical and Electron Microscopy (ScopeM), ETH Zurich, Zurich, Switzerland
- *Correspondence: Umar F. Shahul Hameed, ; Stefan T. Arold, ; Bilal M. Qureshi,
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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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Lan W, Zheng S, Yang P, Qiu Y, Xu Y, Miao Y. Establishment of a Landscape of UPL5-Ubiquitinated on Multiple Subcellular Components of Leaf Senescence Cell in Arabidopsis. Int J Mol Sci 2022; 23:ijms23105754. [PMID: 35628561 PMCID: PMC9145402 DOI: 10.3390/ijms23105754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
Catabolism of macromolecules is a major event in senescent cells, especially involving proteolysis of organelles and abnormally aggregated proteins, circulation of nutrients, and precise control of intracellular environmental balance. Proteasomes are distributed in the nucleus and cytoplasm; however, proteasomes in organelles are limited. In this study, multi-omics proteomic analyses of ubiquitinated proteins enriched by using antibody against “di-Gly-Lys” via a free labeling were used to investigate the global changes of protein levels and ubiquitination modification levels of upl5 mutant relative to wild-type plant; subcellular localization analysis of UPL5 was found to be located in the nucleus, cytoplasm, and plastid within the cell; and the direct lysine site patterns of UPL5 were screened by the H89R substitution in the tagged ubiquitinated assay. It suggests that UPL5 acting as a candidate of organelle E3 ligase either in the nucleus or cytoplasm or plastid modifies numerous targets related to nuclear transcription and plastid photosynthesis involving in Ca2+ and hormone signaling pathway in plant senescence and in response to (a)biotic stress protection.
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Affiliation(s)
| | | | | | | | | | - Ying Miao
- Correspondence: ; Tel.: +86-59186392987
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45
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Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis. Proc Natl Acad Sci U S A 2022; 119:e2121362119. [PMID: 35549553 PMCID: PMC9171785 DOI: 10.1073/pnas.2121362119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Photoinhibitory high light stress in plants leads to increases in markers of protein degradation and transcriptional up-regulation of proteases and proteolytic machinery, but protein homeostasis (proteostasis) of most enzymes is largely maintained under high light, so we know little about the metabolic consequences of it beyond photosystem damage. We developed a technique to look for rapid protein turnover events in response to high light through 13C partial labeling and detailed peptide mass spectrometry. This analysis reveals a light-induced transcriptional program for nuclear-encoded genes, beyond the regulation of photosystem II, to replace key protein degradation targets in plants and ensure proteostasis under high light stress. Photoinhibitory high light stress in Arabidopsis leads to increases in markers of protein degradation and transcriptional up-regulation of proteases and proteolytic machinery, but proteostasis is largely maintained. We find significant increases in the in vivo degradation rate for specific molecular chaperones, nitrate reductase, glyceraldehyde-3 phosphate dehydrogenase, and phosphoglycerate kinase and other plastid, mitochondrial, peroxisomal, and cytosolic enzymes involved in redox shuttles. Coupled analysis of protein degradation rates, mRNA levels, and protein abundance reveal that 57% of the nuclear-encoded enzymes with higher degradation rates also had high light–induced transcriptional responses to maintain proteostasis. In contrast, plastid-encoded proteins with enhanced degradation rates showed decreased transcript abundances and must maintain protein abundance by other processes. This analysis reveals a light-induced transcriptional program for nuclear-encoded genes, beyond the regulation of the photosystem II (PSII) D1 subunit and the function of PSII, to replace key protein degradation targets in plants and ensure proteostasis under high light stress.
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46
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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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47
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Calvanese E, Gu Y. Towards understanding inner nuclear membrane protein degradation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2266-2274. [PMID: 35139191 DOI: 10.1093/jxb/erac037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
The inner nuclear membrane (INM) hosts a unique set of membrane proteins that play essential roles in various aspects of the nuclear function. However, overaccumulation or malfunction of INM protein has been associated with a range of rare genetic diseases; therefore, maintaining the homeostasis and integrity of INM proteins by active removal of aberrantly accumulated proteins and replacing defective molecules through proteolysis is of critical importance. Within the last decade, it has been shown that INM proteins are degraded in yeasts by a process very similar to endoplasmic reticulum-associated degradation (ERAD), which is accomplished by retrotranslocation of membrane substrates followed by proteasome-dependent proteolysis, and this process was named inner nuclear membrane-associated degradation (INMAD). INMAD is distinguished from ERAD by specific INM-localized E3 ubiquitin ligases and proteolysis regulators. While much is yet to be determined about the INMAD pathway in yeasts, virtually no knowledge of it exists for higher eukaryotes, and only very recently have several critical regulators that participate in INM protein degradation been discovered in plants. Here, we review key molecular components of the INMAD pathway and draw parallels between the yeast and plant system to discuss promising directions in the future study of the plant INMAD process.
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Affiliation(s)
- Enrico Calvanese
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
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48
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Li J, Yuan J, Li Y, Sun H, Ma T, Huai J, Yang W, Zhang W, Lin R. The CDC48 complex mediates ubiquitin-dependent degradation of intra-chloroplast proteins in plants. Cell Rep 2022; 39:110664. [PMID: 35417702 DOI: 10.1016/j.celrep.2022.110664] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/19/2022] [Accepted: 03/20/2022] [Indexed: 11/03/2022] Open
Abstract
Chloroplasts are the site of numerous biochemical reactions including photosynthesis, but they also produce reactive oxygen species (ROS) that negatively affect chloroplast integrity. The chaperone-like CDC48 complex plays critical roles in ubiquitin-dependent protein degradation in yeast and mammals, but its function in plants is largely unknown. Here, we show that defects in CDC48A and its cofactors UFD1 and NPL4 lead to the accumulation of ubiquitinated chloroplast proteins in Arabidopsis thaliana. We reveal that two plastid genome-encoded proteins, RbcL and AtpB, associate with the CDC48 complex. Strikingly, RbcL and AtpB are ubiquitinated and degraded by the 26S proteasome pathway upon ROS stress, and these processes are impaired by defects of the CDC48 complex. Functional analysis demonstrates that the CDC48 complex is required for plant tolerance to ROS. This study reveals a role for the plant CDC48 complex in modulating ubiquitin-dependent degradation of intra-chloroplast proteins in response to oxidative stress.
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Affiliation(s)
- Jialong Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jiarui Yuan
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhong Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huilun Sun
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Ma
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Junling Huai
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wenqiang Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenhao Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Rongcheng Lin
- 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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49
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Woodson JD. Control of chloroplast degradation and cell death in response to stress. Trends Biochem Sci 2022; 47:851-864. [DOI: 10.1016/j.tibs.2022.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/25/2022] [Accepted: 03/14/2022] [Indexed: 12/16/2022]
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50
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TIC236 gain-of-function mutations unveil the link between plastid division and plastid protein import. Proc Natl Acad Sci U S A 2022; 119:e2123353119. [PMID: 35275795 PMCID: PMC8931380 DOI: 10.1073/pnas.2123353119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although plastid division is critical for plant development, how components of the plastid division machinery (PDM) are imported into plastids remains unexplored. A forward genetic screen to identify suppressors of a crumpled leaf (crl) mutant deficient in plastid division led us to find dominant gain-of-function (GF) mutations in TIC236, which significantly increases the import of PDM components and completely rescues crl phenotypes. The defective plastid division phenotypes in crl and tic236-knockdown mutants and CRL-TIC236 association in a functional complex indicate that the CRL-TIC236 module is vital for plastid division. Hence, we report the first GF translocon mutants and unveil CRL as a novel functional partner of TIC236 for PDM import. TIC236 is an essential component of the translocon for protein import into chloroplasts, as evidenced by the embryonic lethality of the knockout mutant. Here, we unveil a TIC236-allied component, the chloroplast outer membrane protein CRUMPLED LEAF (CRL), absence of which impairs plastid division and induces autoimmune responses in Arabidopsis thaliana. A forward genetic screen exploring CRL function found multiple dominant TIC236 gain-of-function (tic236-gf) mutations that abolished crl-induced phenotypes. Moreover, CRL associates with TIC236, and a tic236-knockdown mutant exhibited multiple lesions similar to the crl mutant, supporting their shared functionality. Consistent with the defective plastid division phenotype of crl, CRL interacts with the transit peptides of proteins essential in plastid division, with tic236-gf mutations reinforcing their import via increased TIC236 stability. Ensuing reverse genetic analyses further revealed genetic interaction between CRL and SP1, a RING-type ubiquitin E3 ligase, as well as with the plastid protease FTSH11, which function in TOC and TIC protein turnover, respectively. Loss of either SP1 or FTSH11 rescued crl mutant phenotypes to varying degrees due to increased translocon levels. Collectively, our data shed light on the links between plastid protein import, plastid division, and plant stress responses.
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