A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism
Andrew F. Schober,
Andrew D. Mathis,
Christine Ingle,
Junyoung O. Park,
Li Chen,
Joshua D. Rabinowitz,
Ivan Junier,
Olivier Rivoire,
Kimberly A. Reynolds
Affiliations
Andrew F. Schober
The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Andrew D. Mathis
The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Christine Ingle
The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Junyoung O. Park
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
Li Chen
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
Joshua D. Rabinowitz
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
Ivan Junier
Centre National de la Recherche Scientifique, Université Grenoble Alpes, TIMC-IMAG, F-38000 Grenoble, France
Olivier Rivoire
Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, F-75005 Paris, France
Kimberly A. Reynolds
The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Corresponding author
Summary: 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. : Comparative genomics identified the enzymes DHFR and TYMS as an evolutionary module embedded within folate metabolism. Schober et al. show experimentally that these enzymes adapt as a unit in response to DHFR inhibition with an antibiotic. Extending comparative genomics analyses genome wide suggests >200 additional candidate adaptive units throughout bacterial metabolism. Keywords: co-evolution, comparative genomics, synteny, folate metabolism, dihydrofolate reductase, DHFR, thymidylate synthase, TYMS, experimental evolution, forward evolution, trimethoprim, adaptive unit
