Preferential cleavage of the coronavirus defective viral genome by cellular endoribonuclease with characteristics of RNase L
Abstract In testing whether coronavirus defective viral genome 12.7 (DVG12.7) with transcription regulating sequence (TRS) can synthesize subgenomic mRNA (sgmRNA) in coronavirus-infected cells, it was unexpectedly found by Northern blot assay that not only sgmRNA (designated sgmDVG 12.7) but also an...
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BMC
2024-11-01
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| Series: | Virology Journal |
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| Online Access: | https://doi.org/10.1186/s12985-024-02549-x |
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| author | Ching-Hung Lin Hsuan-Yung Lin Chun-Chun Yang Hsuan-Wei Hsu Feng-Cheng Hsieh Cheng-Yao Yang Hung-Yi Wu |
| author_facet | Ching-Hung Lin Hsuan-Yung Lin Chun-Chun Yang Hsuan-Wei Hsu Feng-Cheng Hsieh Cheng-Yao Yang Hung-Yi Wu |
| author_sort | Ching-Hung Lin |
| collection | DOAJ |
| description | Abstract In testing whether coronavirus defective viral genome 12.7 (DVG12.7) with transcription regulating sequence (TRS) can synthesize subgenomic mRNA (sgmRNA) in coronavirus-infected cells, it was unexpectedly found by Northern blot assay that not only sgmRNA (designated sgmDVG 12.7) but also an RNA fragment with a size less than sgmDVG 12.7 was identified. A subsequent study demonstrated that the identified RNA fragment (designated clvDVG) was a cleaved RNA product originating from DVG12.7, and the cleaved sites were located in the loop region of stem‒loop structure and after UU and UA dinucleotides. clvDVG was also identified in mock-infected HRT-18 cells transfected with DVG12.7 transcript, indicating that cellular endoribonuclease is responsible for the cleavage. In addition, the sequence and structure surrounding the cleavage sites can affect the cleavage efficiency of DVG12.7. The cleavage features are therefore consistent with the general criteria for RNA cleavage by cellular RNase L. Furthermore, both the cleavage of rRNA and the synthesis of clvDVG were also identified in A549 cells. Because (i) the cleavage sites occurred predominantly after single-stranded UA and UU dinucleotides, (ii) the sequence and structure surrounding the cleavage sites affected the cleavage efficiency, (iii) the cleavage of rRNA is an index of the activation of RNase L, and (iv) the cleavage of both rRNA and DVG12.7 was identified in A549 cells, the results together indicated that the preferential cleavage of DVG12.7 is correlated with cellular endoribonuclease with the characteristics of RNase L and such cleavage features have not been previously characterized in coronaviruses. |
| format | Article |
| id | doaj-art-151918d2b83c4cf7b0fb1b72ac104afc |
| institution | OA Journals |
| issn | 1743-422X |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj-art-151918d2b83c4cf7b0fb1b72ac104afc2025-08-20T02:18:24ZengBMCVirology Journal1743-422X2024-11-012111910.1186/s12985-024-02549-xPreferential cleavage of the coronavirus defective viral genome by cellular endoribonuclease with characteristics of RNase LChing-Hung Lin0Hsuan-Yung Lin1Chun-Chun Yang2Hsuan-Wei Hsu3Feng-Cheng Hsieh4Cheng-Yao Yang5Hung-Yi Wu6Department of Veterinary Medicine, National Pingtung University of Science and TechnologyGraduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing UniversityGraduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing UniversityGraduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing UniversityGraduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing UniversityGraduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing UniversityGraduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing UniversityAbstract In testing whether coronavirus defective viral genome 12.7 (DVG12.7) with transcription regulating sequence (TRS) can synthesize subgenomic mRNA (sgmRNA) in coronavirus-infected cells, it was unexpectedly found by Northern blot assay that not only sgmRNA (designated sgmDVG 12.7) but also an RNA fragment with a size less than sgmDVG 12.7 was identified. A subsequent study demonstrated that the identified RNA fragment (designated clvDVG) was a cleaved RNA product originating from DVG12.7, and the cleaved sites were located in the loop region of stem‒loop structure and after UU and UA dinucleotides. clvDVG was also identified in mock-infected HRT-18 cells transfected with DVG12.7 transcript, indicating that cellular endoribonuclease is responsible for the cleavage. In addition, the sequence and structure surrounding the cleavage sites can affect the cleavage efficiency of DVG12.7. The cleavage features are therefore consistent with the general criteria for RNA cleavage by cellular RNase L. Furthermore, both the cleavage of rRNA and the synthesis of clvDVG were also identified in A549 cells. Because (i) the cleavage sites occurred predominantly after single-stranded UA and UU dinucleotides, (ii) the sequence and structure surrounding the cleavage sites affected the cleavage efficiency, (iii) the cleavage of rRNA is an index of the activation of RNase L, and (iv) the cleavage of both rRNA and DVG12.7 was identified in A549 cells, the results together indicated that the preferential cleavage of DVG12.7 is correlated with cellular endoribonuclease with the characteristics of RNase L and such cleavage features have not been previously characterized in coronaviruses.https://doi.org/10.1186/s12985-024-02549-xCoronavirusDefective viral genomeRNA cleavageEndoribonucleaseRNase L |
| spellingShingle | Ching-Hung Lin Hsuan-Yung Lin Chun-Chun Yang Hsuan-Wei Hsu Feng-Cheng Hsieh Cheng-Yao Yang Hung-Yi Wu Preferential cleavage of the coronavirus defective viral genome by cellular endoribonuclease with characteristics of RNase L Virology Journal Coronavirus Defective viral genome RNA cleavage Endoribonuclease RNase L |
| title | Preferential cleavage of the coronavirus defective viral genome by cellular endoribonuclease with characteristics of RNase L |
| title_full | Preferential cleavage of the coronavirus defective viral genome by cellular endoribonuclease with characteristics of RNase L |
| title_fullStr | Preferential cleavage of the coronavirus defective viral genome by cellular endoribonuclease with characteristics of RNase L |
| title_full_unstemmed | Preferential cleavage of the coronavirus defective viral genome by cellular endoribonuclease with characteristics of RNase L |
| title_short | Preferential cleavage of the coronavirus defective viral genome by cellular endoribonuclease with characteristics of RNase L |
| title_sort | preferential cleavage of the coronavirus defective viral genome by cellular endoribonuclease with characteristics of rnase l |
| topic | Coronavirus Defective viral genome RNA cleavage Endoribonuclease RNase L |
| url | https://doi.org/10.1186/s12985-024-02549-x |
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