Effects of σ factor competition are promoter initiation kinetics dependent

Vinodh K. Kandavalli, Huy Tran, Andre S. Ribeiro

    Research output: Contribution to journalArticleScientificpeer-review

    18 Citations (Scopus)


    In Escherichia coli, the expression of a σ factor is expected to indirectly down-regulate the expression of genes recognized by another σ factor, due to σ factor competition for a limited pool of RNA polymerase core enzymes. Evidence suggests that the sensitivity of genes to indirect down-regulation differs widely. We studied the variability in this sensitivity in promoters primarily recognized by RNAP holoenzymes carrying σ70. From qPCR and live single-cell, single-RNA measurements of the transcription kinetics of several σ70-dependent promoters in various conditions and from the analysis of σ factors population-dependent models of transcription initiation, we find that, the smaller is the time-scale of the closed complex formation relative to the open complex formation, the weaker is a promoter's responsiveness to changes in σ38 numbers. We conclude that, in E. coli, a promoter's responsiveness to indirect regulation by σ factor competition is determined by the sequence-dependent kinetics of the rate limiting steps of transcription initiation.

    Original languageEnglish
    Pages (from-to)1281-1288
    Number of pages8
    JournalBiochimica et Biophysica Acta: Gene Regulatory Mechanisms
    Issue number10
    Publication statusPublished - 1 Oct 2016
    Publication typeA1 Journal article-refereed


    • Closed Complex Formation
    • In vivo Transcription dynamics
    • Open Complex Formation
    • Single RNA detection
    • σ Factors competition

    Publication forum classification

    • Publication forum level 1

    ASJC Scopus subject areas

    • Biochemistry
    • Biophysics
    • Genetics
    • Molecular Biology
    • Structural Biology


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