Genetic polymorphism of the Rv3303c-Rv3304 intergenic region in Beijing and non-Beijing genotype Mycobacterium...

To investigate the polymorphism of the Rv3303c-Rv3304 intergenic region (IR) in Beijing and non-Beijing genotype Mycobacterium tuberculosis (M. tuberculosis) strains isolated from China, and to explore its regulatory effects on downstream gene expression.

A total of 223 M. tuberculosis isolates from China were classified into Beijing, non-Beijing genotype and modern Beijing subgenotype based on single nucleotide polymorphisms (SNPs). The polymorphism of Rv3303c-Rv3304 IR was identified by DNA sequencing, and a lacZ reporter system was applied to assess its regulatory role on the expression of Rv3303c.

Of 223 isolates, 151 (67.7%) belonged to the Beijing genotype, 72 (32.3%) to the non-Beijing genotype, and 129 (85.4% of Beijing genotype strains) to the modern Beijing subgenotype. All isolates carried 1 to 7 copies of 58-bp repeating sequences in the Rv3303c-Rv3304 IR, with 3-copy repeats being the most predominant. Notably, the proportions of 3-copy repeats in Beijing and modern Beijing genotype strains were 90.1% and 90.7%, respectively, which were significantly higher than that in non-Beijing genotype strains (54.2%). β-galactosidase activity assays showed significant differences in activity among recombinant strains carrying different copy numbers of the repeating sequences (P < 0.0001).

Significant differences in the polymorphism of the Rv3303c-Rv3304 IR were observed between Beijing and non-Beijing genotype M. tuberculosis strains from China. This polymorphism exhibited repeat copy-dependent regulatory activity toward the downstream gene Rv3303c in a reporter system, suggesting that it may potentially contribute to phenotypic diversity among different genotypes of M. tuberculosis.