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Rani S, Mamathashree MN, Bharthi I U, Patil SS, Krishnamoorthy P, Shueb M, Pandey RK, Suresh KP. Comprehensive examination on codon usage bias pattern of the Bovine Ephemeral fever virus. J Biomol Struct Dyn 2023:1-11. [PMID: 37705249 DOI: 10.1080/07391102.2023.2258220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Bovine Ephemeral Fever Virus (BEFV) is a non-contagious virus that commonly infects cattle and water buffalo, reduces milk productivity, decreases the quality of beef, and causes an adverse economic impact on the global livestock industry. However, the evolution of BEFV is unclear, and uncertainty exists regarding its global geodynamics. Consequently, this study aims to comprehend the pattern of viral evolution and gene expression in the BEFV genes G, M, N, and P, including synonymous codons. Additionally, we performed recombination analyses, which exclusively detected recombination signals in the G- and P-genes. Subsequently, a phylogenetic tree was constructed to validate and support these findings. The codon usage bias results showed that the BEFV-selected genes were influenced by both natural and mutation pressure. Furthermore, nucleotide A is more abundant in all the selected genes. The eNC values, ranging from 42.99 to 47.10, revealed the presence of moderate codon usage bias, where gene P exhibited the highest and gene G had the lowest codon usage bias. The neutrality and PR-2 plots, specified codon usage patterns of the genes, are also being shaped by strong selectional pressure. This comprehensive analysis of BEFV genes (G, M, N, and P) sheds light on the molecular evolutionary patterns, co-adaptation, and different genes expression in diverse regions, facilitating the development of preventative programs and insights into viral pathogenesis and vaccine design.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Swati Rani
- Disease Informatics, Spatial Epidemiology Lab, ICAR - National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
| | - M N Mamathashree
- Disease Informatics, Spatial Epidemiology Lab, ICAR - National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
| | - Uma Bharthi I
- Disease Informatics, Spatial Epidemiology Lab, ICAR - National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
| | - S S Patil
- Disease Informatics, Spatial Epidemiology Lab, ICAR - National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
| | - P Krishnamoorthy
- Disease Informatics, Spatial Epidemiology Lab, ICAR - National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
| | - Mohammad Shueb
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, India
| | - Rajan Kumar Pandey
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - K P Suresh
- Disease Informatics, Spatial Epidemiology Lab, ICAR - National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
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Pyasi S, Jonniya NA, Sk MF, Nayak D, Kar P. Finding potential inhibitors against RNA-dependent RNA polymerase (RdRp) of bovine ephemeral fever virus (BEFV): an in- silico study. J Biomol Struct Dyn 2022; 40:10403-10421. [PMID: 34238122 DOI: 10.1080/07391102.2021.1946714] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The bovine ephemeral fever virus (BEFV) is an enzootic agent that affects millions of bovines and causes major economic losses. Though the virus is seasonally reported with a very high morbidity rate (80-100%) from African, Australian, and Asiatic continents, it remains a neglected pathogen in many of its endemic areas, with no proper therapeutic drugs or vaccines presently available for treatment. The RNA-dependent RNA polymerase (RdRp) catalyzes the viral RNA synthesis and is an appropriate candidate for antiviral drug developments. We utilized integrated computational tools to build the 3D model of BEFV-RdRp and then predicted its probable active binding sites. The virtual screening and optimization against these active sites, using several small-molecule inhibitors from a different category of Life Chemical database and FDA-approved drugs from the ZINC database, was performed. We found nine molecules that have docking scores varying between -6.84 to -10.43 kcal/mol. Furthermore, these complexes were analyzed for their conformational dynamics and thermodynamic stability using molecular dynamics simulations in conjunction with the molecular mechanics generalized Born surface area (MM-GBSA) scheme. The binding free energy calculations depict that the electrostatic interactions play a dominant role in the RdRp-inhibitor binding. The hot spot residues, such as Arg565, Asp631, Glu633, Asp740, and Glu707, were found to control the RdRp-inhibitor interaction. The ADMET analysis strongly suggests favorable pharmacokinetics of these compounds that may prove useful for treating the BEFV ailment. Overall, we anticipate that these findings would help explore and develop a wide range of anti-BEFV therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shruti Pyasi
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Debasis Nayak
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
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Zhao W, Hou P, Ma W, Jiang C, Wang H, He H. Bta-miR-101 suppresses BEFV replication via targeting NKRF. Vet Microbiol 2021; 259:109127. [PMID: 34058703 DOI: 10.1016/j.vetmic.2021.109127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/03/2021] [Accepted: 05/16/2021] [Indexed: 01/02/2023]
Abstract
MicroRNAs (miRNAs), as a kind of small noncoding RNAs, have been proved to play a regulatory role in virus infection. However, the role and mechanism of cellular miRNAs in bovine transient fever virus (BEFV) infection are largely unknown. In the present study, we found that bta-miR-101 was significantly up-regulated in the Madin-Darby Bovine Kidney (MDBK) cells upon BEFV infection. Notably, bta-miR-101 mimic dramatically inhibited BEFV replication, while bta-miR-101 inhibitor facilitated BEFV replication, suggesting that bta-miR-101 acted as an anti-viral host factor restraining BEFV replication. Subsequently, NF-κB repressing factor (NKRF) was identified as a target gene of bta-miR-101 by dual luciferase reporter assay, and bta-miR-101 mimic significantly down-regulated expression of NKRF, while bta-miR-101 inhibitor up-regulated its expression, respectively. Furthermore, NKRF could induce apoptosis, and favored the replication of BEFV. Finally, bta-miR-101 inhibited BEFV-induced apoptosis via targeting NKRF to suppress virus replication. In general, our study provides a novel mechanism for bta-miR-101 to exert its antiviral function, which provides a theoretical basis for the development of antiviral strategy.
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Affiliation(s)
- Wendong Zhao
- Ruminant Disease Research Center, College of Life Science, Shandong Normal University, Shandong Province, China.
| | - Peili Hou
- Ruminant Disease Research Center, College of Life Science, Shandong Normal University, Shandong Province, China.
| | - Wenqing Ma
- Ruminant Disease Research Center, College of Life Science, Shandong Normal University, Shandong Province, China.
| | - Chuan Jiang
- Ruminant Disease Research Center, College of Life Science, Shandong Normal University, Shandong Province, China.
| | - Hongmei Wang
- Ruminant Disease Research Center, College of Life Science, Shandong Normal University, Shandong Province, China.
| | - Hongbin He
- Ruminant Disease Research Center, College of Life Science, Shandong Normal University, Shandong Province, China.
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Zhang Y, Hou P, He DC, Wang H, He H. RACK1 degrades MAVS to promote bovine ephemeral fever virus replication via upregulating E3 ubiquitin ligase STUB1. Vet Microbiol 2021; 257:109096. [PMID: 33940459 DOI: 10.1016/j.vetmic.2021.109096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/25/2021] [Indexed: 11/21/2022]
Abstract
Receptors for activated C kinase 1 (RACK1) could competitively combine with mitochondrial antiviral signaling protein (MAVS) to inhibit the type I interferon (IFN) signaling pathway during viral infection in vitro. However, whether RACK1 can degrade MAVS to enhance viral replication is still unknown. In this study, we found that bovine epidemic fever virus (BEFV) infection triggered the expression of RACK1. Overexpression of RACK1 promoted BEFV replication, while knockdown of RACK1 inhibited the replication of BEFV. Further research showed that RACK1 inhibited the type I IFN signaling pathway during BEFV infection by degrading MAVS, and RACK1 degraded MAVS via the ubiquitin-proteasome system. Mechanistically, RACK1 up-regulated the expression of E3 ubiquitin ligase STIP1 homology and U-box containing protein 1 (STUB1), thereby promoting the ubiquitination and degradation of MAVS. In addition, RACK1 degraded MAVS by enhancing the interaction between STUB1 and MAVS but not via its interaction with STUB1. Overall, our study reveals a novel mechanism by which RACK1 inhibits the type I IFN signaling pathway to BEFV infection through degradation of MAVS, thereby promoting viral infection. These findings provide a new perspective for the MAVS degradation regulated by RACK1.
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Hou P, Wang H, Zhao G, Hu G, Xia X, He H. MiR-3470b promotes bovine ephemeral fever virus replication via directly targeting mitochondrial antiviral signaling protein (MAVS) in baby hamster Syrian kidney cells. BMC Microbiol 2018; 18:224. [PMID: 30587113 PMCID: PMC6307158 DOI: 10.1186/s12866-018-1366-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 12/04/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Bovine ephemeral fever virus (BEFV), the causative agent of bovine ephemeral fever, is an economically important pathogen of cattle and water buffalo. MicroRNAs (miRNAs) are endogenous 21-23 nt small non-coding RNA molecules that binding to a multiple of target mRNAs and functioning in the regulation of viral replication including the miRNA-mediated antiviral defense. However, the reciprocal interaction between bovine ephemeral fever virus replication and host miRNAs still remain poorly understood. The aim of our study herein was to investigate the exact function of miR-3470b and its molecular mechanisms during BEFV infection. RESULTS In this study, we found a set of microRNAs induced by BEFV infection using small RNA deep sequencing, and further identified BEFV infection could significantly up-regulate the miR-3470b expression in Baby Hamster Syrian Kidney cells (BHK-21) after 24 h and 48 h post-infection (pi) compared to normal BHK-21 cells without BEFV infection. Additionally, the target association between miR-3470b and mitochondrial antiviral signaling protein (MAVS) was predicted by target gene prediction tools and further validated using a dual-luciferase reporter assay, and the expression of MAVS mRNA and protein levels was negatively associated with miR-3470b levels. Furthermore, the miR-3470b mimic transfection significantly contributed to increase the BEFV N mRNA, G protein level and viral titer, respectively, whereas the miR-3470b inhibitor had the opposite effect on BEFV replication. Moreover, the overexpression of MAVS or silencing of miR-3470b by its inhibitors suppressed BEFV replication, and knockdown of MAVS by small interfering RNA also promoted the replication of BEFV. CONCLUSIONS Our findings is the first to reveal that miR-3470b as a novel host factor regulates BEFV replication via directly targeting the MAVS gene in BHK-21 cells and may provide a potential strategy for developing effective antiviral therapy.
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Affiliation(s)
- Peili Hou
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Hongmei Wang
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Guimin Zhao
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Guixue Hu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122 People’s Republic of China
| | - Hongbin He
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, 250014 People’s Republic of China
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Pasandideh R, Seyfi Abad Shapouri MR, Beigi Nassiri MT. Immunogenicity of a plasmid DNA vaccine encoding G1 epitope of bovine ephemeral fever virus G glycoprotein in mice. Onderstepoort J Vet Res 2018; 85:e1-e6. [PMID: 30198280 PMCID: PMC6238684 DOI: 10.4102/ojvr.v85i1.1617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to investigate the immunogenicity of a plasmid deoxyribonucleic acid (DNA) vaccine encoding the G1 epitope of bovine ephemeral fever virus (BEFV) G glycoprotein in mice. A plasmid DNA carrying the G1 gene was constructed and designated as pcDNA3.1-G1. The expression of the target gene was confirmed in human embryonic kidney 293 (HEK 293) cells transfected with pcDNA3.1-G1 by indirect immunofluorescent staining. Immunisation experiments were intramuscularly carried out by vaccinating 6-week-old female mice in four groups, including the pcDNA3.1-G1 construct, pcDNA3.1 (+) plasmid alone, BEF-inactivated vaccine and phosphate-buffered saline (PBS) (1X) three times with 2-week intervals. Fourteen days after the last immunisation, the animals were bled and the resulting sera were tested for anti-G1-specific antibodies by immunoblotting analysis, indirect enzyme-linked immunosorbent assay (ELISA) and virus neutralisation (VN) test. Serological assays showed that the pcDNA3.1-G1 construct expressing G1 protein was able to elicit specific antibodies against this antigen. Virus neutralisation test showed that pcDNA3.1-G1 could induce anti-BEFV-neutralising antibodies in mice. Our findings indicated that a new dimension can be added to vaccine studies for bovine ephemeral fever (BEF) using eukaryotic expression plasmids encoding the G1 antigen in the future.
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Affiliation(s)
- Reza Pasandideh
- Department of Animal Science, Khuzestan Agricultural Sciences and Natural Resources University, Ahvaz.
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Hou P, Zhao G, Wang H, He C, Huan Y, He H. Development of a recombinase polymerase amplification combined with lateral-flow dipstick assay for detection of bovine ephemeral fever virus. Mol Cell Probes 2017; 38:31-37. [PMID: 29288049 PMCID: PMC7126596 DOI: 10.1016/j.mcp.2017.12.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 12/07/2017] [Accepted: 12/19/2017] [Indexed: 11/18/2022]
Abstract
Bovine ephemeral fever virus (BEFV), identified as the causative pathogen of bovine ephemeral fever (BEF), is responsible for increasing numbers of epidemics/outbreaks and has a significant harmful effect on the livestock industry. Therefore, a rapid detection assay is imperative for BEFV diagnosis. In this study, we described the development of lateral-flow dipstick isothermal recombinase polymerase amplification (LFD-RPA) assays for detection of BEFV. RPA primers and LF probes were designed by targeting the specific G gene, and the amplification product can be visualized on a simple lateral flow dipstick with the naked eyes. The amplification reaction was performed at 38 °C for 20 min and LFD incubation time within 5 min. The detection limit of this assay was 8 copies per reaction, and there was no cross-reactivity with other bovine infectious viruses such as bovine viral diarrhea virus, infectious bovine rhinotracheitis virus, bovine respiratory syncytial virus, bovine coronavirus, bovine parainfluenza virus type 3, bovine vesicular stomatitis virus. In addition, the assay was performed with total 128 clinical specimens and the diagnostic results were compared with conventional RT-PCR, real-time quantative(q) PCR. The result showed that the coincidence rate of BEFV LFD-RPA and real-time qPCR was 96.09% (123/128), which was higher than conventional RT-PCR. The RPA combined with LFD assay probably provides a rapid and sensitive alternative for diagnosis of BEFV infections outbreak. RPA combined with LFD assay was developed first time to detect BEFV. The detection from cDNA could be completed within 30 min and be easily visualized with the naked eyes. The RPA combined with LFD assay probably provides a alternative for diagnosis of BEFV.
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Affiliation(s)
- Peili Hou
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China.
| | - Guimin Zhao
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China.
| | - Hongmei Wang
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China.
| | - Chengqiang He
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China.
| | - Yanjun Huan
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China.
| | - Hongbin He
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China.
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