New Method to Compare Organism Functionality


Systems biology approaches to bioenergy and environmental research are enabled by reliable models of processes in living cells. Advances in genome sequencing and computational modeling have led to the development of over 100 genome-scale network reconstructions (constraint-based models). Rapid increases in this number are expected, so methods that use algorithms to compare functional characteristics between organisms will be increasingly important. Scientists at the University of Wisconsin have reported a novel approach that embeds two constraint-based models into an optimization model. This combination identifies those genes and reaction pathways that contribute most to differences in metabolic functionality. The authors identified several differences in metabolism in two cyanobacteria that have potential for biofuel production, Synechococcus and Cyanothece. For example, they demonstrated the necessity for a particular protein (plastocyanin) for photosynthesis in Cyanothece, but not in Synechococcus. The new approach also aids the curation of constraint-base models by identifying pathways that are coded by the organism, but that are missing from the model.


Hamilton, J. J., and J. L. Reed. 2012. “Identification of Functional Differences in Metabolic Networks Using Comparative Genomics and Constraint-Based Models,” PLoS ONE 7(4), e34670. DOI:10.1371/journal.pone.0034670.