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Data Integration of Geological Science and Genome Science
Takeshi Kawashima
Hirokazu Chiba, Susumu Goto, Shuichi Kawashima, Haruo Suzuki, Naohisa Goto, Julien Mariethoz
In order to elucidate the adaptation of the organisms to environmental changes on the earth, it is necessary to combine evolutionary biology and geological science from various viewpoints. In this project, following in the past BioHackathon, I will explore an method for integrally handling the branching age of genome sequence and stratigraphic age of geology.
The research topic as a starting point is to investigate ways to easily obtain a list of metal binding proteins. This is because the evolution and diversification of metal binding proteins may have occurred as an adaptation to changes in metal ion concentration in sea water on the earth. Another research topic is to investigate how to obtain enzymes that utilize oxygen in in vivo chemical reactions, because diversification of these enzymes may have occurred when the oxygen concentration on Earth changed significantly. The history of oxygen concentration change can be estimated dating back to hundreds of millions of years by isotope analysis and trace element analysis in geology and is a good model for comparing biological evolution and geological data.
The most comprehensive information on the binding between protein and metal seemed to be UniProt. However, at present, even with UniProt, it is not possible to retrieve metal binding proteins unless a condition search using both DR tag and KW tag information. The search-condition required to obtain a combination of binding protein and metal is to filter with the following two conditions. The first filter is GO information in the DR tag. If GO: 0046872 "metal-binding protein" is described in the list of GO, obtain that entry. Next, only when there is an appropriate metal ion name in the KW tag, the entry is acquired. There is a possibility that Uniprot 's REST-API service provides a simpler search method. I will investigate this further in the future.
Survey on databases of metal binding proteins, metabolic pathways using metails, oxygens and CO2.