PMID:17416652

Citation	Thompson, KM, Rhodius, VA and Gottesman, S (2007) SigmaE regulates and is regulated by a small RNA in Escherichia coli.J. Bacteriol. 189:4243-56
Abstract	RybB is a small, Hfq-binding noncoding RNA originally identified in a screen of conserved intergenic regions in Escherichia coli. Fusions of the rybB promoter to lacZ were used to screen plasmid genomic libraries and genomic transposon mutants for regulators of rybB expression. A number of plasmids, including some carrying rybB, negatively regulated the fusion. An insertion in the rep helicase and one upstream of dnaK decreased expression of the fusion. Multicopy suppressors of these insertions led to identification of two plasmids that stimulated the fusion. One contained the gene for the response regulator OmpR; the second contained mipA, encoding a murein hydrolase. The involvement of MipA and OmpR in cell surface synthesis suggested that the rybB promoter might be dependent on sigma(E). The sequence upstream of the +1 of rybB contains a consensus sigma(E) promoter. The activity of rybB-lacZ was increased in cells lacking the RseA anti-sigma factor and when sigma(E) was overproduced from a heterologous promoter. The activity of rybB-lacZ and the detection of RybB were totally abolished in an rpoE-null strain. In vitro, sigma(E) efficiently transcribes from this promoter. Both a rybB mutation and an hfq mutation significantly increased expression of both rybB-lacZ and rpoE-lacZ fusions, consistent with negative regulation of the sigma(E) response by RybB and other small RNAs. Based on the plasmid screens, NsrR, a repressor sensitive to nitric oxide, was also found to negatively regulate sigma(E)-dependent promoters in an RseA-independent fashion.
Links	PubMed Online version:10.1128/JB.00020-07
Keywords	Base Sequence; Blotting, Northern; Escherichia coli; Escherichia coli Proteins; Gene Expression Regulation, Bacterial; Lac Operon; Molecular Sequence Data; Plasmids; Promoter Regions, Genetic; RNA, Bacterial; RNA, Untranslated; Recombinant Fusion Proteins; Sequence Homology, Nucleic Acid; Sigma Factor; Transcription, Genetic
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Materials and Methods Used

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Phenotype Annotations

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Phenotype of	Taxon Information	Genotype Information (if known)	Condition Information	OMP ID	OMP Term Name	ECO ID	ECO Term Name	Notes	Status
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: MG1655 Substrain: 511145	Genotype of Reference Strain: hfq+ Genotype of Experimental Strain : hfq(del)	Reference Condition:					This is a null mutation, causing a change in the expression of a gene. Specifically, overexpression of rybB in both the exponential and stationary growth phase the strain.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: MG1655 Substrain: 511145	Genotype of Reference Strain: rybB+ Genotype of Experimental Strain : pBAD-rybB	Reference Condition:					There was a mutation that caused the expression of rybB to be altered. To be specific, its expression was decreased during the exponential and stationary growth phase.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: MG1655 Substrain: 511145	Genotype of Reference Strain: rybB+ Genotype of Experimental Strain : pBAD-rybB	Reference Condition:					The mutation resulted in a change in the expression of the rybB gene. Particularly, its over-experision and a decrease in rpoE activity during exponential and stationary growth phase.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: MG1655 Substrain: 511145	Genotype of Reference Strain: mipA+ Genotype of Experimental Strain : Multipcopy mipA	Reference Condition:					This mutation caused an increase in rybB expression.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: MG1655 Substrain: 511145	Genotype of Reference Strain: mipA+ Genotype of Experimental Strain : Multicopy mipA ompR(del)	Reference Condition:					This mutation caused an increase in rybB expression.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: MG1655 Substrain: 511145	Genotype of Reference Strain: mipA+ Genotype of Experimental Strain : Multipcopy mipA	Reference Condition:					This mutation resulted in the over-expression of degP gene.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: MG1655 Substrain: 511145	Genotype of Reference Strain: rseA+ Genotype of Experimental Strain : resA(del)	Reference Condition:					The expression of rybB is increased in both the Exponential and Stationary growth phase due to this mutation.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: MG1655 Substrain: 511145	Genotype of Reference Strain: rpoE+ Genotype of Experimental Strain : rpoE(del)	Reference Condition:					The mutated strain had an increase in the expression of its rybB strain.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: MG1655 Substrain: 511145	Genotype of Reference Strain: ompR+ Genotype of Experimental Strain : ompR(del)	Reference Condition:					The expression of the rybB gene was decreased.
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References

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