Project description:By genome comparison of 30 MTBC strains, we identified three SNPs affecting the phoPR genes of members of the animal and M. africanum lineages that were not seen in the M. tuberculosis sensu-stricto genomes. The genes phoPR encode a two component regulatory system that is known for its strong impact on virulence and immunogenicity of M. tuberculosis due to its key role in the regulation of genes involved in lipid synthesis and secretion of the 6 kDa secreted antigenic target ESAT-6. To explore whether these SNPs affect the expression of the PhoP regulon, we compared the transcriptome of M. tuberculosis mutants lacking the endogenous phoPR genes (M-NM-^TphoPR) and their complemented derivatives expressing either the M. bovis or M. tuberculosis allele of phoPR (phoPR-bovis and phoPR-TB respectively). These comparisons were performed in parallel in two M. tuberculosis strains from distinct genetic backgrounds, i.e. strain GC1237 from lineage 2 (also named East-Asia or Beijing cluster) and the H37Rv reference strain from lineage 4 (also named Euro-American cluster). To perform the transcriptomic comparison of the different M. tuberculosis variants (M-NM-^TphoPR, complemented and wt) from the two distinct genetic background, a customized micro-array has been designed then manufactured by Agilent (8 x 15k format). The design of oligonucleotides covering all protein coding sequences was done using OligoArray version 2.1 on the basis of the 3924 predicted coding sequences composing the entire M. tuberculosis H37Rv reference genome. The experimental data for each of the comparison consisted of 4 hybridizations (2 biological replicates with dye-swap); 16 in the end for each genetic background.
