1
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Sprankel L, Vizarraga D, Martín J, Manger S, Meier-Credo J, Marcos M, Julve J, Rotllan N, Scheffer MP, Escolà-Gil JC, Langer JD, Piñol J, Fita I, Frangakis AS. Essential protein P116 extracts cholesterol and other indispensable lipids for Mycoplasmas. Nat Struct Mol Biol 2023; 30:321-329. [PMID: 36782049 PMCID: PMC10023570 DOI: 10.1038/s41594-023-00922-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/06/2023] [Indexed: 02/15/2023]
Abstract
Mycoplasma pneumoniae, responsible for approximately 30% of community-acquired human pneumonia, needs to extract lipids from the host environment for survival and proliferation. Here, we report a comprehensive structural and functional analysis of the previously uncharacterized protein P116 (MPN_213). Single-particle cryo-electron microscopy of P116 reveals a homodimer presenting a previously unseen fold, forming a huge hydrophobic cavity, which is fully accessible to solvent. Lipidomics analysis shows that P116 specifically extracts lipids such as phosphatidylcholine, sphingomyelin and cholesterol. Structures of different conformational states reveal the mechanism by which lipids are extracted. This finding immediately suggests a way to control Mycoplasma infection by interfering with lipid uptake.
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Affiliation(s)
- Lasse Sprankel
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - David Vizarraga
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Spain
| | - Jesús Martín
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Spain
| | - Sina Manger
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | | | - Marina Marcos
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Josep Julve
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau and CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Noemi Rotllan
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau and CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Margot P Scheffer
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Joan Carles Escolà-Gil
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau and CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Julian D Langer
- Proteomics, Max Planck Institute of Biophysics, Frankfurt, Germany
- Proteomics, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Jaume Piñol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ignacio Fita
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Spain.
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany.
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2
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Vizarraga D, Torres-Puig S, Aparicio D, Pich OQ. The Sialoglycan Binding Adhesins of Mycoplasma genitalium and Mycoplasma pneumoniae. Trends Microbiol 2021; 29:477-481. [PMID: 33593698 DOI: 10.1016/j.tim.2021.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/23/2021] [Accepted: 01/25/2021] [Indexed: 01/20/2023]
Abstract
Mycoplasma genitalium (Mge) and Mycoplasma pneumoniae (Mpn) are two human pathogens associated with urogenital and respiratory tract infections, respectively. The recent elucidation of the tridimensional structure of their major cytoadhesins by X-ray crystallography and cryo-electron microscopy/tomography, has provided important insights regarding the mechanics of infection and evasion of immune surveillance.
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Affiliation(s)
- David Vizarraga
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Sergi Torres-Puig
- Research Unit of Molecular Microbiology (RUMM), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - David Aparicio
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain.
| | - Oscar Q Pich
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208 Sabadell, Spain; Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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3
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Vizarraga D, Kawamoto A, Matsumoto U, Illanes R, Pérez-Luque R, Martín J, Mazzolini R, Bierge P, Pich OQ, Espasa M, Sanfeliu I, Esperalba J, Fernández-Huerta M, Scheffer MP, Pinyol J, Frangakis AS, Lluch-Senar M, Mori S, Shibayama K, Kenri T, Kato T, Namba K, Fita I, Miyata M, Aparicio D. Immunodominant proteins P1 and P40/P90 from human pathogen Mycoplasma pneumoniae. Nat Commun 2020; 11:5188. [PMID: 33057023 PMCID: PMC7560827 DOI: 10.1038/s41467-020-18777-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Mycoplasma pneumoniae is a bacterial human pathogen that causes primary atypical pneumonia. M. pneumoniae motility and infectivity are mediated by the immunodominant proteins P1 and P40/P90, which form a transmembrane adhesion complex. Here we report the structure of P1, determined by X-ray crystallography and cryo-electron microscopy, and the X-ray structure of P40/P90. Contrary to what had been suggested, the binding site for sialic acid was found in P40/P90 and not in P1. Genetic and clinical variability concentrates on the N-terminal domain surfaces of P1 and P40/P90. Polyclonal antibodies generated against the mostly conserved C-terminal domain of P1 inhibited adhesion of M. pneumoniae, and serology assays with sera from infected patients were positive when tested against this C-terminal domain. P40/P90 also showed strong reactivity against human infected sera. The architectural elements determined for P1 and P40/P90 open new possibilities in vaccine development against M. pneumoniae infections.
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Affiliation(s)
- David Vizarraga
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Akihiro Kawamoto
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - U Matsumoto
- Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan
| | - Ramiro Illanes
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Rosa Pérez-Luque
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Jesús Martín
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Rocco Mazzolini
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain
| | - Paula Bierge
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208, Sabadell, Spain
| | - Oscar Q Pich
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208, Sabadell, Spain.,Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Mateu Espasa
- Departament de Microbiologia, Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208, Sabadell, Spain
| | - Isabel Sanfeliu
- Departament de Microbiologia, Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208, Sabadell, Spain
| | - Juliana Esperalba
- Departament de Microbiologia, Hospital Universitari Vall d´Hebron, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Miguel Fernández-Huerta
- Departament de Microbiologia, Hospital Universitari Vall d´Hebron, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Margot P Scheffer
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Jaume Pinyol
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain
| | - Shigetarou Mori
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Kenri
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takayuki Kato
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,RIKEN Center for Biosystems Dynamics Research and SPring-8 Center, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ignacio Fita
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan. .,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, 558-8585, Japan.
| | - David Aparicio
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain.
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4
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Vizarraga D, Pérez-Luque R, Martín J, Fita I, Aparicio D. Alternative conformation of the C-domain of the P140 protein from Mycoplasma genitalium. Acta Crystallogr F Struct Biol Commun 2020; 76:508-516. [PMID: 33135669 DOI: 10.1107/s2053230x20012297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/07/2020] [Indexed: 11/10/2022]
Abstract
The human pathogen Mycoplasma genitalium is responsible for urethritis in men, and for cervicitis and pelvic inflammatory disease in women. The adherence of M. genitalium to host target epithelial cells is mediated through an adhesion complex called Nap, which is essential for infectivity. Nap is a transmembrane dimer of heterodimers of the immunodominant proteins P110 and P140. The M. genitalium genome contains multiple copies of portions that share homology with the extracellular regions of P140 and P110 encoded by the genes mg191 and mg192, respectively. Homologous recombination between the genes and the copies allows the generation of a large diversity of P140 and P110 variants to overcome surveillance by the host immune system. Interestingly, the C-terminal domain (C-domain) of the extracellular region of P140, which is essential for the function of Nap by acting as a flexible stalk anchoring the protein to the mycoplasma membrane, presents a low degree of sequence variability. In the present work, the X-ray crystal structures of two crystal forms of a construct of the P140 C-domain are reported. In both crystal forms, the construct forms a compact octamer with D4 point-group symmetry. The structure of the C-domain determined in this work presents significant differences with respect to the structure of the C-domain found recently in intact P140. The structural plasticity of the C-domain appears to be a possible mechanism that may help in the functioning of the mycoplasma adhesion complex.
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Affiliation(s)
- David Vizarraga
- Department of Structural Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Rosa Pérez-Luque
- Department of Structural Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Jesús Martín
- Department of Structural Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Ignacio Fita
- Department of Structural Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - David Aparicio
- Department of Structural Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
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5
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Aparicio D, Scheffer MP, Marcos-Silva M, Vizarraga D, Sprankel L, Ratera M, Weber MS, Seybert A, Torres-Puig S, Gonzalez-Gonzalez L, Reitz J, Querol E, Piñol J, Pich OQ, Fita I, Frangakis AS. Structure and mechanism of the Nap adhesion complex from the human pathogen Mycoplasma genitalium. Nat Commun 2020; 11:2877. [PMID: 32513917 PMCID: PMC7280502 DOI: 10.1038/s41467-020-16511-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/06/2020] [Indexed: 11/09/2022] Open
Abstract
Mycoplasma genitalium is a human pathogen adhering to host target epithelial cells and causing urethritis, cervicitis and pelvic inflammatory disease. Essential for infectivity is a transmembrane adhesion complex called Nap comprising proteins P110 and P140. Here we report the crystal structure of P140 both alone and in complex with the N-terminal domain of P110. By cryo-electron microscopy (cryo-EM) and tomography (cryo-ET) we find closed and open Nap conformations, determined at 9.8 and 15 Å, respectively. Both crystal structures and the cryo-EM structure are found in a closed conformation, where the sialic acid binding site in P110 is occluded. By contrast, the cryo-ET structure shows an open conformation, where the binding site is accessible. Structural information, in combination with functional studies, suggests a mechanism for attachment and release of M. genitalium to and from the host cell receptor, in which Nap conformations alternate to sustain motility and guarantee infectivity.
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Affiliation(s)
- David Aparicio
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC) and Maria de Maeztu Unit of Excellence, Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Margot P Scheffer
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Marina Marcos-Silva
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - David Vizarraga
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC) and Maria de Maeztu Unit of Excellence, Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Lasse Sprankel
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Mercè Ratera
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC) and Maria de Maeztu Unit of Excellence, Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Miriam S Weber
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Anja Seybert
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Sergi Torres-Puig
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Luis Gonzalez-Gonzalez
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Julian Reitz
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Enrique Querol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Jaume Piñol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Oscar Q Pich
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | - Ignacio Fita
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC) and Maria de Maeztu Unit of Excellence, Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain.
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany.
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