Variable-number tandem repeat 3690 polymorphism in Indian clinical isolates of Mycobacterium tuberculosis and its influence on transcription

• Published in: Journal of medical microbiology Vol. 58; no. 6; pp. 798 - 805
• Main Authors: Akhtar, Parvez, Singh, Sarman, Bifani, Pablo, Kaur, Satinder, Srivastava, Brahm S, Srivastava, Ranjana
• Format: Journal Article
• Language: English
• Published: Reading Soc General Microbiol 01.06.2009; Society for General Microbiology
• Subjects: Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Bacteriology; Base Sequence; Biological and medical sciences; DNA, Intergenic - genetics; Fundamental and applied biological sciences. Psychology; Gene Expression Regulation, Bacterial; Green Fluorescent Proteins - genetics; Green Fluorescent Proteins - metabolism; Humans; India; Infectious diseases; Medical sciences; Microbiology; Minisatellite Repeats - genetics; Miscellaneous; Molecular Sequence Data; Mycobacterium bovis; Mycobacterium tuberculosis; Mycobacterium tuberculosis - genetics; Mycobacterium tuberculosis - isolation & purification; Mycobacterium tuberculosis - metabolism; Oxidoreductases - genetics; Oxidoreductases - metabolism; Polymorphism, Genetic; Transcription, Genetic; Tuberculosis, Pulmonary - microbiology; Up-Regulation; India; Microbiology; Mycobacterium tuberculosis; Transcription; Mycobacteriales; Minisatellite DNA; Mycobacteriaceae; Bacteria; Actinomycetes; Clinical isolate; Polymorphism
• ISSN: 0022-2615; 1473-5644
• DOI: 10.1099/jmm.0.002550-0

1 Microbiology Division, Central Drug Research Institute, Lucknow 226001, India 2 Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India 3 Molecular Pathology of Tuberculosis, Pasteur Institute, Brussels, Belgium Correspondence Ranjana Srivastava drranjana{at}yahoo.com Received April 12, 2008 Accepted February 8, 2009 Variable-number tandem repeat (VNTRs) occur throughout the chromosome of Mycobacterium tuberculosis . Although these polymorphic VNTRs, also known as mycobacterial interspersed repetitive units (MIRUs), have proved to be useful tools in molecular epidemiology, their biological significance is less well understood. This study investigated the polymorphism of the VNTR 3690 locus located in the intergenic region between rv 3304 and rv 3303c (encoding the gplD2 and lpdA genes, respectively) and its possible function in the regulation of gene expression. The copy number of VNTR 3690 was found to vary among Indian clinical isolates of M. tuberculosis (one to twelve copies), M. tuberculosis H37Rv TMC102 (four copies), M. tuberculosis H37Ra (two to four copies), Mycobacterium bovis BCG (one copy). The expression of lpdA as measured by quantitative RT-PCR was 12-fold higher in M. tuberculosis H37Rv than in M. bovis BCG. Using a GFP reporter system in which the 5'-flanking region of lpdA was fused to the gfp gene, the effect of VNTRs on gene expression was measured in an M. bovis BCG host background by real-time PCR. Compared with one VNTR repeat, a 12.5-fold upregulation of GFP expression was found with a flanking region containing four VNTR 3690 repeats, indicating that there is a good correlation between VNTR copy number and transcription of lpdA . Abbreviations: EAI, East African–Indian; MIRU, mycobacterial interspersed repetitive unit; SNP, single-nucleotide polymorphism; VNTR, variable-number tandem repeat.