The Diversity of the CRISPR-Cas System and Prophages Present in the Genome Reveals the Co-evolution of Bifidobacterium pseudocatenulatum and Phages
Diverse CRISPR-Cas systems constitute an indispensable part of the bacterial adaptive immune system against viral infections. However, to escape from this immune system, bacteriophages have also evolved corresponding anti-defense measures. We investigated the diversity of CRISPR-Cas systems and the...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2020-05-01
|
| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2020.01088/full |
| _version_ | 1828809012547682304 |
|---|---|
| author | Gang Wang Qian Liu Zhangming Pei Linlin Wang Peijun Tian Zhenmin Liu Jianxin Zhao Jianxin Zhao Jianxin Zhao Hao Zhang Hao Zhang Hao Zhang Hao Zhang Hao Zhang Wei Chen Wei Chen Wei Chen Wei Chen |
| author_facet | Gang Wang Qian Liu Zhangming Pei Linlin Wang Peijun Tian Zhenmin Liu Jianxin Zhao Jianxin Zhao Jianxin Zhao Hao Zhang Hao Zhang Hao Zhang Hao Zhang Hao Zhang Wei Chen Wei Chen Wei Chen Wei Chen |
| author_sort | Gang Wang |
| collection | DOAJ |
| description | Diverse CRISPR-Cas systems constitute an indispensable part of the bacterial adaptive immune system against viral infections. However, to escape from this immune system, bacteriophages have also evolved corresponding anti-defense measures. We investigated the diversity of CRISPR-Cas systems and the presence of prophages in the genomes of 66 Bifidobacterium pseudocatenulatum strains. Our findings revealed a high occurrence of complete CRISPR-Cas systems (62%, 41/66) in the B. pseudocatenulatum genomes. Subtypes I-C, I-U and II-A, were found to be widespread in this species. No significant association was found between the number of bacterial CRISPR spacers and its host’s age. This study on prophages within B. pseudocatenulatum genomes revealed that prophage genes related to distinct functional modules became degraded at different levels, indicating that these prophages were not likely to enter lytic cycle spontaneously. Further, the evolutionary analysis of prophages in this study revealed that they might be derived from different phage ancestors. Notably, self-targeting phenomenon within B. pseudocatenulatum and Anti-CRISPR (Acr) coding genes in prophages was observed. Overall, our results indicate that the competition between B. pseudocatenulatum and phages is a major driving factor for the genomic diversity of both partners. |
| first_indexed | 2024-12-12T08:50:15Z |
| format | Article |
| id | doaj.art-4824d6377e9c47848a8d3b66f9840415 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-12T08:50:15Z |
| publishDate | 2020-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-4824d6377e9c47848a8d3b66f98404152022-12-22T00:30:16ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-05-011110.3389/fmicb.2020.01088507694The Diversity of the CRISPR-Cas System and Prophages Present in the Genome Reveals the Co-evolution of Bifidobacterium pseudocatenulatum and PhagesGang Wang0Qian Liu1Zhangming Pei2Linlin Wang3Peijun Tian4Zhenmin Liu5Jianxin Zhao6Jianxin Zhao7Jianxin Zhao8Hao Zhang9Hao Zhang10Hao Zhang11Hao Zhang12Hao Zhang13Wei Chen14Wei Chen15Wei Chen16Wei Chen17State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, ChinaState Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, ChinaState Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, ChinaState Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, ChinaState Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, ChinaState Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai, ChinaState Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, ChinaSchool of Food Science and Technology, Jiangnan University, Wuxi, ChinaInternational Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, ChinaState Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, ChinaSchool of Food Science and Technology, Jiangnan University, Wuxi, China(Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, ChinaNational Engineering Research Center for Functional Food, Jiangnan University, Wuxi, ChinaWuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, ChinaState Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, ChinaSchool of Food Science and Technology, Jiangnan University, Wuxi, ChinaNational Engineering Research Center for Functional Food, Jiangnan University, Wuxi, ChinaBeijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, ChinaDiverse CRISPR-Cas systems constitute an indispensable part of the bacterial adaptive immune system against viral infections. However, to escape from this immune system, bacteriophages have also evolved corresponding anti-defense measures. We investigated the diversity of CRISPR-Cas systems and the presence of prophages in the genomes of 66 Bifidobacterium pseudocatenulatum strains. Our findings revealed a high occurrence of complete CRISPR-Cas systems (62%, 41/66) in the B. pseudocatenulatum genomes. Subtypes I-C, I-U and II-A, were found to be widespread in this species. No significant association was found between the number of bacterial CRISPR spacers and its host’s age. This study on prophages within B. pseudocatenulatum genomes revealed that prophage genes related to distinct functional modules became degraded at different levels, indicating that these prophages were not likely to enter lytic cycle spontaneously. Further, the evolutionary analysis of prophages in this study revealed that they might be derived from different phage ancestors. Notably, self-targeting phenomenon within B. pseudocatenulatum and Anti-CRISPR (Acr) coding genes in prophages was observed. Overall, our results indicate that the competition between B. pseudocatenulatum and phages is a major driving factor for the genomic diversity of both partners.https://www.frontiersin.org/article/10.3389/fmicb.2020.01088/fullBifidobacterium pseudocatenulatumCRISPR-Cas systemsprophageco-evolutiongenomic diversity |
| spellingShingle | Gang Wang Qian Liu Zhangming Pei Linlin Wang Peijun Tian Zhenmin Liu Jianxin Zhao Jianxin Zhao Jianxin Zhao Hao Zhang Hao Zhang Hao Zhang Hao Zhang Hao Zhang Wei Chen Wei Chen Wei Chen Wei Chen The Diversity of the CRISPR-Cas System and Prophages Present in the Genome Reveals the Co-evolution of Bifidobacterium pseudocatenulatum and Phages Frontiers in Microbiology Bifidobacterium pseudocatenulatum CRISPR-Cas systems prophage co-evolution genomic diversity |
| title | The Diversity of the CRISPR-Cas System and Prophages Present in the Genome Reveals the Co-evolution of Bifidobacterium pseudocatenulatum and Phages |
| title_full | The Diversity of the CRISPR-Cas System and Prophages Present in the Genome Reveals the Co-evolution of Bifidobacterium pseudocatenulatum and Phages |
| title_fullStr | The Diversity of the CRISPR-Cas System and Prophages Present in the Genome Reveals the Co-evolution of Bifidobacterium pseudocatenulatum and Phages |
| title_full_unstemmed | The Diversity of the CRISPR-Cas System and Prophages Present in the Genome Reveals the Co-evolution of Bifidobacterium pseudocatenulatum and Phages |
| title_short | The Diversity of the CRISPR-Cas System and Prophages Present in the Genome Reveals the Co-evolution of Bifidobacterium pseudocatenulatum and Phages |
| title_sort | diversity of the crispr cas system and prophages present in the genome reveals the co evolution of bifidobacterium pseudocatenulatum and phages |
| topic | Bifidobacterium pseudocatenulatum CRISPR-Cas systems prophage co-evolution genomic diversity |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2020.01088/full |
| work_keys_str_mv | AT gangwang thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT qianliu thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT zhangmingpei thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT linlinwang thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT peijuntian thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT zhenminliu thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT jianxinzhao thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT jianxinzhao thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT jianxinzhao thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT haozhang thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT haozhang thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT haozhang thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT haozhang thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT haozhang thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT weichen thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT weichen thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT weichen thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT weichen thediversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT gangwang diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT qianliu diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT zhangmingpei diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT linlinwang diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT peijuntian diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT zhenminliu diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT jianxinzhao diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT jianxinzhao diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT jianxinzhao diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT haozhang diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT haozhang diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT haozhang diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT haozhang diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT haozhang diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT weichen diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT weichen diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT weichen diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages AT weichen diversityofthecrisprcassystemandprophagespresentinthegenomerevealsthecoevolutionofbifidobacteriumpseudocatenulatumandphages |