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 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 σ1.1 from the Gram-positive bacterium Bacillus subtilis We found that B. subtilis σ1.1 is highly compact because of additional stabilization not present in σ1.1 from the other two species and that it is more similar to E. coli σ1.1. Moreover, modeling studies suggested that B. subtilis σ1.1 requires minimal conformational changes for accommodating RNAP in the DNA channel, whereas T. maritima σ1.1 must be rearranged to fit therein. Thus, the mesophilic species B. subtilis and E. coli share the same σ1.1 fold, whereas the fold of σ1.1 from the thermophile T. maritima is distinctly different. Finally, we describe an intriguing similarity between σ1.1 and δ, an RNAP-associated protein in B. subtilis, bearing implications for the so-far unknown binding site of δ on RNAP. In conclusion, our results shed light on the conformational changes of σ1.1 required for its accommodation within bacterial RNAP.

Central European Institute of Technology Brno Czech Republic; National Centre for Biomolecular Research Faculty of Science Masaryk University CZ 62500 Brno Czech Republic

Division of Biomolecular Physics Institute of Physics Faculty of Mathematics and Physics Charles University CZ 12116 Prague 2 Czech Republic

Laboratory of Microbial Genetics and Gene Expression Institute of Microbiology The Czech Academy of Sciences CZ 14220 Prague 4 Czech Republic

See more in PubMed

Weiss A., and Shaw L. N. (2015) Small things considered: the small accessory subunits of RNA polymerase in Gram-positive bacteria. FEMS Microbiol. Rev. 39, 541–554 PubMed PMC

Lópezde Saro F. J., Woody A.-Y., and Helmann J. D. (1995) Structural analysis of the Bacillus subtilis δ factor: a protein polyanion which displaces RNA from RNA polymerase. J. Mol. Biol. 252, 189–202 PubMed

Rabatinová A., Šanderová H., Jirát Matějčková J., Korelusová J., Sojka L., Barvík I., Papoušková V., Sklenář V., Źídek L, and Krásný L. (2013) The δ subunit of RNA polymerase is required for rapid changes in gene expression and competitive fitness of the cell. J. Bacteriol. 195, 2603–2611 PubMed PMC

Prajapati R. K., Sengupta S., Rudra P., and Mukhopadhyay J. (2016) Bacillus subtilis δ functions as a transcriptional regulator by facilitating the open complex formation. J. Biol. Chem. 291, 1064–1075 PubMed PMC

Weiss A., Ibarra J. A., Paoletti J., Carroll R. K., and Shaw L. N. (2014) The δ subunit of RNA polymerase guides promoter selectivity and virulence in Staphylococcus aureus. Infect. Immun. 82, 1424–1435 PubMed PMC

Wiedermannová J., Sudzinová P., Koval' T., Rabatinová A., Šanderová H., Ramaniuk O., Rittich Š., Dohnálek J., Fu Z., Halada P., Lewis P., and Krásný L. (2014) Characterization of helD, an interacting partner of RNA polymerase from Bacillus subtilis. Nucleic Acids Res. 42, 5151–5163 PubMed PMC

Keller A. N., Yang X., Wiedermannová J., Delumeau O., Krásný L., and Lewis P. J. (2014) ϵ, a new subunit of RNA polymerase found in Gram-positive bacteria. J. Bacteriol. 196, 3622–3632 PubMed PMC

Murakami K. S., and Darst S. A. (2003) Bacterial RNA polymerases: the wholo story. Curr. Opin. Struct. Biol. 13, 31–39 PubMed

Ma C., Yang X., Kandemir H., Mielczarek M., Johnston E. B., Griffith R., Kumar N., and Lewis P. J. (2013) Inhibitors of bacterial transcription initiation complex formation. ACS Chem. Biol. 8, 1972–1980 PubMed

Paget M. S. (2015) Bacterial sigma factors and anti-sigma factors: structure, function and distribution. Biomolecules 5, 1245–1265 PubMed PMC

Österberg S., del Peso-Santos T., and Shingler V. (2011) Regulation of alternative sigma factor use. Annu. Rev. Microbiol. 65, 37–55 PubMed

Bae B., Davis E., Brown D., Campbell E. A., Wigneshweraraj S., and Darst S. A. (2013) Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of σ70 domain 1.1. Proc. Natl. Acad. Sci. U.S.A. 110, 19772–19777 PubMed PMC

Murakami K. (2013) X-ray crystal structure of Escherichia coli RNA polymerase σ70 holoenzyme. J. Biol. Chem. 288, 9126–9134 PubMed PMC

Dombroski A. J., Walter W. A., and Gross C. A. (1993) Amino-terminal amino acids modulate σ-factor DNA-binding activity. Genes Dev. 7, 2446–2455 PubMed

Schwartz E. C., Shekhtman A., Dutta K., Pratt M. R., Cowburn D., Darst S., and Muir T. W. (2008) A full-length group 1 bacterial sigma factor adopts a compact structure incompatible with DNA binding. Chem. Biol. 15, 1091–1103 PubMed PMC

Korzhnev D., Billeter M., Arseniev A., and Orekhov V. (2001) NMR studies of brownian tumbling and internal motions in proteins. Prog. Nuclear Magn. Reson. Spectrosc. 38, 197–266

Lipari G., and Szabo A. (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules: 1. theory and range of validity. J. Am. Chem. Soc. 104, 4546–4559

Lipari G., and Szabo A. (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules: 2. analysis of experimental results. J. Am. Chem. Soc. 104, 4559–4570

Clore G. M., Szabo A., Bax A., Kay L. E., Driscoll P. C., and Gronenborn A. M. (1990) Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J. Am. Chem. Soc. 112, 4989–4991

Morin S., Linnet T. E., Lescanne M., Schanda P., Thompson G. S., Tollinger M., Teilum K., Gagné S., Marion D., Griesinger C., Blackledge M., and d'Auvergne E. J. (2014) Relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics 30, 2219–2220 PubMed PMC

MacDougall I. J., Lewis P. J., and Griffith R. (2005) Homology modelling of RNA polymerase and associated transcription factors from Bacillus subtilis. J. Mol. Graphics Model. 23, 297–303 PubMed

Zuo Y., and Steitz T. (2015) Crystal structures of the E. coli transcription initiation complexes with a complete bubble. Mol. Cell 58, 534–540 PubMed PMC

Demo G., Papoušková V., Komárek J., Kadeřávek P., Otrusinová O., Srb P., Rabatinová A., Krásný L., Žídek, Sklenář L. V., and Wimmerová M. (2014) X-ray vs. NMR structure of N-terminal domain of δ-subunit of RNA polymerase. J. Struct. Biol. 187, 174–186 PubMed

Papoušková V., Kadeřávek P., Otrusinová O., Rabatinová A., Šanderová, Nováček H. J., Krásný L., Sklenář V., and Žídek L. (2013) Structural study of the partially disordered full-length δ subunit of RNA polymerase from Bacillus subtilis. ChemBioChem 14, 1772–1779 PubMed

Motáčková V., Šanderová H., Žídek L., Nováček J., Padrta P., Švenková A., Korelusová J., Jonák J., Krásný L., and Sklenář V. (2010) Solution structure of the N-terminal domain of Bacillus subtilis δ subunit of RNA polymerase and its classification based on structural homologs. Proteins 78, 1807–1810 PubMed

Sattler M., Schleucher J., and Griesinger C. (1999) Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog. Nuclear Magn. Reson. Spectrosc. 34, 93–158

Ulrich E. L., Akutsu H., Doreleijers J. F., Harano Y., Ioannidis Y. E., Lin J., Livny M., Mading S., Maziuk D., Miller Z., Nakatani E., Schulte C. F., Tolmie D. E., Kent Wenger R., Yao H., et al. (2008) BioMagResBank. Nucleic Acids Res. 36, D402–D408 PubMed PMC

Vuister G. W., and Bax A. (1993) Quantitative J correlation: a new approach for measuring homonuclear three-bond J(HN Hα) coupling constants in 15N-enriched proteins. J. Am. Chem. Soc. 115, 7772–7777

Novák P., Žídek L., Motáčková V., Padrta P., Švenková A., Nuzillard J.-M., Krásný L., and Sklenář V. (2010) S3EPY: a Sparky extension for determination of small scalar couplings from spin-state-selective excitation NMR experiments.. J. Biomol. NMR 46, 191–197 PubMed

Hagen N., Kupinski M., and Dereniak E. L. (2007) Gaussian profile estimation in one dimension. Applied Optics 46, 5374–5383 PubMed PMC

Delaglio F., Grzesiek S., Vuister G. W., Zhu G., Pfeifer J., and Bax A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293 PubMed

Marsh J. A., Singh V. K., Jia Z., and Forman-Kay J. D. (2006) Sensitivity of secondary structure propensities to sequence differences between α- and γ-synuclein: implications for fibrillation. Protein Sci. 15, 2795–2804 PubMed PMC

Herrmann T., Güntert P., and Wüthrich K. (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 319, 209–227 PubMed

Güntert P., and Buchner L. (2015) Combined automated NOE assignment and structure calculation with CYANA. J. Biomol. NMR 62, 453–471 PubMed

Brünger A. T., Adams P. D., Clore G. M., DeLano W. L., Gros P., Grosse-Kunstleve R. W., Jiang J. S., Kuszewski J., Nilges M., Pannu N. S., Read R. J., Rice L. M., Simonson T., and Warren G. L. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 PubMed

Jansen S., Chmelík J., Žídek L., Padrta P., Novák P., Zdráhal Z., Picimbon J. F., Löfstedt C., and Sklenář V. (2007) Structure of Bombyx mori chemosensory protein 1 in solution. Arch. Insect Biochem. Physiol. 66, 135–145 PubMed

Sass H.-J., Musco G., Stahl S. J., Wingfield P. T., and Grzesiek S. (2001) An easy way to include weak alignment constraints into NMR structure calculations. J. Biomol. NMR 21, 275–280 PubMed

Doreleijers J. F., Vranken W. F., Schulte C., Markley J. L., Ulrich E. L., Vriend G., and Vuister G. W. (2012) NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. Nucleic Acids Res. 40, D519–D524 PubMed PMC

Doreleijers J. F., Sousa da Silva A. W., Krieger E., Nabuurs S. B., Spronk C. A., Stevens T. J., Vranken W. F., Vriend G., and Vuister G. W. (2012) CING: an integrated residue-based structure validation program suite. J. Biomol. NMR 54, 267–283 PubMed PMC

Berman H. M., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig H., Shindyalov I. N., and Bourne P. E. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235–242 PubMed PMC

Ferrage F., Cowburn D., and Ghose R. (2009) Accurate sampling of high-frequency motions in proteins by steady-state 15N-1H nuclear Overhauser effect measurements in the presence of cross-correlated relaxation. J. Am. Chem. Soc. 131, 6048–6049 PubMed PMC

Pelupessy P., Espallargas G. M., and Bodenhausen G. (2003) Symmetrical reconversion: measuring cross-correlation rates with enhanced accuracy. J. Magn. Reson. 161, 258–264 PubMed

Pelupessy P., Ferrage F., and Bodenhausen G. (2007) Accurate measurement of longitudinal cross-relaxation rates in nuclear magnetic resonance. J. Chem. Phys. 126, 134508. PubMed

d'Auvergne E. J., and Gooley P. R. (2006) Model-free model elimination: a new step in the model-free dynamic analysis of NMR relaxation data. J. Biomol. NMR 35, 117–135 PubMed

d'Auvergne E. J., and Gooley P. R. (2007) Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm, Mol. BioSyst. 3, 483–494 PubMed

d'Auvergne E. J., and Gooley P. R. (2008) Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR 40, 107–119 PubMed PMC

d'Auvergne E. J., and Gooley P. R. (2008) Optimisation of NMR dynamic models: II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR 40, 121–133 PubMed PMC

Eaton J. W., Bateman D., and Hauberg S. (2008) GNU Octave Manual, Version 3, Network Theory Ltd., Bristol, United Kingdom

Morin S., and Gagné M. S. (2009) Simple tests for the validation of multiple field spin relaxation data. J. Biomol. NMR 45, 361–372 PubMed

d'Auvergne E. J., and Gooley P. R. (2003) The use of model selection in the model-free analysis of protein dynamics. J. Biomol. NMR 25, 25–39 PubMed

Long D., Liu M., and Yang D. (2008) Accurately probing slow motions on millisecond time scales with a robust NMR relaxation experiment. J. Am. Chem. Soc. 130, 2432–2433 PubMed

MoaB2, a newly identified transcription factor, binds to σA in Mycobacterium smegmatis

Mycobacterial HelD connects RNA polymerase recycling with transcription initiation

The Core and Holoenzyme Forms of RNA Polymerase from Mycobacterium smegmatis

See more in PubMed

PDB
4LK1, 4YLN, 5MWW