Difference between revisions of "Part:BBa K847080"

Latest revision as of 03:07, 4 October 2012

''Escherichia coli'' serine deaminase (sdaB)

Alkaliphiles like marine bacteria (pH 8.2) and pyloric duct flora (pH ~10 or higher) rely largely on transmembrane transporter proteins to regulate the pH within the cytoplasm and thrive (Padan, Bibi, Ito, and Krulwich 2005). Most notable of these transporters are ATP synthase and cation/proton antiporters. Both of these use some type of energy from the cell to power the transport of H+ ions across the membrane: in the former, the energy released in the dephosphorylation of ATP is coupled with the transport; in the latter, an electrochemical gradient is exploited (Padan, et al. 2005).

Unfortunately, there are several issues with using this direct method. Just the structural genes (not considering regulation) required for these transmembrane proteins total ~10 kb in length, which is difficult to manage in BioBrick form. Additionally, these proteins are optimized for the membranes of alkaliphilic bacteria which have a different lipid composition than E. coli, making their behavior tricky to control in a planned fashion (Padan, et al. 2005). Finally, the actions of both can be reversed by a strong proton gradient (after all, ATP synthase can synthesize ATP), requiring much more extensive investigation of regulation mechanisms.

However, the the Stanford-Brown iGEM team found it intriguing that E. coli increases the catabolism of amino acids when exposed to high pHs, most researched of which are tryptophan and serine (Padan et al.). This process creates buffers in the cytoplasm to help counter the effects of the high pH. Since the heightened catabolism of tryptophan would require the insertion of a tryptophan transporter, we chose serine catabolism and isolated the gene for serine deaminase from E. coli.

Sequence and Features