Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes

Evolution; International Journal of Organic Evolution
Glen D'SouzaChristian Kost

Abstract

Many bacterial lineages lack seemingly essential metabolic genes. Previous work suggested selective benefits could drive the loss of biosynthetic functions from bacterial genomes when the corresponding metabolites are sufficiently available in the environment. However, the factors that govern this "genome streamlining" remain poorly understood. Here we determine the effect of plasticity and epistasis on the fitness of Escherichia coli genotypes from whose genome biosynthetic genes for one, two, or three different amino acids have been deleted. Competitive fitness experiments between auxotrophic mutants and prototrophic wild-type cells in one of two carbon environments revealed that plasticity and epistasis strongly affected the mutants' fitness individually and interactively. Positive and negative epistatic interactions were prevalent, yet on average cancelled each other out. Moreover, epistasis correlated negatively with the expected effects of combined auxotrophy-causing mutations, thus producing a pattern of diminishing returns. Moreover, computationally analyzing 1,432 eubacterial metabolic networks revealed that most pairs of auxotrophies co-occurred significantly more often than expected by chance, suggesting epistatic in...Continue Reading

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Citations

Aug 20, 2015·Proceedings of the National Academy of Sciences of the United States of America·John Carey
Apr 1, 2016·The FEBS Journal·Silvio WaschinaChristoph Kaleta
Nov 5, 2016·PLoS Genetics·Glen D'Souza, Christian Kost
Nov 10, 2018·Frontiers in Microbiology·Rosemary J Redfield, Shannon M Soucy
Mar 7, 2020·Nature Communications·Jhonatan A Hernandez-ValdesOscar P Kuipers
Feb 28, 2019·Frontiers in Genetics·Bhaskar Chandra Mohan Ramisetty, Pavithra Anantharaman Sudhakari
May 9, 2021·Applied Microbiology and Biotechnology·Tomás G VillaAngeles Sánchez-Pérez

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