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 Table of Contents  
Year : 2018  |  Volume : 2  |  Issue : 3  |  Page : 208-212

Immunoinformatic analysis of glycoprotein from bovine ephemeral fever virus

Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran

Date of Web Publication6-Sep-2018

Correspondence Address:
Dr. Mehran Bakhshesh
Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/bbrj.bbrj_71_18

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Background: Bovine ephemeral fever virus (BEFV) is an arthropod-borne virus that is highly infective for cattle and water buffalo. The infection has important economic losses and is common in tropical and subtropical regions. Surface glycoprotein (G protein) of BEFV is an immunogenic transmembrane G protein and responsible for attachment and entrance to host cells. The aim of this study was to determine immune dominant epitopes of the protein through immunoinformatics approaches. Methods: A reference sequence and some other related sequences of the G protein were retrieved. Three-dimensional structure of the protein was modeled and refined. Variation analysis of the protein sequences was done, and signal peptide and transmembrane topology were predicted. Finally, linear and conformational (discontinues) epitopes of the protein were predicted. Consensus linear and conformational epitopes were selected and reported as immunodominant epitopes. Results: Five regions were characterized as hyper variable regions (HVRs). Selected consensus epitopes included amino acids 46–60 (AA46–60), AA67–74, AA132–149, AA156–188, AA196–225, AA260–282, AA315–456, and AA487–503 were selected as consensus epitopes. Conclusion: Four determined epitopes including AA67–74, AA132–149, AA196–225, and AA315–456 were determined for the first time in this study. Other predicted epitopes in the current study, has been previously identified, however, new start and end regions for them were suggested here. The predicted epitopes may be experimentally tested to confirm as novel immunogenic candidates applicable in preventive and diagnostic tasks.

Keywords: Bovine Ephemeral fever, epitope, glycoprotein, immunoinformatic

How to cite this article:
Bakhshesh M, Ranjbar MM, Almasi S. Immunoinformatic analysis of glycoprotein from bovine ephemeral fever virus. Biomed Biotechnol Res J 2018;2:208-12

How to cite this URL:
Bakhshesh M, Ranjbar MM, Almasi S. Immunoinformatic analysis of glycoprotein from bovine ephemeral fever virus. Biomed Biotechnol Res J [serial online] 2018 [cited 2022 Aug 16];2:208-12. Available from: https://www.bmbtrj.org/text.asp?2018/2/3/208/240715

  Introduction Top

Bovine ephemeral fever virus (BEFV) is an arthropod-borne virus that can cause BEF or 3-day stiff-sickness. BEF is a zoonotic fatal disease and may cause significant economic losses. The virus can affect cattle and water buffalo. The disease has spread in tropical and subtropical zones of the world, especially in the Middle East (e.g., Iran, Turkey, Egypt, and Saudi Arabia).[1],[2],[3],[4] BEFV belongs to Rhabdoviridae family, genus Ephemerovirus. The genome of the virus is a negative-sense single-stranded RNA and contains five structural coding sequences for nucleoprotein (N protein), phosphoprotein, matrix protein, glycoprotein (G protein), and RNA-dependent RNA polymerase.[5]

G protein has been known as a type-specific transmembrane G protein responsible for viral cell adhesion, entrance, and pathogenicity.[6],[7],[8],[9] The protein has five major neutralization sites (G1, G2, G3a, G3b, and G4) for immunoglobulin of the hosts and therefore, is capable to induce antibody secretion and protective humoral immunity.[6],[7],[8],[9] However, all immunogenic peptides (epitopes) of the G protein have not been clearly determined. Experimentally determined epitopes of the protein are demonstrated in [Figure 1].
Figure 1: Positions of the previously determined immunogenic regions in three-dimensional model of the Glycoprotein

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The G1 site of the protein is placed on the outer side of the viral membrane and contacts with the host antibodies.[6],[7],[10] Yazdani et al. showed that a peptide (with 88 amino acid residues) of the G1 site could stimulate immune system and may be used for diagnostic ELISA kits.[11]

Viro-immunoinformatics has been dramatically progressed to allow deep analysis of viral antigens, prediction of linear and conformational (discontinues) epitope and evaluation of immunogenicity and virulence of pathogens. Besides, using immunoinformatics methods, time and costs for designing novel vaccines against existing viruses, kits, and related antibodies can be reduced.[12],[13],[14]

  Methods Top

Retrieving of sequences

The complete sequence of the G protein from BEFV (strain AIW62182) was retrieved from the National Center for Biotechnology Information (NCBI) database as the reference sequence. Some other nonreference sequences were also retrieved from the database. All obtained sequences were aligned using ClustalW2 tool in T-coffee server. The aligned sequences were trimmed and analyzed by Bioedit software version 7.7.9 (mbio, Inc, North Carolina, USA).

Entropy plot, prediction of signal peptides, and transmembrane topology

Shannon entropy value was used to estimate the conservative and mutational regions of the viral protein. Mutational regions of a protein are known as hypervariable regions (HVRs) in an alignment dataset.

SignalP. 4.1 was used to predict signal peptide of the protein.

Basic Local Alignment Search Tool for proteins (Blastp) from NCBI was used to predict the protein domains based on homologous known proteins.

Trans-membrane topology was predicted through THMM (transmembrane helices prediction method based on a hidden Markov model) server and TopCons (consensus prediction of membrane protein topology) program.

Protein modeling

The structure of the G protein from BEFV was not available in the protein data bank (PDB); therefore, three-dimensional (3D) structure of the protein was modeled using Iterative Threading ASSEmbly Refinement (I-TASSER) server. The best models were selected, and energy minimized using the Groningen Molecular Simulation 96 (GROMOS96) method implementation of Swiss-PDB Viewer software (http://www.expasy.org/spdbv/). Rampage server was used to validate the predicted models. Two-dimensional (2D) structure of the protein was predicted through position-specific iterative-BLAST-based secondary structure Prediction server.

Prediction of conformational (discontinues) and linear B-cell epitopes

Discontinues B-cell epitopes were predicted by different servers including DiscoTope 2.0, ElliPro, and CBTOPE servers. Linear epitopes of the protein were determined employing “support vector machine by combining the tri-peptide similarity,” ABCpred, Bepipred, Tongaonkar-Kolaskar Antigenicity, and Emini-Surface Accessibility-Prediction-Mapping tools. Subsequently, predicted discontinues and linear epitopes were exactly analyzed to find consensus immunogenic regions in the original protein.

Selection of consensus epitopes and epitope engineering

The predicted epitopes by all mentioned servers were investigated to find consensus linear and conformational epitopes of the protein. In addition, to achieve broader spectrum and immunogenic epitopes, some modification and replacements were done on the epitopes.

  Results and Discussion Top

Modeling, minimization, and validation of the protein structure

The model structure of the G protein is presented in [Figure 2]. Considering the figure, the structure of the protein is composed of different secondary structures such as alpha-helix, turn, coil, and beta-turn. Results of secondary structure prediction showed that coils and beta strands are major 2D structures of the protein [Figure 3]. In [Figure 3], feature predictions are color-coded onto the sequence.
Figure 2: Predicted model of the Glycoprotein of bovine ephemeral fever virus

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Figure 3: Predicted secondary structure of the Glycoprotein

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Variation analysis and prediction of signal peptide and transmembrane topology of the protein

Variation analysis of 196 selected sequences of G protein showed that there is no considerable conserved region among the selected sequences [Figure 4]. Therefore, there are concerns about the selection of only one strain to design global vaccine, since the protein of one isolate does not cause fully protection against other isolates. By analysis of variations among aligned sequences, near fine high variable regions (HVRs) were detected in 12 sites of the protein. Many variable and semi-variable regions were located at the C terminal of the protein [Figure 4].
Figure 4: Entropy plot (Shannon entropy plot) showing variability among Glycoprotein sequences of the bovine ephemeral fever virus

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Signal peptide and transmembrane topology

Results of the signal peptide prediction showed that amino acids 1–25 can be considered as a signal peptide. Besides, results of transmembrane topology prediction showed that near 25 percent of the protein sequence is extracellular and consequently can expose to the host antibodies.

Prediction of B-cell epitopes and selection of consensus peptides

Results of B-cell epitope prediction are represented in [Table 1]. The predicted epitopes (conformational and linear), structural information, and variation plot were employed to determine consensus antigenic regions of the G protein. Consequently, eight highly antigenic regions in the protein were predicted as follow; AA46–60(sequence: LSLQAHHNLAKDEHY), AA67–74(sequence: QLKDDDHL), AA132–149(sequence: AGCFWNTEMNQEIEFYVL), AA156–188(sequence: LNPYDNLIYDSRFLTPCTINDSKTKGCPLKDIT), AA196–225(sequence: RVKEISEHCNSKHWECITVKSFRSELNETE), AA260–282(sequence: WSIENQTESDFQNFKIERCKGKK), AA315–456(sequence: ILNKENINTLDMSYL APTRPGRDYAYLFEQTSWQEKLCLSLPDSGRVSKDCSI DWRTSTRGGMVKKNHYGIGSYKRAWCEYRPFIDKNE DGYIDIQELNGHNMSRNHAILETAPAGGSSGTKLNVT LNGMIFVEPTKLYLHT), and AA487–503(sequence: YEEDEKFKPVNLSPHEK).
Table 1: Predicted epitopes from the G protein of bovine ephemeral fever virus

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3D structures of the predicted antigenic regions are represented in [Figure 5].
Figure 5: Tertiary structures of the predicted consensus epitopes

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  Conclusion Top

Results of the protein modeling showed that there are a large number of coils and protruded regions in the G protein that reflects high immunogenicity of the protein as it has been evaluated in previous studies.[15]

Results of consensus epitope predictions represented that four novel epitopes including AA67–74, AA132–149, AA196–225, and AA315–456 can be reported. As it was mentioned afore, other predicted epitopes in this study were identified in previous studies.[9],[16] However, the epitopes identified in the current study was seen to have different start and end regions. The predicted epitopes can be experimentally tested as novel immunogenic peptide candidates for preventive and diagnostic purposes.

Prediction of vigorous peptides from antigenic proteins can provide more precise and helpful information before wet-laboratory experiments.[17],[18],[19],[20] Therefore, identifying the powerful immunogenic epitopes of antigens could assist in developing novel effective and safe peptide-based vaccines as well as improving immunodiagnostics methods for identification of photogenes.

Financial support and sponsorship


Conflicts of interest

There are no conflicts of interest

  References Top

Maclachlan NJ, Dubovi EJ, editors. Fenner's Veterinary Virology. 5th ed. Oxford, UK and Waltham, MA, USA: Academic Press; 2016.  Back to cited text no. 1
Walker PJ, Klement E. Epidemiology and control of bovine ephemeral fever. Vet Res 2015;46:124.  Back to cited text no. 2
Young PL, Spradbrow PB. Clinical response of cattle to experimental infection with bovine ephemeral fever virus. Vet Rec 1990;126:86-8.  Back to cited text no. 3
St George TD. Bovine ephemeral fever: A review. Trop Anim Health Prod 1988;20:194-202.  Back to cited text no. 4
Nandi S, Negi BS. Bovine ephemeral fever: A review. Comp Immunol Microbiol Infect Dis 1999;22:81-91.  Back to cited text no. 5
Zheng FY, Lin GZ, Qiu CQ. Expression, purification and antigenic characterization of the epitope-G1 gene of bovine ephemeral fever virus in Escherichia coli. Wei Sheng Wu Xue Bao 2007;47:498-502.  Back to cited text no. 6
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Kongsuwan K, Cybinski DH, Cooper J, Walker PJ. Location of neutralizing epitopes on the G protein of bovine ephemeral fever rhabdovirus. J Gen Virol 1998;79(Pt 11):2573-81.  Back to cited text no. 9
Ting LJ, Lee MS, Lee SH, Tsai HJ, Lee F. Relationships of bovine ephemeral fever epizootics to population immunity and virus variation. Vet Microbiol 2014;173:241-8.  Back to cited text no. 10
Yazdani F, Bakhshesh M, Esmaelizad M, Sadigh ZA. Expression of G1- epitope of bovine ephemeral fever virus in E. Coli: A novel candidate to develop ELISA kit. Vet Res Forum 2017;8:209-13.  Back to cited text no. 11
Ranjbar MM, Ahmadi NA, Ghorban K, Ghalyanchi Langeroudi A, Dadmanesh M, Amini H, et al. Immnoinformatics: Novel view in understanding of immune system function, databases and prediction of immunogenic epitopes. Koomesh 2015;17:18-26.  Back to cited text no. 12
Ranjbar MM, Ghorban K, Alavian SM, Keyvani H, Dadmanesh M, Roayaei Ardakany A, et al. GB virus C/Hepatitis G virus envelope glycoprotein E2: Computational molecular features and immunoinformatics study. Hepat Mon 2013;13:e15342.  Back to cited text no. 13
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Trinidad L, Blasdell KR, Joubert DA, Davis SS, Melville L, Kirkland PD, et al. Evolution of bovine ephemeral fever virus in the Australian episystem. J Virol 2014;88:1525-35.  Back to cited text no. 15
Johal J, Gresty K, Kongsuwan K, Walker PJ. Antigenic characterization of bovine ephemeral fever rhabdovirus G and GNS glycoproteins expressed from recombinant Baculoviruses. Arch Virol 2008;153:1657-65.  Back to cited text no. 16
Dadmanesh M, Ranjbar MM, Alavian SM, Ghorban K. Sequencing and phylogenetic study of partial NS3 gene of Iranian GB virus C/Hepatitis G virus (HGV) originated from hemodialysis patients in Tehran. Hepat Mon 2015;15:e24173.  Back to cited text no. 17
Malekan M, Vasfi Marandi M, Ranjbar MM, Bashashati M. Molecular evaluation of M2 protein of Iranian avian influenza viruses of H9N2 subtype in order to find mutations of adamantane drug resistance. Iran J Vet Med 2016;10:253-62.  Back to cited text no. 18
Keyvani H, Ahmadi N A, Ranjbar MM, Ataei Kachooei S, Ghorban K, Dadmanesh M. Immunoinformatics study of gp120 of human immunodeficiency virus type 1 subtype CRF35_AD isolated from Iranian patients, Arch Clin Infect Dis 2016;11(4):e36270. doi: 10.5812/archcid.36270.  Back to cited text no. 19
Ranjbar MM, Ghelian-Chian A, Nazoktabar A, Ahmadi N, Khoshnevisan R, et al. Immnoinformatics and epitope prediction methods dynamic science with promising achievements. J Ilam Univ Med Sci 2013;21:300-9.  Back to cited text no. 20


  [Figure 1], [Figure 2], [Figure 3], [Figure 4], [Figure 5]

  [Table 1]

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