Bacteria and other microorganisms rely on a complex sensory and regulatory network in order to respond appropriately to hazards and opportunities in their surroundings. This network, shaped over the evolutionary history of the organism, must provide an internal representation of frequently encountered environmental patterns and encode an optimized response. How, then, will a bacterial population adapt to a completely novel environment? Is fitness under new conditions limited primarily by the biochemical capacity of the organism, or by its proper application of existing capabilities? Through a detailed investigation into the fitness effects of a point mutation in the transcriptional terminator Rho, we have recently shown that a purely regulatory mutation can simultaneously improve the fitness of bacteria under a wide variety of experimental conditions, and dramatically alter the future evolutionary path open to an adapting population. Using a meta-analysis of recent experimental data on the fitness patterns of mutagenized E. coli populations, we also show that that the Rho mutation that we studied is not unique, but rather, that purely regulatory mutations provide access to a previously unappreciated reservoir of phenotypic diversity that can be accessed by populations encountering new conditions. Thus, the biochemical and biophysical capabilities of bacteria to survive and thrive under new conditions far outstrip their regulatory capabilities.
Our findings further show that the adaptive mechanisms through which regulatory mutations reshape the cellular fitness landscape reach throughout the cell's regulatory and metabolic networks, underscoring the need for systems-level data in attempting to understand adaptation to new conditions. Existing approaches for directly measuring the regulatory state of cells, however, must target a single transcription factor at a time, requiring a combinatorially increasing number of experiments to obtain measurements on multiple factors under multiple environmental conditions. We have recently developed a method enabling the simultaneous measurement of the complete regulatory state of bacterial cells, by physically separating protein-DNA complexes from bulk genomic DNA, sequencing the footprinted complexes, and then applying a statistical mechanics-based model to identify protein occupancies. The newly developed method is applicable to any bacterium without the need for prior knowledge of its regulatory network, and will allow the rapid dissection of bacterial responses to environmental stresses.