Prediction of gene functions by use of molecular evolutionary approach

利用分子进化方法预测基因功能

• 批准号: 07504009
• 负责人: GOJOBORI Takashi
• 金额: $ 13.12万
• 依托单位: National Institute of Genetics
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (A)
• 财政年份: 1995
• 资助国家: 日本
• 起止时间: 1995 至 1997
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-07504009/
• 关键词: molecular evolution; prediction of gene function; functional domain; Molecular Phylogenetic Tree; serine protease; MHC (major histocompatibility complex); nucleotide sequence; sequencing; セリンプロテアーゼ

The main purpose of the present research project is to extract functional domains from the nucleotide sequences of homologous gene groups by use of molecular evolutionary approach. To attain this purpose, we first developed the the new method for constructing phylogenetic trees based upon the minimum description length principle. By using this new method, we identified several functional domains of serine protease genes as an example. Because this method was so successful, weextended our approach to all homologous gene groups. Then, we constructed the 'so-called' sequence motif database, where sequence motif represents characteristics of the sequence specific to a particular function. Moreover, we produced nucleotide sequences of genes whose data availability is sos limited by conducting the PCR experiments. In order to establish the sequence techniques in our laboratory, we practiced the PCR experiment by using fish mitochondrial DNAs. These results obtained in this research project is significant for identifying and predicting the gene functions from the nucleotide sepuence data.

本研究的主要目的是利用分子进化方法从同源基因群的核苷酸序列中提取功能域。为了达到这一目的，我们首先提出了基于最小描述长度原则构建系统发育树的新方法。以丝氨酸蛋白酶基因的几个功能域为例进行了分析。由于这种方法非常成功，我们将方法扩展到所有同源基因群。然后，我们构建了“所谓的”序列motif数据库，其中序列motif表示特定于特定功能的序列特征。此外，我们通过进行PCR实验产生了数据可用性有限的基因核苷酸序列。为了建立本实验室的序列技术，我们利用鱼类线粒体dna进行了PCR实验。这些结果对于从核苷酸序列数据中识别和预测基因功能具有重要意义。

项目成果

Watanabe H.: "Bacterial features in the genome of Methanococcus Jannaschii in terms of gene composition and biased base composition in ORFs and their surrounding regions" Gene. 205. 7-18 (1997)

Watanabe H.：“Jannaschii 甲烷球菌基因组中的细菌特征，包括 ORF 及其周围区域的基因组成和偏向碱基组成”Gene。

Endo,T.: "Large-scale search for genes on which positive selection may operate." Mol.Biol.Evol.13・5. 685-690 (1996)

Endo, T.：“大规模搜索可进行正选择的基因。”Mol.Biol.Evol.13・5（1996）。

Nakamura Y.: "Codon usage tabulated from the international DNA sequence databases." Nucl.Acids Res.25・1. 244-245 (1997)

Nakamura Y.：“国际 DNA 序列数据库中的密码子使用列表。”Nucl.Acids Res.25·1（1997）。

Tanaka, H.: "Inference of molecular phylogenetic tree based on minimum model-based complexity method." Proceedings of Fifth internationa1 conference on intelligent systems for molecular biology.319-328 (1997)

Tanaka, H.：“基于最小模型复杂性方法的分子系统发育树推断。”

Gojobori, T.: "Sequence divergence estimation.In:Molecular Biology and Biotechnology.A Comprehensive Desk Reference.(Ed.,R.A.Meyers)" VCH Publishers,Inc.863-866 (1995)

Gojobori, T.：“序列分歧估计。见：分子生物学和生物技术。综合案头参考。（Ed.，R.A.Meyers）”VCH Publishers,Inc.863-866 (1995)