Comprehensive study of instable regions in Pseudomonas aeruginosa and Mycobacterium tuberculosis
Dan Wang1, Jingyu Li1, Lusheng Wang2,3
1Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave., Hong Kong, People's Republic of China.
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.
Insights
Instable genomic regions in Pseudomonas aeruginosa and Mycobacterium tuberculosis are short, site-specific, and strain-variable. Directed repeats, transposons, and integrons are likely associated with these variations, impacting bacterial evolution and infectious potential.
Area of Science:
- Genomics
- Microbiology
- Molecular Evolution
Background:
- Pseudomonas aeruginosa is a significant cause of hospital-acquired infections, known for antibiotic resistance.
- Mycobacterium tuberculosis causes tuberculosis, a leading cause of mortality.
- Accessory genomic sequences influence bacterial evolution, antibiotic resistance, and pathogenicity.
Purpose of the Study:
- To investigate the characteristics of instable genomic regions in P. aeruginosa and M. tuberculosis.
- To identify potential DNA elements associated with the variation in these instable regions.
Main Methods:
- Genome segmentation into core and dispensable blocks using multiple sequence alignment.
- Construction of chromosomal scaffolds and identification of instable regions.
- Analysis of directed repeats (DRs), transposons, and integrons in relation to instable regions.
Main Results:
- Instable regions were found to be short, site-specific, and varied across strains for both bacteria.
- DR pairs were identified in instable regions of both P. aeruginosa (27 pairs) and M. tuberculosis (6 pairs).
- Instable regions in P. aeruginosa contained an average of 14% transposase and 12% integrase genes; in M. tuberculosis, 43% contained transposase and 8% integrase genes.
Conclusions:
- Instable genomic regions exhibit consistent characteristics (short, site-specific, variable) in P. aeruginosa and M. tuberculosis.
- Directed repeats, transposons, and integrons are implicated as potential drivers of variation in these instable regions.
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