FIG 3.

Regulons affected during competence. (Top panels) Expression profiles of genes previously reported to be ComE, ComX, CiaR, or VraR activated. Each line shows the fold changes (versus t = 0) for a single gene from the corresponding regulon. Except for the VraR regulon (all genes shown), only genes that fell into the appropriate WGCNA cluster (cl. 29 for ComE, cl. 11 for ComX, cl. 33 for CiaR) were included. (Bottom panels) Position weight matrices of the recognition sites for ComE, ComX, CiaR, and VraR, as determined with MEME (94), from the promoters of the HC members of the corresponding regulons (ComE, ComX, and CiaR) or from three pneumococcal and six L. lactis promoters (VraR [15]).