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«IZVESTIYA IRKUTSKOGO GOSUDARSTVENNOGO UNIVERSITETA». SERIYA «BIOLOGIYA. ECOLOGIYA»
«THE BULLETIN OF IRKUTSK STATE UNIVERSITY». SERIES «BIOLOGY. ECOLOGY»
ISSN 2073-3372 (Print)

List of issues > Series «Biology. Ecology». 2023. Vol 45

In Silico Analysis of the Structural Diversity of CRISPR-Cas Systems in Genomes of Salmonella enterica and Phage Species Detected by Them

Author(s)
A. Yu. Borisenko, N. A. Arefieva, Yu. P. Dzhioev, S. V. Erdyneev, Yu. S. Bukin, G. A. Teterina, A. A. Pristavka, G. V. Yurinova, D. A. Antipin, K. B. Kahiani, A. E. Makarova, V. P. Salovarova, V. I. Zlobin
Abstract
The problem of resistance of pathogenic bacteria to antibiotics has become global and, therefore, there is renewed interest in the use of bacteriophages. However, bacteria also have phage defense structures, the CRISPR/Cas system. Therefore, the analysis of the structural diversity of CRISPR-Cas systems in the genomes of pathogenic bacteria and phages is an important fundamental and applied direction. The aim. Investigation of the diversity of structures of CRISPR/Cas systems in the genomes of S. enterica strains from the NCBI database using bioinformatics programs and assessment of the possibilities to identify phage protection of strains through spacers in CRISPR cassettes. The studies were carried out with the genomes of 449 S. enterica strains from the NCBI database. A number of bioinformation software methods were used: 1) MacSyFinder, 2) CRISPR Interactive database, 3) CRISPR R Tool, 4) CRISPI: a CRISPR Interactive database, 5) CRISPRFinder. Screening of phages through spacers CRISPR cassettes was used: 1) CRISPRTarget, 2) Mycobacteriophage Database, 3) Phages database. In the genomes of the studied strains of S. enterica, one type of CRISPR/Cas system, I-E, was identified. Protein genes were present in each locus of the CRISPR/Cas systems: Cas1_0_I-E_7, Cas2_0_I-E_8, Cas3_0_I_1, Cas5_0_I-E_5, Cas6_0_I-E_6, Cas7_0_I-E_4, Cse1_0_I-E_2, Cse2_0_I-E_3. The number of cassettes was from 1 to 3, and the spacers in them varied from 8 to 30. Repeats in CRISPR cassettes varied from 27 to 29 base pairs. The identified phages belonged to bacteria of the genera: Salmonella – 60%, Escherichia – 18%, Enterobacter – 9%, Salmonella – 8%, and Staphylococcus and Enterococcus were up to 5%. The obtained data on the diversity of CRISPR/Cas systems in the genomes of the studied S. enterica strains demonstrate their unique structures. The homogeneity of CRISPR/Cas systems and the rooting of CAS types I-E in genomes can be explained by their participation in the interspecific transmission of these CRISPR systems.
About the Authors

Borisenko Andrey Yurievich, Candidate of Science (Biology), Senior Lecturer, Irkutsk State Medical University, 1, Krasnogo Vosstaniya st., Irkutsk, 664003, Russian Federation, e-mail: 89500720225@mail.ru

Arefieva Nadezhda Aleksandrovna, Junior Research Scientist, Scientific Сentre for Family Health and Human Reproduction Problems, 16, Timiryazev st., Irkutsk, 664003, Russian Federation, Junior Research Scientist, Irkutsk Anti-Plague Research Institute of Siberia and Far East of Rospotrebnadzor, 78, Trilisser st., Irkutsk. 664047, Russian Federation, Research Assistant, Irkutsk State Medical University, 1, Krasnogo Vosstaniya, Irkutsk, 664003, Russian Federation, Postgraduate, Irkutsk State University, 1, K. Marx st., Irkutsk, 664003, Russian Federation, e-mail: arefieva.n4@gmail.com

Dzhioev Yuri Pavlovich, Candidate of Science (Biology), Leading Research Scientist, Irkutsk State Medical University, 1, Krasnogo Vosstaniya st., Irkutsk, 664003, Russian Federation, e-mail: alanir07@mail.ru

Erdyneev Sergey Viktorovich, Postgraduate Student, Irkutsk State Medical University, 1, Krasnoe Vosstanie st., Irkutsk, 664003, Russian Federation, Research Assistant, Irkutsk Anti-Plague Research Institute of Siberia and Far East of Rospotrebnadzor, 78, Trilisser st., Irkutsk. 664047, Russian Federation, e-mail: orry230@yandex.ru

Bukin Yuri Sergeevich, Candidate of Science (Biology), Senior Research Scientist, Limnological Institute SB RAS, 3, Ulaanbaatar st., Irkutsk, 664033, Russian Federation, Associate Professor, Irkutsk State University, 1, K. Marx st., Irkutsk, 664003, Russian Federation, e-mail: bukinyura@mail.ru

Teterina Galina Aleksandrovna, Senior Lecturer, Irkutsk State University, 1, K. Marx st., Irkutsk, 664003, Russian Federation, e-mail: galina.teterina.91@mail.ru

Pristavka Aleksey Aleksandrovich, Candidate of Sciences (Biology), Associate Professor, Irkutsk State University, 1, K. Marx st., Irkutsk, 664003, Russian Federation, e-mail: pristavk@gmail.com

Yurinova Galina Valerievna, Candidate of Sciences (Biology), Associate Professor, Irkutsk State University, 1, K. Marx st., Irkutsk, 664003, Russian Federation, e-mail: yurinova@yandex.ru

Antipin Dmitry Andreevich, Postgraduate, Irkutsk State Medical University, 1, Krasnogo Vosstaniya st., Irkutsk, 664003, Russian Federation, e-mail: kagkkris12@gmail.com

Kakhiani Kistina Besikovna, Student, Irkutsk State Medical University, 1, Krasnogo Vosstaniya st., Irkutsk, 664003, Russian Federation, kagkkris12@gmail.com

Makarova Angelina Eduardovna, Student, Irkutsk State Medical University, 1, Krasnogo Vosstaniya st., Irkutsk, 664003, Russian Federation, e-mail: eamak18@mail.ru

Salovarova Valentina Petrovna, Doctor of Sciences (Biology), Professor, Head of Chair, Irkutsk State University, 1, K. Marx st., Irkutsk, 664003, Russian Federation, e-mail: vsalovarova@gmail.com

Zlobin Vladimir Igorevich, Doctor of Sciences (Medicine), Professor, Academician RAS, Irkutsk State Medical University, 11, Krasnogo Vosstaniya st., Irkutsk, 664003, Russian Federation, GamaleyaNational Research Center for Epidemiology and Microbiology, 18, Gamaleya st., Moscow, 123098, Russian Federation, e-mail: vizlobin@mail.ru

For citation
Borisenko A.Yu., Arefieva N.A., Dzhioev Yu.P., Erdyneev S.V., Bukin Yu.S., Teterina G.A., Pristavka A.A., Yurinova G.V., Antipin D.A., Kahiani K.B., Makarova A.E., Salovarova V.P., Zlobin V.I. In Silico Analysis of the Structural Diversity of CRISPR-Cas Systems in Genomes of Salmonella enterica and Phage Species Detected by Them. The Bulletin of Irkutsk State University. Series Biology. Ecology, 2023, vol. 45, pp. 3-20. https://doi.org/10.26516/2073-3372.2023.45.3 (in Russian)
Keywords
Salmonella enterica, in silico approaches, genomics and bioinformatics software, CRISPR/Cas system, spacers, repeats, protospacers, phages.
UDC
579.61:616-078+575.112
DOI
https://doi.org/10.26516/2073-3372.2023.45.3
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