Team:NYMU-Taipei/ymis2.html

From 2012.igem.org

NYMU iGEM

Paper-Based Research

Paper Survey and Bioinformatic Searching

In order to realize whole sulfur metabolism pathway, we use several bioinformation web site such as KEGG(http://www.genome.jp/kegg) and NCBI(http://www.ncbi.nlm.nih.gov/pubmed) . We can find out several important enzyme to reach our goal- digest SOX and produce H2S for further metabolism pathway in our artificial creatures. According to a research done by Prof. Werner Badziong (Growth Yields and Growth Rates of. Desulfovibrio  vulgaris (Marburg) Growing on Hydrogen plus Sulfate and Hydrogen plus Thiosulfate as the Sole Energy Sources, Arch. Microbiol. 117, 209-214 [1978]), four enzyme are involved to produace H2S. They are ATP sulfurylase, APS reductase, sulfite reductase and pyrophosphatase. Completing 1.8.99.1, sulfite reductase, we clone it from a sulfur reducing bacteria(SRB), desulfovibrio desulfuricans, known as DsrI and DsrII. We also clone 1.8.99.1, sulfite reductase from pseudomonas aeruginosa PAOI, which is Cys I.


Desulfovibrio desulfuricans under microscopy and culture with Desulfovibrio medium http://en.wikipedia.org/wiki/File:Dvulgaris_micrograph.JPG



We want to complete the sulfur metabolism pathway of cyanobacteria
http://www.genome.jp/kegg-bin/show_pathway?map00920


Bioinformatic Analysis of Enzyme Trans-Membrane Domain

Sulfite reductases have two types, that is, membrane form(located on cell membrane) and free form(located inside cell membrane). Among which, free form are the best choice since the folding and structure are more stable. We use bioinformation tools- ExPASy(http://expasy.org/) to predict the transmembrane domain of each sulfite reductase. The result shows that Dsr I, DsrI and Cys I enzymes don’t have any transmembrane domain. That is, they might be free form enzymes. As the result, we combine DsrI and DsrII gene to form “Dsr”. We use “Dsr” and “CysI” gene, two sulfite reductase from different bacteria, as our target gene in this part.


Membrane electronic prediction shows that no transmembrane domain exist(from left to right: Cys I domain I, Cys I domain II, Dsr domain I,Dsr domain II)

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