Comprehensive study of instable regions in Pseudomonas aeruginosa and Mycobacterium tuberculosis

Pseudomonas aeruginosa is recognized for its intrinsically advanced antibiotic resistance mechanisms. Dispensable genome which includes sequences shared by a subset of strains in a species is important to the study of a species’ evolution, antibiotic resistance and infectious potential. In this paper, by using a multiple sequence aligner, we segmented the genomes of 25 Pseudomonas aeruginosa strains into core blocks (shared by all the 25 genomes) and dispensable blocks (shared by a subset of the 25 genomes). In this paper, we use the term instable blocks to refer to dispensable blocks since blocks shared by a subset of the 25 genomes may be vitally important. We then built 25 scaffolds which consisted of core and instable blocks sorted by blocks’ starting positions in the chromosomes for each of the 25 strains. In these scaffolds, consecutive instable blocks formed instable regions. We conducted a comprehensive study on these instable regions and found three characteristics of instable regions: instable regions were short, site specific and varied in different strains. We then studied three DNA elements which may contribute to the variation of instable regions: directed repeats (DRs), transposons and integrons. Past studies have shown that sequences flanked by a pair of DRs can be deleted from their host chromosomes or be inserted into new host chromosomes. We developed a pipeline to search for DR pairs on the flank of every instable sequence and found 27 pairs of DRs existing in the instable regions between 21 distinct pairs of core blocks. We also found that in the average, 14% and 12% of instable regions in the 25 scaffolds covered transposase genes and integrase genes, respectively.

[1]  William C. Nierman,et al.  The Early Stage of Bacterial Genome-Reductive Evolution in the Host , 2010, PLoS pathogens.

[2]  B. Michel,et al.  Mechanisms of illegitimate recombination. , 1993, Gene.

[3]  Lee H. Harrison,et al.  Deletion of fetA Gene Sequences in Serogroup B and C Neisseria meningitidis Isolates , 2007, Journal of Clinical Microbiology.

[4]  David R. Riley,et al.  Ten years of pan-genome analyses. , 2015, Current opinion in microbiology.

[5]  Jaideep P. Sundaram,et al.  Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[6]  M. Chandler,et al.  Bacterial transposases and retroviral integrases , 1995, Molecular microbiology.

[7]  R. Kolodner,et al.  Homologous pairing and strand exchange promoted by the Escherichia coli RecT protein. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Stan J. J. Brouns,et al.  CRISPR-based adaptive and heritable immunity in prokaryotes. , 2009, Trends in biochemical sciences.

[9]  C. R. Osorio,et al.  Integrating conjugative elements of the SXT/R391 family from fish-isolated Vibrios encode restriction-modification systems that confer resistance to bacteriophages. , 2013, FEMS microbiology ecology.

[10]  D. Leach,et al.  Bacterial Genome Instability , 2014, Microbiology and Molecular Reviews.

[11]  A. Janulaitis,et al.  Identification of a gene encoding a DNA invertase-like enzyme adjacent to the PaeR7I restriction-modification system. , 1995, Gene.

[12]  Steven Salzberg,et al.  Mugsy: fast multiple alignment of closely related whole genomes , 2010, Bioinform..

[13]  Thomas L. Madden,et al.  BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. , 1999, FEMS microbiology letters.

[14]  P. H. Roy,et al.  A transposon-like sequence adjacent to the AccI restriction-modification operon. , 1995, Gene.

[15]  V. Kunin,et al.  CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea , 2008, Nature Reviews Microbiology.