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Mendonça DC, Morais STB, Ciol H, Pinto APA, Leonardo DA, Pereira HD, Valadares NF, Portugal RV, Klaholz BP, Garratt RC, Araujo APU. Structural Insights into Ciona intestinalis Septins: Complexes Suggest a Mechanism for Nucleotide-dependent Interfacial Cross-talk. J Mol Biol 2024; 436:168693. [PMID: 38960133 DOI: 10.1016/j.jmb.2024.168693] [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: 04/28/2024] [Revised: 06/19/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024]
Abstract
Septins are filamentous nucleotide-binding proteins which can associate with membranes in a curvature-dependent manner leading to structural remodelling and barrier formation. Ciona intestinalis, a model for exploring the development and evolution of the chordate lineage, has only four septin-coding genes within its genome. These represent orthologues of the four classical mammalian subgroups, making it a minimalist non-redundant model for studying the modular assembly of septins into linear oligomers and thereby filamentous polymers. Here, we show that C. intestinalis septins present a similar biochemistry to their human orthologues and also provide the cryo-EM structures of an octamer, a hexamer and a tetrameric sub-complex. The octamer, which has the canonical arrangement (2-6-7-9-9-7-6-2) clearly shows an exposed NC-interface at its termini enabling copolymerization with hexamers into mixed filaments. Indeed, only combinations of septins which had CiSEPT2 occupying the terminal position were able to assemble into filaments via NC-interface association. The CiSEPT7-CiSEPT9 tetramer is the smallest septin particle to be solved by Cryo-EM to date and its good resolution (2.7 Å) provides a well-defined view of the central NC-interface. On the other hand, the CiSEPT7-CiSEPT9 G-interface shows signs of fragility permitting toggling between hexamers and octamers, similar to that seen in human septins but not in yeast. The new structures provide insights concerning the molecular mechanism for cross-talk between adjacent interfaces. This indicates that C. intestinalis may represent a valuable tool for future studies, fulfilling the requirements of a complete but simpler system to understand the mechanisms behind the assembly and dynamics of septin filaments.
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Affiliation(s)
| | | | - Heloísa Ciol
- São Carlos Institute of Physics, USP, São Carlos, SP, Brazil
| | | | | | | | | | - Rodrigo V Portugal
- Brazilian Nanotechnology National Laboratory, CNPEM, Campinas, SP, Brazil; Biotechnosciency Program, Federal University of ABC, Santo André, SP, Brazil
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 67404 Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, 67404 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France
| | | | - Ana P U Araujo
- São Carlos Institute of Physics, USP, São Carlos, SP, Brazil.
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Grupp B, Denkhaus L, Gerhardt S, Vögele M, Johnsson N, Gronemeyer T. The structure of a tetrameric septin complex reveals a hydrophobic element essential for NC-interface integrity. Commun Biol 2024; 7:48. [PMID: 38184752 PMCID: PMC10771490 DOI: 10.1038/s42003-023-05734-w] [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: 07/12/2023] [Accepted: 12/20/2023] [Indexed: 01/08/2024] Open
Abstract
The septins of the yeast Saccharomyces cerevisiae assemble into hetero-octameric rods by alternating interactions between neighboring G-domains or N- and C-termini, respectively. These rods polymerize end to end into apolar filaments, forming a ring beneath the prospective new bud that expands during the cell cycle into an hourglass structure. The hourglass finally splits during cytokinesis into a double ring. Understanding these transitions as well as the plasticity of the higher order assemblies requires a detailed knowledge of the underlying structures. Here we present the first X-ray crystal structure of a tetrameric Shs1-Cdc12-Cdc3-Cdc10 complex at a resolution of 3.2 Å. Close inspection of the NC-interfaces of this and other septin structures reveals a conserved contact motif that is essential for NC-interface integrity of yeast and human septins in vivo and in vitro. Using the tetrameric structure in combination with AlphaFold-Multimer allowed us to propose a model of the octameric septin rod.
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Affiliation(s)
- Benjamin Grupp
- Institute of Molecular Genetics and Cell Biology, Ulm University, Ulm, Germany
| | - Lukas Denkhaus
- Institute of Biochemistry, Albert-Ludwigs University, Freiburg, Germany
| | - Stefan Gerhardt
- Institute of Biochemistry, Albert-Ludwigs University, Freiburg, Germany
| | - Matthis Vögele
- Institute of Molecular Genetics and Cell Biology, Ulm University, Ulm, Germany
| | - Nils Johnsson
- Institute of Molecular Genetics and Cell Biology, Ulm University, Ulm, Germany
| | - Thomas Gronemeyer
- Institute of Molecular Genetics and Cell Biology, Ulm University, Ulm, Germany.
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Hussain A, Nguyen VT, Reigan P, McMurray M. Evolutionary degeneration of septins into pseudoGTPases: impacts on a hetero-oligomeric assembly interface. Front Cell Dev Biol 2023; 11:1296657. [PMID: 38125875 PMCID: PMC10731463 DOI: 10.3389/fcell.2023.1296657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
The septin family of eukaryotic proteins comprises distinct classes of sequence-related monomers that associate in a defined order into linear hetero-oligomers, which are capable of polymerizing into cytoskeletal filaments. Like actin and ⍺ and β tubulin, most septin monomers require binding of a nucleotide at a monomer-monomer interface (the septin "G" interface) for assembly into higher-order structures. Like ⍺ and β tubulin, where GTP is bound by both subunits but only the GTP at the ⍺-β interface is subject to hydrolysis, the capacity of certain septin monomers to hydrolyze their bound GTP has been lost during evolution. Thus, within septin hetero-oligomers and filaments, certain monomers remain permanently GTP-bound. Unlike tubulins, loss of septin GTPase activity-creating septin "pseudoGTPases"-occurred multiple times in independent evolutionary trajectories, accompanied in some cases by non-conservative substitutions in highly conserved residues in the nucleotide-binding pocket. Here, we used recent septin crystal structures, AlphaFold-generated models, phylogenetics and in silico nucleotide docking to investigate how in some organisms the septin G interface evolved to accommodate changes in nucleotide occupancy. Our analysis suggests that yeast septin monomers expressed only during meiosis and sporulation, when GTP is scarce, are evolving rapidly and might not bind GTP or GDP. Moreover, the G dimerization partners of these sporulation-specific septins appear to carry compensatory changes in residues that form contacts at the G interface to help retain stability despite the absence of bound GDP or GTP in the facing subunit. During septin evolution in nematodes, apparent loss of GTPase activity was also accompanied by changes in predicted G interface contacts. Overall, our observations support the conclusion that the primary function of nucleotide binding and hydrolysis by septins is to ensure formation of G interfaces that impose the proper subunit-subunit order within the hetero-oligomer.
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Affiliation(s)
- Alya Hussain
- Program in Structural Biology and Biochemistry, Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Vu T. Nguyen
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Philip Reigan
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Michael McMurray
- Program in Structural Biology and Biochemistry, Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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Yekeen AA, Durojaye OA, Idris MO, Muritala HF, Arise RO. CHAPERON g: A tool for automated GROMACS-based molecular dynamics simulations and trajectory analyses. Comput Struct Biotechnol J 2023; 21:4849-4858. [PMID: 37854635 PMCID: PMC10579869 DOI: 10.1016/j.csbj.2023.09.024] [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: 07/25/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 10/20/2023] Open
Abstract
Molecular dynamics (MD) simulation is a powerful computational tool used in biomolecular studies to investigate the dynamics, energetics, and interactions of a wide range of biological systems at the atomic level. GROMACS is a widely used free and open-source biomolecular MD simulation software recognized for its efficiency, accuracy, and extensive range of simulation options. However, the complexity of setting up, running, and analyzing MD simulations for diverse systems often poses a significant challenge, requiring considerable time, effort, and expertise. Here, we introduce CHAPERONg, a tool that automates the GROMACS MD simulation pipelines for protein and protein-ligand systems. CHAPERONg also integrates seamlessly with GROMACS modules and third-party tools to provide comprehensive analyses of MD simulation trajectories, offering up to 20 post-simulation processing and trajectory analyses. It also streamlines and automates established pipelines for conducting and analyzing biased MD simulations via the steered MD-umbrella sampling workflow. Thus, CHAPERONg makes MD simulations more accessible to beginner GROMACS users whilst empowering experts to focus on data interpretation and other less programmable aspects of MD simulation workflows. CHAPERONg is written in Bash and Python, and the source code is freely available at https://github.com/abeebyekeen/CHAPERONg. Detailed documentation and tutorials are available online at dedicated web pages accessible via https://abeebyekeen.com/chaperong-online.
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Affiliation(s)
- Abeeb Abiodun Yekeen
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Olanrewaju Ayodeji Durojaye
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Department of Chemical Sciences, Coal City University, Emene, Enugu State, Nigeria
| | - Mukhtar Oluwaseun Idris
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Hamdalat Folake Muritala
- Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Rotimi Olusanya Arise
- Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
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Marques da Silva R, Christe Dos Reis Saladino G, Antonio Leonardo D, D'Muniz Pereira H, Andréa Sculaccio S, Paula Ulian Araujo A, Charles Garratt R. A key piece of the puzzle: The central tetramer of the Saccharomyces cerevisiae septin protofilament and its implications for self-assembly. J Struct Biol 2023; 215:107983. [PMID: 37315820 DOI: 10.1016/j.jsb.2023.107983] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/02/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
Septins, often described as the fourth component of the cytoskeleton, are structural proteins found in a vast variety of living beings. They are related to small GTPases and thus, generally, present GTPase activity which may play an important (although incompletely understood) role in their organization and function. Septins polymerize into long non-polar filaments, in which each subunit interacts with two others by alternating interfaces, NC and G. In Saccharomyces cerevisiae four septins are organized in the following manner, [Cdc11-Cdc12-Cdc3-Cdc10-Cdc10-Cdc3-Cdc12-Cdc11]n in order to form filaments. Although septins were originally discovered in yeast and much is known regarding their biochemistry and function, only limited structural information about them is currently available. Here we present crystal structures of Cdc3/Cdc10 which provide the first view of the physiological interfaces formed by yeast septins. The G-interface has properties which place it in between that formed by SEPT2/SEPT6 and SEPT7/SEPT3 in human filaments. Switch I from Cdc10 contributes significantly to the interface, whereas in Cdc3 it is largely disorded. However, the significant negative charge density of the latter suggests it may have a unique role. At the NC-interface, we describe an elegant means by which the sidechain of a glutamine from helix α0 imitates a peptide group in order to retain hydrogen-bond continuity at the kink between helices α5 and α6 in the neighbouring subunit, thereby justifying the conservation of the helical distortion. Its absence from Cdc11, along with this structure's other unusual features are critically discussed by comparison with Cdc3 and Cdc10.
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Affiliation(s)
- Rafael Marques da Silva
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-723, Brazil
| | | | - Diego Antonio Leonardo
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-723, Brazil
| | - Humberto D'Muniz Pereira
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-723, Brazil
| | - Susana Andréa Sculaccio
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-723, Brazil
| | - Ana Paula Ulian Araujo
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-723, Brazil
| | - Richard Charles Garratt
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-723, Brazil.
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Mostowy S, Bertin A, Ewers H. Introduction to the Special Issue of Cytoskeleton on the molecular and cell biology of septins. Cytoskeleton (Hoboken) 2023; 80:139-140. [PMID: 37278438 DOI: 10.1002/cm.21764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023]
Affiliation(s)
- Serge Mostowy
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Aurelie Bertin
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 168, Laboratoire Physico Chimie Curie, Paris, France
| | - Helge Ewers
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
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