[Computerized analysis of inverted repeats in Mycobacterium tuberculosis genome]

Thermodynamic stable inverted repeats, capable of stabilizing nuclease-influenced mRNA, have been determined for M. tuberculosis slowly growing isolates H37Rv and CDC1551 with the completely sequenced genome. The genome of laboratory strain H37Rv may contain 50 pin structures formed by inverted repeats, whose stem varies in length from 11 to 28 nucleotide pairs (n.p.), the loop size being equal to 4-5 nucleotides and free energy deltaG=-15.2 to -56.2 kcal/mol. The genome of strain CDC1551 (clinical isolate) having a high level of virulence contains 47 pins. Each of the two isolates contains 8 long inverted repeats with a length of 48-62 nucleotides and free energy deltaG=-38.9 to -56.2 kcal/mol; of these, 6 pins are completely similar. At the same time in the genome of strain CDC1551, in contrast to that of strain H37Rv, a highly stable pin 58 nucleotides long is localized at 5'-end. The localization of the highly stable pin with deltaG=-53.9 kcal/mol in the area of 5'-end of isolate CDC1551 may lead to a different degree of stabilization of RNA-transcripts in M. tuberculosis CDC1551 in comparison with isolate H37Rv. This may, in its turn, serve as one of the reasons of differences in the virulence of strains. The possibility of the formation of pins with stems of 11 n.p. and longer has been visually cofirmed with the use of atomic power microscopy. The possibility of the participation of the secondary structures formed by pins in the protection of mRNA of slowly growing pathogenic M. tuberculosis from the degrading activity of RNases is discussed.