Environmental DNA Lesions and Mutagenesis: Molecular Mechanisms of Lesion Recognition for Repair and Polymerase Bypass

环境 DNA 损伤和诱变：损伤识别修复和聚合酶旁路的分子机制

• 批准号: 10460604
• 负责人: Suse Broyde
• 金额: $ 37.2万
• 依托单位: NEW YORK UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-06-01 至 2026-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10460604
• 关键词: Acetylation; Address; Affect; Air; Airborne Particulate Matter; Antineoplastic Agents; Aromatic Compounds; Aromatic Polycyclic Hydrocarbons; Base Sequence; Binding; Biological Markers; Bypass; Characteristics; Chemical Structure; Chemicals; Complement; Cryoelectron Microscopy; Cytosine; DNA; DNA Damage; DNA Sequence; DNA lesion; DNA-Directed DNA Polymerase; DNA-protein crosslink; Disease; Environmental Exposure; Environmental Pollutants; Excision; Failure; Food; Fossil Fuels; Free Energy; Genomics; Guanine; Histone Acetylation; Homologous Gene; Human; Human Genome; Impairment; Induced Mutation; Lead; Lesion; Malignant Neoplasms; Methods; Modeling; Modification; Molecular; Molecular Conformation; Mutagenesis; Mutation; Nature; Nucleosomes; Nucleotide Excision Repair; Orthologous Gene; Outcome; Pathologic Mutagenesis; Peptides; Pharmaceutical Preparations; Pharmacotherapy; Play; Polymerase; Positioning Attribute; Predisposition; Process; Property; Proteins; Reactive Oxygen Species; Resistance; Ribonucleotides; Risk; Rotation; Shapes; Site; Source; Structure; Testing; Thermodynamics; Tobacco; Ultraviolet Rays; Water; Work; Xeroderma Pigmentosum; Yeasts; adduct; base; carcinogenicity; chemotherapy; crosslink; design; disease-causing mutation; exhaust; experimental study; frontier; gene repair; genotoxicity; helicase; human disease; insight; interest; molecular dynamics; mutant; predictive tools; repaired; sound; stereochemistry; superfund site; transcription factor TFIIH; tumor; wasting

PROJECT SUMMARY The human genome is constantly attacked from sources that include environmental pollutants, other exogenous origins that include drug treatment, endogenous reactive oxygen species, and UV light. Among the lesions/adducts are ones derived from polycyclic aromatic compounds, widespread byproducts of fossil fuel combustion found at toxic waste dumps, superfund sites, in our air, food and water. The resulting DNA lesions cause mutations that lead to cancer. However, not all DNA lesions are equally carcinogenic, as their mutagenic propensities vary: a cascade of processes determines whether they are repaired, or survive for mutagenic or error-free bypass by DNA polymerases. Human nucleotide excision repair (NER) is a key mechanism for removal of many such DNA lesions. The vital importance of NER is demonstrated in the devastating human disorder xeroderma pigmentosum, caused by mutations in NER genes. Notably, some lesions are rapidly repaired, some slowly, and some are resistant and thus particularly genotoxic, a phenomenon that is poorly understood. Likewise, there is a gap in our understanding of the mechanisms underlying DNA lesion bypass by polymerases that can lead to a mutagenic or error-free outcome. The objective of this project is to provide mechanistic insights into the puzzling variability of DNA lesion mutagenicity, focusing on the key steps of lesion recognition for repair and mutagenic bypass, to yield integrated new molecular and dynamic understanding of lesion mutagenic proclivity in unprecedented atomistic detail, using molecular dynamics simulations. Our overall hypothesis is that the structure of the lesion and its base sequence context determine its overall mutagenic propensity. In Aim 1, we will utilize a selected set of DNA lesions/adducts whose structures differ greatly in size and shape, placed in differing sequence contexts, to determine structural, energetic and dynamic characteristics of the lesion-containing DNAs as they bind to Rad4/XPC, the yeast homolog of the human XPC lesion recognition protein. We will reveal how those that bind for productive recognition leading to excision differ from those that fail to do so. In Aim 2 we will determine how the human XPD helicase in TFIIH, that verifies the presence of lesions for NER by stalling, processes lesions of different sizes and shapes, and how XPD mutations that cause human disease inhibit XPD’s function. In Aim 3 we will determine how differing lesion structures in varying nucleosomal positions impose different distortions on the nucleosome and how selected histone acetylations modulate these distortions, to promote or inhibit access for repair. In Aim 4 we investigate endogenous and exogenous DNA peptide crosslink lesions, to determine how selected DNA bypass polymerases process them error-free or mutagenically, in differing DNA sequence contexts. Focusing on the most mutagenic lesions, our work will facilitate identification of appropriate biomarkers for determining risk of developing cancer, advance design of chemotherapy drugs that are less repaired, and yield a predictive tool to identify mutational hotspot sequences induced by different lesions in human tumors.

项目摘要 人类基因组不断受到包括环境污染物的来源的攻击，其他 外源性起源，包括药物治疗，内源性活性氧和紫外线。在 病变/加合物是源自多环芳族化合物，化石燃料的宽度副产品 在我们的空气，食物和水中发现了有毒废物垃圾场，超级基金地点的燃烧。产生的DNA病变 导致导致癌症的突变。但是，并非所有DNA病变都同样具有致癌性 倾向各不相同：一系列过程确定它们是修复的还是为诱变或生存 DNA聚合酶无错误旁路。人核苷酸惊喜维修（NER）是关键机制 去除许多此类DNA病变。 NER的至关重要性在毁灭性的人类中得到了证明 由NER基因突变引起的疾病静脉皮肤色素。值得注意的是，有些病变迅速 修复，有些缓慢，有些是抗性的，因此尤其是遗传毒性，这种现象很差 理解。同样，我们对DNA病变绕过的机制的理解也存在差距 可以导致诱变或无误效果的聚合酶。该项目的目的是提供 对DNA病变诱变性的拼图变异性的机械洞察力，重点是病变的关键步骤 对修复和诱变旁路的识别，以产生对新的分子和动态理解 使用分子动力学模拟，史无前例的原子细节中的病变诱变倾向。 我们的总体假设是病变及其基本序列的结构决定了其 总体诱变的希望。在AIM 1中，我们将利用一组选定的DNA病变/加合物的结构 不同的大小和形状不同，以不同的序列环境放置，以确定结构，能量和 含有病变DNA的动态特征与Rad4/XPC结合时，它们是酵母菌的同源物 人XPC病变识别蛋白。我们将揭示那些如何绑定产品识别的人 切除与不这样做的切除不同。在AIM 2中，我们将确定tfiih中的人XPD解旋酶如何 这通过失速，多种大小和形状的病变以及 引起人类疾病的XPD突变如何抑制XPD的功能。在AIM 3中，我们将确定如何差异 不同核小体位置的病变结构对核小体造成了不同的畸变，以及如何 选定的组蛋白乙酰化会调节这些扭曲，以促进或抑制修复的通道。在目标4中我们 研究内源性和外源性DNA剥离的交联病变，以确定选择选择DNA 绕过聚合酶在区分DNA序列上下文中无误或诱变处理它们。 关注最诱变的病变，我们的工作将有助于识别适当的生物标志物 为了确定患癌症的风险，修复较少的化学疗法药物的预先设计，以及 产生一种预测工具，以鉴定人类肿瘤不同病变诱导的突变热点序列。