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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] [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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Guo L, Huang P, Li Z, Shin YC, Yan P, Lu M, Chen M, Xiao Y. Auto-inhibition and activation of a short Argonaute-associated TIR-APAZ defense system. Nat Chem Biol 2024; 20:512-520. [PMID: 37932527 DOI: 10.1038/s41589-023-01478-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023]
Abstract
Short prokaryotic Ago accounts for most prokaryotic Argonaute proteins (pAgos) and is involved in defending bacteria against invading nucleic acids. Short pAgo associated with TIR-APAZ (SPARTA) has been shown to oligomerize and deplete NAD+ upon guide-mediated target DNA recognition. However, the molecular basis of SPARTA inhibition and activation remains unknown. In this study, we determined the cryogenic electron microscopy structures of Crenotalea thermophila SPARTA in its inhibited, transient and activated states. The SPARTA monomer is auto-inhibited by its acidic tail, which occupies the guide-target binding channel. Guide-mediated target binding expels this acidic tail and triggers substantial conformational changes to expose the Ago-Ago dimerization interface. As a result, SPARTA assembles into an active tetramer, where the four TIR domains are rearranged and packed to form NADase active sites. Together with biochemical evidence, our results provide a panoramic vision explaining SPARTA auto-inhibition and activation and expand understanding of pAgo-mediated bacterial defense systems.
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Affiliation(s)
- Lijie Guo
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Pingping Huang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhaoxing Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Young-Cheul Shin
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Purui Yan
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Meiling Lu
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Meirong Chen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Yibei Xiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, China.
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3
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Finocchio G, Koopal B, Potocnik A, Heijstek C, Westphal AH, Jinek M, Swarts DC. Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA. Nucleic Acids Res 2024; 52:2012-2029. [PMID: 38224450 PMCID: PMC10899771 DOI: 10.1093/nar/gkad1248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/16/2024] Open
Abstract
In both prokaryotic and eukaryotic innate immune systems, TIR domains function as NADases that degrade the key metabolite NAD+ or generate signaling molecules. Catalytic activation of TIR domains requires oligomerization, but how this is achieved varies in distinct immune systems. In the Short prokaryotic Argonaute (pAgo)/TIR-APAZ (SPARTA) immune system, TIR NADase activity is triggered upon guide RNA-mediated recognition of invading DNA by an unknown mechanism. Here, we describe cryo-EM structures of SPARTA in the inactive monomeric and target DNA-activated tetrameric states. The monomeric SPARTA structure reveals that in the absence of target DNA, a C-terminal tail of TIR-APAZ occupies the nucleic acid binding cleft formed by the pAgo and TIR-APAZ subunits, inhibiting SPARTA activation. In the active tetrameric SPARTA complex, guide RNA-mediated target DNA binding displaces the C-terminal tail and induces conformational changes in pAgo that facilitate SPARTA-SPARTA dimerization. Concurrent release and rotation of one TIR domain allow it to form a composite NADase catalytic site with the other TIR domain within the dimer, and generate a self-complementary interface that mediates cooperative tetramerization. Combined, this study provides critical insights into the structural architecture of SPARTA and the molecular mechanism underlying target DNA-dependent oligomerization and catalytic activation.
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Affiliation(s)
- Giada Finocchio
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Balwina Koopal
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Ana Potocnik
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Clint Heijstek
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Daan C Swarts
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
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4
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Palukaitis P, Yoon JY. Defense signaling pathways in resistance to plant viruses: Crosstalk and finger pointing. Adv Virus Res 2024; 118:77-212. [PMID: 38461031 DOI: 10.1016/bs.aivir.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2024]
Abstract
Resistance to infection by plant viruses involves proteins encoded by plant resistance (R) genes, viz., nucleotide-binding leucine-rich repeats (NLRs), immune receptors. These sensor NLRs are activated either directly or indirectly by viral protein effectors, in effector-triggered immunity, leading to induction of defense signaling pathways, resulting in the synthesis of numerous downstream plant effector molecules that inhibit different stages of the infection cycle, as well as the induction of cell death responses mediated by helper NLRs. Early events in this process involve recognition of the activation of the R gene response by various chaperones and the transport of these complexes to the sites of subsequent events. These events include activation of several kinase cascade pathways, and the syntheses of two master transcriptional regulators, EDS1 and NPR1, as well as the phytohormones salicylic acid, jasmonic acid, and ethylene. The phytohormones, which transit from a primed, resting states to active states, regulate the remainder of the defense signaling pathways, both directly and by crosstalk with each other. This regulation results in the turnover of various suppressors of downstream events and the synthesis of various transcription factors that cooperate and/or compete to induce or suppress transcription of either other regulatory proteins, or plant effector molecules. This network of interactions results in the production of defense effectors acting alone or together with cell death in the infected region, with or without the further activation of non-specific, long-distance resistance. Here, we review the current state of knowledge regarding these processes and the components of the local responses, their interactions, regulation, and crosstalk.
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Affiliation(s)
- Peter Palukaitis
- Graduate School of Plant Protection and Quarantine, Jeonbuk National University, Jeonju, Jeollabuk-do, Republic of Korea.
| | - Ju-Yeon Yoon
- Graduate School of Plant Protection and Quarantine, Jeonbuk National University, Jeonju, Jeollabuk-do, Republic of Korea.
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5
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López-Márquez D, Del-Espino Á, Ruiz-Albert J, Bejarano ER, Brodersen P, Beuzón CR. Regulation of plant immunity via small RNA-mediated control of NLR expression. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6052-6068. [PMID: 37449766 PMCID: PMC10575705 DOI: 10.1093/jxb/erad268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Plants use different receptors to detect potential pathogens: membrane-anchored pattern recognition receptors (PRRs) activated upon perception of pathogen-associated molecular patterns (PAMPs) that elicit pattern-triggered immunity (PTI); and intracellular nucleotide-binding leucine-rich repeat proteins (NLRs) activated by detection of pathogen-derived effectors, activating effector-triggered immunity (ETI). The interconnections between PTI and ETI responses have been increasingly reported. Elevated NLR levels may cause autoimmunity, with symptoms ranging from fitness cost to developmental arrest, sometimes combined with run-away cell death, making accurate control of NLR dosage key for plant survival. Small RNA-mediated gene regulation has emerged as a major mechanism of control of NLR dosage. Twenty-two nucleotide miRNAs with the unique ability to trigger secondary siRNA production from target transcripts are particularly prevalent in NLR regulation. They enhance repression of the primary NLR target, but also bring about repression of NLRs only complementary to secondary siRNAs. We summarize current knowledge on miRNAs and siRNAs in the regulation of NLR expression with an emphasis on 22 nt miRNAs and propose that miRNA and siRNA regulation of NLR levels provides additional links between PTI and NLR defense pathways to increase plant responsiveness against a broad spectrum of pathogens and control an efficient deployment of defenses.
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Affiliation(s)
- Diego López-Márquez
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Ángel Del-Espino
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Javier Ruiz-Albert
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Peter Brodersen
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Carmen R Beuzón
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
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6
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Kadirvelraj R, Boruah BM, Wang S, Chapla D, Huang C, Ramiah A, Hudson KL, Prudden AR, Boons GJ, Withers SG, Wood ZA, Moremen KW. Structural basis for Lewis antigen synthesis by the α1,3-fucosyltransferase FUT9. Nat Chem Biol 2023; 19:1022-1030. [PMID: 37202521 PMCID: PMC10726971 DOI: 10.1038/s41589-023-01345-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 04/20/2023] [Indexed: 05/20/2023]
Abstract
Mammalian cell surface and secreted glycoproteins exhibit remarkable glycan structural diversity that contributes to numerous physiological and pathogenic interactions. Terminal glycan structures include Lewis antigens synthesized by a collection of α1,3/4-fucosyltransferases (CAZy GT10 family). At present, the only available crystallographic structure of a GT10 member is that of the Helicobacter pylori α1,3-fucosyltransferase, but mammalian GT10 fucosyltransferases are distinct in sequence and substrate specificity compared with the bacterial enzyme. Here, we determined crystal structures of human FUT9, an α1,3-fucosyltransferase that generates Lewisx and Lewisy antigens, in complex with GDP, acceptor glycans, and as a FUT9-donor analog-acceptor Michaelis complex. The structures reveal substrate specificity determinants and allow prediction of a catalytic model supported by kinetic analyses of numerous active site mutants. Comparisons with other GT10 fucosyltransferases and GT-B fold glycosyltransferases provide evidence for modular evolution of donor- and acceptor-binding sites and specificity for Lewis antigen synthesis among mammalian GT10 fucosyltransferases.
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Affiliation(s)
- Renuka Kadirvelraj
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
| | - Bhargavi M Boruah
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Shuo Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Chin Huang
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Annapoorani Ramiah
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Kieran L Hudson
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zachary A Wood
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA.
| | - Kelley W Moremen
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
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7
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Hao Y, Pan Y, Chen W, Rashid MAR, Li M, Che N, Duan X, Zhao Y. Contribution of Duplicated Nucleotide-Binding Leucine-Rich Repeat (NLR) Genes to Wheat Disease Resistance. PLANTS (BASEL, SWITZERLAND) 2023; 12:2794. [PMID: 37570947 PMCID: PMC10420896 DOI: 10.3390/plants12152794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023]
Abstract
Wheat has a large and diverse repertoire of NLRs involved in disease resistance, with over 1500 NLRs detected in some studies. These NLR genes occur as singletons or clusters containing copies of NLRs from different phylogenetic clades. The number of NLRs and cluster size can differ drastically among ecotypes and cultivars. Primarily, duplication has led to the evolution and diversification of NLR genes. Among the various mechanisms, whole genome duplication (WGD) is the most intense and leading cause, contributing to the complex evolutionary history and abundant gene set of hexaploid wheat. Tandem duplication or recombination is another major mechanism of NLR gene expansion in wheat. The diversity and divergence of duplicate NLR genes are responsible for the broad-spectrum resistance of most plant species with limited R genes. Understanding the mechanisms underlying the rapid evolution and diversification of wheat NLR genes will help improve disease resistance in crops. The present review focuses on the diversity and divergence of duplicate NLR genes and their contribution to wheat disease resistance. Moreover, we provide an overview of disease resistance-associated gene duplication and the underlying strategies in wheat.
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Affiliation(s)
- Yongchao Hao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Yinghua Pan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Wuying Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Muhammad Abdul Rehman Rashid
- Department of Agricultural Sciences/Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Mengyao Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Naixiu Che
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Xu Duan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
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8
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Panzer B, Kopp CW, Neumayer C, Koppensteiner R, Jozkowicz A, Poledniczek M, Gremmel T, Jilma B, Wadowski PP. Toll-like Receptors as Pro-Thrombotic Drivers in Viral Infections: A Narrative Review. Cells 2023; 12:1865. [PMID: 37508529 PMCID: PMC10377790 DOI: 10.3390/cells12141865] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Toll-like receptors (TLRs) have a critical role in the pathogenesis and disease course of viral infections. The induced pro-inflammatory responses result in the disturbance of the endovascular surface layer and impair vascular homeostasis. The injury of the vessel wall further promotes pro-thrombotic and pro-coagulatory processes, eventually leading to micro-vessel plugging and tissue necrosis. Moreover, TLRs have a direct role in the sensing of viruses and platelet activation. TLR-mediated upregulation of von Willebrand factor release and neutrophil, as well as macrophage extra-cellular trap formation, further contribute to (micro-) thrombotic processes during inflammation. The following review focuses on TLR signaling pathways of TLRs expressed in humans provoking pro-thrombotic responses, which determine patient outcome during viral infections, especially in those with cardiovascular diseases.
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Affiliation(s)
- Benjamin Panzer
- Department of Cardiology, Wilhelminenspital, 1090 Vienna, Austria
| | - Christoph W Kopp
- Division of Angiology, Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria
| | - Christoph Neumayer
- Division of Vascular Surgery, Department of Surgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Renate Koppensteiner
- Division of Angiology, Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria
| | - Alicja Jozkowicz
- Faculty of Biophysics, Biochemistry and Biotechnology, Department of Medical Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Michael Poledniczek
- Division of Cardiology, Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria
| | - Thomas Gremmel
- Institute of Cardiovascular Pharmacotherapy and Interventional Cardiology, Karl Landsteiner Society, 3100 St. Pölten, Austria
- Department of Internal Medicine I, Cardiology and Intensive Care Medicine, Landesklinikum Mistelbach-Gänserndorf, 2130 Mistelbach, Austria
| | - Bernd Jilma
- Department of Clinical Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Patricia P Wadowski
- Division of Angiology, Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria
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9
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Alsamman AM, Mousa KH, Nassar AE, Faheem MM, Radwan KH, Adly MH, Hussein A, Istanbuli T, Mokhtar MM, Elakkad TA, Kehel Z, Hamwieh A, Abdelsattar M, El Allali A. Identification, characterization, and validation of NBS-encoding genes in grass pea. Front Genet 2023; 14:1187597. [PMID: 37408775 PMCID: PMC10318170 DOI: 10.3389/fgene.2023.1187597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/01/2023] [Indexed: 07/07/2023] Open
Abstract
Grass pea is a promising crop with the potential to provide food and fodder, but its genomics has not been adequately explored. Identifying genes for desirable traits, such as drought tolerance and disease resistance, is critical for improving the plant. Grass pea currently lacks known R-genes, including the nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family, which plays a key role in protecting the plant from biotic and abiotic stresses. In our study, we used the recently published grass pea genome and available transcriptomic data to identify 274 NBS-LRR genes. The evolutionary relationships between the classified genes on the reported plants and LsNBS revealed that 124 genes have TNL domains, while 150 genes have CNL domains. All genes contained exons, ranging from 1 to 7. Ten conserved motifs with lengths ranging from 16 to 30 amino acids were identified. We found TIR-domain-containing genes in 132 LsNBSs, with 63 TIR-1 and 69 TIR-2, and RX-CCLike in 84 LsNBSs. We also identified several popular motifs, including P-loop, Uup, kinase-GTPase, ABC, ChvD, CDC6, Rnase_H, Smc, CDC48, and SpoVK. According to the gene enrichment analysis, the identified genes undergo several biological processes such as plant defense, innate immunity, hydrolase activity, and DNA binding. In the upstream regions, 103 transcription factors were identified that govern the transcription of nearby genes affecting the plant excretion of salicylic acid, methyl jasmonate, ethylene, and abscisic acid. According to RNA-Seq expression analysis, 85% of the encoded genes have high expression levels. Nine LsNBS genes were selected for qPCR under salt stress conditions. The majority of the genes showed upregulation at 50 and 200 μM NaCl. However, LsNBS-D18, LsNBS-D204, and LsNBS-D180 showed reduced or drastic downregulation compared to their respective expression levels, providing further insights into the potential functions of LsNBSs under salt stress conditions. They provide valuable insights into the potential functions of LsNBSs under salt stress conditions. Our findings also shed light on the evolution and classification of NBS-LRR genes in legumes, highlighting the potential of grass pea. Further research could focus on the functional analysis of these genes, and their potential use in breeding programs to improve the salinity, drought, and disease resistance of this important crop.
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Affiliation(s)
- Alsamman M. Alsamman
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Khaled H. Mousa
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Ahmed E. Nassar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Mostafa M. Faheem
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Khaled H. Radwan
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Monica H. Adly
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Ahmed Hussein
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Tawffiq Istanbuli
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon
| | - Morad M. Mokhtar
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Tamer Ahmed Elakkad
- Department of Genetics and Genetic Engineering, Faculty of Agriculture at Moshtohor, Benha University, Benha, Egypt
- Moshtohor Research Park, Molecular Biology Lab, Benha University, Benha, Egypt
| | - Zakaria Kehel
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Aladdin Hamwieh
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Mohamed Abdelsattar
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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10
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Abstract
Investigation of fungal biology has been frequently motivated by the fact that many fungal species are important plant and animal pathogens. Such efforts have contributed significantly toward our understanding of fungal pathogenic lifestyles (virulence factors and strategies) and the interplay with host immune systems. In parallel, work on fungal allorecognition systems leading to the characterization of fungal regulated cell death determinants and pathways, has been instrumental for the emergent concept of fungal immunity. The uncovered evolutionary trans-kingdom parallels between fungal regulated cell death pathways and innate immune systems incite us to reflect further on the concept of a fungal immune system. Here, I briefly review key findings that have shaped the fungal immunity paradigm, providing a perspective on what I consider its most glaring knowledge gaps. Undertaking to fill such gaps would establish firmly the fungal immune system inside the broader field of comparative immunology.
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Affiliation(s)
- Asen Daskalov
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- ImmunoConcEpT, CNRS UMR 5164, University of Bordeaux, Bordeaux, France
- Corresponding author
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11
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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. CURRENT OPINION IN PLANT BIOLOGY 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] [Abstract] [MESH Headings] [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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12
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Wang J, Zhang J, Wang J, Hu X, Ouyang L, Wang Y. Small-Molecule Modulators Targeting Toll-like Receptors for Potential Anticancer Therapeutics. J Med Chem 2023; 66:6437-6462. [PMID: 37163340 DOI: 10.1021/acs.jmedchem.2c01655] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Toll-like receptors (TLRs) are key components of the innate immune system and serve as a crucial link between innate and acquired immunity. In addition to immune function, TLRs are involved in other important pathological processes, including tumorigenesis. TLRs have dual regulatory effects on tumor immunity by activating nuclear factor κ-B signaling pathways, which induce tumor immune evasion or enhance the antitumor immune response. Therefore, TLRs have become a popular target for cancer prevention and treatment, and TLR agonists and antagonists offer considerable potential for drug development. The TLR7 agonist imiquimod (1) has been approved by the U.S. Food and Drug Administration as a treatment for malignant skin cancer. Herein, the structure, signaling pathways, and function of the TLR family are summarized, and the structure-activity relationships associated with TLR selective and multitarget modulators and their potential application in tumor therapy are systematically discussed.
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Affiliation(s)
- Jiayu Wang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Jifa Zhang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Xinyue Hu
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Liang Ouyang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yuxi Wang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
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13
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Bernoux M, Chen J, Zhang X, Newell K, Hu J, Deslandes L, Dodds P. Subcellular localization requirements and specificities for plant immune receptor Toll-interleukin-1 receptor signaling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36932864 DOI: 10.1111/tpj.16195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 06/02/2023]
Abstract
Recent work shed light on how plant intracellular immune receptors of the nucleotide-binding leucine-rich repeat (NLR) family are activated upon pathogen effector recognition to trigger immune responses. Activation of Toll-interleukin-1 receptor (TIR) domain-containing NLRs (TNLs) induces receptor oligomerization and close proximity of the TIR domain, which is required for TIR enzymatic activity. TIR-catalyzed small signaling molecules bind to EDS1 family heterodimers and subsequently activate downstream helper NLRs, which function as Ca2+ permeable channel to activate immune responses eventually leading to cell death. Subcellular localization requirements of TNLs and signaling partners are not well understood, although they are required to understand fully the mechanisms underlying NLR early signaling. TNLs show diverse subcellular localization while EDS1 shows nucleocytosolic localization. Here, we studied the impact of TIR and EDS1 mislocalization on the signaling activation of different TNLs. In Nicotiana benthamiana, our results suggest that close proximity of TIR domains isolated from flax L6 and Arabidopsis RPS4 and SNC1 TNLs drives signaling activation from different cell compartments. Nevertheless, both Golgi-membrane anchored L6 and nucleocytosolic RPS4 have the same requirements for EDS1 subcellular localization in Arabidopsis thaliana. By using mislocalized variants of EDS1, we found that autoimmune L6 and RPS4 TIR domain can induce seedling cell death when EDS1 is present in the cytosol. However, when EDS1 is restricted to the nucleus, both induce a stunting phenotype but no cell death. Our data point out the importance of thoroughly investigating the dynamics of TNLs and signaling partners subcellular localization to understand TNL signaling fully.
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Affiliation(s)
- Maud Bernoux
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), UMR 2594/441 CNRS, INRAE, 31326, Castanet-Tolosan, France
| | - Jian Chen
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT 2601, Australia
| | - Xiaoxiao Zhang
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Kim Newell
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT 2601, Australia
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100094, People's Republic of China
| | - Laurent Deslandes
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), UMR 2594/441 CNRS, INRAE, 31326, Castanet-Tolosan, France
| | - Peter Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT 2601, Australia
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14
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Andolfo G, Di Donato A, Ercolano MR. NB-LRR Lineage-Specific Equipment Is Sorted Out by Sequence Pattern Adaptation and Domain Segment Shuffling. Int J Mol Sci 2022; 23:ijms232214269. [PMID: 36430746 PMCID: PMC9696612 DOI: 10.3390/ijms232214269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
The nucleotide-binding and leucine-rich repeat (NB-LRR) genes, also known as resistance (R)-genes, play an important role in the activation of immune responses. In recent years, large-scale studies have been performed to highlight the diversification of plant NB-LRR repertories. It is well known that, to provide new functionalities, NB-LRR sequences are subject to duplication, domain fusions and acquisition and other kinds of mutations. Although some mechanisms that govern NB-LRR protein domain adaptations have been uncovered, to retrace the plant-lineage-specific evolution routes of R protein structure, a multi-genome comparative analysis was performed. This study allowed us to define groups of genes sharing homology relationships across different species. It is worth noting that the most populated groups contained well-characterized R proteins. The arsenal profile of such groups was investigated in five botanical families, including important crop species, to underline specific adaptation signatures. In addition, the dissection of 70 NB domains of well-characterized R-genes revealed the NB core motifs from which the three main R protein classes have been diversified. The structural remodeling of domain segments shaped the specific NB-LRR repertoires observed in each plant species. This analysis provided new evolutionary and functional insights on NB protein domain shuffling. Taken together, such findings improved our understanding of the molecular adaptive selection mechanisms occurring at plant R loci.
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15
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Zheng Y, Zhang S, Luo Y, Li F, Tan J, Wang B, Zhao Z, Lin H, Zhang T, Liu J, Liu X, Guo J, Xie X, Chen L, Liu YG, Chu Z. Rice OsUBR7 modulates plant height by regulating histone H2B monoubiquitination and cell proliferation. PLANT COMMUNICATIONS 2022; 3:100412. [PMID: 35836378 PMCID: PMC9700165 DOI: 10.1016/j.xplc.2022.100412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/20/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Plant height is an important agronomic trait for lodging resistance and yield. Here, we report a new plant-height-related gene, OsUBR7 in rice (Oryza sativa L.); knockout of OsUBR7 caused fewer cells in internodes, resulting in a semi-dwarf phenotype. OsUBR7 encodes a putative E3 ligase containing a plant homeodomain finger and a ubiquitin protein ligase E3 component N-recognin 7 (UBR7) domain. OsUBR7 interacts with histones and monoubiquitinates H2B (H2Bub1) at lysine148 in coordination with the E2 conjugase OsUBC18. OsUBR7 mediates H2Bub1 at a number of chromatin loci for the normal expression of target genes, including cell-cycle-related and pleiotropic genes, consistent with the observation that cell-cycle progression was suppressed in the osubr7 mutant owing to reductions in H2Bub1 and expression levels at these loci. The genetic divergence of OsUBR7 alleles among japonica and indica cultivars affects their transcriptional activity, and these alleles may have undergone selection during rice domestication. Overall, our results reveal a novel mechanism that mediates H2Bub1 in plants, and UBR7 orthologs could be utilized as an untapped epigenetic resource for crop improvement.
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Affiliation(s)
- Yangyi Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Sensen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yanqiu Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Fuquan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jiantao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Bin Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zhe Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Huifang Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Tingting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jianhong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xupeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Zhizhan Chu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou 510642, China.
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16
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Eastman S, Bayless A, Guo M. The Nucleotide Revolution: Immunity at the Intersection of Toll/Interleukin-1 Receptor Domains, Nucleotides, and Ca 2. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:964-976. [PMID: 35881867 DOI: 10.1094/mpmi-06-22-0132-cr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The discovery of the enzymatic activity of the toll/interleukin-1 receptor (TIR) domain protein SARM1 five years ago preceded a flood of discoveries regarding the nucleotide substrates and products of TIR domains in plants, animals, bacteria, and archaea. These discoveries into the activity of TIR domains coincide with major advances in understanding the structure and mechanisms of NOD-like receptors and the mutual dependence of pattern recognition receptor- and effector-triggered immunity (PTI and ETI, respectively) in plants. It is quickly becoming clear that TIR domains and TIR-produced nucleotides are ancestral signaling molecules that modulate immunity and that their activity is closely associated with Ca2+ signaling. TIR domain research now bridges the separate disciplines of molecular plant- and animal-microbe interactions, neurology, and prokaryotic immunity. A cohesive framework for understanding the role of enzymatic TIR domains in diverse organisms will help unite the research of these disparate fields. Here, we review known products of TIR domains in plants, animals, bacteria, and archaea and use context gained from animal and prokaryotic TIR domain systems to present a model for TIR domains, nucleotides, and Ca2+ at the intersection of PTI and ETI in plant immunity. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Samuel Eastman
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
| | - Adam Bayless
- Department of Biology, Colorado State University, Fort Collins, CO 80521, U.S.A
| | - Ming Guo
- Department of Agriculture and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
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17
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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] [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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18
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Zhang B, Liu M, Wang Y, Yuan W, Zhang H. Plant NLRs: Evolving with pathogen effectors and engineerable to improve resistance. Front Microbiol 2022; 13:1018504. [PMID: 36246279 PMCID: PMC9554439 DOI: 10.3389/fmicb.2022.1018504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/09/2022] [Indexed: 11/13/2022] Open
Abstract
Pathogens are important threats to many plants throughout their lifetimes. Plants have developed different strategies to overcome them. In the plant immunity system, nucleotide-binding domain and leucine-rich repeat-containing proteins (NLRs) are the most common components. And recent studies have greatly expanded our understanding of how NLRs function in plants. In this review, we summarize the studies on the mechanism of NLRs in the processes of effector recognition, resistosome formation, and defense activation. Typical NLRs are divided into three groups according to the different domains at their N termini and function in interrelated ways in immunity. Atypical NLRs contain additional integrated domains (IDs), some of which directly interact with pathogen effectors. Plant NLRs evolve with pathogen effectors and exhibit specific recognition. Meanwhile, some NLRs have been successfully engineered to confer resistance to new pathogens based on accumulated studies. In summary, some pioneering processes have been obtained in NLR researches, though more questions arise as a result of the huge number of NLRs. However, with a broadened understanding of the mechanism, NLRs will be important components for engineering in plant resistance improvement.
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19
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Liu N, Chen H, Wang X, Wang D, Fu ZQ. TIRggering cell death via two enzymatic reactions. MOLECULAR PLANT 2022; 15:1263-1265. [PMID: 35808828 DOI: 10.1016/j.molp.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/28/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Na Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Huan Chen
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Xu Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450002, China.
| | - Zheng Qing Fu
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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20
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Zhou J, Xiao Y, Ren Y, Ge J, Wang X. Structural basis of the IL-1 receptor TIR domain-mediated IL-1 signaling. iScience 2022; 25:104508. [PMID: 35754719 PMCID: PMC9213720 DOI: 10.1016/j.isci.2022.104508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 05/02/2022] [Accepted: 05/27/2022] [Indexed: 11/28/2022] Open
Abstract
The cytoplasmic Toll/interleukin-1 receptor (TIR) domains of IL-1 receptors (IL-1Rs) are evolutionally conserved and essential for transmitting signals. IL-1RAcP is a shared co-receptor in the IL-1R family for signaling. Its splicing form IL-1RAcPb contains a different TIR domain and is unable to transduce NF-κB signaling. Here, we determined crystal structures of TIR domains of IL-1RAcPb and other IL-1Rs including IL-18Rβ, IL-1RAPL2, and zebrafish SIGIRR (zSIGIRR). Structurally variant regions in the TIR domain important for signaling were revealed by structural comparisons. Taking advantage of the IL-1RAcP/IL-1RAcPb pair, we demonstrated that differential TIR domain determines signaling discrepancies between IL-1RAcP and IL-1RAcPb. We also proved the functional importance of two helices (αC and αD) in the structurally variable regions and pinpointed critical residues in αC and αD for signaling. These results collectively provide additional and important knowledge for fully understanding the molecular basis of IL-1R TIR domain in mediating signaling. The crystal structures of several IL-1R TIR domains were determinated Structurally variant regions in TIR domains were revealed by structural comparisons Differential TIR domain determines signaling discrepancy between IL-1RAcP and IL-1RAcPb αC/αD regions and several residues there were proved to be vital for IL-1 signaling
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Affiliation(s)
- Jianjie Zhou
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yu Xiao
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yifei Ren
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiwan Ge
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
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21
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Essuman K, Milbrandt J, Dangl JL, Nishimura MT. Shared TIR enzymatic functions regulate cell death and immunity across the tree of life. Science 2022; 377:eabo0001. [DOI: 10.1126/science.abo0001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the 20th century, researchers studying animal and plant signaling pathways discovered a protein domain shared across diverse innate immune systems: the Toll/Interleukin-1/Resistance-gene (TIR) domain. The TIR domain is found in several protein architectures and was defined as an adaptor mediating protein-protein interactions in animal innate immunity and developmental signaling pathways. However, studies of nerve degeneration in animals, and subsequent breakthroughs in plant, bacterial and archaeal systems, revealed that TIR domains possess enzymatic activities. We provide a synthesis of TIR functions and the role of various related TIR enzymatic products in evolutionarily diverse immune systems. These studies may ultimately guide interventions that would span the tree of life, from treating human neurodegenerative disorders and bacterial infections, to preventing plant diseases.
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Affiliation(s)
- Kow Essuman
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marc T. Nishimura
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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22
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Brace EJ, Essuman K, Mao X, Palucki J, Sasaki Y, Milbrandt J, DiAntonio A. Distinct developmental and degenerative functions of SARM1 require NAD+ hydrolase activity. PLoS Genet 2022; 18:e1010246. [PMID: 35737728 PMCID: PMC9223315 DOI: 10.1371/journal.pgen.1010246] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/10/2022] [Indexed: 11/25/2022] Open
Abstract
SARM1 is the founding member of the TIR-domain family of NAD+ hydrolases and the central executioner of pathological axon degeneration. SARM1-dependent degeneration requires NAD+ hydrolysis. Prior to the discovery that SARM1 is an enzyme, SARM1 was studied as a TIR-domain adaptor protein with non-degenerative signaling roles in innate immunity and invertebrate neurodevelopment, including at the Drosophila neuromuscular junction (NMJ). Here we explore whether the NADase activity of SARM1 also contributes to developmental signaling. We developed transgenic Drosophila lines that express SARM1 variants with normal, deficient, and enhanced NADase activity and tested their function in NMJ development. We find that NMJ overgrowth scales with the amount of NADase activity, suggesting an instructive role for NAD+ hydrolysis in this developmental signaling pathway. While degenerative and developmental SARM1 signaling share a requirement for NAD+ hydrolysis, we demonstrate that these signals use distinct upstream and downstream mechanisms. These results identify SARM1-dependent NAD+ hydrolysis as a heretofore unappreciated component of developmental signaling. SARM1 now joins sirtuins and Parps as enzymes that regulate signal transduction pathways via mechanisms that involve NAD+ cleavage, greatly expanding the potential scope of SARM1 TIR NADase functions. SARM1 is the central executioner of axon loss, and inhibition of SARM1 is a therapeutic target for many devastating neurodegenerative disorders. SARM1 is the founding member of the TIR-domain family of NAD+ cleaving enzymes, destroying the essential metabolite NAD+ and inducing an energetic crisis in the axon. This was a surprising finding, as previously studied TIR-domain proteins were characterized as scaffolds that bind signaling proteins to coordinate signal transduction cascades. Indeed, before the discovery of the role of SARM1 in axon degeneration, SARM1 was studied as a regulator of intracellular signaling in immunity and neurodevelopment where it was assumed to act as a scaffold. Here we investigate whether the recently described SARM1 enzymatic activity also regulates such signal transduction pathways. Indeed, we show that a developmental signaling pathway scales with the amount of NADase activity, suggesting an instructive role for NAD+ cleavage. While degenerative and developmental SARM1 signaling share a requirement for NAD+ cleavage, they utilize distinct upstream and downstream mechanisms. With these findings, SARM1 now joins sirtuins and Parps as enzymes that regulate signal transduction pathways via mechanisms that involve NAD+ cleavage, greatly expanding the potential scope of SARM1 TIR NADase functions.
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Affiliation(s)
- E J Brace
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kow Essuman
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Xianrong Mao
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - John Palucki
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yo Sasaki
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jeff Milbrandt
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.,Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Aaron DiAntonio
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America.,Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine, St. Louis, Missouri, United States of America
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23
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Lu Q, Botchway BOA, Zhang Y, Jin T, Liu X. SARM1 can be a potential therapeutic target for spinal cord injury. Cell Mol Life Sci 2022; 79:161. [PMID: 35224705 PMCID: PMC11072485 DOI: 10.1007/s00018-022-04195-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 01/26/2022] [Accepted: 02/05/2022] [Indexed: 01/03/2023]
Abstract
Injury to the spinal cord is devastating. Studies have implicated Wallerian degeneration as the main cause of axonal destruction in the wake of spinal cord injury. Therefore, the suppression of Wallerian degeneration could be beneficial for spinal cord injury treatment. Sterile alpha and armadillo motif-containing protein 1 (SARM1) is a key modulator of Wallerian degeneration, and its impediment can improve spinal cord injury to a significant degree. In this report, we analyze the various signaling domains of SARM1, the recent findings on Wallerian degeneration and its relation to axonal insults, as well as its connection to SARM1, the mitogen-activated protein kinase (MAPK) signaling, and the survival factor, nicotinamide mononucleotide adenylyltransferase 2 (NMNAT2). We then elaborate on the possible role of SARM1 in spinal cord injury and explicate how its obstruction could potentially alleviate the injury.
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Affiliation(s)
- Qicheng Lu
- Department of Histology and Embryology, Medical College, Shaoxing University, Shaoxing, China
| | - Benson O A Botchway
- Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Zhang
- Department of Histology and Embryology, Medical College, Shaoxing University, Shaoxing, China
| | - Tian Jin
- Department of Histology and Embryology, Medical College, Shaoxing University, Shaoxing, China
| | - Xuehong Liu
- Department of Histology and Embryology, Medical College, Shaoxing University, Shaoxing, China.
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24
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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] [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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25
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Peterson ND, Icso JD, Salisbury JE, Rodríguez T, Thompson PR, Pukkila-Worley R. Pathogen infection and cholesterol deficiency activate the C. elegans p38 immune pathway through a TIR-1/SARM1 phase transition. eLife 2022; 11:e74206. [PMID: 35098926 PMCID: PMC8923663 DOI: 10.7554/elife.74206] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Intracellular signaling regulators can be concentrated into membrane-free, higher ordered protein assemblies to initiate protective responses during stress - a process known as phase transition. Here, we show that a phase transition of the Caenorhabditis elegans Toll/interleukin-1 receptor domain protein (TIR-1), an NAD+ glycohydrolase homologous to mammalian sterile alpha and TIR motif-containing 1 (SARM1), underlies p38 PMK-1 immune pathway activation in C. elegans intestinal epithelial cells. Through visualization of fluorescently labeled TIR-1/SARM1 protein, we demonstrate that physiologic stresses, both pathogen and non-pathogen, induce multimerization of TIR-1/SARM1 into visible puncta within intestinal epithelial cells. In vitro enzyme kinetic analyses revealed that, like mammalian SARM1, the NAD+ glycohydrolase activity of C. elegans TIR-1 is dramatically potentiated by protein oligomerization and a phase transition. Accordingly, C. elegans with genetic mutations that specifically block either multimerization or the NAD+ glycohydrolase activity of TIR-1/SARM1 fail to induce p38 PMK phosphorylation, are unable to increase immune effector expression, and are dramatically susceptible to bacterial infection. Finally, we demonstrate that a loss-of-function mutation in nhr-8, which alters cholesterol metabolism and is used to study conditions of sterol deficiency, causes TIR-1/SARM1 to oligomerize into puncta in intestinal epithelial cells. Cholesterol scarcity increases p38 PMK-1 phosphorylation, primes immune effector induction in a manner that requires TIR-1/SARM1 oligomerization and its intrinsic NAD+ glycohydrolase activity, and reduces pathogen accumulation in the intestine during a subsequent infection. These data reveal a new adaptive response that allows a metazoan host to anticipate pathogen threats during cholesterol deprivation, a time of relative susceptibility to infection. Thus, a phase transition of TIR-1/SARM1 as a prerequisite for its NAD+ glycohydrolase activity is strongly conserved across millions of years of evolution and is essential for diverse physiological processes in multiple cell types.
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Affiliation(s)
- Nicholas D Peterson
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Janneke D Icso
- Program in Chemical Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - J Elizabeth Salisbury
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Tomás Rodríguez
- RNA Therapeutics Institute, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Paul R Thompson
- Program in Chemical Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Read Pukkila-Worley
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
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26
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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: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [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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27
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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] [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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28
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Research Progress of ATGs Involved in Plant Immunity and NPR1 Metabolism. Int J Mol Sci 2021; 22:ijms222212093. [PMID: 34829975 PMCID: PMC8623690 DOI: 10.3390/ijms222212093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 12/12/2022] Open
Abstract
Autophagy is an important pathway of degrading excess and abnormal proteins and organelles through their engulfment into autophagosomes that subsequently fuse with the vacuole. Autophagy-related genes (ATGs) are essential for the formation of autophagosomes. To date, about 35 ATGs have been identified in Arabidopsis, which are involved in the occurrence and regulation of autophagy. Among these, 17 proteins are related to resistance against plant pathogens. The transcription coactivator non-expressor of pathogenesis-related genes 1 (NPR1) is involved in innate immunity and acquired resistance in plants, which regulates most salicylic acid (SA)-responsive genes. This paper mainly summarizes the role of ATGs and NPR1 in plant immunity and the advancement of research on ATGs in NPR1 metabolism, providing a new idea for exploring the relationship between ATGs and NPR1.
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29
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Matamoros‐Recio A, Franco‐Gonzalez JF, Perez‐Regidor L, Billod J, Guzman‐Caldentey J, Martin‐Santamaria S. Full-Atom Model of the Agonist LPS-Bound Toll-like Receptor 4 Dimer in a Membrane Environment. Chemistry 2021; 27:15406-15425. [PMID: 34569111 PMCID: PMC8596573 DOI: 10.1002/chem.202102995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Indexed: 01/06/2023]
Abstract
The Toll-like receptor 4 (TLR4)/myeloid differentiation factor 2 (MD-2) innate immunity system is a membrane receptor of paramount importance as therapeutic target. Its assembly, upon binding of Gram-negative bacteria lipopolysaccharide (LPS), and also dependent on the membrane composition, finally triggers the immune response cascade. We have combined ab-initio calculations, molecular docking, all-atom molecular dynamics simulations, and thermodynamics calculations to provide the most realistic and complete 3D models of the active full TLR4 complex embedded into a realistic membrane to date. Our studies give functional and structural insights into the transmembrane domain behavior in different membrane environments, the ectodomain bouncing movement, and the dimerization patterns of the intracellular Toll/Interleukin-1 receptor domain. Our work provides TLR4 models as reasonable 3D structures for the (TLR4/MD-2/LPS)2 architecture accounting for the active (agonist) state of the TLR4, and pointing to a signal transduction mechanism across cell membrane. These observations unveil relevant molecular aspects involved in the TLR4 innate immune pathways and will promote the discovery of new TLR4 modulators.
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Affiliation(s)
- Alejandra Matamoros‐Recio
- Department of Structural and Chemical BiologyCentre for Biological Research Margarita Salas, CIB-CSICC/ Ramiro de Maeztu, 928040MadridSpain
| | - Juan Felipe Franco‐Gonzalez
- Department of Structural and Chemical BiologyCentre for Biological Research Margarita Salas, CIB-CSICC/ Ramiro de Maeztu, 928040MadridSpain
| | - Lucia Perez‐Regidor
- Department of Structural and Chemical BiologyCentre for Biological Research Margarita Salas, CIB-CSICC/ Ramiro de Maeztu, 928040MadridSpain
| | - Jean‐Marc Billod
- Department of Structural and Chemical BiologyCentre for Biological Research Margarita Salas, CIB-CSICC/ Ramiro de Maeztu, 928040MadridSpain
| | - Joan Guzman‐Caldentey
- Department of Structural and Chemical BiologyCentre for Biological Research Margarita Salas, CIB-CSICC/ Ramiro de Maeztu, 928040MadridSpain
| | - Sonsoles Martin‐Santamaria
- Department of Structural and Chemical BiologyCentre for Biological Research Margarita Salas, CIB-CSICC/ Ramiro de Maeztu, 928040MadridSpain
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30
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El Kasmi F. How activated NLRs induce anti-microbial defenses in plants. Biochem Soc Trans 2021; 49:2177-2188. [PMID: 34623378 PMCID: PMC8589443 DOI: 10.1042/bst20210242] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/16/2021] [Accepted: 08/24/2021] [Indexed: 12/21/2022]
Abstract
Plants utilize cell-surface localized and intracellular leucine-rich repeat (LRR) immune receptors to detect pathogens and to activate defense responses, including transcriptional reprogramming and the initiation of a form of programmed cell death of infected cells. Cell death initiation is mainly associated with the activation of nucleotide-binding LRR receptors (NLRs). NLRs recognize the presence or cellular activity of pathogen-derived virulence proteins, so-called effectors. Effector-dependent NLR activation leads to the formation of higher order oligomeric complexes, termed resistosomes. Resistosomes can either form potential calcium-permeable cation channels at cellular membranes and initiate calcium influxes resulting in activation of immunity and cell death or function as NADases whose activity is needed for the activation of downstream immune signaling components, depending on the N-terminal domain of the NLR protein. In this mini-review, the current knowledge on the mechanisms of NLR-mediated cell death and resistance pathways during plant immunity is discussed.
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Affiliation(s)
- Farid El Kasmi
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen Germany
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31
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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: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [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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32
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Toll-Like Receptors: General Molecular and Structural Biology. J Immunol Res 2021; 2021:9914854. [PMID: 34195298 PMCID: PMC8181103 DOI: 10.1155/2021/9914854] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/19/2021] [Indexed: 12/11/2022] Open
Abstract
Background/Aim Toll-like receptors (TLRs) are pivotal biomolecules in the immune system. Today, we are all aware of the importance of TLRs in bridging innate and adaptive immune system to each other. The TLRs are activated through binding to damage/danger-associated molecular patterns (DAMPs), microbial/microbe-associated molecular patterns (MAMPs), pathogen-associated molecular patterns (PAMPs), and xenobiotic-associated molecular patterns (XAMPs). The immunogenetic molecules of TLRs have their own functions, structures, coreceptors, and ligands which make them unique. These properties of TLRs give us an opportunity to find out how we can employ this knowledge for ligand-drug discovery strategies to control TLRs functions and contribution, signaling pathways, and indirect activities. Hence, the authors of this paper have a deep observation on the molecular and structural biology of human TLRs (hTLRs). Methods and Materials To prepare this paper and fulfill our goals, different search engines (e.g., GOOGLE SCHOLAR), Databases (e.g., MEDLINE), and websites (e.g., SCOPUS) were recruited to search and find effective papers and investigations. To reach this purpose, we tried with papers published in the English language with no limitation in time. The iCite bibliometrics was exploited to check the quality of the collected publications. Results Each TLR molecule has its own molecular and structural biology, coreceptor(s), and abilities which make them unique or a complementary portion of the others. These immunogenetic molecules have remarkable roles and are much more important in different sections of immune and nonimmune systems rather than that we understand to date. Conclusion TLRs are suitable targets for ligand-drug discovery strategies to establish new therapeutics in the fields of infectious and autoimmune diseases, cancers, and other inflammatory diseases and disorders.
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Jonkheer EM, Brankovics B, Houwers IM, van der Wolf JM, Bonants PJM, Vreeburg RAM, Bollema R, de Haan JR, Berke L, Smit S, de Ridder D, van der Lee TAJ. The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool. BMC Genomics 2021; 22:265. [PMID: 33849459 PMCID: PMC8045196 DOI: 10.1186/s12864-021-07583-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/26/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Bacterial plant pathogens of the Pectobacterium genus are responsible for a wide spectrum of diseases in plants, including important crops such as potato, tomato, lettuce, and banana. Investigation of the genetic diversity underlying virulence and host specificity can be performed at genome level by using a comprehensive comparative approach called pangenomics. A pangenomic approach, using newly developed functionalities in PanTools, was applied to analyze the complex phylogeny of the Pectobacterium genus. We specifically used the pangenome to investigate genetic differences between virulent and avirulent strains of P. brasiliense, a potato blackleg causing species dominantly present in Western Europe. RESULTS Here we generated a multilevel pangenome for Pectobacterium, comprising 197 strains across 19 species, including type strains, with a focus on P. brasiliense. The extensive phylogenetic analysis of the Pectobacterium genus showed robust distinct clades, with most detail provided by 452,388 parsimony-informative single-nucleotide polymorphisms identified in single-copy orthologs. The average Pectobacterium genome consists of 47% core genes, 1% unique genes, and 52% accessory genes. Using the pangenome, we zoomed in on differences between virulent and avirulent P. brasiliense strains and identified 86 genes associated to virulent strains. We found that the organization of genes is highly structured and linked with gene conservation, function, and transcriptional orientation. CONCLUSION The pangenome analysis demonstrates that evolution in Pectobacteria is a highly dynamic process, including gene acquisitions partly in clusters, genome rearrangements, and loss of genes. Pectobacterium species are typically not characterized by a set of species-specific genes, but instead present themselves using new gene combinations from the shared gene pool. A multilevel pangenomic approach, fusing DNA, protein, biological function, taxonomic group, and phenotypes, facilitates studies in a flexible taxonomic context.
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Affiliation(s)
- Eef M Jonkheer
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Balázs Brankovics
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Ilse M Houwers
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jan M van der Wolf
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Peter J M Bonants
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Robert A M Vreeburg
- Nederlandse Algemene Keuringsdienst voor zaaizaad en pootgoed van landbouwgewassen, Randweg 14, 8304 AS, Emmeloord, The Netherlands
| | - Robert Bollema
- Nederlandse Algemene Keuringsdienst voor zaaizaad en pootgoed van landbouwgewassen, Randweg 14, 8304 AS, Emmeloord, The Netherlands
| | - Jorn R de Haan
- Genetwister Technologies B.V, Nieuwe Kanaal 7b, 6709 PA, Wageningen, The Netherlands
| | - Lidija Berke
- Genetwister Technologies B.V, Nieuwe Kanaal 7b, 6709 PA, Wageningen, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Theo A J van der Lee
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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Ma Y, Chhapekar SS, Lu L, Oh S, Singh S, Kim CS, Kim S, Choi GJ, Lim YP, Choi SR. Genome-wide identification and characterization of NBS-encoding genes in Raphanus sativus L. and their roles related to Fusarium oxysporum resistance. BMC PLANT BIOLOGY 2021; 21:47. [PMID: 33461498 PMCID: PMC7814608 DOI: 10.1186/s12870-020-02803-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/16/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND The nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes are important for plant development and disease resistance. Although genome-wide studies of NBS-encoding genes have been performed in several species, the evolution, structure, expression, and function of these genes remain unknown in radish (Raphanus sativus L.). A recently released draft R. sativus L. reference genome has facilitated the genome-wide identification and characterization of NBS-encoding genes in radish. RESULTS A total of 225 NBS-encoding genes were identified in the radish genome based on the essential NB-ARC domain through HMM search and Pfam database, with 202 mapped onto nine chromosomes and the remaining 23 localized on different scaffolds. According to a gene structure analysis, we identified 99 NBS-LRR-type genes and 126 partial NBS-encoding genes. Additionally, 80 and 19 genes respectively encoded an N-terminal Toll/interleukin-like domain and a coiled-coil domain. Furthermore, 72% of the 202 NBS-encoding genes were grouped in 48 clusters distributed in 24 crucifer blocks on chromosomes. The U block on chromosomes R02, R04, and R08 had the most NBS-encoding genes (48), followed by the R (24), D (23), E (23), and F (17) blocks. These clusters were mostly homogeneous, containing NBS-encoding genes derived from a recent common ancestor. Tandem (15 events) and segmental (20 events) duplications were revealed in the NBS family. Comparative evolutionary analyses of orthologous genes among Arabidopsis thaliana, Brassica rapa, and Brassica oleracea reflected the importance of the NBS-LRR gene family during evolution. Moreover, examinations of cis-elements identified 70 major elements involved in responses to methyl jasmonate, abscisic acid, auxin, and salicylic acid. According to RNA-seq expression analyses, 75 NBS-encoding genes contributed to the resistance of radish to Fusarium wilt. A quantitative real-time PCR analysis revealed that RsTNL03 (Rs093020) and RsTNL09 (Rs042580) expression positively regulates radish resistance to Fusarium oxysporum, in contrast to the negative regulatory role for RsTNL06 (Rs053740). CONCLUSIONS The NBS-encoding gene structures, tandem and segmental duplications, synteny, and expression profiles in radish were elucidated for the first time and compared with those of other Brassicaceae family members (A. thaliana, B. oleracea, and B. rapa) to clarify the evolution of the NBS gene family. These results may be useful for functionally characterizing NBS-encoding genes in radish.
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Affiliation(s)
- Yinbo Ma
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Sushil Satish Chhapekar
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Lu Lu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Sangheon Oh
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Sonam Singh
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Chang Soo Kim
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Seungho Kim
- Neo Seed Co., 256-45 Jingeonjung-gil, Gongdo-eup, Anseong, Gyeonggi Province 17565 Republic of Korea
| | - Gyung Ja Choi
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, 34114 Republic of Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Su Ryun Choi
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134 Republic of Korea
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Rodríguez Gama A, Miller T, Halfmann R. Mechanics of a molecular mousetrap-nucleation-limited innate immune signaling. Biophys J 2021; 120:1150-1160. [PMID: 33460595 PMCID: PMC8059202 DOI: 10.1016/j.bpj.2021.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/17/2022] Open
Abstract
Innate immune responses, such as cell death and inflammatory signaling, are typically switch-like in nature. They also involve "prion-like" self-templating polymerization of one or more signaling proteins into massive macromolecular assemblies known as signalosomes. Despite the wealth of atomic-resolution structural information on signalosomes, how the constituent polymers nucleate and whether the switch-like nature of that event at the molecular scale relates to the digital nature of innate immune signaling at the cellular scale remains unknown. In this perspective, we review current knowledge of innate immune signalosome assembly, with an emphasis on structural constraints that allow the proteins to accumulate in inactive soluble forms poised for abrupt polymerization. We propose that structurally encoded nucleation barriers to protein polymerization kinetically regulate the corresponding pathways, which allows for extremely sensitive, rapid, and decisive signaling upon pathogen detection. We discuss how nucleation barriers satisfy the rigorous on-demand functions of the innate immune system but also predispose the system to precocious activation that may contribute to progressive age-associated inflammation.
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Affiliation(s)
| | - Tayla Miller
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Randal Halfmann
- Stowers Institute for Medical Research, Kansas City, Missouri; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas.
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Abstract
ABSTRACT Host cells recognize molecules that signal danger using pattern recognition receptors (PRRs). Toll-like receptors (TLRs) are the most studied class of PRRs and detect pathogen-associated molecular patterns and danger-associated molecular patterns. Cellular TLR activation and signal transduction can therefore contain, combat, and clear danger by enabling appropriate gene transcription. Here, we review the expression, regulation, and function of different TLRs, with an emphasis on TLR-4, and how TLR adaptor protein binding directs intracellular signaling resulting in activation or termination of an innate immune response. Finally, we highlight the recent progress of research on the involvement of S100 proteins as ligands for TLR-4 in inflammatory disease.
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NOD-like receptor-mediated plant immunity: from structure to cell death. Nat Rev Immunol 2020; 21:305-318. [PMID: 33293618 DOI: 10.1038/s41577-020-00473-z] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2020] [Indexed: 12/25/2022]
Abstract
Animal and plant immune systems use intracellular nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) to detect pathogens, resulting in the activation of immune responses that are often associated with localized host cell death. Whereas vertebrate NLRs detect evolutionarily conserved molecular patterns and have undergone comparatively little copy number expansion, plant NLRs detect virulence factors that have often diversified in plant pathogen populations, and thus plant NLRs have been subject to parallel diversification. Plant NLRs sense the presence of virulence factors with enzymatic virulence activity often indirectly through their modification of host target proteins. By contrast, phytopathogenic virulence factors without enzymatic activity are usually recognized by NLRs directly by their structure. Structural and biochemical analyses have shown that both indirect and direct recognition of plant pathogens trigger the oligomerization of plant NLRs into active complexes. Assembly into three-layered ring-like structures has emerged as a common principle of NLR activation in plants and animals, but with distinct amino-terminal domains initiating different signalling pathways. Collectively, these analyses point to host cell membranes as a convergence point for activated plant NLRs and the disruption of cellular ion homeostasis as a possible major factor in NLR-triggered cell death signalling.
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Alaidarous M. In silico structural homology modeling and characterization of multiple N-terminal domains of selected bacterial Tcps. PeerJ 2020; 8:e10143. [PMID: 33194392 PMCID: PMC7646307 DOI: 10.7717/peerj.10143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/19/2020] [Indexed: 11/20/2022] Open
Abstract
Several bacterial pathogens produce Toll/interleukin-1 receptor (TIR) domain-containing protein homologs that are important for subverting the Toll-like receptor (TLR) signaling cascades in hosts. Consequently, promoting the persistence and survival of the bacterial pathogens. However, the exact molecular mechanisms elucidating the functional characteristics of these bacterial proteins are not clear. Physicochemical and homology modeling characterization studies have been conducted to predict the conditions suitable for the stability and purification of these proteins and to predict their structural properties. The outcomes of these studies have provided important preliminary data for the drug discovery pipeline projects. Here, using in silico physicochemical and homology modeling tools, we have reported the primary, secondary and tertiary structural characteristics of multiple N-terminal domains of selected bacterial TIR domain-containing proteins (Tcps). The results show variations between the primary amino acid sequences, secondary structural components and three-dimensional models of the proteins, suggesting the role of different molecular mechanisms in the functioning of these proteins in subverting the host immune system. This study could form the basis of future experimental studies advancing our understanding of the molecular basis of the inhibition of the host immune response by the bacterial Tcps.
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Affiliation(s)
- Mohammed Alaidarous
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, Saudi Arabia.,Health and Basic Sciences Research Center, Majmaah University, Majmaah, Saudi Arabia
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Chakraborty J, Ghosh P. Advancement of research on plant NLRs evolution, biochemical activity, structural association, and engineering. PLANTA 2020; 252:101. [PMID: 33180185 DOI: 10.1007/s00425-020-03512-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
In this review, we have included evolution of plant intracellular immune receptors, oligomeric complex formation, enzymatic action, engineering, and mechanisms of immune inspection for appropriate defense outcomes. NLR (Nucleotide binding oligomerization domain containing leucine-rich repeat) proteins are the intracellular immune receptors that recognize pathogen-derived virulence factors to confer effector-triggered immunity (ETI). Activation of plant defense by the NLRs are often conveyed through N-terminal Toll-like/ IL-1 receptor (TIR) or non-TIR (coiled-coils or CC) domains. Homodimerization or self-association property of CC/ TIR domains of plant NLRs contribute to their auto-activity and induction of in planta ectopic cell death. High resolution crystal structures of Arabidopsis thaliana RPS4TIR, L6TIR, SNC1TIR, RPP1TIR and Muscadinia rotundifolia RPV1TIR showed that interaction is mediated through one or two distinct interfaces i.e., αA and αE helices comprise AE interface and αD and αE helices were found to form DE interface. By contrast, conserved helical regions were determined for CC domains of plant NLRs. Evolutionary history of NLRs diversification has shown that paired forms were originated from NLR singletons. Plant TIRs executed NAD+ hydrolysis activity for cell death promotion. Plant NLRs were found to form large oligomeric complexes as observed in animal inflammasomes. We have also discussed different protein engineering methods includes domain shuffling, and decoy modification that increase effector recognition spectrum of plant NLRs. In summary, our review highlights structural basis of perception of the virulence factors by NLRs or NLR pairs to design novel classes of plant immune receptors.
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Affiliation(s)
| | - Prithwi Ghosh
- Department of Botany, Narajole Raj College, Narajole, Paschim Medinipur, 721211, West Bengal, India
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40
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Bentham AR, De la Concepcion JC, Mukhi N, Zdrzałek R, Draeger M, Gorenkin D, Hughes RK, Banfield MJ. A molecular roadmap to the plant immune system. J Biol Chem 2020; 295:14916-14935. [PMID: 32816993 PMCID: PMC7606695 DOI: 10.1074/jbc.rev120.010852] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/17/2020] [Indexed: 12/15/2022] Open
Abstract
Plant diseases caused by pathogens and pests are a constant threat to global food security. Direct crop losses and the measures used to control disease (e.g. application of pesticides) have significant agricultural, economic, and societal impacts. Therefore, it is essential that we understand the molecular mechanisms of the plant immune system, a system that allows plants to resist attack from a wide variety of organisms ranging from viruses to insects. Here, we provide a roadmap to plant immunity, with a focus on cell-surface and intracellular immune receptors. We describe how these receptors perceive signatures of pathogens and pests and initiate immune pathways. We merge existing concepts with new insights gained from recent breakthroughs on the structure and function of plant immune receptors, which have generated a shift in our understanding of cell-surface and intracellular immunity and the interplay between the two. Finally, we use our current understanding of plant immunity as context to discuss the potential of engineering the plant immune system with the aim of bolstering plant defenses against disease.
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Affiliation(s)
- Adam R Bentham
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | | | - Nitika Mukhi
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Rafał Zdrzałek
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Markus Draeger
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Danylo Gorenkin
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Richard K Hughes
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom.
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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] [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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Peng Y, Chen T, Luo L, Li L, Cao W, Xu X, Zhang Y, Yue P, Dai X, Ji Z, Jian M, Bai R, Ding Z, Wang F, Wen S, Zhou G, Kong J, Luo S, Liu A, Bao F. Isoforskolin and Cucurbitacin IIa promote the expression of anti-inflammatory regulatory factor SIGIRR in human macrophages stimulated with Borrelia burgdorferi basic membrane protein A. Int Immunopharmacol 2020; 88:106914. [PMID: 32829087 DOI: 10.1016/j.intimp.2020.106914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/01/2020] [Accepted: 08/16/2020] [Indexed: 11/29/2022]
Abstract
Certain natural products, derived from medicinal plants, exhibit anti-inflammatory properties, but the mechanism of action of many remains unclear. Borrelia burgdorferi spirochetes are responsible for causing Lyme arthritis through activation of the Toll-like receptor (TLR) signaling pathway. In this study, we investigated the mechanisms by which Isoforskolin (ISOF) and Cucurbitacin IIa (CuIIa), compounds derived from Chinese herbs, can exert anti-inflammatory effects by modulating single immunoglobulin interleukin-1 receptor-related receptor (SIGIRR; also known as Toll/interleukin-1 receptor 8, TIR8) and thereby inhibiting B. burgdorferi basic membrane protein A (BmpA)-induced TLR signaling in human macrophages, specifically the THP-1 human monocytic cell line. After THP-1 cells were exposed in vitro to: i) recombinant (r)BmpA, ii) rBmpA and ISOF or iii) rBmpA and CuIIa, Cytotoxicity assay (Cell Counting Kit-8, CCK-8) are used to measure the effects of ISOF and CuIIa on cell viability. Meanwhile, real-time polymerase chain reaction and Western blotting were used to quantify SIGIRR mRNA and protein levels, respectively, at 6, 12, 24 and 48 h time points post-stimulation. In addition, proinflammatory cytokine tumor necrosis factor-α (TNF-α) was determined by ELISA analysis. Our study showed that rBmpA stimulation of THP-1 cells resulted in a drop in SIGIRR levels in THP-1 cells. More importantly, SIGIRR levels increased significantly in rBmpA-stimulated THP-1 cells following ISOF or CuIIa administration, and the results of ELISA analysis suggested that ISOF or CuIIa reduced the secretion of the proinflammatory cytokine TNF-α. In conclusion, These results reveal new possibilities for the treatment of Lyme arthritis.
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Affiliation(s)
- Yun Peng
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Taigui Chen
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Lisha Luo
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China
| | - Lianbao Li
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Wenjing Cao
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China
| | - Xin Xu
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Yu Zhang
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Peng Yue
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China
| | - Xiting Dai
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Zhenhua Ji
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Miaomiao Jian
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China
| | - Ruolan Bai
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China
| | - Zhe Ding
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Feng Wang
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Shiyuan Wen
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Guozhong Zhou
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Jing Kong
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China
| | - Suyi Luo
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China
| | - Aihua Liu
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming 650500, China; Yunnan Province Key Laboratory of Children's Major Diseases Research, The Children's Hospital of Kunming/Kunming Medical University, Kunming 650030, China; The Institute for Tropical Medicine, Kunming Medical University, Kunming 650500, China; Yunnan Demonstration Base of International Science and Technology Cooperation for Tropical Diseases, Kunming 650500, China.
| | - Fukai Bao
- Department of Microbiology and Immunology, Kunming Medical University, Kunming 650500, China; Yunnan Province Key Laboratory of Children's Major Diseases Research, The Children's Hospital of Kunming/Kunming Medical University, Kunming 650030, China; The Institute for Tropical Medicine, Kunming Medical University, Kunming 650500, China; Yunnan Demonstration Base of International Science and Technology Cooperation for Tropical Diseases, Kunming 650500, China.
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43
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Ghosh SK, Saha B, Banerjee R. Insight into the sequence-structure relationship of TLR cytoplasm's Toll/Interleukin-1 receptor domain towards understanding the conserved functionality of TLR 2 heterodimer in mammals. J Biomol Struct Dyn 2020; 39:5348-5357. [PMID: 32643540 DOI: 10.1080/07391102.2020.1786457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The signaling response of TLR2 to ligands has always been as a homodimer or in heterodimerization with TLR1/TLR6. The Toll/Interleukin-1 Receptor (TIR) domain of the TLR cytoplasmic region regulates the dimerization and interactions with adaptor molecules to build an active signaling complex. To understand the conservation of functionality of the TLR2-heterodimers between the distantly related species human(h) and mice(m), the pattern of TIR-TIR interaction in heterodimers has been studied through the sequence-structural point of view. Comparative analysis of primary sequence and structural pattern of TLRs(1/2/6) corroborates higher sequence homology between TLR1 and TLR6. Molecular docking analysis of TLR2-TLR1 and TLR2-TLR6 cytoplasmic dimers in both mouse and human have identified that for interaction the BB loop/near-BB loop residues of TLR2 are involved with the near-DD loop of TLR1 and DD loop residues of TLR6 within the TIR domains, which may cause to differential signaling. Molecular dynamics simulation of dimers for both human and mice species recognize stable interface between near-BB/BB loop region of TLR2 and discrete near-DD and DD loop region of TLR1 and TLR6 respectively. The observed dimerization pattern in both the species is further supported by Alanine scanning mutation study. However, Solvent Accessible Surface Area (SASA) of BB and DD loop regions of the cytoplasmic monomers and the heterodimers suggests that while TLR2 BB loop is actively associated as the dimer interface with its heterodimer partners in both the species, the DD loop acts as the active interfacing region in hTLR1 and mTLR6. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soumya Kanti Ghosh
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Kolkata, India
| | | | - Raja Banerjee
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Kolkata, India.,Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Kolkata, India
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44
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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: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [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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45
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Bayless AM, Nishimura MT. Enzymatic Functions for Toll/Interleukin-1 Receptor Domain Proteins in the Plant Immune System. Front Genet 2020; 11:539. [PMID: 32582284 PMCID: PMC7282519 DOI: 10.3389/fgene.2020.00539] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/04/2020] [Indexed: 01/09/2023] Open
Abstract
Rationally engineered improvements to crop plants will be needed to keep pace with increasing demands placed on agricultural systems by population growth and climate change. Engineering of plant immune systems provides an opportunity to increase yields by limiting losses to pathogens. Intracellular immune receptors are commonly used as agricultural disease resistance traits. Despite their importance, how intracellular immune receptors confer disease resistance is still unknown. One major class of immune receptors in dicots contains a Toll/Interleukin-1 Receptor (TIR) domain. The mechanisms of TIR-containing proteins during plant immunity have remained elusive. The TIR domain is an ancient module found in archaeal, bacterial and eukaryotic proteins. In animals, TIR domains serve a structural role by generating innate immune signaling complexes. The unusual animal TIR-protein, SARM1, was recently discovered to function instead as an enzyme that depletes cellular NAD+ (nicotinamide adenine dinucleotide) to trigger axonal cell death. Two recent reports have found that plant TIR proteins also have the ability to cleave NAD+. This presents a new paradigm from which to consider how plant TIR immune receptors function. Here, we will review recent reports of the structure and function of TIR-domain containing proteins. Intriguingly, it appears that TIR proteins in all kingdoms may use similar enzymatic mechanisms in a variety of cell death and immune pathways. We will also discuss TIR structure–function hypotheses in light of the recent publication of the ZAR1 resistosome structure. Finally, we will explore the evolutionary context of plant TIR-containing proteins and their downstream signaling components across phylogenies and the functional implications of these findings.
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Affiliation(s)
- Adam M Bayless
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Marc T Nishimura
- Department of Biology, Colorado State University, Fort Collins, CO, United States
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46
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The TIR-domain containing effectors BtpA and BtpB from Brucella abortus impact NAD metabolism. PLoS Pathog 2020; 16:e1007979. [PMID: 32298382 PMCID: PMC7188309 DOI: 10.1371/journal.ppat.1007979] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 04/28/2020] [Accepted: 03/26/2020] [Indexed: 12/20/2022] Open
Abstract
Brucella species are facultative intracellular Gram-negative bacteria relevant to animal and human health. Their ability to establish an intracellular niche and subvert host cell pathways to their advantage depends on the delivery of bacterial effector proteins through a type IV secretion system. Brucella Toll/Interleukin-1 Receptor (TIR)-domain-containing proteins BtpA (also known as TcpB) and BtpB are among such effectors. Although divergent in primary sequence, they interfere with Toll-like receptor (TLR) signaling to inhibit the innate immune responses. However, the molecular mechanisms implicated still remain unclear. To gain insight into the functions of BtpA and BtpB, we expressed them in the budding yeast Saccharomyces cerevisiae as a eukaryotic cell model. We found that both effectors were cytotoxic and that their respective TIR domains were necessary and sufficient for yeast growth inhibition. Growth arrest was concomitant with actin depolymerization, endocytic block and a general decrease in kinase activity in the cell, suggesting a failure in energetic metabolism. Indeed, levels of ATP and NAD+ were low in yeast cells expressing BtpA and BtpB TIR domains, consistent with the recently described enzymatic activity of some TIR domains as NAD+ hydrolases. In human epithelial cells, both BtpA and BtpB expression reduced intracellular total NAD levels. In infected cells, both BtpA and BtpB contributed to reduction of total NAD, indicating that their NAD+ hydrolase functions are active intracellularly during infection. Overall, combining the yeast model together with mammalian cells and infection studies our results show that BtpA and BtpB modulate energy metabolism in host cells through NAD+ hydrolysis, assigning a novel role for these TIR domain-containing effectors in Brucella pathogenesis. Brucella is a genus of zoonotic bacteria that cause severe disease in a variety of mammals, ranging from farm animals (as bovines, swine and ovine) to marine mammals. Transmission to humans, often by ingestion of non-treated dairy products, leads to serious systemic infection. Brucella abortus invades host cells and replicates intracellularly. Such behavior relies on the injection of bacterial proteins into the host cytoplasm via specialized secretion systems. Our work focuses on the study of two of these factors, BtpA and BtpB, previously described to contain Toll/Interleukin-1 Receptor (TIR)-domains that modulate innate immunity. We use here two biological models: the yeast Saccharomyces cerevisiae and human cell lines. We found that the TIR domains of both Brucella proteins were necessary and sufficient to collapse energy metabolism in yeast by depleting ATP and NAD+. This result was translatable to higher cells and consistent with the recently described NADase activity of some TIR domains both in mammalian and bacterial proteins. Importantly, we demonstrate that Brucella down-regulates total NAD levels in host cells by using both BtpA and BtpB effectors. Our results show that NAD+ is targeted by Brucella during infection, which may constitute a novel mechanism for its pathogenicity.
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Dolatabadian A, Bayer PE, Tirnaz S, Hurgobin B, Edwards D, Batley J. Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:969-982. [PMID: 31553100 PMCID: PMC7061875 DOI: 10.1111/pbi.13262] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 08/30/2019] [Accepted: 09/13/2019] [Indexed: 05/18/2023]
Abstract
Methods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor-bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R-genes harbour more SNPs than variable genes. More nucleotide binding site-leucine-rich repeat (NBS-LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics-based improvement and improved disease resistance.
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Affiliation(s)
- Aria Dolatabadian
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Philipp E. Bayer
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Soodeh Tirnaz
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Bhavna Hurgobin
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Jacqueline Batley
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
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48
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Purifying selection shaping the evolution of the Toll-like receptor 2 TIR domain in brown hares (Lepus europaeus) from Europe and the Middle East. Mol Biol Rep 2020; 47:2975-2984. [PMID: 32236892 DOI: 10.1007/s11033-020-05382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 03/19/2020] [Indexed: 10/24/2022]
Abstract
Toll-like receptors (TLRs) are transmembrane proteins of the innate immune system, composed of the ectodomain involved in pathogen recognition and the intracellular Toll/interleukin-1 receptor (TIR) domain important for downstream signal transduction. Here, we analyze the genetic variability of TIR nucleotide and amino-acid sequences of the TLR2 gene in 243 brown hares from Europe and the Middle East and tested for the presence of selection signals and spatial structuring. TLR2 TIR domain sequences were PCR amplified and sequenced, while genotyping was performed by phasing. Genetic diversity indices were calculated in DnaSP and Arlequin, while presence of selection signals was tested using MEGA and the Datamonkey web server. The presence of spatial patterns in TIR sequence distribution was tested by spatial Principal Component Analysis (sPCA) in adegenet. A total of 13 haplotypes were revealed with haplotype diversity of 0.424, and nucleotide diversity (π) of 0.00138. Two spatial clusters were revealed: "Anatolia/Middle East" and "Europe". In Anatolia the two most prevalent amino-acid variants, A and B (the latter being the most ancestral) were maintained at similar frequencies; but in Europe a shift in genotype frequencies was observed as well as a higher number of nonsynonymous substitutions giving rise to novel amino-acid protein variants originating from the evolutionarily younger protein variant. Molecular diversity (haplotype and nucleotide diversity) indices were significantly higher in the "Anatolia/Middle East" cluster. A signal of purifying selection was detected acting on the TIR sequences.
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49
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Gusev EY, Zotova NV. Cellular Stress and General Pathological Processes. Curr Pharm Des 2020; 25:251-297. [PMID: 31198111 DOI: 10.2174/1381612825666190319114641] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/13/2019] [Indexed: 02/06/2023]
Abstract
From the viewpoint of the general pathology, most of the human diseases are associated with a limited number of pathogenic processes such as inflammation, tumor growth, thrombosis, necrosis, fibrosis, atrophy, pathological hypertrophy, dysplasia and metaplasia. The phenomenon of chronic low-grade inflammation could be attributed to non-classical forms of inflammation, which include many neurodegenerative processes, pathological variants of insulin resistance, atherosclerosis, and other manifestations of the endothelial dysfunction. Individual and universal manifestations of cellular stress could be considered as a basic element of all these pathologies, which has both physiological and pathophysiological significance. The review examines the causes, main phenomena, developmental directions and outcomes of cellular stress using a phylogenetically conservative set of genes and their activation pathways, as well as tissue stress and its role in inflammatory and para-inflammatory processes. The main ways towards the realization of cellular stress and its functional blocks were outlined. The main stages of tissue stress and the classification of its typical manifestations, as well as its participation in the development of the classical and non-classical variants of the inflammatory process, were also described. The mechanisms of cellular and tissue stress are structured into the complex systems, which include networks that enable the exchange of information with multidirectional signaling pathways which together make these systems internally contradictory, and the result of their effects is often unpredictable. However, the possible solutions require new theoretical and methodological approaches, one of which includes the transition to integral criteria, which plausibly reflect the holistic image of these processes.
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Affiliation(s)
- Eugeny Yu Gusev
- Laboratory of the Immunology of Inflammation, Institute of Immunology and Physiology, Yekaterinburg, Russian Federation
| | - Natalia V Zotova
- Laboratory of the Immunology of Inflammation, Institute of Immunology and Physiology, Yekaterinburg, Russian Federation.,Department of Medical Biochemistry and Biophysics, Ural Federal University named after B.N.Yeltsin, Yekaterinburg, Russian Federation
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50
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Toshchakov VY, Neuwald AF. A survey of TIR domain sequence and structure divergence. Immunogenetics 2020; 72:181-203. [PMID: 32002590 PMCID: PMC7075850 DOI: 10.1007/s00251-020-01157-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/20/2020] [Indexed: 12/31/2022]
Abstract
Toll-interleukin-1R resistance (TIR) domains are ubiquitously present in all forms of cellular life. They are most commonly found in signaling proteins, as units responsible for signal-dependent formation of protein complexes that enable amplification and spatial propagation of the signal. A less common function of TIR domains is their ability to catalyze nicotinamide adenine dinucleotide degradation. This survey analyzes 26,414 TIR domains, automatically classified based on group-specific sequence patterns presumably determining biological function, using a statistical approach termed Bayesian partitioning with pattern selection (BPPS). We examine these groups and patterns in the light of available structures and biochemical analyses. Proteins within each of thirteen eukaryotic groups (10 metazoans and 3 plants) typically appear to perform similar functions, whereas proteins within each prokaryotic group typically exhibit diverse domain architectures, suggesting divergent functions. Groups are often uniquely characterized by structural fold variations associated with group-specific sequence patterns and by herein identified sequence motifs defining TIR domain functional divergence. For example, BPPS identifies, in helices C and D of TIRAP and MyD88 orthologs, conserved surface-exposed residues apparently responsible for specificity of TIR domain interactions. In addition, BPPS clarifies the functional significance of the previously described Box 2 and Box 3 motifs, each of which is a part of a larger, group-specific block of conserved, intramolecularly interacting residues.
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Affiliation(s)
- Vladimir Y Toshchakov
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Andrew F Neuwald
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
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