Data for "Indirect and Suboptimal Control of Gene Expression is Widespread in Bacteria"

Morgan N. Price, Adam M. Deutschbauer, Jeffrey M. Skerker, Kelly M. Wetmore, Troy Ruths, Jordan S. Mar, Jennifer V. Kuehl, Wenjun Shao, and Adam P. Arkin
Lawrence Berkeley Lab Physical Biosciences Division
UC Berkeley Dept. of Bioengineering
Energy Biosciences Institute
UCB Dept. of Molecular and Cell Biology
Molecular Systems Biology 9:660

Abstract: Gene regulation in bacteria is usually described as an adaptive response to an environmental change so that genes are expressed when they are required. We instead propose that most genes are under indirect control: their expression responds to signal(s) that are not directly related to the genes' function. Indirect control should perform poorly in artificial conditions, and we show that gene regulation is often maladaptive in the laboratory. In Shewanella oneidensis MR-1, 24% of genes are detrimental to fitness in some conditions, and detrimental genes tend to be highly expressed instead of being repressed when not needed. In diverse bacteria, there is little correlation between when genes are important for optimal growth or fitness and when those genes are upregulated. Two common types of indirect control are constitutive expression and regulation by growth rate; these occur for genes with diverse functions and often seem to be suboptimal. Because genes that have closely-related functions can have dissimilar expression patterns, regulation may be suboptimal in the wild as well as in the laboratory.

Tab-delimited data for Shewanella oneidensis MR-1

Tab-delimited data for Zymomonas mobils ZM4

Tab-delimited data for Desulfovibrio alaskensis G20

GEO Accessions

Links to Gene Expression omnibus:

Supplementary Table S1: Pairs of functionally-related genes in Shewanella oneidensis MR-1 that are not in the same operon and are not coexpressed.

See tab-delimited table.

We list pairs of genes that are cofit and in the same functional category (TIGR subrole) but are not in the same operon, near each other in the genome, or coexpressed. For each pair, we manually examined their annotations and their fitness patterns to determine if they truly had closely-related functions or not. For pairs of flagellar genes, we also report whether they are coregulated and in the same ``class'' in Pseudomonas aeruginosa according to Dasgupta et al 2003.

R source code and image

Morgan Price, July 2012