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: 10683108
• 负责人: Dirk Iwata-Reuyl
• 金额: $ 39.71万
• 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/10683108
• 关键词: 7-deazaguanine; ATP phosphohydrolase; ATPase Domain; Address; Archaeal Viruses; Bacteria; Bacteriophages; Biochemical; Biochemistry; Bioinformatics; Biotechnology; Chemicals; Chemistry; Complex; DNA; DNA Modification Process; DNA Restriction-Modification Enzymes; Development; Discipline; Elements; Engineering; Enzymes; Epigenetic Process; Experimental Designs; Family; Foundations; Future; Genetic; Genome; In Vitro; Interdisciplinary Study; Joints; Knowledge; Lead; Microbial Genetics; Modeling; Modification; Molecular; Molecular Biology; Nitriles; Nucleic Acids; Nucleoside Q; Nucleosides; Nucleotides; Organism; Organism Modification; Positioning Attribute; Prevalence; Process; Productivity; Proteins; Publications; RNA; Reaction; Research; Research Methodology; Research Project Grants; Role; Site; Specificity; Structure; System; Viral; Work; base; biological systems; biophysical techniques; enzyme structure; epigenetic regulation; in vivo; innovation; novel; nuclease; nucleobase; structural biology; tool; viral DNA

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.

概括。酶指导的核苷酸修饰是核酸的关键组成部分 加工并被所有生物体使用，以满足多种基本需求 信息传输系统，包括保护DNA，转化保真度，RNA稳定， 和表观遗传调节。在RNA和DNA之间的串扰的显着例子中 处理，我们最近发现，已知的最复杂的修饰系统之一 发生在RNA中，负责7-二唑烷修改Queuosine（Q）和 考古（G+）也被多种生物用于DNA的修饰。确实，在 细菌一组大约10种蛋白质包括精心限制修饰（RM）系统 基于2'-Deoxy-7-Cyano-和2'-Deoxy-7-Amido-7-Deazaguanosine的形成（DPREQ0 分别在DNA中，这些核外侧以及DG+和2'-脱氧-7-- 在噬菌体的DNA和 古细菌病毒。已经确定了与形成7-的相关蛋白质 基于Deazaguanine的DNA修饰，我们现在提议阐明分子基础 为了它们的功能。特定目的1和2中描述的研究解决了修改 细菌，蛋白质DPDA，DPDB和DPDC中的机械，共同负责 DPREQ0和DADG的形成，并用作基于7-二氮氨酸修饰的模型 在DNA中。在特定目标3中，我们更广泛地研究DPDA家族，并考虑这些系统 缺少DPDB并包含DPDAC融合以及噬菌体DPDA，以便更好地理解 DPDB在细菌修饰中的加密ATPase活性和结构基础的需求 细菌和病毒系统中的序列特异性。