CAREER: DNA as a Nutrient-A Role for Competence Gene Homologs in Long-Term Survival

大多数关于细菌自然史的模型都包括“盛宴和饥荒”的循环，在这个循环中，生物体经历了营养丰富和营养紧张。然而，对于大多数微生物来说，营养物质的可用性通常是有限的。为了了解细菌在实验室条件下的生存机制，更好地反映自然环境，我们研究了大肠杆菌生命周期的营养限制固定阶段。我们已经确定了大肠杆菌在固定阶段存活的长期孵育所必需的基因家族。这些基因的活动使细菌能够利用细胞外DNA作为碳和能量的唯一来源。这些基因与已知参与水平基因转移的其他生物体中的基因同源，使细胞能够进行自然转化。因此，它们被称为“com”基因。然而，与流感嗜血杆菌或枯草芽孢杆菌等具有自然遗传转化能力的细菌不同，大肠杆菌并不具有自然转化能力。在大肠杆菌中发现这些基因表明，这种有机体吸收DNA并不一定是为了作为遗传信息，也可以作为碳和能源来源。本项目的重点是了解大肠杆菌利用DNA作为营养物质的能力，确定这些com基因在DNA分解代谢中的作用，阐明com基因的表达和调控模式。该项目还包括引入一门新课程，“细菌生存、适应和进化机制”，该课程的重点是探索各种微生物在不同环境中生存的机制，使它们能够适应环境变化。

Most models of the natural history of bacteria include cycles of "feast and famine," where the organism experiences nutrient abundance as well as nutrient stress. However, for most microorganisms, nutrient availability is usually restricted. To understand mechanisms of bacterial survival under laboratory conditions that better reflect the natural environment, we study the nutrient-limited stationary phase of the E. coli life cycle. We have identified a gene family essential for E. coli to survive long-term incubation during stationary phase. The activities of these genes enable the bacteria to use extracellular DNA as the sole source of carbon and energy. These genes are homologs of genes in other organisms known to be involved in horizontal gene transfer, making the cells competent for natural transformation. Therefore, they are known as "com" genes. However, unlike bacteria such as Haemophilus influenzae or Bacillus subtilis that are naturally competent for genetic transformation, E. coli is not known to be naturally transformable. The identification of these genes in E. coli suggests that the organism takes up DNA not necessarily to be used as genetic information, but also to be used as a carbon and energy source. The focus of this project is to understand the ability of E. coli to use DNA as a nutrient, determine the roles of these com genes in DNA catabolism, and elucidate the patterns of com gene expression and regulation. This project also includes the introduction of a new course, "Mechanisms of Bacterial Survival, Adaptation & Evolution", whose focus is to explore the mechanisms used by a variety of microorganisms to survive in disparate environments, allowing them to adapt to environmental change.