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.

Základní údaje

Originální název

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

Autoři

TUŽINČIN, Dávid; Petr PADRTA; Hana ŠANDEROVÁ; Alžběta RABATINOVÁ; Kateřina BENDOVÁ; Libor KRÁSNÝ; Lukáš ŽÍDEK a Pavel KADEŘÁVEK

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Konferenční abstrakt

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/23:00130951

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

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

Příznaky

Mezinárodní význam

Změněno: 13. 6. 2023 13:42, Mgr. Dávid Tužinčin

Anotace

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

Návaznosti

EF18_070/0009846, projekt VaV

Název: MSCAfellow2@MUNI

GJ18-04197Y, projekt VaV

Název: Charakterizace flexibilních oblastí RNA polymerázy Bacillus subtilis

Investor: Grantová agentura ČR, Characterization of dynamical regions in RNA polymerase from Bacillus subtilis

LM2018127, projekt VaV

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

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

MUNI/A/1413/2022, interní kód MU

Název: Struktura a dynamika biopolymerů

Investor: Masarykova univerzita, Struktura a dynamika biopolymerů

Citovat

TUŽINČIN, Dávid; Petr PADRTA; Hana ŠANDEROVÁ; Alžběta RABATINOVÁ; Kateřina BENDOVÁ; Libor KRÁSNÝ; Lukáš ŽÍDEK a 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 a 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.

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