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Wang X, Sun J, Zheng Y, Xie F. Dispersion of synonymous codon usage patterns in hepatitis E virus genomes derived from various hosts. J Basic Microbiol 2022; 62:975-983. [PMID: 35778820 DOI: 10.1002/jobm.202200072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/01/2022] [Accepted: 06/11/2022] [Indexed: 11/09/2022]
Abstract
Hepatitis E virus (HEV) is an important zoonotic pathogen infecting a wide range of host species. It has a positive-sense, single-stranded RNA genome encoding three open reading frames (ORFs). Synonymous codon usages of viruses essentially determine their survival and adaptation to susceptible hosts. To better understand the interplay between the ever-expanding host range and synonymous codon usages of HEV, we quantified the dispersion of synonymous codon usages of HEV genomes isolated from different hosts via Vs calculation and information entropy. HEV ORFs show species-specific synonymous codon usage patterns. Ruminant-derived HEV ORFs own the most synonymous codons with stable usage patterns (Vs value <0.1) which leads to the stable overall codon usage patterns (R value being close to zero). Swine-derived HEV ORFs own more concentrated synonymous codons than those from wild boar. Compared with HEV strains isolated from other hosts, the human-derived HEV exhibits a distinct pattern at the overall codon usage (R < 0). Generally, ORF1 contains more synonymous codons with stable usage patterns (Vs < 0.1) than those of ORFs 2 and 3. Moreover, ORF3 contains more synonymous codons with varied patterns (Vs > 1.0) than ORFs 1 and 2. The host factor serving as one of the evolutionary dynamics probably influences synonymous codon usage patterns of the HEV genome. Taken together, synonymous codons with stable usage patterns in ORF1 might help to sustain the infection, while that with varied usage patterns in ORF3 may facilitate cross-species infection and expand the host range.
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Affiliation(s)
- Xin Wang
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, China
| | - Jing Sun
- Department of Endocrine, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yueyan Zheng
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, China
| | - Fuqiang Xie
- Department of Stomatology, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
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The genetic divergences of codon usage shed new lights on transmission of hepatitis E virus from swine to human. INFECTION GENETICS AND EVOLUTION 2019; 68:23-29. [DOI: 10.1016/j.meegid.2018.11.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 11/22/2018] [Accepted: 11/30/2018] [Indexed: 12/27/2022]
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Ma XX, Ma LN, Chang QY, Ma P, Li LJ, Wang YY, Ma ZR, Cao X. Type I Interferon Induced and Antagonized by Foot-and-Mouth Disease Virus. Front Microbiol 2018; 9:1862. [PMID: 30150977 PMCID: PMC6099088 DOI: 10.3389/fmicb.2018.01862] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/24/2018] [Indexed: 12/20/2022] Open
Abstract
Viral infections trigger the innate immune system, serving as the first line of defense, and are characterized by the production of type I interferon (IFN). Type I IFN is expressed in a broad spectrum of cells and tissues in the host and includes various subtypes (IFN-α, IFN-β, IFN-δ, IFN-ε, IFN-κ, IFN-τ, IFN-ω, IFN-ν, and IFN-ζ). Since the discovery of type I IFN, our knowledge of the biology of type I IFN has accumulated immensely, and we now have a substantial amount of information on the molecular mechanisms of the response and induction of type I IFN, as well as the strategies utilized by viruses to evade the type I IFN response. Foot-and-mouth disease virus (FMDV) can selectively alter cellular pathways to promote viral replication and evade antiviral immune activation of type I IFN. RNA molecules generated by FMDV are sensed by the cellular receptor for pathogen-associated molecular patterns (PAMPs). FMDV preferentially activates different sensor molecules and various signal transduction pathways. Based on knowledge of the virus or RNA pathogen specificity as well as the function-structure relationship of RNA sensing, it is necessary to summarize numerous signaling adaptors that are reported to participate in the regulation of IFN gene activation.
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Affiliation(s)
- Xiao-Xia Ma
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Li-Na Ma
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Qiu-Yan Chang
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Peng Ma
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Lin-Jie Li
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Yue-Ying Wang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zhong-Ren Ma
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Xin Cao
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China.,State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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Ma XX, Chang QY, Ma P, Li LJ, Zhou XK, Zhang DR, Li MS, Cao X, Ma ZR. Analyses of nucleotide, codon and amino acids usages between peste des petits ruminants virus and rinderpest virus. Gene 2017; 637:115-123. [PMID: 28947301 DOI: 10.1016/j.gene.2017.09.045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 09/03/2017] [Accepted: 09/21/2017] [Indexed: 10/18/2022]
Abstract
Peste des petits ruminants virus (PPRV) and rinderpest virus (RPV) are two causative agents of an economically important disease for ruminants (i.e., sheep, cattle and goat). In this study, the nucleotide, codon and amino acid usages for PPRV and RPV have been analyzed by multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis represents that ACG for Thr and GCG for Ala are selected with under-representation in both PPRV and RPV, and AGA for Arg in PPRV and AGG for Arg in RPV are used with over-representation. The usage of nucleotide pair (CpG) tends to be removed from viral genes of the two viruses, suggesting that other evolutionary forces take part in evolutionary processes for viral genes in addition to mutation pressure from nucleotide usage at the third codon position. The overall nucleotide usage of viral gene is not major factor in shaping synonymous codon usage patterns, while the nucleotide usages at the third codon position and the nucleotide pairs play important roles in shaping synonymous codon usage patterns. Although PPRV and RPV are closely related antigenically, the codon and amino acid usage patterns for viral genes represent a significant genetic diversity between PPRV and RPV. Moreover, the overall codon usage trends for viral genes between PPRV and RPV are mainly influenced by mutation pressure from nucleotide usage at the third codon position and translation selection from hosts. Taken together, this is first comprehensive analyses for nucleotide, codon and amino acid usages of viral genes of PPRV and RPV and the findings are expected to increase our understanding of evolutionary forces influencing viral evolutionary pathway and adaptation toward hosts.
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Affiliation(s)
- Xiao-Xia Ma
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Qiu-Yan Chang
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Peng Ma
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Lin-Jie Li
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Xiao-Kai Zhou
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - De-Rong Zhang
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Ming-Sheng Li
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Xin Cao
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China.
| | - Zhong-Ren Ma
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China.
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Zhou JH, Ding YZ, He Y, Chu YF, Zhao P, Ma LY, Wang XJ, Li XR, Liu YS. The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis genome. PLoS One 2014; 9:e108949. [PMID: 25350396 PMCID: PMC4211681 DOI: 10.1371/journal.pone.0108949] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/26/2014] [Indexed: 11/19/2022] Open
Abstract
Mycoplasma bovis is a major pathogen causing arthritis, respiratory disease and mastitis in cattle. A better understanding of its genetic features and evolution might represent evidences of surviving host environments. In this study, multiple factors influencing synonymous codon usage patterns in M. bovis (three strains’ genomes) were analyzed. The overall nucleotide content of genes in the M. bovis genome is AT-rich. Although the G and C contents at the third codon position of genes in the leading strand differ from those in the lagging strand (p<0.05), the 59 synonymous codon usage patterns of genes in the leading strand are highly similar to those in the lagging strand. The over-represented codons and the under-represented codons were identified. A comparison of the synonymous codon usage pattern of M. bovis and cattle (susceptible host) indicated the independent formation of synonymous codon usage of M. bovis. Principal component analysis revealed that (i) strand-specific mutational bias fails to affect the synonymous codon usage pattern in the leading and lagging strands, (ii) mutation pressure from nucleotide content plays a role in shaping the overall codon usage, and (iii) the major trend of synonymous codon usage has a significant correlation with the gene expression level that is estimated by the codon adaptation index. The plot of the effective number of codons against the G+C content at the third codon position also reveals that mutation pressure undoubtedly contributes to the synonymous codon usage pattern of M. bovis. Additionally, the formation of the overall codon usage is determined by certain evolutionary selections for gene function classification (30S protein, 50S protein, transposase, membrane protein, and lipoprotein) and translation elongation region of genes in M. bovis. The information could be helpful in further investigations of evolutionary mechanisms of the Mycoplasma family and heterologous expression of its functionally important proteins.
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Affiliation(s)
- Jian-hua Zhou
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Yao-zhong Ding
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Ying He
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Yue-feng Chu
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Ping Zhao
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Li-ya Ma
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Xin-jun Wang
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Xue-rui Li
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
- * E-mail: (XRL); (YSL)
| | - Yong-sheng Liu
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
- * E-mail: (XRL); (YSL)
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