Genome mining approach reveals the CRISPR-Cas systems features and characteristics in Lactobacillus delbrueckii strains
This study employed a comprehensive genome-mining approach to characterize CRISPR-Cas systems in Lactobacillus delbrueckii strains. The analysis involved retrieving 105 genome sequences to explore the variety, occurrence, and evolution of CRISPR-Cas systems within the species. Homology analysis of s...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-11-01
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| Series: | Heliyon |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844024159518 |
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| author | Bahman Panahi Mohaddeseh Rostampour Mohammad Reza Ghaffari Yousef Nami |
| author_facet | Bahman Panahi Mohaddeseh Rostampour Mohammad Reza Ghaffari Yousef Nami |
| author_sort | Bahman Panahi |
| collection | DOAJ |
| description | This study employed a comprehensive genome-mining approach to characterize CRISPR-Cas systems in Lactobacillus delbrueckii strains. The analysis involved retrieving 105 genome sequences to explore the variety, occurrence, and evolution of CRISPR-Cas systems within the species. Homology analysis of spacer sequences in detected CRISPR arrays was conducted to assess the variety of target phages and plasmids. The evolutionary trajectories of spaceromes in each subtype of CRISPR arrays were determined by analyzing acquisition and deletion events under the selection pressure of foreign plasmids and phages. Among the analyzed strains, 53 contained only one CRISPR-Cas locus, 11 had two loci, and 21 featured three loci with complete CRISPR-Cas systems. Subtype designation of the results of current study revealed that 56 % of these systems belong to subtypes I-E/I-C, 23 % to subtypes III-A/III-D, and 17 % to subtype II-A. Notably, certain plasmids were found to be specifically targeted by distinct CRISPR array systems. The comparison of spacer sequences with phage genomes indicated that strains containing only CRISPR-Cas type-I systems targeted a broader range of phages. In conclusion, this study highlights the diversity of the three identified CRISPR-Cas types in L. delbrueckii strains and emphasizes their significant role in defense against phage invasion. |
| format | Article |
| id | doaj-art-a4ddd2afe3d24fa7a154bb6706dd5976 |
| institution | DOAJ |
| issn | 2405-8440 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Heliyon |
| spelling | doaj-art-a4ddd2afe3d24fa7a154bb6706dd59762025-08-20T02:48:58ZengElsevierHeliyon2405-84402024-11-011022e3992010.1016/j.heliyon.2024.e39920Genome mining approach reveals the CRISPR-Cas systems features and characteristics in Lactobacillus delbrueckii strainsBahman Panahi0Mohaddeseh Rostampour1Mohammad Reza Ghaffari2Yousef Nami3Department of Genomics, Branch for Northwest & West region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, IranDepartment of Food Biotechnology, Branch for Northwest & West region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, IranDepartment of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 31535-1897, Karaj, IranDepartment of Food Biotechnology, Branch for Northwest & West region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran; Corresponding author.This study employed a comprehensive genome-mining approach to characterize CRISPR-Cas systems in Lactobacillus delbrueckii strains. The analysis involved retrieving 105 genome sequences to explore the variety, occurrence, and evolution of CRISPR-Cas systems within the species. Homology analysis of spacer sequences in detected CRISPR arrays was conducted to assess the variety of target phages and plasmids. The evolutionary trajectories of spaceromes in each subtype of CRISPR arrays were determined by analyzing acquisition and deletion events under the selection pressure of foreign plasmids and phages. Among the analyzed strains, 53 contained only one CRISPR-Cas locus, 11 had two loci, and 21 featured three loci with complete CRISPR-Cas systems. Subtype designation of the results of current study revealed that 56 % of these systems belong to subtypes I-E/I-C, 23 % to subtypes III-A/III-D, and 17 % to subtype II-A. Notably, certain plasmids were found to be specifically targeted by distinct CRISPR array systems. The comparison of spacer sequences with phage genomes indicated that strains containing only CRISPR-Cas type-I systems targeted a broader range of phages. In conclusion, this study highlights the diversity of the three identified CRISPR-Cas types in L. delbrueckii strains and emphasizes their significant role in defense against phage invasion.http://www.sciencedirect.com/science/article/pii/S2405844024159518CRISPRGenomeSubtypeSpacerPhagePlasmid |
| spellingShingle | Bahman Panahi Mohaddeseh Rostampour Mohammad Reza Ghaffari Yousef Nami Genome mining approach reveals the CRISPR-Cas systems features and characteristics in Lactobacillus delbrueckii strains Heliyon CRISPR Genome Subtype Spacer Phage Plasmid |
| title | Genome mining approach reveals the CRISPR-Cas systems features and characteristics in Lactobacillus delbrueckii strains |
| title_full | Genome mining approach reveals the CRISPR-Cas systems features and characteristics in Lactobacillus delbrueckii strains |
| title_fullStr | Genome mining approach reveals the CRISPR-Cas systems features and characteristics in Lactobacillus delbrueckii strains |
| title_full_unstemmed | Genome mining approach reveals the CRISPR-Cas systems features and characteristics in Lactobacillus delbrueckii strains |
| title_short | Genome mining approach reveals the CRISPR-Cas systems features and characteristics in Lactobacillus delbrueckii strains |
| title_sort | genome mining approach reveals the crispr cas systems features and characteristics in lactobacillus delbrueckii strains |
| topic | CRISPR Genome Subtype Spacer Phage Plasmid |
| url | http://www.sciencedirect.com/science/article/pii/S2405844024159518 |
| work_keys_str_mv | AT bahmanpanahi genomeminingapproachrevealsthecrisprcassystemsfeaturesandcharacteristicsinlactobacillusdelbrueckiistrains AT mohaddesehrostampour genomeminingapproachrevealsthecrisprcassystemsfeaturesandcharacteristicsinlactobacillusdelbrueckiistrains AT mohammadrezaghaffari genomeminingapproachrevealsthecrisprcassystemsfeaturesandcharacteristicsinlactobacillusdelbrueckiistrains AT yousefnami genomeminingapproachrevealsthecrisprcassystemsfeaturesandcharacteristicsinlactobacillusdelbrueckiistrains |