Saxer_et_al_PlosGen_PopulationKey_corrected

This files contains the name of all the populations and ancestors, their selection regime and the accession number for the genomic and proteomics data, if applicable

Saxer_et_al_PlosGen_GrowthOD600_BHI

OD readings of E. coli and C. freundii populations evolved in BHI over the course of a growth cycle in BH

Saxer_et_al_PlosGen_GrowthOD600_LB

OD readings of LB-evolved populations of E. coli and C. freundii in LB with the respective ancestor

Saxer_et_al_PlosGen_CarbohydrateData

Data from carbohydrate analyses of cell extract and spend media from E. coli RU1 ancestor and E. coli RU1-BHI evolved population

Saxer_et_al_PlosGen_pH

pH of stationary phase cultures of the ancestor and evolved populations of E. coli RU1 and C. freundii RU2 in LB and BHI (in their selective media

Mutations in <i>arcA</i> evolved repeatedly and with remarkable diversity both within and among populations of <i>E. coli</i> evolved in LB (A) and BHI (C) and <i>C. freundii</i> populations evolved in LB (B) and BHI (D).

<p>Specific mutations to <i>arcA</i> identified in the evolved populations are indicated. The red dots represent the number of populations with that specific mutation (out of twelve LB and eleven BHI populations for each strain). The red star indicates the mutation that was fixed in LB5. No mutations in <i>arcA</i> were identified in the BHI-evolved <i>C. freundii</i> populations. The receiver domain that includes the site of phosphorylation (Asp-54) is indicated in blue and the DNA binding domain in green.</p

Frequencies of <i>arcA</i> and <i>rpoS</i> mutants in the evolved populations <i>arcA</i> mutations (black bars) reached high frequencies in all LB-evolved populations (A, B) and reach fixation in LB5, while <i>rpoS</i> mutations (red) were more common in BHI-evolved populations (C, D).

<p>The frequencies represent the total frequencies of all <i>arcA</i> or respectively, identified in a particular population.</p

Population genomics and population proteomics were used to identify the biochemical basis for phenotypic convergence and parallel evolution during adaptation to novel resource rich environments.

<p>Clones of two species, <i>E. coli</i> RU1 and <i>C. freundii</i> RU2, were isolated <i>de novo</i> from human stool. Single clones were used to inoculate twelve replicated populations and evolved in LB or BHI for 500 or 765 generations respectively by daily transfers into fresh media. Adaptive mutations were identified as mutations that evolved repeatedly across species and media. We performed a mutation accumulation experiment by transferring a single colony of twelve replicated lines for 200 days as control experiment. The relaxed selection allowed the random accumulation of mutations, and makes the parallel evolution of adaptive mutations unlikely.</p

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

<div><p>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 <i>arcA</i> and the stress response regulator <i>rpoS.</i> We identified 46 unique single-nucleotide variants of <i>arcA</i> and 18 mutations in <i>rpoS</i>, nine of which resulted in stop codons or large deletions, suggesting that subtle modulations of ArcA function and knockouts of <i>rpoS</i> 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 <i>E. coli</i> 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 <i>arcA</i> and <i>rpoS</i> 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.</p></div

Global regulators <i>arcA</i> and <i>rpoS</i> provide a comprehensive metabolic shift during adaptation that circumvents epistatic bottlenecks.

<p>Adaptation to the amino acid rich conditions of BHI by <i>E.coli</i> are consistent with a ‘metabolic selection’ that provides a facile strategy for shifting environments. Up-regulated systems (green) are associated with the movement of abundant amino acids into the cell coupled with an increased capacity for catabolic metabolism through the TCA cycle with excess nitrogen being secreted as putrescine. Down-regulated systems (red) include components of the starvation stress response consistent with the maintenance of a new nutrient rich homeostasis.</p