Pseudohyphal differentiation inKomagataella phaffii: investigating theFLOgene family

Abstract

Many yeasts differentiate into multicellular phenotypes in adverse environmental conditions. Here we investigate pseudohyphal growth in Komagataella phaffii and the involvement of the flocculin (FLO) gene family in its regulation. The K. phaffii FLO family consists of 13 members, and the conditions inducing pseudohyphal growth are different from Saccharomyces cerevisiae. So far, this phenotype was only observed when K. phaffii was cultivated at slow growth rates in glucose-limited chemostats, but not upon nitrogen starvation or the presence of fusel alcohols. Transcriptional analysis identified that FLO11, FLO400 and FLO5–1 are involved in the phenotype, all being controlled by the transcriptional regulator Flo8. The three genes exhibit a complex mechanism of expression and repression during transition from yeast to pseudohyphal form. Unlike in S. cerevisiae, deletion of FLO11 does not completely prevent the phenotype. In contrast, deletion of FLO400 or FLO5–1 prevents pseudohyphae formation, and hampers FLO11 expression. FAIRE-Seq data shows that the expression and repression of FLO400 and FLO5–1 are correlated to open or closed chromatin regions upstream of these genes, respectively. Our findings indicate that K. phaffii Flo400 and/or Flo5–1 act as upstream signals that lead to the induction of FLO11 upon glucose limitation in chemostats at slow growth and chromatin modulation is involved in the regulation of their expression.

What makes Komagataella phaffii non-conventional?

“…However, while also in K. phaffii Flo8 contains an N-terminal LisH domain no Mss11 homolog was identified (De et al . 2020 ), suggesting that Flo8 acts as a homodimer in this organism. While there is a clear ortholog of FLO11 , for the other structural FLO genes no distinct homologs can be identified (Kock et al .…”

“…K. phaffii possesses an expanded FLO gene family consisting of 12 members containing different Flo-domains, and a Flo8-type TF (De et al . 2020 ). Pseudohyphae formation and surface adherence are absent when Flo8 is deleted, indicating that Flo8 is also the major regulator of filamentous growth in K. phaffii (Rebnegger et al .…”

“… 2016 ; De et al . 2020 ). In both, S. cerevisiae and C. albicans , Flo8 was demonstrated to form a heterodimer with Mss11 via their N-terminal LisH domains that cooperatively regulates filamentous growth (Su et al .…”

“…Unlike in S. cerevisiae , no silencing of the subtelomeric FLO genes was observed in exponential growth conditions at pH 5.0 (De et al . 2020 ).…”

“…Also the environmental triggers leading to pseudohyphal growth are different between the two species: In contrast to S. cerevisiae , K. phaffii morphology is not affected by fusel alcohols or nitrogen starvation (De et al . 2020 ). So far, an elongated phenotype representing pseudohyphae was only observed when K. phaffii was cultivated at slow growth rates below µ = 0.075/h in glucose-limited chemostats (Rebnegger et al .…”