Polymorphism in the RD1 locus and its effect on downstream genes among South Indian clinical isolates of Mycobacterium tuberculosis.
ABSTRACT RD1, the region of difference between the virulent strains of Mycobacterium tuberculosis and Mycobacterium bovis BCG, is the most explored region in terms of mycobacterial virulence and vaccine design. This study found a polymorphic intergenic region between two genes, Rv3870 and Rv3871, in the RD1 region. Sequence analysis revealed a 53 bp repeat element that created a polymorphism among the clinical isolates, reported previously as the mycobacterial interspersed repetitive unit (MIRU) 39 locus. The discriminatory power of this locus was found to be high for EAI strains, as indicated by a Hunter-Gaston diversity index value of 0.58, and low for Beijing (0.26) and CAS (0.29) strains. The presence and variability of MIRU 39 in the intergenic region led us to investigate the functional role of the repeat element by measuring the transcription levels of the downstream genes Rv3871 and Rv3874 by quantitative RT-PCR among the different clades of clinical strains. Higher transcription levels of Rv3871 were observed in strains with four copies of the repeat element in the upstream region, whereas the transcription level of Rv3874 was higher in strains with six copies of the repeat element. These data suggest that changes in transcription levels resulting from insertion of different copy numbers of the repeat element may affect regulation of gene expression in M. tuberculosis.