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Mutations in global regulators lead to metabolic selection during adaptation to complex environments.

Saxer G, Krepps MD, Merkley ED, Ansong C, Deatherage Kaiser BL, Valovska MT, Ristic N, Yeh PT, Prakash VP, Leiser OP, Nakhleh L, Gibbons HS, Kreuzer HW, Shamoo Y - PLoS Genet. (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of BioSciences, Rice University, Houston, Texas, United States of America.

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.

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The total number of mutations in coding regions was substantial in the evolved populations.The accumulation of hundreds of mutations is consistent with weak selection, where many mutations can have small consequences for the fitness of organism. Overall, more mutations evolved in LB (A, B) than in BHI (C, D), both in the E. coli (A, C) and the C. freundii (B, D) populations. Two LB- and two BHI-evolved E. coli populations acquired considerably more mutations than the remaining populations evolved in the same media, suggesting that these populations evolved to become mutators. Total number of mutations in coding regions (black) and non-synonymous mutations (red) are shown for each population. Populations BHI5 and BHI20 were not included in the genomic analyses.
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pgen-1004872-g003: The total number of mutations in coding regions was substantial in the evolved populations.The accumulation of hundreds of mutations is consistent with weak selection, where many mutations can have small consequences for the fitness of organism. Overall, more mutations evolved in LB (A, B) than in BHI (C, D), both in the E. coli (A, C) and the C. freundii (B, D) populations. Two LB- and two BHI-evolved E. coli populations acquired considerably more mutations than the remaining populations evolved in the same media, suggesting that these populations evolved to become mutators. Total number of mutations in coding regions (black) and non-synonymous mutations (red) are shown for each population. Populations BHI5 and BHI20 were not included in the genomic analyses.

Mentions: To assess the evolved genetic variation and identify adaptive mutations, we sequenced the evolved populations and identified mutations in coding regions that occurred at a minimum frequency of 0.05 in a population. Two BHI-evolved populations (E.coli BHI5 and C. freundii BHI20) could not be aligned properly and were omitted from further genomic analyses. The number of mutations ranged from 29 to 725 per population. The number of mutations per population did not differ significantly among the E. coli populations evolved in LB or BHI (Fig. 3; Table 1). Two populations evolved to become mutators in each environment (LB4, LB11, BHI6, and BHI10, S1 Text). If the mutator populations are excluded, the average number of mutations between the LB and BHI-evolved populations was reduced, although there was still no significant difference in the number of mutations across environments. In contrast, the LB-evolved C. freundii populations accumulated significantly more mutations than the BHI-evolved populations. Overall, the number of mutations differed significantly both between media and species (Full factor ANOVA with Media and Strain as fixed factors: Media F1,42 = 15.1, p = 0.0004, Species F1,42 = 4.5, p = 0.039, Media×Species F1,42 = 9.5, p = 0.0036). While synonymous mutations can have fitness effects [46], [47], we focused our analyses on non-synonymous mutations, which include SNPs, insertions, and deletions. The number of non-synonymous mutations ranged from 5 to 198 in a population, with more mutations arising in the LB than in BHI in the E. coli population (Fig. 3, Table 1). Excluding the mutator populations reduced the average non-synonymous mutations per population further (LB: 21±15, BHI: 12±7). Among the C. freundii populations, the average number of non-synonymous mutations was significantly higher in the LB-evolved populations than in the BHI-evolved populations. Again, we observed significant differences among media and species (Media  = F1,42 = 23.8, p<0.0001, Species: F1,42 = 13.2, p = 0.0007, Media×Species: F1,42 = 9.4, p = 0.0037).


Mutations in global regulators lead to metabolic selection during adaptation to complex environments.

Saxer G, Krepps MD, Merkley ED, Ansong C, Deatherage Kaiser BL, Valovska MT, Ristic N, Yeh PT, Prakash VP, Leiser OP, Nakhleh L, Gibbons HS, Kreuzer HW, Shamoo Y - PLoS Genet. (2014)

The total number of mutations in coding regions was substantial in the evolved populations.The accumulation of hundreds of mutations is consistent with weak selection, where many mutations can have small consequences for the fitness of organism. Overall, more mutations evolved in LB (A, B) than in BHI (C, D), both in the E. coli (A, C) and the C. freundii (B, D) populations. Two LB- and two BHI-evolved E. coli populations acquired considerably more mutations than the remaining populations evolved in the same media, suggesting that these populations evolved to become mutators. Total number of mutations in coding regions (black) and non-synonymous mutations (red) are shown for each population. Populations BHI5 and BHI20 were not included in the genomic analyses.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4263409&req=5

pgen-1004872-g003: The total number of mutations in coding regions was substantial in the evolved populations.The accumulation of hundreds of mutations is consistent with weak selection, where many mutations can have small consequences for the fitness of organism. Overall, more mutations evolved in LB (A, B) than in BHI (C, D), both in the E. coli (A, C) and the C. freundii (B, D) populations. Two LB- and two BHI-evolved E. coli populations acquired considerably more mutations than the remaining populations evolved in the same media, suggesting that these populations evolved to become mutators. Total number of mutations in coding regions (black) and non-synonymous mutations (red) are shown for each population. Populations BHI5 and BHI20 were not included in the genomic analyses.
Mentions: To assess the evolved genetic variation and identify adaptive mutations, we sequenced the evolved populations and identified mutations in coding regions that occurred at a minimum frequency of 0.05 in a population. Two BHI-evolved populations (E.coli BHI5 and C. freundii BHI20) could not be aligned properly and were omitted from further genomic analyses. The number of mutations ranged from 29 to 725 per population. The number of mutations per population did not differ significantly among the E. coli populations evolved in LB or BHI (Fig. 3; Table 1). Two populations evolved to become mutators in each environment (LB4, LB11, BHI6, and BHI10, S1 Text). If the mutator populations are excluded, the average number of mutations between the LB and BHI-evolved populations was reduced, although there was still no significant difference in the number of mutations across environments. In contrast, the LB-evolved C. freundii populations accumulated significantly more mutations than the BHI-evolved populations. Overall, the number of mutations differed significantly both between media and species (Full factor ANOVA with Media and Strain as fixed factors: Media F1,42 = 15.1, p = 0.0004, Species F1,42 = 4.5, p = 0.039, Media×Species F1,42 = 9.5, p = 0.0036). While synonymous mutations can have fitness effects [46], [47], we focused our analyses on non-synonymous mutations, which include SNPs, insertions, and deletions. The number of non-synonymous mutations ranged from 5 to 198 in a population, with more mutations arising in the LB than in BHI in the E. coli population (Fig. 3, Table 1). Excluding the mutator populations reduced the average non-synonymous mutations per population further (LB: 21±15, BHI: 12±7). Among the C. freundii populations, the average number of non-synonymous mutations was significantly higher in the LB-evolved populations than in the BHI-evolved populations. Again, we observed significant differences among media and species (Media  = F1,42 = 23.8, p<0.0001, Species: F1,42 = 13.2, p = 0.0007, Media×Species: F1,42 = 9.4, p = 0.0037).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of BioSciences, Rice University, Houston, Texas, United States of America.

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.

Show MeSH
Related in: MedlinePlus