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Eckardt NA, Avin-Wittenberg T, Bassham DC, Chen P, Chen Q, Fang J, Genschik P, Ghifari AS, Guercio AM, Gibbs DJ, Heese M, Jarvis RP, Michaeli S, Murcha MW, Mursalimov S, Noir S, Palayam M, Peixoto B, Rodriguez PL, Schaller A, Schnittger A, Serino G, Shabek N, Stintzi A, Theodoulou FL, Üstün S, van Wijk KJ, Wei N, Xie Q, Yu F, Zhang H. The lowdown on breakdown: Open questions in plant proteolysis. THE PLANT CELL 2024; 36:2931-2975. [PMID: 38980154 PMCID: PMC11371169 DOI: 10.1093/plcell/koae193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/16/2024] [Accepted: 06/19/2024] [Indexed: 07/10/2024]
Abstract
Proteolysis, including post-translational proteolytic processing as well as protein degradation and amino acid recycling, is an essential component of the growth and development of living organisms. In this article, experts in plant proteolysis pose and discuss compelling open questions in their areas of research. Topics covered include the role of proteolysis in the cell cycle, DNA damage response, mitochondrial function, the generation of N-terminal signals (degrons) that mark many proteins for degradation (N-terminal acetylation, the Arg/N-degron pathway, and the chloroplast N-degron pathway), developmental and metabolic signaling (photomorphogenesis, abscisic acid and strigolactone signaling, sugar metabolism, and postharvest regulation), plant responses to environmental signals (endoplasmic-reticulum-associated degradation, chloroplast-associated degradation, drought tolerance, and the growth-defense trade-off), and the functional diversification of peptidases. We hope these thought-provoking discussions help to stimulate further research.
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Affiliation(s)
| | - Tamar Avin-Wittenberg
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Poyu Chen
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Qian Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory for Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jun Fang
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Pascal Genschik
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, Strasbourg 67084, France
| | - Abi S Ghifari
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Angelica M Guercio
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA 95616, USA
| | - Daniel J Gibbs
- School of Biosciences, University of Birmingham, Edgbaston B1 2RU, UK
| | - Maren Heese
- Department of Developmental Biology, University of Hamburg, Ohnhorststr. 18, Hamburg 22609, Germany
| | - R Paul Jarvis
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Simon Michaeli
- Department of Postharvest Sciences, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7505101, Israel
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Sergey Mursalimov
- Department of Postharvest Sciences, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7505101, Israel
| | - Sandra Noir
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, Strasbourg 67084, France
| | - Malathy Palayam
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA 95616, USA
| | - Bruno Peixoto
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, Valencia ES-46022, Spain
| | - Andreas Schaller
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart 70599, Germany
| | - Arp Schnittger
- Department of Developmental Biology, University of Hamburg, Ohnhorststr. 18, Hamburg 22609, Germany
| | - Giovanna Serino
- Department of Biology and Biotechnology, Sapienza Universita’ di Roma, p.le A. Moro 5, Rome 00185, Italy
| | - Nitzan Shabek
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA 95616, USA
| | - Annick Stintzi
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart 70599, Germany
| | | | - Suayib Üstün
- Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Bochum 44780, Germany
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14853, USA
| | - Ning Wei
- School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feifei Yu
- College of Grassland Science and Technology, China Agricultural University, Beijing 100083, China
| | - Hongtao Zhang
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden AL5 2JQ, UK
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Wen C, Luo T, He Z, Li Y, Yan J, Xu W. Regulation of Tomato Fruit Autophagic Flux and Promotion of Fruit Ripening by the Autophagy-Related Gene SlATG8f. PLANTS (BASEL, SWITZERLAND) 2023; 12:3339. [PMID: 37765504 PMCID: PMC10536916 DOI: 10.3390/plants12183339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/07/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
Autophagy is a highly conserved self-degradation process that involves the degradation and recycling of cellular components and organelles. Although the involvement of autophagy in metabolic changes during fruit ripening has been preliminarily demonstrated, the variations in autophagic flux and specific functional roles in tomato fruit ripening remain to be elucidated. In this study, we analyzed the variations in autophagic flux during tomato fruit ripening. The results revealed differential expression of the SlATG8 family members during tomato fruit ripening. Transmission electron microscopy observations and dansylcadaverine (MDC) staining confirmed the presence of autophagy at the cellular level in tomato fruits. Furthermore, the overexpression of SlATG8f induced the formation of autophagosomes, increased autophagic flux within tomato fruits, and effectively enhanced the expression of ATG8 proteins during the color-transition phase of fruit ripening, thus promoting tomato fruit maturation. SlATG8f overexpression also led to the accumulation of vitamin C (VC) and soluble solids while reducing acidity in the fruit. Collectively, our findings highlight the pivotal role of SlATG8f in enhancing tomato fruit ripening, providing insights into the mechanistic involvement of autophagy in this process. This research contributes to a better understanding of the key factors that regulate tomato fruit quality and offers a theoretical basis for tomato variety improvement.
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Affiliation(s)
- Cen Wen
- College of Agriculture, Guizhou University, Guizhou 550025, China; (C.W.); (T.L.); (Z.H.); (Y.L.)
| | - Taimin Luo
- College of Agriculture, Guizhou University, Guizhou 550025, China; (C.W.); (T.L.); (Z.H.); (Y.L.)
- Xingyi City Bureau of Agriculture and Rural Development, Guizhou 562400, China
| | - Zhuo He
- College of Agriculture, Guizhou University, Guizhou 550025, China; (C.W.); (T.L.); (Z.H.); (Y.L.)
| | - Yunzhou Li
- College of Agriculture, Guizhou University, Guizhou 550025, China; (C.W.); (T.L.); (Z.H.); (Y.L.)
| | - Jianmin Yan
- College of Agriculture, Guizhou University, Guizhou 550025, China; (C.W.); (T.L.); (Z.H.); (Y.L.)
- Guizhou Higher Education Facility Vegetable Engineering Research Center, Guizhou 550025, China
| | - Wen Xu
- College of Agriculture, Guizhou University, Guizhou 550025, China; (C.W.); (T.L.); (Z.H.); (Y.L.)
- Guizhou Higher Education Facility Vegetable Engineering Research Center, Guizhou 550025, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
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Baldwin A, Dhorajiwala R, Roberts C, Dimitrova S, Tu S, Jones S, Ludlow RA, Cammarisano L, Davoli D, Andrews R, Kent NA, Spadafora ND, Müller CT, Rogers HJ. Storage of halved strawberry fruits affects aroma, phytochemical content and gene expression, and is affected by pre-harvest factors. FRONTIERS IN PLANT SCIENCE 2023; 14:1165056. [PMID: 37324675 PMCID: PMC10264638 DOI: 10.3389/fpls.2023.1165056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023]
Abstract
Introduction Strawberry fruit are highly valued for their aroma which develops during ripening. However, they have a short shelf-life. Low temperature storage is routinely used to extend shelf-life for transport and storage in the supply chain, however cold storage can also affect fruit aroma. Some fruit continue to ripen during chilled storage; however, strawberries are a non-climacteric fruit and hence ripening postharvest is limited. Although most strawberry fruit is sold whole, halved fruit is also used in ready to eat fresh fruit salads which are of increasing consumer demand and pose additional challenges to fresh fruit storage. Methods To better understand the effects of cold storage, volatilomic and transcriptomic analyses were applied to halved Fragaria x ananassa cv. Elsanta fruit stored at 4 or 8°C for up to 12 days over two growing seasons. Results and discussion The volatile organic compound (VOC) profile differed between 4 or 8°C on most days of storage. Major differences were detected between the two different years of harvest indicating that aroma change at harvest and during storage is highly dependent on environmental factors during growth. The major component of the aroma profile in both years was esters. Over 3000 genes changed in expression over 5 days of storage at 8°C in transcriptome analysis. Overall, phenylpropanoid metabolism, which may also affect VOCs, and starch metabolism were the most significantly affected pathways. Genes involved in autophagy were also differentially expressed. Expression of genes from 43 different transcription factor (TF) families changed in expression: mostly they were down-regulated but NAC and WRKY family genes were mainly up-regulated. Given the high ester representation amongst VOCs, the down-regulation of an alcohol acyl transferase (AAT) during storage is significant. A total of 113 differentially expressed genes were co-regulated with the AAT gene, including seven TFs. These may be potential AAT regulators.
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Affiliation(s)
- Ashley Baldwin
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | | | - Callum Roberts
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Simone Dimitrova
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Sarah Tu
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Stephanie Jones
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | | | | | - Daniela Davoli
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Robert Andrews
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Nicholas A. Kent
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Natasha D. Spadafora
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | | | - Hilary J. Rogers
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
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Zhang C, Shang D, Zhang Y, Gao X, Liu D, Gao Y, Li Y, Qi Y, Qiu L. Two Hybrid Histidine Kinases Involved in the Ethylene Regulation of the Mycelial Growth and Postharvest Fruiting Body Maturation and Senescence of Agaricus bisporus. Microbiol Spectr 2022; 10:e0241122. [PMID: 36125274 PMCID: PMC9603746 DOI: 10.1128/spectrum.02411-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/02/2022] [Indexed: 01/04/2023] Open
Abstract
Ethylene regulates mycelial growth, primordium formation, and postharvest mushroom maturation and senescence in the white button mushroom, Agaricus bisporus. However, it remains unknown how ethylene is detected by the mushroom. In this study, we found that two hybrid histidine kinases in the mushroom, designated AbETR1 and AbETR2, showed domain structures similar to those of plant ethylene receptors. The transmembrane helices of AbETR1 and AbETR2 were expressed in yeast cells and showed ethylene-binding activities. Mushroom strains with downregulated expressions of AbETR1 and AbETR2 showed reduced sensitivity to the ethylene inhibition of mycelial growth, ethylene regulation of their own synthesis, postharvest mushroom maturation, and senescence and expression of maturation- and senescence-related genes. Therefore, AbETR1 and AbETR2 are expected to be biologically functional ethylene receptors and exhibit a different mode of action from that of the receptors of plants. Here, we fill gaps in the knowledge pertaining to higher fungus ethylene receptors, discover a novel mode of action of ethylene receptors, confirm ethylene as a novel fungal hormone, and provide a facilitated approach for preventing the maturation and senescence of postharvest button mushrooms. IMPORTANCE Ethylene regulates diverse physiological activities in bacteria, cyanobacteria, fungi, and plants, but how to perceive ethylene by fungi only remains unknown. In this study, we identify two biologically functional ethylene receptors in the basidiomycete fungus Agaricus bisporus, which fills the gaps of deficient fungal ethylene receptors. Furthermore, we found that decreased expression of the ethylene receptors facilitates preventing the maturation and senescence of postharvest button mushrooms, indicating that the two fungal ethylene receptors positively regulate the ethylene response, in contrast to that in plants.
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Affiliation(s)
- Chaohui Zhang
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
- College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Di Shang
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Yan Zhang
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Xiyang Gao
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Dehai Liu
- Institute of Biology Co., Ltd., Henan Academy of Science, Zhengzhou, China
| | - Yuqian Gao
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Yanan Li
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Yuancheng Qi
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Liyou Qiu
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
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Song I, Hong S, Huh SU. Identification and Expression Analysis of the Solanum tuberosum StATG8 Family Associated with the WRKY Transcription Factor. PLANTS (BASEL, SWITZERLAND) 2022; 11:2858. [PMID: 36365311 PMCID: PMC9659186 DOI: 10.3390/plants11212858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Autophagy is an evolutionarily well-conserved cellular catabolic pathway in eukaryotic cells and plays an important role in cellular processes. Autophagy is regulated by autophagy-associated (ATG) proteins. Among these ATG proteins, the ubiquitin-like protein ATG8/LC3 is essential for autophagosome formation and function. In this study, the potato StATG8 family showed clade I and clade II with significantly different sequences. Expression of the StATG8 family was also increased in senescence. Interestingly, the expression of the StATG8 and other core StATG genes decreased in potato tubers as the tubers matured. The StATG8 family also responded to a variety of stresses such as heat, wounding, salicylic acid, and salt stress. We also found that some Arabidopsis WRKY transcription factors interacted with the StATG8 protein in planta. Based on group II-a WRKY, StATG8-WRKY interaction is independent of the ATG8 interacting motif (AIM) or LC3 interacting region (LIR) motif. This study showed that the StATG8 family had diverse functions in tuber maturation and multiple stress responses in potatoes. Additionally, StATG8 may have an unrelated autophagy function in the nucleus with the WRKY transcription factor.
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Affiliation(s)
| | | | - Sung Un Huh
- Department of Biological Science, Kunsan National University, Gunsan 54150, Korea
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Wang J, Miao S, Liu Y, Wang Y. Linking Autophagy to Potential Agronomic Trait Improvement in Crops. Int J Mol Sci 2022; 23:ijms23094793. [PMID: 35563184 PMCID: PMC9103229 DOI: 10.3390/ijms23094793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/18/2022] [Accepted: 04/25/2022] [Indexed: 12/10/2022] Open
Abstract
Autophagy is an evolutionarily conserved catabolic process in eukaryotic cells, by which the superfluous or damaged cytoplasmic components can be delivered into vacuoles or lysosomes for degradation and recycling. Two decades of autophagy research in plants uncovers the important roles of autophagy during diverse biological processes, including development, metabolism, and various stress responses. Additionally, molecular machineries contributing to plant autophagy onset and regulation have also gradually come into people’s sights. With the advancement of our knowledge of autophagy from model plants, autophagy research has expanded to include crops in recent years, for a better understanding of autophagy engagement in crop biology and its potentials in improving agricultural performance. In this review, we summarize the current research progress of autophagy in crops and discuss the autophagy-related approaches for potential agronomic trait improvement in crop plants.
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Magen S, Seybold H, Laloum D, Avin-Wittenberg T. Metabolism and autophagy in plants - A perfect match. FEBS Lett 2022; 596:2133-2151. [PMID: 35470431 DOI: 10.1002/1873-3468.14359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 01/18/2023]
Abstract
Autophagy is a eukaryotic cellular transport mechanism that delivers intracellular macromolecules, proteins, and even organelles to a lytic organelle (vacuole in yeast and plants/lysosome in animals) for degradation and nutrient recycling. The process is mediated by highly conserved Autophagy-Related (ATG) proteins. In plants, autophagy maintains cellular homeostasis under favorable conditions, guaranteeing normal plant growth and fitness. Severe stress such as nutrient starvation and plant senescence further induce it, thus ensuring plant survival under unfavorable conditions by providing nutrients through the removal of damaged or aged proteins, or organelles. In this article, we examine the interplay between metabolism and autophagy, focusing on the different aspects of this reciprocal relationship. We show that autophagy has a strong influence on a range of metabolic processes, whereas, at the same time, even single metabolites can activate autophagy. We highlight the involvement of ATG genes in metabolism, examine the role of the macronutrients carbon and nitrogen, as well as various micronutrients, and take a closer look at how the interaction between autophagy and metabolism impacts on plant phenotypes and yield.
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Affiliation(s)
- Sahar Magen
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Israel
| | - Heike Seybold
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Israel
| | - Daniel Laloum
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Israel
| | - Tamar Avin-Wittenberg
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Israel
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