Diversity-Generating Retroelements in Phage and Bacterial Genomes

噬菌体和细菌基因组中产生多样性的逆转录因子

• 批准号: 7673471
• 负责人: JEFFERY F. MILLER
• 金额: $ 35.39万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-08-01 至 2011-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7673471
• 关键词: Adenine; Amino Acid Sequence; Antigenic Variation; Bacterial Genome; Bacteriophages; Bacteroides thetaiotaomicron; Biochemical; Biology; Bordetella; C-Type Lectins; Characteristics; Coupled; DNA Sequence; Data; Disease; Family; Gene Targeting; Genes; Genetic; Genome; Growth; Health; Homing; Human; Immune; In Vitro; Indium; Ligands; Location; Mammals; Mediating; Mutagenesis; Nucleotides; Parasites; Periodontal Diseases; Phage Receptors; Population; Process; Proteins; RNA-Directed DNA Polymerase; Recurrence; Respiratory Tract Infections; Retroelements; Role; Site; Specific qualifier value; Surface; Testing; Treponema denticola; Tropism; Variant; base; family genetics; gastrointestinal; genetic element; in vivo; interest; member; novel; oral bacteria; pertactin; polypeptide; prototype; receptor; scaffold

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.

描述（由申请人提供）：我们发现了一个新的逆转录元件家族，命名为多样性生成逆转录元件（DGR），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鉴定的，基于其在指定博德特氏菌属物种上受体分子的向性的基因中产生变异性的能力。博德特氏菌引起人类和其他哺乳动物的呼吸道感染。向性转换是一种模板依赖性逆转录酶介导的过程，其在靶基因内的限定位置引入核苷酸取代。这种基于盒的机制在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，提供了潜在的配体-受体相互作用的巨大库。使用博德特氏菌噬菌体DGR作为签名，我们已经确定了许多细菌基因组中的同源元件。特别值得注意的是DGR，其被预测为使多形拟杆菌（Bacteroides thetaiotaomicron）（胃肠植物群中最丰富的成员之一）和齿垢密螺旋体（Treponema denticola）（一种与牙周病相关的口腔细菌）表面上的蛋白质多样化。前体DGRs代表了产生蛋白质多样性的全新机制。除了它们作为新发现的遗传元件家族的基本重要性及其在人类健康和疾病中的潜在作用之外，DGR由于其潜在应用而受到关注。我们的具体目标是：1.对博德特氏菌噬菌体中存在的原型多样性生成逆转录元件进行机制分析。2.通过DGR编码的受体蛋白探测受体库和配体识别的结构基础。3.研究人胃肠道多形拟杆菌DGR功能。