Structural basis for RNA-guided DNA degradation by Cas5-HNH/Cascade complex
Abstract Type I-E CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated proteins) system is one of the most extensively studied RNA-guided adaptive immune systems in prokaryotes, providing defense against foreign genetic elements. Unlike the previously characteriz...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-02-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-55716-7 |
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| _version_ | 1823861785241845760 |
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| author | Yanan Liu Lin Wang Qian Zhang Pengyu Fu Lingling Zhang Ying Yu Heng Zhang Hongtao Zhu |
| author_facet | Yanan Liu Lin Wang Qian Zhang Pengyu Fu Lingling Zhang Ying Yu Heng Zhang Hongtao Zhu |
| author_sort | Yanan Liu |
| collection | DOAJ |
| description | Abstract Type I-E CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated proteins) system is one of the most extensively studied RNA-guided adaptive immune systems in prokaryotes, providing defense against foreign genetic elements. Unlike the previously characterized Cas3 nuclease, which exhibits progressive DNA cleavage in the typical type I-E system, a recently identified HNH-comprising Cascade system enables precise DNA cleavage. Here, we present several near-atomic cryo-electron microscopy (cryo-EM) structures of the Candidatus Cloacimonetes bacterium Cas5-HNH/Cascade complex, both in its DNA-bound and unbound states. Our analysis reveals extensive interactions between the HNH domain and adjacent subunits, including Cas6 and Cas11, with mutations in these key interactions significantly impairing enzymatic activity. Upon DNA binding, the Cas5-HNH/Cascade complex adopts a more compact conformation, with subunits converging toward the center of nuclease, leading to its activation. Notably, we also find that divalent ions such as zinc, cobalt, and nickel down-regulate enzyme activity by destabilizing the Cascade complex. Together, these findings offer structural insights into the assembly and activation of the Cas5-HNH/Cascade complex. |
| format | Article |
| id | doaj-art-20793591fe964e4f9f3a173df36b78f2 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-20793591fe964e4f9f3a173df36b78f22025-02-09T12:46:30ZengNature PortfolioNature Communications2041-17232025-02-0116111110.1038/s41467-024-55716-7Structural basis for RNA-guided DNA degradation by Cas5-HNH/Cascade complexYanan Liu0Lin Wang1Qian Zhang2Pengyu Fu3Lingling Zhang4Ying Yu5Heng Zhang6Hongtao Zhu7Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of SciencesBeijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of SciencesDepartment of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical UniversityDepartment of Pharmacology, School of Basic Medical Sciences, Tianjin Medical UniversityDepartment of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical UniversityDepartment of Pharmacology, School of Basic Medical Sciences, Tianjin Medical UniversityDepartment of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical UniversityBeijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of SciencesAbstract Type I-E CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated proteins) system is one of the most extensively studied RNA-guided adaptive immune systems in prokaryotes, providing defense against foreign genetic elements. Unlike the previously characterized Cas3 nuclease, which exhibits progressive DNA cleavage in the typical type I-E system, a recently identified HNH-comprising Cascade system enables precise DNA cleavage. Here, we present several near-atomic cryo-electron microscopy (cryo-EM) structures of the Candidatus Cloacimonetes bacterium Cas5-HNH/Cascade complex, both in its DNA-bound and unbound states. Our analysis reveals extensive interactions between the HNH domain and adjacent subunits, including Cas6 and Cas11, with mutations in these key interactions significantly impairing enzymatic activity. Upon DNA binding, the Cas5-HNH/Cascade complex adopts a more compact conformation, with subunits converging toward the center of nuclease, leading to its activation. Notably, we also find that divalent ions such as zinc, cobalt, and nickel down-regulate enzyme activity by destabilizing the Cascade complex. Together, these findings offer structural insights into the assembly and activation of the Cas5-HNH/Cascade complex.https://doi.org/10.1038/s41467-024-55716-7 |
| spellingShingle | Yanan Liu Lin Wang Qian Zhang Pengyu Fu Lingling Zhang Ying Yu Heng Zhang Hongtao Zhu Structural basis for RNA-guided DNA degradation by Cas5-HNH/Cascade complex Nature Communications |
| title | Structural basis for RNA-guided DNA degradation by Cas5-HNH/Cascade complex |
| title_full | Structural basis for RNA-guided DNA degradation by Cas5-HNH/Cascade complex |
| title_fullStr | Structural basis for RNA-guided DNA degradation by Cas5-HNH/Cascade complex |
| title_full_unstemmed | Structural basis for RNA-guided DNA degradation by Cas5-HNH/Cascade complex |
| title_short | Structural basis for RNA-guided DNA degradation by Cas5-HNH/Cascade complex |
| title_sort | structural basis for rna guided dna degradation by cas5 hnh cascade complex |
| url | https://doi.org/10.1038/s41467-024-55716-7 |
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