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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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Related in: MedlinePlus

Mutations in arcA evolved repeatedly and with remarkable diversity both within and among populations of E. coli evolved in LB (A) and BHI (C) and C. freundii populations evolved in LB (B) and BHI (D).Specific mutations to arcA 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 arcA were identified in the BHI-evolved C. freundii populations. The receiver domain that includes the site of phosphorylation (Asp-54) is indicated in blue and the DNA binding domain in green.
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pgen-1004872-g007: Mutations in arcA evolved repeatedly and with remarkable diversity both within and among populations of E. coli evolved in LB (A) and BHI (C) and C. freundii populations evolved in LB (B) and BHI (D).Specific mutations to arcA 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 arcA were identified in the BHI-evolved C. freundii populations. The receiver domain that includes the site of phosphorylation (Asp-54) is indicated in blue and the DNA binding domain in green.

Mentions: We observed 46 unique mutations in arcA, both within and among populations (Fig. 7). Strikingly, none of these mutations introduced a stop codon or a frame shift; 44 of these 46 unique mutations were non-synonymous substitutions, one mutation resulted in a C-terminal deletion of three amino acids, and one mutation was an insertion of one amino acid. To independently confirm some of the mutations identified from population genomics, we directly sequenced arcA from eight single colonies isolated from six of the LB-evolved E. coli populations. We were able to confirm eleven of the 46 mutations identified in the whole population samples (L2: I122M, Y137C, I22S, L4: N116T, L6: R16H, A76T; L8: E94K; L10: A25T, G59S, L50Q; and L12: L50Q). In addition, we identified two new mutations (L8: G62D and 218ΔTPE; and L12: G62D) suggesting that our cutoff of 5% in the deep sequencing population analysis still missed many arcA variants. Each clone had only one mutation in arcA, suggesting that the one mutation was sufficient to achieve a beneficial effect.


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)

Mutations in arcA evolved repeatedly and with remarkable diversity both within and among populations of E. coli evolved in LB (A) and BHI (C) and C. freundii populations evolved in LB (B) and BHI (D).Specific mutations to arcA 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 arcA were identified in the BHI-evolved C. freundii populations. The receiver domain that includes the site of phosphorylation (Asp-54) is indicated in blue and the DNA binding domain in green.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4263409&req=5

pgen-1004872-g007: Mutations in arcA evolved repeatedly and with remarkable diversity both within and among populations of E. coli evolved in LB (A) and BHI (C) and C. freundii populations evolved in LB (B) and BHI (D).Specific mutations to arcA 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 arcA were identified in the BHI-evolved C. freundii populations. The receiver domain that includes the site of phosphorylation (Asp-54) is indicated in blue and the DNA binding domain in green.
Mentions: We observed 46 unique mutations in arcA, both within and among populations (Fig. 7). Strikingly, none of these mutations introduced a stop codon or a frame shift; 44 of these 46 unique mutations were non-synonymous substitutions, one mutation resulted in a C-terminal deletion of three amino acids, and one mutation was an insertion of one amino acid. To independently confirm some of the mutations identified from population genomics, we directly sequenced arcA from eight single colonies isolated from six of the LB-evolved E. coli populations. We were able to confirm eleven of the 46 mutations identified in the whole population samples (L2: I122M, Y137C, I22S, L4: N116T, L6: R16H, A76T; L8: E94K; L10: A25T, G59S, L50Q; and L12: L50Q). In addition, we identified two new mutations (L8: G62D and 218ΔTPE; and L12: G62D) suggesting that our cutoff of 5% in the deep sequencing population analysis still missed many arcA variants. Each clone had only one mutation in arcA, suggesting that the one mutation was sufficient to achieve a beneficial effect.

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