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Thermodynamic Modeling of Variations in the Rate of RNA Chain Elongation of E-coli rrn Operons
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
2014 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 1, 55-64 p.Article in journal (Refereed) Published
Abstract [en]

Previous electron-microscopic imaging has shown high RNA polymerase occupation densities in the 16S and 23S encoding regions and low occupation densities in the noncoding leader, spacer, and trailer regions of the rRNA (rrn) operons in E. coli. This indicates slower transcript elongation within the coding regions and faster elongation within the noncoding regions of the operon. Inactivation of four of the seven rrn operons increases the transcript initiation frequency at the promoters of the three intact operons and reduces the time for RNA polymerase to traverse the operon. We have used the DNA sequence-dependent standard free energy variation of the transcription complex to model the experimentally observed changes in the elongation rate along the rrnB operon. We also model the stimulation of the average transcription rate over the whole operon by increasing rate of transcript initiation. Monte Carlo simulations, taking into account initiation of transcription, translocation, and backward and forward tracking of RNA polymerase, partially reproduce the observed transcript elongation rate variations along the rrn operon and fully account for the increased average rate in response to increased frequency of transcript initiation.

Place, publisher, year, edition, pages
2014. Vol. 106, no 1, 55-64 p.
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-217653DOI: 10.1016/j.bpj.2013.11.4487ISI: 000329407700010OAI: oai:DiVA.org:uu-217653DiVA: diva2:695771
Available from: 2014-02-12 Created: 2014-02-04 Last updated: 2017-12-06Bibliographically approved
In thesis
1. Speed and accuracy in transcription and translation: Modelling of transcript and polypeptide elongation
Open this publication in new window or tab >>Speed and accuracy in transcription and translation: Modelling of transcript and polypeptide elongation
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Place, publisher, year, edition, pages
Uppsala Universitet, 2015
National Category
Biochemistry and Molecular Biology
Research subject
Biology with specialization in Molecular Biotechnology
Identifiers
urn:nbn:se:uu:diva-262698 (URN)
Public defence
2015-10-30, BMC A1:111a, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Funder
Knut and Alice Wallenberg FoundationVINNOVASwedish Research Council
Available from: 2015-10-08 Created: 2015-09-18 Last updated: 2015-11-23

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Fange, DavidMellenius, HarrietEhrenberg, Måns

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