Identification of metabolism pathways directly regulated by sigma54 factor in Bacillus thuringiensis

Abstract

Sigma54 (σ54) regulates nitrogen and carbon utilization in bacteria. Promoters that are σ54-dependent are highly conserved and contain short sequences located at the -24 and -12 positions upstream of the transcription initiation site. σ54 requires regulatory proteins known as bacterial enhancer-binding proteins (bEBPs) to activate gene transcription. We show that σ54 regulates the capacity to grow on various nitrogen sources using a Bacillus thuringiensis HD73 mutant lacking the sigL gene encoding σ54 (ΔsigL). A 2-fold-change cutoff and a false discovery rate cutoff of P < 0.05 were used to analyze the DNA microarray data, which revealed 255 genes that were downregulated and 121 that were upregulated in the ΔsigL mutant relative to the wild-type HD73 strain. The σ54 regulon (stationary phase) was characterized by DNA microarray, bioinformatics, and functional assay; 16 operons containing 47 genes were identified whose promoter regions contain the conserved -12/-24 element and whose transcriptional activities were abolished or reduced in the ΔsigL mutant. Eight σ54-dependent transcriptional bEBPs were found in the Bt HD73 genome, and they regulated nine σ54-dependent promoters. The metabolic pathways activated by σ54 in this process have yet to be identified in Bacillus thuringiensis; nonetheless, the present analysis of the σ54 regulon provides a better understanding of the physiological roles of s factors in bacteria.