title: Growth Trade-Offs Accompany the Emergence of Glycolytic Metabolism in Shewanella oneidensis MR-1.
abstract: Bacteria increase their metabolic capacity via the acquisition of genetic material or by the mutation of genes already present in the genome. Here, we explore the mechanisms and trade-offs involved whenShewanella oneidensis, a bacterium that typically consumes small organic and amino acids, rapidly evolves to expand its metabolic capacity to catabolize glucose after a short period of adaptation to a glucose-rich environment. Using whole-genome sequencing and genetic approaches, we discovered that deletions in a region including the transcriptional repressor (nagR) that regulates the expression of genes associated with catabolism ofN-acetylglucosamine are the common basis for evolved glucose metabolism across populations. The loss ofnagRresults in the constitutive expression of genes for anN-acetylglucosamine permease (nagP) and kinase (nagK). We demonstrate that promiscuous activities of both NagP and NagK toward glucose allow for the transport and phosphorylation of glucose to glucose-6-phosphate, the initial events of glycolysis otherwise thought to be absent inS. oneidensis13C-based metabolic flux analysis uncovered that subsequent utilization was mediated by the Entner-Doudoroff pathway. This is an example whereby gene loss and preexisting enzymatic promiscuity, and not gain-of-function mutations, were the drivers of increased metabolic capacity. However, we observed a significant decrease in the growth rate on lactate after adaptation to glucose catabolism, suggesting that trade-offs may explain why glycolytic function may not be readily observed inS. oneidensisin natural environments despite it being readily accessible through just a single mutational event.IMPORTANCEGains in metabolic capacity are frequently associated with the acquisition of novel genetic material via natural or engineered horizontal gene transfer events. Here, we explored how a bacterium that typically consumes small organic acids and amino acids expands its metabolic capacity to include glucose via a loss of genetic material, a process frequently associated with a deterioration of metabolic function. Our findings highlight how the natural promiscuity of transporters and enzymes can be a key driver in expanding metabolic diversity and that many bacteria may possess a latent metabolic capacity accessible through one or a few mutations that remove regulatory functions. Our discovery of trade-offs between growth on lactate and on glucose suggests why this easily gained trait is not observed in nature.
authors.affiliation: Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, USA chubizl@umsl.edu.|Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
authors.forename: Lon M
authors.identifier: http://orcid.org/0000-0003-3370-1308
authors.initials: LM
authors.lastname: Chubiz
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.|Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.|Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho, USA.|Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Marx
mesh_terms: D000117:Acetylglucosamine / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D005947:Glucose / Q000378:metabolism*; D006019:Glycolysis; D009004:Monosaccharide Transport Proteins / Q000235:genetics / Q000378:metabolism; D020592:Shewanella / Q000201:enzymology / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D009004:Monosaccharide Transport Proteins; C103152:N-acetylglucosamine permease; D005947:Glucose; D000117:Acetylglucosamine
keywords: adaptive mutations; glycolysis; metabolic capacity; substrate promiscuity; trade-offs