Bioinformational analysis of Yersinia pseudotuberculosis IP32953 CRISPR/cas system
https://doi.org/10.12737/23384
Abstract
The results of this study include Yersinia pseudotuberculosis CRISPR/Cas system structure analysis. CRISPR/Cas system is a specific adaptive protection against heterogeneous genetic elements. The object of research was the complete genome of Y. pseudotuberculosis IP32953 (NC_006155). CRISPR/Cas system screening was performed by program modelling methods MacSyFinder ver. 1.0.2. CRISPR loci screening and analyzing were carried out by program package: CRISPR Recognition tool (CRT), CR1SP1: a CRISPR Interactive database, CRISPRFinder, and PilerCR. Spacer sequences were used in order to find protospacers in ACLAME, GenBank-Phage and RefSeq-Plasmid databases by BLASTn search algorithm. Protospacer sequences could be found in genomes of phages, plasmids and bacteria. In last case complete genomes of bacteria were analyzed by online-tool PHAST: PHAge Search Tool. Y. pseudotuberculosis IP329353 has CRISPR/Cas system that consists of one sequence of cas-genes and three loci. These loci are far away from each other. Locus YP1 is situated in close proximity to cas-genes. Protospacers were found in genomes of Y. pseudotuberculosis PB1/+, Y. intermedia Y228, Y. similis str. 228, Salmonella phage, Enterobacteria phage, Y. pseudotuberculosis 1P32953 plasmid pYV and plasmid of Y. pseudotuberculosis 1P31758. Thus, the combination of four program methods allows finding CRISPR/Cas system more precisely. Spacer sequences could be used for protospacer screening.
About the Authors
N. P. Peretolchina
Irkutsk state Medical university
Russian Federation
Russian Federation
Y. P. Dzhioev
Irkutsk state Medical university; Scientific centre of Family Health and Human Reproduction problems
Russian Federation
Russian Federation
A. Y. Borisenko
Irkutsk state Medical university
Russian Federation
Russian Federation
E. A. Voskresenskaya
Saint Petersburg pasteur Institute
Russian Federation
Russian Federation
A. I. Paramonov
Scientific centre of Family Health and Human Reproduction problems
Russian Federation
Russian Federation
L. A. Stepanenko
Irkutsk state Medical university
Russian Federation
Russian Federation
O. V. Kolbaseeva
Irkutsk state Medical university
Russian Federation
Russian Federation
V. I. Zlobin
Irkutsk state Medical university
Russian Federation
Russian Federation
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Review
For citations:
Peretolchina N.P., Dzhioev Y.P., Borisenko A.Y., Voskresenskaya E.A., Paramonov A.I., Stepanenko L.A., Kolbaseeva O.V., Zlobin V.I. Bioinformational analysis of Yersinia pseudotuberculosis IP32953 CRISPR/cas system. Acta Biomedica Scientifica. 2016;1(5):64-67. (In Russ.) https://doi.org/10.12737/23384
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