Identification and Characterization of Novel Molecular Markers for the Proteobacteria (Beta and Gamma) and Firmicutes Phyla

微生物(即细菌)在生活的各个方面都发挥着核心作用，包括有机物质的循环利用、固氮、光合作用、废物分解以及对人类健康和疾病的影响。因此，清楚地区分不同的微生物群并确定它们具有哪些独特的性质是非常重要的。虽然目前培养的“细菌”大约分为25个主要类群，但大多数这些类群的独特分子、生化或生理特性尚不清楚。因此，确定不同细菌群体特有的特征是非常重要的。利用基因组序列，我的团队率先发现了两种类型的分子标记(I)蛋白质序列中保守的插入或缺失(Indels)和(Ii)针对不同细菌谱系的完整蛋白质。这些标记除了为鉴定不同种类的细菌提供高度特异性的手段外，还为遗传和生化研究提供了有价值的探针。这项提议将在许多重要方面扩展我们先前广泛的工作。我们的主要目标是： 1.对变形杆菌和菌门变形杆菌的基因组序列进行详细的比较分析，以确定对它们具有特异性的分子标记。变形杆菌和细菌是细菌中最大的两个类群，包含了许多具有工业、临床、农业和环境意义的生物。因此，所发现的分子标记将对各种研究有用。 2.利用新发现的分子标记，开发更灵敏和特异的方法来鉴定一些重要的细菌群(如链球菌、李斯特菌、木霉、细小杆菌、迪克氏杆菌、拉氏杆菌、奈瑟氏菌等)。它们是这些门的一部分。 3.对一些分子标记进行遗传和生化研究，以了解它们的功能意义。在这方面，将对一些保守的Indels进行功能研究，这些Indels在重要的看家蛋白(即。旋转酶A、旋转酶B、DNAK和SecA)。

Microorganisms (i.e. bacteria) play a central role in all aspects of life including recycling of organic materials, nitrogen fixation, photosynthesis, waste decomposition, and in human health and diseases. Therefore, it is of much importance to clearly distinguish different groups of microbes and determine what unique properties they possess. Although the cultured "Bacteria" are presently divided into about 25 main groups, for most of these groups no unique molecular, biochemical or physiological characteristics are known. Hence, it is of much importance to identify characteristics that are unique to different groups of bacteria. Using genome sequences, my group has pioneered the discovery of two types of molecular markers (i) conserved inserts or deletions (indels) in protein sequences and (ii) whole proteins that are specific for different bacterial lineages. These markers in addition to providing highly specific means for identification of different groups of bacteria also provide valuable probes for genetic and biochemical studies. This proposal will extend our extensive earlier work in a number of important ways. Our main objectives are: 1. Undertake detailed comparative analyses of genome sequences from the Proteobacteria and Firmicutes phyla to identify molecular markers that are specific for them. The Proteobacteria and Firmicutes are two of the largest groups within bacteria containing numerous organisms of industrial, clinical, agricultural and environmental interest. Hence, the discovered molecular markers will be useful for a variety of studies. 2. Use the newly discovered molecular markers to develop more sensitive and specific methods for identification of a number of important bacterial groups (e.g. Streptococcus, Listeria, Xylella, Pectobacterium, Dickeya, Ralstonia, Neisseria, etc.) that are part of these phyla. 3. Perform genetic and biochemical studies on a number of molecular markers to understand their functional significance. In this regard, functional studies will be carried out on a number of conserved indels in important housekeeping proteins (viz. Gyrase A, Gyrase B, DnaK and SecA).