Schematic of reconstructed genetic landscapes based on gene activity data. Image credit: Westmann et al. (CC BY 4.0)
Organisms regulate the activity of their genes by turning them up or down at the right time and place. To do so, they use proteins called transcription factors, which bind to short stretches of DNA near a gene known as binding sites.
How tightly a transcription factor binds to its binding site determines how strongly it regulates the gene's activity. As genomes evolve, mutations can create new binding sites, establishing entirely new connections within a cell's regulatory network. This is an important way in which organisms adapt to new environments during evolution. Yet the evolutionary steps that transform a random DNA sequence into a strong, functional binding site remain poorly understood, especially in bacteria. Mapping all possible binding sites for a transcription factor can reveal how readily evolution can generate new regulatory interactions.
To test how evolution builds a strong binding site from scratch, Westmann, Goldbach and Wagner studied three major transcription factors in the bacterium Escherichia coli. For each transcription factor, they measured how strongly 30,000 different DNA sequences regulated a gene. To do this, they linked each sequence to a reporter gene that emitted light when activated and measured light emission in millions of cells.
Using these data, the researchers constructed genetic landscapes, in which each DNA sequence occupied a position in the landscape and its height (or elevation, analogous to the height of a hill) represented the strength of gene regulation. Higher peaks, therefore, corresponded to greater gene activation, likely reflecting stronger transcription factor binding.
All three landscapes contained thousands of distinct peaks, far more than comparable landscapes reported for animals and plants. Most of these peaks corresponded to only weak or moderate gene regulation, while peaks of strong regulation were rare. Despite this complexity, the analyses showed that evolution could still reach these rare, strong peaks through a series of small beneficial mutations more often than expected by chance. In other words, even highly complex landscapes can contain accessible routes to strong new binding sites.
The work of Westmann et al. sheds light on how evolution creates and refines the simplest elements of gene regulation. These findings improve our understanding of how bacteria adapt to new environments, including the evolution of antibiotic resistance. In addition, the experimental and analytical approaches developed in this study provide valuable tools for researchers investigating the evolution of gene regulation and for those engineering synthetic genetic circuits in the laboratory.
