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

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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