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Transhydrogenase promotes the robustness and evolvability of E. coli deficient in NADPH production.

Chou HH, Marx CJ, Sauer U - PLoS Genet. (2015)

Bottom Line: Notably, mTH displays broad phylogenetic distribution and has also played a predominant role in laboratory evolution of Methylobacterium extorquens deficient in NADPH production.Convergent evolution of two phylogenetically and metabolically distinct species suggests mTH as a conserved buffering mechanism that promotes the robustness and evolvability of metabolism.Moreover, adaptive diversification via evolving dual substrate consumption highlights the flexibility of physiological systems to exploit ecological opportunities.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland; Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

ABSTRACT
Metabolic networks revolve around few metabolites recognized by diverse enzymes and involved in myriad reactions. Though hub metabolites are considered as stepping stones to facilitate the evolutionary expansion of biochemical pathways, changes in their production or consumption often impair cellular physiology through their system-wide connections. How does metabolism endure perturbations brought immediately by pathway modification and restore hub homeostasis in the long run? To address this question we studied laboratory evolution of pathway-engineered Escherichia coli that underproduces the redox cofactor NADPH on glucose. Literature suggests multiple possibilities to restore NADPH homeostasis. Surprisingly, genetic dissection of isolates from our twelve evolved populations revealed merely two solutions: (1) modulating the expression of membrane-bound transhydrogenase (mTH) in every population; (2) simultaneously consuming glucose with acetate, an unfavored byproduct normally excreted during glucose catabolism, in two subpopulations. Notably, mTH displays broad phylogenetic distribution and has also played a predominant role in laboratory evolution of Methylobacterium extorquens deficient in NADPH production. Convergent evolution of two phylogenetically and metabolically distinct species suggests mTH as a conserved buffering mechanism that promotes the robustness and evolvability of metabolism. Moreover, adaptive diversification via evolving dual substrate consumption highlights the flexibility of physiological systems to exploit ecological opportunities.

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Effects of adaptive mutations on growth rates and diauxic shifts.Dashed lines indicate the phenotype of E. coli ZED. Error bars are 95% C.I. based on six independent measurements. ND, no diauxic growth.
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pgen.1005007.g003: Effects of adaptive mutations on growth rates and diauxic shifts.Dashed lines indicate the phenotype of E. coli ZED. Error bars are 95% C.I. based on six independent measurements. ND, no diauxic growth.

Mentions: To investigate the phenotypic effects of Z-specific mutations, we introduced seven of them into the ancestral ZED background (pntAB2.4, cyaA8.4, cyaA11.1, crp11.1, ptsI12.1, ptsG2.2, ptsG10.1). We left out pntAB12.1 and two large amplification mutations (pntAB10.2, ptsA10.2) because the former was a point mutation identical to pntAB2.4 and the latter was not amenable to genetic manipulation. These seven mutations caused diverse changes in growth profiles (Fig. 3). Four mutations (pntAB2.4, cyaA8.4, cyaA11.1, ptsI12.1) conferred clear selective advantages through increasing growth rates on glucose by 15–27% and shortening diauxic shifts by 16–78%. Among these, pntAB2.4 alone was able to restore the growth rate of E. coli ZED back to the WT level, which indicated the NADPH shortage of the ZED strain as the major cause of its slow growth on glucose. In contrast, the remaining three mutations (crp11.1, ptsG2.2, ptsG10.1) reduced growth rates by 10–28% and nearly or completely abolished diauxic growth (Fig. 3, Fig. 4). Despite the benefit of shortening diauxic shifts, the significant growth rate defect incurred by crp and ptsG mutations was surprising since they were preserved in lineages thriving through long-term growth selection. Could phenotypes observed here be confounded by epistatic interactions between these and other mutations present in evolved isolates? We tested this possibility by reverting the mutated ptsG alleles (ptsG2.2, ptsG10.1) in two SG isolates Z2.2 and Z10.1 back to wild-type (ptsGWT). If ptsG2.2 and ptsG10.1 exerted an opposite effect in the evolved genetic background, we expected allelic reversion to slow down growth of Z2.2 and Z10.1. Instead, reverting ptsG alleles in both evolved isolates increased growth rates by 31% and 21%, respectively (Fig. 3). In addition, allelic reversion lengthened the diauxic shifts of both evolved isolates, consistent with the phenotypes of ptsG2.2 and ptsG10.1 in the ancestral ZED background. Results indicated that the poor growth of SG isolates on glucose was partly explained by ptsG mutations. Moreover, harmful effects of these mutations on glucose growth were qualitatively independent of the genetic context.


Transhydrogenase promotes the robustness and evolvability of E. coli deficient in NADPH production.

Chou HH, Marx CJ, Sauer U - PLoS Genet. (2015)

Effects of adaptive mutations on growth rates and diauxic shifts.Dashed lines indicate the phenotype of E. coli ZED. Error bars are 95% C.I. based on six independent measurements. ND, no diauxic growth.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4340650&req=5

pgen.1005007.g003: Effects of adaptive mutations on growth rates and diauxic shifts.Dashed lines indicate the phenotype of E. coli ZED. Error bars are 95% C.I. based on six independent measurements. ND, no diauxic growth.
Mentions: To investigate the phenotypic effects of Z-specific mutations, we introduced seven of them into the ancestral ZED background (pntAB2.4, cyaA8.4, cyaA11.1, crp11.1, ptsI12.1, ptsG2.2, ptsG10.1). We left out pntAB12.1 and two large amplification mutations (pntAB10.2, ptsA10.2) because the former was a point mutation identical to pntAB2.4 and the latter was not amenable to genetic manipulation. These seven mutations caused diverse changes in growth profiles (Fig. 3). Four mutations (pntAB2.4, cyaA8.4, cyaA11.1, ptsI12.1) conferred clear selective advantages through increasing growth rates on glucose by 15–27% and shortening diauxic shifts by 16–78%. Among these, pntAB2.4 alone was able to restore the growth rate of E. coli ZED back to the WT level, which indicated the NADPH shortage of the ZED strain as the major cause of its slow growth on glucose. In contrast, the remaining three mutations (crp11.1, ptsG2.2, ptsG10.1) reduced growth rates by 10–28% and nearly or completely abolished diauxic growth (Fig. 3, Fig. 4). Despite the benefit of shortening diauxic shifts, the significant growth rate defect incurred by crp and ptsG mutations was surprising since they were preserved in lineages thriving through long-term growth selection. Could phenotypes observed here be confounded by epistatic interactions between these and other mutations present in evolved isolates? We tested this possibility by reverting the mutated ptsG alleles (ptsG2.2, ptsG10.1) in two SG isolates Z2.2 and Z10.1 back to wild-type (ptsGWT). If ptsG2.2 and ptsG10.1 exerted an opposite effect in the evolved genetic background, we expected allelic reversion to slow down growth of Z2.2 and Z10.1. Instead, reverting ptsG alleles in both evolved isolates increased growth rates by 31% and 21%, respectively (Fig. 3). In addition, allelic reversion lengthened the diauxic shifts of both evolved isolates, consistent with the phenotypes of ptsG2.2 and ptsG10.1 in the ancestral ZED background. Results indicated that the poor growth of SG isolates on glucose was partly explained by ptsG mutations. Moreover, harmful effects of these mutations on glucose growth were qualitatively independent of the genetic context.

Bottom Line: Notably, mTH displays broad phylogenetic distribution and has also played a predominant role in laboratory evolution of Methylobacterium extorquens deficient in NADPH production.Convergent evolution of two phylogenetically and metabolically distinct species suggests mTH as a conserved buffering mechanism that promotes the robustness and evolvability of metabolism.Moreover, adaptive diversification via evolving dual substrate consumption highlights the flexibility of physiological systems to exploit ecological opportunities.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland; Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

ABSTRACT
Metabolic networks revolve around few metabolites recognized by diverse enzymes and involved in myriad reactions. Though hub metabolites are considered as stepping stones to facilitate the evolutionary expansion of biochemical pathways, changes in their production or consumption often impair cellular physiology through their system-wide connections. How does metabolism endure perturbations brought immediately by pathway modification and restore hub homeostasis in the long run? To address this question we studied laboratory evolution of pathway-engineered Escherichia coli that underproduces the redox cofactor NADPH on glucose. Literature suggests multiple possibilities to restore NADPH homeostasis. Surprisingly, genetic dissection of isolates from our twelve evolved populations revealed merely two solutions: (1) modulating the expression of membrane-bound transhydrogenase (mTH) in every population; (2) simultaneously consuming glucose with acetate, an unfavored byproduct normally excreted during glucose catabolism, in two subpopulations. Notably, mTH displays broad phylogenetic distribution and has also played a predominant role in laboratory evolution of Methylobacterium extorquens deficient in NADPH production. Convergent evolution of two phylogenetically and metabolically distinct species suggests mTH as a conserved buffering mechanism that promotes the robustness and evolvability of metabolism. Moreover, adaptive diversification via evolving dual substrate consumption highlights the flexibility of physiological systems to exploit ecological opportunities.

Show MeSH
Related in: MedlinePlus