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

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

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 evoluti...

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Autores principales: 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
Formato: article
Lenguaje:RU
Publicado: Scientific Сentre for Family Health and Human Reproduction Problems 2018
Materias:
crispr/cas-система
bacillus thuringiensis subsp. chinensis ct-43
Science
Q
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spelling oai:doaj.org-article:58090053a027448da97943a8485f794e2021-11-23T06:14:41ZBIOINFORMATIC SEARCH OF CRISPR/CAS SYSTEM STRUCTURES IN GENOME OF PCT281 PLASMID OF BACILLUS THURINGIENSIS SUBSP. CHINENSIS STRAIN CT-432541-94202587-959610.29413/ABS.2018-3.5.5https://doaj.org/article/58090053a027448da97943a8485f794e2018-09-01T00:00:00Zhttps://www.actabiomedica.ru/jour/article/view/704https://doaj.org/toc/2541-9420https://doaj.org/toc/2587-9596Background. 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.N. A. ArefyevaYu. P. DzhioevA. Yu. BorisenkoV. I. ChemerilovaO. F. VyatchinaO. A. SekerinaL. A. StepanenkoYu. A. MarkovaG. V. YurinovaV. P. SalovarovaA. A. PristavkaV. A. KuzminovaO. N. RevaV. I. ZlobinScientific Сentre for Family Health and Human Reproduction Problemsarticlecrispr/cas-системаbacillus thuringiensis subsp. chinensis ct-43ScienceQRUActa Biomedica Scientifica, Vol 3, Iss 5, Pp 33-38 (2018)
institution DOAJ
collection DOAJ
language RU
topic crispr/cas-система
bacillus thuringiensis subsp. chinensis ct-43
Science
Q
spellingShingle crispr/cas-система
bacillus thuringiensis subsp. chinensis ct-43
Science
Q
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
BIOINFORMATIC SEARCH OF CRISPR/CAS SYSTEM STRUCTURES IN GENOME OF PCT281 PLASMID OF BACILLUS THURINGIENSIS SUBSP. CHINENSIS STRAIN CT-43
description 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.
format article
author 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
author_facet 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
author_sort N. A. Arefyeva
title BIOINFORMATIC SEARCH OF CRISPR/CAS SYSTEM STRUCTURES IN GENOME OF PCT281 PLASMID OF BACILLUS THURINGIENSIS SUBSP. CHINENSIS STRAIN CT-43
title_short BIOINFORMATIC SEARCH OF CRISPR/CAS SYSTEM STRUCTURES IN GENOME OF PCT281 PLASMID OF BACILLUS THURINGIENSIS SUBSP. CHINENSIS STRAIN CT-43
title_full BIOINFORMATIC SEARCH OF CRISPR/CAS SYSTEM STRUCTURES IN GENOME OF PCT281 PLASMID OF BACILLUS THURINGIENSIS SUBSP. CHINENSIS STRAIN CT-43
title_fullStr BIOINFORMATIC SEARCH OF CRISPR/CAS SYSTEM STRUCTURES IN GENOME OF PCT281 PLASMID OF BACILLUS THURINGIENSIS SUBSP. CHINENSIS STRAIN CT-43
title_full_unstemmed BIOINFORMATIC SEARCH OF CRISPR/CAS SYSTEM STRUCTURES IN GENOME OF PCT281 PLASMID OF BACILLUS THURINGIENSIS SUBSP. CHINENSIS STRAIN CT-43
title_sort bioinformatic search of crispr/cas system structures in genome of pct281 plasmid of bacillus thuringiensis subsp. chinensis strain ct-43
publisher Scientific Сentre for Family Health and Human Reproduction Problems
publishDate 2018
url https://doaj.org/article/58090053a027448da97943a8485f794e
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