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Escherichia coli YmdB regulates biofilm formation independently of its role as an RNase III modulator.

Kim T, Lee J, Kim KS - BMC Microbiol. (2013)

Bottom Line: Of these, ten are involved in biofilm formation.Moreover, biofilm formation is interdependently regulated by RpoS, a known stress response regulator and biofilm inhibitor, and by YmdB.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.

View Article: PubMed Central - HTML - PubMed

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.

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.

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Interdependency on YmdB and RpoS for biofilm formation. (A) Effect of knocking out ymdB or rpoS on biofilm formation. Biofilm formation was measured in wild-type (ymdB + or rpoS+), KSK002 (∆ymdB) and rpoS mutant (Keio-∆rpoS) cells. (B) Dependency of RpoS and YmdB phenotype on biofilm formation. The effect of ectopic expression of RpoS or YmdB in the absence of ymdB or rpoS, respectively, on biofilm formation was determined. (C) Expression of RpoS and YmdB. Protein expression was detected by immunoblotting using antibodies against RpoS and 6xHistidine tagged YmdB (His-YmdB) as described in Methods. S1 protein level was used as a loading control. All biofilm formation data were obtained as described in Methods. Data represent the mean values from ten independent experiments.
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Figure 3: Interdependency on YmdB and RpoS for biofilm formation. (A) Effect of knocking out ymdB or rpoS on biofilm formation. Biofilm formation was measured in wild-type (ymdB + or rpoS+), KSK002 (∆ymdB) and rpoS mutant (Keio-∆rpoS) cells. (B) Dependency of RpoS and YmdB phenotype on biofilm formation. The effect of ectopic expression of RpoS or YmdB in the absence of ymdB or rpoS, respectively, on biofilm formation was determined. (C) Expression of RpoS and YmdB. Protein expression was detected by immunoblotting using antibodies against RpoS and 6xHistidine tagged YmdB (His-YmdB) as described in Methods. S1 protein level was used as a loading control. All biofilm formation data were obtained as described in Methods. Data represent the mean values from ten independent experiments.

Mentions: While it was clear that YmdB induction decreased biofilm formation (Figure 1), biofilm formation also decreased by ~ 35% in the absence of ymdB (ΔymdB) gene in the chromosome (Figure 3A). This could indicate that YmdB is involved in, but not essential for, the inhibition of biofilm formation in E. coli, or that increased levels of YmdB affect biofilm formation by modulating associated cellular proteins and their pathways. To test this hypothesis, we sought to identify candidate genes whose mRNA levels were increased by YmdB (Table 1) and which have a known effect on the biofilm phenotype. One strong candidate is RpoS, a stress-responsive sigma factor [21], which when overexpressed led to a reduction in biofilm formation (Figures 3B,C; [25]). To determine whether YmdB-mediated inhibition of biofilm formation is dependent on the presence or absence of rpoS, we measured biofilm formation in an rpoS knockout strain (Keio-ΔrpoS). Biofilm formation was activated in the rpoS knockout (Figures 3A,C). Subsequent introduction of a plasmid overexpressing YmdB only decreased biofilm inhibition by 12% in the rpoS knockout (Figure 3B) whereas it resulted in 70% inhibition in wild-type cells (Figure 2A); thus, the inhibition of biofilm formation by YmdB is RpoS-dependent.


Escherichia coli YmdB regulates biofilm formation independently of its role as an RNase III modulator.

Kim T, Lee J, Kim KS - BMC Microbiol. (2013)

Interdependency on YmdB and RpoS for biofilm formation. (A) Effect of knocking out ymdB or rpoS on biofilm formation. Biofilm formation was measured in wild-type (ymdB + or rpoS+), KSK002 (∆ymdB) and rpoS mutant (Keio-∆rpoS) cells. (B) Dependency of RpoS and YmdB phenotype on biofilm formation. The effect of ectopic expression of RpoS or YmdB in the absence of ymdB or rpoS, respectively, on biofilm formation was determined. (C) Expression of RpoS and YmdB. Protein expression was detected by immunoblotting using antibodies against RpoS and 6xHistidine tagged YmdB (His-YmdB) as described in Methods. S1 protein level was used as a loading control. All biofilm formation data were obtained as described in Methods. Data represent the mean values from ten independent experiments.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4222554&req=5

Figure 3: Interdependency on YmdB and RpoS for biofilm formation. (A) Effect of knocking out ymdB or rpoS on biofilm formation. Biofilm formation was measured in wild-type (ymdB + or rpoS+), KSK002 (∆ymdB) and rpoS mutant (Keio-∆rpoS) cells. (B) Dependency of RpoS and YmdB phenotype on biofilm formation. The effect of ectopic expression of RpoS or YmdB in the absence of ymdB or rpoS, respectively, on biofilm formation was determined. (C) Expression of RpoS and YmdB. Protein expression was detected by immunoblotting using antibodies against RpoS and 6xHistidine tagged YmdB (His-YmdB) as described in Methods. S1 protein level was used as a loading control. All biofilm formation data were obtained as described in Methods. Data represent the mean values from ten independent experiments.
Mentions: While it was clear that YmdB induction decreased biofilm formation (Figure 1), biofilm formation also decreased by ~ 35% in the absence of ymdB (ΔymdB) gene in the chromosome (Figure 3A). This could indicate that YmdB is involved in, but not essential for, the inhibition of biofilm formation in E. coli, or that increased levels of YmdB affect biofilm formation by modulating associated cellular proteins and their pathways. To test this hypothesis, we sought to identify candidate genes whose mRNA levels were increased by YmdB (Table 1) and which have a known effect on the biofilm phenotype. One strong candidate is RpoS, a stress-responsive sigma factor [21], which when overexpressed led to a reduction in biofilm formation (Figures 3B,C; [25]). To determine whether YmdB-mediated inhibition of biofilm formation is dependent on the presence or absence of rpoS, we measured biofilm formation in an rpoS knockout strain (Keio-ΔrpoS). Biofilm formation was activated in the rpoS knockout (Figures 3A,C). Subsequent introduction of a plasmid overexpressing YmdB only decreased biofilm inhibition by 12% in the rpoS knockout (Figure 3B) whereas it resulted in 70% inhibition in wild-type cells (Figure 2A); thus, the inhibition of biofilm formation by YmdB is RpoS-dependent.

Bottom Line: Of these, ten are involved in biofilm formation.Moreover, biofilm formation is interdependently regulated by RpoS, a known stress response regulator and biofilm inhibitor, and by YmdB.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.

View Article: PubMed Central - HTML - PubMed

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.

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.

Show MeSH
Related in: MedlinePlus