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Volumn 193, Issue 6, 2011, Pages 1461-1472

Core and panmetabolism in Escherichia coli

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL METABOLISM; BIOSYNTHESIS; ESCHERICHIA COLI; GENETIC DISTANCE; NONHUMAN; PATHOGENICITY; PHYLOGENETIC TREE; PRIORITY JOURNAL; SHIGELLA;

EID: 79952393752     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.01192-10     Document Type: Article
Times cited : (45)

References (55)
  • 1
    • 0023901495 scopus 로고
    • Nutritional requirements of shigellae for growth in a minimal medium
    • Ahmed, Z. U., M. R. Sarker, and D. A. Sack. 1988. Nutritional requirements of shigellae for growth in a minimal medium. Infect. Immun. 56:1007-1009.
    • (1988) Infect. Immun. , vol.56 , pp. 1007-1009
    • Ahmed, Z.U.1    Sarker, M.R.2    Sack, D.A.3
  • 4
    • 70349971144 scopus 로고    scopus 로고
    • Mass spectrometry based metabolomics and enzymatic assays for functional genomics
    • Baran, R., W. Reindl, and T. R. Northen. 2009. Mass spectrometry based metabolomics and enzymatic assays for functional genomics. Curr. Opin. Microbiol. 12:547-552.
    • (2009) Curr. Opin. Microbiol. , vol.12 , pp. 547-552
    • Baran, R.1    Reindl, W.2    Northen, T.R.3
  • 5
    • 70349863392 scopus 로고    scopus 로고
    • Reactome array: Forging a link between metabolome and genome
    • Beloqui, A., et al. 2009. Reactome array: forging a link between metabolome and genome. Science 326:252-257.
    • (2009) Science , vol.326 , pp. 252-257
    • Beloqui, A.1
  • 7
    • 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
    • Caspi, R.1
  • 8
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540-552.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 540-552
    • Castresana, J.1
  • 9
    • 77649289609 scopus 로고    scopus 로고
    • Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042
    • Chaudhuri, R. R., et al. 2010. Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042. PLoS One 5:e8801.
    • (2010) PLoS One , vol.5
    • Chaudhuri, R.R.1
  • 11
    • 79952407065 scopus 로고    scopus 로고
    • Population genetics of pathogenic Escherichia coli
    • D. A. Robinson, D. Falush, and E. J. Feil (ed.), Wiley-Blackwell, West Sussex, United Kingdom
    • Denamur, E., B. Picard, and O. Tenaillon. 2010. Population genetics of pathogenic Escherichia coli, p. 269-286. In D. A. Robinson, D. Falush, and E. J. Feil (ed.), Bacterial population genetics in infectious disease. Wiley-Blackwell, West Sussex, United Kingdom.
    • (2010) Bacterial Population Genetics in Infectious Disease , pp. 269-286
    • Denamur, E.1    Picard, B.2    Tenaillon, O.3
  • 13
    • 57549102595 scopus 로고    scopus 로고
    • Genome-scale models pof bacterial metabolism: Reconstruction and applications
    • Durot, M., P. Bourguignon, and V. Schachter. 2009. Genome-scale models pof bacterial metabolism: reconstruction and applications. FEMS Microbiol. Rev. 33:164-190.
    • (2009) FEMS Microbiol. Rev. , vol.33 , pp. 164-190
    • Durot, M.1    Bourguignon, P.2    Schachter, V.3
  • 14
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • DOI 10.1093/nar/gkh340
    • Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797. (Pubitemid 38832724)
    • (2004) Nucleic Acids Research , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 15
    • 0042386134 scopus 로고    scopus 로고
    • The evolutionary history of Shigella and enteroinvasive Escherichia coli revised
    • Escobar-Páramo, P., C. Giudicelli, C. Parsot, and E. Denamur. 2003. The evolutionary history of Shigella and enteroinvasive Escherichia coli revised. J. Mol. Evol. 57:140-148.
    • (2003) J. Mol. Evol. , vol.57 , pp. 140-148
    • Escobar-Páramo, P.1    Giudicelli, C.2    Parsot, C.3    Denamur, E.4
  • 16
    • 34347332311 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
    • Feist, A. M., 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.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 121
    • Feist, A.M.1
  • 17
    • 53849112279 scopus 로고    scopus 로고
    • Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5
    • Fricke, W. F., et al. 2008. Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5. J. Bacteriol. 190:6779-6794.
    • (2008) J. Bacteriol. , vol.190 , pp. 6779-6794
    • Fricke, W.F.1
  • 18
    • 2942571207 scopus 로고    scopus 로고
    • Extensive genomic diversity in pathogenic Escherichia coli and Shigella strains revealed by comparative genomic hybridization microarray
    • Fukiya, S., H. Mizoguchi, T. Tobe, and H. Mori. 2004. Extensive genomic diversity in pathogenic Escherichia coli and Shigella strains revealed by comparative genomic hybridization microarray. J. Bacteriol. 186:3911-3921.
    • (2004) J. Bacteriol. , vol.186 , pp. 3911-3921
    • Fukiya, S.1    Mizoguchi, H.2    Tobe, T.3    Mori, H.4
  • 19
    • 13244268322 scopus 로고    scopus 로고
    • A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
    • Green, M. L., and P. D. Karp. 2004. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinform. 5:76.
    • (2004) BMC Bioinform. , vol.5 , pp. 76
    • Green, M.L.1    Karp, P.D.2
  • 20
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 21
    • 25144456056 scopus 로고    scopus 로고
    • Computational cluster validation in post-genomic data analysis
    • Handl, J., J. Knowles, and D. B. Kell. 2005. Computational cluster validation in post-genomic data analysis. Bioinformatics 21:3201-3212.
    • (2005) Bioinformatics , vol.21 , pp. 3201-3212
    • Handl, J.1    Knowles, J.2    Kell, D.B.3
  • 22
    • 39749173921 scopus 로고    scopus 로고
    • Reduced selection leads to accelerated gene loss in Shigella
    • Hershberg, R., H. Tang, and D. A. Petrov. 2007. Reduced selection leads to accelerated gene loss in Shigella. Genome Biol. 8:R164.
    • (2007) Genome Biol. , vol.8
    • Hershberg, R.1    Tang, H.2    Petrov, D.A.3
  • 23
    • 58149498183 scopus 로고    scopus 로고
    • Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69
    • Iguchi, A., et al. 2009. Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J. Bacteriol. 191:347-354.
    • (2009) J. Bacteriol. , vol.191 , pp. 347-354
    • Iguchi, A.1
  • 24
    • 0036778151 scopus 로고    scopus 로고
    • Adaptation of sucrose metabolism in the Escherichia coli wild-type strain EC3132
    • Jahreis, K., et al. 2002. Adaptation of sucrose metabolism in the Escherichia coli wild-type strain EC3132. J. Bacteriol. 184:5307-5316.
    • (2002) J. Bacteriol. , vol.184 , pp. 5307-5316
    • Jahreis, K.1
  • 25
    • 60549112381 scopus 로고    scopus 로고
    • Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains
    • Jaureguy, F., et al. 2008. Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains. BMC Genomics 9:560.
    • (2008) BMC Genomics , vol.9 , pp. 560
    • Jaureguy, F.1
  • 26
    • 38549126643 scopus 로고    scopus 로고
    • KEGG for linking genomes to life and the environment
    • Kanehisa, M., et al. 2007. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36:D480-D484.
    • (2007) Nucleic Acids Res. , vol.36
    • Kanehisa, M.1
  • 28
    • 75849133666 scopus 로고    scopus 로고
    • Pathway Tools version 13.0: Integrated software for pathway/genome informatics and systems biology
    • Karp, P. D., et al. 2010. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief. Bioinform. 11:40-79.
    • (2010) Brief. Bioinform. , vol.11 , pp. 40-79
    • Karp, P.D.1
  • 30
    • 0025777130 scopus 로고
    • Molecular and evolutionary relationships among enteric bacteria
    • Lawrence, J. G., H. Ochman, and D. L. Hartl. 1991. Molecular and evolutionary relationships among enteric bacteria. J. Gen. Microbiol. 137:1911-1921.
    • (1991) J. Gen. Microbiol. , vol.137 , pp. 1911-1921
    • Lawrence, J.G.1    Ochman, H.2    Hartl, D.L.3
  • 31
    • 46749110034 scopus 로고    scopus 로고
    • FactoMineR: An R package for multivariate analysis
    • Lê, S., J. Josse, and F. Husson. 2008. FactoMineR: an R package for multivariate analysis. J. Stat. Softw. 25:1-18.
    • (2008) J. Stat. Softw. , vol.25 , pp. 1-18
    • Lê, S.1    Josse, J.2    Husson, F.3
  • 32
    • 34447296715 scopus 로고    scopus 로고
    • Cyclone: Java-based querying and computing with Pathway/Genome databases
    • DOI 10.1093/bioinformatics/btm107
    • Le Fèvre, F., S. Smidtas, and V. Schächter. 2007. Cyclone: Java-based querying and computing with Pathway/Genome databases. Bioinformatics 23:1299-1300. (Pubitemid 47050550)
    • (2007) Bioinformatics , vol.23 , Issue.10 , pp. 1299-1300
    • Le, F.F.1    Smidtas, S.2    Schachter, V.3
  • 33
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li, L., C. J. Stoeckert, and D. S. Roos. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13:2178-2189.
    • (2003) Genome Res. , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 34
    • 67649872627 scopus 로고    scopus 로고
    • Toolbox model of evolution of prokaryotic metabolic networks and their regulation
    • Maslov, S., S. Krishna, T. Y. Pang, and K. Sneppen. 2009. Toolbox model of evolution of prokaryotic metabolic networks and their regulation. Proc. Natl. Acad. Sci. U. S. A. 106:9743-9748.
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 9743-9748
    • Maslov, S.1    Krishna, S.2    Pang, T.Y.3    Sneppen, K.4
  • 35
    • 0032584169 scopus 로고    scopus 로고
    • "Black holes" and bacterial pathogenicity: A large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli
    • Maurelli, A. T., R. E. Fernández, C. A. Bloch, C. K. Rode, and A. Fasano. 1998. "Black holes" and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 95:3943-3948.
    • (1998) Proc. Natl. Acad. Sci. U. S. A. , vol.95 , pp. 3943-3948
    • Maurelli, A.T.1    Fernández, R.E.2    Bloch, C.A.3    Rode, C.K.4    Fasano, A.5
  • 36
    • 77958603351 scopus 로고    scopus 로고
    • Complete genome sequence of Crohn's disease-associated adherent-invasive E. coli strain LF82
    • Miquel, S., et al. 2010. Complete genome sequence of Crohn's disease-associated adherent-invasive E. coli strain LF82. PLoS One 5:e12714.
    • (2010) PLoS One , vol.5
    • Miquel, S.1
  • 37
    • 79952429171 scopus 로고    scopus 로고
    • Reference deleted
    • Reference deleted.
  • 39
    • 59149104994 scopus 로고    scopus 로고
    • Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult
    • Oshima, K., et al. 2008. Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult. DNA Res. 15:375-386.
    • (2008) DNA Res. , vol.15 , pp. 375-386
    • Oshima, K.1
  • 40
    • 28444475529 scopus 로고    scopus 로고
    • Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
    • Pál, C., B. Papp, and M. J. Lercher. 2005. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat. Genet. 37:1372-1375.
    • (2005) Nat. Genet. , vol.37 , pp. 1372-1375
    • Pál, C.1    Papp, B.2    Lercher, M.J.3
  • 41
    • 1042304216 scopus 로고    scopus 로고
    • APE: Analyses of phylogenetics and evolution in R language
    • DOI 10.1093/bioinformatics/btg412
    • Paradis, E., J. Claude, and K. Strimmer. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290. (Pubitemid 38195693)
    • (2004) Bioinformatics , vol.20 , Issue.2 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 42
    • 0025885026 scopus 로고
    • Identification of two genes, kpsM and kpsT, in region 3 of the polysialic acid gene cluster of Escherichia coli K1
    • Pavelka, M. S., L. F. Wright, and R. P. Silver. 1991. Identification of two genes, kpsM and kpsT, in region 3 of the polysialic acid gene cluster of Escherichia coli K1. J. Bacteriol. 173:4603-4610.
    • (1991) J. Bacteriol. , vol.173 , pp. 4603-4610
    • Pavelka, M.S.1    Wright, L.F.2    Silver, R.P.3
  • 43
    • 34447500541 scopus 로고    scopus 로고
    • NadA and nadB of Shigella flexneri 5a are antivirulence loci responsible for the synthesis of quinolinate, a small molecule inhibitor of Shigella pathogenicity
    • DOI 10.1099/mic.0.2007/006916-0
    • Prunier, A., et al. 2007. nadA and nadB of Shigella flexneri 5a are antivirulence loci responsible for the synthesis of quinolinate, a small molecule inhibitor of Shigella pathogenicity. Microbiology 153:2363-2372. (Pubitemid 47074089)
    • (2007) Microbiology , vol.153 , Issue.7 , pp. 2363-2372
    • Prunier, A.-L.1    Schuch, R.2    Fernandez, R.E.3    Kohler, H.4    McCormick, B.A.5    Maurelli, A.T.6
  • 44
    • 34548514828 scopus 로고    scopus 로고
    • Genetic structure of the nadA and nadB antivirulence loci in Shigella spp
    • Prunier, A., R. Schuch, R. E. Fernández, and A. T. Maurelli. 2007. Genetic structure of the nadA and nadB antivirulence loci in Shigella spp. J. Bacteriol. 189:6482-6486.
    • (2007) J. Bacteriol. , vol.189 , pp. 6482-6486
    • Prunier, A.1    Schuch, R.2    Fernández, R.E.3    Maurelli, A.T.4
  • 45
    • 0034641731 scopus 로고    scopus 로고
    • Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics
    • Pupo, G. M., R. Lan, and P. R. Reeves. 2000. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc. Natl. Acad. Sci. U. S. A. 97:10567-10572.
    • (2000) Proc. Natl. Acad. Sci. U. S. A. , vol.97 , pp. 10567-10572
    • Pupo, G.M.1    Lan, R.2    Reeves, P.R.3
  • 46
    • 53849104729 scopus 로고    scopus 로고
    • The pangenome structure of Escherichia coli: Comparative genomic analysis of E. coli commensal and pathogenic isolates
    • Rasko, D. A., et al. 2008. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J. Bacteriol. 190:6881-6893.
    • (2008) J. Bacteriol. , vol.190 , pp. 6881-6893
    • Rasko, D.A.1
  • 48
    • 33947205482 scopus 로고    scopus 로고
    • Autotransporter-encoding sequences are phylogenetically distributed among Escherichia coli clinical isolates and reference strains
    • Restieri, C., G. Garriss, M. Locas, and C. M. Dozois. 2007. Autotransporter-encoding sequences are phylogenetically distributed among Escherichia coli clinical isolates and reference strains. Appl. Environ. Microbiol. 73:1553-1562.
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 1553-1562
    • Restieri, C.1    Garriss, G.2    Locas, M.3    Dozois, C.M.4
  • 49
    • 79952408058 scopus 로고    scopus 로고
    • Reference deleted
    • Reference deleted.
  • 51
    • 29244461323 scopus 로고    scopus 로고
    • In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: Comparing predictions of nutrient requirements with those from growth experiments
    • Teusink, B., et al. 2005. In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments. Appl. Environ. Microbiol. 71:7253-7262.
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 7253-7262
    • Teusink, B.1
  • 52
    • 59249089471 scopus 로고    scopus 로고
    • Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
    • Touchon, M., et al. 2009. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 5:e1000344.
    • (2009) PLoS Genet. , vol.5
    • Touchon, M.1
  • 53
    • 84908096911 scopus 로고    scopus 로고
    • MicroScope: A platform for microbial genome annotation and comparative genomics
    • Vallenet, D., et al. 2009. MicroScope: a platform for microbial genome annotation and comparative genomics. Database 2009:bap021.
    • (2009) Database , vol.2009
    • Vallenet, D.1
  • 54
    • 33746356503 scopus 로고    scopus 로고
    • Biosynthesis and assembly of capsular polysaccharides in Escherichia coli
    • Whitfield, C. 2006. Biosynthesis and assembly of capsular polysaccharides in Escherichia coli. Annu. Rev. Biochem. 75:39-68.
    • (2006) Annu. Rev. Biochem. , vol.75 , pp. 39-68
    • Whitfield, C.1
  • 55
    • 0026019818 scopus 로고
    • Virulence plasmids of enteroinvasive Escherichia coli and Shigella flexneri integrate into a specific site on the host chromosome: Integration greatly reduces expression of plasmid-carried virulence genes
    • Zagaglia, C., et al. 1991. Virulence plasmids of enteroinvasive Escherichia coli and Shigella flexneri integrate into a specific site on the host chromosome: integration greatly reduces expression of plasmid-carried virulence genes. Infect. Immun. 59:792-799.
    • (1991) Infect. Immun. , vol.59 , pp. 792-799
    • Zagaglia, C.1


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