title: Escherichia coli YmdB regulates biofilm formation independently of its role as an RNase III modulator.
abstract: BACKGROUND
  Ribonuclease 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.
  
  
  RESULTS
  The 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.
  
  
  CONCLUSIONS
  This 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.
authors.affiliation: Superbacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea. sunny06@kribb.re.kr.
authors.forename: Taeyeon
authors.initials: T
authors.lastname: Kim
authors.forename: Juyeon
authors.initials: J
authors.lastname: Lee
authors.forename: Kwang-sun
authors.initials: KS
authors.lastname: Kim
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D018441:Biofilms / Q000254:growth & development*; D002352:Carrier Proteins / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D015870:Gene Expression; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D046228:Microarray Analysis; D043244:Ribonuclease III / Q000378:metabolism*; D012808:Sigma Factor / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D002352:Carrier Proteins; D029968:Escherichia coli Proteins; D012808:Sigma Factor; C534806:YmdB protein, E coli; C069567:sigma factor KatF protein, Bacteria; D043244:Ribonuclease III