The RNA-Binding Protein Whi3 Is a Key Regulator of Developmental Signaling and Ploidy inSaccharomyces cerevisiae

Abstract

In Saccharomyces cerevisiae, the RNA-binding protein Whi3 controls cell cycle progression, biofilm formation, and stress response by post-transcriptional regulation of the Cdc28-Cln3 cyclin-dependent protein kinase and the dual-specificity protein kinase Yak1. Previous work has indicated that Whi3 might govern these processes by additional, yet unknown mechanisms. In this study, we have identified additional effectors of Whi3 that include the G 1 cyclins Cln1/Cln2 and two known regulators of biofilm formation, the catalytic PKA subunit Tpk1 and the transcriptional activator Tec1. We also provide evidence that Whi3 regulates production of these factors by post-transcriptional control and might exert this function by affecting translational elongation. Unexpectedly, we also discovered that Whi3 is a key regulator of cellular ploidy, because haploid whi3Δ mutant strains exhibit a significant increase-in-ploidy phenotype that depends on environmental conditions. Our data further suggest that Whi3 might control stability of ploidy by affecting the expression of many key genes involved in sister chromatid cohesion and of NIP100 that encodes a component of the yeast dynactin complex for chromosome distribution. Finally, we show that absence of Whi3 induces a transcriptional stress response in haploid cells that is relieved by whole-genome duplication. In summary, our study suggests that the RNA-binding protein Whi3 acts as a central regulator of cell division and development by post-transcriptional control of key genes involved in chromosome distribution and cell signaling. E UKARYOTIC organisms have evolved highly complex signaling networks to control cell division and development. The functionality of signal transduction pathways crucially depends on the timely availability of individual components at sufficient levels to ensure adequate signaling capacity. A number of studies in different eukaryotes have shown that the production of individual signaling proteins is under the control not only of transcriptional regulators, but also of RNA-binding proteins (Lasko 2003;Sugiura et al. 2003;Prinz et al. 2007;Stewart et al. 2007;Malcher et al. 2011). This suggests that RNA-binding proteins could regulate the performance of whole signaling networks, but a precise view of key interconnections is often lacking.In the budding yeast Saccharomyces cerevisiae, the Pumilio family (PUF) protein Mpt5/Puf5 is a good example of an RNA-binding protein that controls cellular development by targeting signaling components. Mpt5 has been found to negatively affect the performance of at least two different mitogen-activated protein kinase (MAPK) signaling pathways that regulate adhesion/biofilm formation and cell wall integrity (Prinz et al. 2007;Stewart et al. 2007). In general, PUF proteins are known to bind to the 39-UTR of target mRNAs and reduce their stability or translatability (Quenault et al. 2011). This is also true for S. cerevisiae Mpt5, which represses the protein levels of key components of the MAPK cascade that regu...

Molecular Mechanism of Flocculation Self-Recognition in Yeast and Its Role in Mating and Survival

“…S4 ), the downregulated WHI3 is directly linked to the upregulated FLO11 and Cdc28-Cln3p cyclin-dependent protein kinase, which plays a role in the control of the cell size at the G 1 /S transition ( 55 , 56 ). Whi3p is also linked to the cell cycle by controlling the production of the G 1 cyclins Cln1p and Cln2p and also targets, besides Tpk1, the Tec1p transcription factor ( 57 ), which is well known to activate FLO11 expression ( 46 , 58 – 60 ). It is also able to negatively control stress-regulated genes via a currently unknown repressor and might be able to control the stability of ploidy by affecting the expression of many genes involved in sister chromatid cohesion ( 57 ).…”

“…Whi3p is also linked to the cell cycle by controlling the production of the G 1 cyclins Cln1p and Cln2p and also targets, besides Tpk1, the Tec1p transcription factor ( 57 ), which is well known to activate FLO11 expression ( 46 , 58 – 60 ). It is also able to negatively control stress-regulated genes via a currently unknown repressor and might be able to control the stability of ploidy by affecting the expression of many genes involved in sister chromatid cohesion ( 57 ). Additionally, the differentially upregulated SNF1 and SNF4 genes in the network (see C2 and C3 in Fig.…”

A protein condensation network contextualises cell fate decisions

“…In old cells, however, Whi3 targets had significantly reduced translation efficiency scores compared to the other transcripts ( Figure S1D ). Notably, many of the targets are involved in cell cycle control 35,38,46 ( Figures S1B and S1E ) and some of the lowest scores belonged to transcripts of the G1 cyclins Cln2 and Cln3 ( Figure S1E) . Thus, Whi3 may promote senescence by repressing the translation of its target mRNAs.…”

“…Notably, many of the targets are involved in cell cycle control 35,38,46 (Figures S1B and S1E) and some of the lowest scores belonged to transcripts of the G1 cyclins Cln2 and Cln3 (Figure S1E). Thus, Whi3 may promote senescence by repressing the translation of its target mRNAs.…”

Investigating the Quantitative Trait Loci Contributing to Individual Variation in Drug Response

“…and WHI3 (Chen & Madura, 2008;D'Aquino et al, 2005;Nash et al, 1988;Schladebeck & Mosch, 2013;Tye, 1999;Zachariae & Nasmyth, 1999). These processes are well-linked to microtubule function within the literature.…”