Diversity of opisthokont septin proteins reveals structural constraints and conserved motifs

Abstract

BackgroundSeptins are cytoskeletal proteins important in cell division and in establishing and maintaining cell polarity. Although septins are found in various eukaryotes, septin genes had the richest history of duplication and diversification in the animals, fungi and protists that comprise opisthokonts. Opisthokont septin paralogs encode modular proteins that assemble into heteropolymeric higher order structures. The heteropolymers can create physical barriers to diffusion or serve as scaffolds organizing other morphogenetic proteins. How the paralogous septin modules interact to form heteropolymers is still unclear. Through comparative analyses, we hoped to clarify the evolutionary origin of septin diversity and to suggest which amino acid residues were responsible for subunit binding specificity.ResultsHere we take advantage of newly sequenced genomes to reconcile septin gene trees with a species phylogeny from 22 animals, fungi and protists. Our phylogenetic analysis divided 120 septins representing the 22 taxa into seven clades (Groups) of paralogs. Suggesting that septin genes duplicated early in opisthokont evolution, animal and fungal lineages share septin Groups 1A, 4 and possibly also 1B and 2. Group 5 septins were present in fungi but not in animals and whether they were present in the opisthokont ancestor was unclear. Protein homology folding showed that previously identified conserved septin motifs were all located near interface regions between the adjacent septin monomers. We found specific interface residues associated with each septin Group that are candidates for providing subunit binding specificity.ConclusionsThis work reveals that duplication of septin genes began in an ancestral opisthokont more than a billion years ago and continued through the diversification of animals and fungi. Evidence for evolutionary conservation of ~ 49 interface residues will inform mutagenesis experiments and lead to improved understanding of the rules guiding septin heteropolymer formation and from there, to improved understanding of development of form in animals and fungi.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1297-8) contains supplementary material, which is available to authorized users.

Cellular functions of actin- and microtubule-associated septins

“…Septins are a family of GTP-binding proteins that assemble into oligomeric complexes and polymers that lack end-to-end polarity and are more stable than actin filaments and microtubules 2,3,14,15 . Encoded by paralogous genes that expanded through evolution, septins are classified into four groups that vary mainly in GTPase activity and in the amino-and carboxy-terminal extensions of their core GTP-binding domain (Figure 1A) 16,17 . Septins assemble in a combinatorial fashion by oligomerizing in tandem through homomeric and heteromeric interactions of their GTP-binding domains; this oligomerization is partly instructed by GTP binding and hydrolysis [18][19][20][21][22][23] .…”

Biophysical properties governing septin assembly

“…Microtubules and F-actin, two well studied cytoskeletal elements, are composed of dimeric and monomeric subunits, respectively, and form dynamic micron-scale assemblies essential for numerous cell processes. Similarly, septins, GTP-binding proteins conserved in many branches of eukaryotes, are a class of cytoskeletal-like proteins that form micron-scale higher-order assemblies from nanometer-scale building blocks (Auxier et al, 2019; Onishi and Pringle, 2016; Pan et al, 2007; Spiliotis and McMurray, 2020). Septin assemblies act as scaffolds for microtubules and F-actin, recruit essential proteins to the site of cytokinesis, and can organize the plasma membrane (Bridges et al, 2016; Clay et al, 2014; Gilden et al, 2012; Lew and Reed, 1995; Longtine et al, 2000; Spiliotis, 2010).…”

Reconstructed evolutionary history of the yeast septins Cdc11 and Shs1

“…Septin-based structures in eukaryotes have a deeply rooted evolutionary history and a highly conserved overall organization in the opisthokont lineage from single-celled yeast to humans ( Nishihama et al 2011 ; Auxier et al 2019 ; McMurray and Thorner 2019 ). Yet, within any given fungal or mammalian organism (or, in metazoans, cell type), septin hetero-octamers can be assembled from alternative sets of subunits, which, it has been proposed, arose from gene duplication and divergence ( Cao et al 2009 ; Valadares et al 2017 ).…”

“…Septins comprise a fourth cytoskeletal element, conserved from fungi to metazoans ( Pan et al 2007 ; Nishihama et al 2011 ; Auxier et al 2019 ). Each septin contains a GTP-binding fold (G domain) preceded by an N-terminal extension (NTE) of variable length and trailed by a C-terminal extension (CTE) of variable length.…”

“…However, the hetero-octameric complex with distinct subunits occupying specific positions within the structure has been conserved from yeast to humans ( Bertin et al 2008 ; McMurray and Thorner 2019 ; Mendonca et al 2019 ; Soroor et al 2020 ). Phylogenetic analyses indicate that during fungal and metazoan evolution gene duplications gave rise to the current repertoire of septin subunits ( Pan et al 2007 ; Nishihama et al 2011 ; Auxier et al 2019 ). Such increases in biological complexity across deep evolutionary time wherein a multi-subunit complex acquires additional functional components through gene duplication and divergence have clearly occurred in other instances, including the V-type ATPase ( Finnigan et al 2011 , 2012 ), the proteasome ( Wollenberg and Swaffield 2001 ), the TRiC/CCT chaperonin ( Gestaut et al 2019 ), and the NADH:ubiquinone oxidoreductase ( Gabaldon et al 2005 ).…”