A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli
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
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.Attached Files
Published - Silander2012p17511Plos_Genet.pdf
Supplemental Material - journal.pgen.1002443.s001.pdf
Supplemental Material - journal.pgen.1002443.s002.pdf
Supplemental Material - journal.pgen.1002443.s003.pdf
Supplemental Material - journal.pgen.1002443.s004.pdf
Supplemental Material - journal.pgen.1002443.s005.pdf
Supplemental Material - journal.pgen.1002443.s006.pdf
Supplemental Material - journal.pgen.1002443.s007.pdf
Supplemental Material - journal.pgen.1002443.s008.pdf
Supplemental Material - journal.pgen.1002443.s009.doc
Supplemental Material - journal.pgen.1002443.s010.xls
Supplemental Material - journal.pgen.1002443.s011
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Additional details
- PMCID
- PMC3261926
- Eprint ID
- 29877
- Resolver ID
- CaltechAUTHORS:20120328-120118068
- Swiss National Science Foundation (SNSF)
- Created
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2012-03-30Created from EPrint's datestamp field
- Updated
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2021-11-09Created from EPrint's last_modified field