IS6110-Mediated Deletion Polymorphism in the Direct Repeat Region of Clinical Isolates of Mycobacterium tuberculosis

This study investigates the phenomenon of IS6110-mediated deletion polymorphism in the direct repeat (DR) region of the genome of Mycobacterium tuberculosis. Clinical isolates and their putative predecessors were compared using a combination of DR region restriction fragment length polymorphism, IS6110 DNA fingerprinting, spoligotyping, and DNA sequencing, which allowed the mapping of chromosome structure and deletion junctions. The data suggest that adjacently situated IS6110 elements mediate genome deletion. However, in contrast to previous reports, deletions appear to be mediated by inversely oriented IS6110 elements. This suggests that these events may occur via mechanisms other than RecA-mediated homologous recombination. The results underscore the important role of IS6110-associated deletion hypervariability in driving M. tuberculosis genome evolution.

[1]  N Rastogi,et al.  Spacer oligonucleotide typing of bacteria of the Mycobacterium tuberculosis complex: recommendations for standardised nomenclature. , 2001, The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease.

[2]  J. W. Dale.  Mobile genetic elements in mycobacteria. , 1995, The European respiratory journal. Supplement.

[3]  D. Botstein,et al.  Inversions and deletions of the Salmonella chromosome generated by the translocatable tetracycline resistance element Tn10. , 1979, Journal of molecular biology.

[4]  K. Lok,et al.  Identification of a Contaminating Mycobacterium tuberculosis Strain with a Transposition of an IS6110Insertion Element Resulting in an Altered Spoligotype , 2001, Journal of Clinical Microbiology.

[5]  K. Forbes,et al.  A Mycobacterium tuberculosis IS6110 preferential locus (ipl) for insertion into the genome , 1997, Journal of clinical microbiology.

[6]  R. Warren,et al.  Mapping of IS6110 flanking regions in clinical isolates of M.tuberculosis demonstrates genome plasticity. , 2000 .

[7]  P. Groenen,et al.  Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method , 1993, Molecular microbiology.

[8]  P. V. van Helden,et al.  Unexpectedly high strain diversity of Mycobacterium tuberculosis in a high-incidence community. , 1996, South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde.

[9]  J. Musser,et al.  Negligible genetic diversity of mycobacterium tuberculosis host immune system protein targets: evidence of limited selective pressure. , 2000, Genetics.

[10]  D. Young,et al.  Differentiation of Mycobacterium tuberculosis isolates by spoligotyping and IS6110 restriction fragment length polymorphism , 1997, Journal of clinical microbiology.

[11]  P. V. van Helden,et al.  DNA fingerprinting and molecular epidemiology of tuberculosis: Use and interpretation in an epidemic setting , 1999, Electrophoresis.

[12]  A. Albertini,et al.  On the formation of spontaneous deletions: The importance of short sequence homologies in the generation of large deletions , 1982, Cell.

[13]  W. Jacobs,et al.  An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis H37Rv, and comparison with Mycobacterium leprae. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[14]  P. V. van Helden,et al.  IS6110 Insertions in Mycobacterium tuberculosis: Predominantly into Coding Regions , 2001, Journal of Clinical Microbiology.

[15]  N Rastogi,et al.  Detection of a Previously Unamplified Spacer within the DR Locus of Mycobacterium tuberculosis: Epidemiological Implications , 2000, Journal of Clinical Microbiology.

[16]  T. Petes,et al.  Recombination between repeated genes in microorganisms. , 1988, Annual review of genetics.

[17]  T. Whittam,et al.  Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Dale Jw.  Mobile genetic elements in mycobacteria. , 1995 .

[19]  G. Mahairas,et al.  Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis , 1996, Journal of bacteriology.

[20]  D van Soolingen,et al.  Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains , 1991, Infection and immunity.

[21]  N. Morrison,et al.  IS6110 Transposition and Evolutionary Scenario of the Direct Repeat Locus in a Group of Closely Related Mycobacterium tuberculosis Strains , 1998, Journal of bacteriology.

[22]  G. Schoolnik,et al.  Comparative genomics of BCG vaccines by whole-genome DNA microarray. , 1999, Science.

[23]  B. Robertson,et al.  Comparison of Mycobacterium Tuberculosis Genomes Reveals Frequent Deletions in a 20 kb Variable Region in Clinical Isolates , 2000, Yeast.

[24]  P. Palittapongarnpim,et al.  IS6110-Mediated Deletions of Wild-Type Chromosomes of Mycobacterium tuberculosis , 1999, Journal of bacteriology.

[25]  T. Galitski,et al.  Rearrangements of the Bacterial Chromosome : Formation and Applications , 1999 .

[26]  S. Cole,et al.  Genomic Analysis Reveals Variation between Mycobacterium tuberculosis H37Rv and the AttenuatedM. tuberculosis H37Ra Strain , 1999, Infection and Immunity.

[27]  M. Donald Cave,et al.  Mapping of IS6110 Insertion Sites in Two Epidemic Strains of Mycobacterium tuberculosis , 2000, Journal of Clinical Microbiology.

[28]  B. Barrell,et al.  Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence , 1998, Nature.

[29]  D van Soolingen,et al.  Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology , 1997, Journal of clinical microbiology.

[30]  R M Warren,et al.  Disruption of coding regions by IS6110 insertion in Mycobacterium tuberculosis. , 1999, Tubercle and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease.

[31]  Winston A Hide,et al.  Molecular evolution of Mycobacterium tuberculosis: phylogenetic reconstruction of clonal expansion. , 2001, Tuberculosis.

[32]  T. Gingeras,et al.  Comparing genomes within the species Mycobacterium tuberculosis. , 2001, Genome research.

[33]  W. Heyer,et al.  Homologous recombination , 2005, Experientia.

[34]  Ruud Jansen,et al.  Genetic Variation and Evolutionary Origin of the Direct Repeat Locus of Mycobacterium tuberculosis Complex Bacteria , 2000, Journal of bacteriology.

[35]  A. Cataldi,et al.  A 12.7 kb fragment of the Mycobacterium tuberculosis genome is not present in Mycobacterium bovis. , 1999, Microbiology.

[36]  S. Cole,et al.  Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays , 1999, Molecular microbiology.

[37]  H. Nash.  Site-Specific Recombination : Integration , Excision , Resolution , and Inversion of Defined DNA Segments , 1999 .

[38]  J. Musser,et al.  Characterization of the phylogenetic distribution and chromosomal insertion sites of five IS6110 elements in Mycobacterium tuberculosis: non-random integration in the dnaA-dnaN region. , 1998, Tubercle and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease.

[39]  S. Salzberg,et al.  Whole-Genome Comparison of Mycobacterium tuberculosis Clinical and Laboratory Strains , 2002, Journal of bacteriology.

[40]  M. Behr,et al.  Microevolution of the Direct Repeat Region of Mycobacterium tuberculosis: Implications for Interpretation of Spoligotyping Data , 2002, Journal of Clinical Microbiology.

[41]  J. T. Crawford,et al.  Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology , 1993, Journal of clinical microbiology.

[42]  Barun Mathema,et al.  Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains. , 2002, Trends in microbiology.

[43]  D. Sherratt,et al.  Transposition and site-specific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements. , 1997, FEMS microbiology reviews.