Phylogenetic Analysis of Fungal Centromere H3 Proteins

Abstract

Centromere H3 proteins (CenH3's) are variants of histone H3 specialized for packaging centromere DNA. Unlike canonical H3, which is among the most conserved of eukaryotic proteins, CenH3's are rapidly evolving, raising questions about orthology and conservation of function across species. To gain insight on CenH3 evolution and function, a phylogenetic analysis was undertaken on CenH3 proteins drawn from a single, ancient lineage, the Fungi. Using maximum-likelihood methods, a credible phylogeny was derived for the conserved histone fold domain (HFD) of 25 fungal CenH3's. The collection consisted mostly of hemiascomycetous yeasts, but also included basidiomycetes, euascomycetes, and an archaeascomycete. The HFD phylogeny closely recapitulated known evolutionary relationships between the species, supporting CenH3 orthology. The fungal CenH3's lacked significant homology in their N termini except for those of the Saccharomyces/Kluyveromyces clade that all contained a region homologous to the essential N-terminal domain found in Saccharomyces cerevisiae Cse4. The ability of several heterologous CenH3's to function in S. cerevisiae was tested and found to correlate with evolutionary distance. Domain swapping between S. cerevisiae Cse4 and the noncomplementing Pichia angusta ortholog showed that species specificity could not be explained by the presence or absence of any recognized secondary structural element of the HFD.

Absence of positive selection on CenH3 inLuzulasuggests that holokinetic chromosomes may suppress centromere drive

“…in those offering an opportunity for centromere drive (Melters et al, 2013). Similarly, adaptively evolving CenH3 has so far been detected only in lineages with asymmetric meiosis (Henikoff et al, 2001;Talbert et al, 2004Talbert et al, , 2008Hirsch et al, 2009;Schueler et al, 2010;Zedek and Bures, 2012;Finseth et al, 2015) and not in lineages displaying symmetric meiosis (Talbert et al, 2004(Talbert et al, , 2008Baker and Rogers, 2006), which is in accordance with the centromere drive model.…”

The Rapidly Evolving Centromere-Specific Histone Has Stringent Functional Requirements inArabidopsis thaliana

“…This has been shown for fungal CENH3's (Baker and Rogers 2006), but it is important to confirm this property for an organism with large tandem repeat centromeres that are likely specified epigenetically, rather than by sequence-specific DNA binding proteins. A previous study using plant tissue culture cells found that CENH3 from tobacco (Nicotiana tabacum) could localize to A. thaliana kinetochores when tagged at its C termini with GFP and expressed from the strong constitutive 35S promoter (Nagaki et al 2010).…”

Rapid Evolution of Yeast Centromeres in the Absence of Drive

“…Due to the small size of CDEII we were not able to accurately assess the extent of heterogeneity in polymorphism among centromeres on different chromosomes; more data from more isolates and centromeres would be useful in this regard. Interestingly, the two proteins directly interacting with CDEII, Cse4 and Mif2 (homologous to the fast-evolving mammalian CENPC protein), appear to be under strong purifying selection in yeast, with no indication of recurrent directional selection (Henikoff and Dalal 2005;Baker and Rogers 2006).…”