Chapter 11 : The Genome of V583: a Tool for Discovery

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The strain chosen for genome DNA sequencing was V583, the first vancomycin-resistant clinical isolate in the United States. The genome of strain V583 was sequenced by The Institute for Genome Research (TIGR) using the random sequencing method. The predicted open reading frames (ORFs) are organized by functional category in the online annotation database and are summarized in a table. The strain V583 contains four DNA molecules: the main 3,218,030-bp bacterial chromosome and three circular plasmids. The three plasmids are circular DNA molecules identified as Plasmid-1, Plasmid-2, and Plasmid-3, containing 66,320, 17,963, and 57,660 bp, respectively. TTGR has assembled a number of tools for the analysis of the genome and its comparison to other bacterial genomes through the Comprehensive Microbial Resource (CMR). A particularly useful tool is the CMR Gene Attribute Download resource, which allows a user to configure and download a database from the TTGR annotation based on all or part of the assigned role categories. The information contained within the genome of V583 greatly aids one's understanding of how this organism has adapted to be a versatile, opportunistic human pathogen. Comparative genomics and functional genome analysis will begin to unravel the role that regulatory elements play in physiologic responses to environmental stress and in the expression of potential virulence factors.

Citation: McShan W, Shankar N. 2002. The Genome of V583: a Tool for Discovery, p 409-415. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch11
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Figure 1

Percent G+C composition of the V583 genome. The average percent G+C composition (37.38%) along the length of the 3.2-Mb genome is shown. The region containing the large deviation from the average is the vancomycin resistance gene cluster positioned around 2.22 Mb. The average percent G+C analysis was calculated using the software package Artemis with a window size of 500 bases ( ).

Citation: McShan W, Shankar N. 2002. The Genome of V583: a Tool for Discovery, p 409-415. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch11
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1.Anonymous. 1999. National Nosocomial Infections Surveillance (NNIS) System report, data summary from January 1990–May 1999, issued June 1999. Am. J. Infect Control 27:520532.
2.Bolotin, A., P. Wincker, S. Mauger, O. Jaillon, K. Malarme, J. Weissenbach, S. D. Ehrlich, and A. Sorokin. 2001. The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res. 11:731753.
3.Bult, C, O. White, G. Olsen, L. Zhou, R. Fleischmann, G. Sutton, J. Blake, G. L. Fitz, R. Clayton, J. Gocayne, A. Kerlavage, B. Dougherty, J. Tomb, M. Adams, C. Reich, R. Overbeek, E. Kirkness, K. Weinstock, J. Merrick, A. Glodek, J. Scott, N. Geoghagen, and J. Venter. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:10581073.
4. Delcher, A. L.,, S. Kasif,, R. D. Fleischmann,, J. Peterson,, O. White,, and S. L. Salzberg. 1999. Alignment of whole genomes. Nucleic Acids Res. 27:23692376.
5. Ferretti, J. J.,, W. M. McShan,, D. Ajdic,, D. J. Savic,, G. Savic,, K. Lyon,, C. Primeaux,, S. Sezate,, A. N. Suvorov,, S. Kenton,, H. Lai,, S. Lin,, Y. Qian,, H. G. Jia, F. Z. Najar, Q. Ren, H. Zhu, L. Song, J. White, X. Yuan, S. W. Clifton, B. A. Roe, and R. McLaughlin. 2001. Complete genome sequence of an Ml strain of Streptococcus pyogenes. Proc. Natl. Acad. Sci. USA 98:46584663.
6. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton, E. F. Kirkness, A. R. Kerlavage, C. J. Bult, J.-F. Tomb, B. A. Dougherty, J. M. Merrick, K. McKenney, G. Sutton, W. FitzHugh, C. Fields, J. D. Gocayne, J. Scott, R. Shirley, L.-I. Liu, A. Glodek, J. M. Kelly, J. F. Weidman, C. A. Phillips, T. Spriggs, E. Hedblom, M. D. Cotton, T. R. Utterback, M. C. Hanna, D. T. Nguyen, D. M. Saudek, R. C. Brandon, L. D. Fine, J. L. Fritchman, J. L. Fuhrmann, N. S. M. Geoghagen, C. L. Gnehm, L. A. McDonald, K. V. Small, C. M. Fraser, H. O. Smith, and J. C. Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496512.
7.Fraser, C, S. Norris, G. Weinstock, O. White, G. Sutton, R. Dodson, M. Gwinn, E. Hickey, R. Clayton, K. Ketchum, E. Sodergren, J. Hardham, M. McLeod, S. Salzberg, J. Peterson, H. Khalak, D. Richardson, J. Howell, M. Chidambaram, T. Utterback, L. McDonald, P. Artiach, C. Bowman, M. Cotton, J. Venter, et al. 1998. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 281:375388.
8. Hofmann, K.,, P. Bucher,, L. Falquet,, and A. Bairoch. 1999. The PROSITE database, its status in 1999. Nucleic Acids Res. 27:215219.
9. Kunst, F.,, N. Ogasawara,, I. Moszer,, A. Albertini,, G. Alloni,, V. Azevedo,, M. Bertero,, P. Bessieres,, A. Bolotin,, S. Borchert,, R. Borriss,, L. Boursier,, A. Brans,, M. Braun,, S. Brignell,, S. Bron,, S. Brouillet,, C. Bruschi,, B. Caldwell,, V. Capuano,, N. Carter,, S. Choi,, J. Codani,, I. Connexion,, A. Danchin, et al. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature (London) 390:249256.
10. Peterson, J. D.,, L. A. Umayam,, T. Dickinson, E. K. Hickey, and O. White. 2001. The Comprehensive Microbial Resource. Nucleic Acids Res. 29:123125.
11. Rutherford, K.,, J. Parkhill,, J. Crook,, T. Horsnell,, P. Rice,, M. A. Rajandream,, and B. Barrell. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944945.
12. Sahm, D. E, J. Kissinger, M. S. Gilmore, P. R. Murray, R. Mulder, J. Solliday, and B. Clarke. 1989. In vitro susceptibility studies of vancomycin-resistant Enterococcus faecalis. Antimicrob. Agents Chemother. 33:15881591.
13. Tomb, J.,, O. White,, A. Kerlavage,, R. Clayton,, G. Sutton,, R. Fleischmann,, K. Ketchum,, H. Klenk,, S. Gill,, B. Dougherty,, K. Nelson,, J. Quackenbush,, L. Zhou,, E. Kirkness,, S. Peterson,, B. Loftus,, D. Richardson,, R. Dodson,, H. Khalak,, A. Glodek,, K. McKenney,, L. Fitzegerald,, N. Lee,, M. Adams,, J. Venter, et al. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature (London) 388:539547.


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Table 1

Functional distribution of putative genes identified on the genome

Citation: McShan W, Shankar N. 2002. The Genome of V583: a Tool for Discovery, p 409-415. In Gilmore M, Clewell D, Courvalin P, Dunny G, Murray B, Rice L (ed), The Enterococci. ASM Press, Washington, DC. doi: 10.1128/9781555817923.ch11

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