Abstract
ABSTRACTThe alternative sigma factor D is known to be involved in at least three biological processes in Bacilli: flagellin synthesis, methyl-accepting chemotaxis and autolysin synthesis. Although many Bacillus genes have been identified as SigD regulon, the list may be not be complete. With microarray-based systemic screening, we found a set of genes downregulated in the sigD knockout mutant of the plant growth-promoting rhizobacterium B. amyloliquefaciens subsp. plantarum FZB42. Eight genes (appA, blsA, dhaS, spoVG, yqgA, RBAM_004640, RBAM_018080 and ytk) were further confirmed by quantitative PCR and/or northern blot to be controlled by SigD at the transcriptional level. These genes are hitherto not reported to be controlled by SigD. Among them, four genes are of unknown function and two genes (RBAM_004640 and RBAM_018080), absent in the model strain B. subtilis 168, are unique to B. amyloliquefaciens stains. The eight genes are involved in sporulation, biofilm formation, metabolite transport and several other functions. These findings extend our knowledge of the regulatory network governed by SigD in Bacillus and will further help to decipher the roles of the genes.
Highlights
In prokaryotes, which lack a nuclear membrane, transcription and translation take place simultaneously
Total RNAs were extracted from three cultures of FZB42 wild type and the ΔsigD mutant, respectively
A False Discovery Rate (FDR) significance test was performed for the data
Summary
In prokaryotes, which lack a nuclear membrane, transcription and translation take place simultaneously. The holoenzyme of a bacterial RNA polymerase (RNAP) consists of two parts: the catalysing core enzyme and an additional σ factor, which permits the holoenzyme to anchor on certain promoter sites and initiate transcription from the regions. The σ subunit associates with the core RNAP and determines most, if not all, of the specificity of bacterial RNAPs to their cognate promoter.
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