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PseudoCyc, A Pathway-Genome Database for <i>Pseudomonas aeruginosa</i>

2003; Volume: 5; Issue: 4 Linguagem: Inglês

10.1159/000071075

2673-1673

Pedro Romero, Peter D. Karp,

Microbial Natural Products and Biosynthesis

A pathway-genome database (PGDB) describes the entire genome of an organism, as well as its biochemical pathways, reactions, and enzymes. Our PathoLogic software can generate a PGDB from an annotated genome of an organism, predicting the metabolic reactions and pathways corresponding to the enzymes present in the annotation. We have used PathoLogic to generate a PGDB for <i>Pseudomonas aeruginosa</i>, strain PAO1, called ‘PseudoCyc’, which includes 139 predicted pathways and 800 predicted reactions involving 623 chemical species and 718 enzymes. Analysis of the PathoLogic predictions of arginine metabolism and the β-ketoadipate pathway, which are landmark pathways in <i>P. aeruginosa</i>, showed that they were for the most part correctly predicted. These studies also provided possible locations for two genes involved in the β-ketoadipate pathway, <i>pcaI</i> and <i>pcaJ,</i> which are missing from the PAO1 annotation. PseudoCyc adds an extended dimension to the genome of <i>P. aeruginosa</i>, providing researchers with a helpful tool for the analysis of the genomic, proteomic, and metabolic information of the organism. The finding of the probable location of the <i>pcaI</i> and <i>pcaJ</i> genes is but one example of the discoveries facilitated by such a PGDB. PseudoCyc, along with PGDBs for 12 other organisms, is available at http://BioCyc.org/.