Though MaMsvR only shares 33% identity with the previously described MthMsvR, they share a common DNA binding sequence motif. Additionally, the behavior of MaMsvR under non-reduced and reduced conditions represents a straightforward regulatory mechanism at its own promoter and represents a model for investigating the mechanism of MsvR family proteins and the role of the V4R domain cysteines in that mechanism. MaMsvR does not bind intergenic regions in a predicted M. acetivorans oxidative stress response operon The M. acetivorans genes MA4664/MA3734-3743 comprise a putative operon encoding a variety of oxidative stress
response proteins . Although not apparent from the gene numbers, these genes are indeed adjacent on the Mdm2 antagonist chromosome
(http://img.jgi.doe.gov) . Since the MA3743 gene encodes a homologue BAY 63-2521 datasheet of Mth FpaA, an F420H2 oxidase whose expression in M. thermautotrophicus is regulated by MthMsvR, we hypothesized that MaMsvR may regulate expression of this putative operon. However, EMSA did not show binding of MaMsvR to the upstream region of the 5′ gene in the putative operon (Figure 3c, Ma P 4664 , R). A second homologue of Mth FpaA is encoded by MA3381, which appears to be a monocistronic open reading frame. As with the putative oxidative stress operon, MaMsvR failed to bind the MA3381 upstream region in EMSA experiments (see Additional file 3: Figure S2a, b). These results implied that, unlike MthMsvR, MaMsvR might not be involved in regulating the expression of FpaA homologues. However, several other intergenic regions within the reported oxidative stress operon (MA4664/MA3734-3743) contain putative TATA box and BRE sequences that may represent alternate Adavosertib datasheet transcription start sites. To assess whether MaMsvR might be involved in regulating transcription from these sites, the upstream intergenic regions of the MA3734 and MA3736 genes were amplified and tested for MaMsvR binding by EMSA. The Ma histone A promoter (P hmaA ) was used as a control to illustrate that MaMsvR binding is not non-specific. None of these regions exhibited any indication of MaMsvR binding (Figure 3c, P 3734
and P 3736 , R lanes). Therefore, MaMsvR does not appear to directly Acesulfame Potassium regulate one of the putative oxidative stress operons in M. acetivorans. Next, we tested whether MaMsvR might interact with any fragment of DNA containing the TTCGN7-9CGAA sequence that is important for MaMsvR binding to Ma P msvR . The Ma rpoK gene houses the MsvR binding motif within its open reading frame. MaMsvR did not bind to this template (Figure 3c, Ma rpoK, R lane), indicating that the presence of this sequence is not sufficient for MaMsvR binding. These results suggest that multiple factors, such as the surrounding promoter context , play a role in MaMsvR binding. Indeed, when the seventeen base pairs (<20% GC) on both sides of the MaMsvR binding sites are replaced with a different sequence (>40% GC) MaMsvR fails to bind (see Additional file 1: Figure S1).