Linking genotypic and phenotypic changes in the E. coli long-term evolution experiment using metabolomics

TY - JOUR

T1 - Linking genotypic and phenotypic changes in the E. coli long-term evolution experiment using metabolomics

AU - Favate, John S.

AU - Skalenko, Kyle S.

AU - Chiles, Eric

AU - Su, Xiaoyang

AU - Yadavalli, Srujana Samhita

AU - Shah, Premal

N1 - Publisher Copyright: © 2023, Favate et al.

PY - 2023/11/22

Y1 - 2023/11/22

N2 - Changes in an organism's environment, genome, or gene expression patterns can lead to changes in its metabolism. The metabolic phenotype can be under selection and contributes to adaptation. However, the networked and convoluted nature of an organism's metabolism makes relating mutations, metabolic changes, and effects on fitness challenging. To overcome this challenge, we use the long-term evolution experiment (LTEE) with E. coli as a model to understand how mutations can eventually affect metabolism and perhaps fitness. We used mass spectrometry to broadly survey the metabolomes of the ancestral strains and all 12 evolved lines. We combined this metabolic data with mutation and expression data to suggest how mutations that alter specific reaction pathways, such as the biosynthesis of nicotinamide adenine dinucleotide, might increase fitness in the system. Our work provides a better understanding of how mutations might affect fitness through the metabolic changes in the LTEE and thus provides a major step in developing a complete genotype-phenotype map for this experimental system.

AB - Changes in an organism's environment, genome, or gene expression patterns can lead to changes in its metabolism. The metabolic phenotype can be under selection and contributes to adaptation. However, the networked and convoluted nature of an organism's metabolism makes relating mutations, metabolic changes, and effects on fitness challenging. To overcome this challenge, we use the long-term evolution experiment (LTEE) with E. coli as a model to understand how mutations can eventually affect metabolism and perhaps fitness. We used mass spectrometry to broadly survey the metabolomes of the ancestral strains and all 12 evolved lines. We combined this metabolic data with mutation and expression data to suggest how mutations that alter specific reaction pathways, such as the biosynthesis of nicotinamide adenine dinucleotide, might increase fitness in the system. Our work provides a better understanding of how mutations might affect fitness through the metabolic changes in the LTEE and thus provides a major step in developing a complete genotype-phenotype map for this experimental system.

KW - E. coli

KW - LTEE

KW - adaptation

KW - bacteria

KW - evolutionary biology

KW - metabolomics

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U2 - 10.7554/eLife.87039

DO - 10.7554/eLife.87039

M3 - Article

C2 - 37991493

SN - 2050-084X

VL - 12

JO - eLife

JF - eLife

ER -