Discovery of an Unconventional Centromere in Budding Yeast Redefines Evolution of Point Centromeres

Norihiko Kobayashi,Yutaka Suzuki,Lori W Schoenfeld,Carolin A Müller,Conrad Nieduszynski,Kenneth H Wolfe,Tomoyuki U Tanaka

doi:10.1016/j.cub.2015.06.023

Abstract

SummaryCentromeres are the chromosomal regions promoting kinetochore assembly for chromosome segregation. In many eukaryotes, the centromere consists of up to mega base pairs of DNA. On such “regional centromeres,” kinetochore assembly is mainly defined by epigenetic regulation [1]. By contrast, a clade of budding yeasts (Saccharomycetaceae) has a “point centromere” of 120–200 base pairs of DNA, on which kinetochore assembly is defined by the consensus DNA sequence [2, 3]. During evolution, budding yeasts acquired point centromeres, which replaced ancestral, regional centromeres [4]. All known point centromeres among different yeast species share common consensus DNA elements (CDEs) [5, 6], implying that they evolved only once and stayed essentially unchanged throughout evolution. Here, we identify a yeast centromere that challenges this view: that of the budding yeast Naumovozyma castellii is the first unconventional point centromere with unique CDEs. The N. castellii centromere CDEs are essential for centromere function but have different DNA sequences from CDEs in other point centromeres. Gene order analyses around N. castellii centromeres indicate their unique, and separate, evolutionary origin. Nevertheless, they are still bound by the ortholog of the CBF3 complex, which recognizes CDEs in other point centromeres. The new type of point centromere originated prior to the divergence between N. castellii and its close relative Naumovozyma dairenensis and disseminated to all N. castellii chromosomes through extensive genome rearrangement. Thus, contrary to the conventional view, point centromeres can undergo rapid evolutionary changes. These findings give new insights into the evolution of point centromeres.

Highlights

To identify N. castellii centromeres, we added epitope tags to Ndc10, Cep3, and Ndc80 at their original loci, carried out chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq), and analyzed in reference to t
We conclude that they make point centromeres, because (1) consensus DNA elements are found among all ten centromeres, (2) these DNA elements are important for the centromere activity, and (3) a short DNA fragment (110 bp) containing the consensus DNA elements is sufficient for centromere function
The gene order analyses give the following insights: first, most N. castellii centromeres are not located in intergenic regions orthologous to those containing standard CDEI,II,III-type point centromeres in other species (Figure S1D), these two are often in close proximity (Figure S4C)

Summary

Graphical Abstract

All known point centromeres share common DNA sequences and a single evolutionary origin. Kobayashi et al have identified a new type of point centromere in budding yeast N. castellii. Its DNA sequence and evolutionary origin are different from other point centromeres. Discovery of the new centromere redefines the evolution of point centromeres. Highlights d A new type of point centromere has been identified in budding yeast N. castellii d Its DNA sequence and evolutionary origin are different from other point centromeres d N. castellii centromeres are bound by CBF3 that recognizes other point centromeres d Contrary to the conventional view, point centromeres can change rapidly in evolution.

RESULTS AND DISCUSSION

Findings

Conclusions