PMID:19542274

Citation	Preis, H, Eckart, RA, Gudipati, RK, Heidrich, N and Brantl, S (2009) CodY activates transcription of a small RNA in Bacillus subtilis. J. Bacteriol. 191:5446-57
Abstract	Regulatory small RNAs (sRNAs) in bacterial genomes have become a focus of research over the past 8 years. Whereas more than 100 such sRNAs have been found in Escherichia coli, relatively little is known about sRNAs in gram-positive bacteria. Using a computational approach, we identified two sRNAs in intergenic regions of the Bacillus subtilis genome, SR1 and SR2 (renamed BsrF). Recently, we demonstrated that SR1 inhibits the translation initiation of the transcriptional activator AhrC. Here, we describe detection of BsrF, its expression profile, and its regulation by CodY. Furthermore, we mapped the secondary structure of BsrF. BsrF is expressed in complex and minimal media in all growth phases in B. subtilis and, with a similar expression profile, also in Bacillus amyloliquefaciens. Neither overexpression nor deletion of bsrF affected the growth of B. subtilis. BsrF was found to be long-lived in complex and minimal media. Analysis of 13 putative transcription factor binding sites upstream of bsrF revealed only an effect for CodY. Here, we showed by using Northern blotting, lacZ reporter gene fusions, in vitro transcription, and DNase I footprinting that the transcription of bsrF is activated by CodY in the presence of branched-chain amino acids and GTP. Furthermore, BsrF transcription was increased 1.5- to 2-fold by glucose in the presence of branched-chain amino acids, and this increase was independent of the known glucose-dependent regulators. BsrF is the second target for which transcriptional activation by CodY has been discovered.
Links	PubMed PMC2725614 Online version:10.1128/JB.00602-09
Keywords	Amino Acids, Branched-Chain/metabolism; Bacillus subtilis/physiology; Bacterial Proteins/physiology; Base Sequence; Blotting, Northern; DNA Footprinting; DNA, Bacterial/metabolism; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genes, Reporter; Guanosine Triphosphate/metabolism; Molecular Sequence Data; Nucleic Acid Conformation; Promoter Regions, Genetic; Protein Binding; RNA, Small Interfering/biosynthesis; RNA, Small Interfering/chemistry; RNA, Small Interfering/genetics; Trans-Activators/physiology; Transcription, Genetic; beta-Galactosidase/biosynthesis; beta-Galactosidase/genetics
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
BACSU:CODY		GO:0006355: regulation of transcription, DNA-dependent	ECO:0000315:		P		Figure 5.	complete CACAO 2633
BACSU:CODY	involved_in	GO:0006355: regulation of transcription, DNA-templated	ECO:0000315: mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete

References

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