A comparative analysis of metabolic pathways based on metabolic steady states

Abstract

A comparative analysis of organisms with metabolic pathways provides important information about functions within organisms. In this paper, we discuss problem of comparing organisms using partial metabolic structures that contain many biological characteristics and propose a pathway comparison method based on an elementary flux mode (EFM) - the minimal metabolic pathway that satisfies a steady state. By the extraction of the 'elementary flux mode,' we obtain biologically significant metabolic substructures. To compare metabolic pathways based on EFMs, we propose a new pseudo alignment method with a penalty based on the importance of enzymes. The distance among organisms can be calculated based on the pseudo alignment of EFMs. To confirm its effectivity, we apply the proposed method to the pathway datasets from 38 organisms. We successfully reconstructed a "three domain theory" from the aspect of the biological function. Moreover, we evaluated the results in terms of the accuracy of organism classification from the biological function and confirmed that the obtained classification was related deeply to such habitats as aerobe or anaerobe. © 2009 Information Processing Society of Japan.