BER launches Environmental System Science Program. Visit our new website under construction!

U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights

Challenging Traditional Understanding of Microbial Gene Regulation
Published: April 16, 2013
Posted: June 20, 2013

The traditional view of adaptive gene regulation is that bacteria adapt to sense their environment and then selectively tune the expression of their genes for optimal growth efficiency and survival (i.e., fitness) under those conditions. Numerous observations of seemingly nonoptimal gene expression in various microbes suggest, however, that reality is more complex. Researchers at Lawrence Berkeley National Laboratory’s ENIGMA Science Focus Area are gaining a more sophisticated understanding of bacterial gene regulation by examining over a thousand different combinations of gene expression patterns and growth conditions to determine their relation to overall fitness. Four genetically tractable bacterial species representing a broad diversity of microbial lifestyles have been studied: the aquatic metal-reducing environmental microbe Shewanella oneidensis, common intestinal bacterium Escherichia coli, ethanol-producing bacterium Zymomonas mobilis, and anaerobic sulfate-reducing bacterium Desulfovibrio alaskensis. In all four organisms, evidence of adaptive gene regulation was observed for only a small minority of genes; most gene expression was determined to be neutral or even detrimental to growth efficiency and fitness under experimental conditions. While these observations need testing in more realistic environmental settings and in microbial communities, the team concludes that under laboratory conditions, most gene expression is nonadaptive and reflects some form of indirect control unrelated to functional properties of specific genes. These study results add a new layer of complexity to our knowledge of the forces governing gene expression in microorganisms. They have important implications in understanding fundamental systems biology of microbes and attempts to engineer organisms with modified functional capabilities. This publication was selected as a research highlight in the June 2013 issue of Nature Reviews Microbiology.

Reference: Price, M. N., A. M. Deutschbauer, J. M. Skerker, K. M. Wetmore, T. Ruths, J. S. Mar, J. V Kuehl, W. Shao, and A. P. Arkin. 2013. “Indirect and Suboptimal Control of Gene Expression Is Widespread in Bacteria,” Molecular Systems Biology 9(660), DOI: 10.1038/msb.2013.16. (Reference link)

Research Highlight: Hofer, U. 2013. “Unfit Expression,” Nature Reviews Microbiology 11, 362–63. DOI: 10.1038/nrmicro3035. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: Sustainable Biofuels and Bioproducts
  • Research Area: Biosystems Design

Division: SC-33.2 Biological Systems Science Division, BER


BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

Mar 23, 2021
Molecular Connections from Plants to Fungi to Ants
Lipids transfer energy and serve as an inter-kingdom communication tool in leaf-cutter ants&rsqu [more...]

Mar 19, 2021
Microbes Use Ancient Metabolism to Cycle Phosphorus
Microbial cycling of phosphorus through reduction-oxidation reactions is older and more widespre [more...]

Feb 22, 2021
Warming Soil Means Stronger Microbe Networks
Soil warming leads to more complex, larger, and more connected networks of microbes in those soi [more...]

Jan 27, 2021
Labeling the Thale Cress Metabolites
New data pipeline identifies metabolites following heavy isotope labeling.

Analysis [more...]

Aug 31, 2020
Novel Bacterial Clade Reveals Origin of Form I Rubisco

  • All plant biomass is sourced from the carbon-fixing enzyme Rub [more...]

List all highlights (possible long download time)