Activators, deactivators and deactivated activators

Transcriptional regulation of the agr locus and the identification of DNA binding residues of the global regulatory protein SarR in Staphylococcus aureus

Many members of the transcriptional regulator SarA protein family are winged-helix proteins that are involved in gene regulation essential to Staphylococcus aureus pathogenesis. Investigation of the mechanism by which this family of genes acts at the molecular level will likely contribute to the understanding of the pathogenesis process and enhance the potential for the development of inhibitors capable of controlling S. aureus infections. Our previously published studies demonstrate that SarR is a repressor of sarA expression. Here, we show that SarR (a member of the SarA protein family) in part regulates agr expression by direct binding to the agr intergenic promoter region as determined by gel shift and DNase I footprinting assays. Analysis of the double sarA/sarR mutant in the early phase of growth reveals its significant role in regulating agr expression as compared with single mutants. Based on the previously reported crystal structure of SarR, we conducted site-specific mutagenesis and demonstrate that K52 residues within helix-turn-helix (HTH), K80, R82 and R88 (in the wing) and L105 (in the alpha5 helix) are important for DNA binding. Interestingly, SarR and SarA binding sites on the agr promoter are confined within the same region of DNA. Additional gel shift studies with SarR and SarA suggest that these two proteins may bind the same region of the agr promoter.

Crystal structure of the SarR protein from Staphylococcus aureus

The expression of virulence determinants in Staphylococcus aureus is controlled by global regulatory loci (e.g., sarA and agr). The sar (Staphylococcus accessory regulator) locus is composed of three overlapping transcripts (sarA P1, P3, and P2, transcripts initiated from the P1, P3, and P2 promoters, respectively), all encoding the 124-aa SarA protein. The level of SarA, the major regulatory protein, is partially controlled by the differential activation of the sarA promoters. We previously partially purified a 13.6-kDa protein, designated SarR, that binds to the sarA promoter region to down-modulate sarA transcription from the P1 promoter and subsequently SarA expression. SarR shares sequence similarity to SarA, and another SarA homolog, SarS. Here we report the 2.3 A-resolution x-ray crystal structure of the dimeric SarR-MBP (maltose binding protein) fusion protein. The structure reveals that the SarR protein not only has a classic helix-turn-helix module for DNA binding at the major grooves, but also has an additional loop region involved in DNA recognition at the minor grooves. This interaction mode could represent a new functional class of the "winged helix" family. The dimeric SarR structure could accommodate an unusually long stretch of approximately 27 nucleotides with two or four bending points along the course, which could lead to the bending of DNA by 90 degrees or more, similar to that seen in the catabolite activator protein (CAP)-DNA complex. The structure also demonstrates the molecular basis for the stable dimerization of the SarR monomers and possible motifs for interaction with other proteins.

Involvement of iclR and rpoS in the induction of acs, the gene for acetyl coenzyme A synthetase of Escherichia coli K-12

Two independent pathways in Escherichia coli convert acetate to acetyl CoA: reversal of acetate production by phosphotransacetylase and acetate kinase, and the acetyl-CoA synthetase (Acs) pathway that scavenges acetate. We investigated acs gene expression by using a cat transcriptional fusion. It was observed that acs expression varies depending on the carbon sources used and occurs in the stationary phase of growth even in the absence of acetate. Mutations in iclR for the repressor of the glyoxylate shunt and in rpoS for the stationary phase sigma factor reduced the consumption of acetate mediated by Acs, indicating that both are involved in acs regulation.