Diversity-Generating Retroelements in Phage and Bacterial Genomes

描述（由申请人提供）：我们发现了一个新的逆转录因子家族，称为多样性生成逆转录因子（DGRs），其功能是使编码蛋白质的DNA序列多样化。原型DGR是在噬菌体基因组中确定的，其基础是它能够在一个基因中产生变异性，该基因指定了博德特拉菌物种的受体分子的趋向性。博德泰拉菌会引起人类和其他哺乳动物的呼吸道感染。趋向性转换是一种模板依赖性、逆转录酶介导的过程，在靶基因的特定位置引入核苷酸替换。这种基于卡带的机制理论上能够在单个多肽中产生数万亿个不同的氨基酸序列，提供了大量潜在的配体-受体相互作用。利用博德特拉噬菌体DGR作为标记，我们已经在许多细菌基因组中鉴定了同源元件。特别值得注意的是，预计dgr会使胃肠道菌群中最丰富的拟杆菌（Bacteroides thetaiotaomicron）和齿龈密螺旋体（Treponema denticola）表面的蛋白质多样化，密螺旋体是一种与牙周病相关的口腔细菌。原核生物的dgr代表了一种产生蛋白质多样性的全新机制。除了作为新发现的遗传元件家族及其在人类健康和疾病中的潜在作用的根本重要性外，dgr还因其潜在的应用而引起人们的兴趣。我们的具体目标是：1。对博德特拉菌噬菌体中产生多样性的原型逆转录因子进行机理分析。2. 探索受体库和配体识别的结构基础由dgr编码的受体蛋白。3. 探讨DGR在人胃肠道共生拟杆菌中的功能。

DESCRIPTION (provided by applicant): We have discovered a new family of retroelements, designated diversity-generating retroelements (DGRs) that function to diversify protein-encoding DNA sequences. The prototype DGR was identified in a bacteriophage genome on the basis of its ability to generate variability in a gene that specifies tropism for receptor molecules on Bordetella species. Bordetella cause respiratory infections in humans and other mammals. Tropism switching is a template-dependent, reverse transcriptase-mediated process that introduces nucleotide substitutions at defined locations within a target gene. This cassette-based mechanism is theoretically capable of generating trillions of different amino acid sequences in a single polypeptide, providing a vast repertoire of potential ligand-receptor interactions. Using the Bordetella phage DGR as a signature, we have identified homologous elements in numerous bacterial genomes. Of particular note are DGRs that are predicted to diversify proteins on the surface of Bacteroides thetaiotaomicron, one of the most abundant members of the gastrointestinal flora, and Treponema denticola, an oral bacterium associated with periodontal disease. Prokaryotic DGRs represent an entirely novel mechanism for generating protein diversity. In addition to their fundamental importance as a newly discovered family of genetic elements and their potential roles in human health and disease, DGRs are of interest as a result of their potential applications. Our specific aims are to: 1. Conduct a mechanistic analysis of the prototype diversity-generating retroelement present in Bordetella bacteriophage. 2. Probe the receptor repertoire and the structural basis of ligand recognition by a DGR-encoded receptor protein. 3. Investigate DGR function in the human gastrointestinal commensal Bacteroides thetaiotaomicron.