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Li Z, Bi Y, Xiao H, Sun L, Ren Y, Li Y, Chen C, Cun W. CRISPR-Cas9 system-driven site-specific selection pressure on Herpes simplex virus genomes. Virus Res 2018; 244:286-295. [PMID: 28279800 DOI: 10.1016/j.virusres.2017.03.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/03/2017] [Accepted: 03/05/2017] [Indexed: 01/05/2023]
Abstract
The CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9) system has been widely used for viral genome editing, transcription regulation and chromosomal localization in eukaryotic cells. In this study, a guide RNA (gRNA) that specifically recognizes HSV-1 viral genomes was used in the CRISPR-Cas9 system to inhibit viral replication. This inhibition could be achieved with both wild type Cas9 protein and Cas9 nickase (D10A). By targeting viral genomes containing sequences recognized by the gRNA, the CRISPR-Cas9 system distinguished between different viral genome sequences and provided single nucleotide-specific selection pressure to significantly change the proportions of viruses in a mixed viral pool. This finding indicates the utility of this tool for virus selection without the need for antibiotics or reporter genes, which could potentially save time compared to other methods used for screening and purifying mutant viruses.
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Affiliation(s)
- Zhihua Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, 935 Jiaoling Road, Wuhua District, Kunming, Yunnan, 650118 China; Yunnan Key Laboratory of Vaccine Research and Development of Severe Infectious Disease, Kunming, Yunnan, China; Centre for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yanwei Bi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, 935 Jiaoling Road, Wuhua District, Kunming, Yunnan, 650118 China; Yunnan Key Laboratory of Vaccine Research and Development of Severe Infectious Disease, Kunming, Yunnan, China; Centre for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Hongjian Xiao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, 935 Jiaoling Road, Wuhua District, Kunming, Yunnan, 650118 China; Yunnan Key Laboratory of Vaccine Research and Development of Severe Infectious Disease, Kunming, Yunnan, China; Centre for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Le Sun
- Kunming Medical University, 1168 West Chunrong Road, Kunming, Yunnan, 650500, China.
| | - Yuan Ren
- Baoshan College of Traditional Chinese Medicine, No. 20, The sixth Community, Yaowan Village, Longyang District, Baoshan, Yunnan, 678000, China.
| | - Yadong Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, 935 Jiaoling Road, Wuhua District, Kunming, Yunnan, 650118 China; Yunnan Key Laboratory of Vaccine Research and Development of Severe Infectious Disease, Kunming, Yunnan, China.
| | - Chen Chen
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, 935 Jiaoling Road, Wuhua District, Kunming, Yunnan, 650118 China; Yunnan Key Laboratory of Vaccine Research and Development of Severe Infectious Disease, Kunming, Yunnan, China.
| | - Wei Cun
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, 935 Jiaoling Road, Wuhua District, Kunming, Yunnan, 650118 China; Yunnan Key Laboratory of Vaccine Research and Development of Severe Infectious Disease, Kunming, Yunnan, China; Centre for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Tan YW, Fung TS, Shen H, Huang M, Liu DX. Coronavirus infectious bronchitis virus non-structural proteins 8 and 12 form stable complex independent of the non-translated regions of viral RNA and other viral proteins. Virology 2017; 513:75-84. [PMID: 29035788 PMCID: PMC7112110 DOI: 10.1016/j.virol.2017.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/27/2017] [Accepted: 10/02/2017] [Indexed: 02/03/2023]
Abstract
The cleavage products from coronavirus polyproteins, known as the non-structural proteins (nsps), are believed to make up the major components of the viral replication/transcription complex. In this study, several nsps encoded by avian gammacoronavirus infectious bronchitis virus (IBV) were screened for RNA-binding activity and interaction with its RNA-dependent RNA polymerase, nsp12. Nsp2, nsp5, nsp8, nsp9 and nsp10 were found to bind to untranslated regions (UTRs), while nsp8 was confirmed to interact with nsp12. Nsp8 has been reported to interact with nsp7 and functions as a primase synthesizing RNA primers for nsp12. Further characterization revealed that nsp8-nsp12 interaction is independent of the UTRs of viral RNA, and nsp8 interacts with both the N- and C-terminal regions of nsp12. These results have prompted a proposal of how the nsp7-nsp8 complex could possibly function in tandem with nsp12, forming a highly efficient complex that could synthesize both the RNA primer and viral RNA during coronavirus infection.
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Affiliation(s)
- Yong Wah Tan
- South China Agricultural University, Guangdong Province Key Laboratory Microbial Signals & Disease Co, and Integrative Microbiology Research Centre, Guangzhou 510642, Guangdong, People's Republic of China; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 63755, Singapore; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos 138673, Singapore
| | - To Sing Fung
- South China Agricultural University, Guangdong Province Key Laboratory Microbial Signals & Disease Co, and Integrative Microbiology Research Centre, Guangzhou 510642, Guangdong, People's Republic of China
| | - Hongyuan Shen
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos 138673, Singapore
| | - Mei Huang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 63755, Singapore
| | - Ding Xiang Liu
- South China Agricultural University, Guangdong Province Key Laboratory Microbial Signals & Disease Co, and Integrative Microbiology Research Centre, Guangzhou 510642, Guangdong, People's Republic of China.
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Ream DC, Murakami ST, Schmidt EE, Huang GH, Liang C, Friedberg I, Cheng XW. Comparative analysis of error-prone replication mononucleotide repeats across baculovirus genomes. Virus Res 2013; 178:217-25. [PMID: 24140718 DOI: 10.1016/j.virusres.2013.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 10/04/2013] [Accepted: 10/07/2013] [Indexed: 11/25/2022]
Abstract
Genome replication by the baculovirus DNA polymerase often generates errors in mononucleotide repeat (MNR) sequences due to replication slippage. This results in the inactivation of genes that affects different stages of the cell infection cycle. Here we mapped these MNRs in the 59 baculovirus genomes. We found that the MNR frequencies of baculovirus genomes are different and not correlated with the genome sizes. Although the average A/T content of baculoviruses is 58.67%, the A/T MNR frequency is significantly higher than that of the G/C MNRs. Furthermore, the A7/T7 MNRs are the most frequent of those we studied. Finally, MNR frequencies in different classes of baculovirus genes, such as immediate early genes, show differences between baculovirus genomes, suggesting that the distribution and frequency of different MNRs are unique to each baculovirus species or strain. Therefore, the results of this study can help select appropriate baculoviruses for the development of biological insecticides.
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Affiliation(s)
- David C Ream
- Department of Microbiology, Miami University, Oxford, OH, USA
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