Chubiz Lon M, Marx Christopher J
Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, USA
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
J Bacteriol. 2017 May 9;199(11). doi: 10.1128/JB.00827-16. Print 2017 Jun 1.
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 when , 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 () that regulates the expression of genes associated with catabolism of -acetylglucosamine are the common basis for evolved glucose metabolism across populations. The loss of results in the constitutive expression of genes for an -acetylglucosamine permease () and kinase (). 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 in C-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 in in natural environments despite it being readily accessible through just a single mutational event. 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 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.
细菌通过获取遗传物质或基因组中已有基因的突变来提高其代谢能力。在此，我们探究了一种通常消耗小分子有机物和氨基酸的细菌，在短时间适应富含葡萄糖的环境后迅速进化以扩展其代谢能力来分解葡萄糖时所涉及的机制和权衡。通过全基因组测序和遗传学方法，我们发现一个包含转录阻遏物（）的区域发生缺失，该阻遏物调控与N - 乙酰葡糖胺分解代谢相关基因的表达，这是群体中进化出葡萄糖代谢的共同基础。的缺失导致N - 乙酰葡糖胺通透酶（）和激酶（）基因的组成型表达。我们证明NagP和NagK对葡萄糖的混杂活性允许葡萄糖转运并磷酸化为6 - 磷酸葡萄糖，这是糖酵解的起始步骤，否则在基于碳的代谢通量分析中被认为不存在。发现随后的利用由Entner - Doudoroff途径介导。这是一个基因缺失和已有酶混杂性而非功能获得性突变驱动代谢能力增加的例子。然而，我们观察到适应葡萄糖分解代谢后，乳酸生长速率显著下降，这表明权衡可能解释了为什么尽管通过单个突变事件就能轻易获得糖酵解功能，但在自然环境中却不易观察到。代谢能力的增加通常与通过自然或工程水平基因转移事件获取新的遗传物质有关。在此，我们探究了一种通常消耗小分子有机酸和氨基酸的细菌如何通过遗传物质的丢失来扩展其代谢能力以包括葡萄糖，这一过程通常与代谢功能的恶化相关。我们的发现突出了转运蛋白和酶的自然混杂性如何能够成为扩展代谢多样性的关键驱动力，以及许多细菌可能拥有通过一个或几个去除调控功能的突变就能获得的潜在代谢能力。我们在乳酸和葡萄糖生长之间发现的权衡表明了为什么这种容易获得的性状在自然界中未被观察到。
