A strategy for dissecting the kinetics of transcription repression mechanisms

Cristina S.D. Palma, Sofia Startceva, Ramakanth Neeli-Venkata, Marzieh Zare, Nadia S.M. Goncalves, Jose M. Fonseca, Samuel M.D. Oliveira, Andre S. Ribeiro

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

    1 Citation (Scopus)
    1 Downloads (Pure)

    Abstract

    Promoters in Escherichia coli include an ‘OFF’ state, during which transcription is halted. Here, we propose a novel empirical method for assessing the time-length spent by promoters in this state. It relies on direct measurements of RNA production kinetics at the single molecule level at different induction levels, followed by an estimation of the RNA production rate under infinite induction, which is then compared to this rate under real, maximum induction. We apply it to the LacO3O1 promoter and infer that, under full induction, on average, 15% of the time between successful transcription events is spent in the OFF state. We verify this result by comparing the kinetics of a mutant strain lacking repressor molecules with that of the inferred rate under infinite induction. We expect this strategy of dissecting the kinetics of transcription repression to be applicable to a wide number of promoters in E. coli.

    Original languageEnglish
    Title of host publicationEMBEC and NBC 2017 - Joint Conference of the European Medical and Biological Engineering Conference EMBEC 2017 and the Nordic-Baltic Conference on Biomedical Engineering and Medical Physics, NBC 2017
    PublisherSpringer Verlag
    Pages1097-1100
    Number of pages4
    ISBN (Print)9789811051210
    DOIs
    Publication statusPublished - 2018
    Publication typeA4 Article in conference proceedings
    EventJoint Conference of the European Medical and Biological Engineering Conference (EMBEC) and the Nordic-Baltic Conference on Biomedical Engineering and Medical Physics (NBC) -
    Duration: 1 Jan 1900 → …

    Publication series

    NameIFMBE Proceedings
    Volume65
    ISSN (Print)1680-0737

    Conference

    ConferenceJoint Conference of the European Medical and Biological Engineering Conference (EMBEC) and the Nordic-Baltic Conference on Biomedical Engineering and Medical Physics (NBC)
    Period1/01/00 → …

    Keywords

    • Induction
    • OFF state
    • Transcription
    • τ plot

    Publication forum classification

    • Publication forum level 1

    ASJC Scopus subject areas

    • Biomedical Engineering
    • Bioengineering

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