Divergence Involving Global Regulatory Gene Mutations in an Escherichia coli Population Evolving under Phosphate Limitation

Abstract

Many of the important changes in evolution are regulatory in nature. Sequenced bacterial genomes point to flexibility in regulatory circuits but we do not know how regulation is remodeled in evolving bacteria. Here, we study the regulatory changes that emerge in populations evolving under controlled conditions during experimental evolution of Escherichia coli in a phosphate-limited chemostat culture. Genomes were sequenced from five clones with different combinations of phenotypic properties that coexisted in a population after 37 days. Each of the distinct isolates contained a different mutation in 1 of 3 highly pleiotropic regulatory genes (hfq, spoT, or rpoS). The mutations resulted in dissimilar proteomic changes, consistent with the documented effects of hfq, spoT, and rpoS mutations. The different mutations do share a common benefit, however, in that the mutations each redirect cellular resources away from stress responses that are redundant in a constant selection environment. The hfq mutation lowers several individual stress responses as well the small RNA–dependent activation of rpoS translation and hence general stress resistance. The spoT mutation reduces ppGpp levels, decreasing the stringent response as well as rpoS expression. The mutations in and upstream of rpoS resulted in partial or complete loss of general stress resistance. Our observations suggest that the degeneracy at the core of bacterial stress regulation provides alternative solutions to a common evolutionary challenge. These results can explain phenotypic divergence in a constant environment and also how evolutionary jumps and adaptive radiations involve altered gene regulation.

Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

“…The mutational degeneracy of changing RpoS levels reinforces the huge diversity in RpoS across the species E. coli (51,98). The similar effect on SPaNC is accompanied by very different phenotypic changes with, for example, hfq and spoT mutations (353). These secondary differences provide the ingredients for phenotypic diversification seen in populations and across the species.…”

“…The level of RpoS in the cell responds to external and internal stresses and is influenced by over 20 environmental signal inputs (142). The alternative input pathways controlling rpoS expression provide degenerate ways of affecting regulation, and indeed many alternative genes can change the particular regulatory circuit controlling RpoS levels (353). Even within a single adapting population, heterogeneities can arise, and regulatory mutations are the most frequent type in experimental evolution studies (52,264,353).…”

“…This degeneracy aids adaptation because the capacity to lose or change by mutation some component of function or regulation does not kill the cell. Redundancy and robustness built into bacteria not only help survival in the presence of deleterious mutations (183,351,354) but could actually increase the number of loci for beneficial, adaptive changes (175,353). In this respect, degeneracy contributes to the selectability of diversity that can evolve during adaptation, as discussed in "Genetic Heterogeneity within Populations" above.…”

“…A good example of this is within the general stress response controlled by RpoS (17) and the cost that this imposes on the SPaNC balance (95). Recent evidence of degenerate mechanisms to obtain mutational adaptive shifts in the SPaNC balance and RpoS levels comes from population changes in adaptation to nutrient limitation in the laboratory (353) or in pathogen populations adapting to an extraintestinal environment (177). A similar phenotype in terms of SPaNC balance can come from mutations in rpoS itself, hfq, spoT, and rssB (198a, 353) and others that indirectly influence RpoS levels (177).…”

Parallel evolution of transcriptome architecture during genome reorganization

“…Experimental evolution studies combined with genome resequencing have correlated specific mutations to phenotypic changes to demonstrate that these dynamic genome reorganizational events are tightly coupled to adaptive evolution (Herring et al 2006;Barrick et al 2009). Interestingly, several studies have reported that, along with metabolic and structural genes, mutations within regulatory genes are also adaptive (Harris et al 2009;Wang et al 2010), which suggests that altering gene regulatory programs is an effective strategy for adaptation over short time intervals. Despite benefits of efficient coordinate regulation due to operonization, there is a surprisingly low level of conservation in operon structures across organisms.…”