1
|
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] [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.
Collapse
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.
| |
Collapse
|
2
|
Delic S, Shuman B, Lee S, Bahmanyar S, Momany M, Onishi M. The evolutionary origins and ancestral features of septins. Front Cell Dev Biol 2024; 12:1406966. [PMID: 38994454 PMCID: PMC11238149 DOI: 10.3389/fcell.2024.1406966] [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: 03/25/2024] [Accepted: 05/08/2024] [Indexed: 07/13/2024] Open
Abstract
Septins are a family of membrane-associated cytoskeletal guanine-nucleotide binding proteins that play crucial roles in various cellular processes, such as cell division, phagocytosis, and organelle fission. Despite their importance, the evolutionary origins and ancestral function of septins remain unclear. In opisthokonts, septins form five distinct groups of orthologs, with subunits from multiple groups assembling into heteropolymers, thus supporting their diverse molecular functions. Recent studies have revealed that septins are also conserved in algae and protists, indicating an ancient origin from the last eukaryotic common ancestor. However, the phylogenetic relationships among septins across eukaryotes remained unclear. Here, we expanded the list of non-opisthokont septins, including previously unrecognized septins from glaucophyte algae. Constructing a rooted phylogenetic tree of 254 total septins, we observed a bifurcation between the major non-opisthokont and opisthokont septin clades. Within the non-opisthokont septins, we identified three major subclades: Group 6 representing chlorophyte green algae (6A mostly for species with single septins, 6B for species with multiple septins), Group 7 representing algae in chlorophytes, heterokonts, haptophytes, chrysophytes, and rhodophytes, and Group 8 representing ciliates. Glaucophyte and some ciliate septins formed orphan lineages in-between all other septins and the outgroup. Combining ancestral-sequence reconstruction and AlphaFold predictions, we tracked the structural evolution of septins across eukaryotes. In the GTPase domain, we identified a conserved GAP-like arginine finger within the G-interface of at least one septin in most algal and ciliate species. This residue is required for homodimerization of the single Chlamydomonas septin, and its loss coincided with septin duplication events in various lineages. The loss of the arginine finger is often accompanied by the emergence of the α0 helix, a known NC-interface interaction motif, potentially signifying the diversification of septin-septin interaction mechanisms from homo-dimerization to hetero-oligomerization. Lastly, we found amphipathic helices in all septin groups, suggesting that membrane binding is an ancestral trait. Coiled-coil domains were also broadly distributed, while transmembrane domains were found in some septins in Group 6A and 7. In summary, this study advances our understanding of septin distribution and phylogenetic groupings, shedding light on their ancestral features, potential function, and early evolution.
Collapse
Affiliation(s)
- Samed Delic
- Department of Biology, Duke University, Durham, NC, United States
| | - Brent Shuman
- Fungal Biology Group and Plant Biology Department, University of Georgia, Athens, GA, United States
| | - Shoken Lee
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, United States
| | - Shirin Bahmanyar
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, United States
| | - Michelle Momany
- Fungal Biology Group and Plant Biology Department, University of Georgia, Athens, GA, United States
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, NC, United States
| |
Collapse
|
3
|
Delic S, Shuman B, Lee S, Bahmanyar S, Momany M, Onishi M. The Evolutionary Origins and Ancestral Features of Septins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586683. [PMID: 38585751 PMCID: PMC10996617 DOI: 10.1101/2024.03.25.586683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Septins are a family of membrane-associated cytoskeletal GTPases that play crucial roles in various cellular processes, such as cell division, phagocytosis, and organelle fission. Despite their importance, the evolutionary origins and ancestral function of septins remain unclear. In opisthokonts, septins form five distinct groups of orthologs, with subunits from multiple groups assembling into heteropolymers, thus supporting their diverse molecular functions. Recent studies have revealed that septins are also conserved in algae and protists, indicating an ancient origin from the last eukaryotic common ancestor. However, the phylogenetic relationships among septins across eukaryotes remained unclear. Here, we expanded the list of non-opisthokont septins, including previously unrecognized septins from rhodophyte red algae and glaucophyte algae. Constructing a rooted phylogenetic tree of 254 total septins, we observed a bifurcation between the major non-opisthokont and opisthokont septin clades. Within the non-opisthokont septins, we identified three major subclades: Group 6 representing chlorophyte green algae (6A mostly for species with single septins, 6B for species with multiple septins), Group 7 representing algae in chlorophytes, heterokonts, haptophytes, chrysophytes, and rhodophytes, and Group 8 representing ciliates. Glaucophyte and some ciliate septins formed orphan lineages in-between all other septins and the outgroup. Combining ancestral-sequence reconstruction and AlphaFold predictions, we tracked the structural evolution of septins across eukaryotes. In the GTPase domain, we identified a conserved GAP-like arginine finger within the G-interface of at least one septin in most algal and ciliate species. This residue is required for homodimerization of the single Chlamydomonas septin, and its loss coincided with septin duplication events in various lineages. The loss of the arginine finger is often accompanied by the emergence of the α0 helix, a known NC-interface interaction motif, potentially signifying the diversification of septin-septin interaction mechanisms from homo-dimerization to hetero-oligomerization. Lastly, we found amphipathic helices in all septin groups, suggesting that curvature-sensing is an ancestral trait of septin proteins. Coiled-coil domains were also broadly distributed, while transmembrane domains were found in some septins in Group 6A and 7. In summary, this study advances our understanding of septin distribution and phylogenetic groupings, shedding light on their ancestral features, potential function, and early evolution.
Collapse
Affiliation(s)
- Samed Delic
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Brent Shuman
- Fungal Biology Group and Plant Biology Department, University of Georgia, Athens, Georgia, USA
| | - Shoken Lee
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Shirin Bahmanyar
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Michelle Momany
- Fungal Biology Group and Plant Biology Department, University of Georgia, Athens, Georgia, USA
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, North Carolina, USA
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|