COMPREHENSIVE COMPUTER ANALYSIS OF E COLI GENES

大肠杆菌基因的全面计算机分析

• 批准号: 3781286
• 负责人: E V KOONIN
• 金额: --
• 依托单位: NATIONAL LIBRARY OF MEDICINE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/3781286
• 关键词: Escherichia coli; bacterial genetics; bacterial proteins; biochemical evolution; computer assisted sequence analysis; computer system design /evaluation; genome; information system analysis; information systems; protein sequence; protein structure function

With the fraction of known sequences in the Escherichia coli chromosome now-exceeding 50 per cent, the goal of comprehensive computer analysis of the bacterial genome is becoming realistic. The scope of this project includes development of an optimal strategy for analysis of the genetic contents of the genome; assessment of the utility of different computer-assisted methods in large-scale genome projects; identification of all genes in the bacterial chromosome; and extraction of maximal amount of information on possible functions and evolutionary relationships of gene products; delineation off possible regularities in the distribution of related genes in the bacterial chromosome. Comparison of the 1400 protein sequences contained in the EcoSeq6 database with the complete amino acid sequence databases was performed, with particular emphasis on the relationship between various E.coli proteins. A variety of computer methods for database search, motif identification, and multiple sequence alignment were employed, including newly developed algorithms. As the result, probable functions were predicted for a number of previously uncharacterized putative open reading frame products, and several new proteins families and highly conserved, probably functionally important sequence motifs were described. The most interesting findings included: a putative new system of regulated, GTP-dependent proteolysis; a family of putative GTP phosphohydrolases related to the antimutator protein MutT, with an apparent GTP-binding motif of a novel type; two previously uncharacterized DNA or RNA helicases belonging to distinct groups within the "DEAD/H" superfamily; several unknown putative methyltransferases. New, unexpected relationships were found for proteins that have been previously characterized functionally, but not structurally, e.g. it was shown that diadenosine tetraphosphate phosphohydrolase (ApaH) is related to protein phosphatases; and RNase T is related to DNA proofreading exonucleases. Regions of the E.coli chromosome that have been annotated as untranslated in the EcoSeq6 database were explored using the GENMARK method for coding region prediction and BLASTX program for database search. As the result, about 100 new genes were predicted to exist in the E.coli chromosome encoding putative enzymes, membrane proteins, and regulatory proteins. Strong correlation was established between the results of GENMARK prediction and similarity search, suggesting that the coding regions predicted by GENMARK, but not showing similarity to sequences available in current databases are still likely to correspond to new genes. The significance of the project lies in the potential for development of optimal strategy for computer analysis of gene functions and arrangement at the whole genome scale; and in the prediction of likely functions for many gene products leading to stimulation of further experimental dissection.

大肠杆菌染色体中已知序列的比例 目前已超过50%，全面计算机分析的目标 细菌基因组的研究正在变得现实。本项目的范围 包括开发一种最佳策略， 基因组的内容;评估不同基因组的效用 大规模基因组计划中的计算机辅助方法;识别 细菌染色体中的所有基因;以及提取最大的 关于可能的功能和进化的信息量 基因产物的关系;可能的遗传变异的描述 相关基因在细菌染色体中的分布。 EcoSeq 6中包含的1400个蛋白质序列的比较 数据库与完整的氨基酸序列数据库进行比对， 特别强调各种大肠杆菌之间的关系 proteins.用于数据库搜索、基序的多种计算机方法 鉴定和多重序列比对，包括 新开发的算法。因此，可能的函数是 预测了一些以前没有特征的假定开放 阅读框产物，以及几个新的蛋白质家族和高度表达的蛋白质。 保守的，可能具有重要功能的序列基序， 介绍了最有趣的发现包括：一个假定的新系统 受调节的GTP依赖性蛋白水解;一个推定的GTP家族 与抗突变蛋白MutT相关的磷酸水解酶， 一种新类型的表观GTP结合基序;两个先前 未表征的DNA或RNA解旋酶属于不同的组内 “DEAD/H”超家族;几种未知的推定甲基转移酶。 新的，意想不到的关系被发现的蛋白质， 以前的特点功能，但不是结构，例如，它是 表明二腺苷四磷酸磷酸水解酶（ApaH）与 RNase T与DNA校对有关 核酸外切酶已注释的大肠杆菌染色体区域 使用GENMARK对EcoSeq 6数据库中未翻译的 编码区域预测的方法和用于数据库的BLASTX程序 搜索结果，预计其中存在约100个新基因 大肠杆菌染色体编码推定的酶，膜蛋白，和 调节蛋白强相关性建立在 GENMARK预测和相似性搜索的结果，表明 GENMARK预测的编码区，但未显示与 现有数据库中的序列仍然可能与 到新的基因 该项目的意义在于开发的潜力， 基因功能和排列计算机分析的最优策略 在全基因组规模;并在预测可能的功能， 许多基因产物导致进一步的实验刺激， 解剖