Open Access Highly Accessed Open Badges Research article

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

Kechi Fang1, Hansheng Zhao12, Changyue Sun1, Carolyn M C Lam3, Suhua Chang14, Kunlin Zhang1, Gurudutta Panda3, Miguel Godinho35, Vítor A P Martins dos Santos36* and Jing Wang1*

Author Affiliations

1 Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China

2 College of Biological Sciences, China Agricultural University, Beijing 100193, China

3 Systems and Synthetic Biology Group, Helmholtz Center for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany

4 Graduate University of Chinese Academy of Sciences, Beijing 100101, China

5 Lifewizz Lda, Rua Pero de Alenquer 123 7 E, 4150-616 Porto, Portugal

6 Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands

For all author emails, please log on.

BMC Systems Biology 2011, 5:83  doi:10.1186/1752-0509-5-83

Published: 25 May 2011



Burkholderia cenocepacia is a threatening nosocomial epidemic pathogen in patients with cystic fibrosis (CF) or a compromised immune system. Its high level of antibiotic resistance is an increasing concern in treatments against its infection. Strain B. cenocepacia J2315 is the most infectious isolate from CF patients. There is a strong demand to reconstruct a genome-scale metabolic network of B. cenocepacia J2315 to systematically analyze its metabolic capabilities and its virulence traits, and to search for potential clinical therapy targets.


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.