research-article

Effects of Extrinsic Noise are Promoter Kinetics Dependent

Authors:

Mohamed N. M. Bahrudeen,

Sofia Startceva,

Andre S. RibeiroAuthors Info & Claims

ICBBT '17: Proceedings of the 9th International Conference on Bioinformatics and Biomedical Technology

Pages 44 - 47

https://doi.org/10.1145/3093293.3093295

Published: 14 May 2017 Publication History

Abstract

Studies in Escherichia coli using in vivo single-RNA detection and time-lapse confocal microscopy showed that transcription is a multiple rate-limiting steps process, in agreement with previous in vitro measurements. Here, from simulations of a stochastic model of transcription validated empirically that accounts for cell-to-cell variability in RNA polymerase (RNAP) numbers, we investigate the hypothesis that the cell-to-cell variability in RNA numbers due to RNAP variability differs with the promoter rate-limiting steps dynamics. We find that increasing the cell-to-cell variability in RNAP numbers increases the cell-to-cell diversity in RNA numbers, but the degree with which it increases is promoter kinetics dependent. Namely, promoters whose open complex formation is relatively longer lasting dampen more efficiently this noise propagation phenomenon. We conclude that cell-to-cell variability in RNA numbers due to variability in RNAP numbers is promoter-sequence dependent and, thus, evolvable.

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Digital Library

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Cited By

Oliveira SBahrudeen MStartceva SKandavalli VRibeiro A(2018)Modeling and Engineering Promoters with Pre-defined RNA Production Dynamics in Escherichia ColiComputational Methods in Systems Biology10.1007/978-3-319-99429-1_1(3-20)Online publication date: 24-Aug-2018
https://doi.org/10.1007/978-3-319-99429-1_1
Oliveira SBahrudeen MStartceva SRibeiro A(2018)Estimating Effects of Extrinsic Noise on Model Genes and Circuits with Empirically Validated KineticsArtificial Life and Evolutionary Computation10.1007/978-3-319-78658-2_14(181-193)Online publication date: 1-Apr-2018
https://doi.org/10.1007/978-3-319-78658-2_14

Index Terms

Effects of Extrinsic Noise are Promoter Kinetics Dependent
1. Computing methodologies
  1. Modeling and simulation
    1. Model development and analysis

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cover image ACM Other conferences

ICBBT '17: Proceedings of the 9th International Conference on Bioinformatics and Biomedical Technology

May 2017

123 pages

ISBN:9781450348799

DOI:10.1145/3093293

Copyright © 2017 ACM.

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Department of Computer Science, University of Szeged: Department of Computer Science, University of Szeged
University of Lisbon: University of Lisbon

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New York, NY, United States

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Published: 14 May 2017

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ICBBT '17

ICBBT '17: 9th International Conference on Bioinformatics and Biomedical Technology

May 14 - 16, 2017

Lisbon, Portugal

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Cited By

Oliveira SBahrudeen MStartceva SKandavalli VRibeiro A(2018)Modeling and Engineering Promoters with Pre-defined RNA Production Dynamics in Escherichia ColiComputational Methods in Systems Biology10.1007/978-3-319-99429-1_1(3-20)Online publication date: 24-Aug-2018
https://doi.org/10.1007/978-3-319-99429-1_1
Oliveira SBahrudeen MStartceva SRibeiro A(2018)Estimating Effects of Extrinsic Noise on Model Genes and Circuits with Empirically Validated KineticsArtificial Life and Evolutionary Computation10.1007/978-3-319-78658-2_14(181-193)Online publication date: 1-Apr-2018
https://doi.org/10.1007/978-3-319-78658-2_14

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