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Zhou JH, You YN, Chen HT, Zhang J, Ma LN, Ding YZ, Pejsak Z, Liu YS. The effects of the synonymous codon usage and tRNA abundance on protein folding of the 3C protease of foot-and-mouth disease virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2013; 16:270-4. [PMID: 23499709 DOI: 10.1016/j.meegid.2013.02.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 02/18/2013] [Accepted: 02/22/2013] [Indexed: 11/22/2022]
Abstract
The 3C protease of foot-and-mouth disease virus (FMDV) has a conserved amino acid sequence and is responsible for most cleavage in the viral polyprotein. The effects of the synonymous codon usage of FMDV 3C gene and tRNA abundance of the hosts on shaping different folding units (α-helix, β-strand and the coil) in the 3C protease were analyzed based on the structural information of the FMDV 3C protease from Protein Data Bank (PDB: 2BHG) and 210 genes of 3C for all serotypes of FMDV. The strong correlation between some codons usage and the specific folding unit in the FMDV 3C protease is found. As for the effect of translation speed caused by tRNA abundance on the formation of folding units, the codon positions with lowly abundant tRNA scatter in the 3C gene and there is the obvious fluctuation of tRNA abundance locating in the transition boundaries from the β-strand to the α-helix and the coil, respectively. However, codon positions with lowly abundant tRNA clustering into these boundaries are not found, suggesting that the adjustment of translation speed is likely also achieved by the single codon position with low tRNA abundance rather than a cluster. The observations can provide the information for insight into the role of the synonymous codon usage in the formation of 3C protease of FMDV and effect of the tRNA abundance of the hosts on this formation of protease.
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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, 730046 Gansu, PR China
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Esmaelizad M, Jelokhani-Niaraki S, Hashemnejad K, Kamalzadeh M, Lotfi M. Molecular characterization of amino acid deletion in VP1 (1D) protein and novel amino acid substitutions in 3D polymerase protein of foot and mouth disease virus subtype A/Iran87. J Vet Sci 2012; 12:363-71. [PMID: 22122902 PMCID: PMC3232396 DOI: 10.4142/jvs.2011.12.4.363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nucleotide sequence of the VP1 (1D) and partial 3D polymerase (3Dpol) coding regions of the foot and mouth disease virus (FMDV) vaccine strain A/Iran87, a highly passaged isolate (~150 passages), was determined and aligned with previously published FMDV serotype A sequences. Overall analysis of the amino acid substitutions revealed that the partial 3Dpol coding region contained four amino acid alterations. Amino acid sequence comparison of the VP1 coding region of the field isolates revealed deletions in the highly passaged Iranian isolate (A/Iran87). The prominent G-H loop of the FMDV VP1 protein contains the conserved arginine-glycine-aspartic acid (RGD) tripeptide, which is a well-known ligand for a specific cell surface integrin. Despite losing the RGD sequence of the VP1 protein and an Asp26→Glu substitution in a beta sheet located within a small groove of the 3Dpol protein, the virus grew in BHK 21 suspension cell cultures. Since this strain has been used as a vaccine strain, it may be inferred that the RGD deletion has no critical role in virus attachment to the cell during the initiation of infection. It is probable that this FMDV subtype can utilize other pathways for cell attachment.
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Affiliation(s)
- Majid Esmaelizad
- Department of Biotechnology, Razi Vaccine and Serum Research Institute, Karaj 3197619751, Iran.
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Lee YJ, Chu JQ, Lee SY, Kim SM, Lee KN, Ko YJ, Lee HS, Cho IS, Nam SH, Park JH. Analysis of protective genotype of foot-and-mouth disease (FMD) Asia1 vaccine. ACTA ACUST UNITED AC 2011. [DOI: 10.7853/kjvs.2011.34.2.103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Yang X, Zhou YS, Wang HN, Zhang Y, Wei K, Wang T. Isolation, identification and complete genome sequence analysis of a strain of foot-and-mouth disease virus serotype Asia1 from pigs in southwest of China. Virol J 2011; 8:175. [PMID: 21496298 PMCID: PMC3094298 DOI: 10.1186/1743-422x-8-175] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 04/16/2011] [Indexed: 12/04/2022] Open
Abstract
Backgroud Foot-and-mouth disease virus (FMDV) serotype Asia1 generally infects cattle and sheep, while its infection of pigs is rarely reported. In 2005-2007, FMD outbreaks caused by Asia1 type occurred in many regions of China, as well as some parts of East Asia countries. During the outbreaks, there was not any report that pigs were found to be clinically infected. Results In this study, a strain of FMDV that isolated from pigs was identified as serotype Asia1, and designated as "Asia1/WHN/CHA/06". To investigate the genomic feature of the strain, complete genome of Asia1/WHN/CHA/06 was sequenced and compared with sequences of other FMDVs by phylogenetic and recombination analysis. The complete genome of Asia1/WHN/CHA/06 was 8161 nucleotides (nt) in length, and was closer to JS/CHA/05 than to all other strains. Potential recombination events associated with Asia1/WHN/CHA/06 were found between JS/CHA/05 and HNK/CHA/05 strains with partial 3B and 3C fragments. Conclusion This is the first report of the isolation and identification of a strain of FMDV type Asia1 from naturally infected pigs. The Asia1/WHN/CHA/06 strain may evolve from the recombination of JS/CHA/05 and HNK/CHA/05 strains.
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Affiliation(s)
- Xin Yang
- School of Life science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province," 985 Project" Science Innovative Platform for Resource and environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, Sichuan, 610064, China
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Jelokhani-Niaraki S, Esmaelizad M, Daliri M, Vaez-Torshizi R, Kamalzadeh M, Lotfi M. Sequence and phylogenetic analysis of the non-structural 3A and 3B protein-coding regions of foot-and-mouth disease virus subtype A Iran 05. J Vet Sci 2010; 11:243-7. [PMID: 20706032 PMCID: PMC2924486 DOI: 10.4142/jvs.2010.11.3.243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The A Iran 05 foot-and-mouth disease virus (FMDV) subtype was detected in Iran during 2005 and has proven to be highly virulent. This study was undertaken to focus on molecular and phylogenetic analysis of 3A and 3B coding-regions in the A Iran 05 field isolate. To assess the genetic relatedness of A Iran 05 isolate the nucleotide and predicted amino acid sequences of the 3AB region of type A FMDV isolates were compared with twenty previously described type A FMDV isolates. The phylogenetic tree based on the 672 bp 3AB gene sequences of type A FMDV from thirteen different locations clustered them into five distinct lineages. The A Iran 05 isolate clustered in lineage A along with four type A variants and was closely matched with viruses isolated in Turkey and Pakistan during 2005~2006. The number of protein sequence differences exhibited by each of the isolates revealed that A Iran 05 isolate contains three amino acid substitutions at positions 47 and 119 of 3A and 27 of the 3B coding region. The nucleotide identity between A Iran 05 and the other four isolates of lineage A was estimated to be 98%.
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Affiliation(s)
- Saber Jelokhani-Niaraki
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
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Genome analysis and development of infectious cDNA clone of a virulence-attenuated strain of foot-and-mouth disease virus type Asia 1 from China. Vet Microbiol 2009; 138:273-80. [PMID: 19410387 DOI: 10.1016/j.vetmic.2009.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 03/09/2009] [Accepted: 04/03/2009] [Indexed: 11/22/2022]
Abstract
The RNA genome sequence of the rabbit passage-attenuated strain of foot-and-mouth disease virus (FMDV) Asia 1, ZB/CHA/58(att), was determined to be 8165 nt in length excluding the poly(C) tract in the 5' UTR and the poly(A) tail at the 3' end. ZB/CHA/58(att) was most similar to the vaccine strain Asia 1/YNBS/58 in genome sequence and there were no deletions or insertions within the deduced polyprotein between ZB/CHA/58(att) and YNBS/58, but there were a total of 25 substitutions at the amino acid level and an extra 19-nt stretch in the 5' UTR was found in ZB/CHA/58(att). An infectious full-length cDNA clone of ZB/CHA/58(att) was developed. Infectious virus could be recovered in BHK-21 cells transfected with the synthetic viral RNA transcribed in vitro. The plaque morphology, growth kinetics and antigenic profile of the infectious clone-derived virus (termed tZB) were indistinguishable from those induced by the parental virus. Furthermore, the virulence properties of ZB/CHA/58(att) and tZB were found to be highly similar in the mouse model. The availability of genome sequence information and infectious cDNA clone of the FMDV ZB/CHA/58(att) lays a new ground for further investigation of FMDV virulence determinants and development of new potent vaccine to FMD.
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Cooke JN, Westover KM. Serotype-specific differences in antigenic regions of foot-and-mouth disease virus (FMDV): A comprehensive statistical analysis. INFECTION GENETICS AND EVOLUTION 2008; 8:855-63. [DOI: 10.1016/j.meegid.2008.08.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Revised: 08/11/2008] [Accepted: 08/15/2008] [Indexed: 10/21/2022]
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Klein J. Understanding the molecular epidemiology of foot-and-mouth-disease virus. INFECTION GENETICS AND EVOLUTION 2008; 9:153-61. [PMID: 19100342 PMCID: PMC7172361 DOI: 10.1016/j.meegid.2008.11.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Revised: 11/20/2008] [Accepted: 11/20/2008] [Indexed: 12/28/2022]
Abstract
The use of molecular epidemiology is an important tool in understanding and consequently controlling FMDV. In this review I will present basic information about the disease, needed to perform molecular epidemiology. I will give a short introduction to the history and impact of foot-and-mouth disease, clinical picture, infection route, subclinical and persistent infections, general aspects of the transmission of FMDV, serotype-specific epidemiological characteristics, field epidemiology of FMDV, evolution and molecular epidemiology of FMDV. This is followed by two chapters describing the molecular epidemiology of foot-and-mouth disease in global surveillance and molecular epidemiology of foot-and-mouth disease in outbreak investigation.
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Affiliation(s)
- Joern Klein
- Norwegian University of Science and Technology, Faculty of Medicine, Department of Cancer Research and Molecular Medicine, N-7489 Trondheim, Norway.
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Comparative genomics of serotype Asia 1 foot-and-mouth disease virus isolates from India sampled over the last two decades. Virus Res 2008; 136:16-29. [DOI: 10.1016/j.virusres.2008.04.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 04/03/2008] [Accepted: 04/11/2008] [Indexed: 11/21/2022]
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Sequence analysis of the protein-coding regions of foot-and-mouth disease virus O/HK/2001. Vet Microbiol 2008; 130:238-46. [PMID: 18343054 DOI: 10.1016/j.vetmic.2008.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 01/19/2008] [Accepted: 01/29/2008] [Indexed: 11/23/2022]
Abstract
The nucleotide sequence of the protein-coding region of foot-mouth-disease virus (FMDV) strain O/HK/2001 was determined and compared with the sequences of other FMDVs that were registered in GenBank. The protein-coding region was 6966 nucleotides in length and encoded a protein of 2322 amino acid residues. Comparison of the nucleotide sequence and its deduced amino acid sequence with those of other isolates indicated that O/HK/2001 belonged to the Cathay topotype. A genomic coding region nucleotide sequence phylogenetic tree of several FMDV-O isolates showed that O/HK/2001 was most closely related to FMDV isolates found in Taiwan during 1997, and especially shared significant similarity to HKN/2002, suggesting that the virus causing outbreaks in Hong Kong was genetically most-closely related to that causing an outbreak of type O in Taiwan. Mutations in O/HK/2001 were revealed, including frequent substitutions in the VP1 and L proteins, and deletions involving 10 amino acid residues in the 3A protein. This study was undertaken to assess the regional variation of prevalent FMDV type O viruses and to establish a sequence database for FMDV molecular epidemiological investigation.
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Moratorio G, Martínez M, Gutiérrez MF, González K, Colina R, López-Tort F, López L, Recarey R, Schijman AG, Moreno MP, García-Aguirre L, Manascero AR, Cristina J. Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region. Virol J 2007; 4:79. [PMID: 17683527 PMCID: PMC1973069 DOI: 10.1186/1743-422x-4-79] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Accepted: 08/02/2007] [Indexed: 12/21/2022] Open
Abstract
Background Hepatitis C virus (HCV) has been the subject of intense research and clinical investigation as its major role in human disease has emerged. Previous and recent studies have suggested a diversification of type 1 HCV in the South American region. The degree of genetic variation among HCV strains circulating in Bolivia and Colombia is currently unknown. In order to get insight into these matters, we performed a phylogenetic analysis of HCV 5' non-coding region (5'NCR) sequences from strains isolated in Bolivia, Colombia and Uruguay, as well as available comparable sequences of HCV strains isolated in South America. Methods Phylogenetic tree analysis was performed using the neighbor-joining method under a matrix of genetic distances established under the Kimura-two parameter model. Signature pattern analysis, which identifies particular sites in nucleic acid alignments of variable sequences that are distinctly representative relative to a background set, was performed using the method of Korber & Myers, as implemented in the VESPA program. Prediction of RNA secondary structures was done by the method of Zuker & Turner, as implemented in the mfold program. Results Phylogenetic tree analysis of HCV strains isolated in the South American region revealed the presence of a distinct genetic lineage inside genotype 1. Signature pattern analysis revealed that the presence of this lineage is consistent with the presence of a sequence signature in the 5'NCR of HCV strains isolated in South America. Comparisons of these results with the ones found for Europe or North America revealed that this sequence signature is characteristic of the South American region. Conclusion Phylogentic analysis revealed the presence of a sequence signature in the 5'NCR of type 1 HCV strains isolated in South America. This signature is frequent enough in type 1 HCV populations circulating South America to be detected in a phylogenetic tree analysis as a distinct type 1 sub-population. The coexistence of distinct type 1 HCV subpopulations is consistent with quasispecies dynamics, and suggests that multiple coexisting subpopulations may allow the virus to adapt to its human host populations.
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Affiliation(s)
- Gonzalo Moratorio
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| | - Mariela Martínez
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| | - María F Gutiérrez
- Laboratorio de Virología, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7 # 43-82 Ed 50 of 313, Bogotá, Colombia
| | - Katiuska González
- Facultad de Ciencias Médicas y Bioquímicas, Universidad Mayor de San Andrés, Av. Villazón No. 1995 Monoblock Central, La Paz, Bolivia
| | - Rodney Colina
- Department of Biochemistry and McGill Cancer Center, McGill University, Montreal, Quebec, Canada H3G 1Y6
| | - Fernando López-Tort
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| | - Lilia López
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| | - Ricardo Recarey
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| | - Alejandro G Schijman
- Laboratorio de Biología Molecular, Grupo CentraLab, Buenos Aires, Argentina
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Vuelta de Obligado 2490, Second Floor, 1428 Buenos Aires, Argentina
| | - María P Moreno
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| | - Laura García-Aguirre
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| | - Aura R Manascero
- Laboratorio de Virología, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7 # 43-82 Ed 50 of 313, Bogotá, Colombia
| | - Juan Cristina
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
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