Tracing the evolutionary histories of winged-helix domains in Dam1 and Ska complexes via structure and profile-based homology networks

Abstract

Accurate chromosome segregation depends on the kinetochore, a multiprotein complex critical for anchoring chromosomes to spindle microtubules. Two of its key assemblies, the Dam1 and Ska complexes, share analogous functions in generating load-bearing attachments but exhibit little direct similarity in either sequence or structure. Nevertheless, we discovered that both complexes harbor winged-helix domains (WHDs) at the unstructured C-termini of some subunits—a striking integrative feature not previously described as common to these otherwise distinct assemblies.

In this study, we examined whether both complexes acquired their WHDs from a common ancestor or via separate evolutionary events. To tackle the complexities posed by these short and highly divergent domains, we combined a profile-versus-profile search (HHsearch) with a structure-versus-structure search (Foldseek) and then constructed networks of WHD relationships to visualize and cluster potential homologs. We further assessed deeper evolutionary patterns through multiple phylogenetic inference methods, including amino acid–based maximum likelihood, neighbor joining with structure-derived distance metrics, and maximum likelihood in a three-dimensional (3Di) alphabet.

Our results reveal that, although both Dam1 and Ska complexes contain WHDs at the unstructured C-termini of some subunits, these domains appear to have evolved independently. Specifically, the Ska WHDs show strong intra-complex homology, suggesting they originated from duplications of a proto-Ska protein. By contrast, the Dam1 subunits Spc34, Ask1, Dam1, and Spc19 form separate WHD clades in network analyses, indicative of multiple acquisition events within the Dam1 complex.

While classic phylogenetic trees struggled to resolve these relationships—largely due to the short length and high divergence of the WHDs—the network-based approaches consistently recovered clear evidence that Spc34 differs from Ask1, Dam1, and Spc19 in its evolutionary history.

Taken together, our findings support independent origins for the Dam1 and Ska WHDs, highlight both the potential and limitations of current phylogenetic tools in analyzing short domains, and propose that integrative strategies combining sequence and structural data may be key to untangling the evolutionary histories of these and other ancient molecular assemblies.