Challenging Traditional Understanding of Microbial Gene Regulation


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.


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.

Hofer, U. 2013. “Unfit Expression,” Nature Reviews Microbiology 11, 362–63. DOI: 10.1038/nrmicro3035.