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Region 4 of the RNA polymerase σ subunit counteracts pausing during initial transcription

All cellular genetic information is transcribed into RNA by multisubunit RNA polymerases (RNAPs). The basal transcription initiation factors of cellular RNAPs stimulate the initial RNA synthesis via poorly understood mechanisms. Here, we explored the mechanism employed by the bacterial factor σ in p...

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Detalles Bibliográficos
Autores principales: Brodolin, Konstantin, Morichaud, Zakia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Biochemistry and Molecular Biology 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7948647/
https://www.ncbi.nlm.nih.gov/pubmed/33380428
http://dx.doi.org/10.1074/jbc.RA120.016299
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author Brodolin, Konstantin
Morichaud, Zakia
author_facet Brodolin, Konstantin
Morichaud, Zakia
author_sort Brodolin, Konstantin
collection PubMed
description All cellular genetic information is transcribed into RNA by multisubunit RNA polymerases (RNAPs). The basal transcription initiation factors of cellular RNAPs stimulate the initial RNA synthesis via poorly understood mechanisms. Here, we explored the mechanism employed by the bacterial factor σ in promoter-independent initial transcription. We found that the RNAP holoenzyme lacking the promoter-binding domain σ4 is ineffective in de novo transcription initiation and displays high propensity to pausing upon extension of RNAs 3 to 7 nucleotides in length. The nucleotide at the RNA 3' end determines the pause lifetime. The σ4 domain stabilizes short RNA:DNA hybrids and suppresses pausing by stimulating RNAP active-center translocation. The antipausing activity of σ4 is modulated by its interaction with the β subunit flap domain and by the σ remodeling factors AsiA and RbpA. Our results suggest that the presence of σ4 within the RNA exit channel compensates for the intrinsic instability of short RNA:DNA hybrids by increasing RNAP processivity, thus favoring productive transcription initiation. This “RNAP boosting” activity of the initiation factor is shaped by the thermodynamics of RNA:DNA interactions and thus, should be relevant for any factor-dependent RNAP.
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spelling pubmed-79486472021-03-19 Region 4 of the RNA polymerase σ subunit counteracts pausing during initial transcription Brodolin, Konstantin Morichaud, Zakia J Biol Chem Research Article All cellular genetic information is transcribed into RNA by multisubunit RNA polymerases (RNAPs). The basal transcription initiation factors of cellular RNAPs stimulate the initial RNA synthesis via poorly understood mechanisms. Here, we explored the mechanism employed by the bacterial factor σ in promoter-independent initial transcription. We found that the RNAP holoenzyme lacking the promoter-binding domain σ4 is ineffective in de novo transcription initiation and displays high propensity to pausing upon extension of RNAs 3 to 7 nucleotides in length. The nucleotide at the RNA 3' end determines the pause lifetime. The σ4 domain stabilizes short RNA:DNA hybrids and suppresses pausing by stimulating RNAP active-center translocation. The antipausing activity of σ4 is modulated by its interaction with the β subunit flap domain and by the σ remodeling factors AsiA and RbpA. Our results suggest that the presence of σ4 within the RNA exit channel compensates for the intrinsic instability of short RNA:DNA hybrids by increasing RNAP processivity, thus favoring productive transcription initiation. This “RNAP boosting” activity of the initiation factor is shaped by the thermodynamics of RNA:DNA interactions and thus, should be relevant for any factor-dependent RNAP. American Society for Biochemistry and Molecular Biology 2021-01-08 /pmc/articles/PMC7948647/ /pubmed/33380428 http://dx.doi.org/10.1074/jbc.RA120.016299 Text en © 2021 THE AUTHORS https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Research Article
Brodolin, Konstantin
Morichaud, Zakia
Region 4 of the RNA polymerase σ subunit counteracts pausing during initial transcription
title Region 4 of the RNA polymerase σ subunit counteracts pausing during initial transcription
title_full Region 4 of the RNA polymerase σ subunit counteracts pausing during initial transcription
title_fullStr Region 4 of the RNA polymerase σ subunit counteracts pausing during initial transcription
title_full_unstemmed Region 4 of the RNA polymerase σ subunit counteracts pausing during initial transcription
title_short Region 4 of the RNA polymerase σ subunit counteracts pausing during initial transcription
title_sort region 4 of the rna polymerase σ subunit counteracts pausing during initial transcription
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7948647/
https://www.ncbi.nlm.nih.gov/pubmed/33380428
http://dx.doi.org/10.1074/jbc.RA120.016299
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