1
|
Xu Q, Cao J, Rai KR, Zhu B, Liu D, Wan C. Codon usage bias of goose circovirus and its adaptation to host. Poult Sci 2024; 103:103775. [PMID: 38713985 DOI: 10.1016/j.psj.2024.103775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 04/03/2024] [Accepted: 04/13/2024] [Indexed: 05/09/2024] Open
Abstract
Goose circovirus (GoCV), a potential immunosuppressive virus possessing a circular single-stranded DNA genome, is widely distributed in both domesticated and wild geese. This virus infection causes significant economic losses in the waterfowl industry. The codon usage patterns of viruses reflect the evolutionary history and genetic architecture, allowing them to adapt quickly to changes in the external environment, particularly to their hosts. In this study, we retrieved the coding sequences (Rep and Cap) and the genome of GoCV from GenBank, conducting comprehensive research to explore the codon usage patterns in 144 GoCV strains. The overall codon usage of the GoCV strains was relatively similar and exhibited a slight bias. The effective number of codons (ENC) indicated a low overall extent of codon usage bias (CUB) in GoCV. Combined with the base composition and relative synonymous codon usage (RSCU) analysis, the results revealed a bias toward A- and G-ending codons in the overall codon usage. Analysis of the ENC-GC3s plot and neutrality plot suggested that natural selection plays an important role in shaping the codon usage pattern of GoCV, with mutation pressure having a minor influence. Furthermore, the correlations between ENC and relative indices, as well as correspondence analysis (COA), showed that hydrophobicity and geographical distribution also contribute to codon usage variation in GoCV, suggesting the possible involvement of natural selection. In conclusion, GoCV exhibits comparatively slight CUB, with natural selection being the major factor shaping the codon usage pattern of GoCV. Our research contributes to a deeper understanding of GoCV evolution and its host adaptation, providing valuable insights for future basic studies and vaccine design related to GoCV.
Collapse
Affiliation(s)
- Quanming Xu
- Scientific Research and Experiment Center, Fujian Police College, Fuzhou 350007, China
| | - Jie Cao
- Scientific Research and Experiment Center, Fujian Police College, Fuzhou 350007, China
| | - Kul Raj Rai
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Binling Zhu
- Department of Forensic Science, Fujian Police College, Fuzhou 350007, China
| | - Dan Liu
- China Institute of Veterinary Drug Control, Beijing, 100081, China
| | - Chunhe Wan
- Institute of Animal Husbandry and Veterinary Medicine/Fujian Key Laboratory for Avian Diseases Control and Prevention/Fujian Animal Diseases Control Technology Development Centre, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China.
| |
Collapse
|
2
|
Khandia R, Ali Khan A, Alexiou A, Povetkin SN, Nikolaevna VM. Codon Usage Analysis of Pro-Apoptotic Bim Gene Isoforms. J Alzheimers Dis 2022; 86:1711-1725. [DOI: 10.3233/jad-215691] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Background: Bim is a Bcl-2 homology 3 (BH3)-only proteins, a group of pro-apoptotic proteins involved in physiological and pathological conditions. Both the overexpression and under-expression of Bim protein are associated with the diseased condition, and various isoforms of Bim protein are present with differential apoptotic potential. Objective: The present study attempted to envisage the association of various molecular signatures with the codon choices of Bim isoforms. Methods: Molecular signatures like composition, codon usage, nucleotide skews, the free energy of mRNA transcript, physical properties of proteins, codon adaptation index, relative synonymous codon usage, and dinucleotide odds ratio were determined and analyzed for their associations with codon choices of Bim gene. Results: Skew analysis of the Bim gene indicated the preference of C nucleotide over G, A, and T and preference of G over T and A nucleotides was observed. An increase in C content at the first and third codon position increased gene expression while it decreased at the second codon position. Compositional constraints on nucleotide C at all three codon positions affected gene expression. The analysis revealed an exceptionally high usage of CpC dinucleotide in all the envisaged 31 isoforms of Bim. We correlated it with the requirement of rapid demethylation machinery to fine-tune the Bimgene expression. Also, mutational pressure played a dominant role in shaping codon usage bias in Bim isoforms. Conclusion: An exceptionally high usage of CpC dinucleotide in all the envisaged 31 isoforms of Bim indicates a high order selectional force to fine tune Bim gene expression.
Collapse
Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Australia & AFNP Med, Austria
| | | | | |
Collapse
|
3
|
Kokate PP, Techtmann SM, Werner T. Codon usage bias and dinucleotide preference in 29 Drosophila species. G3 GENES|GENOMES|GENETICS 2021; 11:6291245. [PMID: 34849812 PMCID: PMC8496323 DOI: 10.1093/g3journal/jkab191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/13/2021] [Indexed: 12/30/2022]
Abstract
Abstract
Codon usage bias, where certain codons are used more frequently than their synonymous counterparts, is an interesting phenomenon influenced by three evolutionary forces: mutation, selection, and genetic drift. To better understand how these evolutionary forces affect codon usage bias, an extensive study to detect how codon usage patterns change across species is required. This study investigated 668 single-copy orthologous genes independently in 29 Drosophila species to determine how the codon usage patterns change with phylogenetic distance. We found a strong correlation between phylogenetic distance and codon usage bias and observed striking differences in codon preferences between the two subgenera Drosophila and Sophophora. As compared to the subgenus Sophophora, species of the subgenus Drosophila showed reduced codon usage bias and a reduced preference specifically for codons ending with C, except for codons with G in the second position. We found that codon usage patterns in all species were influenced by the nucleotides in the codon’s 2nd and 3rd positions rather than the biochemical properties of the amino acids encoded. We detected a concordance between preferred codons and preferred dinucleotides (at positions 2 and 3 of codons). Furthermore, we observed an association between speciation, codon preferences, and dinucleotide preferences. Our study provides the foundation to understand how selection acts on dinucleotides to influence codon usage bias.
Collapse
Affiliation(s)
- Prajakta P Kokate
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Stephen M Techtmann
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Thomas Werner
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| |
Collapse
|
4
|
Chen-Fei L, Chou-Min C, Jiun-Yan L. Feasibility of vaccination against Macrobrachium rosenbergii nodavirus infection in giant freshwater prawn. FISH & SHELLFISH IMMUNOLOGY 2020; 104:431-438. [PMID: 32580003 DOI: 10.1016/j.fsi.2020.06.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/14/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
The giant freshwater prawn/giant river prawn, Macrobrachium rosenbergii is one of the high market value crustaceans cultured worldwide. The intensified aquaculture of the species has led to the outbreak of infectious diseases, prominently, the white tail disease (WTD). It is caused by the infection of Macrobrachium rosenbergii nodavirus (MrNV), which was classified in the family of Nodaviridae. To-date, there are no effective prophylactic and therapeutic agents available against MrNV infection. Vaccination is known to be the most effective prophylactic agent in disease prevention. However, vaccine development against virus infection in crustaceans is equivocal. The feasibility of vaccination in conferring immune protection in crustaceans against infectious diseases is disputable. The argument lies in the fact that crustaceans do not possess adaptive immunity, which is the main immune component that functions to establish immunological memory upon vaccination. Nevertheless, an increasing number of literatures has been documented, which concerns the development of vaccines against infectious diseases in crustaceans. The current review deliberates different approaches in vaccine development against MrNV, which were documented in the past years. It is noteworthy that the live-attenuated MrNV vaccine has not been experimented by far. Thus, the potential of live-attenuated MrNV vaccine in conferring long-term immune protection through the establishment of innate immune memory is currently being discussed.
Collapse
Affiliation(s)
- Low Chen-Fei
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
| | - Chong Chou-Min
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
| | - Loh Jiun-Yan
- Faculty of Applied Sciences, UCSI University, 56000 Cheras, Kuala Lumpur, Malaysia
| |
Collapse
|
5
|
Chen YM, Tan CS, Wang TY, Hwong CL, Chen TY. Characterization of betanodavirus quasispecies influences on the subcellular localization and expression of tumor necrosis factor (TNF). FISH & SHELLFISH IMMUNOLOGY 2020; 103:332-341. [PMID: 32446969 DOI: 10.1016/j.fsi.2020.05.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
The aim of this study was to investigate the influence of variant coat proteins (CPs) from different quasispecies of betanodavirus on diverse aspects of nodavirus-induced pathogenesis. It is known that variant CPs can acquire either nuclear or cytoplasmic localization, depending on the nodavirus CP genotype, and this variation may arise during viral replication and influence the regulation of host and viral gene transcription. To investigate the role of these variant CPs in pathogenesis, six variant CP expression plasmids were constructed, each containing different quasispecies CP variants from nodavirus genotype red spotted grouper nervous necrosis virus (RGNNV). The CP expression plasmids were transiently transfected into grouper GF-1 cells. At different times, the cell cycle and cell proliferation were assayed using flow cytometry and methyl thiazolyl tetrazolium (MTT) assays, respectively. The proportion of G2/M-phase GF-1 cells transfected with CP expression plasmids was higher than that of cells transfected with the blank plasmid, especially in regards to quasispecies 2 (QS2). The proliferation ratio of cells transfected with the CP expression plasmids was significantly higher than that of cells transfected with the blank plasmid, with the exception of QS6. We also found that the different quasispecies CPs downregulated the promoter activity of the tumor necrosis factor (TNF) gene to different degrees. In addition, this is the first report showing the betanodavirus CP derived from different quasispecies of RGNNV provide evidence of a chronically nodavirus-infected grouper. Overall, this study represents the first comprehensive analysis of variant CPs from grouper with persistent nodavirus infections and their effects on different aspects of pathogenesis.
Collapse
Affiliation(s)
- Young-Mao Chen
- Laboratory of Molecular Genetics, Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Agriculture Biotechnology Research Center, National Cheng Kung University, Tainan, Taiwan; Bachelor Degree Program in Marine Biotechnology, College of Life Sciences, National Taiwan Ocean University, Keelung, Taiwan; Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Chor Siong Tan
- Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Ting-Yu Wang
- Laboratory of Molecular Genetics, Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Agriculture Biotechnology Research Center, National Cheng Kung University, Tainan, Taiwan; Translational Center for Marine Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Long Hwong
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsung, Taiwan.
| | - Tzong-Yueh Chen
- Laboratory of Molecular Genetics, Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Agriculture Biotechnology Research Center, National Cheng Kung University, Tainan, Taiwan; Translational Center for Marine Biotechnology, National Cheng Kung University, Tainan, Taiwan; University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
| |
Collapse
|
6
|
Xu T, Liu S, Li X, Zhang Q. Genomic characterization of covert mortality nodavirus from farming shrimp: Evidence for a new species within the family Nodaviridae. Virus Res 2020; 286:198092. [PMID: 32659308 DOI: 10.1016/j.virusres.2020.198092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 12/21/2022]
Abstract
The prevalence of covert mortality nodavirus (CMNV) has become one of the major threats to the shrimp farming industry in Asia and South America recently. Here, the genomic RNA1 and RNA2 of CMNV were characterized by using transcriptome sequencing and RT-PCR. Our study revealed that RNA1 is 3228 bp in length, and contains two putative Open Reading Frames (ORFs), one encoding the RNA dependent RNA polymerase (RdRp) of length 1043 amino acids and another encoding the protein B2 with a length of 132 amino acids. RNA2 is 1448 bp in length and encodes a capsid protein of 437 amino acids. CMNV shared the highest similarity of 51.78 % for RdRp with the other known nodaviruses. Phylogenetic analyses on the basis of RdRp, B2 and capsid proteins indicated that CMNV might represent a novel viral species in the family Nodaviridae. This study reported the first genome sequence of CMNV and it would be helpful for further studies of CMNV in relation to its evolution, diagnostic technique and control strategy.
Collapse
Affiliation(s)
- Tingting Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Marine Aquaculture Disease Control, Ministry of Agriculture, Key Laboratory of Marine Aquaculture Epidemiology and Biosecurity, Qingdao, 266071, China
| | - Shuang Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Marine Aquaculture Disease Control, Ministry of Agriculture, Key Laboratory of Marine Aquaculture Epidemiology and Biosecurity, Qingdao, 266071, China
| | - Xiaoping Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Marine Aquaculture Disease Control, Ministry of Agriculture, Key Laboratory of Marine Aquaculture Epidemiology and Biosecurity, Qingdao, 266071, China
| | - Qingli Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Marine Aquaculture Disease Control, Ministry of Agriculture, Key Laboratory of Marine Aquaculture Epidemiology and Biosecurity, Qingdao, 266071, China; Marine Fisheries Science and Food Production Process Function Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
| |
Collapse
|
7
|
Zhuang SF, Hu J, Qiao N, Lan ZH, Lai JY, Wu JG, Wu XY. Low-grade fever during COVID-19 convalescence: A report of 3 cases. World J Clin Cases 2020; 8:2655-2661. [PMID: 32607346 PMCID: PMC7322412 DOI: 10.12998/wjcc.v8.i12.2655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/05/2020] [Accepted: 05/21/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Low-grade fever during convalescence is an atypical symptom of coronavirus disease 2019 (COVID-19). Reports of such cases are rare, and the mechanism and outcome of low-grade fever during COVID-19 convalescence are not completely clear. We report 3 cases with low-grade fever during COVID-19 convalescence and highlight the main clinical, radiographic, and laboratory characteristics, thereby increasing the level of expertise in the clinical management of COVID-19 during convalescence and facilitating individualized decision-making.
CASE SUMMARY We describe 3 patients with COVID-19, two females aged 62 and 66 years and a male 55 years, who had low-grade fever during COVID-19 convalescence. All 3 patients had no other discomfort or comorbidities during low-grade process. Lesions on computed tomography in all 3 patients had resolved during this period. Two patients tested negative on two consecutive severe acute respiratory syndrome coronavirus 2 tests with an interval of at least 24 h between tests. Body temperature in all 3 patients returned to normal after several days without treatment, and fever recurrence was not observed.
CONCLUSION Enhancing the knowledge of low-grade fever during COVID-19 convalescence may increase the expertise in the delivery of optimal healthcare services.
Collapse
Affiliation(s)
- Shu-Fan Zhuang
- Department of Gastroenterology, The Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang 330006, Jiangxi Province, China
| | - Jia Hu
- Department of Gastroenterology, The Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang 330006, Jiangxi Province, China
| | - Nan Qiao
- Department of Student Affairs, Jiangxi Institute of Economic Administrators, Nanchang 330088, Jiangxi Province, China
| | - Zhi-Hui Lan
- Department of Respiration, The Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang 330006, Jiangxi Province, China
| | - Jun-Yu Lai
- Department of Cardiology, The Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang 330006, Jiangxi Province, China
| | - Jian-Guang Wu
- Department of Cardiology, The Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang 330006, Jiangxi Province, China
| | - Xiao-Yong Wu
- Department of Radiology, The Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang 330006, Jiangxi Province, China
| |
Collapse
|