Abstract
SigF is an alternative sigma factor that is highly conserved among species of the genus
Mycobacterium
. In this study we identified the SigF regulon in
Mycobacterium smegmatis
using whole-genome microarray and promoter consensus analyses. In total, 64 genes in exponential phase and 124 genes in stationary phase are SigF dependent (
P
< 0.01, >2-fold expression change). Our experimental data reveal the SigF-dependent promoter consensus GTTT-N
(15-17)
-GGGTA for
M. smegmatis
, and we propose 130 potential genes under direct control of SigF, of which more than 50% exhibited reduced expression in a Δ
sigF
strain. We previously reported an increased susceptibility of the Δ
sigF
strain to heat and oxidative stress, and our expression data indicate a molecular basis for these phenotypes. We observed SigF-dependent expression of several genes purportedly involved in oxidative stress defense, namely, a heme-containing catalase, a manganese-containing catalase, a superoxide dismutase, the starvation-induced DNA-protecting protein MsDps1, and the biosynthesis genes for the carotenoid isorenieratene. Our data suggest that SigF regulates the biosynthesis of the thermoprotectant trehalose, as well as an uptake system for osmoregulatory compounds, and this may explain the increased heat susceptibility of the Δ
sigF
strain. We identified the regulatory proteins SigH3, PhoP, WhiB1, and WhiB4 as possible genes under direct control of SigF and propose four novel anti-sigma factor antagonists that could be involved in the posttranslational regulation of SigF in
M. smegmatis
. This study emphasizes the importance of this sigma factor for stationary-phase adaptation and stress response in mycobacteria.