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Sunil S, Beeh S, Stöbbe E, Fischer K, Wilhelm F, Meral A, Paris C, Teasdale L, Jiang Z, Zhang L, Urban M, Aguilar Parras E, Nürnberger T, Weigel D, Lozano-Duran R, El Kasmi F. Activation of an atypical plant NLR with an N-terminal deletion initiates cell death at the vacuole. EMBO Rep 2024:10.1038/s44319-024-00240-4. [PMID: 39242777 DOI: 10.1038/s44319-024-00240-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 07/26/2024] [Accepted: 08/12/2024] [Indexed: 09/09/2024] Open
Abstract
Plants evolve nucleotide-binding leucine-rich repeat receptors (NLRs) to induce immunity. Activated coiled-coil (CC) domain containing NLRs (CNLs) oligomerize and form apparent cation channels promoting calcium influx and cell death, with the alpha-1 helix of the individual CC domains penetrating the plasma membranes. Some CNLs are characterized by putative N-myristoylation and S-acylation sites in their CC domain, potentially mediating permanent membrane association. Whether activated Potentially Membrane Localized NLRs (PMLs) mediate cell death and calcium influx in a similar way is unknown. We uncovered the cell-death function at the vacuole of an atypical but conserved Arabidopsis PML, PML5, which has a significant deletion in its CCG10/GA domain. Active PML5 oligomers localize in Golgi membranes and the tonoplast, alter vacuolar morphology, and induce cell death, with the short N-terminus being sufficient. Mutant analysis supports a potential role of PMLs in plant immunity. PML5-like deletions are found in several Brassicales paralogs, pointing to the evolutionary importance of this innovation. PML5, with its minimal CC domain, represents the first identified CNL utilizing vacuolar-stored calcium for cell death induction.
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Affiliation(s)
- Sruthi Sunil
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Simon Beeh
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Eva Stöbbe
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Kathrin Fischer
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Franziska Wilhelm
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Aron Meral
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Celia Paris
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Luisa Teasdale
- Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
| | - Zhihao Jiang
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Lisha Zhang
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Moritz Urban
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Emmanuel Aguilar Parras
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Depto. Biología Celular, Genética y Fisiología, 29010, Málaga, Spain
| | - Thorsten Nürnberger
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Detlef Weigel
- Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076, Tübingen, Germany
| | - Rosa Lozano-Duran
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Farid El Kasmi
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany.
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Diplock N, Baudin M, Xiang XD, Liang LY, Dai W, Murphy JM, Lucet IS, Hassan JA, Lewis JD. Molecular dissection of the pseudokinase ZED1 expands effector recognition to the tomato immune receptor ZAR1. PLANT PHYSIOLOGY 2024; 196:651-666. [PMID: 38748589 DOI: 10.1093/plphys/kiae268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/11/2024] [Indexed: 09/03/2024]
Abstract
The highly conserved angiosperm immune receptor HOPZ-ACTIVATED RESISTANCE 1 (ZAR1) is a bacterial pathogen recognition hub that mediates resistance by guarding host kinases for modification by pathogen effectors. The pseudokinase HOPZ-ETI DEFICIENT 1 (ZED1) is the only known ZAR1-guarded protein that interacts directly with a pathogen effector, HopZ1a, from the bacterial pathogen Pseudomonas syringae, making it a promising system for rational design of effector recognition for plant immunity. Here, we conducted an in-depth molecular analysis of ZED1. We generated a library of 164 random ZED1 mutants and identified 50 mutants that could not recognize the effector HopZ1a when transiently expressed in Nicotiana benthamiana. Based on our random mutants, we generated a library of 27 point mutants and found evidence of minor functional divergence between Arabidopsis (Arabidopsis thaliana) and N. benthamiana ZAR1 orthologs. We leveraged our point mutant library to identify regions in ZED1 critical for ZAR1 and HopZ1a interactions and identified two likely ZED1-HopZ1a binding conformations. We explored ZED1 nucleotide and cation binding activity and showed that ZED1 is a catalytically dead pseudokinase, functioning solely as an allosteric regulator upon effector recognition. We used our library of ZED1 point mutants to identify the ZED1 activation loop regions as the most likely cause of interspecies ZAR1-ZED1 incompatibility. Finally, we identified a mutation that abolished ZAR1-ZED1 interspecies incompatibility while retaining the ability to mediate HopZ1a recognition, which enabled recognition of HopZ1a through tomato (Solanum lycopersicum) ZAR1. This provides an example of expanded effector recognition through a ZAR1 ortholog from a non-model species.
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Affiliation(s)
- Nathan Diplock
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Maël Baudin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Xincheng Derek Xiang
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Lung-Yu Liang
- Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne 3052, Australia
| | - Weiwen Dai
- Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne 3052, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne 3052, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Isabelle S Lucet
- Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne 3052, Australia
| | - Jana A Hassan
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jennifer D Lewis
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Plant Gene Expression Center, United States Department of Agriculture, Agriculture Research Service, Albany, CA 94710, USA
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3
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Yang Y, Tan L, Xu X, Tang Q, Wang J, Xing S, Wang R, Zou T, Wang S, Zhu J, Li S, Liang Y, Deng Q, Li P. Activation and Autoinhibition Mechanisms of NLR Immune Receptor Pi36 in Rice. Int J Mol Sci 2024; 25:7301. [PMID: 39000408 PMCID: PMC11242311 DOI: 10.3390/ijms25137301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/23/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Nucleotide-binding and leucine-rich repeat receptors (NLRs) are the most important and largest class of immune receptors in plants. The Pi36 gene encodes a canonical CC-NBS-LRR protein that confers resistance to rice blast fungal infections. Here, we show that the CC domain of Pi36 plays a role in cell death induction. Furthermore, self-association is required for the CC domain-mediated cell death, and the self-association ability is correlated with the cell death level. In addition, the NB-ARC domain may suppress the activity of the CC domain through intramolecular interaction. The mutations D440G next to the RNBS-D motif and D503V in the MHD motif autoactivated Pi36, but the mutation K212 in the P-loop motif inhibited this autoactivation, indicating that nucleotide binding of the NB-ARC domain is essential for Pi36 activation. We also found that the LRR domain is required for D503V- and D440G-mediated Pi36 autoactivation. Interestingly, several mutations in the CC domain compromised the CC domain-mediated cell death without affecting the D440G- or D503V-mediated Pi36 autoactivation. The autoactivate Pi36 variants exhibited stronger self-associations than the inactive variants. Taken together, we speculated that the CC domain of Pi36 executes cell death activities, whereas the NB-ARC domain suppressed CC-mediated cell death via intermolecular interaction. The NB-ARC domain releases its suppression of the CC domain and strengthens the self-association of Pi36 to support the CC domain, possibly through nucleotide exchange.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Liu Tan
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Xingzhe Xu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Qiaoyi Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Q.T.); (J.W.); (R.W.); (S.L.); (Y.L.)
| | - Ji Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Q.T.); (J.W.); (R.W.); (S.L.); (Y.L.)
| | - Shiyue Xing
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Rui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Q.T.); (J.W.); (R.W.); (S.L.); (Y.L.)
| | - Ting Zou
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Shiquan Wang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Jun Zhu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Shuangcheng Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Q.T.); (J.W.); (R.W.); (S.L.); (Y.L.)
| | - Yueyang Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Q.T.); (J.W.); (R.W.); (S.L.); (Y.L.)
| | - Qiming Deng
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Ping Li
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
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Lee HY, Choi J, Kang M, Lee JH, Kim MS, Choi D. Protein stability governed by α1-2 helices in Pvr4 is essential for localization and cell death. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:510-523. [PMID: 37433739 DOI: 10.1111/tpj.16388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/13/2023]
Abstract
Plant nucleotide-binding domain leucine-rich-repeat receptor (NLR) confers disease resistance to various pathogens by recognizing effectors derived from the pathogen. Previous studies have shown that overexpression of the CC domain in several NLRs triggers cell death, implying that the CC domain plays an important role as a signaling module. However, how CC domain transduces immune signals remains largely unknown. A Potyvirus-resistant NLR protein, Pvr4, possesses a CC domain (CCPvr4 ) that induces cell death upon transient overexpression in Nicotiana benthamiana. In this study, loss-of-function mutants were generated by error-prone PCR-based random mutagenesis to understand the molecular mechanisms underlying CCPvr4 -mediated cell death. Cell biology and biochemical studies revealed that M16 and Q52 in the α1 and α2 helices, respectively, are crucial for protein stability, and mutation of these residues disrupts localization to the plasma membrane and oligomerization activity. The increase of the protein stability of these mutants by tagging a green fluorescent protein (GFP) variant led to restoration of cell death-inducing activity and plasma membrane localization. Another mutant, I7E in the very N-terminal region, lost cell death-inducing activity by weakening the interaction with plasma membrane H+ -ATPase compared to CCPvr4 , although the protein remained in the plasma membrane. Moreover, most of the mutated residues are on the outer surface of the funnel shape in the predicted pentameric CCPvr4 , implying that the disordered N-terminal region plays a crucial role in association with PMA as well as targeting to the plasma membrane. This work could provide insights into the molecular mechanisms of cell death induced by NLR immune receptors.
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Affiliation(s)
- Hye-Young Lee
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jeen Choi
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Horticultural Science and Biotechnology Program, Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Minji Kang
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Horticultural Science and Biotechnology Program, Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Joo Hyun Lee
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Myung-Shin Kim
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Biosciences and Bioinformatics, Myongji University, Yongin, 17058, Republic of Korea
| | - Doil Choi
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Horticultural Science and Biotechnology Program, Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
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5
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Adachi H, Sakai T, Kourelis J, Pai H, Gonzalez Hernandez JL, Utsumi Y, Seki M, Maqbool A, Kamoun S. Jurassic NLR: Conserved and dynamic evolutionary features of the atypically ancient immune receptor ZAR1. THE PLANT CELL 2023; 35:3662-3685. [PMID: 37467141 PMCID: PMC10533333 DOI: 10.1093/plcell/koad175] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 07/21/2023]
Abstract
Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors generally exhibit hallmarks of rapid evolution, even at the intraspecific level. We used iterative sequence similarity searches coupled with phylogenetic analyses to reconstruct the evolutionary history of HOPZ-ACTIVATED RESISTANCE1 (ZAR1), an atypically conserved NLR that traces its origin to early flowering plant lineages ∼220 to 150 million yrs ago (Jurassic period). We discovered 120 ZAR1 orthologs in 88 species, including the monocot Colocasia esculenta, the magnoliid Cinnamomum micranthum, and most eudicots, notably the Ranunculales species Aquilegia coerulea, which is outside the core eudicots. Ortholog sequence analyses revealed highly conserved features of ZAR1, including regions for pathogen effector recognition and cell death activation. We functionally reconstructed the cell death activity of ZAR1 and its partner receptor-like cytoplasmic kinase (RLCK) from distantly related plant species, experimentally validating the hypothesis that ZAR1 evolved to partner with RLCKs early in its evolution. In addition, ZAR1 acquired novel molecular features. In cassava (Manihot esculenta) and cotton (Gossypium spp.), ZAR1 carries a C-terminal thioredoxin-like domain, and in several taxa, ZAR1 duplicated into 2 paralog families, which underwent distinct evolutionary paths. ZAR1 stands out among angiosperm NLR genes for having experienced relatively limited duplication and expansion throughout its deep evolutionary history. Nonetheless, ZAR1 also gave rise to noncanonical NLRs with integrated domains and degenerated molecular features.
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Affiliation(s)
- Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Toshiyuki Sakai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
| | - Jiorgos Kourelis
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hsuan Pai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jose L Gonzalez Hernandez
- Agronomy, Horticulture and Plant Sciences Department, South Dakota State University, Brookings, SD 57007, USA
| | - Yoshinori Utsumi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan
| | - Abbas Maqbool
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
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6
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Diplock N, Baudin M, Harden L, Silva CJ, Erickson-Beltran ML, Hassan JA, Lewis JD. Utilising natural diversity of kinases to rationally engineer interactions with the angiosperm immune receptor ZAR1. PLANT, CELL & ENVIRONMENT 2023. [PMID: 37157998 DOI: 10.1111/pce.14603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/13/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
The highly conserved angiosperm immune receptor HOPZ-ACTIVATED RESISTANCE1 (ZAR1) recognises the activity of diverse pathogen effector proteins by monitoring the ZED1-related kinase (ZRK) family. Understanding how ZAR1 achieves interaction specificity for ZRKs may allow for the expansion of the ZAR1-kinase recognition repertoire to achieve novel pathogen recognition outside of model species. We took advantage of the natural diversity of Arabidopsis thaliana kinases to probe the ZAR1-kinase interaction interface and found that A. thaliana ZAR1 (AtZAR1) can interact with most ZRKs, except ZRK7. We found evidence of alternative splicing of ZRK7, resulting in a protein that can interact with AtZAR1. Despite high sequence conservation of ZAR1, interspecific ZAR1-ZRK pairings resulted in the autoactivation of cell death. We showed that ZAR1 interacts with a greater diversity of kinases than previously thought, while still possessing the capacity for specificity in kinase interactions. Finally, using AtZAR1-ZRK interaction data, we rationally increased ZRK10 interaction strength with AtZAR1, demonstrating the feasibility of the rational design of a ZAR1-interacting kinase. Overall, our findings advance our understanding of the rules governing ZAR1 interaction specificity, with promising future directions for expanding ZAR1 immunodiversity.
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Affiliation(s)
- Nathan Diplock
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Maël Baudin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Leslie Harden
- United States Department of Agriculture, Agriculture Research Service, Western Regional Research Center, Albany, California, USA
| | - Christopher J Silva
- United States Department of Agriculture, Agriculture Research Service, Western Regional Research Center, Albany, California, USA
| | - Melissa L Erickson-Beltran
- United States Department of Agriculture, Agriculture Research Service, Western Regional Research Center, Albany, California, USA
| | - Jana A Hassan
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Jennifer D Lewis
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
- United States Department of Agriculture, Agriculture Research Service, Plant Gene Expression Center, Albany, California, USA
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7
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Wang Q, Li Y, Kosami KI, Liu C, Li J, Zhang D, Miki D, Kawano Y. Three highly conserved hydrophobic residues in the predicted α2-helix of rice NLR protein Pit contribute to its localization and immune induction. PLANT, CELL & ENVIRONMENT 2022; 45:1876-1890. [PMID: 35312080 DOI: 10.1111/pce.14315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 02/20/2022] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Nucleotide-binding leucine-rich repeat (NLR) proteins work as crucial intracellular immune receptors. N-terminal domains of NLRs fall into two groups, coiled-coil (CC) and Toll-interleukin 1 receptor domains, which play critical roles in signal transduction and disease resistance. However, the activation mechanisms of NLRs, and how their N-termini function in immune induction, remain largely unknown. Here, we revealed that the CC domain of a rice NLR Pit contributes to self-association. The Pit CC domain possesses three conserved hydrophobic residues that are known to be involved in oligomer formation in two NLRs, barley MLA10 and Arabidopsis RPM1. Interestingly, the function of these residues in Pit differs from that in MLA10 and RPM1. Although three hydrophobic residues are important for Pit-induced disease resistance against rice blast fungus, they do not participate in self-association or binding to downstream signalling molecules. By homology modelling of Pit using the Arabidopsis ZAR1 structure, we tried to clarify the role of three conserved hydrophobic residues and found that they are located in the predicted α2-helix of the Pit CC domain and involved in the plasma membrane localization. Our findings provide novel insights for understanding the mechanisms of NLR activation as well as the relationship between subcellular localization and immune induction.
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Affiliation(s)
- Qiong Wang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yuying Li
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ken-Ichi Kosami
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- Fruit Tree Research Center, Ehime Research Institute of Agriculture, Forestry and Fisheries, Ehime, Japan
| | - Chaochao Liu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Jing Li
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dan Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Daisuke Miki
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yoji Kawano
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
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8
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Harant A, Pai H, Sakai T, Kamoun S, Adachi H. A vector system for fast-forward studies of the HOPZ-ACTIVATED RESISTANCE1 (ZAR1) resistosome in the model plant Nicotiana benthamiana. PLANT PHYSIOLOGY 2022; 188:70-80. [PMID: 34633454 PMCID: PMC8774824 DOI: 10.1093/plphys/kiab471] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/08/2021] [Indexed: 05/25/2023]
Abstract
Nicotiana benthamiana has emerged as a complementary experimental system to Arabidopsis thaliana. It enables fast-forward in vivo analyses primarily through transient gene expression and is particularly popular in the study of plant immunity. Recently, our understanding of nucleotide-binding leucine-rich repeat (NLR) plant immune receptors has greatly advanced following the discovery of the Arabidopsis HOPZ-ACTIVATED RESISTANCE1 (ZAR1) resistosome. Here, we describe a vector system of 72 plasmids that enables functional studies of the ZAR1 resistosome in N. benthamiana. We showed that ZAR1 stands out among the coiled coil class of NLRs (CC-NLRs) for being highly conserved across distantly related dicot plant species and confirmed NbZAR1 as the N. benthamiana ortholog of Arabidopsis ZAR1. Effector-activated and autoactive NbZAR1 triggers the cell death response in N. benthamiana and this activity is dependent on a functional N-terminal α1 helix. C-terminally tagged NbZAR1 remains functional in N. benthamiana, thus enabling cell biology and biochemical studies in this plant system. We conclude that the NbZAR1 open source pZA plasmid collection forms an additional experimental system to Arabidopsis for in planta resistosome studies.
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Affiliation(s)
- Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hsuan Pai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Toshiyuki Sakai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
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9
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Martin EC, Spiridon L, Goverse A, Petrescu AJ. NLRexpress-A bundle of machine learning motif predictors-Reveals motif stability underlying plant Nod-like receptors diversity. FRONTIERS IN PLANT SCIENCE 2022; 13:975888. [PMID: 36186050 PMCID: PMC9519389 DOI: 10.3389/fpls.2022.975888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/19/2022] [Indexed: 05/13/2023]
Abstract
Examination of a collection of over 80,000 Plant Nod-like receptors (NLRs) revealed an overwhelming sequence diversity underlying functional specificity of pathogen detection, signaling and cooperativity. The NLR canonical building blocks-CC/TIR/RPW8, NBS and LRR-contain, however, a number of conserved sequence motifs showing a significant degree of invariance amongst different NLR groups. To identify these motifs we developed NLRexpress-a bundle of 17 machine learning (ML)-based predictors, able to swiftly and precisely detect CC, TIR, NBS, and LRR motifs while minimizing computing time without accuracy losses-aimed as an instrument scalable for screening overall proteomes, transcriptomes or genomes for identifying integral NLRs and discriminating them against incomplete sequences lacking key motifs. These predictors were further used to screen a subset of ∼34,000 regular plant NLR sequences. Motifs were analyzed using unsupervised ML techniques to assess the structural correlations hidden underneath pattern variabilities. Both the NB-ARC switch domain which admittedly is the most conserved region of NLRs and the highly diverse LRR domain with its vastly variable lengths and repeat irregularities-show well-defined relations between motif subclasses, highlighting the importance of structural invariance in shaping NLR sequence diversity. The online NLRexpress webserver can be accessed at https://nlrexpress.biochim.ro.
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Affiliation(s)
- Eliza C. Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Laurentiu Spiridon
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Andrei-José Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
- *Correspondence: Andrei-José Petrescu,
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10
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Schreiber KJ, Chau-Ly IJ, Lewis JD. What the Wild Things Do: Mechanisms of Plant Host Manipulation by Bacterial Type III-Secreted Effector Proteins. Microorganisms 2021; 9:1029. [PMID: 34064647 PMCID: PMC8150971 DOI: 10.3390/microorganisms9051029] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 01/05/2023] Open
Abstract
Phytopathogenic bacteria possess an arsenal of effector proteins that enable them to subvert host recognition and manipulate the host to promote pathogen fitness. The type III secretion system (T3SS) delivers type III-secreted effector proteins (T3SEs) from bacterial pathogens such as Pseudomonas syringae, Ralstonia solanacearum, and various Xanthomonas species. These T3SEs interact with and modify a range of intracellular host targets to alter their activity and thereby attenuate host immune signaling. Pathogens have evolved T3SEs with diverse biochemical activities, which can be difficult to predict in the absence of structural data. Interestingly, several T3SEs are activated following injection into the host cell. Here, we review T3SEs with documented enzymatic activities, as well as T3SEs that facilitate virulence-promoting processes either indirectly or through non-enzymatic mechanisms. We discuss the mechanisms by which T3SEs are activated in the cell, as well as how T3SEs modify host targets to promote virulence or trigger immunity. These mechanisms may suggest common enzymatic activities and convergent targets that could be manipulated to protect crop plants from infection.
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Affiliation(s)
- Karl J. Schreiber
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA; (K.J.S.); (I.J.C.-L.)
| | - Ilea J. Chau-Ly
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA; (K.J.S.); (I.J.C.-L.)
| | - Jennifer D. Lewis
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA; (K.J.S.); (I.J.C.-L.)
- Plant Gene Expression Center, United States Department of Agriculture, University of California, Berkeley, CA 94710, USA
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11
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Wang Z, Huang J, Nie L, Hu Y, Zhang N, Guo Q, Guo J, Du B, Zhu L, He G, Chen R. Molecular and functional analysis of a brown planthopper resistance protein with two nucleotide-binding site domains. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2657-2671. [PMID: 33345280 DOI: 10.1093/jxb/eraa586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 12/15/2020] [Indexed: 05/26/2023]
Abstract
The brown planthopper (Nilaparvata lugens Stål, BPH) resistance gene BPH9 encodes an unusual coiled-coil (CC) nucleotide-binding leucine-rich repeat (LRR) protein with two nucleotide-binding site (NBS) domains. To understand how this CC-NBS-NBS-LRR (CNNL) protein regulates defense signaling and BPH resistance, we dissected each domain's functions. The CC domain of BPH9 self-associated and was sufficient to induce cell death. The region of 97-115 residues in the CC domain is crucial for self-association and activation. NBS2, which contains a complete set of NBS function motifs and inhibits CC domain activation, rather than NBS1, acts as a molecular switch to regulate the activity of BPH9. We demonstrated that the CC domain, the NBS domain, and the LRR domain of BPH9 associate with each other and themselves in planta. Further domain swapping experiments revealed that the CC domains of BPH9 and susceptible alleles were similarly competent to induce resistance and the hypersensitive response, while the LRR domain of BPH9 confers resistance specificity to BPH. These findings provide new insights into the regulatory mechanisms governing the activity of CNNL proteins.
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Affiliation(s)
- Zhizheng Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jin Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lingyun Nie
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yinxia Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ning Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qin Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jianping Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bo Du
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lili Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Rongzhi Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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12
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Sun L, Zhang J. Regulatory role of receptor-like cytoplasmic kinases in early immune signaling events in plants. FEMS Microbiol Rev 2021; 44:845-856. [PMID: 32717059 DOI: 10.1093/femsre/fuaa035] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/25/2020] [Indexed: 12/22/2022] Open
Abstract
Receptor-like cytoplasmic kinases (RLCKs) play crucial roles in regulating plant development and immunity. Conserved pathogen-associated molecular patterns (PAMPs) derived from microbes are recognized by plant pattern recognition receptors to activate PAMP-triggered immunity (PTI). Microbial effectors, whose initial function is to promote virulence, are recognized by plant intracellular nucleotide-binding domain and leucine-rich repeat receptors (NLRs) to initiate effector-triggered immunity (ETI). Both PTI and ETI trigger early immune signaling events including the production of reactive oxygen species, induction of calcium influx and activation of mitogen-activated protein kinases. Research progress has revealed the important roles of RLCKs in the regulation of early PTI signaling. Accordingly, RLCKs are often targeted by microbial effectors that are evolved to evade PTI via diverse modulations. In some cases, modulation of RLCKs by microbial effectors triggers the activation of NLRs. This review covers the mechanisms by which RLCKs engage diverse substrates to regulate early PTI signaling and the regulatory roles of RLCKs in triggering NLR activation. Accumulating evidence suggests evolutionary links and close connections between PAMP- and effector-triggered early immune signaling that are mediated by RLCKs. As key immune regulators, RLCKs can be considered targets with broad prospects for the improvement of plant resistance via genetic engineering.
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Affiliation(s)
- Lifan Sun
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing 100049, China
| | - Jie Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing 100049, China
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13
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Baudin M, Martin EC, Sass C, Hassan JA, Bendix C, Sauceda R, Diplock N, Specht CD, Petrescu AJ, Lewis JD. A natural diversity screen in Arabidopsis thaliana reveals determinants for HopZ1a recognition in the ZAR1-ZED1 immune complex. PLANT, CELL & ENVIRONMENT 2021; 44:629-644. [PMID: 33103794 DOI: 10.1111/pce.13927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
Pathogen pressure on hosts can lead to the evolution of genes regulating the innate immune response. By characterizing naturally occurring polymorphisms in immune receptors, we can better understand the molecular determinants of pathogen recognition. ZAR1 is an ancient Arabidopsis thaliana NLR (Nucleotide-binding [NB] Leucine-rich-repeat [LRR] Receptor) that recognizes multiple secreted effector proteins from the pathogenic bacteria Pseudomonas syringae and Xanthomonas campestris through its interaction with receptor-like cytoplasmic kinases (RLCKs). ZAR1 was first identified for its role in recognizing P. syringae effector HopZ1a, through its interaction with the RLCK ZED1. To identify additional determinants of HopZ1a recognition, we performed a computational screen for ecotypes from the 1001 Genomes project that were likely to lack HopZ1a recognition, and tested ~300 ecotypes. We identified ecotypes containing polymorphisms in ZAR1 and ZED1. Using our previously established Nicotiana benthamiana transient assay and Arabidopsis ecotypes, we tested for the effect of naturally occurring polymorphisms on ZAR1 interactions and the immune response. We identified key residues in the NB or LRR domain of ZAR1 that impact the interaction with ZED1. We demonstrate that natural diversity combined with functional assays can help define the molecular determinants and interactions necessary to regulate immune induction in response to pathogens.
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Affiliation(s)
- Maël Baudin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Eliza C Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Chodon Sass
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Jana A Hassan
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Claire Bendix
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Rolin Sauceda
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Nathan Diplock
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Chelsea D Specht
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, New York, USA
| | - Andrei J Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Jennifer D Lewis
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
- Plant Gene Expression Center, United States Department of Agriculture, Albany, California, USA
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14
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Deutschmeyer VE, Richter AM. The ZAR1 protein in cancer; from epigenetic silencing to functional characterisation and epigenetic therapy of tumour suppressors. Biochim Biophys Acta Rev Cancer 2020; 1874:188417. [PMID: 32828887 DOI: 10.1016/j.bbcan.2020.188417] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022]
Abstract
ZAR1, zygote arrest 1, is a zinc finger protein (C-terminus), which was initially identified in mouse oocytes. Later it was found that its expression is present in various human tissues e.g. lung and kidney. Interestingly, it was observed that in various tumour types the ZAR1 transcript is missing due to hypermethylation of its CpG island promoter, but not ZAR2. Since methylation of the ZAR1 promoter is described as a frequent event in tumourigenesis, ZAR1 could serve as a useful diagnostic marker in cancer screens. ZAR1 was described as a useful prognostic/diagnostic cancer marker for lung cancer, kidney cancer, melanoma and possibly liver carcinoma. Furthermore, ZAR1 was reactivated as a tumour suppressor by epigenetic therapy using CRISPR-dCas9 method. This method holds the potential to precisely target not only ZAR1 and reactivate tumour suppressors in a tailored cancer therapy. ZAR1 is highly conserved amongst vertebrates, especially its zinc finger, which is the relevant domain for its protein and RNA binding ability. ZAR1 is implicated in various cellular mechanisms including regulation of oocyte/embryo development, cell cycle control and mRNA binding, though little was known about the underlying mechanisms. ZAR1 was reported to regulate and activate translation through the binding to TCS translation control sequences in the 3'UTRs of its target mRNA the kinase WEE1. ZAR1 has a tumour suppressing function by inhibiting cell cycle progression. Here we review the current literature on ZAR1 focusing on structural, functional and epigenetic aspects. Characterising the cellular mechanisms that regulate the signalling pathways ZAR1 is involved in, could lead to a deeper understanding of tumour development and, furthermore, to new strategies in cancer treatment.
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Affiliation(s)
| | - Antje M Richter
- Institute for Genetics, University of Giessen, 35392 Giessen, Germany; Max-Planck Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany.
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15
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Laflamme B, Dillon MM, Martel A, Almeida RND, Desveaux D, Guttman DS. The pan-genome effector-triggered immunity landscape of a host-pathogen interaction. Science 2020; 367:763-768. [PMID: 32054757 DOI: 10.1126/science.aax4079] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 10/18/2019] [Accepted: 01/17/2020] [Indexed: 12/24/2022]
Abstract
Effector-triggered immunity (ETI), induced by host immune receptors in response to microbial effectors, protects plants against virulent pathogens. However, a systematic study of ETI prevalence against species-wide pathogen diversity is lacking. We constructed the Pseudomonas syringae Type III Effector Compendium (PsyTEC) to reduce the pan-genome complexity of 5127 unique effector proteins, distributed among 70 families from 494 strains, to 529 representative alleles. We screened PsyTEC on the model plant Arabidopsis thaliana and identified 59 ETI-eliciting alleles (11.2%) from 19 families (27.1%), with orthologs distributed among 96.8% of P. syringae strains. We also identified two previously undescribed host immune receptors, including CAR1, which recognizes the conserved effectors AvrE and HopAA1, and found that 94.7% of strains harbor alleles predicted to be recognized by either CAR1 or ZAR1.
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Affiliation(s)
- Bradley Laflamme
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Marcus M Dillon
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Alexandre Martel
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Renan N D Almeida
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Darrell Desveaux
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
| | - David S Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada. .,Center for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada
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16
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LRRpredictor-A New LRR Motif Detection Method for Irregular Motifs of Plant NLR Proteins Using an Ensemble of Classifiers. Genes (Basel) 2020; 11:genes11030286. [PMID: 32182725 PMCID: PMC7140858 DOI: 10.3390/genes11030286] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 12/17/2022] Open
Abstract
Leucine-rich-repeats (LRRs) belong to an archaic procaryal protein architecture that is widely involved in protein-protein interactions. In eukaryotes, LRR domains developed into key recognition modules in many innate immune receptor classes. Due to the high sequence variability imposed by recognition specificity, precise repeat delineation is often difficult especially in plant NOD-like Receptors (NLRs) notorious for showing far larger irregularities. To address this problem, we introduce here LRRpredictor, a method based on an ensemble of estimators designed to better identify LRR motifs in general but particularly adapted for handling more irregular LRR environments, thus allowing to compensate for the scarcity of structural data on NLR proteins. The extrapolation capacity tested on a set of annotated LRR domains from six immune receptor classes shows the ability of LRRpredictor to recover all previously defined specific motif consensuses and to extend the LRR motif coverage over annotated LRR domains. This analysis confirms the increased variability of LRR motifs in plant and vertebrate NLRs when compared to extracellular receptors, consistent with previous studies. Hence, LRRpredictor is able to provide novel insights into the diversification of LRR domains and a robust support for structure-informed analyses of LRRs in immune receptor functioning.
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