These results demonstrate differences in Pitavastatin cell line the stoichiometry of the protein:DNA complexes Ruboxistaurin cost produced by MaMsvR and MthMsvR and suggests that the modes of oligomerization upon DNA binding may differ between the two proteins. MaMsvR binds an inverted repeat sequence conserved in all msvR promoters The two MsvR binding boxes in Ma P msvR , Boxes A and B, are found upstream of all known MsvR-encoding genes (Figure 1b,c; Figure 3a). Mth P msvR/fpaA boxes 2 and 3, corresponding to Ma P msvR boxes A and B represent a partial inverted repeat TTCGTAN4TACGAA, whereas Mth
P msvR/fpaA Box 1 is a partial direct repeat of Box 3. The numbering of the boxes is based on order of discovery and not the order of MsvR binding. These binding boxes were previously identified by sequence alignments and their role in MthMsvR binding to Mth P msvR/fpaA has been described [9]. MthMsvR complexes bound to all three boxes and DNaseI footprinting indicated involvement of upstream regions in conjunction with Box 1[9]. To determine if boxes A and B in Ma P msvR were bound by MaMsvR, EMSAs were performed with fifty base-pair oligonucleotides spanning the binding boxes of Ma P msvR (Figure 3). Mutations in either box A or box B eliminated MaMsvR binding, suggesting that this conserved sequence motif is involved in MsvR binding and auto-regulation (Figure 3b) [9].
Additionally, EMSA experiments with a single insertion or deletion between boxes A and B had
no impact on MaMsvR binding suggesting that minor changes in selleck kinase inhibitor spacing can be accommodated and that MaMsvR binding sites in the genome could be represented by the TTCGN7-9 CGAA motif (see Additional file 1: Figure S1). There are over forty occurrences of such a motif upstream of structural genes in M. acetivorans. The structural genes are annotated to encode proteins involved in a variety of cellular functions including iron transport, divalent cation transport, efflux pumps, control of cell division, and many others (Additional file 2: Table S1). Figure 3 MsvR binding and regulatory targets assessed by EMSA. (a) Sequences of the 50 bp region of Ma P msvR used to confirm MaMsvR Exoribonuclease binding to boxes A and B. Sequence changes within the binding boxes are shown. (b) EMSA assays with the template (50 nM) variations shown in (a) and 1 μM (20-fold excess over DNA) reduced MaMsvR (R, 5 mM DTT). A 50 bp region of Ma P msvR was included as a binding control. The gel wells are indicated (W). (c) EMSA analysis with reduced MaMsvR (R, 5 mM DTT) and its own promoter (Ma P msvR , 10 nM), various intergenic regions of an oxidative stress response cluster (Ma P 4664 , P 3734 , P 3736 , 10 nM) as well as the control Ma histone A promoter (Ma P hmaA , 10 nM). A region of rpoK (10 nM) was tested for binding because an MsvR binding site (TTCGN8CGAA) is present in the coding region.