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

基本信息

批准号：
6750690
负责人：
ASHOK S BHAGWAT
金额：
$ 12.55万
依托单位：
WAYNE STATE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2003
资助国家：
美国
起止时间：
2003-05-22 至 2006-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/6750690
关键词：
DNA repair N glycosidase biochemistry bioinformatics biotechnology complementary DNA computer program /software computer system design /evaluation enzyme activity functional /structural genomics human genetic material tag interdisciplinary collaboration molecular cloning nucleic acid chemical synthesis protein sequence proteomics

项目摘要

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为生物学家带来了前所未有的机会和挑战。尽管蛋白质产物众所周知的基因序列的访问为检验假设提供了新的机会，但没有已知功能的基因序列的可用性却带来了关键的挑战。为了开发一个如何使用生物信息学预测未表征基因的功能的模型，我们将搜索人类基因组以获取新的DNA修复基因，然后通过测试假定的修复蛋白进行预测的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的方法来寻找潜在的人DNA糖基酶。这些工具将包括开发糖基酶家族的改进序列谱以及这些曲线的利用以及用于人蛋白质组穿线分析的结构信息。该提案的R33部分将使用基于非理学的方法，包括鉴定催化中心和在其他已知的DNA修饰酶中对DNA糖基酶进行的联想搜索。此外，我们的搜索中还将包括另外两个类别的DNA修复酶。这项工作将是三个研究小组之间的合作。一个在开发生物信息学工具方面具有专业知识，这是一个在应用该软件的丰富经验的第二组，以及在DNA维修酶生物化学方面具有专业知识的最后一组。虽然前两个组将建立必要的计算机硬件，开发新软件并执行可以预测新的DNA修复基因的分析，但后一组将为推定的修复酶设置必要的生化测试，克隆相应的cDNA中的cDNA中的埃斯切里希亚大肠杆菌，并测试它们的活动。这种综合的预测验证方法应该优于纯生物信息学或纯化的生化方法，并且可以作为在所有生物体基因组中搜索生化功能的范式。