Analysis of the sigS regulon

The sigS gene in S. aureus encodes an ECF sigma factor. ECF sigma factors bind to core-RNA polymerase and redirecting promoter recognition to coordinate gene expression. To determine all of the genes in S. aureus whose expression is SigS dependent we preformed a microarray analysis of a wild type and sigS mutant strain. Genes showing altered expression levels in the sigS mutant versus the wild type were deemed SigS dependent. Two strains of S. aureus were used, the wild type RN4220 strain, and RN4220 containing a sigS mutation. Each strain was grown in triplicate, in TSB broth, at 37°C with shaking. The RN4220 sigS mutant has an increased lag phase. Therefore to synchronize cultures and isolate RNA from cells in the same phase of growth samples for microarray analysis were taken following 3 h growth of the wild type (which corresponds to a timepoint when sigS expression is at its highest) and 5 h growth of the sigS mutant.