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Invariant Distribution of Promoter Activities in Escherichia coli

Zaslaver, Alon and Kaplan, Shai and Bren, Anat and Jinich, Adrian and Mayo, Avi and Dekel, Erez and Alon, Uri and Itzkovitz, Shalev (2009) Invariant Distribution of Promoter Activities in Escherichia coli. PLoS Computational Biology, 5 (10). e1000545. ISSN 1553-734X. https://resolver.caltech.edu/CaltechAUTHORS:20091207-141858548

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Abstract

Cells need to allocate their limited resources to express a wide range of genes. To understand how Escherichia coli partitions its transcriptional resources between its different promoters, we employ a robotic assay using a comprehensive reporter strain library for E. coli to measure promoter activity on a genomic scale at high-temporal resolution and accuracy. This allows continuous tracking of promoter activity as cells change their growth rate from exponential to stationary phase in different media. We find a heavy-tailed distribution of promoter activities, with promoter activities spanning several orders of magnitude. While the shape of the distribution is almost completely independent of the growth conditions, the identity of the promoters expressed at different levels does depend on them. Translation machinery genes, however, keep the same relative expression levels in the distribution across conditions, and their fractional promoter activity tracks growth rate tightly. We present a simple optimization model for resource allocation which suggests that the observed invariant distributions might maximize growth rate. These invariant features of the distribution of promoter activities may suggest design constraints that shape the allocation of transcriptional resources.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1371/journal.pcbi.1000545DOIUNSPECIFIED
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000545PublisherUNSPECIFIED
Additional Information:© Zaslaver 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 January 16, 2009; accepted September 23, 2009; published October 23, 2009. We thank Paul Sternberg for providing lab space and resources. We also thank Eran Segal, Naama Barkai and Arbel Tadmor for valuable comments. We thank the Kahn Family Foundation and the Israel Science Foundation for support. Alon Zaslaver is supported by the Human Frontier Science Program (HFSP) and the European Molecular Biology Organization (EMBO). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Author Contributions: Conceived and designed the experiments: AZ UA SI. Performed the experiments: AZ SI. Analyzed the data: AZ SI. Contributed reagents/ materials/analysis tools: AZ SK AB AJ AM ED UA SI. Wrote the paper: AZ UA SI.
Funders:
Funding AgencyGrant Number
Kahn Family FoundationUNSPECIFIED
Israel Science FoundationUNSPECIFIED
Human Frontier Science Program (HFSP)UNSPECIFIED
European Molecular Biology Organization (EMBO)UNSPECIFIED
Issue or Number:10
Record Number:CaltechAUTHORS:20091207-141858548
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20091207-141858548
Official Citation:Zaslaver A, Kaplan S, Bren A, Jinich A, Mayo A, et al. (2009) Invariant Distribution of Promoter Activities in Escherichia coli. PLoS Comput Biol 5(10): e1000545. doi:10.1371/journal.pcbi.1000545
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:16895
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:08 Dec 2009 19:09
Last Modified:03 Oct 2019 01:19

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