Variable-number tandem repeat 3690 polymorphism in Indian clinical isolates of and its influence on transcription Free

Abstract

Variable-number tandem repeat (VNTRs) occur throughout the chromosome of . Although these polymorphic VNTRs, also known as mycobacterial interspersed repetitive units (MIRUs), have proved to be useful tools in molecular epidemiology, their biological significance is less well understood. This study investigated the polymorphism of the VNTR 3690 locus located in the intergenic region between 3304 and 3303c (encoding the and genes, respectively) and its possible function in the regulation of gene expression. The copy number of VNTR 3690 was found to vary among Indian clinical isolates of (one to twelve copies), H37Rv TMC102 (four copies), H37Ra (two to four copies), BCG (one copy). The expression of as measured by quantitative RT-PCR was 12-fold higher in H37Rv than in BCG. Using a GFP reporter system in which the 5′-flanking region of was fused to the gene, the effect of VNTRs on gene expression was measured in an BCG host background by real-time PCR. Compared with one VNTR repeat, a 12.5-fold upregulation of GFP expression was found with a flanking region containing four VNTR 3690 repeats, indicating that there is a good correlation between VNTR copy number and transcription of .

Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.002550-0
2009-06-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/jmm/58/6/798.html?itemId=/content/journal/jmm/10.1099/jmm.0.002550-0&mimeType=html&fmt=ahah

References

  1. Akhtar P., Srivastava S., Srivastava A., Srivastava M., Srivastava B. S., Srivastava R. 2006; Rv3303c of Mycobacterium tuberculosis protects tubercle bacilli against oxidative stress in vivo and contributes to virulence in mice. Microbes Infect 8:2855–2862 [CrossRef]
    [Google Scholar]
  2. Amano S., Tatsumi K., Tanabe N., Kasahara Y., Kurosu K., Takiguchi Y., Kasuya Y., Kimura S., Kuriyama T. 2004; Polymorphism of the promoter region of prostacyclin synthase gene in chronic thromboembolic pulmonary hypertension. Respirology 9:184–189 [CrossRef]
    [Google Scholar]
  3. Argyrou A., Vetting M. W., Blanchard J. S. 2004; Characterization of a new member of the flavoprotein disulfide reductase family of enzymes from Mycobacterium tuberculosis . J Biol Chem 279:52694–52702 [CrossRef]
    [Google Scholar]
  4. Bifani P. J., Plikaytis B. B., Kapur V., Stockbauer K., Pan X., Lutfey M. L., Moghazeh S. L., Eisner W., Daniel T. M. other authors 1996; Origin and interstate spread of a New York City multidrug-resistant Mycobacterium tuberculosis clone family. JAMA 275:452–457 [CrossRef]
    [Google Scholar]
  5. Bifani P. J., Mathema B., Liu Z., Moghazeh S. L., Shopsin B., Tempalski B., Driscol J., Frothingham R., Musser J. M. other authors 1999; Identification of a W variant outbreak of Mycobacterium tuberculosis via population-based molecular epidemiology. JAMA 282:2321–2327 [CrossRef]
    [Google Scholar]
  6. Bifani P., Moghazeh S., Shopsin B., Driscoll J., Ravikovitch A., Kreiswirth B. N. 2000; Molecular characterization of Mycobacterium tuberculosis H37Rv/Ra variants: distinguishing the mycobacterial laboratory strain. J Clin Microbiol 38:3200–3204
    [Google Scholar]
  7. Cole S. T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S. V., Eiglmeier K., Gas S. other authors 1998; Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537–544 [CrossRef]
    [Google Scholar]
  8. Deb D. K., Dahiya P., Srivastava K. K., Srivastava R., Srivastava B. S. 2002; Selective identification of new therapeutic targets of Mycobacterium tuberculosis by IVIAT approach. Tuberculosis (Edinb 82:175–182 [CrossRef]
    [Google Scholar]
  9. Eerligh P., Roep B. O., Giphart M. J., Koeleman B. P. C. 2004; Insulin-like growth factor 1 promoter polymorphism influences insulin gene variable number of tandem repeat-associated risk for juvenile onset type 1 diabetes. Tissue Antigens 63:568–571 [CrossRef]
    [Google Scholar]
  10. Fabre M., Koeck J. L., Le Fleche P., Simon F., Herve V., Vergnaud G., Pourcel C. 2004; High genetic diversity revealed by variable-number tandem repeat genotyping and analysis of hsp65 gene polymorphism in a large collection of “ Mycobacterium canettii ” strains indicates that the Mycobacterium tuberculosis complex is a recently emerged clone of “ M. canettii ”. J Clin Microbiol 42:3248–3255 [CrossRef]
    [Google Scholar]
  11. Frothingham R., Meeker-O'Connell W. A. 1998; Genetic diversity in the Mycobacterium tuberculosis complex based on variable number of tandem DNA repeats. Microbiology 144:1189–1196 [CrossRef]
    [Google Scholar]
  12. Gutacker M. M., Mathema B., Soini H., Shashkine E., Kreiswirth B. N., Graviss E. A., Musser J. M. 2006; Single-nucleotide polymorphism-based population genetic analysis of Mycobacterium tuberculosis strains from 4 geographical sites. J Infect Dis 193:121–128 [CrossRef]
    [Google Scholar]
  13. Jeffreys A. J., Wilson V., Thein S. L. 1985; Hypervariable minisatellite regions in human DNA. Nature 314:67–73 [CrossRef]
    [Google Scholar]
  14. Keim P., Price L. B., Klevytska A. M., Smith K. L., Schupp J. M., Okinaka R., Jackson P. J., Hugh-Jones M. E. 2000; Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis . J Bacteriol 182:2928–2936 [CrossRef]
    [Google Scholar]
  15. Le Flèche P., Fabre M., Denoeud F., Koeck J., Vergnaud G. 2002; High resolution, on-line identification of strains from the Mycobacterium tuberculosis complex based on tandem repeat typing. BMC Microbiol 2:37–49 [CrossRef]
    [Google Scholar]
  16. Livak K. J., Schmittgen T. D. 2001; Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCt method. Methods 25:402–408 [CrossRef]
    [Google Scholar]
  17. Saxena A., Srivasrtava V., Srivastava R., Srivastava B. S. 2008; Identification of genes of Mycobacterium tuberculosis upregulated during anaerobic persistence by fluorescence and kanamycin resistance selection. Tuberculosis (Edinb) 88:518–525 [CrossRef]
    [Google Scholar]
  18. Skuce R. A., McCorry T. P., McCarroll J. F., Roring S. M. M., Scott A. N., Brittain D., Hughes S. L., Hewinson R. G., Neill S. D. 2002; Discrimination of Mycobacterium tuberculosis complex bacteria using novel VNTR-PCR targets. Microbiology 148:519–528
    [Google Scholar]
  19. Smittipat N., Billamas P., Palittapongarnpim M., Thong-on A., Temu M. M., Thanakijcharoen P., Karnkawinpong O., Palittapongarnpim P. 2005; Polymorphism of variable number tandem repeats at multiple loci in Mycobacterium tuberculosis . J Clin Microbiol 43:5034–5043 [CrossRef]
    [Google Scholar]
  20. Spire-Vayron de la Moureyre C., Debuysère H., Fazio F., Sergent E., Bernard C., Sabbagh N., Marez D., Lo Guidice J. M., D'halluin J. C., Broly F. 1999; Characterization of a variable number tandem repeat region in the thiopurine S -methyltransferase gene promoter. Pharmacogenetics 9:189–198
    [Google Scholar]
  21. Sreevatsan S., Pan X., Stockbauer K. E., Connell N. D., Kreiswirth B. N., Whittam T. S., Musser J. M. 1997; Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci U S A 94:9869–9874 [CrossRef]
    [Google Scholar]
  22. Srivastava V., Rouanet C., Srivastava R., Ramalingam B., Locht C., Srivastava B. S. 2007; Macrophage-specific M. tuberculosis genes identified by green fluorescent protein and kanamycin resistance selection. Microbiology 153:659–666 [CrossRef]
    [Google Scholar]
  23. Srivastava V., Jain A., Srivastava B. S., Srivastava R. 2008; Selection of genes of Mycobacterium tuberculosis upregulated during residence in lungs of infected mice. Tuberculosis (Edinb 88:171–177 [CrossRef]
    [Google Scholar]
  24. Steenken W. Jr, Gardner L. U. 1946; History of H37 strain of tubercle bacillus. Am Rev Tuberc 54:62–66
    [Google Scholar]
  25. Supply P., Magdalena J., Himpens S., Locht C. 1997; Identification of novel intergenic repetitive units in a mycobacterial two-component system operon. Mol Microbiol 26:991–1003 [CrossRef]
    [Google Scholar]
  26. Supply P., Mazars E., Lesjean S., Vincent V., Gicquel B., Locht C. 2000; Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome. Mol Microbiol 36:762–771
    [Google Scholar]
  27. Supply P., Lesjean S., Savine E., Kremer L., Van Soolingen D., Locht C. 2001; Automated high-throughput genotyping for study of global epidemiology of Mycobacterium tuberculosis based on mycobacterial interspersed repetitive units. J Clin Microbiol 39:3563–3571 [CrossRef]
    [Google Scholar]
  28. Supply P., Allix C., Lesjean S., Cardoso-Oelemann M., Rüsch-Gerdes S., Willery E., Savine E., de Haas P., van Deutekom H. other authors 2006; Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis . J Clin Microbiol 44:4498–4510 [CrossRef]
    [Google Scholar]
  29. Valway S. E., Sanchez M. P., Shinnick T. F., Orme I., Agerton T., Hoy D., Jones J. S., Westmoreland H., Onorato I. M. 1998; An outbreak involving extensive transmission of a virulent strain of Mycobacterium tuberculosis . N Engl J Med 338:633–639 [CrossRef]
    [Google Scholar]
  30. Van Belkum A., Scherer S., van Leeuwen W., Willemse D., van Alphen L., Verbrugh H. 1997; Variable number of tandem repeats in clinical strains of Haemophilus influenzae . Infect Immun 65:5017–5027
    [Google Scholar]
  31. Van Belkum A., Scherer S., Van Alphen L., Verbrugh H. 1998; Short-sequence repeats in prokaryotic genomes. Microbiol Mol Biol Rev 62:275–293
    [Google Scholar]
  32. Wang G., Maier R. J. 2004; An NADPH quinone reductase of Helicobacter pylori plays an important role in oxidative stress resistance and host colonization. Infect Immun 72:1391–1396 [CrossRef]
    [Google Scholar]
  33. Zheng H., Lu L., Wang B., Pu S., Zhang X., Zhu G., Shi W., Zhang L., Wang H. other authors 2008; Genetic basis of virulence attenuation revealed by comparative genomic analysis of Mycobacterium tuberculosis strain H37Ra versus H37Rv. PLoS One 3:e2375 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.002550-0
Loading
/content/journal/jmm/10.1099/jmm.0.002550-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed