RG Sytems and synthetic biology (SSBI)http://hdl.handle.net/10033/481562024-03-29T11:00:07Z2024-03-29T11:00:07ZExploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstructionFang, KechiZhao, HanshengSun, ChangyueLam, Carolyn M CChang, SuhuaZhang, KunlinPanda, GuruduttaGodinho, MiguelMartins dos Santos, Vítor A PWang, Jinghttp://hdl.handle.net/10033/6206832019-08-30T11:35:39Z2011-05-25T00:00:00ZExploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction
Fang, Kechi; Zhao, Hansheng; Sun, Changyue; Lam, Carolyn M C; Chang, Suhua; Zhang, Kunlin; Panda, Gurudutta; Godinho, Miguel; Martins dos Santos, Vítor A P; Wang, Jing
Abstract Background 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. Results 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. Conclusions 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.
2011-05-25T00:00:00ZGenotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains.Varga, John JBarbier, MarietteMulet, XavierBielecki, PiotrBartell, Jennifer AOwings, Joshua PMartinez-Ramos, InmaculadaHittle, Lauren EDavis, Michael RDamron, F HeathLiechti, George WPuchałka, JacekDos Santos, Vitor A P MartinsErnst, Robert KPapin, Jason AAlbertí, SebastianOliver, AntonioGoldberg, Joanna Bhttp://hdl.handle.net/10033/5831652019-08-30T11:36:05Z2015-01-01T00:00:00ZGenotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains.
Varga, John J; Barbier, Mariette; Mulet, Xavier; Bielecki, Piotr; Bartell, Jennifer A; Owings, Joshua P; Martinez-Ramos, Inmaculada; Hittle, Lauren E; Davis, Michael R; Damron, F Heath; Liechti, George W; Puchałka, Jacek; Dos Santos, Vitor A P Martins; Ernst, Robert K; Papin, Jason A; Albertí, Sebastian; Oliver, Antonio; Goldberg, Joanna B
Pseudomonas aeruginosa is an environmentally ubiquitous Gram-negative bacterium and important opportunistic human pathogen, causing severe chronic respiratory infections in patients with underlying conditions such as cystic fibrosis (CF) or bronchiectasis. In order to identify mechanisms responsible for adaptation during bronchiectasis infections, a bronchiectasis isolate, PAHM4, was phenotypically and genotypically characterized.
2015-01-01T00:00:00ZThe ten grand challenges of synthetic life.Porcar, ManuelDanchin, Antoinede Lorenzo, VictorDos Santos, Vitor AKrasnogor, NatalioRasmussen, SteenMoya, Andréshttp://hdl.handle.net/10033/3390362019-08-30T11:36:32Z2011-06-01T00:00:00ZThe ten grand challenges of synthetic life.
Porcar, Manuel; Danchin, Antoine; de Lorenzo, Victor; Dos Santos, Vitor A; Krasnogor, Natalio; Rasmussen, Steen; Moya, Andrés
The construction of artificial life is one of the main scientific challenges of the Synthetic Biology era. Advances in DNA synthesis and a better understanding of regulatory processes make the goal of constructing the first artificial cell a realistic possibility. This would be both a fundamental scientific milestone and a starting point of a vast range of applications, from biofuel production to drug design. However, several major issues might hamper the objective of achieving an artificial cell. From the bottom-up to the selection-based strategies, this work encompasses the ten grand challenges synthetic biologists will have to be aware of in order to cope with the task of creating life in the lab.
2011-06-01T00:00:00ZExploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction.Fang, KechiZhao, HanshengSun, ChangyueLam, Carolyn M CChang, SuhuaZhang, KunlinPanda, GuruduttaGodinho, MiguelMartins dos Santos, Vítor A PWang, Jinghttp://hdl.handle.net/10033/3243472019-08-30T11:36:04Z2011-01-01T00:00:00ZExploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction.
Fang, Kechi; Zhao, Hansheng; Sun, Changyue; Lam, Carolyn M C; Chang, Suhua; Zhang, Kunlin; Panda, Gurudutta; Godinho, Miguel; Martins dos Santos, Vítor A P; Wang, Jing
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.
2011-01-01T00:00:00Z