Reconstruction of a metabolic pathway network from genomicinformation and its application to wastewater processing

摘要

Biological treatment is one of the common technologies used to process organiccompounds found in the wastewater stream. With the availability of abundant bio-information, thereconstruction of a metabolic pathway network becomes possible for investigating cellular physiology,and subsequently links it to the presence of a variety of extra-cellular pollutants.In this study, PERL language was used to develop software tools toward the reconstruction of a metabolicpathway network for Pseudomonas putida. Genomic data for P. putida retrieved from the KyotoEncyclopedia of Genes and Genomes (KEGG) contains 5441 open reading frames (ORFs) among which1374 genes are defined. These genes are distributed into 101 pathways involving various cellularfunctions. Each pathway is governed by different genes encoding corresponding proteins. Thereconstruction is made by integrating the genes, enzymes, pathways, and reactions and the relationshipbetween genes and pathways can be visualized using the graphic tool, Pajek.