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Yuen ELH, Leary AY, Clavel M, Tumtas Y, Mohseni A, Zhao J, Picchianti L, Jamshidiha M, Pandey P, Duggan C, Cota E, Dagdas Y, Bozkurt TO. A RabGAP negatively regulates plant autophagy and immune trafficking. Curr Biol 2024; 34:2049-2065.e6. [PMID: 38677281 DOI: 10.1016/j.cub.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 03/11/2024] [Accepted: 04/02/2024] [Indexed: 04/29/2024]
Abstract
Plants rely on autophagy and membrane trafficking to tolerate stress, combat infections, and maintain cellular homeostasis. However, the molecular interplay between autophagy and membrane trafficking is poorly understood. Using an AI-assisted approach, we identified Rab3GAP-like (Rab3GAPL) as a key membrane trafficking node that controls plant autophagy negatively. Rab3GAPL suppresses autophagy by binding to ATG8, the core autophagy adaptor, and deactivating Rab8a, a small GTPase essential for autophagosome formation and defense-related secretion. Rab3GAPL reduces autophagic flux in three model plant species, suggesting that its negative regulatory role in autophagy is conserved in land plants. Beyond autophagy regulation, Rab3GAPL modulates focal immunity against the oomycete pathogen Phytophthora infestans by preventing defense-related secretion. Altogether, our results suggest that Rab3GAPL acts as a molecular rheostat to coordinate autophagic flux and defense-related secretion by restraining Rab8a-mediated trafficking. This unprecedented interplay between a RabGAP-Rab pair and ATG8 sheds new light on the intricate membrane transport mechanisms underlying plant autophagy and immunity.
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Affiliation(s)
- Enoch Lok Him Yuen
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Alexandre Y Leary
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Marion Clavel
- Gregor Mendel Institute of Molecular Plant Biology, Vienna BioCenter, Dr. Bohr-Gasse, 1030 Vienna, Austria; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Yasin Tumtas
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Azadeh Mohseni
- Gregor Mendel Institute of Molecular Plant Biology, Vienna BioCenter, Dr. Bohr-Gasse, 1030 Vienna, Austria
| | - Jierui Zhao
- Gregor Mendel Institute of Molecular Plant Biology, Vienna BioCenter, Dr. Bohr-Gasse, 1030 Vienna, Austria
| | - Lorenzo Picchianti
- Gregor Mendel Institute of Molecular Plant Biology, Vienna BioCenter, Dr. Bohr-Gasse, 1030 Vienna, Austria
| | - Mostafa Jamshidiha
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Pooja Pandey
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Cian Duggan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Ernesto Cota
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Yasin Dagdas
- Gregor Mendel Institute of Molecular Plant Biology, Vienna BioCenter, Dr. Bohr-Gasse, 1030 Vienna, Austria.
| | - Tolga O Bozkurt
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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2
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Bentham AR, Wang W, Trusch F, Varden FA, Birch PRJ, Banfield MJ. The WY Domain of an RxLr Effector Drives Interactions with a Host Target Phosphatase to Mimic Host Regulatory Proteins and Promote Phytophthora infestans Infection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:239-249. [PMID: 37921637 DOI: 10.1094/mpmi-08-23-0118-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Plant pathogens manipulate the cellular environment of the host to facilitate infection and colonization that often lead to plant diseases. To accomplish this, many specialized pathogens secrete virulence proteins called effectors into the host cell, which subvert processes such as immune signaling, gene transcription, and host metabolism. Phytophthora infestans, the causative agent of potato late blight, employs an expanded repertoire of RxLR effectors with WY domains to manipulate the host through direct interaction with protein targets. However, our understanding of the molecular mechanisms underlying the interactions between WY effectors and their host targets remains limited. In this study, we performed a structural and biophysical characterization of the P. infestans WY effector Pi04314 in complex with the potato Protein Phosphatase 1-c (PP1c). We elucidate how Pi04314 uses a WY domain and a specialized C-terminal loop carrying a KVxF motif that interact with conserved surfaces on PP1c, known to be used by host regulatory proteins for guiding function. Through biophysical and in planta analyses, we demonstrate that Pi04314 WY or KVxF mutants lose their ability to bind PP1c. The loss of PP1c binding correlates with changes in PP1c nucleolar localization and a decrease in lesion size in plant infection assays. This study provides insights into the manipulation of plant hosts by pathogens, revealing how effectors exploit key regulatory interfaces in host proteins to modify their function and facilitate disease. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Adam R Bentham
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Wei Wang
- Department of Cell and Molecular Sciences, James Hutton Institute, Invergowrie DD2 5DA, Dundee, U.K
- Division of Plant Sciences, College of Life Science, University of Dundee (at JHI), Invergowrie DD2 5DA, Dundee, U.K
| | - Franziska Trusch
- Department of Cell and Molecular Sciences, James Hutton Institute, Invergowrie DD2 5DA, Dundee, U.K
- Division of Plant Sciences, College of Life Science, University of Dundee (at JHI), Invergowrie DD2 5DA, Dundee, U.K
| | - Freya A Varden
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Paul R J Birch
- Department of Cell and Molecular Sciences, James Hutton Institute, Invergowrie DD2 5DA, Dundee, U.K
- Division of Plant Sciences, College of Life Science, University of Dundee (at JHI), Invergowrie DD2 5DA, Dundee, U.K
| | - Mark J Banfield
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
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3
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Noda NN. Structural view on autophagosome formation. FEBS Lett 2024; 598:84-106. [PMID: 37758522 DOI: 10.1002/1873-3468.14742] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/02/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023]
Abstract
Autophagy is a conserved intracellular degradation system in eukaryotes, involving the sequestration of degradation targets into autophagosomes, which are subsequently delivered to lysosomes (or vacuoles in yeasts and plants) for degradation. In budding yeast, starvation-induced autophagosome formation relies on approximately 20 core Atg proteins, grouped into six functional categories: the Atg1/ULK complex, the phosphatidylinositol-3 kinase complex, the Atg9 transmembrane protein, the Atg2-Atg18/WIPI complex, the Atg8 lipidation system, and the Atg12-Atg5 conjugation system. Additionally, selective autophagy requires cargo receptors and other factors, including a fission factor, for specific sequestration. This review covers the 30-year history of structural studies on core Atg proteins and factors involved in selective autophagy, examining X-ray crystallography, NMR, and cryo-EM techniques. The molecular mechanisms of autophagy are explored based on protein structures, and future directions in the structural biology of autophagy are discussed, considering the advancements in the era of AlphaFold.
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Affiliation(s)
- Nobuo N Noda
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
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4
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Rogov VV, Nezis IP, Tsapras P, Zhang H, Dagdas Y, Noda NN, Nakatogawa H, Wirth M, Mouilleron S, McEwan DG, Behrends C, Deretic V, Elazar Z, Tooze SA, Dikic I, Lamark T, Johansen T. Atg8 family proteins, LIR/AIM motifs and other interaction modes. AUTOPHAGY REPORTS 2023; 2:27694127.2023.2188523. [PMID: 38214012 PMCID: PMC7615515 DOI: 10.1080/27694127.2023.2188523] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
The Atg8 family of ubiquitin-like proteins play pivotal roles in autophagy and other processes involving vesicle fusion and transport where the lysosome/vacuole is the end station. Nuclear roles of Atg8 proteins are also emerging. Here, we review the structural and functional features of Atg8 family proteins and their protein-protein interaction modes in model organisms such as yeast, Arabidopsis, C. elegans and Drosophila to humans. Although varying in number of homologs, from one in yeast to seven in humans, and more than ten in some plants, there is a strong evolutionary conservation of structural features and interaction modes. The most prominent interaction mode is between the LC3 interacting region (LIR), also called Atg8 interacting motif (AIM), binding to the LIR docking site (LDS) in Atg8 homologs. There are variants of these motifs like "half-LIRs" and helical LIRs. We discuss details of the binding modes and how selectivity is achieved as well as the role of multivalent LIR-LDS interactions in selective autophagy. A number of LIR-LDS interactions are known to be regulated by phosphorylation. New methods to predict LIR motifs in proteins have emerged that will aid in discovery and analyses. There are also other interaction surfaces than the LDS becoming known where we presently lack detailed structural information, like the N-terminal arm region and the UIM-docking site (UDS). More interaction modes are likely to be discovered in future studies.
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Affiliation(s)
- Vladimir V. Rogov
- Institute for Pharmaceutical Chemistry, Department of Biochemistry, Chemistry and Pharmacy, Goethe University, 60438 Frankfurt, am Main, and Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Ioannis P. Nezis
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
| | | | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China and College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yasin Dagdas
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo 060-0815, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Martina Wirth
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Stephane Mouilleron
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | | | - Christian Behrends
- Munich Cluster of Systems Neurology, Ludwig-Maximilians-Universität München, München, Germany
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM and Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Zvulun Elazar
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Ivan Dikic
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt am Main, and Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Trond Lamark
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Terje Johansen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
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5
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Wang S, McLellan H, Boevink PC, Birch PRJ. RxLR Effectors: Master Modulators, Modifiers and Manipulators. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:754-763. [PMID: 37750829 DOI: 10.1094/mpmi-05-23-0054-cr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Cytoplasmic effectors with an Arg-any amino acid-Arg-Leu (RxLR) motif are encoded by hundreds of genes within the genomes of oomycete Phytophthora spp. and downy mildew pathogens. There has been a dramatic increase in our understanding of the evolution, function, and recognition of these effectors. Host proteins with a wide range of subcellular localizations and functions are targeted by RxLR effectors. Many processes are manipulated, including transcription, post-translational modifications, such as phosphorylation and ubiquitination, secretion, and intracellular trafficking. This involves an array of RxLR effector modes-of-action, including stabilization or destabilization of protein targets, altering or disrupting protein complexes, inhibition or utility of target enzyme activities, and changing the location of protein targets. Interestingly, approximately 50% of identified host proteins targeted by RxLR effectors are negative regulators of immunity. Avirulence RxLR effectors may be directly or indirectly detected by nucleotide-binding leucine-rich repeat resistance (NLR) proteins. Direct recognition by a single NLR of RxLR effector orthologues conserved across multiple Phytophthora pathogens may provide wide protection of diverse crops. Failure of RxLR effectors to interact with or appropriately manipulate target proteins in nonhost plants has been shown to restrict host range. This knowledge can potentially be exploited to alter host targets to prevent effector interaction, providing a barrier to host infection. Finally, recent evidence suggests that RxLR effectors, like cytoplasmic effectors from fungal pathogen Magnaporthe oryzae, may enter host cells via clathrin-mediated endocytosis. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Shumei Wang
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, U.S.A
| | - Hazel McLellan
- Division of Plant Sciences, School of Life Sciences, University of Dundee, at James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Petra C Boevink
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Paul R J Birch
- Division of Plant Sciences, School of Life Sciences, University of Dundee, at James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
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6
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Ji C, Zhou J, Yang D, Yuan B, Tang R, Liu Y, Xi D. ATG8f Interacts with Chilli Veinal Mottle Virus 6K2 Protein to Limit Virus Infection. Viruses 2023; 15:2324. [PMID: 38140565 PMCID: PMC10747504 DOI: 10.3390/v15122324] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Autophagy, as a conserved protein degradation pathway in plants, has also been reported to be intricately associated with antiviral defense mechanisms. However, the relationship between chilli veinal mottle virus (ChiVMV) and autophagy has not been investigated in the existing research. Here, we reveal that ChiVMV infection caused the accumulation of autophagosomes in infected Nicotiana benthamiana leaves and the upregulation of autophagy-related genes (ATGs). Moreover, the changes in gene expression were correlated with the development of symptoms. Treatment with autophagy inhibitors (3-MA or E-64D) could increase the infection sites and facilitate virus infection, whereas treatment with the autophagy activator (Rapamycin) limited virus infection. Then, ATG8f was identified to interact with ChiVMV 6K2 protein directly in vitro and in vivo. The silencing of ATG8f promoted virus infection, whereas the overexpression of ATG8f inhibited virus infection. Furthermore, the expression of 6K2-GFP in ATG8f- or ATG7-silenced plants was significantly higher than that in control plants. Rapamycin treatment reduced the accumulation of 6K2-GFP in plant cells, whereas treatment with the inhibitor of the ubiquitin pathway (MG132), 3-MA, or E-64D displayed little impact on the accumulation of 6K2-GFP. Thus, our results demonstrated that ATG8f interacts with the ChiVMV 6K2 protein, promoting the degradation of 6K2 through the autophagy pathway.
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Affiliation(s)
- Chenglong Ji
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (C.J.)
| | - Jingya Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (C.J.)
| | - Daoyong Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (C.J.)
| | - Bowen Yuan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (C.J.)
| | - Rongxia Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (C.J.)
| | - Yong Liu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Dehui Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (C.J.)
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7
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Chepsergon J, Moleleki LN. "Order from disordered": Potential role of intrinsically disordered regions in phytopathogenic oomycete intracellular effector proteins. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102402. [PMID: 37329857 DOI: 10.1016/j.pbi.2023.102402] [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: 11/28/2022] [Revised: 05/13/2023] [Accepted: 05/17/2023] [Indexed: 06/19/2023]
Abstract
There is a continuous arms race between pathogens and their host plants. However, successful pathogens, such as phytopathogenic oomycetes, secrete effector proteins to manipulate host defense responses for disease development. Structural analyses of these effector proteins reveal the existence of regions that fail to fold into three-dimensional structures, intrinsically disordered regions (IDRs). Because of their flexibility, these regions are involved in important biological functions of effector proteins, such as effector-host protein interactions that perturb host immune responses. Despite their significance, the role of IDRs in phytopathogenic oomycete effector-host protein interactions is not clear. This review, therefore, searched the literature for functionally characterized oomycete intracellular effectors with known host interactors. We further classify regions that mediate effector-host protein interactions into globular or disordered binding sites in these proteins. To fully appreciate the potential role of IDRs, five effector proteins encoding potential disordered binding sites were used as case studies. We also propose a pipeline that can be used to identify, classify as well as characterize potential binding regions in effector proteins. Understanding the role of IDRs in these effector proteins can aid in the development of new disease-control strategies.
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Affiliation(s)
- Jane Chepsergon
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa.
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8
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Zeng Y, Liang Z, Liu Z, Li B, Cui Y, Gao C, Shen J, Wang X, Zhao Q, Zhuang X, Erdmann PS, Wong KB, Jiang L. Recent advances in plant endomembrane research and new microscopical techniques. THE NEW PHYTOLOGIST 2023; 240:41-60. [PMID: 37507353 DOI: 10.1111/nph.19134] [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: 05/12/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023]
Abstract
The endomembrane system consists of various membrane-bound organelles including the endoplasmic reticulum (ER), Golgi apparatus, trans-Golgi network (TGN), endosomes, and the lysosome/vacuole. Membrane trafficking between distinct compartments is mainly achieved by vesicular transport. As the endomembrane compartments and the machineries regulating the membrane trafficking are largely conserved across all eukaryotes, our current knowledge on organelle biogenesis and endomembrane trafficking in plants has mainly been shaped by corresponding studies in mammals and yeast. However, unique perspectives have emerged from plant cell biology research through the characterization of plant-specific regulators as well as the development and application of the state-of-the-art microscopical techniques. In this review, we summarize our current knowledge on the plant endomembrane system, with a focus on several distinct pathways: ER-to-Golgi transport, protein sorting at the TGN, endosomal sorting on multivesicular bodies, vacuolar trafficking/vacuole biogenesis, and the autophagy pathway. We also give an update on advanced imaging techniques for the plant cell biology research.
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Affiliation(s)
- Yonglun Zeng
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Zizhen Liang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Zhiqi Liu
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Baiying Li
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yong Cui
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xiangfeng Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qiong Zhao
- School of Life Sciences, East China Normal University, Shanghai, 200062, China
| | - Xiaohong Zhuang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Philipp S Erdmann
- Human Technopole, Viale Rita Levi-Montalcini, 1, Milan, I-20157, Italy
| | - Kam-Bo Wong
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong (CUHK), Shatin, Hong Kong, China
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- The CUHK Shenzhen Research Institute, Shenzhen, 518057, China
- Institute of Plant Molecular Biology and Agricultural Biotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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9
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Mallén-Ponce MJ, Gámez-Arcas S, Pérez-Pérez ME. Redox partner interactions in the ATG8 lipidation system in microalgae. Free Radic Biol Med 2023; 203:58-68. [PMID: 37028463 DOI: 10.1016/j.freeradbiomed.2023.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/09/2023]
Abstract
Autophagy is a catabolic pathway that functions as a degradative and recycling process to maintain cellular homeostasis in most eukaryotic cells, including photosynthetic organisms such as microalgae. This process involves the formation of double-membrane vesicles called autophagosomes, which engulf the material to be degraded and recycled in lytic compartments. Autophagy is mediated by a set of highly conserved autophagy-related (ATG) proteins that play a fundamental role in the formation of the autophagosome. The ATG8 ubiquitin-like system catalyzes the conjugation of ATG8 to the lipid phosphatidylethanolamine, an essential reaction in the autophagy process. Several studies identified the ATG8 system and other core ATG proteins in photosynthetic eukaryotes. However, how ATG8 lipidation is driven and regulated in these organisms is not fully understood yet. A detailed analysis of representative genomes from the entire microalgal lineage revealed a high conservation of ATG proteins in these organisms with the remarkable exception of red algae, which likely lost ATG genes before diversification. Here, we examine in silico the mechanisms and dynamic interactions between different components of the ATG8 lipidation system in plants and algae. Moreover, we also discuss the role of redox post-translational modifications in the regulation of ATG proteins and the activation of autophagy in these organisms by reactive oxygen species.
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Affiliation(s)
- Manuel J Mallén-Ponce
- Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 75005, Paris, France
| | - Samuel Gámez-Arcas
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092, Sevilla, Spain
| | - María Esther Pérez-Pérez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092, Sevilla, Spain.
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10
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Vo KTX, Yi Q, Jeon JS. Engineering effector-triggered immunity in rice: Obstacles and perspectives. PLANT, CELL & ENVIRONMENT 2023; 46:1143-1156. [PMID: 36305486 DOI: 10.1111/pce.14477] [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: 06/29/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Improving rice immunity is one of the most effective approaches to reduce yield loss by biotic factors, with the aim of increasing rice production by 2050 amidst limited natural resources. Triggering a fast and strong immune response to pathogens, effector-triggered immunity (ETI) has intrigued scientists to intensively study and utilize the mechanisms for engineering highly resistant plants. The conservation of ETI components and mechanisms across species enables the use of ETI components to generate broad-spectrum resistance in plants. Numerous efforts have been made to introduce new resistance (R) genes, widen the effector recognition spectrum and generate on-demand R genes. Although engineering ETI across plant species is still associated with multiple challenges, previous attempts have provided an enhanced understanding of ETI mechanisms. Here, we provide a survey of recent reports in the engineering of rice R genes. In addition, we suggest a framework for future studies of R gene-effector interactions, including genome-scale investigations in both rice and pathogens, followed by structural studies of R proteins and effectors, and potential strategies to use important ETI components to improve rice immunity.
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Affiliation(s)
- Kieu Thi Xuan Vo
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Korea
| | - Qi Yi
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Korea
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Korea
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11
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Lovelace AH, Dorhmi S, Hulin MT, Li Y, Mansfield JW, Ma W. Effector Identification in Plant Pathogens. PHYTOPATHOLOGY 2023; 113:637-650. [PMID: 37126080 DOI: 10.1094/phyto-09-22-0337-kd] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Effectors play a central role in determining the outcome of plant-pathogen interactions. As key virulence proteins, effectors are collectively indispensable for disease development. By understanding the virulence mechanisms of effectors, fundamental knowledge of microbial pathogenesis and disease resistance have been revealed. Effectors are also considered double-edged swords because some of them activate immunity in disease resistant plants after being recognized by specific immune receptors, which evolved to monitor pathogen presence or activity. Characterization of effector recognition by their cognate immune receptors and the downstream immune signaling pathways is instrumental in implementing resistance. Over the past decades, substantial research effort has focused on effector biology, especially concerning their interactions with virulence targets or immune receptors in plant cells. A foundation of this research is robust identification of the effector repertoire from a given pathogen, which depends heavily on bioinformatic prediction. In this review, we summarize methodologies that have been used for effector mining in various microbial pathogens which use different effector delivery mechanisms. We also discuss current limitations and provide perspectives on how recently developed analytic tools and technologies may facilitate effector identification and hence generation of a more complete vision of host-pathogen interactions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
| | - Sara Dorhmi
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
- Department of Microbiology and Plant Pathology, University of California Riverside, CA 92521, U.S.A
| | | | - Yufei Li
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
| | - John W Mansfield
- Faculty of Natural Sciences, Imperial College London, London, SW7 2BX, U.K
| | - Wenbo Ma
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
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12
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Yan H, Zhuang M, Xu X, Li S, Yang M, Li N, Du X, Hu K, Peng X, Huang W, Wu H, Tse YC, Zhao L, Wang H. Autophagy and its mediated mitochondrial quality control maintain pollen tube growth and male fertility in Arabidopsis. Autophagy 2023; 19:768-783. [PMID: 35786359 PMCID: PMC9980518 DOI: 10.1080/15548627.2022.2095838] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Macroautophagy/autophagy, a major catabolic pathway in eukaryotes, participates in plant sexual reproduction including the processes of male gametogenesis and the self-incompatibility response. Rapid pollen tube growth is another essential reproductive process that is metabolically highly demanding to drive the vigorous cell growth for delivery of male gametes for fertilization in angiosperms. Whether and how autophagy operates to maintain the homeostasis of pollen tubes remains unknown. Here, we provide evidence that autophagy is elevated in growing pollen tubes and critically required during pollen tube growth and male fertility in Arabidopsis. We demonstrate that SH3P2, a critical non-ATG regulator of plant autophagy, colocalizes with representative ATG proteins during autophagosome biogenesis in growing pollen tubes. Downregulation of SH3P2 expression significantly disrupts Arabidopsis pollen germination and pollen tube growth. Further analysis of organelle dynamics reveals crosstalk between autophagosomes and prevacuolar compartments following the inhibition of phosphatidylinositol 3-kinase. In addition, time-lapse imaging and tracking of ATG8e-labeled autophagosomes and depolarized mitochondria demonstrate that they interact specifically via the ATG8-family interacting motif (AIM)-docking site to mediate mitophagy. Ultrastructural identification of mitophagosomes and two additional forms of autophagosomes imply that multiple types of autophagy are likely to function simultaneously within pollen tubes. Altogether, our results suggest that autophagy is functionally crucial for mediating mitochondrial quality control and canonical cytoplasm recycling during pollen tube growth.Abbreviations: AIM: ATG8-family interacting motif; ATG8: autophagy related 8; ATG5: autophagy related 5; ATG7: autophagy related 7; BTH: acibenzolar-S-methyl; DEX: dexamethasone; DNP: 2,4-dinitrophenol; GFP: green fluorescent protein; YFP: yellow fluorescent protein; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; PVC: prevacuolar compartment; SH3P2: SH3 domain-containing protein 2.
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Affiliation(s)
- He Yan
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, Hong Kong, China
| | - Menglong Zhuang
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, Hong Kong, China
| | - Xiaoyu Xu
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, Hong Kong, China
| | - Shanshan Li
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, Hong Kong, China
| | - Mingkang Yang
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, Hong Kong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou null China
| | - Nianle Li
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, Hong Kong, China
| | - Xiaojuan Du
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, Hong Kong, China
| | - Kangwei Hu
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, Hong Kong, China
| | - Xiaomin Peng
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, Hong Kong, China
| | - Wei Huang
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, Hong Kong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou null China
| | - Hong Wu
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, Hong Kong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou null China
| | - Yu Chung Tse
- Core Research Facilities, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lifeng Zhao
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, Hong Kong, China
| | - Hao Wang
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, Hong Kong, China
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13
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Ibrahim T, Khandare V, Mirkin FG, Tumtas Y, Bubeck D, Bozkurt TO. AlphaFold2-multimer guided high-accuracy prediction of typical and atypical ATG8-binding motifs. PLoS Biol 2023; 21:e3001962. [PMID: 36753519 PMCID: PMC9907853 DOI: 10.1371/journal.pbio.3001962] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/15/2022] [Indexed: 02/09/2023] Open
Abstract
Macroautophagy/autophagy is an intracellular degradation process central to cellular homeostasis and defense against pathogens in eukaryotic cells. Regulation of autophagy relies on hierarchical binding of autophagy cargo receptors and adaptors to ATG8/LC3 protein family members. Interactions with ATG8/LC3 are typically facilitated by a conserved, short linear sequence, referred to as the ATG8/LC3 interacting motif/region (AIM/LIR), present in autophagy adaptors and receptors as well as pathogen virulence factors targeting host autophagy machinery. Since the canonical AIM/LIR sequence can be found in many proteins, identifying functional AIM/LIR motifs has proven challenging. Here, we show that protein modelling using Alphafold-Multimer (AF2-multimer) identifies both canonical and atypical AIM/LIR motifs with a high level of accuracy. AF2-multimer can be modified to detect additional functional AIM/LIR motifs by using protein sequences with mutations in primary AIM/LIR residues. By combining protein modelling data from AF2-multimer with phylogenetic analysis of protein sequences and protein-protein interaction assays, we demonstrate that AF2-multimer predicts the physiologically relevant AIM motif in the ATG8-interacting protein 2 (ATI-2) as well as the previously uncharacterized noncanonical AIM motif in ATG3 from potato (Solanum tuberosum). AF2-multimer also identified the AIM/LIR motifs in pathogen-encoded virulence factors that target ATG8 members in their plant and human hosts, revealing that cross-kingdom ATG8-LIR/AIM associations can also be predicted by AF2-multimer. We conclude that the AF2-guided discovery of autophagy adaptors/receptors will substantially accelerate our understanding of the molecular basis of autophagy in all biological kingdoms.
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Affiliation(s)
- Tarhan Ibrahim
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Virendrasinh Khandare
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Agrotechnology and Food Sciences, Biochemistry, Wageningen University and Research, Wageningen, the Netherlands
| | - Federico Gabriel Mirkin
- Department of Life Sciences, Imperial College London, London, United Kingdom
- INGEBI-CONICET, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | - Yasin Tumtas
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Doryen Bubeck
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail: (DB); (TOB)
| | - Tolga O. Bozkurt
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail: (DB); (TOB)
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14
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Macquet J, Mounichetty S, Raffaele S. Genetic co-option into plant-filamentous pathogen interactions. TRENDS IN PLANT SCIENCE 2022; 27:1144-1158. [PMID: 35909010 DOI: 10.1016/j.tplants.2022.06.011] [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: 02/23/2022] [Revised: 06/16/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Plants are engaged in a coevolutionary arms race with their pathogens that drives rapid diversification and specialization of genes involved in resistance and virulence. However, some major innovations in plant-pathogen interactions, such as molecular decoys, trans-kingdom RNA interference, two-speed genomes, and receptor networks, evolved through the expansion of the functional landscape of genes. This is a typical outcome of genetic co-option, the evolutionary process by which available genes are recruited into new biological functions. Co-option into plant-pathogen interactions emerges generally from (i) cis-regulatory variation, (ii) horizontal gene transfer (HGT), (iii) mutations altering molecular promiscuity, and (iv) rewiring of gene networks and protein complexes. Understanding these molecular mechanisms is key for the functional and predictive biology of plant-pathogen interactions.
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Affiliation(s)
- Joris Macquet
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France
| | - Shantala Mounichetty
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France.
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15
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Regressive evolution of an effector following a host jump in the Irish potato famine pathogen lineage. PLoS Pathog 2022; 18:e1010918. [DOI: 10.1371/journal.ppat.1010918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 11/08/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
In order to infect a new host species, the pathogen must evolve to enhance infection and transmission in the novel environment. Although we often think of evolution as a process of accumulation, it is also a process of loss. Here, we document an example of regressive evolution of an effector activity in the Irish potato famine pathogen (Phytophthora infestans) lineage, providing evidence that a key sequence motif in the effector PexRD54 has degenerated following a host jump. We began by looking at PexRD54 and PexRD54-like sequences from across Phytophthora species. We found that PexRD54 emerged in the common ancestor of Phytophthora clade 1b and 1c species, and further sequence analysis showed that a key functional motif, the C-terminal ATG8-interacting motif (AIM), was also acquired at this point in the lineage. A closer analysis showed that the P. mirabilis PexRD54 (PmPexRD54) AIM is atypical, the otherwise-conserved central residue mutated from a glutamate to a lysine. We aimed to determine whether this PmPexRD54 AIM polymorphism represented an adaptation to the Mirabilis jalapa host environment. We began by characterizing the M. jalapa ATG8 family, finding that they have a unique evolutionary history compared to previously characterized ATG8s. Then, using co-immunoprecipitation and isothermal titration calorimetry assays, we showed that both full-length PmPexRD54 and the PmPexRD54 AIM peptide bind weakly to the M. jalapa ATG8s. Through a combination of binding assays and structural modelling, we showed that the identity of the residue at the position of the PmPexRD54 AIM polymorphism can underpin high-affinity binding to plant ATG8s. Finally, we conclude that the functionality of the PexRD54 AIM was lost in the P. mirabilis lineage, perhaps owing to as-yet-unknown selection pressure on this effector in the new host environment.
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16
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Kotsaridis K, Tsakiri D, Sarris PF. Understanding enemy's weapons to an effective prevention: common virulence effects across microbial phytopathogens kingdoms. Crit Rev Microbiol 2022:1-15. [PMID: 35709325 DOI: 10.1080/1040841x.2022.2083939] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Plant-pathogens interaction is an ongoing confrontation leading to the emergence of new diseases. The majority of the invading microorganisms inject effector proteins into the host cell, to bypass the sophisticated defense system of the host. However, the effectors could also have other specialized functions, which can disrupt various biological pathways of the host cell. Pathogens can enrich their effectors arsenal to increase infection success or expand their host range. This usually is accomplished by the horizontal gene transfer. Nowadays, the development of specialized software that can predict proteins structure, has changed the experimental designing in effectors' function research. Different effectors of distinct plant pathogens tend to fold alike and have the same function and focussed structural studies on microbial effectors can help to uncover their catalytic/functional activities, while the structural similarity can enable cataloguing the great number of pathogens' effectors. In this review, we collectively present phytopathogens' effectors with known enzymatic functions and proteins structure, originated from all the kingdoms of microbial plant pathogens. Presentation of their common domains and motifs is also included. We believe that the in-depth understanding of the enemy's weapons will help the development of new strategies to prevent newly emerging or re-emerging plant pathogens.
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Affiliation(s)
| | | | - Panagiotis F Sarris
- Department of Biology, University of Crete, Crete, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Crete, Greece.,Biosciences, University of Exeter, Exeter, UK
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17
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Sun S, Feng L, Chung KP, Lee KM, Cheung HHY, Luo M, Ren K, Law KC, Jiang L, Wong KB, Zhuang X. Mechanistic insights into an atypical interaction between ATG8 and SH3P2 in Arabidopsis thaliana. Autophagy 2022; 18:1350-1366. [PMID: 34657568 PMCID: PMC9225624 DOI: 10.1080/15548627.2021.1976965] [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: 01/09/2023] Open
Abstract
In selective macroautophagy/autophagy, cargo receptors are recruited to the forming autophagosome by interacting with Atg8 (autophagy-related 8)-family proteins and facilitate the selective sequestration of specific cargoes for autophagic degradation. In addition, Atg8 interacts with a number of adaptors essential for autophagosome biogenesis, including ATG and non-ATG proteins. The majority of these adaptors and receptors are characterized by an Atg8-family interacting motif (AIM) for binding to Atg8. However, the molecular basis for the interaction mode between ATG8 and regulators or cargo receptors in plants remains largely unclear. In this study, we unveiled an atypical interaction mode for Arabidopsis ATG8f with a plant unique adaptor protein, SH3P2 (SH3 domain-containing protein 2), but not with the other two SH3 proteins. By structure analysis of the unbound form of ATG8f, we identified the unique conformational changes in ATG8f upon binding to the AIM sequence of a plant known autophagic receptor, NBR1. To compare the binding affinity of SH3P2-ATG8f with that of ATG8f-NBR1, we performed a gel filtration assay to show that ubiquitin-associated domain of NBR1 outcompetes the SH3 domain of SH3P2 for ATG8f interaction. Biochemical and cellular analysis revealed that distinct interfaces were employed by ATG8f to interact with NBR1 and SH3P2. Further subcellular analysis showed that the AIM-like motif of SH3P2 is essential for its recruitment to the phagophore membrane but is dispensable for its trafficking in endocytosis. Taken together, our study provides an insightful structural basis for the ATG8 binding specificity toward a plant-specific autophagic adaptor and a conserved autophagic receptor.Abbreviations: ATG, autophagy-related; AIM, Atg8-family interacting motif; BAR, Bin-Amphiphysin-Rvs; BFA, brefeldin A; BTH, benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester; CCV, clathrin-coated-vesicle; CLC2, clathrin light chain 2; Conc A, concanamycin A; ER, endoplasmic reticulum; LDS, LIR docking site; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; LIR, LC3-interacting region; PE, phosphatidylethanolamine; SH3P2, SH3 domain containing protein 2; SH3, Src-Homology-3; UBA, ubiquitin-associated; UIM, ubiquitin-interacting motif.
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Affiliation(s)
- Shuangli Sun
- Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Lanlan Feng
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kin Pan Chung
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China,Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Ka-Ming Lee
- Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hayley Hei-Yin Cheung
- Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Mengqian Luo
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kaike Ren
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kai Ching Law
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Liwen Jiang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China,The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Kam-Bo Wong
- Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaohong Zhuang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China,CONTACT Xiaohong Zhuang Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
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18
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Outram MA, Figueroa M, Sperschneider J, Williams SJ, Dodds PN. Seeing is believing: Exploiting advances in structural biology to understand and engineer plant immunity. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102210. [PMID: 35461025 DOI: 10.1016/j.pbi.2022.102210] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/27/2022] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Filamentous plant pathogens cause disease in numerous economically important crops. These pathogens secrete virulence proteins, termed effectors, that modulate host cellular processes and promote infection. Plants have evolved immunity receptors that detect effectors and activate defence pathways, resulting in resistance to the invading pathogen. This leads to an evolutionary arms race between pathogen and host that is characterised by highly diverse effector repertoires in plant pathogens. Here, we review the recent advances in understanding host-pathogen co-evolution provided by the structural determination of effectors alone, and in complex with immunity receptors. We highlight the use of recent advances in structural prediction within this field and its role for future development of designer resistance proteins.
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Affiliation(s)
- Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia.
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19
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Coordinative regulation of ERAD and selective autophagy in plants. Essays Biochem 2022; 66:179-188. [PMID: 35612379 DOI: 10.1042/ebc20210099] [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: 02/24/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 12/30/2022]
Abstract
Endoplasmic reticulum-associated degradation (ERAD) plays important roles in plant development, hormone signaling, and plant-environment stress interactions by promoting the clearance of certain proteins or soluble misfolded proteins through the ubiquitin-proteasome system. Selective autophagy is involved in the autophagic degradation of protein aggregates mediated by specific selective autophagy receptors. These two major degradation routes co-operate with each other to relieve the cytotoxicity caused by ER stress. In this review, we analyze ERAD and different types of autophagy, including nonselective macroautophagy and ubiquitin-dependent and ubiquitin-independent selective autophagy in plants, and specifically summarize the selective autophagy receptors characterized in plants. In addition to being a part of selective autophagy, ERAD components also serve as their cargos. Moreover, an ubiquitinated substrate can be delivered to two distinguishable degradation systems, while the underlying determinants remain elusive. These excellent findings suggest an interdependent but complicated relationship between ERAD and selective autophagy. According to this point, we propose several key issues that need to be addressed in the future.
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20
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Short Linear Motifs (SLiMs) in “Core” RxLR Effectors of
Phytophthora parasitica
var.
nicotianae
: a Case of PpRxLR1 Effector. Microbiol Spectr 2022; 10:e0177421. [PMID: 35404090 PMCID: PMC9045269 DOI: 10.1128/spectrum.01774-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Oomycetes of the genus Phytophthora encompass several of the most successful plant pathogens described to date. The success of infection by Phytophthora species is attributed to the pathogens’ ability to secrete effector proteins that alter the host’s physiological processes. Structural analyses of effector proteins mainly from bacterial and viral pathogens have revealed the presence of intrinsically disordered regions that host short linear motifs (SLiMs). These motifs play important biological roles by facilitating protein-protein interactions as well as protein translocation. Nonetheless, SLiMs in Phytophthora species RxLR effectors have not been investigated previously and their roles remain unknown. Using a bioinformatics pipeline, we identified 333 candidate RxLR effectors in the strain INRA 310 of Phytophthora parasitica. Of these, 71 (21%) were also found to be present in 10 other genomes of P. parasitica, and hence, these were designated core RxLR effectors (CREs). Within the CRE sequences, the N terminus exhibited enrichment in intrinsically disordered regions compared to the C terminus, suggesting a potential role of disorder in effector translocation. Although the disorder content was reduced in the C-terminal regions, it is important to mention that most SLiMs were in this terminus. PpRxLR1 is one of the 71 CREs identified in this study, and its genes encode a 6-amino acid (aa)-long SLiM at the C terminus. We showed that PpRxLR1 interacts with several host proteins that are implicated in defense. Structural analysis of this effector using homology modeling revealed the presence of potential ligand-binding sites. Among key residues that were predicted to be crucial for ligand binding, L102 and Y106 were of interest since they form part of the 6-aa-long PpRxLR1 SLiM. In silico substitution of these two residues to alanine was predicted to have a significant effect on both the function and the structure of PpRxLR1 effector. Molecular docking simulations revealed possible interactions between PpRxLR1 effector and ubiquitin-associated proteins. The ubiquitin-like SLiM carried in this effector was shown to be a potential mediator of these interactions. Further studies are required to validate and elucidate the underlying molecular mechanism of action. IMPORTANCE The continuous gain and loss of RxLR effectors makes the control of Phytophthora spp. difficult. Therefore, in this study, we endeavored to identify RxLR effectors that are highly conserved among species, also known as “core” RxLR effectors (CREs). We reason that these highly conserved effectors target conserved proteins or processes; thus, they can be harnessed in breeding for durable resistance in plants. To further understand the mechanisms of action of CREs, structural dissection of these proteins is crucial. Intrinsically disordered regions (IDRs) that do not adopt a fixed, three-dimensional fold carry short linear motifs (SLiMs) that mediate biological functions of proteins. The presence and potential role of these SLiMs in CREs of Phytophthora spp. have been overlooked. To our knowledge, we have effectively identified CREs as well as SLiMs with the potential of promoting effector virulence. Together, this work has advanced our comprehension of Phytophthora RxLR effector function and may facilitate the development of innovative and effective control strategies.
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21
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Yang Y, Xiang Y, Niu Y. An Overview of the Molecular Mechanisms and Functions of Autophagic Pathways in Plants. PLANT SIGNALING & BEHAVIOR 2021; 16:1977527. [PMID: 34617497 PMCID: PMC9208794 DOI: 10.1080/15592324.2021.1977527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
Autophagy is an evolutionarily conserved pathway for the degradation of damaged or toxic components. Under normal conditions, autophagy maintains cellular homeostasis. It can be triggered by senescence and various stresses. In the process of autophagy, autophagy-related (ATG) proteins not only function as central signal regulators but also participate in the development of complex survival mechanisms when plants suffer from adverse environments. Therefore, ATGs play significant roles in metabolism, development and stress tolerance. In the past decade, both the molecular mechanisms of autophagy and a large number of components involved in the assembly of autophagic vesicles have been identified. In recent studies, an increasing number of components, mechanisms, and receptors have appeared in the autophagy pathway. In this paper, we mainly review the recent progress of research on the molecular mechanisms of plant autophagy, as well as its function under biotic stress and abiotic stress.
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Affiliation(s)
- Yang Yang
- Moe Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences,Lanzhou University, Lanzhou, China
| | - Yun Xiang
- Moe Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences,Lanzhou University, Lanzhou, China
| | - Yue Niu
- Moe Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences,Lanzhou University, Lanzhou, China
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22
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Chepsergon J, Motaung TE, Moleleki LN. "Core" RxLR effectors in phytopathogenic oomycetes: A promising way to breeding for durable resistance in plants? Virulence 2021; 12:1921-1935. [PMID: 34304703 PMCID: PMC8516161 DOI: 10.1080/21505594.2021.1948277] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/11/2021] [Accepted: 06/18/2021] [Indexed: 12/30/2022] Open
Abstract
Phytopathogenic oomycetes are known to successfully infect their hosts due to their ability to secrete effector proteins. Of interest to many researchers are effectors with the N-terminal RxLR motif (Arginine-any amino acid-Leucine-Arginine). Owing to advances in genome sequencing, we can now comprehend the high level of diversity among oomycete effectors, and similarly, their conservation within and among species referred to here as "core" RxLR effectors (CREs). Currently, there is a considerable number of CREs that have been identified in oomycetes. Functional characterization of these CREs propose their virulence role with the potential of targeting central cellular processes that are conserved across diverse plant species. We reason that effectors that are highly conserved and recognized by the host, could be harnessed in engineering plants for durable as well as broad-spectrum resistance.
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Affiliation(s)
- Jane Chepsergon
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Thabiso E. Motaung
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
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23
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Rehman NU, Zeng P, Mo Z, Guo S, Liu Y, Huang Y, Xie Q. Conserved and Diversified Mechanism of Autophagy between Plants and Animals upon Various Stresses. Antioxidants (Basel) 2021; 10:1736. [PMID: 34829607 PMCID: PMC8615172 DOI: 10.3390/antiox10111736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 01/01/2023] Open
Abstract
Autophagy is a highly conserved degradation mechanism in eukaryotes, executing the breakdown of unwanted cell components and subsequent recycling of cellular material for stress relief through vacuole-dependence in plants and yeast while it is lysosome-dependent in animal manner. Upon stress, different types of autophagy are stimulated to operate certain biological processes by employing specific selective autophagy receptors (SARs), which hijack the cargo proteins or organelles to the autophagy machinery for subsequent destruction in the vacuole/lysosome. Despite recent advances in autophagy, the conserved and diversified mechanism of autophagy in response to various stresses between plants and animals still remain a mystery. In this review, we intend to summarize and discuss the characterization of the SARs and their corresponding processes, expectantly advancing the scope and perspective of the evolutionary fate of autophagy between plants and animals.
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Affiliation(s)
- Naveed Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
| | - Peichun Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
| | - Zulong Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
| | - Shaoying Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
| | - Yunfeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences and Technology, Guangxi University, Nanning 530004, China;
| | - Yifeng Huang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310001, China
| | - Qingjun Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
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24
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Pandey P, Leary AY, Tumtas Y, Savage Z, Dagvadorj B, Duggan C, Yuen EL, Sanguankiattichai N, Tan E, Khandare V, Connerton AJ, Yunusov T, Madalinski M, Mirkin FG, Schornack S, Dagdas Y, Kamoun S, Bozkurt TO. An oomycete effector subverts host vesicle trafficking to channel starvation-induced autophagy to the pathogen interface. eLife 2021; 10:65285. [PMID: 34424198 PMCID: PMC8382295 DOI: 10.7554/elife.65285] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 07/20/2021] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic cells deploy autophagy to eliminate invading microbes. In turn, pathogens have evolved effector proteins to counteract antimicrobial autophagy. How adapted pathogens co-opt autophagy for their own benefit is poorly understood. The Irish famine pathogen Phytophthora infestans secretes the effector protein PexRD54 that selectively activates an unknown plant autophagy pathway that antagonizes antimicrobial autophagy at the pathogen interface. Here, we show that PexRD54 induces autophagosome formation by bridging vesicles decorated by the small GTPase Rab8a with autophagic compartments labeled by the core autophagy protein ATG8CL. Rab8a is required for pathogen-triggered and starvation-induced but not antimicrobial autophagy, revealing specific trafficking pathways underpin selective autophagy. By subverting Rab8a-mediated vesicle trafficking, PexRD54 utilizes lipid droplets to facilitate biogenesis of autophagosomes diverted to pathogen feeding sites. Altogether, we show that PexRD54 mimics starvation-induced autophagy to subvert endomembrane trafficking at the host-pathogen interface, revealing how effectors bridge distinct host compartments to expedite colonization. With its long filaments reaching deep inside its prey, the tiny fungi-like organism known as Phytophthora infestans has had a disproportionate impact on human history. Latching onto plants and feeding on their cells, it has caused large-scale starvation events such as the Irish or Highland potato famines. Many specialized proteins allow the parasite to accomplish its feat. For instance, PexRD54 helps P. infestans hijack a cellular process known as autophagy. Healthy cells use this ‘self-eating’ mechanism to break down invaders or to recycle their components, for example when they require specific nutrients. The process is set in motion by various pathways of molecular events that result in specific sac-like ‘vesicles’ filled with cargo being transported to specialized compartments for recycling. PexRD54 can take over this mechanism by activating one of the plant autophagy pathways, directing cells to form autophagic vesicles that Phytophthora could then possibly use to feed on or to destroy antimicrobial components. How or why this is the case remains poorly understood. To examine these questions, Pandey, Leary et al. used a combination of genetic and microscopy techniques and tracked how PexRD54 alters autophagy as P. infestans infects a tobacco-related plant. The results show that PexRD54 works by bridging two proteins: one is present on cellular vesicles filled with cargo, and the other on autophagic structures surrounding the parasite. This allows PexRD54 to direct the vesicles to the feeding sites of P. infestans so the parasite can potentially divert nutrients. Pandey, Leary et al. then went on to develop a molecule called the AIM peptide, which could block autophagy by mimicking part of PexRD54. These results help to better grasp how a key disease affects crops, potentially leading to new ways to protect plants without the use of pesticides. They also shed light on autophagy: ultimately, a deeper understanding of this fundamental biological process could allow the development of plants which can adapt to changing environments.
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Affiliation(s)
| | | | | | | | | | - Cian Duggan
- Imperial College London, London, United Kingdom
| | | | | | - Emily Tan
- Imperial College London, London, United Kingdom
| | | | | | - Temur Yunusov
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, United Kingdom
| | - Mathias Madalinski
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Federico Gabriel Mirkin
- Imperial College London, London, United Kingdom.,Sainsbury Laboratory Cambridge University (SLCU), Cambridge, United Kingdom.,Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.,INGEBI-CONICET, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | | | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
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25
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Pandey P, Leary AY, Tumtas Y, Savage Z, Dagvadorj B, Duggan C, Yuen EL, Sanguankiattichai N, Tan E, Khandare V, Connerton AJ, Yunusov T, Madalinski M, Mirkin FG, Schornack S, Dagdas Y, Kamoun S, Bozkurt TO. An oomycete effector subverts host vesicle trafficking to channel starvation-induced autophagy to the pathogen interface. eLife 2021; 10:65285. [PMID: 34424198 DOI: 10.1101/2020.03.20.000117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 07/20/2021] [Indexed: 05/26/2023] Open
Abstract
Eukaryotic cells deploy autophagy to eliminate invading microbes. In turn, pathogens have evolved effector proteins to counteract antimicrobial autophagy. How adapted pathogens co-opt autophagy for their own benefit is poorly understood. The Irish famine pathogen Phytophthora infestans secretes the effector protein PexRD54 that selectively activates an unknown plant autophagy pathway that antagonizes antimicrobial autophagy at the pathogen interface. Here, we show that PexRD54 induces autophagosome formation by bridging vesicles decorated by the small GTPase Rab8a with autophagic compartments labeled by the core autophagy protein ATG8CL. Rab8a is required for pathogen-triggered and starvation-induced but not antimicrobial autophagy, revealing specific trafficking pathways underpin selective autophagy. By subverting Rab8a-mediated vesicle trafficking, PexRD54 utilizes lipid droplets to facilitate biogenesis of autophagosomes diverted to pathogen feeding sites. Altogether, we show that PexRD54 mimics starvation-induced autophagy to subvert endomembrane trafficking at the host-pathogen interface, revealing how effectors bridge distinct host compartments to expedite colonization.
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Affiliation(s)
| | | | | | | | | | - Cian Duggan
- Imperial College London, London, United Kingdom
| | | | | | - Emily Tan
- Imperial College London, London, United Kingdom
| | | | | | - Temur Yunusov
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, United Kingdom
| | - Mathias Madalinski
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Federico Gabriel Mirkin
- Imperial College London, London, United Kingdom
- Sainsbury Laboratory Cambridge University (SLCU), Cambridge, United Kingdom
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- INGEBI-CONICET, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | | | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
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26
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Dong S, Ma W. How to win a tug-of-war: the adaptive evolution of Phytophthora effectors. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102027. [PMID: 33684881 DOI: 10.1016/j.pbi.2021.102027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
The 'zigzag' model formulates some of the fundamental principles underpinning the dynamic interactions between pathogen effectors and plant immunity. As key virulence factors, effectors often exhibit a pattern of rapid evolution, presumably as a result of the host-pathogen arms race. Here, we summarize the current knowledge of mechanisms that may accelerate effector evolution in the highly successful Phytophthora pathogens. Recent findings on epigenetic regulation of effector genes that allows evasion of host recognition and maintenance of cost/benefit balance, and a conserved structural unit in effector proteins that may promote the evolution of virulence activities are highlighted.
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Affiliation(s)
- Suomeng Dong
- Department of Plant Pathology and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Wenbo Ma
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom; Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA.
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27
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Petre B, Contreras MP, Bozkurt TO, Schattat MH, Sklenar J, Schornack S, Abd-El-Haliem A, Castells-Graells R, Lozano-Durán R, Dagdas YF, Menke FLH, Jones AME, Vossen JH, Robatzek S, Kamoun S, Win J. Host-interactor screens of Phytophthora infestans RXLR proteins reveal vesicle trafficking as a major effector-targeted process. THE PLANT CELL 2021. [PMID: 33677602 DOI: 10.1101/2020.09.24.308585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Pathogens modulate plant cell structure and function by secreting effectors into host tissues. Effectors typically function by associating with host molecules and modulating their activities. This study aimed to identify the host processes targeted by the RXLR class of host-translocated effectors of the potato blight pathogen Phytophthora infestans. To this end, we performed an in planta protein-protein interaction screen by transiently expressing P. infestans RXLR effectors in Nicotiana benthamiana leaves followed by coimmunoprecipitation and liquid chromatography-tandem mass spectrometry. This screen generated an effector-host protein interactome matrix of 59 P. infestans RXLR effectors x 586 N. benthamiana proteins. Classification of the host interactors into putative functional categories revealed over 35 biological processes possibly targeted by P. infestans. We further characterized the PexRD12/31 family of RXLR-WY effectors, which associate and colocalize with components of the vesicle trafficking machinery. One member of this family, PexRD31, increased the number of FYVE positive vesicles in N. benthamiana cells. FYVE positive vesicles also accumulated in leaf cells near P. infestans hyphae, indicating that the pathogen may enhance endosomal trafficking during infection. This interactome dataset will serve as a useful resource for functional studies of P. infestans effectors and of effector-targeted host processes.
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Affiliation(s)
- Benjamin Petre
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Tolga O Bozkurt
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Martin H Schattat
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Department of Plant Physiology, Institute for Biology, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Schornack
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | | | - Roger Castells-Graells
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA
| | - Rosa Lozano-Durán
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yasin F Dagdas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Alexandra M E Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Jack H Vossen
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Silke Robatzek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
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28
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Petre B, Contreras MP, Bozkurt TO, Schattat MH, Sklenar J, Schornack S, Abd-El-Haliem A, Castells-Graells R, Lozano-Durán R, Dagdas YF, Menke FLH, Jones AME, Vossen JH, Robatzek S, Kamoun S, Win J. Host-interactor screens of Phytophthora infestans RXLR proteins reveal vesicle trafficking as a major effector-targeted process. THE PLANT CELL 2021; 33:1447-1471. [PMID: 33677602 PMCID: PMC8254500 DOI: 10.1093/plcell/koab069] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/19/2021] [Indexed: 05/20/2023]
Abstract
Pathogens modulate plant cell structure and function by secreting effectors into host tissues. Effectors typically function by associating with host molecules and modulating their activities. This study aimed to identify the host processes targeted by the RXLR class of host-translocated effectors of the potato blight pathogen Phytophthora infestans. To this end, we performed an in planta protein-protein interaction screen by transiently expressing P. infestans RXLR effectors in Nicotiana benthamiana leaves followed by coimmunoprecipitation and liquid chromatography-tandem mass spectrometry. This screen generated an effector-host protein interactome matrix of 59 P. infestans RXLR effectors x 586 N. benthamiana proteins. Classification of the host interactors into putative functional categories revealed over 35 biological processes possibly targeted by P. infestans. We further characterized the PexRD12/31 family of RXLR-WY effectors, which associate and colocalize with components of the vesicle trafficking machinery. One member of this family, PexRD31, increased the number of FYVE positive vesicles in N. benthamiana cells. FYVE positive vesicles also accumulated in leaf cells near P. infestans hyphae, indicating that the pathogen may enhance endosomal trafficking during infection. This interactome dataset will serve as a useful resource for functional studies of P. infestans effectors and of effector-targeted host processes.
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Affiliation(s)
- Benjamin Petre
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Tolga O Bozkurt
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Martin H Schattat
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Department of Plant Physiology, Institute for Biology, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Schornack
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | | | - Roger Castells-Graells
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA
| | - Rosa Lozano-Durán
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yasin F Dagdas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Alexandra M E Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Jack H Vossen
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Silke Robatzek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
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29
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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30
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Maidment JHR, Franceschetti M, Maqbool A, Saitoh H, Jantasuriyarat C, Kamoun S, Terauchi R, Banfield MJ. Multiple variants of the fungal effector AVR-Pik bind the HMA domain of the rice protein OsHIPP19, providing a foundation to engineer plant defense. J Biol Chem 2021; 296:100371. [PMID: 33548226 PMCID: PMC7961100 DOI: 10.1016/j.jbc.2021.100371] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 01/24/2023] Open
Abstract
Microbial plant pathogens secrete effector proteins, which manipulate the host to promote infection. Effectors can be recognized by plant intracellular nucleotide-binding leucine-rich repeat (NLR) receptors, initiating an immune response. The AVR-Pik effector from the rice blast fungus Magnaporthe oryzae is recognized by a pair of rice NLR receptors, Pik-1 and Pik-2. Pik-1 contains a noncanonical integrated heavy-metal-associated (HMA) domain, which directly binds AVR-Pik to activate plant defenses. The host targets of AVR-Pik are also HMA-domain-containing proteins, namely heavy-metal-associated isoprenylated plant proteins (HIPPs) and heavy-metal-associated plant proteins (HPPs). Here, we demonstrate that one of these targets interacts with a wider set of AVR-Pik variants compared with the Pik-1 HMA domains. We define the biochemical and structural basis of the interaction between AVR-Pik and OsHIPP19 and compare the interaction to that formed with the HMA domain of Pik-1. Using analytical gel filtration and surface plasmon resonance, we show that multiple AVR-Pik variants, including the stealthy variants AVR-PikC and AVR-PikF, which do not interact with any characterized Pik-1 alleles, bind to OsHIPP19 with nanomolar affinity. The crystal structure of OsHIPP19 in complex with AVR-PikF reveals differences at the interface that underpin high-affinity binding of OsHIPP19-HMA to a wider set of AVR-Pik variants than achieved by the integrated HMA domain of Pik-1. Our results provide a foundation for engineering the HMA domain of Pik-1 to extend binding to currently unrecognized AVR-Pik variants and expand disease resistance in rice to divergent pathogen strains.
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Affiliation(s)
- Josephine H R Maidment
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marina Franceschetti
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Abbas Maqbool
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Hiromasa Saitoh
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Chatchawan Jantasuriyarat
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK; Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok, Thailand
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research Centre, Iwate, Japan; Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK.
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31
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Wood KJ, Nur M, Gil J, Fletcher K, Lakeman K, Gann D, Gothberg A, Khuu T, Kopetzky J, Naqvi S, Pandya A, Zhang C, Maisonneuve B, Pel M, Michelmore R. Effector prediction and characterization in the oomycete pathogen Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif. PLoS Pathog 2020; 16:e1009012. [PMID: 33104763 PMCID: PMC7644090 DOI: 10.1371/journal.ppat.1009012] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/05/2020] [Accepted: 09/29/2020] [Indexed: 12/11/2022] Open
Abstract
Pathogens that infect plants and animals use a diverse arsenal of effector proteins to suppress the host immune system and promote infection. Identification of effectors in pathogen genomes is foundational to understanding mechanisms of pathogenesis, for monitoring field pathogen populations, and for breeding disease resistance. We identified candidate effectors from the lettuce downy mildew pathogen Bremia lactucae by searching the predicted proteome for the WY domain, a structural fold found in effectors that has been implicated in immune suppression as well as effector recognition by host resistance proteins. We predicted 55 WY domain containing proteins in the genome of B. lactucae and found substantial variation in both sequence and domain architecture. These candidate effectors exhibit several characteristics of pathogen effectors, including an N-terminal signal peptide, lineage specificity, and expression during infection. Unexpectedly, only a minority of B. lactucae WY effectors contain the canonical N-terminal RXLR motif, which is a conserved feature in the majority of cytoplasmic effectors reported in Phytophthora spp. Functional analysis of 21 effectors containing WY domains revealed 11 that elicited cell death on wild accessions and domesticated lettuce lines containing resistance genes, indicative of recognition of these effectors by the host immune system. Only two of the 11 recognized effectors contained the canonical RXLR motif, suggesting that there has been an evolutionary divergence in sequence motifs between genera; this has major consequences for robust effector prediction in oomycete pathogens.
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Affiliation(s)
- Kelsey J. Wood
- The Genome Center, University of California, Davis, Davis, California, United States of America
- Integrative Genetics & Genomics Graduate Group, University of California, Davis, Davis, California, United States of America
| | - Munir Nur
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Juliana Gil
- The Genome Center, University of California, Davis, Davis, California, United States of America
- Plant Pathology Graduate Group, University of California, Davis, Davis, California, United States of America
| | - Kyle Fletcher
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | | | - Dasan Gann
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Ayumi Gothberg
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Tina Khuu
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Jennifer Kopetzky
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Sanye Naqvi
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Archana Pandya
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Chi Zhang
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | | | | | - Richard Michelmore
- The Genome Center, University of California, Davis, Davis, California, United States of America
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, Davis, California, United States of America
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Li X, Yang X, Zheng X, Bai M, Hu D. Review on Structures of Pesticide Targets. Int J Mol Sci 2020; 21:E7144. [PMID: 32998191 PMCID: PMC7582455 DOI: 10.3390/ijms21197144] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 12/12/2022] Open
Abstract
Molecular targets play important roles in agrochemical discovery. Numerous pesticides target the key proteins in pathogens, insect, or plants. Investigating ligand-binding pockets and/or active sites in the proteins' structures is usually the first step in designing new green pesticides. Thus, molecular target structures are extremely important for the discovery and development of such pesticides. In this manuscript, we present a review of the molecular target structures, including those of antiviral, fungicidal, bactericidal, insecticidal, herbicidal, and plant growth-regulator targets, currently used in agrochemical research. The data will be helpful in pesticide design and the discovery of new green pesticides.
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Affiliation(s)
- Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China;
| | - Xueqing Yang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China;
| | - Xiaodong Zheng
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China;
| | - Miao Bai
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China;
| | - Deyu Hu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China;
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McLoughlin F, Marshall RS, Ding X, Chatt EC, Kirkpatrick LD, Augustine RC, Li F, Otegui MS, Vierstra RD. Autophagy Plays Prominent Roles in Amino Acid, Nucleotide, and Carbohydrate Metabolism during Fixed-Carbon Starvation in Maize. THE PLANT CELL 2020; 32:2699-2724. [PMID: 32616663 PMCID: PMC7474275 DOI: 10.1105/tpc.20.00226] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/04/2020] [Accepted: 06/27/2020] [Indexed: 05/31/2023]
Abstract
Autophagic recycling of proteins, lipids, nucleic acids, carbohydrates, and organelles is essential for cellular homeostasis and optimal health, especially under nutrient-limiting conditions. To better understand how this turnover affects plant growth, development, and survival upon nutrient stress, we applied an integrated multiomics approach to study maize (Zea mays) autophagy mutants subjected to fixed-carbon starvation induced by darkness. Broad metabolic alterations were evident in leaves missing the core autophagy component ATG12 under normal growth conditions (e.g., lipids and secondary metabolism), while changes in amino acid-, carbohydrate-, and nucleotide-related metabolites selectively emerged during fixed-carbon starvation. Through combined proteomic and transcriptomic analyses, we identified numerous autophagy-responsive proteins, which revealed processes underpinning the various metabolic changes seen during carbon stress as well as potential autophagic cargo. Strikingly, a strong upregulation of various catabolic processes was observed in the absence of autophagy, including increases in simple carbohydrate levels with a commensurate drop in starch levels, elevated free amino acid levels with a corresponding reduction in intact protein levels, and a strong increase in the abundance of several nitrogen-rich nucleotide catabolites. Altogether, this analysis showed that fixed-carbon starvation in the absence of autophagy adjusts the choice of respiratory substrates, promotes the transition of peroxisomes to glyoxysomes, and enhances the retention of assimilated nitrogen.
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Affiliation(s)
- Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Xinxin Ding
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, Wisconsin 53706
| | - Elizabeth C Chatt
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Liam D Kirkpatrick
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Robert C Augustine
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Faqiang Li
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, Wisconsin 53706
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
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Kumbar B, Kandagalla S, Bharath BR, Sharath BS, Mahmood R. Protein-protein Interaction and Molecular Dynamics of Iturin A Gene on Effector Proteins of Phytophthora infestans. Comb Chem High Throughput Screen 2020; 24:259-268. [PMID: 32691704 DOI: 10.2174/1386207323666200720012054] [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: 02/04/2020] [Revised: 05/07/2020] [Accepted: 06/18/2020] [Indexed: 11/22/2022]
Abstract
AIM AND OBJECTIVES Phytophthora infestans (Mont.) de Bary, the fungal pathogen causes late blight, which results in devastating economic loss among the Solanaceae. The bacillus lipopeptides show the antagonistic activity against the many plant pathogens, among bacillus lipopeptides reported as the antifungal gene. Hence, to understand the in silico antifungal activity, we have selected gene iturin A (AXN89987) produced by Bacillus spp to check the molecular dynamics study with the effector proteins of the P. infestanse. In this concern, known effector proteins of P. infestans were subjected to the protein-protein interaction followed by simulation. MATERIALS AND METHODS Iturin A gene was amplified using the soil bacterium Bacillus subtilis with gene-specific primers, cloned into pTZ 57R/T vector and confirmed by sequencing. To get better insights, the protein model was developed for Iturin A using Modeller 9.17, using PDB structure of ID 4MRT (Phosphopantetheine transferase Sfp) and 1QR0 (4'-phosphopantetheinyl moiety of coenzyme A) as a template, it shared the identity 72% and expected P-value: 3e-121, respectively. The model quality was assessed using ProSA and PROCHECK programs. RESULTS The potency of modelled protein against effector proteins of P. infestans were evaluated in silico using the HADDOCK server and the results showed the high affinity of towards the effector protein Host ATG8 (PDB-5L83). Finally, the simulation was performed to the docked conformation of with Host ATG8 to further understand the stability of the complex using the Desmond program. CONCLUSION Altogether, the protein-protein interaction and simulation study propose a new methodology and to uncover possible antifungal activity of iturin A against effector proteins of P. infestans.
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Affiliation(s)
- Bhimanagoud Kumbar
- Department of Biotechnology, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka 577451, India
| | - Shivananda Kandagalla
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, 4540008, Chaikovskogo 20A, Russian Federation
| | | | | | - Riaz Mahmood
- Department of Biotechnology, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka 577451, India
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Franceschetti M, Banfield MJ, Stevenson CEM, De La Concepcion JC. In vitro Assessment of Pathogen Effector Binding to Host Proteins by Surface Plasmon Resonance. Bio Protoc 2020; 10:e3676. [PMID: 33659346 PMCID: PMC7842709 DOI: 10.21769/bioprotoc.3676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/15/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022] Open
Abstract
The mechanisms of virulence and immunity are often governed by molecular interactions between pathogens and host proteins. The study of these interactions has major implications on understanding virulence activities, and how the host immune system recognizes the presence of pathogens to initiate an immune response. Frequently, the association between pathogen molecules and host proteins are assessed using qualitative techniques. As small differences in binding affinity can have a major biological effect, in vitro techniques that can quantitatively compare the binding between different proteins are required. However, these techniques can be manually intensive and often require large amounts of purified proteins. Here we present a simplified Surface Plasmon Resonance (SPR) protocol that allows a reproducible side-by-side quantitative comparison of the binding between different proteins, even in cases where the binding affinity cannot be confidently calculated. We used this method to assess the binding of virulence proteins (termed effectors) from the blast fungus Magnaporthe oryzae, to a domain of a host immune receptor. This approach represents a rapid and quantitative way to study how pathogen molecules bind to host proteins, requires only limited quantities of proteins, and is highly reproducible. Although this method requires the use of an SPR instrument, these can often be accessed through shared scientific services at many institutions. Thus, this technique can be implemented in any study that aims to understand host-pathogen interactions, irrespective of the expertise of the investigator.
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Affiliation(s)
- Marina Franceschetti
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Mark J. Banfield
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Clare E. M. Stevenson
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
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36
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Mochida K, Yamasaki A, Matoba K, Kirisako H, Noda NN, Nakatogawa H. Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes. Nat Commun 2020; 11:3306. [PMID: 32620754 PMCID: PMC7335187 DOI: 10.1038/s41467-020-17163-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 06/11/2020] [Indexed: 12/15/2022] Open
Abstract
The endoplasmic reticulum (ER) is selectively degraded by autophagy (ER-phagy) through proteins called ER-phagy receptors. In Saccharomyces cerevisiae, Atg40 acts as an ER-phagy receptor to sequester ER fragments into autophagosomes by binding Atg8 on forming autophagosomal membranes. During ER-phagy, parts of the ER are morphologically rearranged, fragmented, and loaded into autophagosomes, but the mechanism remains poorly understood. Here we find that Atg40 molecules assemble in the ER membrane concurrently with autophagosome formation via multivalent interaction with Atg8. Atg8-mediated super-assembly of Atg40 generates highly-curved ER regions, depending on its reticulon-like domain, and supports packing of these regions into autophagosomes. Moreover, tight binding of Atg40 to Atg8 is achieved by a short helix C-terminal to the Atg8-family interacting motif, and this feature is also observed for mammalian ER-phagy receptors. Thus, this study significantly advances our understanding of the mechanisms of ER-phagy and also provides insights into organelle fragmentation in selective autophagy of other organelles.
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Affiliation(s)
- Keisuke Mochida
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Akinori Yamasaki
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Kazuaki Matoba
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Hiromi Kirisako
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
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37
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Mukhi N, Gorenkin D, Banfield MJ. Exploring folds, evolution and host interactions: understanding effector structure/function in disease and immunity. THE NEW PHYTOLOGIST 2020; 227:326-333. [PMID: 32239533 DOI: 10.1111/nph.16563] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
Over the past decade, tremendous progress has been made in plant pathology, broadening our understanding of how pathogens colonize their hosts. To manipulate host cell physiology and subvert plant immune responses, pathogens secrete an array of effector proteins. A co-evolutionary arms-race drives the pathogen to constantly reinvent its effector repertoire to undermine plant immunity. In turn, hosts develop novel immune receptors to maintain effector recognition and mount defences. Understanding how effectors promote disease and how they are perceived by the plant's defence network persist as major subjects in the study of plant-pathogen interactions. Here, we focus on recent advances (over roughly the last two years) in understanding structure/function relationships in effectors from bacteria and filamentous plant pathogens. Structure/function studies of bacterial effectors frequently uncover diverse catalytic activities, while structure-informed similarity searches have enabled cataloguing of filamentous pathogen effectors. We also suggest how such advances have informed the study of plant-pathogen interactions.
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Affiliation(s)
- Nitika Mukhi
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Danylo Gorenkin
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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38
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Organize, Don't Agonize: Strategic Success of Phytophthora Species. Microorganisms 2020; 8:microorganisms8060917. [PMID: 32560346 PMCID: PMC7355776 DOI: 10.3390/microorganisms8060917] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022] Open
Abstract
Plants are constantly challenged by various environmental stressors ranging from abiotic-sunlight, elevated temperatures, drought, and nutrient deficits, to biotic factors-microbial pathogens and insect pests. These not only affect the quality of harvest but also the yield, leading to substantial annual crop losses, worldwide. Although plants have a multi-layered immune system, phytopathogens such as species of the oomycete genus Phytophthora, can employ elaborate mechanisms to breach this defense. For the last two decades, researchers have focused on the co-evolution between Phytophthora and interacting hosts to decouple the mechanisms governing their molecular associations. This has provided a comprehensive understanding of the pathobiology of plants affected by oomycetes. Ultimately, this is important for the development of strategies to sustainably improve agricultural production. Therefore, this paper discusses the present-day state of knowledge of the strategic mode of operation employed by species of Phytophthora for successful infection. Specifically, we consider motility, attachment, and host cell wall degradation used by these pathogenic species to obtain nutrients from their host. Also discussed is an array of effector types from apoplastic (hydrolytic proteins, protease inhibitors, elicitins) to cytoplastic (RxLRs, named after Arginine-any amino acid-Leucine-Arginine consensus sequence and CRNs, for CRinkling and Necrosis), which upon liberation can subvert the immune response and promote diseases in plants.
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Bu F, Yang M, Guo X, Huang W, Chen L. Multiple Functions of ATG8 Family Proteins in Plant Autophagy. Front Cell Dev Biol 2020; 8:466. [PMID: 32596242 PMCID: PMC7301642 DOI: 10.3389/fcell.2020.00466] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/19/2020] [Indexed: 11/13/2022] Open
Abstract
Autophagy is a major degradation process of cytoplasmic components in eukaryotes, and executes both bulk and selective degradation of targeted cargos. A set of autophagy-related (ATG) proteins participate in various stages of the autophagic process. Among ATGs, ubiquitin-like protein ATG8 plays a central role in autophagy. The ATG8 protein is conjugated to the membrane lipid phosphatidylethanolamine in a ubiquitin-like conjugation reaction that is essential for autophagosome formation. In addition, ATG8 interacts with various adaptor/receptor proteins to recruit specific cargos for degradation by selective autophagy. The ATG8-interacting proteins usually contain the ATG8-interacting motif (AIM) or the ubiquitin-interacting motif (UIM) for ATG8 binding. Unlike a single ATG8 gene in yeast, multiple ATG8 orthologs have been identified in the plant kingdom. The large diversity within the ATG8 family may explain the various functions of selective autophagy in plants. Here, we discuss and summarize the current view of the structure and function of ATG8 proteins in plants.
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Affiliation(s)
- Fan Bu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Mingkang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xu Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
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Murúa P, Müller DG, Etemadi M, van West P, Gachon CMM. Host and pathogen autophagy are central to the inducible local defences and systemic response of the giant kelp Macrocystis pyrifera against the oomycete pathogen Anisolpidium ectocarpii. THE NEW PHYTOLOGIST 2020; 226:1445-1460. [PMID: 31955420 PMCID: PMC7317505 DOI: 10.1111/nph.16438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/08/2020] [Indexed: 05/20/2023]
Abstract
Kelps are key primary producers of cold and temperate marine coastal ecosystems and exhibit systemic defences against pathogens. Yet, the cellular mechanisms underpinning their immunity remain to be elucidated. We investigated the time course of infection of the kelp Macrocystis pyrifera by the oomycete Anisolpidium ectocarpii using TEM, in vivo autophagy markers and autophagy inhibitors. Over several infection cycles, A. ectocarpii undergoes sequential physiological shifts sensitive to autophagy inhibitors. Initially lipid-rich, pathogen thalli become increasingly lipid-depleted; they subsequently tend to become entirely abortive, irrespective of their lipid content. Moreover, infected algal cells mount local defences and can directly eliminate the pathogen by xenophagy. Finally, autophagy-dependent plastid recycling is induced in uninfected host cells. We demonstrate the existence of local, inducible autophagic processes both in the pathogen and infected host cells, which result in the restriction of pathogen propagation. We also show the existence of a systemic algal response mediated by autophagy. We propose a working model accounting for all our observations, whereby the outcome of the algal-pathogen interaction (i.e. completion or not of the pathogen life cycle) is dictated by the induction, and possibly the mutual hijacking, of the host and pathogen autophagy machineries.
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Affiliation(s)
- Pedro Murúa
- Aberdeen Oomycete LaboratoryInternational Centre for Aquaculture Research and DevelopmentUniversity of AberdeenForesterhillAberdeenAB25 2ZDUK
- The Scottish Association for Marine ScienceScottish Marine InstituteObanPA37 1QAUK
| | - Dieter G. Müller
- Fachbereich Biologie der Universität KonstanzD‐78457KonstanzGermany
| | - Mohammad Etemadi
- Institute of MicrobiologyUniversity of InnsbruckA‐6020InnsbruckTyrolAustria
| | - Pieter van West
- Aberdeen Oomycete LaboratoryInternational Centre for Aquaculture Research and DevelopmentUniversity of AberdeenForesterhillAberdeenAB25 2ZDUK
| | - Claire M. M. Gachon
- The Scottish Association for Marine ScienceScottish Marine InstituteObanPA37 1QAUK
- UMR 7245 - Molécules de Communication et Adaptation des Micro-organismesMuséum National d'Histoire NaturelleCP 54, 57 rue Cuvier75005ParisFrance
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Su T, Li X, Yang M, Shao Q, Zhao Y, Ma C, Wang P. Autophagy: An Intracellular Degradation Pathway Regulating Plant Survival and Stress Response. FRONTIERS IN PLANT SCIENCE 2020; 11:164. [PMID: 32184795 PMCID: PMC7058704 DOI: 10.3389/fpls.2020.00164] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/03/2020] [Indexed: 05/18/2023]
Abstract
Autophagy is an intracellular process that facilitates the bulk degradation of cytoplasmic materials by the vacuole or lysosome in eukaryotes. This conserved process is achieved through the coordination of different autophagy-related genes (ATGs). Autophagy is essential for recycling cytoplasmic material and eliminating damaged or dysfunctional cell constituents, such as proteins, aggregates or even entire organelles. Plant autophagy is necessary for maintaining cellular homeostasis under normal conditions and is upregulated during abiotic and biotic stress to prolong cell life. In this review, we present recent advances on our understanding of the molecular mechanisms of autophagy in plants and how autophagy contributes to plant development and plants' adaptation to the environment.
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Affiliation(s)
| | | | | | | | | | - Changle Ma
- *Correspondence: Changle Ma, ; Pingping Wang,
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Zhang P, Jia Y, Shi J, Chen C, Ye W, Wang Y, Ma W, Qiao Y. The WY domain in the Phytophthora effector PSR1 is required for infection and RNA silencing suppression activity. THE NEW PHYTOLOGIST 2019; 223:839-852. [PMID: 30963588 DOI: 10.1111/nph.15836] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 03/29/2019] [Indexed: 05/27/2023]
Abstract
Phytophthora pathogens manipulate host innate immunity by secreting numerous RxLR effectors, thereby facilitating pathogen colonization. Predicted single and tandem repeats of WY domains are the most prominent C-terminal motifs conserved across the Phytophthora RxLR superfamily. However, the functions of individual WY domains in effectors remain poorly understood. The Phytophthora sojae effector PSR1 promotes infection by suppressing small RNA biogenesis in plant hosts. We identified one single WY domain following the RxLR motif in PSR1. This domain was required for RNA silencing suppression activity and infection in Nicotiana benthamiana, Arabidopsis and soybean. Mutations of the conserved residues in the WY domain did not affect the subcellular localization of PSR1 but abolished its effect on plant development and resistance to viral and Phytophthora pathogens. This is at least in part due to decreased protein stability of the PSR1 mutants in planta. The identification of the WY domain in PSR1 allows predicts that a family of PSR1-like effectors also possess RNA silencing suppression activity. Mutation of the conserved residues in two members of this family, PpPSR1L from P. parasitica and PcPSR1L from P. capsici, perturbed their biological functions, indicating that the WY domain is critical in Phytophthora PSR1 and PSR1-like effectors.
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Affiliation(s)
- Peng Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Yijuan Jia
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jinxia Shi
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Chen Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenbo Ma
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
- Center for Plant Cell Biology, University of California, Riverside, CA, 92521, USA
| | - Yongli Qiao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
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Zess EK, Jensen C, Cruz-Mireles N, De la Concepcion JC, Sklenar J, Stephani M, Imre R, Roitinger E, Hughes R, Belhaj K, Mechtler K, Menke FLH, Bozkurt T, Banfield MJ, Kamoun S, Maqbool A, Dagdas YF. N-terminal β-strand underpins biochemical specialization of an ATG8 isoform. PLoS Biol 2019; 17:e3000373. [PMID: 31329577 PMCID: PMC6675122 DOI: 10.1371/journal.pbio.3000373] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 08/01/2019] [Accepted: 07/09/2019] [Indexed: 02/07/2023] Open
Abstract
Autophagy-related protein 8 (ATG8) is a highly conserved ubiquitin-like protein that modulates autophagy pathways by binding autophagic membranes and a number of proteins, including cargo receptors and core autophagy components. Throughout plant evolution, ATG8 has expanded from a single protein in algae to multiple isoforms in higher plants. However, the degree to which ATG8 isoforms have functionally specialized to bind distinct proteins remains unclear. Here, we describe a comprehensive protein-protein interaction resource, obtained using in planta immunoprecipitation (IP) followed by mass spectrometry (MS), to define the potato ATG8 interactome. We discovered that ATG8 isoforms bind distinct sets of plant proteins with varying degrees of overlap. This prompted us to define the biochemical basis of ATG8 specialization by comparing two potato ATG8 isoforms using both in vivo protein interaction assays and in vitro quantitative binding affinity analyses. These experiments revealed that the N-terminal β-strand-and, in particular, a single amino acid polymorphism-underpins binding specificity to the substrate PexRD54 by shaping the hydrophobic pocket that accommodates this protein's ATG8-interacting motif (AIM). Additional proteomics experiments indicated that the N-terminal β-strand shapes the broader ATG8 interactor profiles, defining interaction specificity with about 80 plant proteins. Our findings are consistent with the view that ATG8 isoforms comprise a layer of specificity in the regulation of selective autophagy pathways in plants.
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Affiliation(s)
- Erin K. Zess
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
| | - Cassandra Jensen
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Neftaly Cruz-Mireles
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Juan Carlos De la Concepcion
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
| | - Madlen Stephani
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Richard Imre
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Elisabeth Roitinger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Richard Hughes
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Khaoula Belhaj
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
| | - Karl Mechtler
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Frank L. H. Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
| | - Tolga Bozkurt
- Imperial College London, Department of Life Sciences, London, United Kingdom
| | - Mark J. Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
| | - Abbas Maqbool
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Yasin F. Dagdas
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
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Wang J, Gao C, Li L, Cao W, Dong R, Ding X, Zhu C, Chu Z. Transgenic RXLR Effector PITG_15718.2 Suppresses Immunity and Reduces Vegetative Growth in Potato. Int J Mol Sci 2019; 20:ijms20123031. [PMID: 31234322 PMCID: PMC6627464 DOI: 10.3390/ijms20123031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 01/25/2023] Open
Abstract
Phytophthora infestans causes the severe late blight disease of potato. During its infection process, P. infestans delivers hundreds of RXLR (Arg-x-Leu-Arg, x behalf of any one amino acid) effectors to manipulate processes in its hosts, creating a suitable environment for invasion and proliferation. Several effectors interact with host proteins to suppress host immunity and inhibit plant growth. However, little is known about how P. infestans regulates the host transcriptome. Here, we identified an RXLR effector, PITG_15718.2, which is upregulated and maintains a high expression level throughout the infection. Stable transgenic potato (Solanum tuberosum) lines expressing PITG_15718.2 show enhanced leaf colonization by P. infestans and reduced vegetative growth. We further investigated the transcriptional changes between three PITG_15718.2 transgenic lines and the wild type Désirée by using RNA sequencing (RNA-Seq). Compared with Désirée, 190 differentially expressed genes (DEGs) were identified, including 158 upregulated genes and 32 downregulated genes in PITG_15718.2 transgenic lines. Eight upregulated and nine downregulated DEGs were validated by real-time RT-PCR, which showed a high correlation with the expression level identified by RNA-Seq. These DEGs will help to explore the mechanism of PITG_15718.2-mediated immunity and growth inhibition in the future.
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Affiliation(s)
- Jiao Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China.
- Shandong Provincial Key Laboratory of Vegetable Disease and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China.
| | - Cungang Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China.
- College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.
| | - Long Li
- College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.
| | - Weilin Cao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China.
- College of Life Science, Shandong Agricultural University, Tai'an, 271018, China.
| | - Ran Dong
- Shandong Provincial Key Laboratory of Vegetable Disease and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China.
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China.
- Shandong Provincial Key Laboratory of Vegetable Disease and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China.
| | - Changxiang Zhu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China.
- College of Life Science, Shandong Agricultural University, Tai'an, 271018, China.
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China.
- College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.
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45
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Marshall RS, Vierstra RD. Dynamic Regulation of the 26S Proteasome: From Synthesis to Degradation. Front Mol Biosci 2019; 6:40. [PMID: 31231659 PMCID: PMC6568242 DOI: 10.3389/fmolb.2019.00040] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/09/2019] [Indexed: 01/12/2023] Open
Abstract
All eukaryotes rely on selective proteolysis to control the abundance of key regulatory proteins and maintain a healthy and properly functioning proteome. Most of this turnover is catalyzed by the 26S proteasome, an intricate, multi-subunit proteolytic machine. Proteasomes recognize and degrade proteins first marked with one or more chains of poly-ubiquitin, the addition of which is actuated by hundreds of ligases that individually identify appropriate substrates for ubiquitylation. Subsequent proteasomal digestion is essential and influences a myriad of cellular processes in species as diverse as plants, fungi and humans. Importantly, dysfunction of 26S proteasomes is associated with numerous human pathologies and profoundly impacts crop performance, thus making an understanding of proteasome dynamics critically relevant to almost all facets of human health and nutrition. Given this widespread significance, it is not surprising that sophisticated mechanisms have evolved to tightly regulate 26S proteasome assembly, abundance and activity in response to demand, organismal development and stress. These include controls on transcription and chaperone-mediated assembly, influences on proteasome localization and activity by an assortment of binding proteins and post-translational modifications, and ultimately the removal of excess or damaged particles via autophagy. Intriguingly, the autophagic clearance of damaged 26S proteasomes first involves their modification with ubiquitin, thus connecting ubiquitylation and autophagy as key regulatory events in proteasome quality control. This turnover is also influenced by two distinct biomolecular condensates that coalesce in the cytoplasm, one attracting damaged proteasomes for autophagy, and the other reversibly storing proteasomes during carbon starvation to protect them from autophagic clearance. In this review, we describe the current state of knowledge regarding the dynamic regulation of 26S proteasomes at all stages of their life cycle, illustrating how protein degradation through this proteolytic machine is tightly controlled to ensure optimal growth, development and longevity.
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Affiliation(s)
- Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
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He Q, McLellan H, Hughes RK, Boevink PC, Armstrong M, Lu Y, Banfield MJ, Tian Z, Birch PRJ. Phytophthora infestans effector SFI3 targets potato UBK to suppress early immune transcriptional responses. THE NEW PHYTOLOGIST 2019; 222:438-454. [PMID: 30536576 DOI: 10.1111/nph.15635] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/19/2018] [Indexed: 05/27/2023]
Abstract
The potato blight agent Phytophthora infestans secretes a range of RXLR effectors to promote disease. Recent evidence indicates that some effectors suppress early pattern-triggered immunity (PTI) following perception of microbe-associated molecular patterns (MAMPs). Phytophthora infestans effector PiSFI3/Pi06087/PexRD16 has been previously shown to suppress MAMP-triggered pFRK1-Luciferase reporter gene activity. How PiSFI3 suppresses immunity is unknown. We employed yeast-two-hybrid (Y2H) assays, co-immunoprecipitation, transcriptional silencing by RNA interference and virus-induced gene silencing (VIGS), and X-ray crystallography for structure-guided mutagenesis, to investigate the function of PiSFI3 in targeting a plant U-box-kinase protein (StUBK) to suppress immunity. We discovered that PiSFI3 is active in the host nucleus and interacts in yeast and in planta with StUBK. UBK is a positive regulator of specific PTI pathways in both potato and Nicotiana benthamiana. Importantly, it contributes to early transcriptional responses that are suppressed by PiSFI3. PiSFI3 forms an unusual trans-homodimer. Mutation to disrupt dimerization prevents nucleolar localisation of PiSFI3 and attenuates both its interaction with StUBK and its ability to enhance P. infestans leaf colonisation. PiSFI3 is a 'WY-domain' RXLR effector that forms a novel trans-homodimer which is required for its ability to suppress PTI via interaction with the U-box-kinase protein StUBK.
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Affiliation(s)
- Qin He
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Division of Plant Science, School of Life Science, University of Dundee (at JHI), Invergowrie, Dundee, DD2 5DA, UK
- Cell and Molecular Science, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Hazel McLellan
- Division of Plant Science, School of Life Science, University of Dundee (at JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Richard K Hughes
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Petra C Boevink
- Cell and Molecular Science, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Miles Armstrong
- Division of Plant Science, School of Life Science, University of Dundee (at JHI), Invergowrie, Dundee, DD2 5DA, UK
- Cell and Molecular Science, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Yuan Lu
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Zhendong Tian
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Paul R J Birch
- Division of Plant Science, School of Life Science, University of Dundee (at JHI), Invergowrie, Dundee, DD2 5DA, UK
- Cell and Molecular Science, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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Structural analysis of Phytophthora suppressor of RNA silencing 2 (PSR2) reveals a conserved modular fold contributing to virulence. Proc Natl Acad Sci U S A 2019; 116:8054-8059. [PMID: 30926664 DOI: 10.1073/pnas.1819481116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Phytophthora are eukaryotic pathogens that cause enormous losses in agriculture and forestry. Each Phytophthora species encodes hundreds of effector proteins that collectively have essential roles in manipulating host cellular processes and facilitating disease development. Here we report the crystal structure of the effector Phytophthora suppressor of RNA silencing 2 (PSR2). PSR2 produced by the soybean pathogen Phytophthora sojae (PsPSR2) consists of seven tandem repeat units, including one W-Y motif and six L-W-Y motifs. Each L-W-Y motif forms a highly conserved fold consisting of five α-helices. Adjacent units are connected through stable, directional linkages between an internal loop at the C terminus of one unit and a hydrophobic pocket at the N terminus of the following unit. This unique concatenation results in an overall stick-like structure of PsPSR2. Genome-wide analyses reveal 293 effectors from five Phytophthora species that have the PsPSR2-like arrangement, that is, containing a W-Y motif as the "start" unit, various numbers of L-W-Y motifs as the "middle" units, and a degenerate L-W-Y as the "end" unit. Residues involved in the interunit interactions show significant conservation, suggesting that these effectors also use the conserved concatenation mechanism. Furthermore, functional analysis demonstrates differential contributions of individual units to the virulence activity of PsPSR2. These findings suggest that the L-W-Y fold is a basic structural and functional module that may serve as a "building block" to accelerate effector evolution in Phytophthora.
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48
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Nuta GC, Gilad Y, Gershoni M, Sznajderman A, Schlesinger T, Bialik S, Eisenstein M, Pietrokovski S, Kimchi A. A cancer associated somatic mutation in LC3B attenuates its binding to E1-like ATG7 protein and subsequent lipidation. Autophagy 2019; 15:438-452. [PMID: 30238850 PMCID: PMC6351123 DOI: 10.1080/15548627.2018.1525476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/30/2018] [Accepted: 09/14/2018] [Indexed: 02/01/2023] Open
Abstract
Macroautophagy/autophagy is a conserved catabolic process that maintains cellular homeostasis under basal growth and stress conditions. In cancer, autophagy can either prevent or promote tumor growth, at early or advanced stages, respectively. We screened public databases to identify autophagy-related somatic mutations in cancer, using a computational approach to identify cancer mutational target sites, employing exact statistics. The top significant hit was a missense mutation (Y113C) in the MAP1LC3B/LC3B (microtubule associated protein 1 light chain 3 beta) protein, which occurred at a significant frequency in cancer, and was detected in early stages in primary tumors of patients with known tumor lineage. The mutation reduced the formation of GFP-LC3B puncta and attenuated LC3B lipidation during Torin1-induced autophagy. Its effect on the direct physical interaction of LC3B with each of the 4 proteins that control its maturation or lipidation was tested by applying a protein-fragment complementation assay and co-immunoprecipitation experiments. Interactions with ATG4A and ATG4B proteases were reduced, yet without perturbing the cleavage of mutant LC3B. Most importantly, the mutation significantly reduced the interaction with the E1-like enzyme ATG7, but not the direct interaction with the E2-like enzyme ATG3, suggesting a selective perturbation in the binding of LC3B to some of its partner proteins. Structure analysis and molecular dynamics simulations of LC3B protein and its mutant suggest that the mutation changes the conformation of a loop that has several contact sites with ATG4B and the ATG7 homodimer. We suggest that this loss-of-function mutation, which attenuates autophagy, may promote early stages of cancer development.
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Affiliation(s)
- Gal Chaim Nuta
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yuval Gilad
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Moran Gershoni
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Arielle Sznajderman
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tomer Schlesinger
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shani Bialik
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Miriam Eisenstein
- Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Shmuel Pietrokovski
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Kimchi
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Ding X, Zhang X, Otegui MS. Plant autophagy: new flavors on the menu. CURRENT OPINION IN PLANT BIOLOGY 2018; 46:113-121. [PMID: 30267997 DOI: 10.1016/j.pbi.2018.09.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
Autophagy mediates the delivery of cytoplasmic content to vacuoles or lysosomes for degradation or storage. The best characterized autophagy route called macroautophagy involves the sequestration of cargo in double-membrane autophagosomes and is conserved in eukaryotes, including plants. Recently, several new receptors, some of them plant-specific, that select cargo for macroautophagy have been identified. Some of these receptors appear to participate in regulation of competing catabolic pathways, for example proteasome-mediated versus autophagic degradation under specific stress conditions. Vacuolar microautophagy, a process by which the vacuole directly engulf cytoplasmic material, also occurs in plants but its underlying molecular mechanisms are yet to be elucidated.
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Affiliation(s)
- Xinxin Ding
- Department of Botany, 430 Lincoln Drive, University of Wisconsin-Madison, WI 53706, United States; Laboratory of Molecular and Cellular Biology, 1525 Linden Drive, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Xiaoguo Zhang
- Department of Botany, 430 Lincoln Drive, University of Wisconsin-Madison, WI 53706, United States; Laboratory of Molecular and Cellular Biology, 1525 Linden Drive, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Marisa S Otegui
- Department of Botany, 430 Lincoln Drive, University of Wisconsin-Madison, WI 53706, United States; Laboratory of Molecular and Cellular Biology, 1525 Linden Drive, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Genetics, 405 Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, United States.
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50
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Bentham AR, Zdrzałek R, De la Concepcion JC, Banfield MJ. Uncoiling CNLs: Structure/Function Approaches to Understanding CC Domain Function in Plant NLRs. PLANT & CELL PHYSIOLOGY 2018; 59:2398-2408. [PMID: 30192967 PMCID: PMC6290485 DOI: 10.1093/pcp/pcy185] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 08/24/2018] [Indexed: 05/20/2023]
Abstract
Plant nucleotide-binding leucine-rich repeat receptors (NLRs) are intracellular pathogen receptors whose N-terminal domains are integral to signal transduction after perception of a pathogen-derived effector protein. The two major plant NLR classes are defined by the presence of either a Toll/interleukin-1 receptor (TIR) or a coiled-coil (CC) domain at their N-terminus (TNLs and CNLs). Our knowledge of how CC domains function in plant CNLs lags behind that of how TIR domains function in plant TNLs. CNLs are the most abundant class of NLRs in monocotyledonous plants, and further research is required to understand the molecular mechanisms of how these domains contribute to disease resistance in cereal crops. Previous studies of CC domains have revealed functional diversity, making categorization difficult, which in turn makes experimental design for assaying function challenging. In this review, we summarize the current understanding of CC domain function in plant CNLs, highlighting the differences in modes of action and structure. To aid experimental design in exploring CC domain function, we present a 'best-practice' guide to designing constructs through use of sequence and secondary structure comparisons and discuss the relevant assays for investigating CC domain function. Finally, we discuss whether using homology modeling is useful to describe putative CC domain function in CNLs through parallels with the functions of previously characterized helical adaptor proteins.
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Affiliation(s)
- Adam R Bentham
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Rafał Zdrzałek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
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