Mechanisms for the repair of oxidative stress-induced DNA damage in Porphyromonas

卟啉单胞菌氧化应激诱导的 DNA 损伤的修复机制

• 批准号: 10441150
• 负责人: Hansel M. Fletcher
• 金额: $ 19.75万
• 依托单位: LOMA LINDA UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10441150
• 关键词: 8-hydroxyguanosine; Address; Affinity; Anaerobic Bacteria; Architecture; Base Excision Repairs; Bioinformatics; Cardiovascular Diseases; Chemicals; Chemistry; Chromosomes; Cytidylate kinase; DNA; DNA Damage; DNA Repair; Data; Development; Disease; Drug Metabolic Detoxication; Environment; Enzymes; Escherichia coli; Etiology; Excision; Exposure to; Fractionation; Future; Genetic Recombination; Genome; Genome Stability; Goals; Guanine; Guanine + Cytosine Composition; Health; Homeostasis; Human; Hydrogen Peroxide; In Vitro; Inflammatory; Knowledge; Lesion; Link; Mediating; Mismatch Repair; Molecular; Nucleotide Excision Repair; Oligonucleotides; Operon; Organism; Oxidation-Reduction; Oxidative Stress; PAWR protein; Pathology; Pathway interactions; Periodontal Diseases; Periodontal Pocket; Peroxidases; Peroxides; Pigments; Play; Porphyromonas; Porphyromonas gingivalis; Prevention; Process; Prokaryotic Cells; Property; Proteins; Recombinants; Research; Resolution; Rheumatoid Arthritis; Role; SWI2/SNF2; Stress; Structure; Surveys; System; Systemic disease; Testing; Virulence; Zinc Fingers; base; biological adaptation to stress; crosslink; cytidylate; experimental study; in silico; inflammatory milieu; microbial host; novel; novel therapeutic intervention; novel therapeutics; oxidation; oxidative DNA damage; oxidative damage; pathogen; periodontopathogen; prevent; repaired; success

Porphyromonas gingivalis, as a “keystone pathogen”, highlights its ability to adapt to the harsh inflammatory conditions of the periodontal pocket. Because the environmental stress response is a major determinant of its virulence, it is our long-term goal to gain a comprehensive understanding of its survival strategy(s). DNA damage is a major consequence of oxidative stress. While more than 20 different oxidatively altered bases might be generated by this stress, 8-oxo-7,8-dihydroguanine (8-oxoG) is one of the most common product of DNA damage. Guanine is the most susceptible base to oxidation and forms mainly 8-oxoG due to its low redox potential. In prokaryotic cells the presence of 8-oxoG is mainly repaired by base excision repair (BER). A survey of the P. gingivalis genome indicate that an important component of the BER system is missing. Because the average G + C content of the genome of P. gingivalis is 49%, a mechanism(s) to prevent or repair lesions resulting from guanine oxidation is vital. There is a gap in our comprehensive knowledge on a mechanism(s) for the repair of oxidative stress-induced DNA damage in P. gingivalis. We have previously demonstrated that there is an accumulation of 8-oxoG in the chromosome of P. gingivalis exposed to H2O2-induced oxidative stress. Neither BER nor nucleotide excision repair (NER), as observed in other strains, appear to be involved in the repair of the 8-oxoG lesion in P. gingivalis. DNA affinity fractionation identified PG1037, a conserved hypothetical protein, among others, that were preferentially bound to the oligonucleotide fragment carrying the 8-oxo-G lesion. PG1037 is part of the uvrA-pg1037-pcrA operon in P. gingivalis which is known to be upregulated under H2O2- induced stress. The purified recombinant PG1037 protein, likely via a reducing function, has the ability to prevent Fenton chemistry-mediated DNA damage in vitro and, under oxidative stress conditions, reduced the cleavage of the 8-oxoG lesion by the E.coli foramidopyrimidine glycosylase (Fpg) enzyme. In silico analysis of PG1037 shows a protein that contains a zinc finger domain, two peroxidase homologous motifs and a cytidylate kinase domain. The goal of the proposal is to test the hypothesis that a novel P. gingivalis protein (PG1037) carrying peroxidase motifs and a zinc finger domain is involved in the repair of oxidatively damaged DNA. Our aims are to confirm the specific role of PG1037 in the removal of 8-oxoG from duplex DNA and to evaluate any interaction of PG1037 with other proteins in that process. The data will provide a major conceptual advance on the molecular bases for the repair of oxidative stress-induced DNA damage in P. gingivalis and could likely support a unique and effective DNA repair mechanism we propose to designate “base redox repair”. It will set the stage, in a future RO1 application, to address specific structure-function questions on the vital components and their corporation in maintaining genomic stability in anaerobes exposed to environmental stress. These components could be targets for the development of novel therapeutic interventions for the control and prevention of P. gingivalis-associated diseases.

牙龈卟啉单胞菌作为“关键病原体”，凸显其适应严酷炎症的能力 牙周袋的状况。因为环境应激反应是其表现的主要决定因素。 毒力，全面了解其生存策略是我们的长期目标。脱氧核糖核酸 损伤是氧化应激的主要后果。超过 20 种不同的氧化改变碱基 可能是由这种压力产生的，8-oxo-7,8-二氢鸟嘌呤（8-oxoG）是最常见的产物之一 DNA损伤。鸟嘌呤是最容易被氧化的碱基，由于其氧化还原性低，主要形成 8-oxoG 潜在的。在原核细胞中，8-oxoG 的存在主要通过碱基切除修复 (BER) 进行修复。一个 对牙龈卟啉单胞菌基因组的调查表明，BER 系统的一个重要组成部分缺失。因为 牙龈卟啉单胞菌基因组的平均 G + C 含量为 49%，这是一种预防或修复病变的机制 鸟嘌呤氧化产生的结果至关重要。我们对机制的全面了解存在差距 牙龈卟啉单胞菌氧化应激诱导的 DNA 损伤的修复。我们之前已经证明了，有 是暴露于 H2O2 诱导的氧化应激的牙龈卟啉单胞菌染色体中 8-oxoG 的积累。 正如在其他菌株中观察到的，BER 和核苷酸切除修复 (NER) 似乎都不参与 牙龈卟啉单胞菌 8-oxoG 损伤的修复。 DNA 亲和分级鉴定出 PG1037，一个保守的假设 其中，优先与携带 8-oxo-G 损伤的寡核苷酸片段结合的蛋白质。 PG1037 是牙龈卟啉单胞菌中 uvrA-pg1037-pcrA 操纵子的一部分，已知该操纵子在 H2O2- 下会上调 诱发的压力。纯化的重组 PG1037 蛋白可能通过还原功能，能够预防 芬顿化学介导的体外 DNA 损伤，在氧化应激条件下，减少了裂解 大肠杆菌甲酰胺嘧啶糖基化酶 (Fpg) 引起的 8-oxoG 损伤。 PG1037 的计算机分析 显示含有锌指结构域、两个过氧化物酶同源基序和胞苷酸激酶的蛋白质 领域。该提案的目标是检验一种新型牙龈卟啉单胞菌蛋白 (PG1037) 的假设 携带过氧化物酶基序和锌指结构域参与氧化损伤的修复 脱氧核糖核酸。我们的目的是确认 PG1037 在从双链 DNA 中去除 8-oxoG 方面的具体作用，并 评估 PG1037 在此过程中与其他蛋白质的任何相互作用。该数据将提供一个主要概念 修复牙龈卟啉单胞菌氧化应激诱导的 DNA 损伤的分子基础研究进展 可能支持一种独特且有效的 DNA 修复机制，我们建议将其命名为“碱基氧化还原修复”。 它将在未来的 RO1 应用中奠定基础，解决重要的结构-功能问题。 组件及其在维持暴露于环境的厌氧菌基因组稳定性方面的作用 压力。这些成分可以作为开发新的治疗干预措施的目标来控制 和预防牙龈卟啉单胞菌相关疾病。

项目成果

Inhibition of β-lactamase function by de novo designed peptide.

• DOI: 10.1371/journal.pone.0290845
• 发表时间: 2023
• 期刊: PloS one
• 影响因子: 3.7

Role of the Filifactor alocis Hypothetical Protein FA519 in Oxidative Stress Resistance.

• DOI: 10.1128/spectrum.01212-21
• 发表时间: 2021-12-22
• 期刊: Microbiology spectrum
• 影响因子: 3.7
• 作者: Aja E;Mishra A;Dou Y;Fletcher HM
• 通讯作者: Fletcher HM

Can periodontal pockets and caries lesions act as reservoirs for coronavirus?

• DOI: 10.1111/omi.12362
• 发表时间: 2022-04
• 期刊: MOLECULAR ORAL MICROBIOLOGY
• 影响因子: 3.7
• 作者: Natto, Zuhair S.;Afeef, Marwah;Bakhrebah, Muhammed A.;Ashi, Heba;Alzahrani, Khaled A.;Alhetheel, Abdulkarim F.;Fletcher, Hansel M.
• 通讯作者: Fletcher, Hansel M.

The Machine-Learning-Mediated Interface of Microbiome and Genetic Risk Stratification in Neuroblastoma Reveals Molecular Pathways Related to Patient Survival.

• DOI: 10.3390/cancers14122874
• 发表时间: 2022-06-10
• 期刊: CANCERS
• 影响因子: 5.2
• 作者: Li, Xin;Wang, Xiaoqi;Huang, Ruihao;Stucky, Andres;Chen, Xuelian;Sun, Lan;Wen, Qin;Zeng, Yunjing;Fletcher, Hansel;Wang, Charles;Xu, Yi;Cao, Huynh;Sun, Fengzhu;Li, Shengwen Calvin;Zhang, Xi;Zhong, Jiang
• 通讯作者: Zhong, Jiang

Characterization of FA1654: A putative DPS protein in Filifactor alocis.

• DOI: 10.1111/omi.12398
• 发表时间: 2023-02
• 期刊: MOLECULAR ORAL MICROBIOLOGY
• 影响因子: 3.7
• 作者: Mangar, Malissa;Mishra, Arunima;Yang, Zhengrong;Deivanayagam, Champion;Fletcher, Hansel M.
• 通讯作者: Fletcher, Hansel M.