Centromeres of the YeastKomagataella phaffii(Pichia pastoris)Have a Simple Inverted-Repeat Structure

Abstract

Centromere organization has evolved dramatically in one clade of fungi, the Saccharomycotina. These yeasts have lost the ability to make normal eukaryotic heterochromatin with histone H3K9 methylation, which is a major component of pericentromeric regions in other eukaryotes. Following this loss, several different types of centromere emerged, including two types of sequence-defined (“point”) centromeres, and the epigenetically defined “small regional” centromeres of Candida albicans. Here we report that centromeres of the methylotrophic yeast Komagataella phaffii (formerly called Pichia pastoris) are structurally defined. Each of its four centromeres consists of a 2-kb inverted repeat (IR) flanking a 1-kb central core (mid) region. The four centromeres are unrelated in sequence. CenH3 (Cse4) binds strongly to the cores, with a decreasing gradient along the IRs. This mode of organization resembles Schizosaccharomyces pombe centromeres but is much more compact and lacks the extensive flanking heterochromatic otr repeats. Different isolates of K. phaffii show polymorphism for the orientation of the mid regions, due to recombination in the IRs. CEN4 is located within a 138-kb region that changes orientation during mating-type switching, but switching does not induce recombination of centromeric IRs. Our results demonstrate that evolutionary transitions in centromere organization have occurred in multiple yeast clades.

Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes

“…VI), 56 (chr. IV), 57 and 58], we observed an inverted repeat structure with a central core region of 1–2 kb surrounded by an inverted repeat of 2.5–5 kb, which is quite similar to the centromere structure of S. pombe [31, 33, 34], Candida albicans [35], Candida tropicalis [36], and Komagataella phaffii (formerly Pichia pastoris ) [37]. Details on this observation are available on Additional file 4 but a complete study on T. reesei centromeres structure would require a full assembly, and chromatin immunoprecipitation sequencing experiments.…”

“…Interestingly, we observed in four centromeric regions (scaffolds 51, 56, 57, 58) a 7- to 10-kb long inverted repeat regions, reminiscent of inverted repeats organization found in yeasts C. albicans, C. tropicalis , K. phaffii , or S. pombe [31, 33–37]. To our knowledge, such an organization has not been described in filamentous fungi, as most data come from the study of N. crassa , whose centromeric region are 150–300 kb long and consist in degenerate transposon sequences.…”

“…To our knowledge, such an organization has not been described in filamentous fungi, as most data come from the study of N. crassa , whose centromeric region are 150–300 kb long and consist in degenerate transposon sequences. This raises the question of whether at least some centromeres in Trichoderma are sequence- or at least inverted repeat-defined, as recently hypothesized for C. tropicalis [37] and not only epigenetically defined. Such observation could have an influence on efforts to develop a plasmid transformation system in this fungus.…”

A Stable, Autonomously Replicating Plasmid Vector Containing Pichia pastoris Centromeric DNA

“…1). This result provided independent confirmation of a similar observation in two earlier reports (45,46). We found that these nontranscribed regions ranged from 8 to 11 kb in length, each containing a nearly complete inverted repeat sequence (2 to 2.7 kb in length) flanking a nonrepetitive central core region (0.9 to 1.4 kb) ( Fig.…”

“…Most recently, Sturmberger et al published a refined reference genome for the CBS7435 strain and also proposed candidate P. pastoris centromeres (45). Coughlan et al structurally defined the centromeres of P. pastoris by transcriptome sequencing (RNA-seq) and chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) using binding by the histone H3-like centromere protein Cse4 (46). Through these studies, these researchers found that each of the putative centromeres on the four P. pastoris chromosomes contained inverted repeat structures.…”