Polymorphism in RD1 locus and its effect on down stream genes among South Indian clinical isolates of M. tuberculosis

RD1, the region of difference between the virulent strains of Mycobacterium tuberculosis, and Mycobacterium bovis BCG, is the most explored region, for mycobacterial virulence and vaccine design. We found a polymorphic intergenic region between two genes rv3870 and rv3871 in RD1 region. Sequence analysis revealed a 53 base pair repeat element which creates polymorphism among the clinical isolates reported earlier as MIRU 39. The discriminatory power of this locus was found to be high for EAI strains as indicated by Hunter Gaston Diversity Index 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 level of downstream genes rv3871 and rv3874 by quantitative RT-PCR among the different clades of clinical strains. Higher transcription of rv3871 was observed in the strains having 4 copies of repeat element in the upstream region. Where as the transcription of rv3874 was higher in the strains having 6 copies of the repeat element. Above data suggest that change in transcription level due to insertion of different copy numbers may affect the regulation of gene expression in M. tuberculosis.