Comparison of metabolic pathways in Escherichia coli by using genetic algorithms

Publication date: Available online 9 April 2015 Source:Computational and Structural Biotechnology Journal Author(s): Patricia Ortegon , Augusto C. Poot-Hernández , Ernesto Perez-Rueda , Katya Rodriguez-Vazquez In order to understand how cellular metabolism has taken its modern form, the conservation and variations between metabolic pathways were evaluated by using a genetic algorithm (GA). The GA approach considered information on the complete metabolism of the bacterium Escherichia coli K-12, as deposited in the KEGG database, and the enzymes belonging to a particular pathway were transformed into chains by using the Breadth-First Search algorithm. These sequences represent contiguous enzymes linked to each other, based on their catalytic activities as they are encoded in the Enzyme Commission numbers. In a posterior step, these sequences were compared using a GA in an all-against-all (pairwise comparisons) approach. Individual reactions were chosen based on their measure of fitness to act as parents of offspring, which constitute the new generation. The sequences compared were used to construct a similarity matrix (of fitness values) that was then considered to be clustered by using a k-medoids algorithm. A total of 34 clusters of conserved reactions were obtained, and their sequences were finally aligned with a multiple-sequence alignment GA optimized to align all the reaction sequences included in each group or cluster. From these comparisons, maps associated wit...
Source: Computational and Structural Biotechnology Journal - Category: Biotechnology Source Type: research