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Yang Q, Feng Y, Zhang Y, Wang M, Jia R, Zhu D, Chen S, Liu M, Zhao X, Wu Y, Zhang S, Tian B, Ou X, Mao S, Huang J, Gao Q, Sun D, Wu Z, He Y, Zhang L, Yu Y, Cheng A. Characteristics of the a sequence of the duck Plague virus genome and specific cleavage of the viral genome based on the a sequence. Vet Res 2024; 55:2. [PMID: 38172999 PMCID: PMC10763189 DOI: 10.1186/s13567-023-01256-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 10/25/2023] [Indexed: 01/05/2024] Open
Abstract
During the replication process, the herpesvirus genome forms the head-to-tail linked concatemeric genome, which is then cleaved and packaged into the capsid. The cleavage and packing process is carried out by the terminase complex, which specifically recognizes and cleaves the concatemeric genome. This process is governed by a cis-acting sequence in the genome, named the a sequence. The a sequence and genome cleavage have been described in some herpesviruses, but it remains unclear in duck plague virus. In this study, we analysed the location, composition, and conservation of a sequence in the duck plague virus genome. The structure of the DPV genome has an a sequence of (DR4)m-(DR2)n-pac1-S termini (32 bp)-L termini (32 bp)-pac2, and the length is 841 bp. Direct repeat (DR) sequences are conserved in different DPV strains, but the number of DR copies is inconsistent. Additionally, the typical DR1 sequence was not found in the DPV a sequence. The Pac1 and pac2 motifs are relatively conserved between DPV and other herpesviruses. Cleavage of the DPV concatemeric genome was detected, and the results showed that the DPV genome can form a concatemer and is cleaved into a monomer at a specific site. We also established a sensitive method, TaqMan dual qRT‒PCR, to analyse genome cleavage. The ratio of concatemer to total viral genome was decreased during the replication process. These results will be critical for understanding the process of DPV genome cleavage, and the application of TaqMan dual qRT‒PCR will greatly facilitate more in-depth research.
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Affiliation(s)
- Qiao Yang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Yaya Feng
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Yuanxin Zhang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Mingshu Wang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Renyong Jia
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Dekang Zhu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Shun Chen
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Mafeng Liu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Xinxin Zhao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Ying Wu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Shaqiu Zhang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Bin Tian
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Xumin Ou
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Sai Mao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Juan Huang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Qun Gao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Di Sun
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Zhen Wu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Yu He
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Ling Zhang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Yanling Yu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China
| | - Anchun Cheng
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China.
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, China.
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Guo P, Driver D, Zhao Z, Zheng Z, Chan C, Cheng X. Controlling the Revolving and Rotating Motion Direction of Asymmetric Hexameric Nanomotor by Arginine Finger and Channel Chirality. ACS NANO 2019; 13:6207-6223. [PMID: 31067030 PMCID: PMC6595433 DOI: 10.1021/acsnano.8b08849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Nanomotors in nanotechnology are as important as engines in daily life. Many ATPases are nanoscale biomotors classified into three categories based on the motion mechanisms in transporting substrates: linear, rotating, and the recently discovered revolving motion. Most biomotors adopt a multisubunit ring-shaped structure that hydrolyzes ATP to generate force. How these biomotors control the motion direction and regulate the sequential action of their multiple subunits is intriguing. Many ATPases are hexameric with each monomer containing a conserved arginine finger. This review focuses on recent findings on how the arginine finger controls motion direction and coordinates adjacent subunit interactions in both revolving and rotating biomotors. Mechanisms of intersubunit interactions and sequential movements of individual subunits are evidenced by the asymmetrical appearance of one dimer and four monomers in high-resolution structural complexes. The arginine finger is situated at the interface of two subunits and extends into the ATP binding pocket of the downstream subunit. An arginine finger mutation results in deficiency in ATP binding/hydrolysis, substrate binding, and transport, highlighting the importance of the arginine finger in regulating energy transduction and motor function. Additionally, the roles of channel chirality and channel size are discussed as related to controlling one-way trafficking and differentiating the revolving and rotating mechanisms. Finally, the review concludes by discussing the conformational changes and entropy conversion triggered by ATP binding/hydrolysis, offering a view different from the traditional concept of ATP-mediated mechanochemical energy coupling. The elucidation of the motion mechanism and direction control in ATPases could facilitate nanomotor fabrication in nanotechnology.
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Affiliation(s)
- Peixuan Guo
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
- E-mail:
| | - Dana Driver
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Zhengyi Zhao
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Zhen Zheng
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Chun Chan
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Xiaolin Cheng
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
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