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Schelle L, Côrte-Real JV, Fayyaz S, del Pozo Ben A, Shnipova M, Petersen M, Lotke R, Menon B, Matzek D, Pfaff L, Pinheiro A, Marques JP, Melo-Ferreira J, Popper B, Esteves PJ, Sauter D, Abrantes J, Baldauf HM. Evolutionary and functional characterization of lagomorph guanylate-binding proteins: a story of gain and loss and shedding light on expression, localization and innate immunity-related functions. Front Immunol 2024; 15:1303089. [PMID: 38348040 PMCID: PMC10859415 DOI: 10.3389/fimmu.2024.1303089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/04/2024] [Indexed: 02/15/2024] Open
Abstract
Guanylate binding proteins (GBPs) are an evolutionarily ancient family of proteins that are widely distributed among eukaryotes. They belong to the dynamin superfamily of GTPases, and their expression can be partially induced by interferons (IFNs). GBPs are involved in the cell-autonomous innate immune response against bacterial, parasitic and viral infections. Evolutionary studies have shown that GBPs exhibit a pattern of gene gain and loss events, indicative for the birth-and-death model of evolution. Most species harbor large GBP gene clusters that encode multiple paralogs. Previous functional and in-depth evolutionary studies have mainly focused on murine and human GBPs. Since rabbits are another important model system for studying human diseases, we focus here on lagomorphs to broaden our understanding of the multifunctional GBP protein family by conducting evolutionary analyses and performing a molecular and functional characterization of rabbit GBPs. We observed that lagomorphs lack GBP3, 6 and 7. Furthermore, Leporidae experienced a loss of GBP2, a unique duplication of GBP5 and a massive expansion of GBP4. Gene expression analysis by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and transcriptome data revealed that leporid GBP expression varied across tissues. Overexpressed rabbit GBPs localized either uniformly and/or discretely to the cytoplasm and/or to the nucleus. Oryctolagus cuniculus (oc)GBP5L1 and rarely ocGBP5L2 were an exception, colocalizing with the trans-Golgi network (TGN). In addition, four ocGBPs were IFN-inducible and only ocGBP5L2 inhibited furin activity. In conclusion, from an evolutionary perspective, lagomorph GBPs experienced multiple gain and loss events, and the molecular and functional characteristics of ocGBP suggest a role in innate immunity.
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Affiliation(s)
- Luca Schelle
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - João Vasco Côrte-Real
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Sharmeen Fayyaz
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
- National Institute of Virology, International Center of Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Augusto del Pozo Ben
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Margarita Shnipova
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Moritz Petersen
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Rishikesh Lotke
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Bhavna Menon
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Dana Matzek
- Biomedical Center (BMC), Core facility Animal Models (CAM), Faculty of Medicine, LMU München, Munich, Germany
| | - Lena Pfaff
- Biomedical Center (BMC), Core facility Animal Models (CAM), Faculty of Medicine, LMU München, Munich, Germany
| | - Ana Pinheiro
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - João Pedro Marques
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- ISEM, University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - José Melo-Ferreira
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Bastian Popper
- Biomedical Center (BMC), Core facility Animal Models (CAM), Faculty of Medicine, LMU München, Munich, Germany
| | - Pedro José Esteves
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- CITS - Center of Investigation in Health Technologies, CESPU, Gandra, Portugal
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Joana Abrantes
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
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2
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Schumann W, Loschwitz J, Reiners J, Degrandi D, Legewie L, Stühler K, Pfeffer K, Poschmann G, Smits SHJ, Strodel B. Integrative modeling of guanylate binding protein dimers. Protein Sci 2023; 32:e4818. [PMID: 37916607 PMCID: PMC10683561 DOI: 10.1002/pro.4818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 11/03/2023]
Abstract
Guanylate-binding proteins (GBPs) are essential interferon-γ-activated large GTPases that play a crucial role in host defense against intracellular bacteria and parasites. While their protective functions rely on protein polymerization, our understanding of the structural intricacies of these multimerized states remains limited. To bridge this knowledge gap, we present dimer models for human GBP1 (hGBP1) and murine GBP2 and 7 (mGBP2 and mGBP7) using an integrative approach, incorporating the crystal structure of hGBP1's GTPase domain dimer, crosslinking mass spectrometry, small-angle X-ray scattering, protein-protein docking, and molecular dynamics simulations. Our investigation begins by comparing the protein dynamics of hGBP1, mGBP2, and mGBP7. We observe that the M/E domain in all three proteins exhibits significant mobility and hinge motion, with mGBP7 displaying a slightly less pronounced motion but greater flexibility in its GTPase domain. These dynamic distinctions can be attributed to variations in the sequences of mGBP7 and hGBP1/mGBP2, resulting in different dimerization modes. Unlike hGBP1 and its close ortholog mGBP2, which exclusively dimerize through their GTPase domains, we find that mGBP7 exhibits three equally probable alternative dimer structures. The GTPase domain of mGBP7 is only partially involved in its dimerization, primarily due to an accumulation of negative charge, allowing mGBP7 to dimerize independently of GTP. Instead, mGBP7 exhibits a strong tendency to dimerize in an antiparallel arrangement across its stalks. The results of this work go beyond the sequence-structure-function relationship, as the sequence differences in mGBP7 and mGBP2/hGBP1 do not lead to different structures, but to different protein dynamics and dimerization. The distinct GBP dimer structures are expected to encode specific functions crucial for disrupting pathogen membranes.
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Affiliation(s)
- Wibke Schumann
- Institute of Theoretical and Computational ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute of Biological Information Processing: Structural BiochemistryForschungszentrum JülichJülichGermany
| | - Jennifer Loschwitz
- Institute of Theoretical and Computational ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute of Biological Information Processing: Structural BiochemistryForschungszentrum JülichJülichGermany
| | - Jens Reiners
- Center for Structural StudiesHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Daniel Degrandi
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine UniversityDüsseldorfGermany
| | - Larissa Legewie
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine UniversityDüsseldorfGermany
| | - Kai Stühler
- Institute of Molecular Medicine, Proteome ResearchMedical Faculty and University Hospital Düsseldorf, Heinrich Heine University DüsseldorfDüsseldorfGermany
- Molecular Proteomics Laboratory, Biomedical Research Centre (BMFZ)Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine UniversityDüsseldorfGermany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome ResearchMedical Faculty and University Hospital Düsseldorf, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Sander H. J. Smits
- Center for Structural StudiesHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute for BiochemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Birgit Strodel
- Institute of Theoretical and Computational ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute of Biological Information Processing: Structural BiochemistryForschungszentrum JülichJülichGermany
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3
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Valeva SV, Degabriel M, Michal F, Gay G, Rohde JR, Randow F, Lagrange B, Henry T. Comparative study of GBP recruitment on two cytosol-dwelling pathogens, Francisella novicida and Shigella flexneri highlights differences in GBP repertoire and in GBP1 motif requirements. Pathog Dis 2023; 81:ftad005. [PMID: 37012222 DOI: 10.1093/femspd/ftad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
Guanylate-Binding Proteins are interferon-inducible GTPases that play a key role in cell autonomous responses against intracellular pathogens. Despite sharing high sequence similarity, subtle differences among GBPs translate into functional divergences that are still largely not understood. A key GBP feature is the formation of supramolecular GBP complexes on the bacterial surface. Such complexes are observed when GBP1 binds lipopolysaccharide (LPS) from Shigella and Salmonella and further recruits GBP2-4. Here, we compared GBP recruitment on two cytosol-dwelling pathogens, Francisella novicida and S. flexneri. Francisella novicida was coated by GBP1 and GBP2 and to a lower extent by GBP4 in human macrophages. Contrary to S. flexneri, F. novicida was not targeted by GBP3, a feature independent of T6SS effectors. Multiple GBP1 features were required to promote targeting to F. novicida while GBP1 targeting to S. flexneri was much more permissive to GBP1 mutagenesis suggesting that GBP1 has multiple domains that cooperate to recognize F. novicida atypical LPS. Altogether our results indicate that the repertoire of GBPs recruited onto specific bacteria is dictated by GBP-specific features and by specific bacterial factors that remain to be identified.
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Affiliation(s)
- Stanimira V Valeva
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ Lyon, F-69007, Lyon, France
| | - Manon Degabriel
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ Lyon, F-69007, Lyon, France
| | - Fanny Michal
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ Lyon, F-69007, Lyon, France
| | - Gabrielle Gay
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ Lyon, F-69007, Lyon, France
| | - John R Rohde
- Department of Microbiology and Immunology, Dalhousie University, Halifax, B3H 4R2, NS, Canada
| | - Felix Randow
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, CB2 0QH, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, CB2 0QH, Cambridge, United Kingdom
| | - Brice Lagrange
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ Lyon, F-69007, Lyon, France
| | - Thomas Henry
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ Lyon, F-69007, Lyon, France
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Loschwitz J, Steffens N, Wang X, Schäffler M, Pfeffer K, Degrandi D, Strodel B. Domain motions, dimerization, and membrane interactions of the murine guanylate binding protein 2. Sci Rep 2023; 13:679. [PMID: 36639389 PMCID: PMC9839784 DOI: 10.1038/s41598-023-27520-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Guanylate-binding proteins (GBPs) are a group of GTPases that are induced by interferon-[Formula: see text] and are crucial components of cell-autonomous immunity against intracellular pathogens. Here, we examine murine GBP2 (mGBP2), which we have previously shown to be an essential effector protein for the control of Toxoplasma gondii replication, with its recruitment through the membrane of the parasitophorous vacuole and its involvement in the destruction of this membrane likely playing a role. The overall aim of our work is to provide a molecular-level understanding of the mutual influences of mGBP2 and the parasitophorous vacuole membrane. To this end, we performed lipid-binding assays which revealed that mGBP2 has a particular affinity for cardiolipin. This observation was confirmed by fluorescence microscopy using giant unilamellar vesicles of different lipid compositions. To obtain an understanding of the protein dynamics and how this is affected by GTP binding, mGBP2 dimerization, and membrane binding, assuming that each of these steps are relevant for the function of the protein, we carried out standard as well as replica exchange molecular dynamics simulations with an accumulated simulation time of more than 30 μs. The main findings from these simulations are that mGBP2 features a large-scale hinge motion in its M/E domain, which is present in each of the studied protein states. When bound to a cardiolipin-containing membrane, this hinge motion is particularly pronounced, leading to an up and down motion of the M/E domain on the membrane, which did not occur on a membrane without cardiolipin. Our prognosis is that this up and down motion has the potential to destroy the membrane following the formation of supramolecular mGBP2 complexes on the membrane surface.
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Affiliation(s)
- Jennifer Loschwitz
- grid.411327.20000 0001 2176 9917Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Nora Steffens
- grid.411327.20000 0001 2176 9917Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Xue Wang
- grid.411327.20000 0001 2176 9917Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Moritz Schäffler
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Klaus Pfeffer
- grid.411327.20000 0001 2176 9917Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Daniel Degrandi
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Birgit Strodel
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany. .,Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425, Jülich, Germany.
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Honkala AT, Tailor D, Malhotra SV. Guanylate-Binding Protein 1: An Emerging Target in Inflammation and Cancer. Front Immunol 2020; 10:3139. [PMID: 32117203 PMCID: PMC7025589 DOI: 10.3389/fimmu.2019.03139] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/24/2019] [Indexed: 12/16/2022] Open
Abstract
Guanylate-binding protein 1 (GBP1) is a large GTPase of the dynamin superfamily involved in the regulation of membrane, cytoskeleton, and cell cycle progression dynamics. In many cell types, such as endothelial cells and monocytes, GBP1 expression is strongly provoked by interferon γ (IFNγ) and acts to restrain cellular proliferation in inflammatory contexts. In immunity, GBP1 activity is crucial for the maturation of autophagosomes infected by intracellular pathogens and the cellular response to pathogen-associated molecular patterns. In chronic inflammation, GBP1 activity inhibits endothelial cell proliferation even as it protects from IFNγ-induced apoptosis. A similar inhibition of proliferation has also been found in some tumor models, such as colorectal or prostate carcinoma mouse models. However, this activity appears to be context-dependent, as in other cancers, such as oral squamous cell carcinoma and ovarian cancer, GBP1 activity appears to anchor a complex, taxane chemotherapy resistance profile where its expression levels correlate with worsened prognosis in patients. This discrepancy in GBP1 function may be resolved by GBP1's involvement in the induction of a cellular senescence phenotype, wherein anti-proliferative signals coincide with potent resistance to apoptosis and set the stage for dysregulated proliferative mechanisms present in growing cancers to hijack GBP1 as a pro- chemotherapy treatment resistance (TXR) and pro-survival factor even in the face of continued cytotoxic treatment. While the structure of GBP1 has been extensively characterized, its roles in inflammation, TXR, senescence, and other biological functions remain under-investigated, although initial findings suggest that GBP1 is a compelling target for therapeutic intervention in a variety of conditions ranging from chronic inflammatory disorders to cancer.
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Affiliation(s)
- Alexander T Honkala
- Department of Radiation Oncology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Dhanir Tailor
- Department of Radiation Oncology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Sanjay V Malhotra
- Department of Radiation Oncology, School of Medicine, Stanford University, Stanford, CA, United States
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