title: Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium.
abstract: Contrary to previous understanding, recent evidence indicates that synonymous codon changes may sometimes face strong selection. However, it remains difficult to generalize the nature, strength, and mechanism(s) of such selection. Previously, we showed that synonymous variants of a key enzyme-coding gene (fae) of Methylobacterium extorquens AM1 decreased enzyme production and reduced fitness dramatically. We now show that during laboratory evolution, these variants rapidly regained fitness via parallel yet variant-specific, highly beneficial point mutations in the N-terminal region of fae These mutations (including four synonymous mutations) had weak but consistently positive impacts on transcript levels, enzyme production, or enzyme activity. However, none of the proposed mechanisms (including internal ribosome pause sites or mRNA structure) predicted the fitness impact of evolved or additional, engineered point mutations. This study shows that synonymous mutations can be fixed through strong positive selection, but the mechanism for their benefit varies depending on the local sequence context.
authors.affiliation: National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India Department of Organismic and Evolutionary Biology, Harvard University dagashe@ncbs.res.in cmarx@uidaho.edu.
authors.forename: Deepa
authors.initials: D
authors.lastname: Agashe
authors.affiliation: National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India.
authors.forename: Mrudula
authors.initials: M
authors.lastname: Sane
authors.affiliation: National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India.
authors.forename: Kruttika
authors.initials: K
authors.lastname: Phalnikar
authors.affiliation: National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India SASTRA University, Thanjavur, India.
authors.forename: Gaurav D
authors.initials: GD
authors.lastname: Diwan
authors.affiliation: National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India.
authors.forename: Alefiyah
authors.initials: A
authors.lastname: Habibullah
authors.affiliation: Department of Microbiology and Molecular Genetics, Michigan State University.
authors.forename: Norma Cecilia
authors.initials: NC
authors.lastname: Martinez-Gomez
authors.affiliation: National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India.
authors.forename: Vinaya
authors.initials: V
authors.lastname: Sahasrabuddhe
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University.
authors.forename: William
authors.initials: W
authors.lastname: Polachek
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University Systems Biology Graduate Program, Harvard University.
authors.forename: Jue
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University.
authors.forename: Lon M
authors.initials: LM
authors.lastname: Chubiz
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Harvard University Department of Biological Sciences, University of Idaho Institute for Bioinformatics and Evolutionary Studies, University of Idaho dagashe@ncbs.res.in cmarx@uidaho.edu.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Marx
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D005075:Biological Evolution; D019731:Carbon-Nitrogen Ligases / Q000235:genetics* / Q000378:metabolism; D003062:Codon; D004843:Epistasis, Genetic; D019143:Evolution, Molecular; D056084:Genetic Fitness; D020601:Methylobacterium extorquens / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D009154:Mutation; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism; D012641:Selection, Genetic; D000069456:Silent Mutation
chemical_list: D001426:Bacterial Proteins; D003062:Codon; D012333:RNA, Messenger; D019731:Carbon-Nitrogen Ligases; C417713:Fae protein, Methylobacterium extorquens
keywords: Shine–Dalgarno sequence; codon use; epistasis; fitness; mRNA folding.