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Rahaman MH, Thygesen SJ, Maxwell MJ, Kim H, Mudai P, Nanson JD, Jia X, Vajjhala PR, Hedger A, Vetter I, Haselhorst T, Robertson AAB, Dymock B, Ve T, Mobli M, Stacey KJ, Kobe B. o-Vanillin binds covalently to MAL/TIRAP Lys-210 but independently inhibits TLR2. J Enzyme Inhib Med Chem 2024; 39:2313055. [PMID: 38416868 PMCID: PMC10903754 DOI: 10.1080/14756366.2024.2313055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 01/28/2024] [Indexed: 03/01/2024] Open
Abstract
Toll-like receptor (TLR) innate immunity signalling protects against pathogens, but excessive or prolonged signalling contributes to a range of inflammatory conditions. Structural information on the TLR cytoplasmic TIR (Toll/interleukin-1 receptor) domains and the downstream adaptor proteins can help us develop inhibitors targeting this pathway. The small molecule o-vanillin has previously been reported as an inhibitor of TLR2 signalling. To study its mechanism of action, we tested its binding to the TIR domain of the TLR adaptor MAL/TIRAP (MALTIR). We show that o-vanillin binds to MALTIR and inhibits its higher-order assembly in vitro. Using NMR approaches, we show that o-vanillin forms a covalent bond with lysine 210 of MAL. We confirm in mouse and human cells that o-vanillin inhibits TLR2 but not TLR4 signalling, independently of MAL, suggesting it may covalently modify TLR2 signalling complexes directly. Reactive aldehyde-containing small molecules such as o-vanillin may target multiple proteins in the cell.
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Affiliation(s)
- Md. Habibur Rahaman
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Sara J. Thygesen
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Michael J. Maxwell
- Centre for Advanced Imaging, University of Queensland, Brisbane, Australia
| | - Hyoyoung Kim
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Prerna Mudai
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Jeffrey D. Nanson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Xinying Jia
- Centre for Advanced Imaging, University of Queensland, Brisbane, Australia
| | - Parimala R. Vajjhala
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Andrew Hedger
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Irina Vetter
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
- School of Pharmacy, University of Queensland, Brisbane, Australia
| | | | - Avril A. B. Robertson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Brian Dymock
- Queensland Emory Drug Discovery Initiative, University of Queensland, Brisbane, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, University of Queensland, Brisbane, Australia
| | - Katryn J. Stacey
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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2
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Thynne E, Kobe B. Mixed-organism enzyme in plant defense. Science 2024; 383:707-708. [PMID: 38359137 DOI: 10.1126/science.adn8306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Plants commandeer a pathogen's virulence factor to bolster immunity.
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Affiliation(s)
- Elisha Thynne
- Botanical Institute, Christian-Albrechts University, Kiel, Germany
- Max Planck Institute for Molecular Biology, Plön, Germany
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences , The University of Queensland, Brisbane, QLD, Australia
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Maruta N, Outram MA, Kobe B. Mildew RALPHs up in arms with cereals. Proc Natl Acad Sci U S A 2023; 120:e2311817120. [PMID: 37611066 PMCID: PMC10483659 DOI: 10.1073/pnas.2311817120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023] Open
Affiliation(s)
- Natsumi Maruta
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD4072, Australia
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD4072, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Megan A. Outram
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, ACT2601, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD4072, Australia
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD4072, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
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McCombe CL, Catanzariti AM, Greenwood JR, Desai AM, Outram MA, Yu DS, Ericsson DJ, Brenner SE, Dodds PN, Kobe B, Jones DA, Williams SJ. A rust-fungus Nudix hydrolase effector decaps mRNA in vitro and interferes with plant immune pathways. New Phytol 2023; 239:222-239. [PMID: 36631975 DOI: 10.1111/nph.18727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/02/2023] [Indexed: 06/02/2023]
Abstract
To infect plants, pathogenic fungi secrete small proteins called effectors. Here, we describe the catalytic activity and potential virulence function of the Nudix hydrolase effector AvrM14 from the flax rust fungus (Melampsora lini). We completed extensive in vitro assays to characterise the enzymatic activity of the AvrM14 effector. Additionally, we used in planta transient expression of wild-type and catalytically dead AvrM14 versions followed by biochemical assays, phenotypic analysis and RNA sequencing to unravel how the catalytic activity of AvrM14 impacts plant immunity. AvrM14 is an extremely selective enzyme capable of removing the protective 5' cap from mRNA transcripts in vitro. Homodimerisation of AvrM14 promoted biologically relevant mRNA cap cleavage in vitro and this activity was conserved in related effectors from other Melampsora spp. In planta expression of wild-type AvrM14, but not the catalytically dead version, suppressed immune-related reactive oxygen species production, altered the abundance of some circadian-rhythm-associated mRNA transcripts and reduced the hypersensitive cell-death response triggered by the flax disease resistance protein M1. To date, the decapping of host mRNA as a virulence strategy has not been described beyond viruses. Our results indicate that some fungal pathogens produce Nudix hydrolase effectors with in vitro mRNA-decapping activity capable of interfering with plant immunity.
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Affiliation(s)
- Carl L McCombe
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Ann-Maree Catanzariti
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Julian R Greenwood
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Anna M Desai
- Plant and Microbial Biology Department, University of California, Berkeley, CA, 94720, USA
| | - Megan A Outram
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel S Yu
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Australian Synchrotron, Macromolecular Crystallography, Clayton, Vic., 3168, Australia
| | - Steven E Brenner
- Plant and Microbial Biology Department, University of California, Berkeley, CA, 94720, USA
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, 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
| | - David A Jones
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Simon J Williams
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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Lang JJ, Lv Y, Kobe B, Chen H, Tan Y, Chen L, Wang X, Mi P, Zheng X, Lin YW. Discovery of C-5 Pyrazole-Substituted Pyrrolopyridine Derivatives as Potent and Selective Inhibitors for Janus Kinase 1. J Med Chem 2023; 66:6725-6742. [PMID: 37163463 DOI: 10.1021/acs.jmedchem.3c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Developing selective inhibitors for Janus kinase 1 (JAK1) is a significant focus for improving the efficacy and alleviating the adverse effects in treating immune-inflammatory diseases. Herein, we report the discovery of a series of C-5 pyrazole-modified pyrrolopyrimidine derivatives as JAK1-selective inhibitors. The potential hydrogen bond between the pyrazole group and E966 in JAK1 is the key point that enhances JAK1 selectivity. These compounds exhibit 10- to 20-fold JAK1 selectivity over JAK2 in enzyme assays. Compound 12b also exhibits excellent JAK1 selectivity in Ba/F3-TEL-JAK cellular assays. Metabolism studies and the results of the hair growth model in mice indicate that compound 12b may be a viable lead compound for the development of highly JAK1-selective inhibitors for immune and inflammatory diseases.
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Affiliation(s)
- Jia-Jia Lang
- Department of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hengyang Medical College, School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
| | - You Lv
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, Shaanxi 710021, China
- Xi'an Amazinggene Co., Ltd, Xi'an, Shaanxi 710026, China
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hongfei Chen
- Department of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Yan Tan
- Department of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Limei Chen
- Department of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Xuechuan Wang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, Shaanxi 710021, China
| | - Pengbing Mi
- Department of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
| | - Xing Zheng
- Department of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Department of Pharmacy, Hunan Vocational College of Science and Technology, Changsha 410004, China
| | - Ying-Wu Lin
- Hengyang Medical College, School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
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Maruta N, Sorbello M, Lim BYJ, McGuinness HY, Shi Y, Ve T, Kobe B. TIR domain-associated nucleotides with functions in plant immunity and beyond. Curr Opin Plant Biol 2023; 73:102364. [PMID: 37086529 DOI: 10.1016/j.pbi.2023.102364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/19/2023] [Accepted: 03/09/2023] [Indexed: 05/03/2023]
Abstract
TIR (Toll/interlukin-1 receptor) domains are found in archaea, bacteria and eukaryotes, featured in proteins generally associated with immune functions. In plants, they are found in a large group of NLRs (nucleotide-binding leucine-rich repeat receptors), NLR-like proteins and TIR-only proteins. They are also present in effector proteins from phytopathogenic bacteria that are associated with suppression of host immunity. TIR domains from plants and bacteria are enzymes that cleave NAD+ (nicotinamide adenine dinucleotide, oxidized form) and other nucleotides. In dicot plants, TIR-derived signalling molecules activate downstream immune signalling proteins, the EDS1 (enhanced disease susceptibility 1) family proteins, and in turn helper NLRs. Recent work has brought major advances in understanding how TIR domains work, how they produce signalling molecules and how these products signal.
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Affiliation(s)
- Natsumi Maruta
- The University of Queensland, School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, Brisbane, QLD 4072, Australia
| | - Mitchell Sorbello
- The University of Queensland, School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, Brisbane, QLD 4072, Australia
| | - Bryan Y J Lim
- The University of Queensland, School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, Brisbane, QLD 4072, Australia
| | - Helen Y McGuinness
- The University of Queensland, School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, Brisbane, QLD 4072, Australia
| | - Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Bostjan Kobe
- The University of Queensland, School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, Brisbane, QLD 4072, Australia.
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7
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Li S, Manik MK, Shi Y, Kobe B, Ve T. Toll/interleukin-1 receptor domains in bacterial and plant immunity. Curr Opin Microbiol 2023; 74:102316. [PMID: 37084552 DOI: 10.1016/j.mib.2023.102316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 04/23/2023]
Abstract
The Toll/interleukin-1 receptor (TIR) domain is found in animal, plant, and bacterial immune systems. It was first described as a protein-protein interaction module mediating signalling downstream of the Toll-like receptor and interleukin-1 receptor families in animals. However, studies of the pro-neurodegenerative protein sterile alpha and TIR motif containing 1, plant immune receptors, and many bacterial TIR domain-containing proteins revealed that TIR domains have enzymatic activities and can produce diverse nucleotide products using nicotinamide adenine dinucleotide (NAD+) or nucleic acids as substrates. Recent work has led to key advances in understanding how TIR domain enzymes work in bacterial and plant immune systems as well as the function of their signalling molecules.
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Affiliation(s)
- Sulin Li
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mohammad K Manik
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia.
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8
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Teng L, Liang M, Wang C, Li Y, Urbach JM, Kobe B, Xing Q, Han W, Ye N. Exon shuffling potentiates a diverse repertoire of brown algal NB-ARC-TPR candidate immune receptor proteins via alternative splicing. Plant J 2023; 114:246-261. [PMID: 36738111 DOI: 10.1111/tpj.16131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 05/10/2023]
Abstract
Like other organisms, brown algae are subject to diseases caused by bacteria, fungi, and viruses. Brown algal immunity mechanisms are not well characterized; however, there is evidence suggesting that pathogen receptors exist in brown algae. One key protein family likely associated with brown algal innate immunity possesses an NB-ARC domain analogous to innate immune proteins in plants and animals. In this study, we conducted an extensive survey of NB-ARC genes in brown algae and obtained insights into the domain organization and evolutionary history of the encoded proteins. Our data show that brown algae possess an ancient NB-ARC-tetratricopeptide repeat (NB-TPR) domain architecture. We identified an N-terminal effector domain, the four-helix bundle, which was not previously found associated with NB-ARC domains. The phylogenetic tree including NB-ARC domains from all kingdoms of life suggests the three clades of brown algal NB-TPRs are likely monophyletic, whereas their TPRs seem to have distinct origins. One group of TPRs exhibit intense exon shuffling, with various alternative splicing and diversifying selection acting on them, suggesting exon shuffling is an important mechanism for evolving ligand-binding specificities. The reconciliation of gene duplication and loss events of the NB-ARC genes reveals that more independent gene gains than losses have occurred during brown algal evolution, and that tandem duplication has played a major role in the expansion of NB-ARC genes. Our results substantially enhance our understanding of the evolutionary history and exon shuffling mechanisms of the candidate innate immune repertoire of brown algae.
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Affiliation(s)
- Linhong Teng
- College of Life Sciences, Dezhou University, Dezhou, 253023, China
| | - Miao Liang
- College of Life Sciences, Dezhou University, Dezhou, 253023, China
| | - Chenghui Wang
- College of Life Sciences, Dezhou University, Dezhou, 253023, China
| | - Yan Li
- College of Life Sciences, Dezhou University, Dezhou, 253023, China
| | - Jonathan M Urbach
- Ragon Institute, 400 Technology Square, Cambridge, Massachusetts, 02139, USA
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Qikun Xing
- Department of Marine Science, Incheon National University, Incheon, 22012, South Korea
| | - Wentao Han
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Naihao Ye
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
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9
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Tao L, Yang G, Sun T, Jie Tao, Zhu C, Yu H, Cheng Y, Yang Z, Xu M, Jiang Y, Zhang W, Wang Z, Ma W, Wu L, Xue D, Wang D, Yang W, Zhao Y, Horsefield S, Kobe B, Zhang Z, Tang Z, Li Q, Zhai Q, Dooley S, Seki E, Liu P, Xu J, Chen H, Liu C. Capsaicin receptor TRPV1 maintains quiescence of hepatic stellate cells in the liver via recruitment of SARM1. J Hepatol 2023; 78:805-819. [PMID: 36669703 DOI: 10.1016/j.jhep.2022.12.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 01/19/2023]
Abstract
BACKGROUND & AIMS Capsaicin receptor, also known as transient receptor potential vanilloid 1 (TRPV1), is involved in pain physiology and neurogenic inflammation. Herein, we discovered the presence of TRPV1 in hepatic stellate cells (HSCs) and aimed to delineate its function in this cell type and liver fibrosis. METHODS TRPV1 expression was examined in liver biopsies from patients with liver fibrosis using quantitative real-time PCR and immunostaining. Its contribution to liver fibrosis was examined in Trpv1-/- mice, upon lentiviral delivery of the TRPV1 gene, and in human and mouse primary HSCs, using patch clamp, intracellular Ca2+ mobilization determination, FACS analyses and gain/loss of function experiments. Binding of sterile alpha and Toll/interleukin-1 receptor motif-containing protein 1 (SARM1) to TRPV1 was determined using mass spectrometry, co-immunoprecipitation, surface plasmon resonance, bioluminescence resonance energy transfer, and NanoBiT. RESULTS TRPV1 mRNA levels are significantly downregulated in patients with liver fibrosis and mouse models, showing a negative correlation with F stage and α-smooth muscle actin expression, a marker of HSC activation. TRPV1 expression and function decrease during HSC activation in fibrotic livers in vivo or during culture. Genetic and pharmacological inhibition of TRPV1 in quiescent HSCs leads to NF-κB activation and pro-inflammatory cytokine production. TRPV1 requires binding of its N-terminal ankyrin repeat domain to the TIR-His583 (Toll/interleukin-1 receptor) domain of SARM1 to prevent HSCs from pro-inflammatory activation. Trpv1-/- mice display increased HSC activation and more severe liver fibrosis, whereas TRPV1 overexpression is antifibrotic in various disease models. CONCLUSION The antifibrotic properties of TRPV1 are attributed to the prevention of HSC activation via the recruitment of SARM1, which could be an attractive therapeutic strategy against liver fibrosis. IMPACT AND IMPLICATIONS We identified the neuronal channel protein TRPV1 as a gatekeeper of quiescence in hepatic stellate cells, a key driver of liver fibrogenesis and chronic liver disease. Physiologically expressed in healthy liver and consistently downregulated during liver fibrosis development, its therapeutic re-expression is expected to have few side effects, making it an attractive target diagnostic tool and drug candidate for industry and clinicians.
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Affiliation(s)
- Le Tao
- Laboratory of Liver Disease, Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China; Department of Infectious Disease, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China
| | - Guangyue Yang
- Laboratory of Liver Disease, Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China
| | - Tiantian Sun
- Laboratory of Liver Disease, Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China
| | - Jie Tao
- Laboratory of Liver Disease, Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China
| | - Chan Zhu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210000, China
| | - Huimin Yu
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yalan Cheng
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zongguo Yang
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201508, China
| | - Mingyi Xu
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200092, China
| | - Yuefeng Jiang
- State Key Laboratory of Membrane Biology, Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Wei Zhang
- Laboratory of Liver Disease, Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China
| | - Zhiyi Wang
- Laboratory of Liver Disease, Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China
| | - Wenting Ma
- Department of Infectious Disease, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China
| | - Liu Wu
- Department of Infectious Disease, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China
| | - Dongying Xue
- Department of Infectious Disease, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China
| | - Dongxue Wang
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China; Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
| | - Wentao Yang
- Department of Organ Transplantation, Second Affiliated Hospital, Nanchang University, No. 1 Minde Road, Nanchang, 330006, China
| | - Yongjuan Zhao
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, China
| | - 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; QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Tumour Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland 4006, 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
| | - Zhe Zhang
- State Key Laboratory of Membrane Biology, Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zongxiang Tang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210000, China
| | - Qigen Li
- Department of Organ Transplantation, Second Affiliated Hospital, Nanchang University, No. 1 Minde Road, Nanchang, 330006, China; Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Qiwei Zhai
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Steven Dooley
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ekihiro Seki
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Ping Liu
- Institute of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Jianrong Xu
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China; Shanghai Frontiers Science Center of TCM Chemical Biology, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China.
| | - Hongzhuan Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China; Shanghai Frontiers Science Center of TCM Chemical Biology, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China; Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.
| | - Cheng Liu
- Laboratory of Liver Disease, Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China; Department of Infectious Disease, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, China; Interventional Cancer Institute of Chinese Integrative Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, 200062 Shanghai, China.
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10
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McGuinness HY, Gu W, Shi Y, Kobe B, Ve T. SARM1-Dependent Axon Degeneration: Nucleotide Signaling, Neurodegenerative Disorders, Toxicity, and Therapeutic Opportunities. Neuroscientist 2023:10738584231162508. [DOI: 10.1177/10738584231162508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Axons are an essential component of the nervous system, and axon degeneration is an early feature of many neurodegenerative disorders. The NAD+ metabolome plays an essential role in regulating axonal integrity. Axonal levels of NAD+ and its precursor NMN are controlled in large part by the NAD+ synthesizing survival factor NMNAT2 and the pro-neurodegenerative NADase SARM1, whose activation triggers axon destruction. SARM1 has emerged as a promising axon-specific target for therapeutic intervention, and its function, regulation, structure, and role in neurodegenerative diseases have been extensively characterized in recent years. In this review, we first introduce the key molecular players involved in the SARM1-dependent axon degeneration program. Next, we summarize recent major advances in our understanding of how SARM1 is kept inactive in healthy neurons and how it becomes activated in injured or diseased neurons, which has involved important insights from structural biology. Finally, we discuss the role of SARM1 in neurodegenerative disorders and environmental neurotoxicity and its potential as a therapeutic target.
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Affiliation(s)
- Helen Y. McGuinness
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Saint Lucia, Australia
| | - Weixi Gu
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Saint Lucia, Australia
| | - Yun Shi
- Institute for Glycomics, Griffith University, Gold Coast, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Saint Lucia, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Gold Coast, Australia
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11
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Bayless AM, Chen S, Ogden SC, Xu X, Sidda JD, Manik MK, Li S, Kobe B, Ve T, Song L, Grant M, Wan L, Nishimura MT. Plant and prokaryotic TIR domains generate distinct cyclic ADPR NADase products. Sci Adv 2023; 9:eade8487. [PMID: 36930706 PMCID: PMC10022894 DOI: 10.1126/sciadv.ade8487] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Toll/interleukin-1 receptor (TIR) domain proteins function in cell death and immunity. In plants and bacteria, TIR domains are often enzymes that produce isomers of cyclic adenosine 5'-diphosphate-ribose (cADPR) as putative immune signaling molecules. The identity and functional conservation of cADPR isomer signals is unclear. A previous report found that a plant TIR could cross-activate the prokaryotic Thoeris TIR-immune system, suggesting the conservation of plant and prokaryotic TIR-immune signals. Here, we generate autoactive Thoeris TIRs and test the converse hypothesis: Do prokaryotic Thoeris TIRs also cross-activate plant TIR immunity? Using in planta and in vitro assays, we find that Thoeris and plant TIRs generate overlapping sets of cADPR isomers and further clarify how plant and Thoeris TIRs activate the Thoeris system via producing 3'cADPR. This study demonstrates that the TIR signaling requirements for plant and prokaryotic immune systems are distinct and that TIRs across kingdoms generate a diversity of small-molecule products.
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Affiliation(s)
- Adam M. Bayless
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Sisi Chen
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Sam C. Ogden
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO 80523, USA
| | - Xiaoyan Xu
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - John D. Sidda
- School of Life Sciences, University of Warwick, Coventry CV47AL, UK
| | - Mohammad K. Manik
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, Brisbane, QLD 4072, Australia
| | - Sulin Li
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, Brisbane, QLD 4072, Australia
| | - Bostjan Kobe
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, Brisbane, QLD 4072, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Lijiang Song
- School of Life Sciences, University of Warwick, Coventry CV47AL, UK
| | - Murray Grant
- School of Life Sciences, University of Warwick, Coventry CV47AL, UK
| | - Li Wan
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Corresponding author. (M.T.N.); (L.W.)
| | - Marc T. Nishimura
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
- Corresponding author. (M.T.N.); (L.W.)
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12
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Foley G, Mora A, Ross CM, Bottoms S, Sützl L, Lamprecht ML, Zaugg J, Essebier A, Balderson B, Newell R, Thomson RES, Kobe B, Barnard RT, Guddat L, Schenk G, Carsten J, Gumulya Y, Rost B, Haltrich D, Sieber V, Gillam EMJ, Bodén M. Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). PLoS Comput Biol 2022; 18:e1010633. [PMID: 36279274 PMCID: PMC9632902 DOI: 10.1371/journal.pcbi.1010633] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 11/03/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
Ancestral sequence reconstruction is a technique that is gaining widespread use in molecular evolution studies and protein engineering. Accurate reconstruction requires the ability to handle appropriately large numbers of sequences, as well as insertion and deletion (indel) events, but available approaches exhibit limitations. To address these limitations, we developed Graphical Representation of Ancestral Sequence Predictions (GRASP), which efficiently implements maximum likelihood methods to enable the inference of ancestors of families with more than 10,000 members. GRASP implements partial order graphs (POGs) to represent and infer insertion and deletion events across ancestors, enabling the identification of building blocks for protein engineering. To validate the capacity to engineer novel proteins from realistic data, we predicted ancestor sequences across three distinct enzyme families: glucose-methanol-choline (GMC) oxidoreductases, cytochromes P450, and dihydroxy/sugar acid dehydratases (DHAD). All tested ancestors demonstrated enzymatic activity. Our study demonstrates the ability of GRASP (1) to support large data sets over 10,000 sequences and (2) to employ insertions and deletions to identify building blocks for engineering biologically active ancestors, by exploring variation over evolutionary time.
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Affiliation(s)
- Gabriel Foley
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Ariane Mora
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Connie M. Ross
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Scott Bottoms
- Campus Straubing for Biotechnology and Sustainability, Technische Universität München, Straubing, Germany
| | - Leander Sützl
- Institut für Lebensmitteltechnologie, Universität für Bodenkultur Wien, Vienna, Austria
| | - Marnie L. Lamprecht
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Julian Zaugg
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Alexandra Essebier
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Brad Balderson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Rhys Newell
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Raine E. S. Thomson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
| | - Ross T. Barnard
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Luke Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Sustainable Minerals Institute, The University of Queensland, Brisbane, Australia
| | - Jörg Carsten
- Zentralinstitut für Katalyseforschung, Technische Universität München, Munich, Germany
| | - Yosephine Gumulya
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Burkhard Rost
- Fakultät für Informatik, Technische Universität München, Munich, Germany
| | - Dietmar Haltrich
- Institut für Lebensmitteltechnologie, Universität für Bodenkultur Wien, Vienna, Austria
| | - Volker Sieber
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Campus Straubing for Biotechnology and Sustainability, Technische Universität München, Straubing, Germany
- Zentralinstitut für Katalyseforschung, Technische Universität München, Munich, Germany
| | - Elizabeth M. J. Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- * E-mail: (MB); (EMJG)
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- * E-mail: (MB); (EMJG)
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13
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Manik MK, Shi Y, Li S, Zaydman MA, Damaraju N, Eastman S, Smith TG, Gu W, Masic V, Mosaiab T, Weagley JS, Hancock SJ, Vasquez E, Hartley-Tassell L, Kargios N, Maruta N, Lim BYJ, Burdett H, Landsberg MJ, Schembri MA, Prokes I, Song L, Grant M, DiAntonio A, Nanson JD, Guo M, Milbrandt J, Ve T, Kobe B. Cyclic ADP ribose isomers: Production, chemical structures, and immune signaling. Science 2022; 377:eadc8969. [PMID: 36048923 DOI: 10.1126/science.adc8969] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cyclic adenosine diphosphate (ADP)-ribose (cADPR) isomers are signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via nicotinamide adenine dinucleotide (oxidized form) (NAD+) hydrolysis. We show that v-cADPR (2'cADPR) and v2-cADPR (3'cADPR) isomers are cyclized by O-glycosidic bond formation between the ribose moieties in ADPR. Structures of 2'cADPR-producing TIR domains reveal conformational changes that lead to an active assembly that resembles those of Toll-like receptor adaptor TIR domains. Mutagenesis reveals a conserved tryptophan that is essential for cyclization. We show that 3'cADPR is an activator of ThsA effector proteins from the bacterial antiphage defense system termed Thoeris and a suppressor of plant immunity when produced by the effector HopAM1. Collectively, our results reveal the molecular basis of cADPR isomer production and establish 3'cADPR in bacteria as an antiviral and plant immunity-suppressing signaling molecule.
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Affiliation(s)
- Mohammad K Manik
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Sulin Li
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mark A Zaydman
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63100, USA
| | - Neha Damaraju
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63100, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63100, USA
| | - Samuel Eastman
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Thomas G Smith
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Weixi Gu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Veronika Masic
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Tamim Mosaiab
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - James S Weagley
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Steven J Hancock
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Eduardo Vasquez
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | | | - Nestoras Kargios
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Natsumi Maruta
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bryan Y J Lim
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Hayden Burdett
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ivan Prokes
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Murray Grant
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Aaron DiAntonio
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63100, USA
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63100, USA
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ming Guo
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Jeffrey Milbrandt
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63100, USA
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD 4072, Australia
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14
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Wizrah MS, Chua SM, Luo Z, Manik MK, Pan M, Whyte JM, Robertson AA, Kappler U, Kobe B, Fraser JA. AICAR transformylase/IMP cyclohydrolase (ATIC) is essential for de novo purine biosynthesis and infection by Cryptococcus neoformans. J Biol Chem 2022; 298:102453. [PMID: 36063996 PMCID: PMC9525906 DOI: 10.1016/j.jbc.2022.102453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 01/27/2023] Open
Abstract
The fungal pathogen Cryptococcus neoformans is a leading cause of meningoencephalitis in the immunocompromised. As current antifungal treatments are toxic to the host, costly, limited in their efficacy, and associated with drug resistance, there is an urgent need to identify vulnerabilities in fungal physiology to accelerate antifungal discovery efforts. Rational drug design was pioneered in de novo purine biosynthesis as the end products of the pathway, ATP and GTP, are essential for replication, transcription, and energy metabolism, and the same rationale applies when considering the pathway as an antifungal target. Here, we describe the identification and characterization of C. neoformans 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/5'-inosine monophosphate cyclohydrolase (ATIC), a bifunctional enzyme that catalyzes the final two enzymatic steps in the formation of the first purine base inosine monophosphate. We demonstrate that mutants lacking the ATIC-encoding ADE16 gene are adenine and histidine auxotrophs that are unable to establish an infection in a murine model of virulence. In addition, our assays employing recombinantly expressed and purified C. neoformans ATIC enzyme revealed Km values for its substrates AICAR and 5-formyl-AICAR are 8-fold and 20-fold higher, respectively, than in the human ortholog. Subsequently, we performed crystallographic studies that enabled the determination of the first fungal ATIC protein structure, revealing a key serine-to-tyrosine substitution in the active site, which has the potential to assist the design of fungus-specific inhibitors. Overall, our results validate ATIC as a promising antifungal drug target.
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Affiliation(s)
- Maha S.I. Wizrah
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Sheena M.H. Chua
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Zhenyao Luo
- School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Mohammad K. Manik
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Mengqi Pan
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Jessica M.L. Whyte
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Avril A.B. Robertson
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Ulrike Kappler
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Bostjan Kobe
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - James A. Fraser
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,For correspondence: James A. Fraser
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15
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Pan M, Hedger A, Nanson J, Pospich S, Ve T, Raunser S, Landsberg M, Kobe B. Structural basis of TIR-domain assembly formation in TRAM- and TRIF- dependent TLR signalling. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322093196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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16
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Holmes S, Kirkwood HJ, Bean R, Giewekemeyer K, Martin AV, Hadian-Jazi M, Wiedorn MO, Oberthür D, Marman H, Adriano L, Al-Qudami N, Bajt S, Barák I, Bari S, Bielecki J, Brockhauser S, Coleman MA, Cruz-Mazo F, Danilevski C, Dörner K, Gañán-Calvo AM, Graceffa R, Fanghor H, Heymann M, Frank M, Kaukher A, Kim Y, Kobe B, Knoška J, Laurus T, Letrun R, Maia L, Messerschmidt M, Metz M, Michelat T, Mills G, Molodtsov S, Monteiro DCF, Morgan AJ, Münnich A, Peña Murillo GE, Previtali G, Round A, Sato T, Schubert R, Schulz J, Shelby M, Seuring C, Sellberg JA, Sikorski M, Silenzi A, Stern S, Sztuk-Dambietz J, Szuba J, Trebbin M, Vagovic P, Ve T, Weinhausen B, Wrona K, Xavier PL, Xu C, Yefanov O, Nugent KA, Chapman HN, Mancuso AP, Barty A, Abbey B, Darmanin C. Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers. Nat Commun 2022; 13:4708. [PMID: 35953469 PMCID: PMC9372077 DOI: 10.1038/s41467-022-32434-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/28/2022] [Indexed: 11/12/2022] Open
Abstract
The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 µs, yield up to 2.1 Å resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX. Free-electron lasers are capable of high repetition rates and it is assumed that protein crystals often do not survive the first X-ray pulse. Here the authors address these issues with a demonstration of multi-hit serial crystallography in which multiple FEL pulses interact with the sample without destroying it.
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Affiliation(s)
- Susannah Holmes
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | | | - Richard Bean
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Andrew V Martin
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
| | - Marjan Hadian-Jazi
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Australian Nuclear Science and Technology Organisation (ANSTO), Sydney, NSW, 2234, Australia
| | - Max O Wiedorn
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Hugh Marman
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Luigi Adriano
- Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Imrich Barák
- Institute of Molecular Biology, SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | | | - Mathew A Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Francisco Cruz-Mazo
- Dept. de Ingeniería Aeroespacial y Mecánica de Fluidos, ETSI, Universidad de Sevilla, 41092, Sevilla, Spain.,Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA
| | | | | | - Alfonso M Gañán-Calvo
- Dept. de Ingeniería Aeroespacial y Mecánica de Fluidos, ETSI, Universidad de Sevilla, 41092, Sevilla, Spain
| | - Rita Graceffa
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Hans Fanghor
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 175, 22761, Hamburg, Germany.,University of Southampton, Southampton, SO17 1BJ, UK
| | - Michael Heymann
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Am Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | | | - Yoonhee Kim
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - 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
| | - Juraj Knoška
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Torsten Laurus
- Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Luis Maia
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marc Messerschmidt
- School of Molecular Science, Arizona State University, Tempe, AZ, 85281, USA
| | - Markus Metz
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | - Grant Mills
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Serguei Molodtsov
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Institute of Experimental Physics, TU Bergakademie Freiberg, Leipziger, Str. 23, 09599, Freiberg, Germany.,ITMO University, Kronverksky pr. 49, St. Petersburg, 197101, Russia
| | - Diana C F Monteiro
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany.,Hauptman-Woodward Medical Research Institute, 700 Ellicott St., Buffalo, NY, 14203, USA
| | - Andrew J Morgan
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,Department of Physics, University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Gisel E Peña Murillo
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | - Adam Round
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tokushi Sato
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | | | - Megan Shelby
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Carolin Seuring
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Jonas A Sellberg
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | | | | | - Stephan Stern
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Janusz Szuba
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Martin Trebbin
- Institute of Experimental Physics, TU Bergakademie Freiberg, Leipziger, Str. 23, 09599, Freiberg, Germany.,Department of Chemistry, State University of New York at Buffalo, 760 Natural Sciences Complex, Buffalo, NY, 14260, USA
| | | | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD, 4222, Australia
| | | | | | - Paul Lourdu Xavier
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 175, 22761, Hamburg, Germany
| | - Chen Xu
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Keith A Nugent
- Department of Quantum Science and Technology, Research School of Physics, Australian National University, Canberra, ACT, 2601, Australia
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Anton Barty
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Brian Abbey
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia. .,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Connie Darmanin
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia. .,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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17
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Hancock SJ, Lo AW, Ve T, Day CJ, Tan L, Mendez AA, Phan MD, Nhu NTK, Peters KM, Richards AC, Fleming BA, Chang C, Ngu DHY, Forde BM, Haselhorst T, Goh KGK, Beatson SA, Jennings MP, Mulvey MA, Kobe B, Schembri MA. Ucl fimbriae regulation and glycan receptor specificity contribute to gut colonisation by extra-intestinal pathogenic Escherichia coli. PLoS Pathog 2022; 18:e1010582. [PMID: 35700218 PMCID: PMC9236248 DOI: 10.1371/journal.ppat.1010582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 06/27/2022] [Accepted: 05/09/2022] [Indexed: 11/25/2022] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) belong to a critical priority group of antibiotic resistant pathogens. ExPEC establish gut reservoirs that seed infection of the urinary tract and bloodstream, but the mechanisms of gut colonisation remain to be properly understood. Ucl fimbriae are attachment organelles that facilitate ExPEC adherence. Here, we investigated cellular receptors for Ucl fimbriae and Ucl expression to define molecular mechanisms of Ucl-mediated ExPEC colonisation of the gut. We demonstrate differential expression of Ucl fimbriae in ExPEC sequence types associated with disseminated infection. Genome editing of strains from two common sequence types, F11 (ST127) and UTI89 (ST95), identified a single nucleotide polymorphism in the ucl promoter that changes fimbriae expression via activation by the global stress-response regulator OxyR, leading to altered gut colonisation. Structure-function analysis of the Ucl fimbriae tip-adhesin (UclD) identified high-affinity glycan receptor targets, with highest affinity for sialyllacto-N-fucopentose VI, a structure likely to be expressed on the gut epithelium. Comparison of the UclD adhesin to the homologous UcaD tip-adhesin from Proteus mirabilis revealed that although they possess a similar tertiary structure, apart from lacto-N-fucopentose VI that bound to both adhesins at low-micromolar affinity, they recognize different fucose- and glucose-containing oligosaccharides. Competitive surface plasmon resonance analysis together with co-structural investigation of UcaD in complex with monosaccharides revealed a broad-specificity glycan binding pocket shared between UcaD and UclD that could accommodate these interactions. Overall, our study describes a mechanism of adaptation that augments establishment of an ExPEC gut reservoir to seed disseminated infections, providing a pathway for the development of targeted anti-adhesion therapeutics. ExPEC infection of the urinary tract and bloodstream is frequently seeded from an intestinal reservoir, necessitating an understanding of the mechanisms that promote gut colonisation. Here we employed molecular and structural approaches to define the regulation and function of ExPEC Ucl fimbriae as a gut colonisation factor. We describe how mutations in the non-coding regulatory region of the ucl promoter cause increased Ucl fimbriae expression and promote enhanced gut colonisation via tuned induction by a global regulator that senses oxygen stress. We further define the glycan receptor targets of Ucl fimbriae and characterise the structural features of the Ucl adhesin that facilitate these interactions. These findings explain how ExPEC can adapt to survival in the gut to seed extra-intestinal infection.
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Affiliation(s)
- Steven J. Hancock
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Alvin W. Lo
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas Ve
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Glycomics, Griffith University Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Christopher J. Day
- Institute for Glycomics, Griffith University Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Alejandra A. Mendez
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Minh-Duy Phan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Nguyen Thi Khanh Nhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Kate M. Peters
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Amanda C. Richards
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Brittany A. Fleming
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Chyden Chang
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Dalton H. Y. Ngu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Brian M. Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Kelvin G. K. Goh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Scott A. Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael P. Jennings
- Institute for Glycomics, Griffith University Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Matthew A. Mulvey
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Mark A. Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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18
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Scholz JL, Eleftherianos I, Kobe B. Editorial: Evolution of Innate Immunity in Eukarya: Advances and Implications. Front Immunol 2022; 13:879429. [PMID: 35514967 PMCID: PMC9066193 DOI: 10.3389/fimmu.2022.879429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jean L Scholz
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Ioannis Eleftherianos
- Infection and Innate Immunity Laboratory, Department of Biological Sciences, The George Washington University, Washington DC, United States
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
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19
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Shi Y, Kerry PS, Nanson JD, Bosanac T, Sasaki Y, Krauss R, Saikot FK, Adams SE, Mosaiab T, Masic V, Mao X, Rose F, Vasquez E, Furrer M, Cunnea K, Brearley A, Gu W, Luo Z, Brillault L, Landsberg MJ, DiAntonio A, Kobe B, Milbrandt J, Hughes RO, Ve T. Structural basis of SARM1 activation, substrate recognition, and inhibition by small molecules. Mol Cell 2022; 82:1643-1659.e10. [PMID: 35334231 PMCID: PMC9188649 DOI: 10.1016/j.molcel.2022.03.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/11/2022] [Accepted: 03/01/2022] [Indexed: 01/04/2023]
Abstract
The NADase SARM1 (sterile alpha and TIR motif containing 1) is a key executioner of axon degeneration and a therapeutic target for several neurodegenerative conditions. We show that a potent SARM1 inhibitor undergoes base exchange with the nicotinamide moiety of nicotinamide adenine dinucleotide (NAD+) to produce the bona fide inhibitor 1AD. We report structures of SARM1 in complex with 1AD, NAD+ mimetics and the allosteric activator nicotinamide mononucleotide (NMN). NMN binding triggers reorientation of the armadillo repeat (ARM) domains, which disrupts ARM:TIR interactions and leads to formation of a two-stranded TIR domain assembly. The active site spans two molecules in these assemblies, explaining the requirement of TIR domain self-association for NADase activity and axon degeneration. Our results reveal the mechanisms of SARM1 activation and substrate binding, providing rational avenues for the design of new therapeutics targeting SARM1.
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Affiliation(s)
- Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Philip S Kerry
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, QLD 4072, Australia
| | - Todd Bosanac
- Disarm Therapeutics, a wholly-owned subsidiary of Eli Lilly & Co., Cambridge, MA, USA
| | - Yo Sasaki
- Needleman Center for Neurometabolism and Axonal Therapeutics and Department of Genetics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - Raul Krauss
- Disarm Therapeutics, a wholly-owned subsidiary of Eli Lilly & Co., Cambridge, MA, USA
| | - Forhad K Saikot
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, QLD 4072, Australia
| | - Sarah E Adams
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
| | - Tamim Mosaiab
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Veronika Masic
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Xianrong Mao
- Needleman Center for Neurometabolism and Axonal Therapeutics and Department of Genetics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - Faith Rose
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Eduardo Vasquez
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Marieke Furrer
- Evotec SE, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Katie Cunnea
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
| | - Andrew Brearley
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
| | - Weixi Gu
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, QLD 4072, Australia
| | - Zhenyao Luo
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, QLD 4072, Australia
| | - Lou Brillault
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Australia
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, QLD 4072, Australia
| | - Aaron DiAntonio
- Needleman Center for Neurometabolism and Axonal Therapeutics and Department of Developmental Biology, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, QLD 4072, Australia
| | - Jeffrey Milbrandt
- Needleman Center for Neurometabolism and Axonal Therapeutics and Department of Genetics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - Robert O Hughes
- Disarm Therapeutics, a wholly-owned subsidiary of Eli Lilly & Co., Cambridge, MA, USA.
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia.
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20
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Maruta N, Burdett H, Lim BYJ, Hu X, Desa S, Manik MK, Kobe B. Structural basis of NLR activation and innate immune signalling in plants. Immunogenetics 2022; 74:5-26. [PMID: 34981187 PMCID: PMC8813719 DOI: 10.1007/s00251-021-01242-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/29/2021] [Indexed: 12/18/2022]
Abstract
Animals and plants have NLRs (nucleotide-binding leucine-rich repeat receptors) that recognize the presence of pathogens and initiate innate immune responses. In plants, there are three types of NLRs distinguished by their N-terminal domain: the CC (coiled-coil) domain NLRs, the TIR (Toll/interleukin-1 receptor) domain NLRs and the RPW8 (resistance to powdery mildew 8)-like coiled-coil domain NLRs. CC-NLRs (CNLs) and TIR-NLRs (TNLs) generally act as sensors of effectors secreted by pathogens, while RPW8-NLRs (RNLs) signal downstream of many sensor NLRs and are called helper NLRs. Recent studies have revealed three dimensional structures of a CNL (ZAR1) including its inactive, intermediate and active oligomeric state, as well as TNLs (RPP1 and ROQ1) in their active oligomeric states. Furthermore, accumulating evidence suggests that members of the family of lipase-like EDS1 (enhanced disease susceptibility 1) proteins, which are uniquely found in seed plants, play a key role in providing a link between sensor NLRs and helper NLRs during innate immune responses. Here, we summarize the implications of the plant NLR structures that provide insights into distinct mechanisms of action by the different sensor NLRs and discuss plant NLR-mediated innate immune signalling pathways involving the EDS1 family proteins and RNLs.
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Affiliation(s)
- Natsumi Maruta
- 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
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Bryan Y J Lim
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xiahao Hu
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sneha Desa
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mohammad Kawsar Manik
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, 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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21
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Nimma S, Gu W, Manik MK, Ve T, Nanson JD, Kobe B. Crystal structure of the Toll/interleukin-1 receptor (TIR) domain of IL-1R10 provides structural insights into TIR domain signaling. FEBS Lett 2022; 596:886-897. [PMID: 35038778 DOI: 10.1002/1873-3468.14288] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/24/2021] [Accepted: 01/03/2022] [Indexed: 11/09/2022]
Abstract
The Toll/interleukin-1 receptor (TIR) domains are key innate immune signaling modules. Here, we present the crystal structure of the TIR domain of human Interleukin-1 receptor 10 (IL-1R10), also called IL-1RAPL2. It is similar to that of IL-1R9 (IL-1RAPL1) but shows significant structural differences to those from Toll-like receptors (TLRs) and the adaptor proteins MAL and MyD88. Interactions of TIR domains in their respective crystals and the higher-order assemblies (MAL and MyD88) reveal the presence of a common 'BCD surface', suggesting its functional significance. We also show that the TIR domains of IL-1R10 and IL-1R9 lack NADase activity, consistent with their structures. Our study provides a foundation for unraveling the functions of IL-1R9 and IL-1R10.
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Affiliation(s)
- Surekha Nimma
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute of Molecular Bioscience, Brisbane, Queensland, 4072, Australia
| | - Weixi Gu
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute of Molecular Bioscience, Brisbane, Queensland, 4072, Australia
| | - Mohammad K Manik
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute of Molecular Bioscience, Brisbane, Queensland, 4072, Australia
| | - Thomas Ve
- Griffith University, Institute for Glycomics, Southport, Queensland, 4222, Australia
| | - Jeffrey D Nanson
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute of Molecular Bioscience, Brisbane, Queensland, 4072, Australia
| | - Bostjan Kobe
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute of Molecular Bioscience, Brisbane, Queensland, 4072, Australia
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22
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Tran TT, Mathmann CD, Gatica-Andrades M, Rollo RF, Oelker M, Ljungberg JK, Nguyen TTK, Zamoshnikova A, Kummari LK, Wyer OJK, Irvine KM, Melo-Bolívar J, Gross A, Brown D, Mak JYW, Fairlie DP, Hansford KA, Cooper MA, Giri R, Schreiber V, Joseph SR, Simpson F, Barnett TC, Johansson J, Dankers W, Harris J, Wells TJ, Kapetanovic R, Sweet MJ, Latomanski EA, Newton HJ, Guérillot RJR, Hachani A, Stinear TP, Ong SY, Chandran Y, Hartland EL, Kobe B, Stow JL, Sauer-Eriksson AE, Begun J, Kling JC, Blumenthal A. Inhibition of the master regulator of Listeria monocytogenes virulence enables bacterial clearance from spacious replication vacuoles in infected macrophages. PLoS Pathog 2022; 18:e1010166. [PMID: 35007292 PMCID: PMC8746789 DOI: 10.1371/journal.ppat.1010166] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/01/2021] [Indexed: 02/04/2023] Open
Abstract
A hallmark of Listeria (L.) monocytogenes pathogenesis is bacterial escape from maturing entry vacuoles, which is required for rapid bacterial replication in the host cell cytoplasm and cell-to-cell spread. The bacterial transcriptional activator PrfA controls expression of key virulence factors that enable exploitation of this intracellular niche. The transcriptional activity of PrfA within infected host cells is controlled by allosteric coactivation. Inhibitory occupation of the coactivator site has been shown to impair PrfA functions, but consequences of PrfA inhibition for L. monocytogenes infection and pathogenesis are unknown. Here we report the crystal structure of PrfA with a small molecule inhibitor occupying the coactivator site at 2.0 Å resolution. Using molecular imaging and infection studies in macrophages, we demonstrate that PrfA inhibition prevents the vacuolar escape of L. monocytogenes and enables extensive bacterial replication inside spacious vacuoles. In contrast to previously described spacious Listeria-containing vacuoles, which have been implicated in supporting chronic infection, PrfA inhibition facilitated progressive clearance of intracellular L. monocytogenes from spacious vacuoles through lysosomal degradation. Thus, inhibitory occupation of the PrfA coactivator site facilitates formation of a transient intravacuolar L. monocytogenes replication niche that licenses macrophages to effectively eliminate intracellular bacteria. Our findings encourage further exploration of PrfA as a potential target for antimicrobials and highlight that intra-vacuolar residence of L. monocytogenes in macrophages is not inevitably tied to bacterial persistence.
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Affiliation(s)
- Thao Thanh Tran
- The University of Queensland Diamantina Institute, Brisbane, Australia
| | | | | | - Rachel F. Rollo
- The University of Queensland Diamantina Institute, Brisbane, Australia
| | | | | | - Tam T. K. Nguyen
- The University of Queensland Diamantina Institute, Brisbane, Australia
| | | | - Lalith K. Kummari
- The University of Queensland School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Orry J. K. Wyer
- The University of Queensland Diamantina Institute, Brisbane, Australia
| | - Katharine M. Irvine
- ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | | | - Annette Gross
- The University of Queensland Diamantina Institute, Brisbane, Australia
| | - Darren Brown
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jeffrey Y. W. Mak
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - David P. Fairlie
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Karl A. Hansford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Matthew A. Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Rabina Giri
- Mater Research Institute – The University of Queensland, Brisbane, Australia
| | - Veronika Schreiber
- Mater Research Institute – The University of Queensland, Brisbane, Australia
| | - Shannon R. Joseph
- The University of Queensland Diamantina Institute, Brisbane, Australia
| | - Fiona Simpson
- The University of Queensland Diamantina Institute, Brisbane, Australia
| | - Timothy C. Barnett
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, Australia
| | | | - Wendy Dankers
- Department of Medicine, School of Clinical Sciences at Monash Health, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, Australia
| | - James Harris
- Department of Medicine, School of Clinical Sciences at Monash Health, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, Australia
| | - Timothy J. Wells
- The University of Queensland Diamantina Institute, Brisbane, Australia
| | - Ronan Kapetanovic
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Matthew J. Sweet
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Eleanor A. Latomanski
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Hayley J. Newton
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Romain J. R. Guérillot
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sze Ying Ong
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash University, Melbourne, Australia
| | - Yogeswari Chandran
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash University, Melbourne, Australia
| | - Elizabeth L. Hartland
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash University, Melbourne, Australia
| | - Bostjan Kobe
- The University of Queensland School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jennifer L. Stow
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | | | - Jakob Begun
- Mater Research Institute – The University of Queensland, Brisbane, Australia
| | - Jessica C. Kling
- The University of Queensland Diamantina Institute, Brisbane, Australia
| | - Antje Blumenthal
- The University of Queensland Diamantina Institute, Brisbane, Australia
- * E-mail:
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23
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Loreto A, Angeletti C, Gu W, Osborne A, Nieuwenhuis B, Gilley J, Merlini E, Arthur-Farraj P, Amici A, Luo Z, Hartley-Tassell L, Ve T, Desrochers LM, Wang Q, Kobe B, Orsomando G, Coleman MP. Neurotoxin-mediated potent activation of the axon degeneration regulator SARM1. eLife 2021; 10:72823. [PMID: 34870595 PMCID: PMC8758145 DOI: 10.7554/elife.72823] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/05/2021] [Indexed: 11/13/2022] Open
Abstract
Axon loss underlies symptom onset and progression in many neurodegenerative disorders. Axon degeneration in injury and disease is promoted by activation of the NAD-consuming enzyme SARM1. Here, we report a novel activator of SARM1, a metabolite of the pesticide and neurotoxin vacor. Removal of SARM1 completely rescues mouse neurons from vacor-induced neuron and axon death in vitro and in vivo. We present the crystal structure of the Drosophila SARM1 regulatory domain complexed with this activator, the vacor metabolite VMN, which as the most potent activator yet known is likely to support drug development for human SARM1 and NMNAT2 disorders. This study indicates the mechanism of neurotoxicity and pesticide action by vacor, raises important questions about other pyridines in wider use today, provides important new tools for drug discovery, and demonstrates that removing SARM1 can robustly block programmed axon death induced by toxicity as well as genetic mutation.
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Affiliation(s)
- Andrea Loreto
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Carlo Angeletti
- Department of Clinical Sciences (DISCO), Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Weixi Gu
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
| | - Andrew Osborne
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Bart Nieuwenhuis
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan Gilley
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Elisa Merlini
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Peter Arthur-Farraj
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Adolfo Amici
- Department of Clinical Sciences (DISCO), Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Zhenyao Luo
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
| | | | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, Australia
| | - Laura M Desrochers
- Neuroscience, BioPharmaceuticals R and D, AstraZeneca, Waltham, United States
| | - Qi Wang
- Neuroscience, BioPharmaceuticals R and D, AstraZeneca, Waltham, United States
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
| | - Giuseppe Orsomando
- Department of Clinical Sciences (DISCO), Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Michael P Coleman
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
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24
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Nimma S, Gu W, Maruta N, Li Y, Pan M, Saikot FK, Lim BYJ, McGuinness HY, Zaoti ZF, Li S, Desa S, Manik MK, Nanson JD, Kobe B. Structural Evolution of TIR-Domain Signalosomes. Front Immunol 2021; 12:784484. [PMID: 34868065 PMCID: PMC8635717 DOI: 10.3389/fimmu.2021.784484] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/25/2021] [Indexed: 01/23/2023] Open
Abstract
TIR (Toll/interleukin-1 receptor/resistance protein) domains are cytoplasmic domains widely found in animals and plants, where they are essential components of the innate immune system. A key feature of TIR-domain function in signaling is weak and transient self-association and association with other TIR domains. An additional new role of TIR domains as catalytic enzymes has been established with the recent discovery of NAD+-nucleosidase activity by several TIR domains, mostly involved in cell-death pathways. Although self-association of TIR domains is necessary in both cases, the functional specificity of TIR domains is related in part to the nature of the TIR : TIR interactions in the respective signalosomes. Here, we review the well-studied TIR domain-containing proteins involved in eukaryotic immunity, focusing on the structures, interactions and their corresponding functional roles. Structurally, the signalosomes fall into two separate groups, the scaffold and enzyme TIR-domain assemblies, both of which feature open-ended complexes with two strands of TIR domains, but differ in the orientation of the two strands. We compare and contrast how TIR domains assemble and signal through distinct scaffolding and enzymatic roles, ultimately leading to distinct cellular innate-immunity and cell-death outcomes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
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25
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Sasaki Y, Zhu J, Shi Y, Gu W, Kobe B, Ve T, DiAntonio A, Milbrandt J. Nicotinic acid mononucleotide is an allosteric SARM1 inhibitor promoting axonal protection. Exp Neurol 2021; 345:113842. [PMID: 34403688 PMCID: PMC8571713 DOI: 10.1016/j.expneurol.2021.113842] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 12/31/2022]
Abstract
SARM1 is an inducible NAD+ hydrolase that is the central executioner of pathological axon loss. Recently, we elucidated the molecular mechanism of SARM1 activation, demonstrating that SARM1 is a metabolic sensor regulated by the levels of NAD+ and its precursor, nicotinamide mononucleotide (NMN), via their competitive binding to an allosteric site within the SARM1 N-terminal ARM domain. In healthy neurons with abundant NAD+, binding of NAD+ blocks access of NMN to this allosteric site. However, with injury or disease the levels of the NAD+ biosynthetic enzyme NMNAT2 drop, increasing the NMN/ NAD+ ratio and thereby promoting NMN binding to the SARM1 allosteric site, which in turn induces a conformational change activating the SARM1 NAD+ hydrolase. Hence, NAD+ metabolites both regulate the activation of SARM1 and, in turn, are regulated by the SARM1 NAD+ hydrolase. This dual upstream and downstream role for NAD+ metabolites in SARM1 function has hindered mechanistic understanding of axoprotective mechanisms that manipulate the NAD+ metabolome. Here we reevaluate two methods that potently block axon degeneration via modulation of NAD+ related metabolites, 1) the administration of the NMN biosynthesis inhibitor FK866 in conjunction with the NAD+ precursor nicotinic acid riboside (NaR) and 2) the neuronal expression of the bacterial enzyme NMN deamidase. We find that these approaches not only lead to a decrease in the levels of the SARM1 activator NMN, but also an increase in the levels of the NAD+ precursor nicotinic acid mononucleotide (NaMN). We show that NaMN inhibits SARM1 activation, and demonstrate that this NaMN-mediated inhibition is important for the long-term axon protection induced by these treatments. Analysis of the NaMN-ARM domain co-crystal structure shows that NaMN competes with NMN for binding to the SARM1 allosteric site and promotes the open, autoinhibited configuration of SARM1 ARM domain. Together, these results demonstrate that the SARM1 allosteric pocket can bind a diverse set of metabolites including NMN, NAD+, and NaMN to monitor cellular NAD+ homeostasis and regulate SARM1 NAD+ hydrolase activity. The relative promiscuity of the allosteric site may enable the development of potent pharmacological inhibitors of SARM1 activation for the treatment of neurodegenerative disorders.
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Affiliation(s)
- Yo Sasaki
- Washington University School of Medicine in Saint Louis, Department of Genetics, St. Louis, MO, USA; Needleman Center for Neurometabolism and Axonal Therapeutics, USA.
| | - Jian Zhu
- Washington University School of Medicine in Saint Louis, Department of Genetics, St. Louis, MO, USA; Needleman Center for Neurometabolism and Axonal Therapeutics, USA
| | - Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Weixi Gu
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, QLD 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, QLD 4072, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Aaron DiAntonio
- Washington University School of Medicine in Saint Louis, Department of Developmental Biology, St. Louis, MO, USA; Needleman Center for Neurometabolism and Axonal Therapeutics, USA
| | - Jeffrey Milbrandt
- Washington University School of Medicine in Saint Louis, Department of Genetics, St. Louis, MO, USA; Needleman Center for Neurometabolism and Axonal Therapeutics, USA
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26
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Gu W, Luo Z, Vonrhein C, Jia X, Ve T, Nanson JD, Kobe B. Crystal structure determination of the armadillo repeat domain of Drosophila SARM1 using MIRAS phasing. Acta Crystallogr F Struct Biol Commun 2021; 77:364-373. [PMID: 34605441 DOI: 10.1107/s2053230x21006786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/29/2021] [Indexed: 11/11/2022]
Abstract
The crystal structure determination of the armadillo repeat motif (ARM) domain of Drosophila SARM1 (dSARM1ARM) is described, which required the combination of a number of sources of phase information in order to obtain interpretable electron-density maps. SARM1 is a central executioner of programmed axon degeneration, a common feature of the early phase of many neurodegenerative diseases. SARM1 is held in the inactive state in healthy axons by its N-terminal auto-inhibitory ARM domain, and is activated to cleave NAD upon injury, triggering subsequent axon degeneration. To characterize the molecular mechanism of SARM1 activation, it was sought to determine the crystal structure of the SARM1 ARM domain. Here, the recombinant production and crystallization of dSARM1ARM is described, as well as the unconventional process used for structure determination. Crystals were obtained in the presence of NMN, a precursor of NAD and a potential activator of SARM1, only after in situ proteolysis of the N-terminal 63 residues. After molecular-replacement attempts failed, the crystal structure of dSARM1ARM was determined at 1.65 Å resolution using the MIRAS phasing technique with autoSHARP, combining data from native, selenomethionine-labelled and bromide-soaked crystals. The structure will further the understanding of SARM1 regulation.
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Affiliation(s)
- Weixi Gu
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Zhenyao Luo
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | | | - Xinying Jia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, Queensland 4222, Australia
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
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27
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Outram MA, Sung YC, Yu D, Dagvadorj B, Rima SA, Jones DA, Ericsson DJ, Sperschneider J, Solomon PS, Kobe B, Williams SJ. The crystal structure of SnTox3 from the necrotrophic fungus Parastagonospora nodorum reveals a unique effector fold and provides insight into Snn3 recognition and pro-domain protease processing of fungal effectors. New Phytol 2021; 231:2282-2296. [PMID: 34053091 DOI: 10.1111/nph.17516] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/20/2021] [Indexed: 05/22/2023]
Abstract
Plant pathogens cause disease through secreted effector proteins, which act to promote infection. Typically, the sequences of effectors provide little functional information and further targeted experimentation is required. Here, we utilized a structure/function approach to study SnTox3, an effector from the necrotrophic fungal pathogen Parastagonospora nodorum, which causes cell death in wheat-lines carrying the sensitivity gene Snn3. We developed a workflow for the production of SnTox3 in a heterologous host that enabled crystal structure determination and functional studies. We show this approach can be successfully applied to study effectors from other pathogenic fungi. The β-barrel fold of SnTox3 is a novel fold among fungal effectors. Structure-guided mutagenesis enabled the identification of residues required for Snn3 recognition. SnTox3 is a pre-pro-protein, and the pro-domain of SnTox3 can be cleaved in vitro by the protease Kex2. Complementing this, an in silico study uncovered the prevalence of a conserved motif (LxxR) in an expanded set of putative pro-domain-containing fungal effectors, some of which can be cleaved by Kex2 in vitro. Our in vitro and in silico study suggests that Kex2-processed pro-domain (designated here as K2PP) effectors are common in fungi and this may have broad implications for the approaches used to study their functions.
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Affiliation(s)
- Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Yi-Chang Sung
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel Yu
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Bayantes Dagvadorj
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Sharmin A Rima
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - David A Jones
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Australian Synchrotron, Macromolecular Crystallography, Clayton, VIC, 3168, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, ACT, 2601, Australia
| | - Peter S Solomon
- Research School of Biology, The Australian National University, 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
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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28
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Outram MA, Sung YC, Yu D, Dagvadorj B, Rima SA, Jones DA, Ericsson DJ, Sperschneider J, Solomon PS, Kobe B, Williams SJ. The crystal structure of SnTox3 from the necrotrophic fungus Parastagonospora nodorum reveals a unique effector fold and provides insight into Snn3 recognition and pro-domain protease processing of fungal effectors. New Phytol 2021; 231:2282-2296. [PMID: 34053091 DOI: 10.1101/2020.05.27.120113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/20/2021] [Indexed: 05/25/2023]
Abstract
Plant pathogens cause disease through secreted effector proteins, which act to promote infection. Typically, the sequences of effectors provide little functional information and further targeted experimentation is required. Here, we utilized a structure/function approach to study SnTox3, an effector from the necrotrophic fungal pathogen Parastagonospora nodorum, which causes cell death in wheat-lines carrying the sensitivity gene Snn3. We developed a workflow for the production of SnTox3 in a heterologous host that enabled crystal structure determination and functional studies. We show this approach can be successfully applied to study effectors from other pathogenic fungi. The β-barrel fold of SnTox3 is a novel fold among fungal effectors. Structure-guided mutagenesis enabled the identification of residues required for Snn3 recognition. SnTox3 is a pre-pro-protein, and the pro-domain of SnTox3 can be cleaved in vitro by the protease Kex2. Complementing this, an in silico study uncovered the prevalence of a conserved motif (LxxR) in an expanded set of putative pro-domain-containing fungal effectors, some of which can be cleaved by Kex2 in vitro. Our in vitro and in silico study suggests that Kex2-processed pro-domain (designated here as K2PP) effectors are common in fungi and this may have broad implications for the approaches used to study their functions.
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Affiliation(s)
- Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Yi-Chang Sung
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel Yu
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Bayantes Dagvadorj
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Sharmin A Rima
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - David A Jones
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Australian Synchrotron, Macromolecular Crystallography, Clayton, VIC, 3168, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, ACT, 2601, Australia
| | - Peter S Solomon
- Research School of Biology, The Australian National University, 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
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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29
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Chua SMH, Wizrah MSI, Luo Z, Lim BYJ, Kappler U, Kobe B, Fraser JA. Structural features of Cryptococcus neoformans bifunctional GAR/AIR synthetase may present novel antifungal drug targets. J Biol Chem 2021; 297:101091. [PMID: 34416230 PMCID: PMC8449271 DOI: 10.1016/j.jbc.2021.101091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 08/06/2021] [Accepted: 08/16/2021] [Indexed: 11/18/2022] Open
Abstract
Cryptococcus neoformans is a fungus that causes life-threatening systemic mycoses. During infection of the human host, this pathogen experiences a major change in the availability of purines; the fungus can scavenge the abundant purines in its environmental niche of pigeon excrement, but must employ de novo biosynthesis in the purine-poor human CNS. Eleven sequential enzymatic steps are required to form the first purine base, IMP, an intermediate in the formation of ATP and GTP. Over the course of evolution, several gene fusion events led to the formation of multifunctional purine biosynthetic enzymes in most organisms, particularly the higher eukaryotes. In C. neoformans, phosphoribosyl-glycinamide synthetase (GARs) and phosphoribosyl-aminoimidazole synthetase (AIRs) are fused into a bifunctional enzyme, while the human ortholog is a trifunctional enzyme that also includes GAR transformylase. Here we functionally, biochemically, and structurally characterized C. neoformans GARs and AIRs to identify drug targetable features. GARs/AIRs are essential for de novo purine production and virulence in a murine inhalation infection model. Characterization of GARs enzymatic functional parameters showed that C. neoformans GARs/AIRs have lower affinity for substrates glycine and PRA compared with the trifunctional metazoan enzyme. The crystal structure of C. neoformans GARs revealed differences in the glycine- and ATP-binding sites compared with the Homo sapiens enzyme, while the crystal structure of AIRs shows high structural similarity compared with its H. sapiens ortholog as a monomer but differences as a dimer. The alterations in functional and structural characteristics between fungal and human enzymes could potentially be exploited for antifungal development.
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Affiliation(s)
- Sheena M H Chua
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Maha S I Wizrah
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Zhenyao Luo
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Bryan Y J Lim
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Ulrike Kappler
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Bostjan Kobe
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - James A Fraser
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
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30
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Holmes S, Clabbers MTB, Muusse TW, Vajjhala PR, Thygesen SJ, Malde AK, Hunter DJB, Croll TI, Flueckiger L, Nanson JD, Rahaman MH, Aquila A, Hunter MS, Liang M, Yoon CH, Zhao J, Zatsepin NA, Abbey B, Sierecki E, Gambin Y, Stacey KJ, Darmanin C, Kobe B, Xu H, Ve T. MyD88 TIR domain higher-order assembly interactions revealed by serial femtosecond crystallography. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321088498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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31
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Ve T, Gu W, Nanson JD, Shi Y, Cunnea K, Kerry PS, Bosanac T, Hughes RO, Kobe B. Crystal and cryo-EM structures provide insight into how pro-neurodegenerative SARM1 is activated and cleaves NAD +. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321092552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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32
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Pan M, Nanson J, Hedger A, Kobe B. Understanding the structural basis of TIR-domain assembly formation in TRAM- and TRIF-dependent TLR signalling. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321085949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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33
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Nimma S, Nanson J, Ve T, Kobe B. Determining the role of TIR domain of Interleukin-1 receptor 8 (SIGIRR) in regulating TLR4 signalling. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321089121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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34
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Clabbers MTB, Holmes S, Muusse TW, Vajjhala P, Thygesen SJ, Malde AK, Hunter DJB, Croll TI, Flueckiger L, Nanson JD, Rahaman MH, Aquila A, Hunter MS, Liang M, Yoon CH, Zhao J, Zatsepin NA, Abbey B, Sierecki E, Gambin Y, Stacey KJ, Darmanin C, Kobe B, Xu H, Ve T. MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321093879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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35
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Hopkins EL, Gu W, Kobe B, Coleman MP. A Novel NAD Signaling Mechanism in Axon Degeneration and its Relationship to Innate Immunity. Front Mol Biosci 2021; 8:703532. [PMID: 34307460 PMCID: PMC8295901 DOI: 10.3389/fmolb.2021.703532] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/28/2021] [Indexed: 12/21/2022] Open
Abstract
Axon degeneration represents a pathological feature of many neurodegenerative diseases, including Alzheimer's disease and Parkinson's disease where axons die before the neuronal soma, and axonopathies, such as Charcot-Marie-Tooth disease and hereditary spastic paraplegia. Over the last two decades, it has slowly emerged that a central signaling pathway forms the basis of this process in many circumstances. This is an axonal NAD-related signaling mechanism mainly regulated by the two key proteins with opposing roles: the NAD-synthesizing enzyme NMNAT2, and SARM1, a protein with NADase and related activities. The crosstalk between the axon survival factor NMNAT2 and pro-degenerative factor SARM1 has been extensively characterized and plays an essential role in maintaining the axon integrity. This pathway can be activated in necroptosis and in genetic, toxic or metabolic disorders, physical injury and neuroinflammation, all leading to axon pathology. SARM1 is also known to be involved in regulating innate immunity, potentially linking axon degeneration to the response to pathogens and intercellular signaling. Understanding this NAD-related signaling mechanism enhances our understanding of the process of axon degeneration and enables a path to the development of drugs for a wide range of neurodegenerative diseases.
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Affiliation(s)
- Eleanor L. Hopkins
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Weixi Gu
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Michael P. Coleman
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
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Lee CH, Hawker NP, Peters JR, Lonhienne TGA, Gursanscky NR, Matthew L, Brosnan CA, Mann CWG, Cromer L, Taochy C, Ngo QA, Sundaresan V, Schenk PM, Kobe B, Borges F, Mercier R, Bowman JL, Carroll BJ. DEFECTIVE EMBRYO AND MERISTEMS genes are required for cell division and gamete viability in Arabidopsis. PLoS Genet 2021; 17:e1009561. [PMID: 33999950 PMCID: PMC8158957 DOI: 10.1371/journal.pgen.1009561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/27/2021] [Accepted: 04/21/2021] [Indexed: 11/19/2022] Open
Abstract
The DEFECTIVE EMBRYO AND MERISTEMS 1 (DEM1) gene encodes a protein of unknown biochemical function required for meristem formation and seedling development in tomato, but it was unclear whether DEM1’s primary role was in cell division or alternatively, in defining the identity of meristematic cells. Genome sequence analysis indicates that flowering plants possess at least two DEM genes. Arabidopsis has two DEM genes, DEM1 and DEM2, which we show are expressed in developing embryos and meristems in a punctate pattern that is typical of genes involved in cell division. Homozygous dem1 dem2 double mutants were not recovered, and plants carrying a single functional DEM1 allele and no functional copies of DEM2, i.e. DEM1/dem1 dem2/dem2 plants, exhibit normal development through to the time of flowering but during male reproductive development, chromosomes fail to align on the metaphase plate at meiosis II and result in abnormal numbers of daughter cells following meiosis. Additionally, these plants show defects in both pollen and embryo sac development, and produce defective male and female gametes. In contrast, dem1/dem1 DEM2/dem2 plants showed normal levels of fertility, indicating that DEM2 plays a more important role than DEM1 in gamete viability. The increased importance of DEM2 in gamete viability correlated with higher mRNA levels of DEM2 compared to DEM1 in most tissues examined and particularly in the vegetative shoot apex, developing siliques, pollen and sperm. We also demonstrate that gamete viability depends not only on the number of functional DEM alleles inherited following meiosis, but also on the number of functional DEM alleles in the parent plant that undergoes meiosis. Furthermore, DEM1 interacts with RAS-RELATED NUCLEAR PROTEIN 1 (RAN1) in yeast two-hybrid and pull-down binding assays, and we show that fluorescent proteins fused to DEM1 and RAN1 co-localize transiently during male meiosis and pollen development. In eukaryotes, RAN is a highly conserved GTPase that plays key roles in cell cycle progression, spindle assembly during cell division, reformation of the nuclear envelope following cell division, and nucleocytoplasmic transport. Our results demonstrate that DEM proteins play an essential role in cell division in plants, most likely through an interaction with RAN1. Up to half of the genes predicted from genome projects lack a known biological and biochemical function. Many of these genes are likely to play essential roles but it is difficult to reveal their function because minor changes in the genetic sequence can result in lethality and genetic redundancy can obscure analysis. Genome projects predict that flowering plants have at least two DEM genes that encode a protein of unknown cellular and biochemical function. In this paper, we use multiple combinations of dem mutants in Arabidopsis to show that DEM genes are essential for cell division and gamete viability. Interestingly, gamete viability depends not only on the number of functional copies of DEM genes in the gametes, but also on the number of functional copies of DEM genes in the parent plant that produces the gametes. We also show that DEM proteins interact with RAN, a highly conserved protein that controls cell division in all eukaryotic organisms.
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Affiliation(s)
- Chin Hong Lee
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Australia
| | - Nathaniel P. Hawker
- Section of Plant Biology, One Shields Avenue, University of California at Davis, Davis, California, United States of America
| | - Jonathan R. Peters
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Australia
| | - Thierry G. A. Lonhienne
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Australia
| | - Nial R. Gursanscky
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Australia
| | - Louisa Matthew
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Australia
| | - Christopher A. Brosnan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Australia
| | - Christopher W. G. Mann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Australia
| | - Laurence Cromer
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Christelle Taochy
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Quy A. Ngo
- Section of Plant Biology, One Shields Avenue, University of California at Davis, Davis, California, United States of America
| | - Venkatesan Sundaresan
- Section of Plant Biology, One Shields Avenue, University of California at Davis, Davis, California, United States of America
| | - Peer M. Schenk
- School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Australia
- Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Australia
| | - Filipe Borges
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - John L. Bowman
- Section of Plant Biology, One Shields Avenue, University of California at Davis, Davis, California, United States of America
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, Victoria, Australia
- * E-mail: (JLB); (BJC)
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Australia
- * E-mail: (JLB); (BJC)
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Clabbers MTB, Holmes S, Muusse TW, Vajjhala PR, Thygesen SJ, Malde AK, Hunter DJB, Croll TI, Flueckiger L, Nanson JD, Rahaman MH, Aquila A, Hunter MS, Liang M, Yoon CH, Zhao J, Zatsepin NA, Abbey B, Sierecki E, Gambin Y, Stacey KJ, Darmanin C, Kobe B, Xu H, Ve T. MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography. Nat Commun 2021; 12:2578. [PMID: 33972532 PMCID: PMC8110528 DOI: 10.1038/s41467-021-22590-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/18/2021] [Indexed: 02/03/2023] Open
Abstract
MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.
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Affiliation(s)
- Max T B Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California, USA
| | - Susannah Holmes
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Timothy W Muusse
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Parimala R Vajjhala
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sara J Thygesen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Alpeshkumar K Malde
- Institute for Glycomics, Griffith University, Southport, Queensland, Australia
| | - Dominic J B Hunter
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Tristan I Croll
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Leonie Flueckiger
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Md Habibur Rahaman
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jingjing Zhao
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Nadia A Zatsepin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Brian Abbey
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Emma Sierecki
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
| | - Yann Gambin
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
| | - Katryn J Stacey
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Connie Darmanin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, Queensland, Australia.
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Struwe MA, Kalimuthu P, Luo Z, Zhong Q, Ellis D, Yang J, Khadanand KC, Harmer JR, Kirk ML, McEwan AG, Clement B, Bernhardt PV, Kobe B, Kappler U. Active site architecture reveals coordination sphere flexibility and specificity determinants in a group of closely related molybdoenzymes. J Biol Chem 2021; 296:100672. [PMID: 33887324 PMCID: PMC8166771 DOI: 10.1016/j.jbc.2021.100672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/11/2021] [Accepted: 04/14/2021] [Indexed: 11/27/2022] Open
Abstract
MtsZ is a molybdenum-containing methionine sulfoxide reductase that supports virulence in the human respiratory pathogen Haemophilus influenzae (Hi). HiMtsZ belongs to a group of structurally and spectroscopically uncharacterized S-/N-oxide reductases, all of which are found in bacterial pathogens. Here, we have solved the crystal structure of HiMtsZ, which reveals that the HiMtsZ substrate-binding site encompasses a previously unrecognized part that accommodates the methionine sulfoxide side chain via interaction with His182 and Arg166. Charge and amino acid composition of this side chain–binding region vary and, as indicated by electrochemical, kinetic, and docking studies, could explain the diverse substrate specificity seen in closely related enzymes of this type. The HiMtsZ Mo active site has an underlying structural flexibility, where dissociation of the central Ser187 ligand affected catalysis at low pH. Unexpectedly, the two main HiMtsZ electron paramagnetic resonance (EPR) species resembled not only a related dimethyl sulfoxide reductase but also a structurally unrelated nitrate reductase that possesses an Asp–Mo ligand. This suggests that contrary to current views, the geometry of the Mo center and its primary ligands, rather than the specific amino acid environment, is the main determinant of the EPR properties of mononuclear Mo enzymes. The flexibility in the electronic structure of the Mo centers is also apparent in two of three HiMtsZ EPR-active Mo(V) species being catalytically incompetent off-pathway forms that could not be fully oxidized.
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Affiliation(s)
- Michel A Struwe
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia; Pharmazeutisches Institut, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Palraj Kalimuthu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia
| | - Zhenyao Luo
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Qifeng Zhong
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia
| | - Daniel Ellis
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia
| | - Jing Yang
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, New Mexico, USA
| | - K C Khadanand
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, New Mexico, USA
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Qld, Australia
| | - Martin L Kirk
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Alastair G McEwan
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia
| | - Bernd Clement
- Pharmazeutisches Institut, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia
| | - Bostjan Kobe
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Ulrike Kappler
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia.
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Figley MD, Gu W, Nanson JD, Shi Y, Sasaki Y, Cunnea K, Malde AK, Jia X, Luo Z, Saikot FK, Mosaiab T, Masic V, Holt S, Hartley-Tassell L, McGuinness HY, Manik MK, Bosanac T, Landsberg MJ, Kerry PS, Mobli M, Hughes RO, Milbrandt J, Kobe B, DiAntonio A, Ve T. SARM1 is a metabolic sensor activated by an increased NMN/NAD + ratio to trigger axon degeneration. Neuron 2021; 109:1118-1136.e11. [PMID: 33657413 PMCID: PMC8174188 DOI: 10.1016/j.neuron.2021.02.009] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/15/2021] [Accepted: 02/08/2021] [Indexed: 12/16/2022]
Abstract
Axon degeneration is a central pathological feature of many neurodegenerative diseases. Sterile alpha and Toll/interleukin-1 receptor motif-containing 1 (SARM1) is a nicotinamide adenine dinucleotide (NAD+)-cleaving enzyme whose activation triggers axon destruction. Loss of the biosynthetic enzyme NMNAT2, which converts nicotinamide mononucleotide (NMN) to NAD+, activates SARM1 via an unknown mechanism. Using structural, biochemical, biophysical, and cellular assays, we demonstrate that SARM1 is activated by an increase in the ratio of NMN to NAD+ and show that both metabolites compete for binding to the auto-inhibitory N-terminal armadillo repeat (ARM) domain of SARM1. We report structures of the SARM1 ARM domain bound to NMN and of the homo-octameric SARM1 complex in the absence of ligands. We show that NMN influences the structure of SARM1 and demonstrate via mutagenesis that NMN binding is required for injury-induced SARM1 activation and axon destruction. Hence, SARM1 is a metabolic sensor responding to an increased NMN/NAD+ ratio by cleaving residual NAD+, thereby inducing feedforward metabolic catastrophe and axonal demise.
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Affiliation(s)
- Matthew D Figley
- Department of Developmental Biology, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA; Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - 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
| | - 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
| | - Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Yo Sasaki
- Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - Katie Cunnea
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK; Evotec SE, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Alpeshkumar K Malde
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Xinying Jia
- Centre for Advanced Imaging, University of Queensland, Brisbane, QLD 4072, Australia
| | - Zhenyao Luo
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Forhad K Saikot
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Tamim Mosaiab
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Veronika Masic
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Stephanie Holt
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | | | - Helen Y McGuinness
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, 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
| | - Todd Bosanac
- Disarm Therapeutics, a wholly owned subsidiary of Eli Lilly & Co., Cambridge, MA, USA
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Philip S Kerry
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK; Evotec SE, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Mehdi Mobli
- Centre for Advanced Imaging, University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert O Hughes
- Disarm Therapeutics, a wholly owned subsidiary of Eli Lilly & Co., Cambridge, MA, USA
| | - Jeffrey Milbrandt
- Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA.
| | - 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.
| | - Aaron DiAntonio
- Department of Developmental Biology, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA; Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA.
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia.
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Sung YC, Outram MA, Breen S, Wang C, Dagvadorj B, Winterberg B, Kobe B, Williams SJ, Solomon PS. PR1-mediated defence via C-terminal peptide release is targeted by a fungal pathogen effector. New Phytol 2021; 229:3467-3480. [PMID: 33277705 DOI: 10.1111/nph.17128] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/24/2020] [Indexed: 05/22/2023]
Abstract
The effector SnTox3 from Parastagonospora nodorum elicits a strong necrotic response in susceptible wheat and also interacts with wheat pathogenesis-related protein 1 (TaPR-1), although the function of this interaction in disease is unclear. Here, we dissect TaPR1 function by studying SnTox3-TaPR1 interaction and demonstrate the dual functionality of SnTox3. We utilized site-directed mutagenesis to identify an SnTox3 variant, SnTox3P173S , that was unable to interact with TaPR1 in yeast-two-hybrid assays. Additionally, using recombinant proteins we established a novel protein-mediated phenotyping assay allowing functional studies to be undertaken in wheat. Wheat leaves infiltrated with TaPR1 proteins showed significantly less disease compared to control leaves, correlating with a strong increase in defence gene expression. This activity was dependent on release of the TaCAPE1 peptide embedded within TaPR1 by an unidentified serine protease. The priming activity of TaPR1 was compromised by SnTox3 but not the noninteracting variant SnTox3P173S , and we demonstrate that SnTox3 prevents TaCAPE1 release from TaPR1 in vitro. SnTox3 independently functions to induce necrosis through recognition by Snn3 and also suppresses host defence through a direct interaction with TaPR1 proteins. Importantly, this study also advances our understanding of the role of PR1 proteins in host-microbe interactions as inducers of host defence signalling.
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Affiliation(s)
- Yi-Chang Sung
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Susan Breen
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Chen Wang
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Bayantes Dagvadorj
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Britta Winterberg
- Research School of Biology, The Australian National University, 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
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Peter S Solomon
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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41
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Oyarzun P, Kashyap M, Fica V, Salas-Burgos A, Gonzalez-Galarza FF, McCabe A, Jones AR, Middleton D, Kobe B. A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach. Front Immunol 2021; 12:598778. [PMID: 33717077 PMCID: PMC7952308 DOI: 10.3389/fimmu.2021.598778] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/11/2021] [Indexed: 01/06/2023] Open
Abstract
Emerging infectious diseases (EIDs) caused by viruses are increasing in frequency, causing a high disease burden and mortality world-wide. The COVID-19 pandemic caused by the novel SARS-like coronavirus (SARS-CoV-2) underscores the need to innovate and accelerate the development of effective vaccination strategies against EIDs. Human leukocyte antigen (HLA) molecules play a central role in the immune system by determining the peptide repertoire displayed to the T-cell compartment. Genetic polymorphisms of the HLA system thus confer a strong variability in vaccine-induced immune responses and may complicate the selection of vaccine candidates, because the distribution and frequencies of HLA alleles are highly variable among different ethnic groups. Herein, we build on the emerging paradigm of rational epitope-based vaccine design, by describing an immunoinformatics tool (Predivac-3.0) for proteome-wide T-cell epitope discovery that accounts for ethnic-level variations in immune responsiveness. Predivac-3.0 implements both CD8+ and CD4+ T-cell epitope predictions based on HLA allele frequencies retrieved from the Allele Frequency Net Database. The tool was thoroughly assessed, proving comparable performances (AUC ~0.9) against four state-of-the-art pan-specific immunoinformatics methods capable of population-level analysis (NetMHCPan-4.0, Pickpocket, PSSMHCPan and SMM), as well as a strong accuracy on proteome-wide T-cell epitope predictions for HIV-specific immune responses in the Japanese population. The utility of the method was investigated for the COVID-19 pandemic, by performing in silico T-cell epitope mapping of the SARS-CoV-2 spike glycoprotein according to the ethnic context of the countries where the ChAdOx1 vaccine is currently initiating phase III clinical trials. Potentially immunodominant CD8+ and CD4+ T-cell epitopes and population coverages were predicted for each population (the Epitope Discovery mode), along with optimized sets of broadly recognized (promiscuous) T-cell epitopes maximizing coverage in the target populations (the Epitope Optimization mode). Population-specific epitope-rich regions (T-cell epitope clusters) were further predicted in protein antigens based on combined criteria of epitope density and population coverage. Overall, we conclude that Predivac-3.0 holds potential to contribute in the understanding of ethnic-level variations of vaccine-induced immune responsiveness and to guide the development of epitope-based next-generation vaccines against emerging pathogens, whose geographic distributions and populations in need of vaccinations are often well-defined for regional epidemics.
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Affiliation(s)
- Patricio Oyarzun
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Sede Concepción, Concepción, Chile
| | - Manju Kashyap
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Sede Concepción, Concepción, Chile
| | - Victor Fica
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Sede Concepción, Concepción, Chile
| | | | - Faviel F Gonzalez-Galarza
- Center for Biomedical Research, Faculty of Medicine, Autonomous University of Coahuila, Torreon, Mexico
| | - Antony McCabe
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Derek Middleton
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
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Abstract
Mononuclear molybdoenzymes are highly versatile catalysts that occur in organisms in all domains of life, where they mediate essential cellular functions such as energy generation and detoxification reactions. Molybdoenzymes are particularly abundant in bacteria, where over 50 distinct types of enzymes have been identified to date. In bacterial pathogens, all aspects of molybdoenzyme biology such as molybdate uptake, cofactor biosynthesis, and function of the enzymes themselves, have been shown to affect fitness in the host as well as virulence. Although current studies are mostly focused on a few key pathogens such as Escherichia coli, Salmonella enterica, Campylobacter jejuni, and Mycobacterium tuberculosis, some common themes for the function and adaptation of the molybdoenzymes to pathogen environmental niches are emerging. Firstly, for many of these enzymes, their role is in supporting bacterial energy generation; and the corresponding pathogen fitness and virulence defects appear to arise from a suboptimally poised metabolic network. Secondly, all substrates converted by virulence-relevant bacterial Mo enzymes belong to classes known to be generated in the host either during inflammation or as part of the host signaling network, with some enzyme groups showing adaptation to the increased conversion of such substrates. Lastly, a specific adaptation to bacterial in-host survival is an emerging link between the regulation of molybdoenzyme expression in bacterial pathogens and the presence of immune system-generated reactive oxygen species. The prevalence of molybdoenzymes in key bacterial pathogens including ESKAPE pathogens, paired with the mounting evidence of their central roles in bacterial fitness during infection, suggest that they could be important future drug targets.
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Affiliation(s)
- Qifeng Zhong
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Bostjan Kobe
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
| | - Ulrike Kappler
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
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Hancock SJ, Phan MD, Luo Z, Lo AW, Peters KM, Nhu NTK, Forde BM, Whitfield J, Yang J, Strugnell RA, Paterson DL, Walsh TR, Kobe B, Beatson SA, Schembri MA. Comprehensive analysis of IncC plasmid conjugation identifies a crucial role for the transcriptional regulator AcaB. Nat Microbiol 2020; 5:1340-1348. [PMID: 32807890 DOI: 10.1038/s41564-020-0775-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 07/16/2020] [Indexed: 01/05/2023]
Abstract
The IncC family of broad-host-range plasmids enables the spread of antibiotic resistance genes among human enteric pathogens1-3. Although aspects of IncC plasmid conjugation have been well studied4-9, many roles of conjugation genes have been assigned based solely on sequence similarity. We applied hypersaturated transposon mutagenesis and transposon-directed insertion-site sequencing to determine the set of genes required for IncC conjugation. We identified 27 conjugation genes, comprising 19 that were previously identified (including two regulatory genes, acaDC) and eight not previously associated with conjugation. We show that one previously unknown gene, acaB, encodes a transcriptional regulator that has a crucial role in the regulation of IncC conjugation. AcaB binds upstream of the acaDC promoter to increase acaDC transcription; in turn, AcaDC activates the transcription of IncC conjugation genes. We solved the crystal structure of AcaB at 2.9-Å resolution and used this to guide functional analyses that reveal how AcaB binds to DNA. This improved understanding of IncC conjugation provides a basis for the development of new approaches to reduce the spread of these multi-drug-resistance plasmids.
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Affiliation(s)
- Steven J Hancock
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Minh-Duy Phan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
| | - Zhenyao Luo
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Alvin W Lo
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Kate M Peters
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Nguyen Thi Khanh Nhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Brian M Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Jason Whitfield
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Ji Yang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - David L Paterson
- The University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia
| | | | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
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44
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Azar DF, Haas M, Fedosyuk S, Rahaman MH, Hedger A, Kobe B, Skern T. Vaccinia Virus Immunomodulator A46: Destructive Interactions with MAL and MyD88 Shown by Negative-Stain Electron Microscopy. Structure 2020; 28:1271-1287.e5. [PMID: 33035450 DOI: 10.1016/j.str.2020.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/27/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022]
Abstract
Vaccinia virus A46 is an anti-inflammatory and non-anti-apoptotic, two-domain member of the poxviral Bcl-2-like protein family that inhibits the cellular innate immune response at the level of the Toll/interleukin-1 receptor (TIR) domain-containing TLR adaptor proteins MAL, MyD88, TRAM, and TRIF. The mechanism of interaction of A46 with its targets has remained unclear. The TIR domains of MAL and MyD88 have been shown to signal by forming filamentous assemblies. We show a clear concentration-dependent destruction of both of these assemblies by A46 by means of negative-stain electron microscopy from molar ratios of 1:15 for MAL and 1:30 for MyD88. Using targeted mutagenesis and protein-protein crosslinking, we show that A46 interacts with MAL and MyD88 through several facets, including residues on helices α1 and α7 and the C-terminal flexible region. We propose a model in which A46 targets the MAL and MyD88 signalosome intra-strand interfaces and gradually destroys their assemblies in a concentration-dependent manner.
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Affiliation(s)
- Daniel F Azar
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Meryl Haas
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Sofiya Fedosyuk
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria; Jenner Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Md Habibur Rahaman
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrew Hedger
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, 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
| | - Tim Skern
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria.
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45
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Sun Y, Kobe B, Qi J. Targeting multiple epitopes on the spike protein: a new hope for COVID-19 antibody therapy. Signal Transduct Target Ther 2020; 5:208. [PMID: 32951007 PMCID: PMC7501506 DOI: 10.1038/s41392-020-00320-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 11/09/2022] Open
Affiliation(s)
- Yeping Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China. .,Savaid Medical School, University of the Chinese Academy of Sciences, 100049, Beijing, China.
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46
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Lai JS, Rost B, Kobe B, Bodén M. Evolutionary model of protein secondary structure capable of revealing new biological relationships. Proteins 2020; 88:1251-1259. [PMID: 32394426 DOI: 10.1002/prot.25898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 10/24/2019] [Accepted: 04/27/2020] [Indexed: 11/09/2022]
Abstract
Ancestral sequence reconstruction has had recent success in decoding the origins and the determinants of complex protein functions. However, phylogenetic analyses of remote homologues must handle extreme amino acid sequence diversity resulting from extended periods of evolutionary change. We exploited the wealth of protein structures to develop an evolutionary model based on protein secondary structure. The approach follows the differences between discrete secondary structure states observed in modern proteins and those hypothesized in their immediate ancestors. We implemented maximum likelihood-based phylogenetic inference to reconstruct ancestral secondary structure. The predictive accuracy from the use of the evolutionary model surpasses that of comparative modeling and sequence-based prediction; the reconstruction extracts information not available from modern structures or the ancestral sequences alone. Based on a phylogenetic analysis of a sequence-diverse protein family, we showed that the model can highlight relationships that are evolutionarily rooted in structure and not evident in amino acid-based analysis.
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Affiliation(s)
- Jhih-Siang Lai
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Burkhard Rost
- Department of Informatics, Institute of Advanced Studies (TUM-IAS), School of Life Sciences (WZW), Technical University of Munich (TUM), Garching, Bavaria, Germany
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
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47
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Shewell LK, Day CJ, Jen FEC, Haselhorst T, Atack JM, Reijneveld JF, Everest-Dass A, James DBA, Boguslawski KM, Brouwer S, Gillen CM, Luo Z, Kobe B, Nizet V, von Itzstein M, Walker MJ, Paton AW, Paton JC, Torres VJ, Jennings MP. All major cholesterol-dependent cytolysins use glycans as cellular receptors. Sci Adv 2020; 6:eaaz4926. [PMID: 32494740 PMCID: PMC7244308 DOI: 10.1126/sciadv.aaz4926] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 03/17/2020] [Indexed: 05/03/2023]
Abstract
Cholesterol-dependent cytolysins (CDCs) form pores in cholesterol-rich membranes, but cholesterol alone is insufficient to explain their cell and host tropism. Here, we show that all eight major CDCs have high-affinity lectin activity that identifies glycans as candidate cellular receptors. Streptolysin O, vaginolysin, and perfringolysin O bind multiple glycans, while pneumolysin, lectinolysin, and listeriolysin O recognize a single glycan class. Addition of exogenous carbohydrate receptors for each CDC inhibits toxin activity. We present a structure for suilysin domain 4 in complex with two distinct glycan receptors, P1 antigen and αGal/Galili. We report a wide range of binding affinities for cholesterol and for the cholesterol analog pregnenolone sulfate and show that CDCs bind glycans and cholesterol independently. Intermedilysin binds to the sialyl-TF O-glycan on its erythrocyte receptor, CD59. Removing sialyl-TF from CD59 reduces intermedilysin binding. Glycan-lectin interactions underpin the cellular tropism of CDCs and provide molecular targets to block their cytotoxic activity.
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Affiliation(s)
- Lucy K. Shewell
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | - Christopher J. Day
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | - Freda E.-C. Jen
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | - John M. Atack
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | | | - Arun Everest-Dass
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | - David B. A. James
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Stephan Brouwer
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Christine M. Gillen
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Zhenyao Luo
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Victor Nizet
- Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | - Mark J. Walker
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Adrienne W. Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide 5005, Australia
| | - James C. Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide 5005, Australia
| | - Victor J. Torres
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Michael P. Jennings
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
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48
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Burdett H, Bentham AR, Williams SJ, Dodds PN, Anderson PA, Banfield MJ, Kobe B. The Plant "Resistosome": Structural Insights into Immune Signaling. Cell Host Microbe 2019; 26:193-201. [PMID: 31415752 DOI: 10.1016/j.chom.2019.07.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Plant innate immunity is triggered via direct or indirect recognition of pathogen effectors by the NLR family immune receptors. Mechanistic understanding of plant NLR function has relied on structural information from individual NLR domains and inferences from studies on animal NLRs. Recent reports of the cryo-EM structures of the Arabidopsis plant immune receptor ZAR1 in monomeric inactive and transition states, as well as the active oligomeric state or the "resistosome," have afforded a quantum leap in our understanding of how plant NLRs function. In this Review, we outline the recent structural findings and examine their implications for the activation of plant immune receptors more broadly. We also discuss how NLR signaling in plants, as illustrated by the ZAR1 structure, is analogous to innate immune receptor signaling mechanisms across kingdoms, drawing particular attention to the concept of signaling by cooperative assembly formation.
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Affiliation(s)
- 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
| | - Adam R Bentham
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Simon J Williams
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra 2601, Australia
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Peter A Anderson
- College of Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - 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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49
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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: 279] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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. New Phytol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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