Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora

Abstract

Background: There is little published regarding metabolism of Salinispora species. In continuation with efforts performed towards this goal, this study is focused on new insights into the metabolism of the three-identified species of Salinispora using constraints-based modeling. At present, only one manually curated genome-scale metabolic model (GSM) for Salinispora tropica strain CNB-440 T has been built despite the role of Salinispora strains in drug discovery. Results: Here, we updated, and expanded the scope of the model of Salinispora tropica CNB-440 T , and GSMs were constructed for two sequenced type strains covering the three-identified species. We also constructed a Salinispora core model that contains the genes shared by 93 sequenced strains and a few non-conserved genes associated with essential reactions. The models predicted no auxotrophies for essential amino acids, which was corroborated experimentally using a defined minimal medium (DMM). Experimen