Domain 1.1 of σA factor of RNA polymerase from Bacillus
subtilis beyond its major state conformation

a 2023

Domain 1.1 of σA factor of RNA polymerase from Bacillus subtilis beyond its major state conformation

TUŽINČIN, Dávid, Petr PADRTA, Hana ŠANDEROVÁ, Alžběta RABATINOVÁ, Kateřina BENDOVÁ et. al.

Basic information

Original name

Domain 1.1 of σA factor of RNA polymerase from Bacillus subtilis beyond its major state conformation

Authors

TUŽINČIN, Dávid (703 Slovakia, belonging to the institution), Petr PADRTA (203 Czech Republic), Hana ŠANDEROVÁ (203 Czech Republic), Alžběta RABATINOVÁ (203 Czech Republic), Kateřina BENDOVÁ (203 Czech Republic), Libor KRÁSNÝ (203 Czech Republic), Lukáš ŽÍDEK (203 Czech Republic) and Pavel KADEŘÁVEK (203 Czech Republic, guarantor)

Edition

Inaugural Biochemistry Symposium Puzzles of (Bio)molecular Structure and Dynamics: NMR spectroscopy and complementary approaches. 2023

Other information

Language

English

Type of outcome

Konferenční abstrakt

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

RIV identification code

RIV/00216224:14310/23:00130951

Organization unit

Faculty of Science

Keywords in English

σA factor; RNA polymerase; Bacillus subtilis; NMR; conformational exchange

Abstract

V originále

σ factors of RNA polymerase in bacteria are one of their key components which recognize promotor sequences and initiate transcription [1]. Domain 1.1 of σ A factors occupies the primary channel of RNA polymerase and prevents binding of the σ factor to promoter DNA [2,3]. Here we are presenting a study of domain 1.1 of σ A from the model organism B. subtilis and we are describing its dynamics at μs—ms timescale using detailed study of nuclear magnetic resonance together with its thermal unfolding characterized by optical and calorimetric methods. The results show that the domain 1.1 of σ A factor has natural ability to form a significantly less compact and more flexible state compared to the previously determined structure [4] at biologically relevant temperatures as documented by the secondary structure propensity (SSP) prediction based on the NMR data (Figure 1) and it is shown that even the hydrophobic core of the protein is affected by the transition of the state of the protein. The study is complemented with the functional characterization of the domain 1.1 in dependence on temperature. It clearly showed that the domain 1.1 is responsible for the response of the transcription process to an increase of the temperature supporting our hypothesis that the conformational plasticity of the domain 1.1 affects its ability to entry or exit the primary channel of RNA polymerase and it allows to increase the transcriptional output at higher temperatures. [1] Murakami K.S. and Darst S.A. (2003) Bacterial rna polymerases: the wholo story. Current opinion in structural biology, 13(1):31–39 [2] 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 σ 70 domain 1.1. Proceedings of the National Academy of Sciences, 110(49):19772–19777 [3] Murakami K.S. (2013) X-ray crystal structure of Escherichia coli RNA polymerase σ 70 holoenzyme. Journal of Biological Chemistry, 288(13):9126–9134

Links

EF18_070/0009846, research and development project

Name: MSCAfellow2@MUNI

GJ18-04197Y, research and development project

Name: Charakterizace flexibilních oblastí RNA polymerázy Bacillus subtilis

Investor: Czech Science Foundation

LM2018127, research and development project

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

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

MUNI/A/1413/2022, interní kód MU

Name: Struktura a dynamika biopolymerů

Investor: Masaryk University

Citovat

TUŽINČIN, Dávid, Petr PADRTA, Hana ŠANDEROVÁ, Alžběta RABATINOVÁ, Kateřina BENDOVÁ, Libor KRÁSNÝ, Lukáš ŽÍDEK and Pavel KADEŘÁVEK. Domain 1.1 of σA factor of RNA polymerase from Bacillus subtilis beyond its major state conformation. In Inaugural Biochemistry Symposium Puzzles of (Bio)molecular Structure and Dynamics: NMR spectroscopy and complementary approaches. 2023.

@proceedings{2291213,
   author = {Tužinčin, Dávid and Padrta, Petr and Šanderová, Hana and Rabatinová, Alžběta and Bendová, Kateřina and Krásný, Libor and Žídek, Lukáš and Kadeřávek, Pavel},
   booktitle = {Inaugural Biochemistry Symposium Puzzles of (Bio)molecular Structure and Dynamics: NMR spectroscopy and complementary approaches.},
   keywords = {σA factor; RNA polymerase; Bacillus subtilis; NMR; conformational exchange},
   language = {eng},
   title = {Domain 1.1 of σA factor of RNA polymerase from Bacillus subtilis beyond its major state conformation},
   url = {https://www.jku.at/fileadmin/gruppen/385/202305-Symposium/BookOfAbstracts.pdf},
   year = {2023}
}

TY  - CONF
ID  - 2291213
AU  - Tužinčin, Dávid - Padrta, Petr - Šanderová, Hana - Rabatinová, Alžběta - Bendová, Kateřina - Krásný, Libor - Žídek, Lukáš - Kadeřávek, Pavel
PY  - 2023
TI  - Domain 1.1 of σA factor of RNA polymerase from Bacillus subtilis beyond its major state conformation
KW  - σA factor
KW  - RNA polymerase
KW  - Bacillus subtilis
KW  - NMR
KW  - conformational exchange
UR  - https://www.jku.at/fileadmin/gruppen/385/202305-Symposium/BookOfAbstracts.pdf
N2  - σ factors of RNA polymerase in bacteria are one of their key components which recognize promotor sequences and initiate transcription [1]. Domain 1.1 of σ A factors occupies the primary channel of RNA polymerase and prevents binding of the σ factor to promoter DNA [2,3]. Here we are presenting a study of domain 1.1 of σ A from the model organism B. subtilis and we are describing its dynamics at μs—ms timescale using detailed study of nuclear magnetic resonance together with its thermal unfolding characterized by optical and calorimetric methods. The results show that the domain 1.1 of σ A factor has natural ability to form a significantly less compact and more flexible state compared to the previously determined structure [4] at biologically relevant temperatures as documented by the secondary structure propensity (SSP) prediction based on the NMR data (Figure 1) and it is shown that even the hydrophobic core of the protein is affected by the transition of the state of the protein. The study is complemented with the functional characterization of the domain 1.1 in dependence on temperature. It clearly showed that the domain 1.1 is responsible for the response of the transcription process to an increase of the temperature supporting our hypothesis that the conformational plasticity of the domain 1.1 affects its ability to entry or exit the primary channel of RNA polymerase and it allows to increase the transcriptional output at higher temperatures. [1] Murakami K.S. and Darst S.A. (2003) Bacterial rna polymerases: the wholo story. Current opinion in structural biology, 13(1):31–39 [2] 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 σ 70 domain 1.1. Proceedings of the National Academy of Sciences, 110(49):19772–19777 [3] Murakami K.S. (2013) X-ray crystal structure of Escherichia coli RNA polymerase σ 70 holoenzyme. Journal of Biological Chemistry, 288(13):9126–9134
ER  -

TUŽINČIN, Dávid, Petr PADRTA, Hana ŠANDEROVÁ, Alžběta RABATINOVÁ, Kateřina BENDOVÁ, Libor KRÁSNÝ, Lukáš ŽÍDEK and Pavel KADEŘÁVEK. Domain 1.1 of σA factor of RNA polymerase from Bacillus subtilis beyond its major state conformation. In \textit{Inaugural Biochemistry Symposium Puzzles of (Bio)molecular Structure and Dynamics: NMR spectroscopy and complementary approaches.}. 2023.

Detailed Information on Publication Record