Characterization of the transcriptional response to cell wall stress in Saccharomyces cerevisiae

Abstract

The cell wall perturbants Calcofluor white and Zymolyase activate the Pkc1-Rho1-controlled Slt2p MAP kinase pathway in Saccharomyces cerevisiae. A downstream transcription factor of this pathway, Rlm1p, is known to control expression of about 20 cell wall-related genes. Global transcript analysis of Calcofluor white and Zymolyase treatment was performed to determine whether cell wall stress affects transcription of these and other genes. Transcript profiles were analysed using two recently developed algorithms, viz. REDUCE, which correlates upstream regulatory motifs with expression, and Quontology, which compares expression of genes from functional groups with overall gene expression. Both methods indicated upregulation of Rlm1p-controlled cell wall genes and STRE-controlled genes, and downregulation of ribosomal genes and rRNA genes. Comparison of these expression profiles with the published profiles of two constitutively active upstream activators of the Slt2p-MAP kinase pathway, viz. Pkc1-R398A and Rho1-Q68A, revealed significant similarity. In addition, a new putative regulatory motif, CCC(N) 10 GGC, was found. In Zymolyase -treated cells a regulatory site was identified, ATGACGT, which resembles the AFT/CRE binding site. Interestingly, Sko1p, a downstream regulator of the high osmolarity pathway is known to bind to the AFT/CRE binding site, suggesting a possible role for the Hog1 pathway in the response to cell wall stress. Finally, using REDUCE, an improved version of the Rlm1 binding motif, viz. TA(W) 4 TAGM, was discovered. We propose that this version can be used in combination with REDUCE as a sensitive indicator of cell wall stress. Taken together, our data indicate that cell wall stress results in activation of various signalling pathways including the cell wall integrity pathway.

Transcript Profiles of Candida albicans Cortical Actin Patch Mutants Reflect Their Cellular Defects: Contribution of the Hog1p and Mkc1p Signaling Pathways

“…Transcript levels of many genes encoding cell wall, secreted, and stress proteins identified in the sla2⌬ and myo5⌬ mutant transcript profiles were also upregulated in S. cerevisiae cells challenged with cell wall perturbations that activate the cell wall integrity pathway (9,20). Because the elevated transcript levels of most of these genes were not dependent on the presence of Mkc1p in the myo5⌬ mutant, this also indicates that if cell wall defects acted as a signal to promote upregulation of key genes then signaling would not involve activation of the Pkc1p-Mkc1p pathway.…”

“…As described above, the transcript levels of genes encoding cell wall organization and biogenesis proteins are affected by deletion of MYO5 or SLA2. The transcript levels for many of these are induced when S. cerevisiae wild-type cells are exposed to chemical challenges to the cell wall (9,20). These observations, together with the observed sensitivity of the myo5⌬ and sla2⌬ mutants to SDS and calcofluor, suggest that the cell wall integrity pathway is differentially modulated in these mutants.…”

“…TOS2 (target of SBF-2) transcript levels in the myo5 mkc1⌬ double mutant were examined despite the absence of chip data because SBF is a known target of the Mkc1p protein kinase. Surprisingly, very few homologues of these genes are modulated when S. cerevisiae is challenged with calcofluor white or zymolyase, causing cell wall perturbations known to activate the Pkc1p-Slt2p signaling pathway (9,20).…”

Architecture and Biosynthesis of the Saccharomyces cerevisiae Cell Wall

“…PIR1, PIR2, and PIR3 show peaks of expression in early G 1 , whereas PIR4 expression is highest in G 2 (Spellman et al 1998). PIR2 is also induced by heat shock, treatment with CFW or Zymolyase, and nitrogen limitation (Russo et al 1993;Toh-e et al 1993;Yun et al 1997;Boorsma et al 2004). Consistent with their upregulation upon wall stress, all four PIR genes show elevated expression in an mpk1 mutant that constitutively activates the protein kinase C-dependent CWI pathway, an effect eliminated in mutants lacking the PKC pathway's target transcription factor, Rlm1 (Jung and Levin 1999).…”

Deglycosylation systematically improves N-glycoprotein identification in liquid chromatography–tandem mass spectrometry proteomics for analysis of cell wall stress responses in Saccharomyces cerevisiae lacking Alg3p

“…Together with other members of the PIR family, gene expression studies have shown upregulation of Cis3p in response to cell wall stress caused by calcofluor white or zymolyase [47], or via the cell wall integrity signalling pathway through Mpk1 [48]. A proteomic study showed upregulation of Cis3p and other proteins involved in the cell wall stability response in Δgas1 cells [34].…”