1887

Abstract

To better understand the biology and the virulence determinants of the two major mycobacterial human pathogens and , their genome sequences have been determined recently. comparisons revealed that among the 1439 genes common to both and , 219 genes code for proteins that show no similarity with proteins from other organisms. Therefore, the latter ‘core’ genes could be specific for mycobacteria or even for the intracellular mycobacterial pathogens. To obtain more information as to whether these genes really were mycobacteria-specific, they were included in a focused macro-array, which also contained genes from previously defined regions of difference (RD) known to be absent from BCG relative to . Hybridization of DNA from 40 strains of the complex and comparison of these genes with the near-complete genome sequences from , and were undertaken to answer this question. The results showed that among the 219 conserved genes, very few were not present in all the strains tested. Some of these missing genes code for proteins of the ESAT-6 family, a group of highly immunogenic small proteins whose presence and number is variable among the genomically highly conserved members of the complex. Indeed, the results suggest that, with few exceptions, the ‘core’ genes conserved among H37Rv and are also highly conserved among other mycobacterial strains, which makes them interesting potential targets for developing new specific anti-mycobacterial drugs. In contrast, the genes from RD regions showed great variability among certain members of the complex, and some new specific deletions in , and seal isolates were identified and further characterized during this study. Together with the distribution of a particular 6 or 7 bp micro-deletion in the gene encoding the polyketide synthase , these results confirm and further extend the revised phylogenetic model for the complex recently presented.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.26662-0
2004-02-01
2019-08-25
Loading full text...

Full text loading...

/deliver/fulltext/micro/150/2/mic1500483.html?itemId=/content/journal/micro/10.1099/mic.0.26662-0&mimeType=html&fmt=ahah

References

  1. Banu, S., Honore, N., Saint-Joanis, B., Philpott, D., Prevost, M. C. & Cole, S. T. ( 2002; ). Are the PE-PGRS proteins of Mycobacterium tuberculosis variable surface antigens? Mol Microbiol 44, 9–19.[CrossRef]
    [Google Scholar]
  2. Behr, M. A., Wilson, M. A., Gill, W. P., Salamon, H., Schoolnik, G. K., Rane, S. & Small, P. M. ( 1999; ). Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284, 1520–1523.[CrossRef]
    [Google Scholar]
  3. Belanger, A. E., Besra, G. S., Ford, M. E., Mikusova, K., Belisle, J. T., Brennan, P. J. & Inamine, J. M. ( 1996; ). The embAB genes of Mycobacterium avium encode an arabinosyl transferase involved in cell wall arabinan biosynthesis that is the target for the antimycobacterial drug ethambutol. Proc Natl Acad Sci U S A 93, 11919–11924.[CrossRef]
    [Google Scholar]
  4. Brodin, P., Eiglmeier, K., Marmiesse, M., Billault, A., Garnier, T., Niemann, S., Cole, S. T. & Brosch, R. ( 2002; ). Bacterial artificial chromosome-based comparative genomic analysis identifies Mycobacterium microti as a natural ESAT-6 deletion mutant. Infect Immun 70, 5568–5578.[CrossRef]
    [Google Scholar]
  5. Brosch, R., Gordon, S. V., Billault, A., Garnier, T., Eiglmeier, K., Soravito, C., Barrell, B. G. & Cole, S. T. ( 1998; ). Use of a Mycobacterium tuberculosis H37Rv bacterial artificial chromosome library for genome mapping, sequencing, and comparative genomics. Infect Immun 66, 2221–2229.
    [Google Scholar]
  6. Brosch, R., Gordon, S. V., Pym, A., Eiglmeier, K., Garnier, T. & Cole, S. T. ( 2000; ). Comparative genomics of the mycobacteria. Int J Med Microbiol 290, 143–152.[CrossRef]
    [Google Scholar]
  7. Brosch, R., Pym, A. S., Gordon, S. V. & Cole, S. T. ( 2001; ). The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol 9, 452–458.[CrossRef]
    [Google Scholar]
  8. Brosch, R., Gordon, S. V., Marmiesse, M. & 12 other authors ( 2002; ). A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci U S A 99, 3684–3689.[CrossRef]
    [Google Scholar]
  9. Camus, J. C., Pryor, M. J., Medigue, C. & Cole, S. T. ( 2002; ). Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology 148, 2967–2973.
    [Google Scholar]
  10. Cole, S. T. ( 2002; ). Comparative mycobacterial genomics as a tool for drug target and antigen discovery. Eur Respir J Suppl 36, 78–86.
    [Google Scholar]
  11. Cole, S. T., Brosch, R., Parkhill, J. & 39 other authors ( 1998; ). Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537–544.[CrossRef]
    [Google Scholar]
  12. Cole, S. T., Eiglmeier, K., Parkhill, J. & 41 other authors ( 2001; ). Massive gene decay in the leprosy bacillus. Nature 409, 1007–1011.[CrossRef]
    [Google Scholar]
  13. Constant, P., Perez, E., Malaga, W., Laneelle, M. A., Saurel, O., Daffe, M. & Guilhot, C. ( 2002; ). Role of the pks15/1 gene in the biosynthesis of phenolglycolipids in the Mycobacterium tuberculosis complex. Evidence that all strains synthesize glycosylated p-hydroxybenzoic methyl esters and that strains devoid of phenolglycolipids harbor a frameshift mutation in the pks15/1 gene. J Biol Chem 277, 38148–38158.[CrossRef]
    [Google Scholar]
  14. Cousins, D. V., Bastida, R., Cataldi, A. & 16 other authors ( 2003; ). Tuberculosis in seals caused by a novel member of the Mycobacterium tuberculosis complex: Mycobacterium pinnipedii sp. nov. Int J Syst Evol Microbiol 53, 1305–1314.[CrossRef]
    [Google Scholar]
  15. Fleischmann, R. D., Alland, D., Eisen, J. A. & 23 other authors ( 2002; ). Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol 184, 5479–5490.[CrossRef]
    [Google Scholar]
  16. Fletcher, H. A., Donoghue, H. D., Taylor, G. M., van der Zanden, A. G. & Spigelman, M. ( 2003; ). Molecular analysis of Mycobacterium tuberculosis DNA from a family of 18th century Hungarians. Microbiology 149, 143–151.[CrossRef]
    [Google Scholar]
  17. Garnier, T., Eiglmeier, K., Camus, J. C. & 19 other authors ( 2003; ). The complete genome sequence of Mycobacterium bovis. Proc Natl Acad Sci U S A 100, 7877–7882.[CrossRef]
    [Google Scholar]
  18. Gey Van Pittius, N. C., Gamieldien, J., Hide, W., Brown, G. D., Siezen, R. J. & Beyers, A. D. ( 2001; ). The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol 2, RESEARCH0044.1-0044.18.
    [Google Scholar]
  19. Gordon, S. V., Brosch, R., Billault, A., Garnier, T., Eiglmeier, K. & Cole, S. T. ( 1999; ). Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays. Mol Microbiol 32, 643–655.[CrossRef]
    [Google Scholar]
  20. Gutacker, M. M., Smoot, J. C., Migliaccio, C. A. & 7 other authors ( 2002; ). Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms. Resolution of genetic relationships among closely related microbial strains. Genetics 162, 1533–1543.
    [Google Scholar]
  21. Ho, T. B., Robertson, B. D., Taylor, G. M., Shaw, R. J. & Young, D. B. ( 2000; ). Comparison of Mycobacterium tuberculosis genomes reveals frequent deletions in a 20 kb variable region in clinical isolates. Yeast 17, 272–282.
    [Google Scholar]
  22. Kato-Maeda, M., Rhee, J. T., Gingeras, T. R., Salamon, H., Drenkow, J., Smittipat, N. & Small, P. M. ( 2001; ). Comparing genomes within the species Mycobacterium tuberculosis. Genome Res 11, 547–554.[CrossRef]
    [Google Scholar]
  23. Lewis, K. N., Liao, R., Guinn, K. M., Hickey, M. J., Smith, S., Behr, M. A. & Sherman, D. R. ( 2003; ). Deletion of RD1 from Mycobacterium tuberculosis mimics bacille Calmette-Guerin attenuation. J Infect Dis 187, 117–123.[CrossRef]
    [Google Scholar]
  24. Mahairas, G. G., Sabo, P. J., Hickey, M. J., Singh, D. C. & Stover, C. K. ( 1996; ). Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis. J Bacteriol 178, 1274–1282.
    [Google Scholar]
  25. Mostowy, S., Cousins, D., Brinkman, J., Aranaz, A. & Behr, M. A. ( 2002; ). Genomic deletions suggest a phylogeny for the Mycobacterium tuberculosis complex. J Infect Dis 186, 74–80.[CrossRef]
    [Google Scholar]
  26. Niobe-Eyangoh, S. N., Kuaban, C., Sorlin, P., Cunin, P., Thonnon, J., Sola, C., Rastogi, N., Vincent, V. & Gutierrez, M. C. ( 2003; ). Genetic biodiversity of Mycobacterium tuberculosis complex strains from patients with pulmonary tuberculosis in Cameroon. J Clin Microbiol 41, 2547–2553.[CrossRef]
    [Google Scholar]
  27. Pallen, M. J. ( 2002; ). The ESAT-6/WXG100 superfamily – and a new Gram-positive secretion system? Trends Microbiol 10, 209–212.[CrossRef]
    [Google Scholar]
  28. Pym, A. S., Brodin, P., Brosch, R., Huerre, M. & Cole, S. T. ( 2002; ). Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovis BCG and Mycobacterium microti. Mol Microbiol 46, 709–717.[CrossRef]
    [Google Scholar]
  29. Pym, A. S., Brodin, P., Majlessi, L. & 7 other authors ( 2003; ). Recombinant BCG exporting ESAT-6 confers enhanced protection against tuberculosis. Nat Med 9, 533–539.[CrossRef]
    [Google Scholar]
  30. Rosenkrands, I., King, A., Weldingh, K., Moniatte, M., Moertz, E. & Andersen, P. ( 2000; ). Towards the proteome of Mycobacterium tuberculosis. Electrophoresis 21, 3740–3756.[CrossRef]
    [Google Scholar]
  31. Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M.-A. & Barrell, B. ( 2000; ). artemis: sequence visualisation and annotation. Bioinformatics 16, 944–945.[CrossRef]
    [Google Scholar]
  32. Skjot, R. L., Brock, I., Arend, S. M., Munk, M. E., Theisen, M., Ottenhoff, T. H. & Andersen, P. ( 2002; ). Epitope mapping of the immunodominant antigen TB10.4 and the two homologous proteins TB10.3 and TB12.9, which constitute a subfamily of the esat-6 gene family. Infect Immun 70, 5446–5453.[CrossRef]
    [Google Scholar]
  33. Soini, H., Pan, X., Amin, A., Graviss, E. A., Siddiqui, A. & Musser, J. M. ( 2000; ). Characterization of Mycobacterium tuberculosis isolates from patients in Houston, Texas, by spoligotyping. J Clin Microbiol 38, 669–676.
    [Google Scholar]
  34. Springer, B., Stockman, L., Teschner, K., Roberts, G. D. & Bottger, E. C. ( 1996; ). Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods. J Clin Microbiol 34, 296–303.
    [Google Scholar]
  35. 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]
  36. Supply, P., Warren, R. M., Banuls, A. L. & 7 other authors ( 2003; ). Linkage disequilibrium between minisatellite loci supports clonal evolution of Mycobacterium tuberculosis in a high tuberculosis incidence area. Mol Microbiol 47, 529–538.[CrossRef]
    [Google Scholar]
  37. Tekaia, F., Gordon, S. V., Garnier, T., Brosch, R., Barrell, B. G. & Cole, S. T. ( 1999; ). Analysis of the proteome of Mycobacterium tuberculosis in silico. Tuber Lung Dis 79, 329–342.[CrossRef]
    [Google Scholar]
  38. Telenti, A., Philipp, W. J., Sreevatsan, S., Bernasconi, C., Stockbauer, K. E., Wieles, B., Musser, J. M. & Jacobs, W. R., Jr ( 1997; ). The emb operon, a gene cluster of Mycobacterium tuberculosis involved in resistance to ethambutol. Nat Med 3, 567–570.[CrossRef]
    [Google Scholar]
  39. van Soolingen, D., Hoogenboezem, T., de Haas, P. E. & 9 other authors ( 1997; ). A novel pathogenic taxon of the Mycobacterium tuberculosis complex, Canetti: characterization of an exceptional isolate from Africa. Int J Syst Bacteriol 47, 1236–1245.[CrossRef]
    [Google Scholar]
  40. Zink, A. R., Sola, C., Reischl, U., Grabner, W., Rastogi, N., Wolf, H. & Nerlich, A. G. ( 2003; ). Characterization of Mycobacterium tuberculosis complex DNAs from Egyptian mummies by spoligotyping. J Clin Microbiol 41, 359–367.[CrossRef]
    [Google Scholar]
  41. Zumarraga, M. J., Bernardelli, A., Bastida, R. & 10 other authors ( 1999; ). Molecular characterization of mycobacteria isolated from seals. Microbiology 145, 2519–2526.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.26662-0
Loading
/content/journal/micro/10.1099/mic.0.26662-0
Loading

Data & Media loading...

vol. , part 2, pp. 483–496

The sequence polymorphism for phylogenetic group 3 strains, as defined by Sreevatsan (1997), shown in Fig. 4(d) should read AGC and not ACC, as shown in the new version of the figure available to download. [PDF]



PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error