A1 Refereed original research article in a scientific journal

Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter




AuthorsBera Subhas C, America Pim PB, Maatsola Santeri, Seifert Mona, Ostrofet Eugeniu, Cnossen Jelmer, Spermann Monika, Papini Flávia S, Depken Martin, Malinen Anssi M, Dulin David

PublisherOxford University Press

Publication year2022

JournalNucleic Acids Research

Journal name in sourceNUCLEIC ACIDS RESEARCH

Journal acronymNUCLEIC ACIDS RES

Article number gkac560

Volume50

Issue13

First page 7511

Last page7528

Number of pages18

ISSN0305-1048

eISSN1362-4962

DOIhttps://doi.org/10.1093/nar/gkac560

Web address https://doi.org/10.1093/nar/gkac560

Self-archived copy’s web addresshttps://research.utu.fi/converis/portal/detail/Publication/177819629


Abstract

Transcription initiation is the first step in gene expression, and is therefore strongly regulated in all domains of life. The RNA polymerase (RNAP) first associates with the initiation factor σ to form a holoenzyme, which binds, bends and opens the promoter in a succession of reversible states. These states are critical for transcription regulation, but remain poorly understood. Here, we addressed the mechanism of open complex formation by monitoring its assembly/disassembly kinetics on individual consensus lacUV5 promoters using high-throughput single-molecule magnetic tweezers. We probed the key protein-DNA interactions governing the open-complex formation and dissociation pathway by modulating the dynamics at different concentrations of monovalent salts and varying temperatures. Consistent with ensemble studies, we observed that RNAP-promoter open (RPO) complex is a stable, slowly reversible state that is preceded by a kinetically significant open intermediate (RPI), from which the holoenzyme dissociates. A strong anion concentration and type dependence indicates that the RPO stabilization may involve sequence-independent interactions between the DNA and the holoenzyme, driven by a non-Coulombic effect consistent with the non-template DNA strand interacting with σ and the RNAP β subunit. The temperature dependence provides the energy scale of open-complex formation and further supports the existence of additional intermediates.


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