Solution structure of domain 1.1 of the sigma(A) factor from
Bacillus subtilis is preformed for binding to the RNA
polymerase core

J 2017

Solution structure of domain 1.1 of the sigma(A) factor from Bacillus subtilis is preformed for binding to the RNA polymerase core

ZACHRDLA, Milan, Petr PADRTA, Alzbeta RABATINOVA, Hana SANDEROVA, Ivan BARVIK et. al.

Basic information

Original name

Solution structure of domain 1.1 of the sigma(A) factor from Bacillus subtilis is preformed for binding to the RNA polymerase core

Authors

ZACHRDLA, Milan (203 Czech Republic, belonging to the institution), Petr PADRTA (203 Czech Republic, belonging to the institution), Alzbeta RABATINOVA (203 Czech Republic), Hana SANDEROVA (203 Czech Republic), Ivan BARVIK (203 Czech Republic), Libor KRASNY (203 Czech Republic) and Lukáš ŽÍDEK (203 Czech Republic, guarantor, belonging to the institution)

Edition

Journal of Biological Chemistry, Bethesda, Amer. Soc. Biochem. Mol. Biol. 2017, 0021-9258

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 4.011

RIV identification code

RIV/00216224:14740/17:00094887

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1074/jbc.M117.784074

UT WoS

000405485600002

Keywords in English

Bacillus; molecular modeling; nuclear magnetic resonance (NMR); protein structure; RNA polymerase; transcription initiation factor

Abstract

V originále

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.

Links

GA13-16842S, research and development project

Name: PODJEDNOTKY URČUJÍCÍ DNA SPECIFICITU BAKTERIÁLNÍ RNA POLYMERÁZY S FLEXIBILNÍMI DOMÉNAMI: FUNKCE A DYNAMIKA

Investor: Czech Science Foundation

LM2015043, research and development project

Name: Česká infrastruktura pro integrativní strukturní biologii (Acronym: CIISB)

Investor: Ministry of Education, Youth and Sports of the CR

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

ZACHRDLA, Milan, Petr PADRTA, Alzbeta RABATINOVA, Hana SANDEROVA, Ivan BARVIK, Libor KRASNY and Lukáš ŽÍDEK. Solution structure of domain 1.1 of the sigma(A) factor from Bacillus subtilis is preformed for binding to the RNA polymerase core. Journal of Biological Chemistry. Bethesda: Amer. Soc. Biochem. Mol. Biol., 2017, vol. 292, No 28, p. 11610-11617. ISSN 0021-9258. Available from: https://dx.doi.org/10.1074/jbc.M117.784074.

@article{1387541,
   author = {Zachrdla, Milan and Padrta, Petr and Rabatinova, Alzbeta and Sanderova, Hana and Barvik, Ivan and Krasny, Libor and Žídek, Lukáš},
   article_location = {Bethesda},
   article_number = {28},
   doi = {http://dx.doi.org/10.1074/jbc.M117.784074},
   keywords = {Bacillus; molecular modeling; nuclear magnetic resonance (NMR); protein structure; RNA polymerase; transcription initiation factor},
   language = {eng},
   issn = {0021-9258},
   journal = {Journal of Biological Chemistry},
   title = {Solution structure of domain 1.1 of the sigma(A) factor from Bacillus subtilis is preformed for binding to the RNA polymerase core},
   url = {http://www.jbc.org/content/292/28/11610},
   volume = {292},
   year = {2017}
}

TY  - JOUR
ID  - 1387541
AU  - Zachrdla, Milan - Padrta, Petr - Rabatinova, Alzbeta - Sanderova, Hana - Barvik, Ivan - Krasny, Libor - Žídek, Lukáš
PY  - 2017
TI  - Solution structure of domain 1.1 of the sigma(A) factor from Bacillus subtilis is preformed for binding to the RNA polymerase core
JF  - Journal of Biological Chemistry
VL  - 292
IS  - 28
SP  - 11610-11617
EP  - 11610-11617
PB  - Amer. Soc. Biochem. Mol. Biol.
SN  - 00219258
KW  - Bacillus
KW  - molecular modeling
KW  - nuclear magnetic resonance (NMR)
KW  - protein structure
KW  - RNA polymerase
KW  - transcription initiation factor
UR  - http://www.jbc.org/content/292/28/11610
L2  - http://www.jbc.org/content/292/28/11610
N2  - 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.
ER  -

ZACHRDLA, Milan, Petr PADRTA, Alzbeta RABATINOVA, Hana SANDEROVA, Ivan BARVIK, Libor KRASNY and Lukáš ŽÍDEK. Solution structure of domain 1.1 of the sigma(A) factor from Bacillus subtilis is preformed for binding to the RNA polymerase core. \textit{Journal of Biological Chemistry}. Bethesda: Amer. Soc. Biochem. Mol. Biol., 2017, vol.~292, No~28, p.~11610-11617. ISSN~0021-9258. Available from: https://dx.doi.org/10.1074/jbc.M117.784074.

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