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.

Základní údaje

Originální název

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

Autoři

ZACHRDLA, Milan (203 Česká republika, domácí), Petr PADRTA (203 Česká republika, domácí), Alzbeta RABATINOVA (203 Česká republika), Hana SANDEROVA (203 Česká republika), Ivan BARVIK (203 Česká republika), Libor KRASNY (203 Česká republika) a Lukáš ŽÍDEK (203 Česká republika, garant, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.011

Kód RIV

RIV/00216224:14740/17:00094887

Organizační jednotka

Středoevropský technologický institut

DOI

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

UT WoS

000405485600002

Klíčová slova anglicky

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

Štítky

CF NMR, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 28. 2. 2018 16:36, Mgr. Pavla Foltynová, Ph.D.

Anotace

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.

Návaznosti

GA13-16842S, projekt VaV

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

Investor: Grantová agentura ČR, Podjednotky urcující DNA specificitu bakteriální RNA polymerázy s flexibilními doménami: funkce a dynamika

LM2015043, projekt VaV

Název: Česká infrastruktura pro integrativní strukturní biologii (Akronym: CIISB)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Czech Infrastructure for Integrative Structural Biology

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

ZACHRDLA, Milan, Petr PADRTA, Alzbeta RABATINOVA, Hana SANDEROVA, Ivan BARVIK, Libor KRASNY a 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, roč. 292, č. 28, s. 11610-11617. ISSN 0021-9258. Dostupné z: 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 a 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, roč.~292, č.~28, s.~11610-11617. ISSN~0021-9258. Dostupné z: https://dx.doi.org/10.1074/jbc.M117.784074.

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