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Horsefield S, Burdett H, Zhang X, Manik MK, Shi Y, Chen J, Qi T, Gilley J, Lai JS, Rank MX, Casey LW, Gu W, Ericsson DJ, Foley G, Hughes RO, Bosanac T, von Itzstein M, Rathjen JP, Nanson JD, Boden M, Dry IB, Williams SJ, Staskawicz BJ, Coleman MP, Ve T, Dodds PN, Kobe B. NAD + cleavage activity by animal and plant TIR domains in cell death pathways. Science 2019; 365:793-799. [PMID: 31439792 DOI: 10.1126/science.aax1911] [Citation(s) in RCA: 288] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/23/2019] [Indexed: 02/02/2023]
Abstract
SARM1 (sterile alpha and TIR motif containing 1) is responsible for depletion of nicotinamide adenine dinucleotide in its oxidized form (NAD+) during Wallerian degeneration associated with neuropathies. Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors recognize pathogen effector proteins and trigger localized cell death to restrict pathogen infection. Both processes depend on closely related Toll/interleukin-1 receptor (TIR) domains in these proteins, which, as we show, feature self-association-dependent NAD+ cleavage activity associated with cell death signaling. We further show that SARM1 SAM (sterile alpha motif) domains form an octamer essential for axon degeneration that contributes to TIR domain enzymatic activity. The crystal structures of ribose and NADP+ (the oxidized form of nicotinamide adenine dinucleotide phosphate) complexes of SARM1 and plant NLR RUN1 TIR domains, respectively, reveal a conserved substrate binding site. NAD+ cleavage by TIR domains is therefore a conserved feature of animal and plant cell death signaling pathways.
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Affiliation(s)
- Shane Horsefield
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Hayden Burdett
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Xiaoxiao Zhang
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia.,Plant Sciences Division, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Mohammad K Manik
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Jian Chen
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia.,Plant Sciences Division, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Tiancong Qi
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jonathan Gilley
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, ED Adrian Building, Forvie Site, Robinson Way, Cambridge CB2 0PY, UK.,Babraham Institute, Babraham, Cambridge CB22 3AT, UK
| | - Jhih-Siang Lai
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Maxwell X Rank
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Lachlan W Casey
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.,Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, QLD 4072, Australia
| | - Weixi Gu
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Daniel J Ericsson
- Macromolecular Crystallography (MX) Beamlines, Australian Synchrotron, Melbourne, VIC 3168, Australia
| | - Gabriel Foley
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert O Hughes
- Disarm Therapeutics, 400 Technology Square, Cambridge, MA 02139, USA
| | - Todd Bosanac
- Disarm Therapeutics, 400 Technology Square, Cambridge, MA 02139, USA
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - John P Rathjen
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Mikael Boden
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Ian B Dry
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Urrbrae, SA 5064, Australia
| | - Simon J Williams
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Brian J Staskawicz
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Michael P Coleman
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, ED Adrian Building, Forvie Site, Robinson Way, Cambridge CB2 0PY, UK.,Babraham Institute, Babraham, Cambridge CB22 3AT, UK
| | - Thomas Ve
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia. .,Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia.
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.
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2
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Newman TE, Lee J, Williams SJ, Choi S, Halane MK, Zhou J, Solomon P, Kobe B, Jones JDG, Segonzac C, Sohn KH. Autoimmunity and effector recognition in Arabidopsis thaliana can be uncoupled by mutations in the RRS1-R immune receptor. THE NEW PHYTOLOGIST 2019; 222:954-965. [PMID: 30500990 DOI: 10.1111/nph.15617] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/23/2018] [Indexed: 05/13/2023]
Abstract
Plant nucleotide-binding leucine-rich repeat (NLR) disease resistance proteins recognize specific pathogen effectors and activate a cellular defense program. In Arabidopsis thaliana (Arabidopsis), Resistance to Ralstonia solanacearum 1 (RRS1-R) and Resistance to Pseudomonas syringae 4 (RPS4) function together to recognize the unrelated bacterial effectors PopP2 and AvrRps4. In the plant cell nucleus, the RRS1-R/RPS4 complex binds to and signals the presence of AvrRps4 or PopP2. The exact mechanism underlying NLR signaling and immunity activation remains to be elucidated. Using genetic and biochemical approaches, we characterized the intragenic suppressors of sensitive to low humidity 1 (slh1), a temperature-sensitive autoimmune allele of RRS1-R. Our analyses identified five amino acid residues that contribute to RRS1-RSLH1 autoactivity. We investigated the role of these residues in the RRS1-R allele by genetic complementation, and found that C15 in the Toll/interleukin-1 receptor (TIR) domain and L816 in the LRR domain were also important for effector recognition. Further characterization of the intragenic suppressive mutations located in the RRS1-R TIR domain revealed differing requirements for RRS1-R/RPS4-dependent autoimmunity and effector-triggered immunity. Our results provide novel information about the mechanisms which, in turn, hold an NLR protein complex inactive and allow adequate activation in the presence of pathogens.
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Affiliation(s)
- Toby E Newman
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
- Bioprotection Centre of Research Excellence, Institute of Agriculture and Environment, Massey University, Palmerston North, 4442, New Zealand
| | - Jungmin Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Simon J Williams
- Division of Plant Sciences, Research School of Biology, Australian National University, Acton, ACT, 2601, Australia
| | - Sera Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Morgan K Halane
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Jun Zhou
- Bioprotection Centre of Research Excellence, Institute of Agriculture and Environment, Massey University, Palmerston North, 4442, New Zealand
| | - Peter Solomon
- Division of Plant Sciences, Research School of Biology, Australian National University, Acton, ACT, 2601, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld, 4072, Australia
| | | | - Cécile Segonzac
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Plant Immunity Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
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Zhang X, Bernoux M, Bentham AR, Newman TE, Ve T, Casey LW, Raaymakers TM, Hu J, Croll TI, Schreiber KJ, Staskawicz BJ, Anderson PA, Sohn KH, Williams SJ, Dodds PN, Kobe B. Multiple functional self-association interfaces in plant TIR domains. Proc Natl Acad Sci U S A 2017; 114:E2046-E2052. [PMID: 28159890 PMCID: PMC5347627 DOI: 10.1073/pnas.1621248114] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The self-association of Toll/interleukin-1 receptor/resistance protein (TIR) domains has been implicated in signaling in plant and animal immunity receptors. Structure-based studies identified different TIR-domain dimerization interfaces required for signaling of the plant nucleotide-binding oligomerization domain-like receptors (NLRs) L6 from flax and disease resistance protein RPS4 from Arabidopsis Here we show that the crystal structure of the TIR domain from the Arabidopsis NLR suppressor of npr1-1, constitutive 1 (SNC1) contains both an L6-like interface involving helices αD and αE (DE interface) and an RPS4-like interface involving helices αA and αE (AE interface). Mutations in either the AE- or DE-interface region disrupt cell-death signaling activity of SNC1, L6, and RPS4 TIR domains and full-length L6 and RPS4. Self-association of L6 and RPS4 TIR domains is affected by mutations in either region, whereas only AE-interface mutations affect SNC1 TIR-domain self-association. We further show two similar interfaces in the crystal structure of the TIR domain from the Arabidopsis NLR recognition of Peronospora parasitica 1 (RPP1). These data demonstrate that both the AE and DE self-association interfaces are simultaneously required for self-association and cell-death signaling in diverse plant NLRs.
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Affiliation(s)
- Xiaoxiao Zhang
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Maud Bernoux
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia;
| | - Adam R Bentham
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
- School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, SA 5001, Australia
| | - Toby E Newman
- Department of Life Sciences, and School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea
- Bioprotection Research Centre, Institute of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand
| | - Thomas Ve
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Lachlan W Casey
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Tom M Raaymakers
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
- Department of Biology, Plant-Microbe Interactions, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Jian Hu
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
- College of Biological Sciences, China Agricultural University, Beijing 100094, People's Republic of China
| | - Tristan I Croll
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Karl J Schreiber
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Brian J Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
| | - Peter A Anderson
- School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, SA 5001, Australia
| | - Kee Hoon Sohn
- Department of Life Sciences, and School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea
- Bioprotection Research Centre, Institute of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand
| | - Simon J Williams
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia;
- Research School of Biology, College of Medicine, Biology, and Environment, Australian National University, Canberra, ACT 0200, Australia
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia;
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia;
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Sun Y, Mui Z, Liu X, Yim AKY, Qin H, Wong FL, Chan TF, Yiu SM, Lam HM, Lim BL. Comparison of Small RNA Profiles of Glycine max and Glycine soja at Early Developmental Stages. Int J Mol Sci 2016; 17:E2043. [PMID: 27929436 PMCID: PMC5187843 DOI: 10.3390/ijms17122043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 11/24/2016] [Accepted: 11/29/2016] [Indexed: 01/22/2023] Open
Abstract
Small RNAs, including microRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs; from PHAS loci), play key roles in plant development. Cultivated soybean, Glycine max, contributes a great deal to food production, but, compared to its wild kin, Glycine soja, it may lose some genetic information during domestication. In this work, we analyzed the sRNA profiles of different tissues in both cultivated (C08) and wild soybeans (W05) at three stages of development. A total of 443 known miRNAs and 15 novel miRNAs showed varying abundances between different samples, but the miRNA profiles were generally similar in both accessions. Based on a sliding window analysis workflow that we developed, 50 PHAS loci generating 55 21-nucleotide phasiRNAs were identified in C08, and 46 phasiRNAs from 41 PHAS loci were identified in W05. In germinated seedlings, phasiRNAs were more abundant in C08 than in W05. Disease resistant TIR-NB-LRR genes constitute a very large family of PHAS loci. PhasiRNAs were also generated from several loci that encode for NAC transcription factors, Dicer-like 2 (DCL2), Pentatricopeptide Repeat (PPR), and Auxin Signaling F-box 3 (AFB3) proteins. To investigate the possible involvement of miRNAs in initiating the PHAS-phasiRNA pathway, miRNA target predictions were performed and 17 C08 miRNAs and 15 W05 miRNAs were predicted to trigger phasiRNAs biogenesis. In summary, we provide a comprehensive description of the sRNA profiles of wild versus cultivated soybeans, and discuss the possible roles of sRNAs during soybean germination.
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Affiliation(s)
- Yuzhe Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Zeta Mui
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Xuan Liu
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Aldrin Kay-Yuen Yim
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Hao Qin
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Fuk-Ling Wong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Siu-Ming Yiu
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Hon-Ming Lam
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Boon Leong Lim
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Williams SJ, Sohn KH, Wan L, Bernoux M, Sarris PF, Segonzac C, Ve T, Ma Y, Saucet SB, Ericsson DJ, Casey LW, Lonhienne T, Winzor DJ, Zhang X, Coerdt A, Parker JE, Dodds PN, Kobe B, Jones JDG. Structural basis for assembly and function of a heterodimeric plant immune receptor. Science 2014; 344:299-303. [PMID: 24744375 DOI: 10.1126/science.1247357] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cytoplasmic plant immune receptors recognize specific pathogen effector proteins and initiate effector-triggered immunity. In Arabidopsis, the immune receptors RPS4 and RRS1 are both required to activate defense to three different pathogens. We show that RPS4 and RRS1 physically associate. Crystal structures of the N-terminal Toll-interleukin-1 receptor/resistance (TIR) domains of RPS4 and RRS1, individually and as a heterodimeric complex (respectively at 2.05, 1.75, and 2.65 angstrom resolution), reveal a conserved TIR/TIR interaction interface. We show that TIR domain heterodimerization is required to form a functional RRS1/RPS4 effector recognition complex. The RPS4 TIR domain activates effector-independent defense, which is inhibited by the RRS1 TIR domain through the heterodimerization interface. Thus, RPS4 and RRS1 function as a receptor complex in which the two components play distinct roles in recognition and signaling.
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Affiliation(s)
- Simon J Williams
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
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