Abstract
BackgroundRibonuclease III (RNase III) activity modulates hundreds of genes in Escherichia coli (E. coli). YmdB, a member of the macrodomain protein family, is one of known trans-acting regulators of RNase III activity; however, the significance of its regulatory role in specific bacterial cellular processes and related genes has not been determined. YmdB overexpression was used to model YmdB-induced RNase III inhibition in vivo, and microarray analysis identified gene targets and cellular processes related to RNase III inhibition.ResultsThe expression of >2,000 E. coli genes was modulated by YmdB induction; 129 genes were strongly regulated, of which 80 have not been reported as RNase III targets. Of these, ten are involved in biofilm formation. Significantly, YmdB overexpression also inhibited biofilm formation via a process that is not uniquely dependent upon RNase III inhibition. Moreover, biofilm formation is interdependently regulated by RpoS, a known stress response regulator and biofilm inhibitor, and by YmdB.ConclusionsThis is the first global profile of target genes modulated by YmdB-induced RNase III inhibition in E. coli, and the data reveal a novel, hitherto unrecognized regulatory role for YmdB in biofilm modulation.
Highlights
Ribonuclease III (RNase III) activity modulates hundreds of genes in Escherichia coli (E. coli)
Analysis of the E. coli transcriptome under conditions mimicking those of an RNase III mutant To identify which pathways and related genes are mediated by YmdB-modulated RNase III inhibition, a genome-wide analysis of mRNA abundance at single gene resolution was performed
The microarray data related to YmdB overexpression were compared with the tiling array data for an RNase III mutant [36], in which 592 genes were affected by the absence of RNase III
Summary
Ribonuclease III (RNase III) activity modulates hundreds of genes in Escherichia coli (E. coli). Several protein identities are proposed for the trans-acting inhibitor(s) and potential targets of their inhibition has been suggested; for example, cellular targets of RNase III activity, such as the RNase III gene itself, rnc [12,13], pnp [14], and rRNA processing by YmdB [18] and the level of bdm mRNA encoding a protein that promotes biofilm formation by unknown trans-acting factor(s) [19]. By cleaving the rpoS mRNA 5′-leader [21], RNase III reduces RpoS production; the presence of YmdB limits this reaction and as a consequence, increases RpoS levels, which supports entry into the stationary phase [7] This hypothesis behind this process came from a study that used an RNase III mutant [21]; to clarify and identify new targets of RNase III inhibition, it is essential to adopt a model that mimics physiological RNase III inhibition via the induction of trans-acting factor(s)
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