vuzbiochemiИзвестия вузов. Прикладная химия и биотехнологияProceedings of Universities. Applied Chemistry and Biotechnology2227-29252500-1558ИРНИТУ10.21285/achb.982NPXLVYvuzbiochemi-1473Research ArticleФИЗИКО-ХИМИЧЕСКАЯ БИОЛОГИЯPHYSICOCHEMICAL BIOLOGYПоиск и анализ разнообразия структур CRISPR-Cas-систем патогенных штаммов Clostridium botulinum с целью создания экологически безопасных фаговых препаратовIdentification and diversity analysis of CRISPR-Cas systems in the pathogenic strains of Clostridium botulinum to create eco-friendly phage preparationshttps://orcid.org/0009-0007-0487-8223ТетеринаГ. А.TeterinaG. A.

Тетерина Галина Александровна, аспирант

664003, г. Иркутск, ул. Карла Маркса, 1

Galina A. Teterina, Postgraduate Student

1, Karl Marx St., Irkutsk, 664003

galina.teterina.91@mail.ruhttps://orcid.org/0000-0002-3693-9058СаловароваВ. П.SalovarovaV. P.

Саловарова Валентина Петровна, д.б.н., профессор, заведующий кафедрой

664003, г. Иркутск, ул. Карла Маркса, 1

Valentina P. Salovarova, Dr. Sci. (Biology), Professor, Head of the Department

1, Karl Marx St., Irkutsk, 664003

vsalovarova@gmail.comhttps://orcid.org/0000-0001-5410-5113ДжиоевЮ. П.DzhioevYu. P.

Джиоев Юрий Павлович, к.б.н., ведущий научный сотрудник

664003, г. Иркутск, ул. Красного Восстания, 1

Yurii P. Dzhioev, Cand. Sci. (Biology), Leading Researcher

1, Krasnogo Vosstaniya St., Irkutsk, 664003

alanir07@mail.ruhttps://orcid.org/0000-0003-2222-4518АрефьеваН. А.ArefievaN. A.

Арефьева Надежда Александровна, аспирант; лаборант-исследователь; младший научный сотрудник

664003, г. Иркутск, ул. Карла Маркса, 1;

664003, г. Иркутск, ул. Красного Восстания, 1;

664003, г. Иркутск, ул. Тимирязева, 16

Nadezhda A. Arefieva, Postgraduate Student; Clinical Research Assistant; Junior Researcher

1, Karl Marx St., Irkutsk, 664003;

1, Krasnogo Vosstaniya, St., Irkutsk, 664003;

16, Timiryazev St., Irkutsk, 664003

arefieva.n4@gmail.comБорисенкоА. Ю.BorisenkoA. Yu.

Борисенко Андрей Юрьевич, к.б.н., доцент

664003, г. Иркутск, ул. Красного Восстания, 1

Andrey Y. Borisenko, Cand. Sci. (Biology), Associate Professor

1, Krasnogo Vosstaniya St., Irkutsk, 664003

89500720225@mail.ruhttps://orcid.org/0000-0002-4534-3846БукинЮ. С.BukinYu. S.

Букин Юрий Сергеевич, к.б.н., доцент; старший научный сотрудник

664003, г. Иркутск, ул. Карла Маркса, 1;

664003, г. Иркутск, ул. Улан-Баторская, 3

Yuri S. Bukin, Cand. Sci. (Biology), Associate Professor; Senior Researcher

1, Karl Marx St., Irkutsk, 664003;

3, Ulanbatorskaya St., Irkutsk, 664033

bukinyura@mail.ruhttps://orcid.org/0009-0006-7937-1382ЭрдынеевС. В.ErdyneevS. V.

Эрдынеев Сергей Викторович, аспирант; младший научный сотрудник

664003, г. Иркутск, ул. Красного Восстания, 1;

664047, г. Иркутск, ул. Трилиссера, 78

Sergey V. Erdyneev, Postgraduate Student; Junior Researcher

1, Krasnogo Vosstaniya St., Irkutsk, 664003;

78, Trilisser St., Irkutsk, 664047

orry230@yandex.ruhttps://orcid.org/0000-0002-5792-7283СтепаненкоЛ. А.StepanenkoL. A.

Степаненко Лилия Александровна, к.м.н., старший научный сотрудник

664003, г. Иркутск, ул. Красного Восстания, 1

Liliya A. Stepanenko, Cand. Sci. (Medicine), Senior Researcher

1, Krasnogo Vosstaniya St., Irkutsk, 664003

steplia@mail.ruhttps://orcid.org/0009-0003-9442-9907АнтипинД. А.AntipinD. A.

Антипин Дмитрий Андреевич, аспирант

664003, г. Иркутск, ул. Красного Восстания, 1

Dmitry A. Antipin, Postgraduate Student

1, Krasnogo Vosstaniya St., Irkutsk, 664003

mieshamecka@yandex.ruhttps://orcid.org/0009-0000-7901-7056КахианиК. Б.KakhianiK. B.

Кахиани Кристина Бесиковна, лаборант

664003, г. Иркутск, ул. Красного Восстания, 1

Kristina B. Kakhiani, Laboratory Assistant

1, Krasnogo Vosstaniya St., Irkutsk, 664003

kagkkris12@gmail.comhttps://orcid.org/0009-0004-2207-5668МакароваА. Э.MakarovaA. E.

Макарова Ангелина Эдуардовна, лаборант

664003, г. Иркутск, ул. Красного Восстания, 1

Angelina E. Makarova, Laboratory Assistant

1, Krasnogo Vosstaniya St., Irkutsk, 664003

eamak18@mail.ruИркутский государственный университетРоссияIrkutsk State UniversityRussian FederationИркутский государственный медицинский университетРоссияIrkutsk State Medical UniversityRussian FederationИркутский государственный университет; Иркутский государственный медицинский университет; Научный центр проблем здоровья семьи и репродукции человекаРоссияIrkutsk State University; Irkutsk State Medical University; Scientific Centre for Family Health and Human Reproduction ProblemsRussian FederationИркутский государственный университет; Лимнологический институт СО РАНРоссияIrkutsk State University; Limnological Institute, Siberian Branch of the Russian Academy of SciencesRussian FederationИркутский государственный медицинский университет; Иркутский научно-исследовательский противочумный институт Сибири и Дальнего ВостокаРоссияIrkutsk State Medical University; Irkutsk Scientific Research Anti-Plague Institute of Siberia and the Far EastRussian Federation202502072025152224233Copyright © Тетерина Г.А., Саловарова В.П., Джиоев Ю.П., Арефьева Н.А., Борисенко А.Ю., Букин Ю.С., Эрдынеев С.В., Степаненко Л.А., Антипин Д.А., Кахиани К.Б., Макарова А.Э., 20252025Тетерина Г.А., Саловарова В.П., Джиоев Ю.П., Арефьева Н.А., Борисенко А.Ю., Букин Ю.С., Эрдынеев С.В., Степаненко Л.А., Антипин Д.А., Кахиани К.Б., Макарова А.Э.Teterina G.A., Salovarova V.P., Dzhioev Y.P., Arefieva N.A., Borisenko A.Y., Bukin Y.S., Erdyneev S.V., Stepanenko L.A., Antipin D.A., Kakhiani K.B., Makarova A.E.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://vuzbiochemi.elpub.ru/jour/article/view/1473

В работе представлено биоинформатическое исследование разнообразия CRISPR-Cas-систем в геномах Clostridium botulinum и детектируемых ими фагов с перспективной целью их таргетного скрининга. Объектом исследования стали 49 полных хромосомных последовательностей бактерий, взятых из базы данных GenBank. Для идентификации cas-генов использовался программный комплекс MacSyFinder с применением профилей HMM из баз данных PFAM и TIGRFAM. Поиск и анализ CRISPR-кассет осуществлялся с помощью трех независимых программ: CRISPRFinder, PILER-CR и CRISPR Recognition Tool, что обеспечило высокую точность определения структуры кассет. Поиск протоспейсеров проводился с использованием программы CRISPRTarget и алгоритма BLASTn против вирусных баз данных RefSeq-Viral. Исследование включало сопоставление последовательностей спейсеров с геномами фагов для выявления комплементарных участков. Анализ фагового иммунитета показал преобладание фагов Cellulophaga (19%), что связано с экологическими особенностями Clostridium botulinum, а также значительную долю фагов Aeromonas и Bacillus (12,5%). Следующую группу фагов, преимущественно направленных на кишечную микрофлору, составили виды Enterococcus, Escherichia, Lactococcus (6–10%). Найдены протоспейсеры редких фагов (по 3%): Acidianus filamentous, Prochlorococcus, Pseudoalteromonas, Stenotrophomonas, Synechococcus. Полученные результаты указывают на сложную структуру CRISPR-Cas-систем Clostridium botulinum, эволюционно формирующихся под влиянием различных экологических ниш.

The article presents a bioinformatic study of the diversity of CRISPR-Cas systems in the genomes of Clostridium botulinum and the phages they detect, with the aim of their targeted screening. The subject matter of the study was 49 complete chromosomal sequences of bacteria obtained from the GenBank database. Cas genes were identified employing the MacSyFinder tool with the use of HMM profiles from the PFAM and TIGRFAM databases. The identification and analysis of CRISPR cassettes were performed using three independent programs: CRISPRFinder, PILER-CR, and CRISPR Recognition Tool, which ensured high accuracy in determining the cassette structure. Protospacers were identified using the CRISPRTarget tool and the BLASTn algorithm against RefSeq-Viral viral databases. The study involved comparing spacer sequences and phage genomes in order to identify complementary sites. A phage immunity analysis revealed a predominance of Cellulophaga phages (19%), which can be attributed to the environmental characteristics of Clostridium botulinum, as well as a significant proportion of Aeromonas and Bacillus phages (12.5%). Another group of phages (predominantly intestinal) included Enterococcus, Escherichia, and Lactococcus species (6–10%). Also, the protospacers of rare phages (3% each) were found: Acidianus filamentous, Prochlorococcus, Pseudoalteromonas, Stenotrophomonas, and Synechococcus. The obtained results indicate complex CRISPR-Cas systems in Clostridium botulinum, evolving under the impact of different ecological niches.

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The authors declare that there are no conflicts of interest present.