Characterization of a major polymorphic tandem repeat in Mycobacterium tuberculosis and its potential use in the epidemiology of Mycobacterium kansasii and Mycobacterium gordonae

Abstract

In this study, the occurrence of repeated DNA sequences in the chromosome of Repetitive DNA sequences have also been found in mycobacteria. The insertion elements IS900 from Mycobacterium paratuberculosis (4, 12), IS901 from Mycobacterium avium (19), IS1096 from Mycobacterium smegmatis (2), IS1081 from Mycobacterium bovis, and the IS3 family of insertion elements present in the species of the Mycobacterium tuberculosis complex (15,22,37) are present in multiple copies in the mycobacterial chromosome (16,40). Additionally, unidentified repeated sequences, or repeats which do not share characteristics with other sequences, have been found in Mycobacterium leprae (3, 13, 43) and M. tuberculosis (6, 14, 15, 27).The mycobacterial repeated DNA sequences described above were selected from gene libraries on the basis of their species specificity or differences in hybridization to particular DNA probes. However, no systematic study has been done on the major classes of repetitive DNA in mycobacteria.In this study, we investigated systematically the occurrence of repetitive DNA in M. tuberculosis. We show that a major repetitive DNA in this species belongs to a family consisting of short tandemly repeated sequences of 10 bp, separated by 5-bp spacer DNA. Furthermore, we analyzed the presence of this DNA family in other mycobacterial species and the potential use of this repetitive DNA for * Corresponding author.subtyping of mycobacterial strains and the epidemiology of mycobacterioses.

Comparative and functional genomics of the Mycobacterium tuberculosis complex a aThis review is based on the 2002 Marjory Stephenson Prize Lecture delivered by the author at the 150th Meeting of the Society for General Microbiology, 9 April 2002.

“…The PGRS encodes the motif AsnGlyGlyAlaGlyGlyAla, or variants thereof, while MPTR encodes Asn-X-Gly-X-Gly-Asn-X-Gly. Multiple tandem repetitions of these motifs are found in the corresponding proteins, which are acidic and exceptionally rich in glycine, and at the gene level variations occur in the repeat copy number and sequence thereby accounting for the genomic polymorphisms observed in hybridization patterns obtained with PGRS or MPTR probes (Hermans et al, 1992 ;Poulet & Cole, 1995a, b ;van Soolingen et al, 1993). Initially, the PGRS and MPTR sequences were thought to correspond to dispersed tandem repeats or microsatellites but the finding that they were part of coding sequences led to reflection about the functions of these proteins.…”

A novel polymorphic genetic locus in members of the Mycobacterium tuberculosis complex

“…Orf6 possesses an N-terminal hydrophobic segment consistent with a lipoprotein signal sequence. Orf6 also has similarity to part of the 1D sequence located in the RD1 region of M. bovis and M. tuberculosis (Mahairas et al, 1996). RD1 is a 9.5 kb DNA segment that is found in virulent laboratory and clinical isolates of M. bovis the fragment that was close to a series of eight 10 bp sequences with some similarity to major polymorphic tandem repeat (MPTR) sequences (Hermans et d.,…”

Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats

“…The MPTR consists of 15-bp repeats with a single consensus sequence but with substantial sequence variability between adjacent repeats (Hermans et al, 1992). We amplified the 48 strains in our panel in five MPTR loci, including four published loci (Hermans et al, 1992;Shinnick, 1987) and one locus identified by our search of cosmid sequences.…”

“…We amplified the 48 strains in our panel in five MPTR loci, including four published loci (Hermans et al, 1992;Shinnick, 1987) and one locus identified by our search of cosmid sequences. One of these MPTR loci (MPTR-A) demonstrated length polymorphism, corresponding to 15,16 or 17 copies of the 15-bp repeat unit (Tables 2 and 3).…”