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

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)10GGC, 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)4TAGM, 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.