212
Views
21
CrossRef citations to date
0
Altmetric
Research Article

Targeting multiple targets in Pseudomonas aeruginosa PAO1 using flux balance analysis of a reconstructed genome-scale metabolic network

, , &
Pages 1-13 | Received 11 Nov 2009, Accepted 25 Jan 2010, Published online: 16 Mar 2010

References

  • Alper H, Jin YS, Moxley JF, Stephanopoulos G. (2005). Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab Eng, 7: 155–164.
  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 25: 3389–3402.
  • Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C. (2002). The Protein Data Bank. Acta Crystallogr D Biol Crystallogr, 58(Pt 6 No 1): 899–907.
  • Borisy AA, Elliott PJ, Hurst NW, Lee MS, Lehar J, Price ER, Serbedzija G, Zimmermann GR, Foley MA, Stockwell BR, Keith CT. (2003). Systematic discovery of multicomponent therapeutics. Proc Natl Acad Sci USA, 100: 7977–7982.
  • Burgard AP, Nikolaev EV, Schilling CH, Maranas CD. (2004). Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res, 14: 301–312.
  • Che D, Zhao J, Cai L, Xu Y. (2007). Operon prediction in microbial genomes using decision tree approach. In: Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology,IEEE California, USA, 135–142.
  • Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. (2004). Integrating high-throughput and computational data elucidates bacterial networks. Nature, 429: 92–96.
  • Csermely P, Agoston V, Pongor S. (2005). The efficiency of multi-target drugs: the network approach might help drug design. Trends Pharmacol Sci, 26: 178–182.
  • Edwards JS, Ibarra RU, Palsson BO. (2001). In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol, 19: 125–130.
  • Jacobs MA, Alwood A, Thaipisuttikul I, Spencer D, Haugen E, Ernst S, Will O, Kaul R, Raymond C, Levy R, Chun-Rong L, Guenthner D, Bovee D, Olson MV, Manoil C. (2003). Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proc Natl Acad Sci USA, 100: 14339–14344.
  • Jamshidi N, Palsson BØ. (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.
  • Joyce AR, Palsson BØ. (2008). Predicting gene essentiality using genome-scale in silico models. Methods Mol Biol, 416: 433–457.
  • Kanehisa M, Goto S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res, 28: 27–30.
  • Korcsmáros T, Szalay MS, Böde C, Kovács IA, Csermely P. (2007). How to design multi-target drugs: target search options in cellular networks. Expert Opin Drug Discov, 2: 799–808.
  • Kuepfer L, Sauer U, Blank LM. (2005). Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res, 15: 1421–1430.
  • Lawrence JG, Roth JR. (1996). Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics, 143: 1843–1860.
  • Lewenza S, Falsafi RK, Winsor G, Gooderham WJ, Mcphee JB, Brinkman FS, Hancock RE. (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.
  • Lindsay MA. (2003). Target discovery. Nat Rev Drug Discov, 2: 831–838.
  • Ma H, Sorokin A, Mazein A, Selkov A, Selkov E, Demin O, Goryanin I. (2007). The Edinburgh human metabolic network reconstruction and its functional analysis. Mol Syst Biol, 3: 135.
  • Oberhardt MA, Puchałka 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.
  • Oltvai ZN, Barabási AL. (2002). Systems biology. Life’s complexity pyramid. Science, 298: 763–764.
  • Palumbo MC, Colosimo A, Giuliani A, Farina L. (2005). Functional essentiality from topology features in metabolic networks: a case study in yeast. FEBS Lett, 579: 4642–4646.
  • Papp B, Pal C, Hurst LD. (2004). Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature, 429: 661–664.
  • Park JH, Lee SY, Kim TY, Kim HU. (2008). Application of systems biology for bioprocess development. Trends Biotechnol, 26: 404–412.
  • Park JH, Lee KH, Kim TY, Lee SY. (2007). Metabolic engineering of Escherichia coli for the production of l-valine based on transcriptome analysis and in silico gene knockout simulation. Proc Natl Acad Sci USA, 104: 7797–7802.
  • Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL. (2009). OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Res, 37: D479–D482.
  • Perumal D, Lim CS, Chow VT, Sakharkar KR, Sakharkar MK. (2008). A combined computational-experimental analyses of selected metabolic enzymes in Pseudomonas species. Int J Biol Sci, 4: 309–317.
  • 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.
  • Price MN, Huang KH, Alm EJ, Arkin AP. (2005). A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res, 33: 880–892.
  • Price ND, Reed JL, Palsson BA. (2004). Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol, 2: 886–897.
  • Raman K, Rajagopalan P, Chandra N. (2005). Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs. PLoS Comput Biol, 1: e46.
  • Reed JL, Vo TD, Schilling CH, Palsson BO. (2003). An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol, 4: R54.
  • Samal A, Singh S, Giri V, Krishna S, Raghuram N, Jain S. (2006). Low degree metabolites explain essential reactions and enhance modularity in biological networks. BMC Bioinformatics, 7: 118.
  • Sams-Dodd F. (2005). Target-based drug discovery: is something wrong? Drug Discov Today, 10: 139–147.
  • Schuster S, Schuster R. (1991). Detecting strictly detailed balanced subnetworks in open chemical reaction networks. J Math Chem, 6: 17–40.
  • Snel B, Van Noort V, Huynen MA. (2004). Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes. Nucleic Acids Res, 32: 4725–4731.
  • Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED. (2002). Metabolic network structure determines key aspects of functionality and regulation. Nature, 420: 190–193.
  • Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ, Lagrou M, Garber RL, Goltry L, Tolentino E, Westbrock-Wadman S, Yuan Y, Brody LL, Coulter SN, Folger KR, Kas A, Larbig K, Lim R, Smith K, Spencer D, Wong GK, Wu Z, Paulsen IT, Reizer J, Saier MH, Hancock RE, Lory S, Olson MV. (2000). Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature, 406: 959–964.
  • Varma A, Palsson BO. (1994). Metabolic flux balancing: basic concepts, scientific and practical use. Nature Biotechnology, 12: 994–998.
  • Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J. (2006). DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res, 34: D668–D672.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.