a 2023

Characterisation of invisible conformation of domain 1.1 of σA factor of RNA polymerase from Bacillus subtilis

TUŽINČIN, Dávid, Petr PADRTA, Hana ŠANDEROVÁ, Alžběta RABATINOVÁ, Libor KRÁSNÝ et. al.

Basic information

Original name

Characterisation of invisible conformation of domain 1.1 of σA factor of RNA polymerase from Bacillus subtilis

Authors

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

Edition

19th European Magnetic Resonance Congress, EUROMAR 2023, 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:

RIV identification code

RIV/00216224:14310/23:00131478

Organization unit

Faculty of Science

Keywords in English

σA factor; RNA polymerase; Bacillus subtilis; NMR; conformational exchange
Změněno: 22/8/2023 20:45, Mgr. Dávid Tužinčin

Abstract

V originále

Introduction: σ factors are essential components of bacterial RNA polymerase (RNAP) as they allow to recognize promotor sequences and initiate transcription. Domain 1.1 of vegetative σ factors occupies the primary channel of RNAP and also prevents binding of the σ factor to promoter DNA alone. Here, we show that domain 1.1 of Bacillus subtilis σA exists in two structurally distinct variants in dynamic equilibrium. Aims: To elucidate the structure and dynamics of minor conformation and to discover how does minor conformation affect transcription. Methods: Relaxation dispersion analysis, chemical exchange saturation transfer analysis, in vitro transcription Results: The major conformation at room temperature is represented by a previously reported well-folded structure solved by nuclear magnetic resonance, but 4 % of the protein molecules are present in a less thermodynamically favorable state. We show that this population increases with temperature and we predict its significant elevation at higher but still biologically relevant temperatures. We found that, in contrast to the major state, the detected minor state is partially unfolded. Its propensity to form secondary structure elements is especially decreased for the first and third α helices, while the second α helix and β strand close to the C-terminus are more stable. Functional experiments with full length σA and its shortened version lacking domain 1.1(σA_∆1.1) then revealed that while full length σA increases transcription activity of RNAP with increasing temperature, transcription with σA_∆1.1 remains constant. Conclusions: In conclusion, this study reveals conformational dynamics of domain 1.1 and provides a basis for studies of its interaction with RNAP and effects on transcription regulation.

Links

EF18_070/0009846, research and development project
Name: MSCAfellow2@MUNI
GA22-12023S, research and development project
Name: Neuspořádanost proteinových struktur vnáší řád do bakteriální transkripce
Investor: Czech Science Foundation, Structural protein disorder brings order into bacterial transcription
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
LX22NPO5103, research and development project
Name: Národní institut virologie a bakteriologie (Acronym: NIVB)
Investor: Ministry of Education, Youth and Sports of the CR, National Institute of Virology and Bacteriology, 5.1 EXCELES
MUNI/A/1413/2022, interní kód MU
Name: Struktura a dynamika biopolymerů
Investor: Masaryk University