Phylogenetic and structural analysis of centromeric DNA and kinetochore proteins

Using computational approaches, ranging from sequence similarity searches to hidden Markov model-based modeling, we show that organisms with CENs resembling those in S. cerevisiae (point CENs) are very closely related and that all contain a set of 11 kinetochore proteins not found in organisms with complex CENs. Conversely, organisms with complex CENs (regional CENs) contain proteins seemingly absent from point-CEN organisms. However, at least three quarters of known kinetochore proteins are present in all fungi regardless of CEN organization. At least six of these proteins have previously unidentified human orthologs. When fungi and metazoa are compared, almost all have kinetochores constructed around Spc105 and three conserved multi-protein linker complexes (MIND, COMA, and the NDC80 complex).Our data suggest that critical structural features of kinetochores have been well conserved from yeast to man. Surprisingly, phylogenetic analysis reveals that human kinetochore proteins are as similar in sequence to their yeast counterparts as to presumptive Drosophila melanogaster or Caenorhabditis elegans orthologs. This finding is consistent with evidence that kinetochore proteins have evolved very rapidly relative to components of other complex cellular structures.Kinetochores are eukaryote-specific structures that assemble on centromeric (CEN) DNA and perform three crucial functions: they bind paired sister chromatids to spindle microtubules (MTs) in a bipolar fashion compatible with chromatid disjunction; they couple MT (+)-end polymer dynamics to chromosome movement during metaphase and anaphase [1]; and they generate the spindle checkpoint signals linking anaphase onset to the completion of kinetochore-MT attachment [2]. Despite the conservation of these functions, and of MT structure and dynamics, CENs in closely related organisms are highly diverged in sequence, as are CENs on different chromosomes in a single organism [2,3]. The simplest known CENs, those in the b