Solution structure of domain 1.1 of the σA factor from Bacillus subtilis is preformed for binding to the RNA polymerase core

Bacterial RNA polymerase (RNAP) requires sigma factors to recognize promoter sequences. Domain 1.1 of primary sigma factors (sigma 1.1) prevents their binding to promoter DNA in the absence of RNAP, and when in complex with RNAP, it occupies the DNA-binding channel of RNAP. Currently, two 3D structures of sigma 1.1 are available: from Escherichia coli in complex with RNAP and from T. maritima solved free in solution. However, these two structures significantly differ, and it is unclear whether this difference is due to an altered conformation upon RNAP binding or to differences in intrinsic properties between the proteins from these two distantly related species. Here, we report the solution structure of sigma 1.1 from the Gram-positive bacterium Bacillus subtilis. We found that B. subtilis sigma 1.1 is highly compact because of additional stabilization not present in sigma 1.1 from the other two species and that it is more similar to E. coli sigma 1.1. Moreover, modeling studies suggested that B. subtilis sigma 1.1 requires minimal conformational changes for accommodating RNAP in the DNA channel, whereas T. maritima sigma 1.1 must be rearranged to fit therein. Thus, the mesophilic species B. subtilis and E. coli share the same sigma 1.1 fold, whereas the fold of sigma 1.1 from the thermophile T. maritima is distinctly different. Finally, we describe an intriguing similarity between sigma 1.1 and , an RNAP-associated protein in B. subtilis, bearing implications for the so-far unknown binding site of on RNAP. In conclusion, our results shed light on the conformational changes of sigma 1.1 required for its accommodation within bacterial RNAP.