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

ABSTRACT: Bacterial RNA polymerase (RNAP) requires ? factors to recognize promoter sequences. Domain 1.1 of primary ? factors (?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 ?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 ?1.1 from the Gram-positive bacterium Bacillus subtilis We found that B. subtilis ?1.1 is highly compact because of additional stabilization not present in ?1.1 from the other two species and that it is more similar to E. coli ?1.1. Moreover, modeling studies suggested that B. subtilis ?1.1 requires minimal conformational changes for accommodating RNAP in the DNA channel, whereas T. maritima ?1.1 must be rearranged to fit therein. Thus, the mesophilic species B. subtilis and E. coli share the same ?1.1 fold, whereas the fold of ?1.1 from the thermophile T. maritima is distinctly different. Finally, we describe an intriguing similarity between ?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 ?1.1 required for its accommodation within bacterial RNAP.

SUBMITTER: Zachrdla M

PROVIDER: S-EPMC5512058 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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

Zachrdla Milan M Padrta Petr P Rabatinová Alžbeta A Šanderová Hana H Barvík Ivan I Krásný Libor L Žídek Lukáš L

The Journal of biological chemistry 20170524 28

Bacterial RNA polymerase (RNAP) requires σ factors to recognize promoter sequences. Domain 1.1 of primary σ factors (σ1.1) 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 σ1.1 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 ...[more]

PMID: 28539362

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Dataset Information

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

Publications

Solution structure of domain 1.1 of the σ<sup>A</sup> factor from <i>Bacillus subtilis</i> is preformed for binding to the RNA polymerase core.

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