14 NSFBIO:Identifying Mechanisms for Environmental Adaptation in CMNR Bacteria: A Systems Analysis of GeneRegulation of AlternativeSubstrateMetabolism

棒状杆菌-分枝杆菌-诺卡氏菌-红球菌（CMNR）细菌组的成员因其对人类健康的影响而得到最好的认可，并且它们包括结核病（TB;结核分枝杆菌）、麻风病（麻风分枝杆菌）和白喉（白喉棒状杆菌）的病原体。然而，这个群体的许多成员对农业、生物技术和环境问题也具有重要意义。CMNR细菌还包括具有广泛宿主范围的动物（牛分枝杆菌、马红球菌以及棒状杆菌和诺卡氏菌属的物种）和植物（红球菌属）病原体。它们也被广泛用于工业。实例包括用于大规模生产氨基酸如L-谷氨酸的谷氨酸棒杆菌和已知积累三酰甘油（TAG）的细菌，三酰甘油是生物柴油的直接构建块的油。此外，一些CMNR细菌也用于称为生物修复的过程，因为它们能够分解环境中的有害和持久性污染物。CMNR细菌中的一个共同主题是富含脂质的细胞包膜，其中含有脂肪酸和脂质，这些脂肪酸和脂质是独特的，在其他细菌中没有发现。这种复杂性反映在这些细菌基因组中脂质代谢相关基因的相对较大比例上。CMNR细菌定居的栖息地的多样性源于它们通过动态改变其独特细胞包膜中复杂脂肪酸的组成来适应新环境的能力。该提案将测试以下假设：根据环境和可用底物，CMNR细菌选择性地改变其细胞包膜的组成。我们提出，细菌通过使用参与细胞被膜“积木”的摄取和生物合成的基因的扩展家族来实现。为了阐明CMNR细菌如何实现这一点，我们将首先测试模型CMNR细菌，耻垢分枝杆菌，在不同基质上生长的能力，这些基质可能作为“积木”。我们将选择导致细胞包膜改变的生长条件，并确定M的转录组（基因表达水平的全局图）。在选择的条件下生长。然后将使用内部计算工具（称为EGRIN 2.0的程序）分析从这些研究中获得的信息，以生成基因调控网络的模型。换句话说，我们将在模型细菌中对这些网络进行“逆向工程”。该模型随后将使我们能够通过比较已发表的基因组来表征CMNR细菌之间的共同和独特的调控机制。将通过分析特定基因缺失对相关条件下代表性CMNR细菌细胞包膜组成的影响来检验模型预测。这个跨机构的建议结合了美国和英国的研究小组的互补专业知识。美国PI的系统生物学专业知识与英国PI在表征CMNR细菌脂质代谢和细胞包膜生物化学方面的专业知识将使我们能够解决CMNR细菌如何适应新环境的基本和生物技术重要问题。

Members of the Corynebacteria-Mycobacteria-Nocardia-Rhodococcus (CMNR) group of bacteria are best recognized for their impact on human health and they include the causative agent of tuberculosis (TB; Mycobacterium tuberculosis), leprosy (Mycobacterium leprae) and diphtheria (Corynebacterium diptheriae). However, many members of this group are also of great significance to agriculture, biotechnology, and environmental issues. CMNR bacteria also include animal (Mycobacterium bovis, Rhodococcus equi, and species of Corynebacteria and Nocardia) and plant (Rhodococcus) pathogens with a broad host range. They also are widely used in industry. Examples include Corynebacterium glutamicum which is used for large-scale manufacturing of amino acids such as L-glutamate and bacteria that are known to accumulate triacyglycerols (TAGs), oils that are the direct building blocks for biodiesel. Furthermore, some CMNR bacteria are also used for a process termed bioremediation due to their ability to break down harmful and persistent pollutants in the environment. A common theme among the CMNR bacteria is a lipid-rich cell envelope that contains fatty acids and lipids that are distinct and not found in other bacteria. This complexity is reflected in the relatively large proportion of lipid metabolism related genes in the genomes of these bacteria. The diversity of habitats colonized by CMNR bacteria is rooted in their ability to adapt to new environments by dynamically altering the composition of complex fatty acids in their unique cell envelope. This proposal will test the hypothesis that depending on the environment and available substrates, the CMNR bacteria selectively alter the composition of their cell envelope. We propose that the bacteria achieve by using expanded families of genes involved in the uptake and biosynthesis of cell envelope 'building blocks'. To elucidate how CMNR bacteria achieve this we will first test the ability of a model CMNR bacterium, Mycobacterium smegmatis, to grow on different substrates that can potentially act as 'building blocks'. We will select growth conditions that lead to cell envelope alterations and determine the transciptome (a global picture of the levels to which genes are expressed) of M. smegmatis growing under the select conditions. The information obtained from these studies will then be analysed using in-house computational tools (a program called EGRIN 2.0) to generate models of gene regulatory networks. In other words, we will 'reverse engineer' these networks in the model bacterium. This model will subsequently allow us, by comparing published genomes, to characterize common and unique regulatory mechanisms across CMNR bacteria. Model predictions will be tested by analyzing consequences of specific gene deletions on cell envelope composition of representative CMNR bacteria under relevant conditions. This inter-institutional proposal combines the complementary expertise of the US and UK based research groups. The systems biology expertise of the US-based PI with the UK-based PI's expertise in characterizing CMNR bacteria lipid metabolism and cell envelope biochemistry will allow us to address the fundamental and biotechnologically important question of how CMNR bacteria adapt to new environments.