Acta biomedica scientifica Acta biomedica scientifica Acta biomedica scientifica 2541-9420 2587-9596 14492 10.12737/23384 новые технологии Innovative Technologies новые технологии BIoInfoRmatIonal analySIS of YersiniapseudotuberculosisIP32953 CRISPR/CaSSyStem Биоинформационный анализ CRISPR/CaS системы штамма Yersiniapseudotuberculosis IP32953 Степаненко Лилия Александровна Stepanenko Liliya Александровна steplia@mail.ru Парамонов Алексей Игоревич Paramonov Aleksey Igorevich paramonov_a.i@mail.ru Колбасеева Ольга Владимировна Kolbaseeva Olga Владимировна kolbaseeva@yandex.ru Воскресенская Екатерина Александровна Voskresenskaya Ekaterina Александровна Борисенко Андрей Юрьевич Borisenko Andrey Юрьевич Перетолчина Надежда Павловна Peretolchina Nadezhda Павловна nadine1lenz@gmail.com Джиоев Юрий Павлович Dzhioev Yuriy Павлович alanir07@mail.ru Злобин Владимир Игоревич Zlobin Vladimir Igorevich vizlobin@mail.ru Научный центр проблем здоровья семьи и репродукции человека Иркутск Россия Scientific Centre for Family Health and Human Reproduction Problems Irkutsk Russian Federation Иркутский государственный медицинский университет Irkutsk State Medical University 09 12 2016 09 12 2016 1 5 64 67 https://zh-szf.ru/en/nauka/article/14492/view

Цель данного исследования: поиск и расшифровка CRISPR/Cas системы с помощью пакета программ в геноме Y.pseudotuberculosis IP32953. С помощью объединения результатов 4программных методов мы обнаружили в геноме штамма Y.pseudotuberculosis IP329353 один набор cas-генов и три локуса: YP1, YP2 и YP3. Через спейсеры кассет были обнаружены протоспейсеры в геномах: Y.pseudotuberculosis, Y.intermedia, Y.similis, Salmonella phage, Enterobacteria phage, и плазмиды Y.pseudotuberculosis IP32953 и Y.pseudotuberculosis IP31758.

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), CRISPI: 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 IP32953 plasmid pYV and plasmid of Y. pseudotuberculosis IP31758. Thus, the combination of four program methods allows finding CRISPR/Cas system more precisely. Spacer sequences could be used for protospacer screening.

 CRISPR/Cas иерсинии биоинформатика CRISPR/Cas Yersinia bioinformatics

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