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

基本信息

批准号：
10293848
负责人：
Suse Broyde
金额：
$ 36.79万
依托单位：
NEW YORK UNIVERSITY
依托单位国家：
美国
项目类别：
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/10293848
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

项目摘要

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.

项目概要人类基因组不断受到环境污染物、其他来源的攻击外源性来源包括药物治疗、内源性活性氧和紫外线。病变/加合物是源自多环芳香族化合物，广泛存在的化石燃料副产品在有毒废物堆、超级基金场所、我们的空气、食物和水中发现了燃烧所造成的 DNA 损伤。然而，并非所有 DNA 损伤都同样具有致癌性，因为它们具有致突变性。倾向各不相同：一连串的过程决定了它们是否被修复，或者是否因突变或突变而存活下来。 DNA聚合酶的无差错旁路是人类核苷酸切除修复（NER）的关键机制。 NER 的重要性在毁灭性的人类身上得到了证明。着色性干皮病，由 NER 基因突变引起，值得注意的是，某些病变会迅速发生。修复，有些缓慢，有些具有抗药性，因此具有特别的遗传毒性，这种现象很少见同样，我们对 DNA 损伤绕过机制的理解也存在差距。该项目的目标是提供可导致突变或无错误结果的聚合酶。对 DNA 损伤致突变性令人费解的变异性的机制见解，重点关注损伤的关键步骤识别修复和诱变旁路，以产生整合的新分子和动态理解使用分子动力学模拟，在前所未有的原子细节中发现病变致突变倾向。我们的总体假设是病变的结构及其碱基序列上下文决定了其在目标 1 中，我们将利用一组选定的 DNA 损伤/加合物，其结构如下。大小和形状差异很大，放置在不同的序列环境中，以确定结构、能量和含有损伤的 DNA 在与 Rad4/XPC（酵母同源物）结合时的动态特征我们将揭示那些结合产生有效识别的蛋白如何导致人类 XPC 损伤识别蛋白。在目标 2 中，我们将确定 TFIIH 中的人类 XPD 解旋酶，通过不同大小和形状的病变过程的停滞来验证 NER 病变的存在，以及在目标 3 中，我们将确定导致人类疾病的 XPD 突变如何抑制 XPD 的功能。不同核小体位置的病变结构对核小体造成不同的扭曲，以及如何在目标 4 中，我们选择组蛋白乙酰化来调节这些扭曲，以促进或抑制修复。研究内源性和外源性DNA肽交联损伤，以确定如何选择DNA 旁路聚合酶在不同的 DNA 序列环境中无差错或诱变地处理它们。我们的工作重点关注最具致突变性的病变，将有助于识别适当的生物标志物用于确定患癌症的风险，提前设计修复较少的化疗药物，以及产生一种预测工具来识别人类肿瘤中不同病变引起的突变热点序列。