The low noise limit in gene expression

Dar, Roy D.; Weinberger, Leor S.; Cox, Chris D.; Simpson, Michael L.; Razooky, Brandon S.

doi:10.1371/journal.pone.0140969

Title: The low noise limit in gene expression

Journal Article · Wed Oct 21 00:00:00 EDT 2015 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0140969· OSTI ID:1255649

Dar, Roy D. ^[1]; Weinberger, Leor S. ^[2]; Cox, Chris D. ^[3]; Simpson, Michael L. ^[4]; Razooky, Brandon S. ^[5]

Gladstone Institute of Virology and Immunology, San Francisco, CA (United States); Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States)
Gladstone Institute of Virology and Immunology, San Francisco, CA (United States); Univ. of California, San Francisco, CA (United States)
Univ. of Tennessee, Knoxville, TN (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); The Rockefeller Univ., New York, NY (United States)

Protein noise measurements are increasingly used to elucidate biophysical parameters. Unfortunately noise analyses are often at odds with directly measured parameters. Here we show that these inconsistencies arise from two problematic analytical choices: (i) the assumption that protein translation rate is invariant for different proteins of different abundances, which has inadvertently led to (ii) the assumption that a large constitutive extrinsic noise sets the low noise limit in gene expression. While growing evidence suggests that transcriptional bursting may set the low noise limit, variability in translational bursting has been largely ignored. We show that genome-wide systematic variation in translational efficiency can-and in the case of E. coli does-control the low noise limit in gene expression. Therefore constitutive extrinsic noise is small and only plays a role in the absence of a systematic variation in translational efficiency. Lastly, these results show the existence of two distinct expression noise patterns: (1) a global noise floor uniformly imposed on all genes by expression bursting; and (2) high noise distributed to only a select group of genes.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1255649

Journal Information:: PLoS ONE, Vol. 10, Issue 10; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 22 works

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59 BASIC BIOLOGICAL SCIENCES
gene expression
E. coli
transcriptional bursting
translational bursting
extrinsic noise
messenger RNA
saccharomyces cerevisiae
protein translation
protein abundance
DNA transcription
bacterial genomics
T cells

Title: The low noise limit in gene expression

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