Comprehensive study of instable regions in Pseudomonas aeruginosa and Mycobacterium tuberculosis

Background: Pseudomonas aeruginosa is a common bacterium which is recognized for its association with hospital-acquired infections and its advanced antibiotic resistance mechanisms. Tuberculosis, one of the major causes of mortality, is initiated by the deposition of Mycobacterium tuberculosis. Accessory sequences shared by a subset of strains of a species play an important role in a species' evolution, antibiotic resistance and infectious potential. 
Results: Here, with a multiple sequence aligner, we segmented 25 P. aeruginosa genomes and 28 M. tuberculosis genomes into core blocks (include sequences shared by all the input genomes) and dispensable blocks (include sequences shared by a subset of the input genomes), respectively. For each input genome, we then constructed a scaffold consisting of its core and dispensable blocks sorted by blocks' locations on the chromosomes. Consecutive dispensable blocks on these scaffold formed instable regions. After a comprehensive study of these instable regions, three characteristics of instable regions are summarized: instable regions were short, site specific and varied in different strains. Three DNA elements (directed repeats (DRs), transposons and integrons) were then studied to see whether these DNA elements are associated with the variation of instable regions. A pipeline was developed to search for DR pairs on the flank of every instable sequence. 27 DR pairs in P. aeruginosa strains and 6 pairs in M. tuberculosis strains were found to exist in the instable regions. On the average, 14% and 12% of instable regions in P. aeruginosa strains covered transposase genes and integrase genes, respectively. In M. tuberculosis strains, an average of 43% and 8% of instable regions contain transposase genes and integrase genes, respectively. 
Conclusions: Instable regions were short, site specific and varied in different strains for both P. aeruginosa and M. tuberculosis. Our experimental results showed that DRs, transposons and integrons may be associated with variation of instable regions.