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Volumn 6, Issue , 2009, Pages 21-34

In silico reconstruction of the metabolic and pathogenic potential of bacterial genomes using subsystems

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DIHYDRONEOPTERIN TRIPHOSPHATE; GUANOSINE TRIPHOSPHATE CYCLOHYDROLASE I; PHOSPHATE; UNCLASSIFIED DRUG; VIRULENCE FACTOR;

EID: 77950628554     PISSN: 16609263     EISSN: None     Source Type: Book Series    
DOI: 10.1159/000235760     Document Type: Review
Times cited : (3)

References (40)
  • 1
    • 0030060689 scopus 로고    scopus 로고
    • Sequence-based identification of microbial pathogens: A reconsideration of Koch's postulates
    • Fredericks DN, Relman DA: Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates. Clin Microbiol Rev 1996;9:18-33.
    • (1996) Clin Microbiol Rev , vol.9 , pp. 18-33
    • Fredericks, D.N.1    Relman, D.A.2
  • 3
    • 0029653518 scopus 로고
    • Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
    • Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, et al: Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995;269:496-512.
    • (1995) Science , vol.269 , pp. 496-512
    • Fleischmann, R.D.1    Adams, M.D.2    White, O.3    Clayton, R.A.4    Kirkness, E.F.5
  • 5
    • 1542377296 scopus 로고    scopus 로고
    • Community structure and metabolism through reconstruction of microbial genomes from the environment
    • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, et al: Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004;428:37-43.
    • (2004) Nature , vol.428 , pp. 37-43
    • Tyson, G.W.1    Chapman, J.2    Hugenholtz, P.3    Allen, E.E.4    Ram, R.J.5
  • 8
    • 77955914167 scopus 로고    scopus 로고
    • National Microbial Pathogen Data Resource [database on the Internet]. Version of March 24, Chicago: Computation Institute, University of Chicago/Argonne National Laboratory/Fellowship for Interpretation of Genomes; 2004- [cited 2008 May 10]. Available from:
    • National Microbial Pathogen Data Resource [database on the Internet]. Version of March 24, 2008. Chicago: Computation Institute, University of Chicago/Argonne National Laboratory/Fellowship for Interpretation of Genomes; 2004- [cited 2008 May 10]. Available from: http://www.nmpdr.org// FIG/seedviewer.cgi?pattern = 71421.1;page = SearchResult
    • (2008)
  • 10
    • 36448974114 scopus 로고    scopus 로고
    • Principia aetiologica: Taking causality beyond Koch's postulates
    • Inglis TJ: Principia aetiologica: taking causality beyond Koch's postulates. J Med Microbiol 2007;56: 1419-1422.
    • (2007) J Med Microbiol , vol.56 , pp. 1419-1422
    • Inglis, T.J.1
  • 11
    • 0024041593 scopus 로고
    • Molecular Koch's postulates applied to microbial pathogenicity
    • Falkow S: Molecular Koch's postulates applied to microbial pathogenicity. Rev Infect Dis 1988;10: S274-S276.
    • (1988) Rev Infect Dis , vol.10
    • Falkow, S.1
  • 12
    • 1842434337 scopus 로고    scopus 로고
    • Molecular Koch's postulates applied to bacterial pathogenicity-A personal recollection 15 years later
    • Falkow S: Molecular Koch's postulates applied to bacterial pathogenicity-a personal recollection 15 years later. Nat Rev Microbiol 2004;2:67-72.
    • (2004) Nat Rev Microbiol , vol.2 , pp. 67-72
    • Falkow, S.1
  • 13
    • 35349003200 scopus 로고    scopus 로고
    • Bacterial pathogenomics
    • Pallen MJ, Wren BW: Bacterial pathogenomics. Nature 2007;449:835-842.
    • (2007) Nature , vol.449 , pp. 835-842
    • Pallen, M.J.1    Wren, B.W.2
  • 14
    • 0029799009 scopus 로고    scopus 로고
    • The plasmin-binding protein Plr of group A streptococci is identified as glyceraldehyde- 3-phosphate dehydrogenase
    • Winram SB, Lottenberg R: The plasmin-binding protein Plr of group A streptococci is identified as glyceraldehyde- 3-phosphate dehydrogenase. Microbiology 1996;142:2311-2320.
    • (1996) Microbiology , vol.142 , pp. 2311-2320
    • Winram, S.B.1    Lottenberg, R.2
  • 15
    • 0029995819 scopus 로고    scopus 로고
    • Cloning, sequencing and functional overexpression of the Streptococcus equisimilis H46A gapC gene encoding a glyceraldehyde-3-phosphate dehydrogenase that also functions as a plasmin(ogen)-binding protein. Purification and biochemical characterization of the protein
    • Gase K, Gase A, Schirmer H, Malke H: Cloning, sequencing and functional overexpression of the Streptococcus equisimilis H46A gapC gene encoding a glyceraldehyde-3-phosphate dehydrogenase that also functions as a plasmin(ogen)-binding protein. Purification and biochemical characterization of the protein. Eur J Biochem 1996;239:42-51.
    • (1996) Eur J Biochem , vol.239 , pp. 42-51
    • Gase, K.1    Gase, A.2    Schirmer, H.3    Malke, H.4
  • 16
    • 77955864378 scopus 로고    scopus 로고
    • The genomics of disease-causing organisms: Mapping a strategy for discovery and defense
    • Buckley M: The genomics of disease-causing organisms: mapping a strategy for discovery and defense. American Academy of Microbiology 2004 (http:// academy.asm.org/index.php?option = com-content &task = blogcategory&id = 22&Itemid = 57).
    • (2004) American Academy of Microbiology
    • Buckley, M.1
  • 17
    • 33748659861 scopus 로고    scopus 로고
    • Genes for the majority of group A streptococcal virulence factors and extracellular surface proteins do not confer an increased propensity to cause invasive disease
    • McMillan DJ, Beiko RG, Geffers R, Buer J, Schouls LM, et al: Genes for the majority of group A streptococcal virulence factors and extracellular surface proteins do not confer an increased propensity to cause invasive disease. Clin Infect Dis 2006;43:884-891.
    • (2006) Clin Infect Dis , vol.43 , pp. 884-891
    • McMillan, D.J.1    Beiko, R.G.2    Geffers, R.3    Buer, J.4    Schouls, L.M.5
  • 18
    • 34249009232 scopus 로고    scopus 로고
    • Strain prevalence, rather than innate virulence potential, is the major factor responsible for an increase in serious group A Streptococcus infections
    • Rogers S, Commons R, Danchin MH, Selvaraj G, Kelpie L, et al: Strain prevalence, rather than innate virulence potential, is the major factor responsible for an increase in serious group A Streptococcus infections. J Infect Dis 2007;195:1625-1633.
    • (2007) J Infect Dis , vol.195 , pp. 1625-1633
    • Rogers, S.1    Commons, R.2    Danchin, M.H.3    Selvaraj, G.4    Kelpie, L.5
  • 19
    • 0036908653 scopus 로고    scopus 로고
    • An immunogenetic and molecular basis for differences in outcomes of invasive group A streptococcal infections
    • Kotb M, Norrby-Teglund A, McGeer A, El-Sherbini H, Dorak MT, et al: An immunogenetic and molecular basis for differences in outcomes of invasive group A streptococcal infections. Nat Med 2002;8: 1398-1404.
    • (2002) Nat Med , vol.8 , pp. 1398-1404
    • Kotb, M.1    Norrby-Teglund, A.2    McGeer, A.3    El-Sherbini, H.4    Dorak, M.T.5
  • 20
    • 0035479288 scopus 로고    scopus 로고
    • Genetic control of susceptibility to group A streptococcal infection in mice
    • Medina E, Goldmann O, Rohde M, Lengeling A, Chhatwals GS: Genetic control of susceptibility to group A streptococcal infection in mice. J Infect Dis 2001;184:846-852.
    • (2001) J Infect Dis , vol.184 , pp. 846-852
    • Medina, E.1    Goldmann, O.2    Rohde, M.3    Lengeling, A.4    Chhatwals, G.S.5
  • 21
    • 25444501564 scopus 로고    scopus 로고
    • A new set of BXD recombinant inbred lines from advanced intercross populations in mice
    • Peirce JL, Lu L, Gu J, Silver LM, Williams RW: A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genet 2004;5:7-23.
    • (2004) BMC Genet , vol.5 , pp. 7-23
    • Peirce, J.L.1    Lu, L.2    Gu, J.3    Silver, L.M.4    Williams, R.W.5
  • 22
    • 34547520746 scopus 로고    scopus 로고
    • Susceptibility to severe streptococcal sepsis: Use of a large set of isogenic mouse lines to study genetic and environmental factors
    • Aziz RK, Kansal R, Abdeltawab NF, Rowe SL, Su Y, et al: Susceptibility to severe streptococcal sepsis: use of a large set of isogenic mouse lines to study genetic and environmental factors. Genes Immun 2007;8:404-415.
    • (2007) Genes Immun , vol.8 , pp. 404-415
    • Aziz, R.K.1    Kansal, R.2    Abdeltawab, N.F.3    Rowe, S.L.4    Su, Y.5
  • 23
    • 43049085937 scopus 로고    scopus 로고
    • An unbiased systems genetics approach to mapping genetic loci modulating susceptibility to severe streptococcal sepsis
    • Abdeltawab NF, Aziz RK, Kansall R, Rowe SL, Su Y, et al: An unbiased systems genetics approach to mapping genetic loci modulating susceptibility to severe streptococcal sepsis. PLoS Pathogens 2008; 4:e1000042.
    • (2008) PLoS Pathogens , vol.4
    • Abdeltawab, N.F.1    Aziz, R.K.2    Kansall, R.3    Rowe, S.L.4    Su, Y.5
  • 24
    • 25644458211 scopus 로고    scopus 로고
    • The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    • Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, et al: The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 2005;33: 5691-5702.
    • (2005) Nucleic Acids Res , vol.33 , pp. 5691-5702
    • Overbeek, R.1    Begley, T.2    Butler, R.M.3    Choudhuri, J.V.4    Chuang, H.Y.5
  • 25
    • 34447271298 scopus 로고    scopus 로고
    • National Institute of Allergy and Infectious Diseases bioinformatics resource centers: New assets for pathogen informatics
    • Greene JM, Collins F, Lefkowitz EJ, Roos D, Scheuermann RH, et al: National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infect Immun 2007;75:3212-3219.
    • (2007) Infect Immun , vol.75 , pp. 3212-3219
    • Greene, J.M.1    Collins, F.2    Lefkowitz, E.J.3    Roos, D.4    Scheuermann, R.H.5
  • 26
    • 33846119130 scopus 로고    scopus 로고
    • The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation
    • McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, et al: The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res 2007;35: D347-D353.
    • (2007) Nucleic Acids Res , vol.35
    • McNeil, L.K.1    Reich, C.2    Aziz, R.K.3    Bartels, D.4    Cohoon, M.5
  • 27
    • 38549144166 scopus 로고    scopus 로고
    • The Genomes OnLine Database (GOLD) in 2007 status of genomic and metagenomic projects and their associated metadata
    • Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC: The Genomes OnLine Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008;36:D475-D479.
    • (2008) Nucleic Acids Res , vol.36
    • Liolios, K.1    Mavromatis, K.2    Tavernarakis, N.3    Kyrpides, N.C.4
  • 28
    • 5044230561 scopus 로고    scopus 로고
    • Two-dimensional annotation of genomes
    • Palsson B: Two-dimensional annotation of genomes. Nat Biotechnol 2004;22:1218-1219.
    • (2004) Nat Biotechnol , vol.22 , pp. 1218-1219
    • Palsson, B.1
  • 30
    • 0037316342 scopus 로고    scopus 로고
    • FluxAnalyzer: Exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps
    • Klamt S, Stelling J, Ginkel M, Gilles ED: FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 2003;19:261-269.
    • (2003) Bioinformatics , vol.19 , pp. 261-269
    • Klamt, S.1    Stelling, J.2    Ginkel, M.3    Gilles, E.D.4
  • 32
    • 34548506752 scopus 로고    scopus 로고
    • Comparative genomics of bacterial and plant folate synthesis and salvage: Predictions and validations
    • de Crécy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD: Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics 2007;8: 245-249.
    • (2007) BMC Genomics , vol.8 , pp. 245-249
    • De Crécy-Lagard, V.1    El Yacoubi, B.2    De La Garza, R.D.3    Noiriel, A.4    Hanson, A.D.5
  • 33
    • 14044254160 scopus 로고    scopus 로고
    • A nudix enzyme removes pyrophosphate from dihydroneopterin triphosphate in the folate synthesis pathway of bacteria and plants
    • Klaus SM, Wegkamp A, Sybesma W, Hugenholtz J, Gregory JF 3rd, Hanson AD: A nudix enzyme removes pyrophosphate from dihydroneopterin triphosphate in the folate synthesis pathway of bacteria and plants. J Biol Chem 2005;280:5274-5280.
    • (2005) J Biol Chem , vol.280 , pp. 5274-5280
    • Klaus, S.M.1    Wegkamp, A.2    Sybesma, W.3    Hugenholtz, J.4    Gregory III, J.F.5    Hanson, A.D.6
  • 34
    • 34547657390 scopus 로고    scopus 로고
    • Structure and function of the E. coli dihydroneopterin triphosphate pyrophosphatase: A Nudix enzyme involved in folate biosynthesis
    • Gabelli SB, Bianchet MA, Xu W, Dunn CA, Niu ZD, et al: Structure and function of the E. coli dihydroneopterin triphosphate pyrophosphatase: a Nudix enzyme involved in folate biosynthesis. Structure 2007;15:1014-1022.
    • (2007) Structure , vol.15 , pp. 1014-1022
    • Gabelli, S.B.1    Bianchet, M.A.2    Xu, W.3    Dunn, C.A.4    Niu, Z.D.5
  • 36
    • 0037007095 scopus 로고    scopus 로고
    • Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks
    • Smoot JC, Barbian KD, Van Gompel JJ, Smoot LM, Chaussee MS, et al: Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks. Proc Natl Acad Sci USA 2002;99:4668-4673.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 4668-4673
    • Smoot, J.C.1    Barbian, K.D.2    Van Gompel, J.J.3    Smoot, L.M.4    Chaussee, M.S.5
  • 37
    • 3943087577 scopus 로고    scopus 로고
    • Progress toward characterization of the group A Streptococcus metagenome: Complete genome sequence of a macrolide-resistant serotype M6 strain
    • Banks DJ, Porcella SF, Barbian KD, Beres SB, Philips LE, et al: Progress toward characterization of the group A Streptococcus metagenome: complete genome sequence of a macrolide-resistant serotype M6 strain. J Infect Dis 2004;190:727-738.
    • (2004) J Infect Dis , vol.190 , pp. 727-738
    • Banks, D.J.1    Porcella, S.F.2    Barbian, K.D.3    Beres, S.B.4    Philips, L.E.5
  • 38
    • 23944510259 scopus 로고    scopus 로고
    • Genome sequence of a serotype M28 strain of group A Streptococcus: Potential new insights into puerperal sepsis and bacterial disease specificity
    • Green NM, Zhang S, Porcella SF, Nagiec MJ, Barbian KD, et al: Genome sequence of a serotype M28 strain of group A Streptococcus: potential new insights into puerperal sepsis and bacterial disease specificity. J Infect Dis 2005;192:760-770.
    • (2005) J Infect Dis , vol.192 , pp. 760-770
    • Green, N.M.1    Zhang, S.2    Porcella, S.F.3    Nagiec, M.J.4    Barbian, K.D.5
  • 39
    • 33646149163 scopus 로고    scopus 로고
    • Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics
    • Collyn F, Guy L, Marceau M, Simonet M, Roten CA: Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics. Bioinformatics 2006;22: 1072-1079.
    • (2006) Bioinformatics , vol.22 , pp. 1072-1079
    • Collyn, F.1    Guy, L.2    Marceau, M.3    Simonet, M.4    Roten, C.A.5
  • 40
    • 33846087685 scopus 로고    scopus 로고
    • Towards pathogenomics: A web-based resource for pathogenicity islands
    • Yoon SH, Park YK, Lee S, Choi D, Oh TK, et al: Towards pathogenomics: a web-based resource for pathogenicity islands. Nucleic Acids Res 2007;35: D395-D400.
    • (2007) Nucleic Acids Res , vol.35
    • Yoon, S.H.1    Park, Y.K.2    Lee, S.3    Choi, D.4    Oh, T.K.5


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