title: Identification of metabolism pathways directly regulated by sigma(54) factor in Bacillus thuringiensis.
abstract: Sigma(54) (σ(54)) regulates nitrogen and carbon utilization in bacteria. Promoters that are σ(54)-dependent are highly conserved and contain short sequences located at the -24 and -12 positions upstream of the transcription initiation site. σ(54) requires regulatory proteins known as bacterial enhancer-binding proteins (bEBPs) to activate gene transcription. We show that σ(54) regulates the capacity to grow on various nitrogen sources using a Bacillus thuringiensis HD73 mutant lacking the sigL gene encoding σ(54) (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 σ(54) 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 σ(54)-dependent transcriptional bEBPs were found in the Bt HD73 genome, and they regulated nine σ(54)-dependent promoters. The metabolic pathways activated by σ(54) in this process have yet to be identified in Bacillus thuringiensis; nonetheless, the present analysis of the σ(54) regulon provides a better understanding of the physiological roles of σ factors in bacteria.
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Peng
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Guannan
authors.initials: G
authors.lastname: Wang
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China.
authors.forename: Guiming
authors.initials: G
authors.lastname: Liu
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Fuping
authors.initials: F
authors.lastname: Song
keywords: Bacillus thuringiensis; DNA microarray; bEBPs; metabolic pathways; sigma54