7-deazaguanines in DNA: mechanism and structure of complex genome modification

DNA 中的 7-脱氮鸟嘌呤：复杂基因组修饰的机制和结构

• 批准号: 10810530
• 负责人: Dirk Iwata-Reuyl
• 金额: $ 1.23万
• 依托单位: PORTLAND STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-08-15 至 2026-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10810530
• 关键词: 7-deazaguanine; ATP phosphohydrolase; Address; Archaeal Viruses; Bacteria; Bacteriophages; Biotechnology; Complex; DNA; DNA Modification Process; DNA Restriction-Modification Enzymes; Development; Family; Foundations; Genome; Modeling; Modification; Molecular; Nucleic Acids; Nucleoside Q; Nucleosides; Nucleotides; Organism; Organism Modification; Proteins; RNA; Research; Role; Specificity; Structure; System; Viral; Work; epigenetic regulation; tool

SUMMARY. Enzymatically-directed nucleotide modification is a key component of nucleic acid processing and is used by all organisms to address a multitude of fundamental needs in information transfer systems, including protection of DNA, translational fidelity, RNA stabilization, and epigenetic regulation. In a remarkable example of the cross-talk between RNA and DNA processing, we recently discovered that one of the most complex modification systems known to occur in RNA, that responsible for the 7-deazaguanine modifications queuosine (Q) and archaeosine (G+), is also utilized by diverse organisms for the modification of DNA. Indeed, in Bacteria a set of roughly 10 proteins comprise an elaborate restriction-modification (RM) system based on the formation of 2’-deoxy-7-cyano- and 2’-deoxy-7-amido-7-deazaguanosine (dPreQ0 and dADG, respectively) in DNA, and these nucleosides, as well as dG+ and 2’-deoxy-7- aminomethyl-7-deazaguanosine (dPreQ1), have also been found in the DNA of phage and archaeal viruses. Having identified the relevant proteins involved in the formation of 7- deazaguanine based DNA modifications, we are now proposing to elucidate the molecular basis for their function. The research described in specific aims 1 & 2 address the modification machinery in bacteria, the proteins DpdA, DpdB, and DpdC, which together are responsible for the formation of dPreQ0 and dADG, and serve as a model for 7-deazaguanine based modification in DNA. In specific aim 3 we take a broader look at the DpdA family and consider systems that lack DpdB and contain DpdAC fusions, as well as a phage DpdA in order to better understand the need for the cryptic ATPase activity of DpdB in bacterial modification, and the structural basis of sequence specificity in the bacterial and viral systems.

摘要：酶促核苷酸修饰是核酸的关键组成部分。 处理并被所有生物体用来满足多种基本需求 信息传输系统，包括 DNA 保护、翻译保真度、RNA 稳定性、 这是 RNA 和 DNA 之间相互作用的一个显着例子。 处理，我们最近发现已知的最复杂的修改系统之一 发生在 RNA 中，负责 7-脱氮鸟嘌呤修饰 queuosine (Q) 和 事实上，古氨酸 (G+) 也被多种生物体用来修饰 DNA。 细菌由大约 10 种蛋白质组成，包含复杂的限制性修饰 (RM) 系统 基于 2’-deoxy-7-cyano- 和 2’-deoxy-7-amido-7-deazaguanosine (dPreQ0 和 dADG，分别）在 DNA 中，以及这些核苷，以及 dG+ 和 2'-deoxy-7- 氨甲基-7-脱氮鸟苷 (dPreQ1) 也被发现存在于噬菌体的 DNA 中 鉴定出参与 7-形成的相关蛋白质。 基于脱氮鸟嘌呤的 DNA 修饰，我们现在提议阐明其分子基础 具体目标 1 和 2 中描述的研究解决了修改问题。 细菌中的机制，即蛋白质 DpdA、DpdB 和 DpdC，它们共同负责 dPreQ0 和 dADG 的形成，并作为基于 7-脱氮鸟嘌呤的修饰的模型 在具体目标 3 中，我们更广泛地审视 DpdA 系列并考虑以下系统： 缺少 DpdB 并包含 DpdAC 融合体，以及噬菌体 DpdA，以便更好地理解 细菌修饰中对 DpdB 隐秘 ATP 酶活性的需求及其结构基础 细菌和病毒系统中的序列特异性。