1. Spontaneous non-canonical assembly of CcmK hexameric components from β-carboxysome shells of cyanobacteria
- Author
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Katharina Root, Eric Lesniewska, Gilles Truan, Nicolas Pocholle, Luis F. Garcia-Alles, Renato Zenobi, Denis Pompon, David Reguera, Nathalie Aubry, Carlos I Mendoza, Konstantin Barylyuk, Eric Bourillot, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Department of Chemistry and Applied Biosciences [ETH Zürich], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Instituto de Investigaciones en Materiales, Universidad Nacional Autonoma de Mexico, ANR-15-IDEX-03 PIA2/iSite-BFC, ANR-15-CE09-0002,BioSound-IR,Plateforme MS-AFM-IR pour l'analyse structurale d'inclusions de lipides dans les micro-organismes oléagineux(2015), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), ANR-15-CE09-0002-02, Laboratoire Interdisciplinaire Carnot de Bourgogne [Dijon] (LICB), Université de Bourgogne (UB)-Université de Technologie de Belfort-Montbeliard (UTBM)-Centre National de la Recherche Scientifique (CNRS), Department of Chemistry and Applied Biosciences [ETH Zürich] (D-CHAB), Universitat de Barcelona (UB), Univ Nacl Autonoma Mexico, Spanish GovernmentEuropean CommissionFIS2015-67837-P, Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), and Universitat de Barcelona
- Subjects
0301 basic medicine ,Protein Structure Comparison ,Topography ,[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,MESH: Protein Structure, Quaternary ,mass spectrum analysis ,lcsh:Medicine ,MESH: Protein Structure, Secondary ,MESH: Solvents ,Random hexamer ,Microscopy, Atomic Force ,Molecular Dynamics ,MESH: Synechocystis ,Biochemistry ,Bacteris ,Mass Spectrometry ,Protein Structure, Secondary ,Molecular dynamics ,Protein structure ,Computational Chemistry ,Bacterial microcompartment ,spectrométrie de masse ,Mica ,Macromolecular Structure Analysis ,MESH: Molecular Dynamics Simulation ,Cromatografia ,Isomeria ,lcsh:Science ,MESH: Bacterial Proteins ,Islands ,MESH: Microscopy, Atomic Force ,Minerals ,Chromatography ,Multidisciplinary ,Crystallography ,biology ,Chemistry ,MESH: Protein Multimerization ,Physics ,Synechocystis ,MESH: Chromatography, Gel ,Condensed Matter Physics ,Mineralogy ,Solutions ,Carboxysome ,protéine ,Physical Sciences ,MESH: Phosphates ,Chromatography, Gel ,Crystal Structure ,Aluminum Silicates ,Research Article ,Protein Structure ,Biophysical Simulations ,MESH: Mutation ,Icosahedral symmetry ,030106 microbiology ,Biophysics ,cyanobactérie ,Biotechnologies ,Molecular Dynamics Simulation ,MESH: Solutions ,Phosphates ,03 medical and health sciences ,Bacterial Proteins ,Isomerism ,Solid State Physics ,MESH: Isomerism ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,patch ,Protein Structure, Quaternary ,Molecular Biology ,MESH: Mass Spectrometry ,Landforms ,Bacteria ,lcsh:R ,Chemical Compounds ,Biology and Life Sciences ,Computational Biology ,Proteins ,Geomorphology ,biology.organism_classification ,030104 developmental biology ,Mutation ,Solvents ,Earth Sciences ,MESH: Aluminum Silicates ,lcsh:Q ,Protein Multimerization ,protein ,Proteïnes ,Biogenesis - Abstract
CcmK proteins are major constituents of icosahedral shells of β-carboxysomes, a bacterial microcompartment that plays a key role for CO2 fixation in nature. Supported by the characterization of bidimensional (2D) layers of packed CcmK hexamers in crystal and electron microscopy structures, CcmK are assumed to be the major components of icosahedral flat facets. Here, we reassessed the validity of this model by studying CcmK isoforms from Synechocystis sp. PCC6803. Native mass spectrometry studies confirmed that CcmK are hexamers in solution. Interestingly, potential pre-assembled intermediates were also detected with CcmK2. Atomic-force microscopy (AFM) imaging under quasi-physiological conditions confirmed the formation of canonical flat sheets with CcmK4. Conversely, CcmK2 formed both canonical and striped-patterned patches, while CcmK1 assembled into remarkable supra-hexameric curved honeycomb-like mosaics. Mutational studies ascribed the propensity of CcmK1 to form round assemblies to a combination of two features shared by at least one CcmK isoform in most β-cyanobacteria: a displacement of an α helical portion towards the hexamer edge, where a potential phosphate binding funnel forms between packed hexamers, and the presence of a short C-terminal extension in CcmK1. All-atom molecular dynamics supported a contribution of phosphate molecules sandwiched between hexamers to bend CcmK1 assemblies. Formation of supra-hexameric curved structures could be reproduced in coarse-grained simulations, provided that adhesion forces to the support were weak. Apart from uncovering unprecedented CcmK self-assembly features, our data suggest the possibility that transitions between curved and flat assemblies, following cargo maturation, could be important for the biogenesis of β-carboxysomes, possibly also of other BMC., PLoS ONE, 12 (9), ISSN:1932-6203
- Published
- 2017