A systems biology approach to drug targets in pseudomonas aeruginosa biofilm

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Sigurdsson, Gunnar ^a   Fleming, Ronan M T ^a   Heinken, Almut ^a   Thiele, Ines ^a  

^a UNIVERSITY OF ICELAND   (Iceland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GROWTH; BACTERIAL METABOLISM; BIOFILM; CHEMICAL COMPOSITION; DRUG TARGETING; GENE DELETION; GENE IDENTIFICATION; MATHEMATICAL MODEL; MICROBIAL COMMUNITY; MICROENVIRONMENT; OXYGEN SUPPLY; PLANKTON; PSEUDOMONAS AERUGINOSA; SYSTEMS BIOLOGY; ANTIBIOTIC RESISTANCE; COMPUTER SIMULATION; DRUG EFFECT; GENETICS; GROWTH, DEVELOPMENT AND AGING; MICROBIOLOGICAL EXAMINATION;

BACTERIA (MICROORGANISMS); PSEUDOMONAS AERUGINOSA;

OXYGEN;

BIOFILMS; COMPUTER SIMULATION; DRUG RESISTANCE, BACTERIAL; GENE DELETION; MICROBIAL SENSITIVITY TESTS; OXYGEN; PSEUDOMONAS AERUGINOSA; SYSTEMS BIOLOGY;

EID: 84859856422     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0034337     Document Type: Article

References (46)

1. Bodey GP, Bolivar R, Fainstein V, Jadeja L, (1983) Infections caused by Pseudomonas aeruginosa. Rev Infect Dis 5: 279-313.
2. Driscoll JA, Brody SL, Kollef MH, (2007) The epidemiology, pathogenesis and treatment of Pseudomonas aeruginosa infections. Drugs 67: 351-368.
3. Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, et al. (2000) Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406: 959-964.
4. Wang Y, Dai Y, Zhang Y, Hu Y, Yang B, et al. (2007) Effects of quorum sensing autoinducer degradation gene on virulence and biofilm formation of Pseudomonas aeruginosa. Sci China C Life Sci 50: 385-391.
5. Carmeli Y, Troillet N, Eliopoulos GM, Samore MH, (1999) Emergence of antibiotic-resistant Pseudomonas aeruginosa: comparison of risks associated with different antipseudomonal agents. Antimicrob Agents Chemother 43: 1379-1382.
6. del Pozo JL, Patel R, (2007) The challenge of treating biofilm-associated bacterial infections. Clin Pharmacol Ther 82: 204-209.
7. Stewart PS, Costerton JW, (2001) Antibiotic resistance of bacteria in biofilms. Lancet 358: 135-138.
8. Hall-Stoodley L, Costerton JW, Stoodley P, (2004) Bacterial biofilms: from the natural environment to infectious diseases. Nat Rev Microbiol 2: 95-108.
9. Borriello G, Werner E, Roe F, Kim AM, Ehrlich GD, et al. (2004) Oxygen limitation contributes to antibiotic tolerance of Pseudomonas aeruginosa in biofilms. Antimicrob Agents Chemother 48: 2659-2664.
10. Moreau-Marquis S, Stanton BA, O'Toole GA, (2008) Pseudomonas aeruginosa biofilm formation in the cystic fibrosis airway. Pulm Pharmacol Ther 21: 595-599.
11. Sriramulu DD, Lunsdorf H, Lam JS, Romling U, (2005) Microcolony formation: a novel biofilm model of Pseudomonas aeruginosa for the cystic fibrosis lung. J Med Microbiol 54: 667-676.
12. Bielecki P, Glik J, Kawecki M, Martins dos Santos VA, (2008) Towards understanding Pseudomonas aeruginosa burn wound infections by profiling gene expression. Biotechnol Lett 30: 777-790.
13. Kell DB, (2006) Systems biology, metabolic modelling and metabolomics in drug discovery and development. Drug Discovery Today 11: 1085-1092.
14. Obrzut S, Tiongson J, Jamshidi N, Phan HM, Hoh C, et al. (2010) Assessment of metabolic phenotypes in patients with non-ischemic dilated cardiomyopathy undergoing cardiac resynchronization therapy. J Cardiovasc Transl Res 3: 643-651.
15. Oberhardt MA, Palsson BO, Papin JA, (2009) Applications of genome-scale metabolic reconstructions. Mol Syst Biol 5: 320.
16. Palsson B, (2009) Metabolic systems biology. FEBS Lett 583: 3900-3904.
17. Thiele I, Vo TD, Price ND, Palsson BO, (2005) Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. J Bacteriol 187: 5818-5830.
18. Lee DS, Burd H, Liu J, Almaas E, Wiest O, et al. (2009) Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets. J Bacteriol 191: 4015-4024.
19. Jamshidi N, Palsson BO, (2007) Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Syst Biol 1: 26.
20. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3: 121.
21. Gonzalez O, Gronau S, Falb M, Pfeiffer F, Mendoza E, et al. (2008) Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism. Mol Biosyst 4: 148-159.
22. Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, et al. (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A 104: 1777-1782.
23. Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BO, (2010) A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. BMC Syst Biol 4: 140.
24. Selvarasu S, Karimi IA, Ghim GH, Lee DY, (2010) Genome-scale modeling and in silico analysis of mouse cell metabolic network. Mol Biosyst 6: 152-161.
25. Price ND, Reed JL, Palsson BO, (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2: 886-897.
26. Palsson B, (2006) Systems biology: properties of reconstructed networks. Cambridge: Cambridge University Press. xii, 322.
27. Orth JD, Thiele I, Palsson BO, (2010) What is flux balance analysis? Nat Biotechnol 28: 245-248.
28. Feist AM, Palsson BO, (2008) The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotech 26: 659-667.
29. Oberhardt MA, Puchalka J, Fryer KE, Martins dos Santos VA, Papin JA, (2008) Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. J Bacteriol 190: 2790-2803.
30. Thiele I, Palsson BO, (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5: 93-121.
31. Silver LL, (2007) Multi-targeting by monotherapeutic antibacterials. Nat Rev Drug Discov 6: 41-55.
32. Zimmermann GR, Lehar J, Keith CT, (2007) Multi-target therapeutics: when the whole is greater than the sum of the parts. Drug Discov Today 12: 34-42.
33. Fleming RM, Thiele I, Nasheuer HP, (2009) Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. Biophys Chem 145: 47-56.
34. Fleming RM, Thiele I, (2011) von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. Bioinformatics 27: 142-143.
35. Price ND, Thiele I, Palsson BO, (2006) Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of loop law thermodynamic constraints. Biophys J 90: 3919-3928.
36. Perumal D, Lim CS, Sakharkar KR, Sakharkar MK, (2007) Differential genome analyses of metabolic enzymes in Pseudomonas aeruginosa for drug target identification. In Silico Biol 7: 453-465.
37. Jacobs MA, Alwood A, Thaipisuttikul I, Spencer D, Haugen E, et al. (2003) Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences 100: 14339-14344.
38. Lewenza S, Falsafi RK, Winsor G, Gooderham WJ, McPhee JB, et al. (2005) Construction of a mini-Tn5-luxCDABE mutant library in Pseudomonas aeruginosa PAO1: a tool for identifying differentially regulated genes. Genome Res 15: 583-589.
39. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, et al. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 36: D901-906.
40. Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, et al. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6: 1290-1307.
41. Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, et al. (2007) Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox. Nat Protocols 2: 727-738.
42. Pommerenke C, Musken M, Becker T, Dotsch A, Klawonn F, et al. (2010) Global genotype-phenotype correlations in Pseudomonas aeruginosa. PLoS Pathog 6: e1001074.
43. Musken M, Di Fiore S, Dotsch A, Fischer R, Haussler S, (2010) Genetic determinants of Pseudomonas aeruginosa biofilm establishment. Microbiology 156: 431-441.
44. Perumal D, Samal A, Sakharkar KR, Sakharkar MK, (2011) Targeting multiple targets in Pseudomonas aeruginosa PAO1 using flux balance analysis of a reconstructed genome-scale metabolic network. J Drug Target 19: 1-13.
45. Fang K, Zhao H, Sun C, Lam CM, Chang S, et al. (2011) Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction. BMC Syst Biol 5: 83.
46. Oberhardt MA, Goldberg JB, Hogardt M, Papin JA, (2010) Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection. J Bacteriol 192: 5534-5548.