The Evolution of Gene Regulatory Mechanisms in Bacteria
Modern bacteria regulate the expression of their genes through a spectrum of mechanisms ranging from the very simple to those that are highly complex. The regulatory mechanisms have evolved in concert with the means to detect changes to the physical or chemical environment, equipping the organism to respond to change. Regulation can be imposed at each stage of gene expression, and the networking of genes through coordinated control makes for multidimensional relationships that vary in time and space. Understanding how this regulatory complexity evolved is not a trivial matter, but it can be attempted. In one popular view, an ‘RNA world’ may have preceded the modern one with its DNA-based genomes. Looking for evidence of RNA-based gene regulation has been very fruitful and shows that gene control at this level is still very much in use: the conversion of genetic information held in RNA into protein by translation involves processes that are open to control at several levels. In DNA-based genomes, transcription is a fundamental process, and over evolutionary time bacterial cells have invested heavily in mechanisms that control it. Mechanisms that influence the activity of RNA polymerase are legion but fall into two categories: those that impede and those that assist the polymerase in the process of reading genetic information. It seems that simply turning genes on or off is rarely sufficient: it was necessary to evolve mechanisms for tuning transcription to the needs of the cell to promote survival, regardless of the size or level of sophistication of the organism’s genome. These regulatory mechanisms have evolved in ways that make their operations ‘noisy’, and this noise can be useful in generating physiological variety among genetically identical bacterial cells. It is becoming clear that the evolutionary forces that shape the bacterial nucleoid also guide the development of gene regulatory elements. For this reason the evolution of bacterial gene regulatory mechanisms will also be considered in the context of bacterial genome architecture.
We thank AP Dorman for useful comments on the manuscript. This work was supported by Science Foundation Ireland Principal Investigator Award 13/IA/1875 to CJD. MJD is supported by the Wellcome Trust (grant 206194).
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