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

微生物（即细菌）在生活的各个方面发挥着核心作用，包括有机材料的回收，固氮，光合作用，废物分解以及人类健康和疾病。因此，明确区分不同的微生物群体并确定它们具有哪些独特的特性非常重要。虽然培养的“细菌”目前被分为大约25个主要组，但对于这些组中的大多数，没有独特的分子、生物化学或生理学特征是已知的。因此，识别不同细菌群所特有的特征非常重要。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）蛋白质序列中的保守插入或缺失（indels），以及（ii）对不同细菌谱系具有特异性的完整蛋白质。这些标记物除了提供用于鉴定不同组细菌的高度特异性手段之外，还为遗传和生物化学研究提供有价值的探针。这一建议将在若干重要方面扩展我们先前广泛的工作。我们的主要目标是：**1。对变形菌门和厚壁菌门的基因组序列进行详细的比较分析，以确定对它们有特异性的分子标记。变形菌门和厚壁菌门是细菌中最大的两个类群，包含许多具有工业、临床、农业和环境意义的生物。因此，所发现的分子标记将用于各种研究。2.利用新发现的分子标记开发更灵敏和特异的方法，用于鉴定一些重要的细菌群（例如链球菌、李斯特菌、木糖杆菌、果胶杆菌、狄氏菌、罗尔斯通氏菌、奈瑟氏菌等）。是这些门的一部分。** 3.对一些分子标记进行遗传和生物化学研究，以了解其功能意义。在这方面，将对重要管家蛋白（即Gyrase A、Gyrase B、DnaK和SecA）中的许多保守indel进行功能研究。

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).**********