Rapid evolution of Cse4p-rich centromeric DNA sequences in closely related pathogenic yeasts, Candida albicans and Candida dubliniensis

Abstract

The Cse4p-containing centromere regions of Candida albicans have unique and different DNA sequences on each of the eight chromosomes. In a closely related yeast, C. dubliniensis, we have identified the centromeric histone, CdCse4p, and shown that it is localized at the kinetochore. We have identified putative centromeric regions, orthologous to the C. albicans centromeres, in each of the eight C. dubliniensis chromosomes by bioinformatic analysis. Chromatin immunoprecipitation followed by PCR using a specific set of primers confirmed that these regions bind CdCse4p in vivo. As in C. albicans, the CdCse4p-associated core centromeric regions are 3–5 kb in length and show no sequence similarity to one another. Comparative sequence analysis suggests that the Cse4p-rich centromere DNA sequences in these two species have diverged faster than other orthologous intergenic regions and even faster than our best estimated “neutral” mutation rate. However, the location of the centromere and the relative position of Cse4p-rich centromeric chromatin in the orthologous regions with respect to adjacent ORFs are conserved in both species, suggesting that centromere identity is not solely determined by DNA sequence. Unlike known point and regional centromeres of other organisms, centromeres in C. albicans and C. dubliniensis have no common centromere-specific sequence motifs or repeats except some of the chromosome-specific pericentric repeats that are found to be similar in these two species. We propose that centromeres of these two Candida species are of an intermediate type between point and regional centromeres.