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RNA polymerase-promoter interactions determining different stability of the Escherichia coli and Thermus aquaticus transcription initiation complexes

Transcription initiation complexes formed by bacterial RNA polymerases (RNAPs) exhibit dramatic species-specific differences in stability, leading to different strategies of transcription regulation. The molecular basis for this diversity is unclear. Promoter complexes formed by RNAP from Thermus aq...

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Autores principales: Mekler, Vladimir, Minakhin, Leonid, Kuznedelov, Konstantin, Mukhamedyarov, Damir, Severinov, Konstantin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526302/
https://www.ncbi.nlm.nih.gov/pubmed/23087380
http://dx.doi.org/10.1093/nar/gks973
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author Mekler, Vladimir
Minakhin, Leonid
Kuznedelov, Konstantin
Mukhamedyarov, Damir
Severinov, Konstantin
author_facet Mekler, Vladimir
Minakhin, Leonid
Kuznedelov, Konstantin
Mukhamedyarov, Damir
Severinov, Konstantin
author_sort Mekler, Vladimir
collection PubMed
description Transcription initiation complexes formed by bacterial RNA polymerases (RNAPs) exhibit dramatic species-specific differences in stability, leading to different strategies of transcription regulation. The molecular basis for this diversity is unclear. Promoter complexes formed by RNAP from Thermus aquaticus (Taq) are considerably less stable than Escherichia coli RNAP promoter complexes, particularly at temperatures below 37°C. Here, we used a fluorometric RNAP molecular beacon assay to discern partial RNAP-promoter interactions. We quantitatively compared the strength of E. coli and Taq RNAPs partial interactions with the −10, −35 and UP promoter elements; the TG motif of the extended −10 element; the discriminator and the downstream duplex promoter segments. We found that compared with Taq RNAP, E. coli RNAP has much higher affinity only to the UP element and the downstream promoter duplex. This result indicates that the difference in stability between E. coli and Taq promoter complexes is mainly determined by the differential strength of core RNAP–DNA contacts. We suggest that the relative weakness of Taq RNAP interactions with DNA downstream of the transcription start point is the major reason of low stability and temperature sensitivity of promoter complexes formed by this enzyme.
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spelling pubmed-35263022013-01-04 RNA polymerase-promoter interactions determining different stability of the Escherichia coli and Thermus aquaticus transcription initiation complexes Mekler, Vladimir Minakhin, Leonid Kuznedelov, Konstantin Mukhamedyarov, Damir Severinov, Konstantin Nucleic Acids Res Gene Regulation, Chromatin and Epigenetics Transcription initiation complexes formed by bacterial RNA polymerases (RNAPs) exhibit dramatic species-specific differences in stability, leading to different strategies of transcription regulation. The molecular basis for this diversity is unclear. Promoter complexes formed by RNAP from Thermus aquaticus (Taq) are considerably less stable than Escherichia coli RNAP promoter complexes, particularly at temperatures below 37°C. Here, we used a fluorometric RNAP molecular beacon assay to discern partial RNAP-promoter interactions. We quantitatively compared the strength of E. coli and Taq RNAPs partial interactions with the −10, −35 and UP promoter elements; the TG motif of the extended −10 element; the discriminator and the downstream duplex promoter segments. We found that compared with Taq RNAP, E. coli RNAP has much higher affinity only to the UP element and the downstream promoter duplex. This result indicates that the difference in stability between E. coli and Taq promoter complexes is mainly determined by the differential strength of core RNAP–DNA contacts. We suggest that the relative weakness of Taq RNAP interactions with DNA downstream of the transcription start point is the major reason of low stability and temperature sensitivity of promoter complexes formed by this enzyme. Oxford University Press 2012-12 2012-10-18 /pmc/articles/PMC3526302/ /pubmed/23087380 http://dx.doi.org/10.1093/nar/gks973 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.
spellingShingle Gene Regulation, Chromatin and Epigenetics
Mekler, Vladimir
Minakhin, Leonid
Kuznedelov, Konstantin
Mukhamedyarov, Damir
Severinov, Konstantin
RNA polymerase-promoter interactions determining different stability of the Escherichia coli and Thermus aquaticus transcription initiation complexes
title RNA polymerase-promoter interactions determining different stability of the Escherichia coli and Thermus aquaticus transcription initiation complexes
title_full RNA polymerase-promoter interactions determining different stability of the Escherichia coli and Thermus aquaticus transcription initiation complexes
title_fullStr RNA polymerase-promoter interactions determining different stability of the Escherichia coli and Thermus aquaticus transcription initiation complexes
title_full_unstemmed RNA polymerase-promoter interactions determining different stability of the Escherichia coli and Thermus aquaticus transcription initiation complexes
title_short RNA polymerase-promoter interactions determining different stability of the Escherichia coli and Thermus aquaticus transcription initiation complexes
title_sort rna polymerase-promoter interactions determining different stability of the escherichia coli and thermus aquaticus transcription initiation complexes
topic Gene Regulation, Chromatin and Epigenetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526302/
https://www.ncbi.nlm.nih.gov/pubmed/23087380
http://dx.doi.org/10.1093/nar/gks973
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