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Studies on probing genome resources and its application from deep-sea microorganism by post-genomic approaches

后基因组方法探测深海微生物基因组资源及其应用研究

基本信息

批准号：
17613006
负责人：
NAKASONE Kaoru
金额：
$ 2.3万
依托单位：
Kinki University
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (C)
财政年份：
2005
资助国家：
日本
起止时间：
2005 至 2006
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-17613006/
关键词：
deep-sea environment genome proteome applied microbiology microarray

项目摘要

In this research funding area, researches on probing several gene and genome resources and its industrial applications by post-genomic approaches were carried out, using deep-sea isolate, Shewanella violacea strain DSS 12 which is already sequenced whole genome (gene candidates ; 4300).Several studies using deep-sea isolate, S. violacea strain DSS12 were included such as 1) development of a software searching efficiently upstream promoters interested in from genome sequence, 2) construction of gene database for several industrially useful enzymes, 3) biochemical analyses of alkaline phosphatases useful in the field of genetic engineering, in terms of high pressure and low temperature.The software is being developed in Perl language, and uses Tk modules for the user interface. It was initially developed to look for high-pressure-response sigma 54 promoter sequences in S. violacea genome, using a fuzzy search algorithm, but it can be used to find other promoter sequences such as sigma 32 … More or sigma 70 promoter sequences, or for example NtrC binding sites. The database for several industrially useful enzymes will be opened after publication of the genome analyses. In biochemical analyses of alkaline phosphatases, three enzymes whose gene is independently distributed on the genome and have different homology each other, were expressed in E. coli after construction expression plasmids. Each enzyme purified has different optimal temperature in dephosphrylation activity, showing its diversity of the enzymes and suggesting adaptation to deep-sea environments.Trying to isolate industrially useful new deep-sea microbes from deep-sea mud of Japan Sea, was also performed. From the several screening procedures, some protease-producing and amylase producing bacteria were isolated. These were suggested to be psychrotolerant isolates. Moreover, spore-forming nitrogen-fixing bacterium (Genus Paenibacillus), first example from deep-sea environment, was isolated. Phylogenetic analyses based on 16S rDNA of these isolates, showed that several bacteria seem to be new species. Less

在该研究基金资助领域，利用已经测序的全基因组（基因候选物; 4300）的深海分离物，紫色希瓦氏菌菌株DSS 12，进行了通过后基因组方法探测几种基因和基因组资源及其工业应用的研究。包括1）从基因组序列中高效搜索感兴趣的上游启动子的软件开发，2）几种工业上有用的酶的基因数据库的构建，3）在高压和低温方面在基因工程领域有用的碱性磷酸酶的生物化学分析。并将Tk模块用于用户界面。它最初是为了在S.使用模糊搜索算法，但它可以用于找到其他启动子序列，如sigma 32 ...更多信息或σ 70启动子序列，或例如NtrC结合位点。几种工业上有用的酶的数据库将在基因组分析发表后开放。在碱性磷酸酶的生化分析中，有三种基因在基因组上独立分布且同源性不同的酶在大肠杆菌中得到表达。coli中表达。从日本海深海泥中分离出了具有工业应用价值的新型深海微生物。通过多次筛选，分离到一些产蛋白酶和淀粉酶的细菌。这些被认为是耐冷的分离物。此外，从深海环境中分离出了第一例产孢子固氮菌（类芽孢杆菌属）。基于16 S rDNA的系统发育分析表明，这些细菌似乎是新的物种。少