Expression noise facilitates the evolution of gene regulation

Although it is often tacitly assumed that gene regulatory interactions are finely tuned, how accurate gene regulation could evolve from a state without regulation is unclear. Moreover, gene expression noise would seem to impede the evolution of accurate gene regulation, and previous investigations have provided circumstantial evidence that natural selection has acted to lower noise levels. By evolving synthetic Escherichia coli promoters de novo, we here show that, contrary to expectations, promoters exhibit low noise by default. Instead, selection must have acted to increase the noise levels of highly regulated E. coli promoters. We present a general theory of the interplay between gene expression noise and gene regulation that explains these observations. The theory shows that propagation of expression noise from regulators to their targets is not an unwanted side-effect of regulation, but rather acts as a rudimentary form of regulation that facilitates the evolution of more accurate regulation. DOI: http://dx.doi.org/10.7554/eLife.05856.001
eLife digest Genes are stretches of DNA that contain the instructions needed to make proteins and other molecules. By changing how much protein is produced from each gene (i.e., its expression), many organisms—including humans—can produce a wide variety of cell types with very different behaviors. Similarly, single-celled organisms, such as bacteria, can adapt to survive and grow in different environments by changing gene expression levels. It is thus thought that gene expression must be precisely controlled. However, the molecular processes involved in gene expression are subject to random fluctuations, and so gene expression is inherently ‘noisy’. This means that even groups of identical cells in identical environments will show variation in their gene expression patterns. Furthermore, different genes show different levels of noise. The DNA sequence of a part of each gene, called the promoter, has a big effect on these noise levels. Consequently, gene expression noise is a genetically encoded trait, and can therefore be shaped by natural selection. But it remains largely unclear how natural selection has affected gene expression noise. Now, Wolf et al. have carefully measured the gene expression noise of hundreds of synthetic promoters that were evolved in the laboratory from random DNA sequences, and a similar number of natural promoters in a bacterium called E. coli. These experiments revealed that, contrary to expectation, most lab-evolved promoters had low levels of noise. On the other hand, many natural promoters had high levels of noise. Wolf et al. also found that noisy promoters tend to be highly regulated by transcription factors: the proteins that control gene expression by binding to promoter regions. Together, these results imply that unregulated promoters start by having low noise as a default state. Selection pressures must then have caused some E. coli promoters to become regulated by transcription factors and raise their noise levels. But, what might these selection pressures have been? Many genes need to be expressed at different levels in different conditions, and it is generally accepted that regulation by transcription factors evolves to ‘satisfy’ these requirements. However, transcription factors are themselves noisy, and this noise necessarily propagates to their target genes. Wolf et al. have now developed a general theory showing that this noise-propagation can often benefit an organism. This explains why natural selection can favor an increase in noise levels for regulated genes. Importantly, by showing that the main role of a transcription factor can be to increase the noise of its targets, it suddenly becomes very easy to see how new gene regulatory interactions can evolve from scratch. The next steps in understanding of how gene expression noise evolves will involve manipulating the expression noise of a gene, and measuring how selection acts on such changes. DOI: http://dx.doi.org/10.7554/eLife.05856.002