Urease
From 2006.igem.org
Making the urease biobrick
To generate an increase in pH, we decided to take advantage of the urease reaction, in which urea is cleaved by urease to yield ammonium and carbon dioxide. This reaction is used in clinical microbiology to identify urease-positive bacteria such as Proteus vulgaris, which in the presence of urea can raise to pH of the growth medium to 9 or higher. The most obvious source of urease would be the urease operon of a urease-positive E. coli strain such as EDL933. The sequence of this operon is available in Genbank. However, the gene cluster consists of almost 5 kb of DNA encoding 7 genes, ureDABCEFG, where ureABC encode the three subunits of urease and the other genes encode proteins required for insertion of the nickel cofactor; also, sequence analysis showed the presence of 5 PstI sites and 1 EcoRI site, all of which would have to be individually mutated out to make this DNA into a biobrick.
Analysis of other sequence urease operons, and a search of the associated literature, showed that the Bacillus subtilis 168 urease operon consisted of only three genes, ureABC, which nevertheless can be assembled into a functional urease in E. coli without the requirement for accessory proteins, although urease activity was relatively low (Kim, J.K., Mulrooney, S.B., and Hausinger, R.P. 2005. Biosynthesis of active Bacillus subtilis urease in the absence of known urease accessory proteins. journal of Bacteriology 187, 7150-7154). We therefore decided to test this urease to see whether it would be suitable for our purposes.
The genes ureABC were amplified from B. subtilis 168 genomic DNA using primers with a SacI site in the forward primer and a BamHI site in the reverse primer. The PCR product was initially ligated into pGemT-easy (Promega), a vector designed for cloning PCR products with AT overhangs. This vector possesses a lac promoter at one end of the insertion site and a T7 promoter at the other. We had hoped to recover a clone with the insert in the correct orientation for expression from the lac promoter, but all clones tested using SacI digests had the insert in the reverse orientation, which could only be expressed from the T7 promoter. One of these plasmids was therefore introduced into E. coli BL21(DE3) which expresses T7 RNA polymerase in the presence of IPTG. Also, in case activity might be different in our normal host strain, JM109, the insert was excised as a SacI-BamHI fragment and inserted into pBluescript SK+ (Stratagene), so that it could be expressed from the lac promoter.
Expression was tested in the two clones: BL21(DE3)/pGemTe-ureABC and JM109/pBluescript-ureABC. In both cases, when expression was induced with IPTG in LB medium with 2% w/v urea, a slow pH increase was seen, with the pH reaching 9 after overnight incubation. In control cultures lacking urea, or using dontrol plasmids pT7-7 or pBluescript SK+, no such pH increase was seen. This indicated that the B. subtilis urease was potentially suitable for our purposes.
