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Analysis of variations, structures, and phylogenic characteristics of bovine leukocyte antigen DRB3 exon2 | ||
| Archives of Razi Institute | ||
| مقاله 1، دوره 72، شماره 3، آذر 2017، صفحه 147-157 اصل مقاله (1.13 M) | ||
| نوع مقاله: Original Articles | ||
| شناسه دیجیتال (DOI): 10.22092/ari.2017.111611 | ||
| نویسندگان | ||
| M. M. Ranjbar1؛ S. Ataei* 2؛ Gh. Nikbakht Brujeni3؛ S. Golabdar3 | ||
| 1Department of Viral Animal Diseases, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran | ||
| 2Department of Avian Bacterial Diseases, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran | ||
| 3Department of Microbiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran | ||
| چکیده | ||
| Bovine leukocyte antigen (BoLA) DRB3 is a highly polymorphic gene in major histocompatibility complex (MHC) class II that plays a central role in immune responses and production factors. As of yet, molecular and evolutionary characteristics of BoLA-DRB3.2* have not been as fully understood as human and mouse. Therefore, we attempted to analyze variability and phylogeny of BoLA-DRB3.2* and illustrate some novel practical evidence on interspecies diversity, the resistance /susceptibility points in cattle breeding, and vaccine design. Initially, BoLA-DRB3.2* alleles and orthologous exons in the selected livestock were retrieved and checked. In the next step, the secondary/tertiary structure of BoLA-DRB3.2*24 gene product was modeled and validated. Then, hypervariable regions (HVRs) of alleles were identified by hybrid approaches. In the last step, interspecies relationship, allele’s phylogeny/grouping, and estimate of average evolutionary divergence were explored. Shannon entropy variation analysis showed eight HVRs and three semi-variable regions in BoLADRB3.2* alleles. These HVRs were present in all the three sub-structures and dominantly existed in alpha helix. In addition, strong relationships and little diversity were noted in phylogenetic trees of cattle, buffaloes, sheep, and goats. Furthermore, there was some evidence on divergence of DRB3 before speciation among the mentioned species and possibility of cross prediction resistance/susceptibility alleles. Finally, DRB3 alleles were grouped into seven clusters, and older and newer alleles were identified. The results show that similar studies should be done in other animals to better understand the nature of the DRB3 attributes. | ||
| کلیدواژه‌ها | ||
| BoLA-DRB3.2؛ Cattle؛ Variation؛ modeling؛ phylogeny | ||
| عنوان مقاله [English] | ||
| آنالیز تغییرات، ساختار و خصوصیات فیلوژنیک اگزون 2 از BoLA-DRB3 درگاو | ||
| چکیده [English] | ||
| اگزون2 از BoLA-DRB3 یکژن با چند شکلی بالا در MHC کلاس 2 بوده، نقش مرکزی در پاسخهای ایمنی و فاکتورهای تولیدی دارد. تا به حال خصوصیات مولکولی و تکاملی BoLA-DRB3.2 به مانند مولکولهای معادل آن درانسانی و موشی به طور کامل درک نشده است. بنابراین آنالیز تغییرپذیری و فیلوژنی BoLA-DRB3.2 صورت گرفت و برخی یافتههای کاربردی جدید در مورد تنوع بین گونهای و حساسیت / مقاوت به بیماری، و طراحی واکسن اشاره شده است. در ابتدا آللهای BoLA-DRB3.2 و اگزونهای ارتولوگ مورد نظر از پایگاه داده استخراج و ارزیابی شد. در گام بعدی ساختار دوم و سوم BoLA-DRB3.2 مدل سازی و مورد اعتبار سنجی قرار گرفت. سپس نواحی بسیار متغیر (HVRs) با رهیافتهای هیبریدی مشخص گردیدند. در گام پایانی ارتباط بین گونهای، فیلوژنی / گروهبندی آللی و تخمین میانگین واگرایی تکاملی انجام گرفت. نتایج حاکی از وجود هشت HVR و سه ناحیه مرزی در آنالیز تغییر پذیری آنتروپی شانون بود. این HVR ها در همه تحت ساختارها وجود داشته و به شکل غالب در آلفاهلیکس مشاهده شد. در بررسی فیلوژنی نیز ارتباط تکاملی بالا و تنوع پایین بین گاو، گاومیش، گوسفند و بز به دست آمد. به علاوه این شواهد حاکی از اشتقاق DRB3 قبل از گونه زایی و امکان پیشگویی متقاطع آلل های مقاومت / حساسیت را فراهم میکند. در پایان DRB3 در 7 خوشه گروهبندی گردید و ردههای آللی قدیمیتر و جدیدتر شناسایی گردید. نتایج نشان میدهد که مطالعات مشابهای نیز میبایست در سایر حیوانات صورت گیرد تا ماهیت ویژگی های DRB3 بهتر درک شود. | ||
| کلیدواژه‌ها [English] | ||
| BoLA-DRB3.2, گاو, تغییرات, مدل سازی, فیلوژنی | ||
| مراجع | ||
|
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 2012, 12.
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., et al., 2000. The Protein Data Bank. Nucleic Acids Res 28, 235-242.
Burt, D.W., 2009. The cattle genome reveals its secrets. J Biol 8, 36.
De, S., Singh, R.K., Butchaiah, G., 2002. MHC-DRB exon 2 allele polymorphism in Indian river buffalo (Bubalus bubalis). Anim Genet 33, 215-219.
Gowane, G.R., Sharma, A.K., Sankar, M., Thirumurugan, P., Narayanan, K., Subramaniam, S., et al., 2013. Evaluation of Genetic and Environmental Parameters Determining Antibody Response Induced by Vaccination Against Foot and Mouth Disease. Agricultural Research 2, 140-147.
Gupta, S.K., Srivastava, M., Akhoon, B.A., Gupta, S.K., Grabe, N., 2012. In silico accelerated identification of structurally conserved CD8+ and CD4+ T-cell epitopes in high-risk HPV types. Infect Genet Evol 12, 1513-1518.
Gupta, S.K., Srivastava, M., Akhoon, B.A., Smita, S., Schmitz, U., Wolkenhauer, O., et al., 2011. Identification of immunogenic consensus T-cell epitopes in globally distributed influenza-A H1N1 neuraminidase. Infect Genet Evol 11, 308-319.
Jeong, H.J., Bhuiyan, M.S.A., Lee, J.S., Yu, S.L., Sang, B.C., Yoon, D., et al., 2007. Characterization of BoLA-DRB3.2 Alleles in Hanwoo (Korean cattle) by Sequence Based Typing (SBT). Asian-Australas J Anim Sci 20, 1791-1797.
Johansson, F., Toh, H., 2010. A comparative study of conservation and variation scores. BMC Bioinformatics 11, 388.
MacCallum, R.M., Martin, A.C., Thornton, J.M., 1996. Antibody-antigen interactions: contact analysis and binding site topography. J Mol Biol 262, 732-745.
Marti-Renom, M.A., Stuart, A.C., Fiser, A., Sanchez, R., Melo, F., Sali, A., 2000. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29, 291-325.
Miyasaka, T., Takeshima, S.N., Matsumoto, Y., Kobayashi, N., Matsuhashi, T., Miyazaki, Y., et al., 2011. The diversity of bovine MHC class II DRB3 and DQA1 alleles in different herds of Japanese Black and Holstein cattle in Japan. Gene 472, 42-49.
Nielsen, M., Justesen, S., Lund, O., Lundegaard, C., Buus, S., 2010. NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure. Immunome Res 6, 9.
Nikbakht, G., Ranjbar, M.M., Ghasemi, F., Asadian, F., 2012. Allelic polymorphism in exon 2 of the BoLA-DRB3 gene in Iranian Holstein cows Method and Material. Anim Prod Res 1, 33- 41.
Paital, B., Kumar, S., Farmer, R., Tripathy, N.K., Chainy, G.B., 2011. In silico prediction and characterization of 3D structure and binding properties of catalase from the commercially important crab, Scylla serrata. Interdiscip Sci 3, 110-120.
Parham, P., Lawlor, D.A., Lomen, C.E., Ennis, P.D., 1989. Diversity and diversification of HLA-A,B,C alleles. J Immunol 142, 3937-3950.
Ranjbar, M.M., Gupta, S.K., Ghorban, K., Nabian, S., Sazmand, A., Taheri, M., et al., 2015. Designing and modeling of complex DNA vaccine based on tropomyosin protein of Boophilus genus tick. Appl Biochem Biotechnol 175, 323-339.
Ranjbar, M.M., Nikbakht, G., Ghadrdan Mashhadi, A.R., Dabbaghyan, M., 2016. Study of BuLA-DRB3 polymorphism in Khuzestan river buffaloes. J Vet Res 71, 33-40.
Rupp, R., Hernandez, A., Mallard, B.A., 2007. Association of bovine leukocyte antigen (BoLA) DRB3.2 with immune response, mastitis, and production and type traits in Canadian Holsteins. J Dairy Sci 90, 1029-1038.
Russell, G.C., Fraser, D.C., Craigmile, S., Oliver, R.A., Dutia, B.M., Glass, E.J., 2000. Sequence and transfection of BoLA-DRB3 cDNAs. Anim Genet 31, 219-222.
Sena, L., Schneider, M.P., Brenig, B., Honeycutt, R.L., Womack, J.E., Skow, L.C., 2003. Polymorphisms in MHC-DRA and -DRB alleles of water buffalo (Bubalus bubalis) reveal different features from cattle DR alleles. Anim Genet 34, 1-10.
Sharif, S., Mallard, B.A., Sargeant, J.M., 2000. Presence of glutamine at position 74 of pocket 4 in the BoLA-DR antigen binding groove is associated with occurrence of clinical mastitis caused by Staphylococcus species. Veterinary Immunology and Immunopathology 76, 231-238.
Sharif, S., Mallard, B.A., Wilkie, B.N., Sargeant, J.M., Scott, H.M., Dekkers, J.C., et al., 1999. Associations of the bovine major histocompatibility complex DRB3 (BoLA-DRB3) with production traits in Canadian dairy cattle. Anim Genet 30, 157-160.
Takeshima, S.-n., Ikegami, M., Morita, M., Nakai, Y., Aida, Y., 2001. Identification of new cattle BoLA-DRB3 alleles by sequence-based typing. Immunogenetics 53, 74-81.
Takeshima, S., Saitou, N., Morita, M., Inoko, H., Aida, Y., 2003. The diversity of bovine MHC class II DRB3 genes in Japanese Black, Japanese Shorthorn, Jersey and Holstein cattle in Japan. Gene 316, 111-118.
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. J Dairy Sci 92, 2965-2970.
Tizard, I.R., 2013. Veterinary Immunology - E-Book, Elsevier Health Sciences.
Tomar, N., De, R.K., 2010. Immunoinformatics: an integrated scenario. Immunology 131, 153-168.
Tramontano, A., Leplae, R., Morea, V., 2001. Analysis and assessment of comparative modeling predictions in CASP4. Proteins Suppl 5, 22-38.
Wang, K., Sun, D., Zhang, Y., 2008. Sequencing of 15 new BoLA-DRB3 alleles. Int J Immunogenet 35, 331-332.
Yoshida, T., Mukoyama, H., Furuta, H., Kondo, Y., Takeshima, S.-n., Aida, Y., et al., 2009a. Association of the amino acid motifs of BoLA-DRB3 alleles with mastitis pathogens in Japanese Holstein cows. Animal Science Journal 80, 510-519.
Yoshida, T., Mukoyama, H., Furuta, H., Kondo, Y., Takeshima, S.N., Aida, Y., et al., 2009b. Association of BoLA-DRB3 alleles identified by a sequence-based typing method with mastitis pathogens in Japanese Holstein cows. Ani m Sci J 80, 498-509.
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