메뉴 건너뛰기




Volumn 589, Issue 3, 2015, Pages 285-294

Construction of a genome-scale metabolic network of the plant pathogen Pectobacterium carotovorum provides new strategies for bactericide discovery

Author keywords

carotovorum PC1; Flux balance analysis; Metabolic network; Pectobacterium carotovorum subsp.; Phenotype microarray; Virtual screening

Indexed keywords

ALKALINE PHOSPHATASE; BACTERICIDE;

EID: 84921483800     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2014.12.010     Document Type: Article
Times cited : (15)

References (52)
  • 1
    • 0036181156 scopus 로고    scopus 로고
    • Potato diseases caused by soft rot erwinias: An overview of pathogenesis
    • Pérombelon, M.C.M. (2002) Potato diseases caused by soft rot erwinias: an overview of pathogenesis. Plant Pathol. 51, 1-12.
    • (2002) Plant Pathol. , vol.51 , pp. 1-12
    • Pérombelon, M.C.M.1
  • 5
    • 0032989255 scopus 로고    scopus 로고
    • Identification and cloning of an Erwinia carotovora subsp. Carotovora bacteriocin regulator gene by insertional mutagenesis
    • Chuang, D.Y., Kyeremeh, A.G., Gunji, Y., Takahara, Y., Ehara, Y. and Kikumoto, T. (1999) Identification and cloning of an Erwinia carotovora subsp. carotovora bacteriocin regulator gene by insertional mutagenesis. J. Bacteriol. 181, 1953-1957.
    • (1999) J. Bacteriol. , vol.181 , pp. 1953-1957
    • Chuang, D.Y.1    Kyeremeh, A.G.2    Gunji, Y.3    Takahara, Y.4    Ehara, Y.5    Kikumoto, T.6
  • 6
    • 84903977461 scopus 로고    scopus 로고
    • Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth
    • Kentner, D. et al. (2014) Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth. Proc. Natl. Acad. Sci. U.S.A. 111, 9929-9934.
    • (2014) Proc. Natl. Acad. Sci. U.S.A. , vol.111 , pp. 9929-9934
    • Kentner, D.1
  • 7
    • 78651467275 scopus 로고    scopus 로고
    • A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella typhimurium LT2
    • Thiele, I. et al. (2011) A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella typhimurium LT2. BMC Syst. Biol. 5, 8.
    • (2011) BMC Syst. Biol. , vol.5 , pp. 8
    • Thiele, I.1
  • 8
    • 84879002382 scopus 로고    scopus 로고
    • Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli
    • McCloskey, D., Palsson, B.Ø. and Feist, A.M. (2013) Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol. Syst. Biol. 9, 661.
    • (2013) Mol. Syst. Biol. , vol.9 , pp. 661
    • McCloskey, D.1    Palsson, B.Ø.2    Feist, A.M.3
  • 9
    • 77958537509 scopus 로고    scopus 로고
    • Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions
    • Bordbar, A., Lewis, N.E., Schellenberger, J., Palsson, B.Ø. and Jamshidi, N. (2010) Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol. Syst. Biol. 6, 422.
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 422
    • Bordbar, A.1    Lewis, N.E.2    Schellenberger, J.3    Palsson, B.Ø.4    Jamshidi, N.5
  • 10
    • 0034625143 scopus 로고    scopus 로고
    • The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
    • Edwards, J.S. and Palsson, B.Ø. (2000) The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. U.S.A. 97, 5528-5533.
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 5528-5533
    • Edwards, J.S.1    Palsson, B.Ø.2
  • 12
    • 0034911878 scopus 로고    scopus 로고
    • Phenotype microarrays for high-throughput phenotypic testing and assay of gene function
    • Bochner, B.R., Gadzinski, P. and Panomitros, E. (2001) Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. Genome Res. 11, 1246-1255.
    • (2001) Genome Res. , vol.11 , pp. 1246-1255
    • Bochner, B.R.1    Gadzinski, P.2    Panomitros, E.3
  • 15
    • 70449449392 scopus 로고    scopus 로고
    • Genome scale reconstruction of a Salmonella metabolic model: Comparison of similarity and differences with a commensal Escherichia coli strain
    • AbuOun, M., Suthers, P.F., Jones, G.I., Carter, B.R., Saunders, M.P., Maranas, C.D., Woodward, M.J. and Anjum, M.F. (2009) Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain. J. Biol. Chem. 284, 29480-29488.
    • (2009) J. Biol. Chem. , vol.284 , pp. 29480-29488
    • AbuOun, M.1    Suthers, P.F.2    Jones, G.I.3    Carter, B.R.4    Saunders, M.P.5    Maranas, C.D.6    Woodward, M.J.7    Anjum, M.F.8
  • 16
    • 34547588704 scopus 로고    scopus 로고
    • KAAS: An automatic genome annotation and pathway reconstruction server
    • Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C. and Kanehisa, M. (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182-W185.
    • (2007) Nucleic Acids Res. , vol.35 , pp. W182-W185
    • Moriya, Y.1    Itoh, M.2    Okuda, S.3    Yoshizawa, A.C.4    Kanehisa, M.5
  • 17
    • 67849104638 scopus 로고    scopus 로고
    • PubChem: A public information system for analyzing bioactivities of small molecules
    • Wang, Y., Xiao, J., Suzek, T.O., Zhang, J., Wang, J. and Bryant, S.H. (2009) PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res. 37, W623-W633.
    • (2009) Nucleic Acids Res. , vol.37 , pp. W623-W633
    • Wang, Y.1    Xiao, J.2    Suzek, T.O.3    Zhang, J.4    Wang, J.5    Bryant, S.H.6
  • 20
    • 75549090505 scopus 로고    scopus 로고
    • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    • Caspi, R. et al. (2010) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 38, D473-D479.
    • (2010) Nucleic Acids Res. , vol.38 , pp. D473-D479
    • Caspi, R.1
  • 21
    • 0346494926 scopus 로고    scopus 로고
    • TransportDB: A relational database of cellular membrane transport systems
    • Ren, Q., Kang, K.H. and Paulsen, I.T. (2004) TransportDB: a relational database of cellular membrane transport systems. Nucleic Acids Res. 32, D284-D288.
    • (2004) Nucleic Acids Res. , vol.32 , pp. D284-D288
    • Ren, Q.1    Kang, K.H.2    Paulsen, I.T.3
  • 22
    • 33644873454 scopus 로고    scopus 로고
    • TCDB: The Transporter Classification Database for membrane transport protein analyses and information
    • Saier Jr., M.H., Tran, C.V. and Barabote, R.D. (2006) TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res. 34, D181-D186.
    • (2006) Nucleic Acids Res. , vol.34 , pp. D181-D186
    • Saier, M.H.1    Tran, C.V.2    Barabote, R.D.3
  • 24
    • 80052564961 scopus 로고    scopus 로고
    • Structure and function of the D-galactose network in enterobacteria
    • Csiszovszki, Z., Krishna, S., Orosz, L., Adhya, S. and Semsey, S. (2011) Structure and function of the D-galactose network in enterobacteria. mBio 2, e00053-e00111.
    • (2011) mBio , vol.2 , pp. e00053-e00111
    • Csiszovszki, Z.1    Krishna, S.2    Orosz, L.3    Adhya, S.4    Semsey, S.5
  • 25
    • 84857982248 scopus 로고    scopus 로고
    • Ferredoxin containing bacteriocins suggest a novel mechanism of iron uptake in Pectobacterium spp
    • Grinter, R., Milner, J. and Walker, D. (2012) Ferredoxin containing bacteriocins suggest a novel mechanism of iron uptake in Pectobacterium spp. PLoS One 7, e33033.
    • (2012) PLoS One , vol.7 , pp. e33033
    • Grinter, R.1    Milner, J.2    Walker, D.3
  • 26
  • 27
    • 34547676311 scopus 로고    scopus 로고
    • Optimization based automated curation of metabolic reconstructions
    • Satish Kumar, V., Dasika, M.S. and Maranas, C.D. (2007) Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 8, 212.
    • (2007) BMC Bioinformatics , vol.8 , pp. 212
    • Satish Kumar, V.1    Dasika, M.S.2    Maranas, C.D.3
  • 28
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 2.8: New features for data integration and network visualization
    • Smoot, M.E., Ono, K., Ruscheinski, J., Wang, P.L. and Ideker, T. (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27, 431-432.
    • (2011) Bioinformatics , vol.27 , pp. 431-432
    • Smoot, M.E.1    Ono, K.2    Ruscheinski, J.3    Wang, P.L.4    Ideker, T.5
  • 29
    • 79551662521 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0
    • Schellenberger, J. et al. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat. Protoc. 6, 1290-1307.
    • (2011) Nat. Protoc. , vol.6 , pp. 1290-1307
    • Schellenberger, J.1
  • 30
    • 77949263661 scopus 로고    scopus 로고
    • Why similar protein sequences encode similar three-dimensional structures?
    • Kaczanowski, S. and Zielenkiewicz, P. (2010) Why similar protein sequences encode similar three-dimensional structures? Theor. Chem. Acc. 125, 543-850.
    • (2010) Theor. Chem. Acc. , vol.125 , pp. 543-850
    • Kaczanowski, S.1    Zielenkiewicz, P.2
  • 31
    • 0029902763 scopus 로고    scopus 로고
    • Computational methods for biomolecular docking
    • Lengauer, T. and Rarey, M. (1996) Computational methods for biomolecular docking. Curr. Opin. Struc. Biol. 6, 402-406.
    • (1996) Curr. Opin. Struc. Biol. , vol.6 , pp. 402-406
    • Lengauer, T.1    Rarey, M.2
  • 33
    • 77956591314 scopus 로고    scopus 로고
    • EasyModeller: A graphical interface to MODELLER
    • Kuntal, B.K., Aparoy, P. and Reddanna, P. (2010) EasyModeller: a graphical interface to MODELLER. BMC Res. Notes 3, 226.
    • (2010) BMC Res. Notes , vol.3 , pp. 226
    • Kuntal, B.K.1    Aparoy, P.2    Reddanna, P.3
  • 34
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G., Willett, P., Glen, R.C., Leach, A.R. and Taylor, R. (1997) Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267, 727-748.
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 35
    • 39449086721 scopus 로고    scopus 로고
    • Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances
    • Wiegand, I., Hilpert, K. and Hancock, R.E. (2008) Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances. Nat. Protoc. 3, 163-175.
    • (2008) Nat. Protoc. , vol.3 , pp. 163-175
    • Wiegand, I.1    Hilpert, K.2    Hancock, R.E.3
  • 39
    • 0033862847 scopus 로고    scopus 로고
    • Bacterial quorum sensing in pathogenic relationships
    • de Kievit, T.R. and Iglewski, B.H. (2000) Bacterial quorum sensing in pathogenic relationships. Infect. Immun. 68, 4839-4849.
    • (2000) Infect. Immun. , vol.68 , pp. 4839-4849
    • De Kievit, T.R.1    Iglewski, B.H.2
  • 40
    • 0000292096 scopus 로고    scopus 로고
    • Quorum sensing in gram-negative bacteria
    • Greenberg, E.P. (1997) Quorum sensing in gram-negative bacteria. ASM News 63, 371-377.
    • (1997) ASM News , vol.63 , pp. 371-377
    • Greenberg, E.P.1
  • 41
    • 84858960203 scopus 로고    scopus 로고
    • Quorum sensing and expression of virulence in pectobacteria
    • Põllumaa, L., Alamäe, T. and Mäe, A. (2012) Quorum sensing and expression of virulence in pectobacteria. Sensors (Basel) 12, 3327-3349.
    • (2012) Sensors (Basel) , vol.12 , pp. 3327-3349
    • Põllumaa, L.1    Alamäe, T.2    Mäe, A.3
  • 43
    • 0023410829 scopus 로고
    • Characterization and virulence properties of Erwinia chrysanthemi lipopolysaccharide-defective, phiEC2-resistant mutants
    • Schoonejans, E., Expert, D. and Toussaint, A. (1987) Characterization and virulence properties of Erwinia chrysanthemi lipopolysaccharide-defective, phiEC2-resistant mutants. J. Bacteriol. 169, 4011-4017.
    • (1987) J. Bacteriol. , vol.169 , pp. 4011-4017
    • Schoonejans, E.1    Expert, D.2    Toussaint, A.3
  • 44
  • 45
  • 46
    • 84859267371 scopus 로고    scopus 로고
    • Therapeutic target database update 2012: A resource for facilitating target-oriented drug discovery
    • Zhu, F. et al. (2012) Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery. Nucleic Acids Res. 40, D1128-D1136.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D1128-D1136
    • Zhu, F.1
  • 47
    • 77955187744 scopus 로고    scopus 로고
    • High-throughput screening of tissue-nonspecific alkaline phosphatase for identification of effectors with diverse modes of action
    • Sergienko, E.A. and Millan, J.L. (2010) High-throughput screening of tissue-nonspecific alkaline phosphatase for identification of effectors with diverse modes of action. Nat. Protoc. 5, 1431-1439.
    • (2010) Nat. Protoc. , vol.5 , pp. 1431-1439
    • Sergienko, E.A.1    Millan, J.L.2
  • 48
    • 0036908733 scopus 로고    scopus 로고
    • Effect of carboxymethyl chitin-glucan on the activity of some hydrolytic enzymes in maize plants
    • Tamás, L., Huttová, J., Mistrk, I. and Kogan, G. (2002) Effect of carboxymethyl chitin-glucan on the activity of some hydrolytic enzymes in maize plants. Chem. Pap. 56, 326-329.
    • (2002) Chem. Pap. , vol.56 , pp. 326-329
    • Tamás, L.1    Huttová, J.2    Mistrk, I.3    Kogan, G.4
  • 49
    • 59149097144 scopus 로고    scopus 로고
    • Medicinal chemistry and the molecular operating environment (MOE): Application of QSAR and molecular docking to drug discovery
    • Vilar, S., Cozza, G. and Moro, S. (2008) Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery. Curr. Top. Med. Chem. 8, 1555-1572.
    • (2008) Curr. Top. Med. Chem. , vol.8 , pp. 1555-1572
    • Vilar, S.1    Cozza, G.2    Moro, S.3
  • 50
    • 84921472288 scopus 로고    scopus 로고
    • Johann Gasteiger-Germany's pioneer in chemoinformatics
    • Engel, T. (2006) Johann Gasteiger-Germany's pioneer in chemoinformatics. J. Chem. Inf. Model. 46, 2191-2192.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 2191-2192
    • Engel, T.1
  • 51
    • 33749598013 scopus 로고    scopus 로고
    • Cheminformatics analysis and learning in a data pipelining environment
    • Hassan, M., Brown, R.D., Varma-O'brien, S. and Rogers, D. (2006) Cheminformatics analysis and learning in a data pipelining environment. Mol. Divers 10, 283-299.
    • (2006) Mol. Divers , vol.10 , pp. 283-299
    • Hassan, M.1    Brown, R.D.2    Varma-O'Brien, S.3    Rogers, D.4
  • 52
    • 84865126690 scopus 로고    scopus 로고
    • Scientific workflow systems: Pipeline Pilot and KNIME
    • Warr, W.A. (2012) Scientific workflow systems: Pipeline Pilot and KNIME. J. Comput. Aid. Mol. Des. 26, 801-804.
    • (2012) J. Comput. Aid. Mol. Des. , vol.26 , pp. 801-804
    • Warr, W.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.