Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction

We reconstructed the genome-scale metabolic network of B. cenocepacia J2315. An iterative reconstruction process led to the establishment of a robust model, iKF1028, which accounts for 1,028 genes, 859 internal reactions, and 834 metabolites. The model iKF1028 captures important metabolic capabilities of B. cenocepacia J2315 with a particular focus on the biosyntheses of key metabolic virulence factors to assist in understanding the mechanism of disease infection and identifying potential drug targets. The model was tested through BIOLOG assays. Based on the model, the genome annotation of B. cenocepacia J2315 was refined and 24 genes were properly re-annotated. Gene and enzyme essentiality were analyzed to provide further insights into the genome function and architecture. A total of 45 essential enzymes were identified as potential therapeutic targets.As the first genome-scale metabolic network of B. cenocepacia J2315, iKF1028 allows a systematic study of the metabolic properties of B. cenocepacia and its key metabolic virulence factors affecting the CF community. The model can be used as a discovery tool to design novel drugs against diseases caused by this notorious pathogen.Burkholderia cenocepacia is a Gram-negative opportunistic pathogen and formerly Genomovar III of Burkholderia cepacia complex (Bcc). The Bcc comprises at least 17 taxonomically related species [1-3], which have developed diverse niches from the natural environment [4] and humans as they have emerged as pathogens in patients with cystic fibrosis (CF), chronic granulomatous disease, and in immunocompromised individuals [5]. B. cenocepacia is the dominant Bcc species in patients with CF, accounting for between 50% and 80% of the infection cases [5]. It also causes many instances of non-CF clinical infections, such as for cancer patients [6,7]. As a representative isolate for the spread of an epidemic CF strain, B. cenocepacia J2315 belongs to a clonal lineage known as ET12, which is of increase