Characterization of a transitionally occupied state and thermal
unfolding of domain 1.1 of  σ A  factor of RNA polymerase from
Bacillus subtilis

J 2023

Characterization of a transitionally occupied state and thermal unfolding of domain 1.1 of σ A factor of RNA polymerase from Bacillus subtilis

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

Základní údaje

Originální název

Characterization of a transitionally occupied state and thermal unfolding of domain 1.1 of σ A factor of RNA polymerase from Bacillus subtilis

Autoři

TUŽINČIN, Dávid (703 Slovensko, domácí), Petr PADRTA (203 Česká republika, domácí), Hana ŠANDEROVÁ, Alžbeta RABATINOVÁ, Kateřina BENDOVÁ (203 Česká republika, domácí), Libor KRÁSNÝ, Lukáš ŽÍDEK (203 Česká republika, garant, domácí) a Pavel KADEŘÁVEK (203 Česká republika, domácí)

Vydání

Proteins: Structure, Function and Bioinformatics, Wiley, 2023, 0887-3585

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.900 v roce 2022

Kód RIV

RIV/00216224:14740/23:00131160

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1002/prot.26531

UT WoS

001019240900001

Klíčová slova anglicky

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

Štítky

CF BIC, CF NMR, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 27. 10. 2024 15:25, Ing. Martina Blahová

Anotace

V originále

σ factors are essential parts 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 σ A exists in more structurally distinct variants in dynamic equilibrium. The major conformation at room temperature is represented by a previously reported well-folded structure solved by nuclear magnetic resonance (NMR), 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 characterized the minor state of the domain 1.1 using specialized methods of NMR. 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. We also analyzed thermal unfolding of the domain 1.1 and performed functional experiments with full length σ A and its shortened version lacking domain 1.1 ( σ A _ Δ 1.1 ). The results revealed that while full length σ A increases transcription activity of RNAP with increasing temperature, transcription with σ A _ Δ 1.1 remains constant. In summary, 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.

Návaznosti

EF18_070/0009846, projekt VaV

Název: MSCAfellow2@MUNI

GA22-12023S, projekt VaV

Název: Neuspořádanost proteinových struktur vnáší řád do bakteriální transkripce

Investor: Grantová agentura ČR, Neuspořádanost proteinových struktur vnáší řád do bakteriální transkripce

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

LX22NPO5103, projekt VaV

Název: Národní institut virologie a bakteriologie (Akronym: NIVB)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Národní institut virologie a bakteriologie, 5.1 EXCELES

MUNI/A/1413/2022, interní kód MU

Název: Struktura a dynamika biopolymerů

Investor: Masarykova univerzita, Struktura a dynamika biopolymerů

90127, velká výzkumná infrastruktura

Název: CIISB II

Přiložené soubory

Proteins_-_2023_-_Tu_in_in_-_Characterization_of_a_transitionally_occupied_state_and_thermal_unfolding_of_domain_1_1_of_A_.pdf

Vyhledat podobné dokumenty

2296078.pdf

Vyhledat podobné dokumenty

Citovat

TUŽINČIN, Dávid, Petr PADRTA, Hana ŠANDEROVÁ, Alžbeta RABATINOVÁ, Kateřina BENDOVÁ, Libor KRÁSNÝ, Lukáš ŽÍDEK a Pavel KADEŘÁVEK. Characterization of a transitionally occupied state and thermal unfolding of domain 1.1 of σ A factor of RNA polymerase from Bacillus subtilis. Proteins: Structure, Function and Bioinformatics. Wiley, 2023, roč. 91, č. 9, s. 1276-1287. ISSN 0887-3585. Dostupné z: https://dx.doi.org/10.1002/prot.26531.

@article{2296078,
   author = {Tužinčin, Dávid and Padrta, Petr and Šanderová, Hana and Rabatinová, Alžbeta and Bendová, Kateřina and Krásný, Libor and Žídek, Lukáš and Kadeřávek, Pavel},
   article_number = {9},
   doi = {http://dx.doi.org/10.1002/prot.26531},
   keywords = {σA factor; Bacillus subtilis; NMR; RNA polymerase; conformational exchange.},
   language = {eng},
   issn = {0887-3585},
   journal = {Proteins: Structure, Function and Bioinformatics},
   title = {Characterization of a transitionally occupied state and thermal unfolding of domain 1.1 of σ A factor of RNA polymerase from Bacillus subtilis},
   url = {https://onlinelibrary.wiley.com/doi/10.1002/prot.26531},
   volume = {91},
   year = {2023}
}

TY  - JOUR
ID  - 2296078
AU  - Tužinčin, Dávid - Padrta, Petr - Šanderová, Hana - Rabatinová, Alžbeta - Bendová, Kateřina - Krásný, Libor - Žídek, Lukáš - Kadeřávek, Pavel
PY  - 2023
TI  - Characterization of a transitionally occupied state and thermal unfolding of domain 1.1 of σ A factor of RNA polymerase from Bacillus subtilis
JF  - Proteins: Structure, Function and Bioinformatics
VL  - 91
IS  - 9
SP  - 1276-1287
EP  - 1276-1287
PB  - Wiley
SN  - 08873585
KW  - σA factor
KW  - Bacillus subtilis
KW  - NMR
KW  - RNA polymerase
KW  - conformational exchange.
UR  - https://onlinelibrary.wiley.com/doi/10.1002/prot.26531
N2  - σ factors are essential parts 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 σ A exists in more structurally distinct variants in dynamic equilibrium. The major conformation at room temperature is represented by a previously reported well-folded structure solved by nuclear magnetic resonance (NMR), 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 characterized the minor state of the domain 1.1 using specialized methods of NMR. 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. We also analyzed thermal unfolding of the domain 1.1 and performed functional experiments with full length σ A and its shortened version lacking domain 1.1 ( σ A _ Δ 1.1 ). The results revealed that while full length σ A increases transcription activity of RNAP with increasing temperature, transcription with σ A _ Δ 1.1 remains constant. In summary, 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.
ER  -

TUŽINČIN, Dávid, Petr PADRTA, Hana ŠANDEROVÁ, Alžbeta RABATINOVÁ, Kateřina BENDOVÁ, Libor KRÁSNÝ, Lukáš ŽÍDEK a Pavel KADEŘÁVEK. Characterization of a transitionally occupied state and thermal unfolding of domain 1.1 of σ A factor of RNA polymerase from Bacillus subtilis. \textit{Proteins: Structure, Function and Bioinformatics}. Wiley, 2023, roč.~91, č.~9, s.~1276-1287. ISSN~0887-3585. Dostupné z: https://dx.doi.org/10.1002/prot.26531.

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