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A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Silander, Olin K. and Nikolic, Nela and Zaslaver, Alon and Bren, Anat and Kikoin, Ilya and Alon, Uri and Ackermann, Martin (2012) A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli. PLoS Genetics, 8 (1). e1002443. ISSN 1553-7390. https://resolver.caltech.edu/CaltechAUTHORS:20120328-120118068

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Abstract

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alone


Item Type:Article
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http://dx.doi.org/10.1371/journal.pgen.1002443DOIUNSPECIFIED
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002443PublisherUNSPECIFIED
Additional Information:© 2012 Silander et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received August 22, 2011; Accepted November 16, 2011; Published January 19, 2012. OKS, NN, and MA were supported by a grant from the Swiss National Science Foundation to MA. OKS was additionally supported by an Ambizione fellowship from the Swiss National Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank T. Bollenbach for sharing bacterial strains, R. Beiko for sharing data on horizontal transfer, E. van Nimwegen for valuable discussions, and three reviewers for helpful comments on the manuscript. Author Contributions: Conceived and designed the experiments: OKS NN MA AZ. Performed the experiments: OKS NN AZ AB IK. Analyzed the data: OKS NN MA. Contributed reagents/materials/analysis tools: AZ AB IK UA. Wrote the paper: OKS NN MA.
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Funding AgencyGrant Number
Swiss National Science Foundation (SNSF)UNSPECIFIED
Swiss National Foundation Ambizione FellowshipUNSPECIFIED
Issue or Number:1
Record Number:CaltechAUTHORS:20120328-120118068
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20120328-120118068
Official Citation:Silander OK, Nikolic N, Zaslaver A, Bren A, Kikoin I, et al. (2012) A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli. PLoS Genet 8(1): e1002443. doi:10.1371/journal.pgen.1002443
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:29877
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:30 Mar 2012 14:42
Last Modified:03 Oct 2019 03:45

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