@article{868f83a4f26443dfa91e0bc723b2700b,
title = "A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism",
abstract = "Enzyme function and evolution are influenced by the larger context of a metabolic pathway. Deleterious mutations or perturbations in one enzyme can often be compensated by mutations to others. We used comparative genomics and experiments to examine evolutionary interactions with the essential metabolic enzyme dihydrofolate reductase (DHFR). Analyses of synteny and co-occurrence across bacterial species indicate that DHFR is coupled to thymidylate synthase (TYMS) but relatively independent from the rest of folate metabolism. Using quantitative growth rate measurements and forward evolution in Escherichia coli, we demonstrate that the two enzymes adapt as a relatively independent unit in response to antibiotic stress. Metabolomic profiling revealed that TYMS activity must not exceed DHFR activity to prevent the depletion of reduced folates and the accumulation of the intermediate dihydrofolate. Comparative genomics analyses identified >200 gene pairs with similar statistical signatures of modular co-evolution, suggesting that cellular pathways may be decomposable into small adaptive units.",
keywords = "DHFR, TYMS, adaptive unit, co-evolution, comparative genomics, dihydrofolate reductase, experimental evolution, folate metabolism, forward evolution, synteny, thymidylate synthase, trimethoprim",
author = "Schober, {Andrew F.} and Mathis, {Andrew D.} and Christine Ingle and Park, {Junyoung O.} and Li Chen and Rabinowitz, {Joshua D.} and Ivan Junier and Olivier Rivoire and Reynolds, {Kimberly A.}",
note = "Funding Information: We thank members of the Reynolds lab for their review of the manuscript, E. Toprak for E. coli MG1655 folA single mutants and extensive advice on morbidostat construction and operation, S. Benkovic for the ER2566 ΔfolA ΔthyA strain, D. Bikard for the E. coli MG1655 strain containing dCas9, T. Kuhlman for molecular biology reagents used in genome editing, S. Thompson for the folA supplementation mix recipe, and T. Bergmiller for the GFP and chloramphenicol resistance marker incorporated into our forward evolution parent strain. This research was funded by the Gordon and Betty Moore Foundation{\textquoteright}s Data-Driven Discovery Initiative through grant GBMF4557 (to K.R.) and by the Green Center for Systems Biology at UT Southwestern Medical Center . A.S. was supported in part by NIH training grant 5T32GM8203-28 . I.J. is supported by an ATIP-Avenir grant ( Centre National de la Recherche Scientifique ). Funding Information: We thank members of the Reynolds lab for their review of the manuscript, E. Toprak for E. coli MG1655 folA single mutants and extensive advice on morbidostat construction and operation, S. Benkovic for the ER2566 ΔfolA ΔthyA strain, D. Bikard for the E. coli MG1655 strain containing dCas9, T. Kuhlman for molecular biology reagents used in genome editing, S. Thompson for the folA supplementation mix recipe, and T. Bergmiller for the GFP and chloramphenicol resistance marker incorporated into our forward evolution parent strain. This research was funded by the Gordon and Betty Moore Foundation's Data-Driven Discovery Initiative through grant GBMF4557 (to K.R.) and by the Green Center for Systems Biology at UT Southwestern Medical Center. A.S. was supported in part by NIH training grant 5T32GM8203-28. I.J. is supported by an ATIP-Avenir grant (Centre National de la Recherche Scientifique). Conceptualization, A.F.S. I.J. O.R. and K.A.R.; Methodology, A.F.S. A.D.M. J.D.R. I.J. O.R. and K.A.R.; Investigation, A.F.S. A.D.M. C.I. J.O.P. L.C. I.J. O.R. and K.A.R.; Writing – Original Draft, A.S. and K.A.R.; Writing – Review & Editing, A.S. A.D.M. C.I. J.O.P. J.D.R. I.J. O.R. and K.A.R.; Supervision, K.A.R. The authors declare no competing interests. Publisher Copyright: {\textcopyright} 2019 The Author(s)",
year = "2019",
month = jun,
day = "11",
doi = "10.1016/j.celrep.2019.05.030",
language = "English (US)",
volume = "27",
pages = "3359--3370.e7",
journal = "Cell Reports",
issn = "2211-1247",
publisher = "Cell Press",
number = "11",
}