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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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A schematic model of biofilm formation and gene expression involving YmdB, RpoS, and RNase III. Two different pathways for biofilm formation are proposed: an RNase III-dependent pathway in which other uncharacterized factor(s) inhibit RNase III activity, thereby upregulating biofilm formation, and an RNase III-independent pathway in which both YmdB and RpoS interdependently regulate the inhibition of biofilm formation. In terms of gene expression, the level of RpoS is post-transcriptionally regulated by YmdB either directly or indirectly via the inhibition of RNase III activity [18,20], while the level of YmdB is regulated transcriptionally by the RpoS protein [18].
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Figure 5: A schematic model of biofilm formation and gene expression involving YmdB, RpoS, and RNase III. Two different pathways for biofilm formation are proposed: an RNase III-dependent pathway in which other uncharacterized factor(s) inhibit RNase III activity, thereby upregulating biofilm formation, and an RNase III-independent pathway in which both YmdB and RpoS interdependently regulate the inhibition of biofilm formation. In terms of gene expression, the level of RpoS is post-transcriptionally regulated by YmdB either directly or indirectly via the inhibition of RNase III activity [18,20], while the level of YmdB is regulated transcriptionally by the RpoS protein [18].

Mentions: The results presented herein demonstrate that YmdB is a major regulator of RNase III activity in E. coli, modulating more than 30% of the genes targeted by RNase III. In addition, the results of a microarray analysis following YmdB overexpression (which identified changes in biofilm-related genes and a decrease in biofilm formation) indicate a novel role for YmdB as a modulator of biofilm formation. Previous results indicated that overexpression of RpoS was associated with decreased biofilm formation [25]. Our microarray, qPCR, and Western blotting data showed that overexpression of YmdB increased the levels of RpoS (Additional file 1: Tables S3, Figures 2, 3 and 4). Moreover, YmdB modulated RpoS levels and activity of biofilm formation (Figures 3, 4). Thus, we propose a model to illustrate the multiple roles played by YmdB during gene expression and biofilm formation (Figure 5).


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

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

A schematic model of biofilm formation and gene expression involving YmdB, RpoS, and RNase III. Two different pathways for biofilm formation are proposed: an RNase III-dependent pathway in which other uncharacterized factor(s) inhibit RNase III activity, thereby upregulating biofilm formation, and an RNase III-independent pathway in which both YmdB and RpoS interdependently regulate the inhibition of biofilm formation. In terms of gene expression, the level of RpoS is post-transcriptionally regulated by YmdB either directly or indirectly via the inhibition of RNase III activity [18,20], while the level of YmdB is regulated transcriptionally by the RpoS protein [18].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: A schematic model of biofilm formation and gene expression involving YmdB, RpoS, and RNase III. Two different pathways for biofilm formation are proposed: an RNase III-dependent pathway in which other uncharacterized factor(s) inhibit RNase III activity, thereby upregulating biofilm formation, and an RNase III-independent pathway in which both YmdB and RpoS interdependently regulate the inhibition of biofilm formation. In terms of gene expression, the level of RpoS is post-transcriptionally regulated by YmdB either directly or indirectly via the inhibition of RNase III activity [18,20], while the level of YmdB is regulated transcriptionally by the RpoS protein [18].
Mentions: The results presented herein demonstrate that YmdB is a major regulator of RNase III activity in E. coli, modulating more than 30% of the genes targeted by RNase III. In addition, the results of a microarray analysis following YmdB overexpression (which identified changes in biofilm-related genes and a decrease in biofilm formation) indicate a novel role for YmdB as a modulator of biofilm formation. Previous results indicated that overexpression of RpoS was associated with decreased biofilm formation [25]. Our microarray, qPCR, and Western blotting data showed that overexpression of YmdB increased the levels of RpoS (Additional file 1: Tables S3, Figures 2, 3 and 4). Moreover, YmdB modulated RpoS levels and activity of biofilm formation (Figures 3, 4). Thus, we propose a model to illustrate the multiple roles played by YmdB during gene expression and biofilm formation (Figure 5).

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