Mutations in Global Regulators Lead to Metabolic Selection during Adaptation to Complex Environments

Abstract

Adaptation to ecologically complex environments can provide insights into the evolutionary dynamics and functional constraints encountered by organisms during natural selection. Adaptation to a new environment with abundant and varied resources can be difficult to achieve by small incremental changes if many mutations are required to achieve even modest gains in fitness. Since changing complex environments are quite common in nature, we investigated how such an epistatic bottleneck can be avoided to allow rapid adaptation. We show that adaptive mutations arise repeatedly in independently evolved populations in the context of greatly increased genetic and phenotypic diversity. We go on to show that weak selection requiring substantial metabolic reprogramming can be readily achieved by mutations in the global response regulator arcA and the stress response regulator rpoS. We identified 46 unique single-nucleotide variants of arcA and 18 mutations in rpoS, nine of which resulted in stop codons or large deletions, suggesting that subtle modulations of ArcA function and knockouts of rpoS are largely responsible for the metabolic shifts leading to adaptation. These mutations allow a higher order metabolic selection that eliminates epistatic bottlenecks, which could occur when many changes would be required. Proteomic and carbohydrate analysis of adapting E. coli populations revealed an up-regulation of enzymes associated with the TCA cycle and amino acid metabolism, and an increase in the secretion of putrescine. The overall effect of adaptation across populations is to redirect and efficiently utilize uptake and catabolism of abundant amino acids. Concomitantly, there is a pronounced spread of more ecologically limited strains that results from specialization through metabolic erosion. Remarkably, the global regulators arcA and rpoS can provide a “one-step” mechanism of adaptation to a novel environment, which highlights the importance of global resource management as a powerful strategy to adaptation.

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution

“…As regulatory networks are ‘aligned’ with particular functional subsystems, mutations that perturb them change phenotypes in a functionally coherent manner (Innocenti and Chenoweth, 2013; Saxer et al, 2014; Wagner et al, 2007). The regulatory rebalancing detailed here occurs along a coherent growth versus hedging trajectory.…”

“…In addition to cis regulatory variation, causal mutations are often found in trans -acting transcriptional regulators (Barrick et al, 2010; Ferenci, 2008; LaCroix et al, 2015; Sandberg et al, 2014; Saxer et al, 2014). Due to transcriptional regulators' involvement in multiple cellular processes, mutations in transcriptional regulators often affect multiple phenotypes (King et al, 2004; Solopova et al, 2014; Venturelli et al, 2015; Wang et al, 2015).…”

Adaptive mutations in RNA polymerase and the transcriptional terminator Rho have similar effects onEscherichia coligene expression

“…In retrospect, it is not surprising that we observed many mutations in rpoB, because mutations in this gene have been found commonly in EMEs (Herring et al 2006;Charusanti et al 2010;Conrad et al 2009), as have mutations in other global regulators of gene expression (GE) (Conrad et al 2011;Le Gac et al 2013;Saxer et al 2014).…”

Evolutionary trade-offs between unicellularity and multicellularity in budding yeast

“…The DNA from the ancestor and each of the three TBR1 EvoTop isolates was extracted from cultures started from individual colonies that were anticipated to be clonal. Clonal mutations are expected to be present at a minimum of 80% -90% in clonal population samples analyzed as if they were polymorphic (Saxer et al 2014). Since the TBR1 A EvoTop isolate appeared to be founded by two clones, with the lower frequency clone present at about 18%, we reasoned that this clone could have other clonal mutations present at as low as 14% (= 0.8*18%) (Table S1).…”