Discovering New Human DNA Repair Genes by Bioinformatics

利用生物信息学发现新的人类DNA修复基因

• 批准号: 6585359
• 负责人: ASHOK S BHAGWAT
• 金额: $ 13.46万
• 依托单位: WAYNE STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-05-22 至 2005-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6585359
• 关键词: DNA repair; N glycosidase; biochemistry; biotechnology; complementary DNA; computer program /software; computer system design /evaluation; enzyme activity; functional /structural genomics; human genetic material tag; informatics; interdisciplinary collaboration; molecular cloning; nucleic acid chemical synthesis; protein sequence; proteomics

DESCRIPTION (provided by applicant): The completion of the human genome sequence presents unprecedented opportunities and challenges to biologists. While the access to complete sequences of genes whose protein products are well known provides new opportunities for testing hypotheses, the availability of sequences of genes with no known function poses critical challenges. To develop a model for how to predict functions of uncharacterized genes using bioinformatics, we will search the human genome for new DNA repair genes and then confirm their identity by testing the putative repair proteins for the predicted biochemical activities. The R21 part of the proposal will use mainly homology based methods to search for potential human DNA glycosylases. These tools will include development of improved sequence profiles of glycosylase families and utilization of these profiles along with the structural information for threading analysis of the human proteome. The R33 part of the proposal will use non-homology based methods including identification of catalytic centers and an associative search for DNA glycosylases in other known DNA modifying enzymes. Additionally, two other classes of DNA repair enzymes will be included in our search. This work will be a collaboration between three research groups; one with expertise in the development bioinformatics tools, a second group with extensive experience in application of this software and the last group with expertise in the biochemistry of DNA repair enzymes. While the first two groups will establish the necessary computer hardware, develop new software and perform the analysis that will predict new DNA repair genes, the latter group will set-up the necessary biochemical tests for the putative repair enzymes, clone the corresponding cDNAs into Escherichia coli and test them for activity. This integrated prediction-validation approach should be superior to a purely bioinformatics or a purely biochemical approach and may serve as a paradigm for searching biochemical functions in genomes of all organisms.

描述（由申请人提供）：人类基因组序列的完成给生物学家带来了前所未有的机遇和挑战。虽然获得其蛋白质产物众所周知的基因的完整序列为检验假设提供了新的机会，但功能未知的基因序列的可用性提出了严峻的挑战。为了开发一个如何使用生物信息学预测未表征基因功能的模型，我们将在人类基因组中搜索新的 DNA 修复基因，然后通过测试假定的修复蛋白的预测生化活性来确认其身份。该提案的R21部分将主要使用基于同源性的方法来寻找潜在的人类DNA糖基化酶。这些工具将包括开发改进的糖基化酶家族序列图谱，以及利用这些图谱以及结构信息进行人类蛋白质组的线索分析。该提案的 R33 部分将使用基于非同源性的方法，包括识别催化中心以及在其他已知的 DNA 修饰酶中关联搜索 DNA 糖基化酶。此外，我们的搜索中还将包括另外两类 DNA 修复酶。这项工作将由三个研究小组合作完成；其中一组拥有开发生物信息学工具的专业知识，第二组拥有该软件应用的丰富经验，最后一组拥有 DNA 修复酶生物化学的专业知识。前两组将建立必要的计算机硬件、开发新软件并进行预测新 DNA 修复基因的分析，而后一组将为假定的修复酶建立必要的生化测试，将相应的 cDNA 克隆到大肠杆菌中大肠杆菌并测试它们的活性。这种综合的预测验证方法应该优于纯粹的生物信息学或纯粹的生化方法，并且可以作为搜索所有生物体基因组中的生化功能的范例。