Estimating effects of extrinsic noise on model genes and circuits with empirically validated kinetics

Samuel M.D. Oliveira, Mohamed N.M. Bahrudeen, Sofia Startceva, Andre S. Ribeiro

    Tutkimustuotos: Conference contributionScientificvertaisarvioitu

    2 Sitaatiot (Scopus)

    Abstrakti

    Recent studies of Escherichia coli transcription dynamics using time-lapse confocal microscopy and in vivo single-RNA detection confirmed that transcription initiation has two main rate-limiting steps. Here, we argue that this allows selective ‘tuning’ of the effects of extrinsic noise on a multi-scale level that ranges from individual genes to large-scale gene networks. First, using empirically validated stochastic models of transcription and translation, we show that the effects of RNA polymerase numbers’ cell-to-cell variability on the cell-to-cell diversity in RNA numbers decrease as the relative time-length of the open complex formation increases. Next, using a stochastic model of a 2-genes symmetric toggle switch, we show that the cell-to-cell diversity of the switching frequency due to cell-to-cell variability in RNA polymerase numbers also depends on the promoter kinetics. Finally, from the binarized protein numbers over time of 50-gene network models where genes interact by repression, we calculate the cell-to-cell variability of the mutual information and Lempel-Ziv complexity of the networks dynamics, and find that, while arising from the cell-to-cell variability in RNA polymerase numbers, these variability levels also depend on the promoter initiation kinetics. Given this, we hypothesize that E. coli may be capitalizing on the 2 rate-limiting steps’ nature of transcription initiation to tune the effects of extrinsic noise at the single gene, motifs, and large gene regulatory network levels.

    AlkuperäiskieliEnglanti
    OtsikkoArtificial Life and Evolutionary Computation - 12th Italian Workshop, WIVACE 2017, Revised Selected Papers
    KustantajaSpringer Verlag
    Sivut181-193
    Sivumäärä13
    ISBN (painettu)9783319786575
    DOI - pysyväislinkit
    TilaJulkaistu - 1 tammik. 2018
    OKM-julkaisutyyppiA4 Artikkeli konferenssijulkaisussa
    TapahtumaItalian Workshop on Artificial Life and Evolutionary Computation -
    Kesto: 1 tammik. 2000 → …

    Julkaisusarja

    NimiCommunications in Computer and Information Science
    Vuosikerta830
    ISSN (painettu)1865-0929

    Conference

    ConferenceItalian Workshop on Artificial Life and Evolutionary Computation
    Ajanjakso1/01/00 → …

    Julkaisufoorumi-taso

    • Jufo-taso 1

    !!ASJC Scopus subject areas

    • Computer Science(all)
    • Mathematics(all)

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