Acta Biomedica Scientifica (Sep 2018)

BIOINFORMATIC SEARCH OF CRISPR/CAS SYSTEM STRUCTURES IN GENOME OF PCT281 PLASMID OF BACILLUS THURINGIENSIS SUBSP. CHINENSIS STRAIN CT-43

  • N. A. Arefyeva,
  • Yu. P. Dzhioev,
  • A. Yu. Borisenko,
  • V. I. Chemerilova,
  • O. F. Vyatchina,
  • O. A. Sekerina,
  • L. A. Stepanenko,
  • Yu. A. Markova,
  • G. V. Yurinova,
  • V. P. Salovarova,
  • A. A. Pristavka,
  • V. A. Kuzminova,
  • O. N. Reva,
  • V. I. Zlobin

DOI
https://doi.org/10.29413/ABS.2018-3.5.5
Journal volume & issue
Vol. 3, no. 5
pp. 33 – 38

Abstract

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Background. CRISPR/Cas systems loci are one of the functionally important patterns in bacterial genome which perform the role of “adaptive immune defense” from foreign nucleic acids. The study of CRISPR/Cas systems structure in genomes of plasmids and phages provide new information about the evolution of this systems in bacterial hosts.Aims. A search of CRISPR/Cas systems structures in pCT281 plasmid from Bacillus thuringiensis subsp. chinensis strain CT-43 using bioinformatic methods.Materials and methods. Search studies using bioinformatics methods were performed with the genome of pCT281 plasmid of B. thuringiensis subsp. chinensis strain CT-43 from the RefSeq database. To search for the CRISPR/Cas system structure MacSyFinder (ver. 1.0.5) and three combined algorithms were used: CRISPRFinder; PILER-CR; CRISPR Recognition Tool (CRT). The consensus repeat sequence was generated in WebLogo 3.Results and discussion. In pCT281 plasmid we detected one locus of CRISPR/Cas system of the type I-C which contains 2 CRISPR-cassettes and 4 cas-genes located between them. The CRISPR-cassette 1 includes 10 spacers from 32 to 35 bp and 11 repeats 32bp in length. 5 spacers (33–35 bp) separated by 6 repeats 32 bp in length were detected in the CRISPR-cassette 2.Conclusions. The bioinformatic methods used in this study enable to conduct a search of CRISPR/Cas systems structures in plasmid genomes. The presence of the CRISPR-Cas locus in pCT281 plasmid confirms a possible transfer of this system from the nucleoid to this plasmid. The detected spacers provide information about phages this bacteria was encountered.

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