Lon M. Chubiz, Christopher J. Marx

Bacteria increase metabolic capacity via acquisition of genetic material or by mutation to genes already present in the genome. Here, we explore the mechanisms and tradeoffs involved when Shewanella 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 expression of genes associated with catabolism of N-acetylglucosamine is the common basis for evolved glucose metabolism across populations. Loss of nagR results in constitutive expression of an N-acetylglucosamine permease (nagP) and kinase (nagK). We demonstrate that promiscuous activities of both NagP and NagK towards glucose allows for transport and phosphorylation of glucose to glucose-6-phosphate, the initial events of glycolysis otherwise thought to be absent in S. oneidensis(13)C-based metabolic flux analysis uncovered that subsequent utilization was mediated by the Entner-Doudoroff pathway. This is an example whereby gene loss and pre-existing enzymatic promiscuity, and not gain-of-function mutations, was the driver of increased metabolic capacity. We observed a significant decrease in growth rate on lactate after adapting to glucose catabolism, however, suggesting that tradeoffs may explain why glycolytic function may not be readily observed in S. oneidensis in natural environments despite it being readily accessible through just a single mutational event.Importance Gains 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 loss of genetic material, a process frequently associated with deterioration of metabolic function. Our findings highlight how natural promiscuity of transporters and enzymes can be key drivers in expanding metabolic diversity, and that many bacteria may possess latent metabolic capacity accessible through one or a few mutations that remove regulatory functions. Our discovery of growth tradeoffs between lactate and glucose growth suggest why this easily gained trait is not observed in nature.