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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：
10612958
负责人：
Suse Broyde
金额：
$ 35.61万
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/10612958
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 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 Productivity Property Proteins Reactive Oxygen Species Resistance Ribonucleotides Risk Shapes Site Source Structure Testing Therapeutic Thermodynamics Tobacco smoke 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.

项目摘要人类基因组不断受到来自环境污染物、其他外源性来源，包括药物治疗，内源性活性氧和紫外线。中损伤/加合物是来自多环芳香族化合物的损伤/加合物，多环芳香族化合物是化石燃料的广泛副产品有毒废物倾倒场、超级基金场所、空气、食物和水中都有燃烧现象。DNA损伤会导致癌症的突变。然而，并不是所有的DNA损伤都是同样致癌的，因为它们的诱变性倾向各不相同：一系列的过程决定了它们是否被修复，或者在诱变或通过DNA聚合酶的无错误旁路。人核苷酸切除修复（NER）是一种关键机制，去除许多这样的DNA损伤。净入学率的至关重要性体现在毁灭性的人类由NER基因突变引起的着色性干皮病。值得注意的是，一些病变迅速修复，有些缓慢，有些是耐药的，因此特别是遗传毒性，这种现象是很差的明白同样，我们对DNA损伤绕过的机制的理解也存在差距。聚合酶，可以导致诱变或无错误的结果。该项目的目标是提供对DNA损伤致突变性的令人困惑的可变性的机制见解，重点是损伤的关键步骤识别修复和诱变旁路，产生综合的新的分子和动态的理解，病变诱变倾向在前所未有的原子细节，使用分子动力学模拟。我们的总体假设是病变的结构及其碱基序列背景决定了其总体致突变倾向。在目标1中，我们将利用一组选定的DNA损伤/加合物，其结构在大小和形状上有很大的不同，放置在不同的序列背景下，以确定结构，能量和含有损伤的DNA的动态特性，因为它们结合到Rad 4/XPC，酵母同系物的人XPC损伤识别蛋白。我们将揭示那些与生产性认可结合的人如何导致切割与未切割的不同。在目标2中，我们将确定TFIIH中的人XPD解旋酶，通过失速验证NER的病变存在，处理不同大小和形状的病变，导致人类疾病的XPD突变如何抑制XPD的功能。在目标3中，我们将确定不同核小体位置的损伤结构对核小体产生不同的扭曲，选择性的组蛋白乙酰化调节这些扭曲，以促进或抑制修复的通路。在目标4中，研究内源性和外源性DNA肽交联病变，以确定如何选择DNA 旁路聚合酶在不同的DNA序列环境中无错误地或诱变地处理它们。我们的工作集中在最具致突变性的病变上，将有助于鉴定适当的生物标志物用于确定发展癌症的风险，先进的化疗药物的设计，较少修复，产生一个预测工具，以识别人类肿瘤中不同病变诱导的突变热点序列。

项目成果

期刊论文数量（20）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Rotational and translational positions determine the structural and dynamic impact of a single ribonucleotide incorporated in the nucleosome.

DOI：
10.1016/j.dnarep.2018.11.012
发表时间：
2019-01
期刊：
DNA repair
影响因子：
3.8
作者：
Iwen Fu;Duncan J. Smith;S. Broyde
通讯作者：
Iwen Fu;Duncan J. Smith;S. Broyde

Mechanism of lesion verification by the human XPD helicase in nucleotide excision repair.

DOI：
10.1093/nar/gkac496
发表时间：
2022-07-08
期刊：
NUCLEIC ACIDS RESEARCH
影响因子：
14.9
作者：
Fu, Iwen;Mu, Hong;Geacintov, Nicholas E.;Broyde, Suse
通讯作者：
Broyde, Suse

Corrigendum: 5-Formylcytosine mediated DNA-protein cross-links block DNA replication and induce mutations in human cells.

勘误表：5-甲酰胞嘧啶介导的 DNA-蛋白质交联可阻断 DNA 复制并诱导人类细胞突变。

DOI：
10.1093/nar/gky809
发表时间：
2018
期刊：
Nucleic acids research
影响因子：
14.9
作者：
Ji,Shaofei;Fu,Iwen;Naldiga,Spandana;Shao,Hongzhao;Basu,AshisK;Broyde,Suse;Tretyakova,NataliaY
通讯作者：
Tretyakova,NataliaY

The Nonbulky DNA Lesions Spiroiminodihydantoin and 5-Guanidinohydantoin Significantly Block Human RNA Polymerase II Elongation in Vitro.

DOI：
10.1021/acs.biochem.7b00295
发表时间：
2017-06-20
期刊：
Biochemistry
影响因子：
2.9
作者：
Kolbanovskiy M;Chowdhury MA;Nadkarni A;Broyde S;Geacintov NE;Scicchitano DA;Shafirovich V
通讯作者：
Shafirovich V

Nucleotide Excision Repair Lesion-Recognition Protein Rad4 Captures a Pre-Flipped Partner Base in a Benzo[a]pyrene-Derived DNA Lesion: How Structure Impacts the Binding Pathway.