Comparative analysis of six Mycobacterium tuberculosis complex genomes
Keywords:
Mycobacterium tuberculosis, genomics, tuberculosis
Abstract
Introduction. A growing number of sequenced genomes belonging to the Mycobacterium tuberculosis complex has enabled a comparison of strain traits and genomic constitution. These analyses may reveal mechanisms of evolution and genomic variation relevant to tuberculosis pathogenesis.
Objective. Multiple alignments were used to analyze the differences between six genomes of the M. tuberculosis complex and to locate regions of variation that may lead to improvements in species identification or in their treatment.
Materials and methods. The Mauve software package was used to perform a multiple alignment of 6 genomes belonging to the M. tuberculosis complex. Regions exclusive to each genome were annotated using the TB database.
Results. Percent similarity among the six genomes ranged between 96.1% and 97.8%. The annotation identified intergenic regions, regions associated with transposable elements of the PE-PGRS and PPE families, and regions associated with resistance against bacteriophage.
Conclusions. In spite of the high genetic similarity among the tuberculosis strains, genomic variations were elucidated that may be relevant to differences in behavior and virulence, as well as for improvement of strain diagnosis. Regions encoding membrane-associated proteins, possibly related with antigenic variation and immune response, are particularly interesting for studies aimed at seeking tuberculosis treatments.
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References
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38. Soto C, Menéndez M, Pérez E, Samper S, Gómez S, García M, et al. IS6110 mediates increased transcription of the phoP virulence gene in a multidrug-resistant clinical isolate responsible for tuberculosis outbreaks. J Clin Microbiol. 2004;42:212-9.
39. Cubillos-Ruíz A, Morales JP, Zambrano MM. Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments. BMC Res Notes. 2008;1:110.
2. World Health Organization. WHO report 2008. Global tuberculosis control. 2008. Fecha de consulta: 2 de octubre 2008. Disponible en: http://www.who.int/tb/publications/global_report/2008/en/
3. Garzón M, Angée D, Llerena C, Orjuela D, Victoria J. Vigilancia de la resistencia de Mycobacterium tuberculosis a los fármacos antituberculosos, Colombia 2004-2005. Biomédica. 2008;28:319-6.
4. Ministerio de la Protección Social, Organización Panamericana de la Salud. Situación de salud en Colombia. Indicadores básicos. Bogotá, D.C.: Ministerio de la Protección Social; 2006.
5. Tiruviluamala P, Reichman LB. Tuberculosis. Annu Rev Public Health. 2002;23:403-26.
6. Imaeda T. Deoxyribonucleic acid relatedness among selected strains of Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium bovis BCG, Mycobacterium micoti and Mycobacterium africanum. Int J Syst Bacteriol. 1985;35:147-50.
7. Fleischmann R, Alland D, Eisen J, Carpenter L, White O, Peterson J, et al. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol. 2002;184:5479-90.
8. Sreevatsan S, Pan X, Stockbauer K, Connell N, Kreiswirth B, Whittam T, et al. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci USA. 1997;94:9869-74.
9. Zheng H, Lu L, Wang B, Pu S, Zhang X, Zhu G, et al. Genetic basis of virulence attenuation revealed by comparative genomic analysis of Mycobacterium tuberculosis strain H37Ra versus H37Rv. PLoS One. 2008;3:e2375.
10. Deshayes C, Perrodou E, Euphrasie D, Frapy E, Poch O, Bifani P, et al. Detecting the molecular scars of evolution in the Mycobacterium tuberculosis complex by analyzing interrupted coding sequences. BMC Evol Biol. 2008;8:78.
11. Tang J, Moret BM. Scaling up accurate phylogenetic reconstruction from gene-order data. Bioinformatics. 2003;19(Suppl.1):i305-12.
12. De Groot A, Bosma A, Chinai N, Frost J, Jesdale B, Gonzalez M, et al. From genome to vaccine: in silico predictions, ex vivo verification. Vaccine. 2001;19:4385-95.
13. Mustafa A. Development of new vaccines and diagnostic reagents against tuberculosis. Mol Immunol. 2002:39:113-9.
14. Raman K, Yetura K, Chandra N. targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC Syst Biol. 2008;2:109.
15. Morris R, Drouin G. Similar ectopic gene conversion frequencies in the backbone genome of pathogenic and nonpathogenic Escherichia coli Strains. Genomics. 2008;92:168-72.
16. Azhikina T, Gvozdevsky N, Botvinnik A, Fushan A, Shemyakin I, Shemyakin V, et al. A genome-wide sequence-independent comparative analysis of insertion-deletion polymorphisms in multiple Mycobacterium tuberculosis strains. Res Microbiol. 2006;157:282-90.
17. Wang X, Galamba A, Warner D, Soetaert K, Merkel J, Kalai M, et al. IS1096-mediated DNA rearrangements play a key role in genome evolution of Mycobacterium smegmatis. Tuberculosis (Edinb). 2008:88:399-409.
18. Fremez R, Faraut T, Fichant T, Gouzy J, Quentin Y. Phylogenetic exploration of bacterial genomic rearrangements. Bioinformatics. 2007:23:72-4.
19. Vishnoi A, Roy R, Bhattacharya A. Comparative analysis of bacterial genomes: identification of divergent regions in mycobacterial strains using an anchor-based approach. Nucleic Acids Res. 2007;35:3654-67.
20. Bourque G, Pevzner PA. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 2002;12:26-36.
21. Moret BM, Wyman S, Bader DA, Warnow T, Yan M. A new implementation and detailed study of breakpoint analysis. Pac Symp Biocomput. 2001:583-94.
22. Darling A, Mau B, Blatter F, Perna N. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14:1394-403.
23. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004;5:113.
24. Domenech P, Barry C, Cole S. Mycobacterium tuberculosis in the post-genomic age. Curr Opin Microbiol. 2001;4:28-34.
25. Malik A, Godfrey-Faussett P. Effects of genetic variability of Mycobacterium tuberculosis strains on the presentation of disease. Lancet Infect Dis. 2005:5:174-83.
26. Field D, Feil E, Wilson G. Databases and software for the comparison of prokaryotic genomes. Microbiology. 2005;151:2125-32.
27. Gordon S, Brosch R, Billault A, Garnier T, Eiglmeier K, Cole S. Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays. Mol Microbiol. 1999;32:643-56.
28. Mahairas G. Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis. J Bacteriol. 1996;178:1274-82.
29. Garnier T, Eiglmeier K, Camus J, Medina N, Mansoor H, Pryor M, et al. The complete genome sequence of Mycobacterium bovis. Proc Natl Acad Sci USA. 2003;100:7877-82.
30. Ou H, Chen L, Lonnen J, Chaudhuri R, Thani A, Smith R, et al. A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Res. 2006;34:1e3.
31. Jang J, Becq J, Gicquel B, Deschavanne P, Neyrolles O. Horizontally acquired genomic islands in the tubercle bacilli. Trends Microbiol. 2008;16:303-8.
32. Delogu G, Pusceddu C, Bua A, Fadda G, Brennan M, Zanetti S. Rv1818c-encoded PE-PGRS protein of Mycobacterium tuberculosis is surface exposed and influences bacterial cell structure. Mol Microbiol. 2004;52:725-33.
33. Banu S, Honore N, Saint-Joanis B, Philpott D, Prevost MC. Are the PE-PGRS proteins of Mycobacterium tuberculosis variable surface antigens? Mol Microbiol. 2002;44:9-19.
34. Brouns S, Jore M. Lundgren M, Westra E, Slijkhuis R, Snijders A, et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008;321:960-3.
35. Barrangou R, Fremaux, C, Deveau H, Richards M, Boyaval P, Moineau S, et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007;315:1709-12.
36. Sorek R, Kunin V, Hugenholtz P. CRISPR- a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol. 2008;6:181-6.
37. Darling A, Miklos I, Ragan M. Dynamics of genome rearrangement in bacterial populations. PLoS Genet. 2008;4:e1000128.
38. Soto C, Menéndez M, Pérez E, Samper S, Gómez S, García M, et al. IS6110 mediates increased transcription of the phoP virulence gene in a multidrug-resistant clinical isolate responsible for tuberculosis outbreaks. J Clin Microbiol. 2004;42:212-9.
39. Cubillos-Ruíz A, Morales JP, Zambrano MM. Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments. BMC Res Notes. 2008;1:110.
How to Cite
1.
Chaves D, Sandoval A, Rodríguez L, García JC, Restrepo S, Zambrano MM. Comparative analysis of six Mycobacterium tuberculosis complex genomes. biomedica [Internet]. 2010 Mar. 1 [cited 2024 May 18];30(1):23-31. Available from: https://revistabiomedica.org/index.php/biomedica/article/view/149
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