Study of structural variations and phylogeny of DQA from MHC class II in cattle

Document Type : Full Research Paper

Authors

1 Asisstant Prefossor, Department of Poultry Bacterial Diseases, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organisation (AREEO), Tehran, Iran.

2 Asisstant Prefossor, Department of Therapeutic Sera, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organisation (AREEO), Tehran Iran.

Abstract

BoLA-DQA protein is a highly polymorphic region in MHC class II and plays a key role in immune responses, resistance and susceptibility to infectious diseases, vaccination and production factors. Compared with other species, there are little data on molecular characteristics, structure, phylogeny and evolution of BoLA-DQA. In the present study, some aspects of these subjects and propose practical points based on findings about variations, structure and phylogeny of this locus in cattle was studies. Protein sequences of BoLA-DQA alleles were retrieved from databases. Variation was evaluated by Shannon entropy plot based on alignment of sequences with ClustalW2 algorithm, and Highly Variable Regions (HVRs) were analyzed. Then, tertiary structure of protein by homology modeling approach under certain circumstances, energy minimization and model validation were achieved. Finally, phylogeny, allelic grouping and estimation of evolutionary divergence were done using Maximum Likelihood method. For heuristic search of initial tree, Neighbor-Joining and BioNJ were used for pairwise distance matrix by JTT model and then, Logs with better Likelihood were appointed. Seven HVRs and some semi-variable regions in variation analysis were obtained. The highest variable region was amino acids 90-93. These HVRs were seen in all substructures after homology modeling of BoLA-DQA protein (with 97.5 validity). Besides, alleles were grouped into five clusters by phylogenetic analysis. Evolutionary analysis of tree showed that more ancient alleles were *2103 and *2602, and probable newer alleles were *1204, *0302 and *2207. Present study helps in designing effective vaccines against infectious diseases and animal breeding in easy prediction of production factors in cattle.

Keywords

Main Subjects

References

1. Abbas, A., Lichtman, A., Pillai S. 2015. Major histocompatibility complex molecules and antigen presentation to T lymphocytes. Cellular and molecular immunology, 8th Edition, USA Philadelphia, Saunders-Elsevier, 107-136.
2. Andersson, L. R. 1988. Characterization of the MHC class II region in cattle. The number of DQ genes varies between haplotypes. Immunogenetics. 27: 110-120.
3. Annette Gelhaus, B. F. 1999. Evidence for an additional cattle DQA locus, BoLA-DQA5. Immunogenetics. 49: 321-327.
4. Ballingall, K.T. 2004. The DY genes of the cattle MHC: expression and comparative analysis of an unusual class II MHC gene pair. Immunogenetics. 55: 748-755.
5. Behl, J.D. 2007. Characterization of Genetic Polymorphism of the Bovine Lymphocyte Antigen DRB3.2 Locus in Kankrej Cattle (Bos indicus). Dairy science. 90: 2997-3-1.
6. Behl, J.D., Verma, N.K., Tyagi, N., Mishra, P., Behl, R., Joshi, B.K., 2012. The Major Histocompatibility Complex in Bovines: A Review. ISRN Veterinary Science.
7. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat T. N., Weissig H., Shindyalov, I. N., Bourne, P. E. 2000. The Protein Data Bank. Nucleic Acids Research. 28: 235–242.
8. Borghans, JA.,Beltman, JB., De Boer, RJ. 2004. MHC polymorphism under host-pathogen coevolution. Immunogenetics. 55(11):732-9.
9. Brown, J. N. 2005. Intrahaplotype and interhaplotype pairing of bovine leukocyte antigen DQA and DQB molecules generate functional DQ molecules important for priming CD4+ T-lymphocyte responses. Immunogenetics. 57: 750-762.
10. Eveline, M., Ibeagha-Awemu, P. K. 2008. Acritical analysis of disease-associated DNA polymorphisms in the genes of cattle, goat, sheep, and pig. Mammalian Genome. 19: 226-245.
11. García-Boronat, M., Diez-Rivero, CM.,Reinherz, Reche, PA. 2008 PVS: A web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery. Nucleic Acids Research. 36:W35–W41.
12. Gelhaus, A., Wippern, C. 1995. Sequence polymorphism of BoLA-DQA. Immunogenetics. 42: 296-298.
13. Gerner, W., Denyer, M.S., Takamatsu, H.H., Wileman, T.E., Wiesmüller, K.H. 2006. Identification of novel foot-and-mouth disease virus specific T-cell epitopes in c/c and d/d haplotype miniature swine. Virus Research. 121: 223–228.
14. Martí-Renom, MA., Stuart, AC., Fiser, A., Sánchez, R., Melo, F., Sali, A. 2000. Comparative protein structure modeling of genes and genomes. Annual Review of Biophysics Bimolecular Structure. 29:291-325.
15. Morooka, A., Asahina, M., Kohda, C., Tajima, S., Niimi, M., Nishino, Y., Sugiyama, M., Aida, Y. 1995. Biochemistry and Biophysics Research Communication. 6, 212(1):110-7.
16. Paital, B., Kumar, S., Farmer, R., Tripathy, NK.,Chainy, GBN. 2011. In silico prediction and characterization of 3D structure and binding properties of catalase from the commercially important crab, Scylla serrata. Interdisciplinary Sciences. Computational Life Science. 3(2):110-20.
17. Pia, M., Untalan, J. H. 2007. Association of the bovine leukocyte antigen major histocompatibility complex class II DRB3*4401 allele with host resistance to the Lone Star tick, Amblyomma americanum. Veterinary parasitology. 145: 190-195.
18. Ranjbar, M.M., Nikbakht, G., GhadrdanMashhadi, A.R., Dabbaghyan, M., 2016. Study of BuLA-DRB3 polymorphism in Khuzestan river buffaloes. Journal of Veterinary Research. 71,1:33-40.
19. Rupp, R. A., 2007. Association of Bovine Leukocyte Antigen(BoLA)DRB3.2 with Immune Responce, mastitis and production and type traits. Dairy science. 90: 1029-1039.
20. Takeshima, S., Aida, Y. 2006. Structure, function and disease susceptibility of the bovine major histocompatibility complex. Animal Science Journal. 77(2): 138-50.
21. Takeshima, S-N., Matsumoto, Y., Aida, Y. 2009. Short communication: Establishment of a new polymerase chain reaction–sequence-based typing method for genotyping cattle major histocompatibility complex class II DRB3. Journal of dairy science. 92(6):2965-70.
22. Tizard, I.R., 2013. Major Histocompatibility Complex. Veterinary Immunology, 9th ed. USA, Philadelphia, Saunders-Elsevier, 102-112.
23. Van der Poel, J. 1990. The nucleotide sequence of the bovine MHC class II alpha genes:DRA, DQA, and DYA. Immunogenetics. 31: 29-36.
24. Xu, a.,van Eijk, M.J., Park, C., Lewin, H.A. 1993. Polymorphism in BoLA-DRB3 exon 2 Correlates with Resistance to Persistent Lymphocytosis Caused by Bovine Leukemia Virus. Journal of Immunology. 151(12): 6977-85.
Veterinary Research & Biological Products
Volume 30, Issue 3 - Serial Number 116
September 2017
Pages 34-42

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History

  • Receive Date: 18 June 2016
  • Revise Date: 21 August 2016
  • Accept Date: 21 August 2016

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