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Volumn 9, Issue 6, 1999, Pages 700-703

Contribution of genomics to bacterial pathogenesis

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENETICS; BACTERIAL INFECTION; NONHUMAN; PATHOGENESIS; PRIORITY JOURNAL; SHORT SURVEY;

EID: 0032762029     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(99)00021-0     Document Type: Review
Times cited : (17)

References (52)
  • 1
    • 85031636166 scopus 로고    scopus 로고
    • Genomes online database (GOLD) The best maintained and most comprehensive internet database of genome projects and related information
    • Genomes online database (GOLD) http://geta.life.uiuc.edu/~nikos/genomes.html The best maintained and most comprehensive internet database of genome projects and related information.
  • 2
    • 0032947528 scopus 로고    scopus 로고
    • Genomes and proteomes: Towards a multidimensional view of biology
    • Williams K.L. Genomes and proteomes: towards a multidimensional view of biology. Electrophoresis. 20:1999;678-688.
    • (1999) Electrophoresis , vol.20 , pp. 678-688
    • Williams, K.L.1
  • 4
    • 0033552961 scopus 로고    scopus 로고
    • Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori
    • Landmark publication of the first duplicate genome sequence from a single (pathogenic) species. Heralds the beginning of the true age of comparative genomics. Analysis of the complete genome sequence of two strains from different continents revealed 206 unshared coding regions, or about 7% coding-region divergence. Almost half of these genes are clustered in a single hypervariable region termed a 'strain-specific plasticity zone'. Overall genome organisation differs by 10 inverted or transposed regions. This study has successfully detected a wide range of strain-specific sequences and has led to a better understanding of the gene pool of the species.
    • Alm R.A., Ling L.S., Moir D.T., King B.L., Brown E.D., Doig P.C., Smith D.R., Noonan B., Guild B.C., deJonge B.L.et al. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature. 397:1999;176-180. Landmark publication of the first duplicate genome sequence from a single (pathogenic) species. Heralds the beginning of the true age of comparative genomics. Analysis of the complete genome sequence of two strains from different continents revealed 206 unshared coding regions, or about 7% coding-region divergence. Almost half of these genes are clustered in a single hypervariable region termed a 'strain-specific plasticity zone'. Overall genome organisation differs by 10 inverted or transposed regions. This study has successfully detected a wide range of strain-specific sequences and has led to a better understanding of the gene pool of the species.
    • (1999) Nature , vol.397 , pp. 176-180
    • Alm, R.A.1    Ling, L.S.2    Moir, D.T.3    King, B.L.4    Brown, E.D.5    Doig, P.C.6    Smith, D.R.7    Noonan, B.8    Guild, B.C.9    Dejonge, B.L.10
  • 6
    • 0032401709 scopus 로고    scopus 로고
    • Implications of sequencing bacterial genomes for pathogenesis and vaccine development
    • Saunders N.J., Moxon E.R. Implications of sequencing bacterial genomes for pathogenesis and vaccine development. Curr Opin Biotechnol. 9:1998;618-623.
    • (1998) Curr Opin Biotechnol , vol.9 , pp. 618-623
    • Saunders, N.J.1    Moxon, E.R.2
  • 9
    • 0032491377 scopus 로고    scopus 로고
    • Predicting function: From genes to genomes and back
    • Detailed review of how function can be ascribed to novel sequences through homology. The computational process of ascribing putative function to protein sequences is benefiting immensely from the sequencing of microbial genomes. This extensive review offers perhaps the first summary of how our knowledge of 'function' has improved since the first microbial genome sequence. This paper emphasises the need to begin examining protein function in light of higher order processes, such as regulation of gene expression, metabolic pathways and signalling cascades.
    • Bork P., Dandekar T., Diaz-Lazcoz Y., Eisenhaber F., Huynen M., Yuan Y. Predicting function: from genes to genomes and back. J Mol Biol. 283:1998;707-725. Detailed review of how function can be ascribed to novel sequences through homology. The computational process of ascribing putative function to protein sequences is benefiting immensely from the sequencing of microbial genomes. This extensive review offers perhaps the first summary of how our knowledge of 'function' has improved since the first microbial genome sequence. This paper emphasises the need to begin examining protein function in light of higher order processes, such as regulation of gene expression, metabolic pathways and signalling cascades.
    • (1998) J Mol Biol , vol.283 , pp. 707-725
    • Bork, P.1    Dandekar, T.2    Diaz-Lazcoz, Y.3    Eisenhaber, F.4    Huynen, M.5    Yuan, Y.6
  • 12
    • 0032502899 scopus 로고    scopus 로고
    • Differential genome analysis applied to the species-specific features of Helicobacter pylori
    • Huynen M., Dandekar T., Bork P. Differential genome analysis applied to the species-specific features of Helicobacter pylori. FEBS Lett. 426:1998;1-5.
    • (1998) FEBS Lett , vol.426 , pp. 1-5
    • Huynen, M.1    Dandekar, T.2    Bork, P.3
  • 13
    • 0032509179 scopus 로고    scopus 로고
    • Comparison of the complete protein sets of worm and yeast: Orthology and divergence
    • Outstanding example of the ability of in silico methods to help find genes responsible for certain phenotypes using the 'species-filter' approach. This comprehensive comparison of the first two eukaryotic genomes sequenced, S. cerevisiae and the latter, identified genes unique to the latter that may prove to be restricted to metazoans and play a role in multicellularity.
    • Chervitz S.A., Aravind L., Sherlock G., Ball C.A., Koonin E.V., Dwight S.S., Harris M.A., Dolinski K., Mohr S., Smith T.et al. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science. 282:1998;2022-2028. Outstanding example of the ability of in silico methods to help find genes responsible for certain phenotypes using the 'species-filter' approach. This comprehensive comparison of the first two eukaryotic genomes sequenced, S. cerevisiae and the latter, identified genes unique to the latter that may prove to be restricted to metazoans and play a role in multicellularity.
    • (1998) Science , vol.282 , pp. 2022-2028
    • Chervitz, S.A.1    Aravind, L.2    Sherlock, G.3    Ball, C.A.4    Koonin, E.V.5    Dwight, S.S.6    Harris, M.A.7    Dolinski, K.8    Mohr, S.9    Smith, T.10
  • 14
    • 0032189860 scopus 로고    scopus 로고
    • Concordance analysis of microbial genomes
    • A rare example showing the importance of combining in silico and experimental approaches to hypothesis testing. Using the 'species-filter' approach in combination with experimental approaches the authors search for drug targets - essential genes restricted to pathogenic prokaryotes. Useful software for comparing shared and unshared genes between complete genomes available on the internet is described.
    • Bruccoleri R.E., Dougherty T.J., Davison D.B. Concordance analysis of microbial genomes. Nucleic Acids Res. 26:1998;4482-4486. A rare example showing the importance of combining in silico and experimental approaches to hypothesis testing. Using the 'species-filter' approach in combination with experimental approaches the authors search for drug targets - essential genes restricted to pathogenic prokaryotes. Useful software for comparing shared and unshared genes between complete genomes available on the internet is described.
    • (1998) Nucleic Acids Res , vol.26 , pp. 4482-4486
    • Bruccoleri, R.E.1    Dougherty, T.J.2    Davison, D.B.3
  • 15
    • 0032173619 scopus 로고    scopus 로고
    • New antibiotic discovery, novel screens, novel targets and impact of microbial genomics
    • Allsop A.E. New antibiotic discovery, novel screens, novel targets and impact of microbial genomics. Curr Opin Microbiol. 1:1998;530-534.
    • (1998) Curr Opin Microbiol , vol.1 , pp. 530-534
    • Allsop, A.E.1
  • 16
    • 0032403024 scopus 로고    scopus 로고
    • Bacterial genome sequencing and drug discovery
    • Allsop A.E. Bacterial genome sequencing and drug discovery. Curr Opin Biotechnol. 9:1998;637-642.
    • (1998) Curr Opin Biotechnol , vol.9 , pp. 637-642
    • Allsop, A.E.1
  • 20
    • 0032408407 scopus 로고    scopus 로고
    • The Mycobacterium tuberculosis genomic sequence: Anatomy of a master adaptor
    • Bishai W. The Mycobacterium tuberculosis genomic sequence: anatomy of a master adaptor. Trends Microbiol. 6:1998;464-465.
    • (1998) Trends Microbiol , vol.6 , pp. 464-465
    • Bishai, W.1
  • 21
    • 0032561243 scopus 로고    scopus 로고
    • Databases in genomic research
    • Gelbart W.M. Databases in genomic research. Science. 282:1998;659-661.
    • (1998) Science , vol.282 , pp. 659-661
    • Gelbart, W.M.1
  • 23
    • 85031628147 scopus 로고    scopus 로고
    • What is there (WIT)? Interactive metabolic reconstruction on the web
    • What is there (WIT)? Interactive metabolic reconstruction on the web. http://wit.mcs.anl.gov/WIT2/.
  • 24
    • 0033515250 scopus 로고    scopus 로고
    • Building working cells 'in silico'
    • The concept of 'in silico' cells is at present an underdeveloped yet exciting possibility that holds the promise of allowing researchers to combine all aspects of cell biology into a single system that 'lives' within a computer. From genes, to metabolic pathways, to information on stochiometric ratios of protein products within a cell - once sufficient information has been collected and entered into these model cells, this will be a technology to watch in the future (see [25]).
    • Normile D. Building working cells 'in silico'. Science. 284:1999;80-81. The concept of 'in silico' cells is at present an underdeveloped yet exciting possibility that holds the promise of allowing researchers to combine all aspects of cell biology into a single system that 'lives' within a computer. From genes, to metabolic pathways, to information on stochiometric ratios of protein products within a cell - once sufficient information has been collected and entered into these model cells, this will be a technology to watch in the future (see [25]).
    • (1999) Science , vol.284 , pp. 80-81
    • Normile, D.1
  • 25
    • 0030739712 scopus 로고    scopus 로고
    • A general computational framework for modeling cellular structure and function
    • Schaff J., Fink C.C., Slepchenko B., Carson J.H., Loew L.M. A general computational framework for modeling cellular structure and function. Biophys J. 73:1997;1135-1146.
    • (1997) Biophys J , vol.73 , pp. 1135-1146
    • Schaff, J.1    Fink, C.C.2    Slepchenko, B.3    Carson, J.H.4    Loew, L.M.5
  • 26
    • 84984932472 scopus 로고    scopus 로고
    • Exploring the new world of the genome with DNA microarrays
    • Review of the subject in a special issue devoted to advances in microarray technology.
    • Brown P.O., Botstein D. Exploring the new world of the genome with DNA microarrays. Nat Genet. 21:1999;33-37. Review of the subject in a special issue devoted to advances in microarray technology.
    • (1999) Nat Genet , vol.21 , pp. 33-37
    • Brown, P.O.1    Botstein, D.2
  • 29
    • 0033614336 scopus 로고    scopus 로고
    • Bacterial population genetics, evolution and epidemiology
    • Spratt B.G., Maiden M.C. Bacterial population genetics, evolution and epidemiology. Philos Trans R Soc Lond Biol. 354:1999;701-710.
    • (1999) Philos Trans R Soc Lond Biol , vol.354 , pp. 701-710
    • Spratt, B.G.1    Maiden, M.C.2
  • 30
    • 0033612136 scopus 로고    scopus 로고
    • Comparative genomics of BCG vaccines by whole-genome DNA microarray
    • A premier example of how microarray technology can be used to survey for heritable genetic variation that may provide the genetic basis for important phenotypes. In this case, genetic variation in tuberculosis vaccine strains that may explain observed temporal and geographic differences in vaccine effectiveness.
    • Behr M.A., Wilson M.A., Gill W.P., Salamon H., Schoolnik G.K., Rane S., Small P.M. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science. 284:1999;1520-1523. A premier example of how microarray technology can be used to survey for heritable genetic variation that may provide the genetic basis for important phenotypes. In this case, genetic variation in tuberculosis vaccine strains that may explain observed temporal and geographic differences in vaccine effectiveness.
    • (1999) Science , vol.284 , pp. 1520-1523
    • Behr, M.A.1    Wilson, M.A.2    Gill, W.P.3    Salamon, H.4    Schoolnik, G.K.5    Rane, S.6    Small, P.M.7
  • 31
    • 0033134861 scopus 로고    scopus 로고
    • Pathoadaptive mutations: Gene loss and variation in bacterial pathogens
    • Sokurenko E.V., Hasty D.L., Dykhuizen D.E. Pathoadaptive mutations: gene loss and variation in bacterial pathogens. Trends Microbiol. 7:1999;191-195.
    • (1999) Trends Microbiol , vol.7 , pp. 191-195
    • Sokurenko, E.V.1    Hasty, D.L.2    Dykhuizen, D.E.3
  • 33
    • 0032899321 scopus 로고    scopus 로고
    • New insertion sequences and a novel repeated sequence in the genome of Mycobacterium tuberculosis H37Rv
    • Gordon S.V., Heym B., Parkhill J., Barrell B., Cole S.T. New insertion sequences and a novel repeated sequence in the genome of Mycobacterium tuberculosis H37Rv. Microbiology. 145:1999;881-892.
    • (1999) Microbiology , vol.145 , pp. 881-892
    • Gordon, S.V.1    Heym, B.2    Parkhill, J.3    Barrell, B.4    Cole, S.T.5
  • 34
    • 0032932427 scopus 로고    scopus 로고
    • Accessing genomic information: Alternatives to PCR
    • Isaksson A., Landegren U. Accessing genomic information: alternatives to PCR. Curr Opin Biotechnol. 10:1999;11-15.
    • (1999) Curr Opin Biotechnol , vol.10 , pp. 11-15
    • Isaksson, A.1    Landegren, U.2
  • 35
    • 0033591094 scopus 로고    scopus 로고
    • Is it time to uproot the tree of life?
    • See papers [36-41]. Excellent synopsis of the current debate over how much horizontal gene transfer contributes to the evolution of bacterial genomes.
    • Pennisi E. Is it time to uproot the tree of life? Science. 284:1999;1305-1307. See papers [36-41]. Excellent synopsis of the current debate over how much horizontal gene transfer contributes to the evolution of bacterial genomes.
    • (1999) Science , vol.284 , pp. 1305-1307
    • Pennisi, E.1
  • 36
    • 0032900532 scopus 로고    scopus 로고
    • Genome phylogeny based on gene content
    • Snel B., Bork P., Huynen M.A. Genome phylogeny based on gene content. Nat Genet. 21:1999;108-110.
    • (1999) Nat Genet , vol.21 , pp. 108-110
    • Snel, B.1    Bork, P.2    Huynen, M.A.3
  • 37
    • 0033043696 scopus 로고    scopus 로고
    • Is there a phylogenetic signal in prokaryote proteins?
    • Teichmann S.A., Mitchison G. Is there a phylogenetic signal in prokaryote proteins? J Mol Evol. 49:1999;98-107.
    • (1999) J Mol Evol , vol.49 , pp. 98-107
    • Teichmann, S.A.1    Mitchison, G.2
  • 38
    • 0033605625 scopus 로고    scopus 로고
    • Mix and match in the tree of life
    • Lake J.A., Jain R., Rivera M.C. Mix and match in the tree of life. Science. 283:1999;2027-2028.
    • (1999) Science , vol.283 , pp. 2027-2028
    • Lake, J.A.1    Jain, R.2    Rivera, M.C.3
  • 39
    • 0342378138 scopus 로고    scopus 로고
    • The record of horizontal gene transfer in Salmonella
    • Baumler A.J. The record of horizontal gene transfer in Salmonella. Trends Microbiol. 5:1997;318-322.
    • (1997) Trends Microbiol , vol.5 , pp. 318-322
    • Baumler, A.J.1
  • 41
    • 0033616714 scopus 로고    scopus 로고
    • Horizontal gene transfer among genomes: The complexity hypothesis
    • Jain R., Rivera M.C., Lake J.A. Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA. 96:1999;3801-3806.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 3801-3806
    • Jain, R.1    Rivera, M.C.2    Lake, J.A.3
  • 42
    • 0030870440 scopus 로고    scopus 로고
    • How Salmonella became a pathogen
    • Groisman E.A., Ochman H. How Salmonella became a pathogen. Trends Microbiol. 5:1997;343-349.
    • (1997) Trends Microbiol , vol.5 , pp. 343-349
    • Groisman, E.A.1    Ochman, H.2
  • 43
    • 0033546021 scopus 로고    scopus 로고
    • NIH urged to fund centers to merge computing and biology
    • Evidence that future funding will place emphasis on the establishment of 'centers of excellence' dedicated to projects that merge computational and empirical approaches. As so many genome projects now focus on pathogenic species, this initiative will hopefully have an important impact on the study of pathogenesis.
    • Malakoff D. NIH urged to fund centers to merge computing and biology. Science. 284:1999;1742. Evidence that future funding will place emphasis on the establishment of 'centers of excellence' dedicated to projects that merge computational and empirical approaches. As so many genome projects now focus on pathogenic species, this initiative will hopefully have an important impact on the study of pathogenesis.
    • (1999) Science , vol.284 , pp. 1742
    • Malakoff, D.1
  • 46
    • 85031632010 scopus 로고    scopus 로고
    • The Sanger Center
    • The Sanger Center. http://www.sanger.ac.uk.
  • 50
    • 0032173615 scopus 로고    scopus 로고
    • Comparative mycobacterial genomics
    • Cole S.T. Comparative mycobacterial genomics. Curr Opin Microbiol. 1:1998;567-571.
    • (1998) Curr Opin Microbiol , vol.1 , pp. 567-571
    • Cole, S.T.1
  • 51
    • 85031618883 scopus 로고    scopus 로고
    • The Institute for Genome Research (TIGR)
    • The Institute for Genome Research (TIGR). http://www.tigr.org.
  • 52
    • 85031632347 scopus 로고    scopus 로고
    • Advanced Center for Genome Technology (ACGT)
    • Advanced Center for Genome Technology (ACGT). http://dna1.chem.ou.edu/.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.