, Volume 68, Issue 5, pp 339–352 | Cite as

Sequence diversity between class I MHC loci of African native and introduced Bos taurus cattle in Theileria parva endemic regions: in silico peptide binding prediction identifies distinct functional clusters

  • Isaiah ObaraEmail author
  • Morten Nielsen
  • Marie Jeschek
  • Ard Nijhof
  • Camila J. Mazzoni
  • Nicholas Svitek
  • Lucilla Steinaa
  • Elias Awino
  • Cassandra Olds
  • Ahmed Jabbar
  • Peter-Henning Clausen
  • Richard P. Bishop
Original Article


There is strong evidence that the immunity induced by live vaccination for control of the protozoan parasite Theileria parva is mediated by class I MHC-restricted CD8+ T cells directed against the schizont stage of the parasite that infects bovine lymphocytes. The functional competency of class I MHC genes is dependent on the presence of codons specifying certain critical amino acid residues that line the peptide binding groove. Compared with European Bos taurus in which class I MHC allelic polymorphisms have been examined extensively, published data on class I MHC transcripts in African taurines in T. parva endemic areas is very limited. We utilized the multiplexing capabilities of 454 pyrosequencing to make an initial assessment of class I MHC allelic diversity in a population of Ankole cattle. We also typed a population of exotic Holstein cattle from an African ranch for class I MHC and investigated the extent, if any, that their peptide-binding motifs overlapped with those of Ankole cattle. We report the identification of 18 novel allelic sequences in Ankole cattle and provide evidence of positive selection for sequence diversity, including in residues that predominantly interact with peptides. In silico functional analysis resulted in peptide binding specificities that were largely distinct between the two breeds. We also demonstrate that CD8+ T cells derived from Ankole cattle that are seropositive for T. parva do not recognize vaccine candidate antigens originally identified in Holstein and Boran (Bos indicus) cattle breeds.


Theileria parva CD8+ T cell epitopes Class I MHC Ankole cattle Pyrosequencing 



We are grateful to Dr. Joerg Jores of ILRI for reviewing the manuscript. We also wish to thank Giles Prettejohn of the Ol Pejeta Conservancy in Kenya whose efforts were instrumental to the completion of this study. The study was funded by the DFG German-African Cooperation Projects in Infectiology: ‘Molecular epidemiology network for promotion and support of delivery of life vaccines against Theileria parva and Theileria annulata infection in Eastern and Northern Africa (SE 862/2-1)’. Some of the work described in this paper was also supported by the CGIAR Consortium research project CRP3.7.

Supplementary material

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Supplementary Fig. 1 (DOCX 29 kb)
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Supplementary Fig. 2 (DOCX 31 kb)
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Supplementary Table 1 (DOCX 82 kb)


  1. Akoolo L, Pellé R, Saya R, Awino E, Nyanjui J, Taracha EL, Kanyari P, Mwangi DM, Graham SP (2008) Evaluation of the recognition of Theileria parva vaccine candidate antigens by cytotoxic T lymphocytes from Zebu cattle. Vet Immunol Immunopathol 121(3–4):216–221CrossRefPubMedGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410CrossRefPubMedGoogle Scholar
  3. Anderung C, Hellborg L, Seddon J, Hanotte O, Götherström A (2007) Investigation of X- and Y-specific single nucleotide polymorphisms in taurine (Bos taurus) and indicine (Bos indicus) cattle. Anim Genet 38(6):595–600CrossRefPubMedGoogle Scholar
  4. Babik W, Kawalko A, Wojcik JM, Radwan J (2012) Low major histocompatibility complex class 1 (MHC I) variation in the European bison (Bison bonasus). J Hered 103:349–359CrossRefPubMedGoogle Scholar
  5. Birch J, Murphy L, MacHugh ND, Ellis SA (2006) Generation and maintenance of diversity in the cattle MHC class I region. Immunogenetics 58(8):670–679CrossRefPubMedGoogle Scholar
  6. Codner GF, Stear MJ, Reeve R, Mathews L, Ellis SA (2011) Selective forces shaping diversity in the class I region of the major histocompatibility complex in dairy cattle. Anim Genet 43:239–249CrossRefPubMedGoogle Scholar
  7. Codner GF, Birch J, Hammond JA, Ellis SA (2012) Constraints on haplotype structure and variable gene frequencies suggest a functional hierarchy within cattle MHC class I. Immunogenetics 64(6):435–445CrossRefPubMedGoogle Scholar
  8. Di Giulio G, Lynen G, Morzaria S, Oura C, Bishop R (2009) Live immunization against East Coast fever—current status. Trends Parasitol 25(2):85–92CrossRefPubMedGoogle Scholar
  9. Di Palma F, Archibald SD, Young JR, Ellis SA (2002) A BAC contig of approximately 400 kb contains the classical class I major histocompatibility complex (MHC) genes of cattle. Eur J Immunogenet 29(1):65–68CrossRefPubMedGoogle Scholar
  10. Dodt M, Roehr J, Ahmed R, Dieterich C (2012) FLEXBAR—flexible barcode and adapter processing for next-generation sequencing platforms. Biology 1(3):895–905CrossRefPubMedPubMedCentralGoogle Scholar
  11. Ellis S (2004) The cattle major histocompatibility complex: is it unique? Vet Immunol Immunopathol 102(1–2):1–8CrossRefPubMedGoogle Scholar
  12. Ellis SA, Holmes EC, Staines KA, Smith KB, Stear MJ, McKeever DJ, MacHugh ND, Morrison WI (1999) Variation in the number of expressed MHC genes in different cattle class I haplotypes. Immunogenetics 50(5–6):319–328CrossRefPubMedGoogle Scholar
  13. Emery DL, Eugui EM, Nelson RT, Tenywa T (1981) Cell-mediated immune responses to Theileria parva (East Coast fever) during immunization and lethal infections in cattle. Immunology 43(2):323–336PubMedPubMedCentralGoogle Scholar
  14. Eugui EM, Emery DL (1981) Genetically restricted cell-mediated cytotoxicity in cattle immune to Theileria parva. Nature 290(5803):251–254CrossRefPubMedGoogle Scholar
  15. Graham SP, Pellé R, Honda Y, Mwangi DM, Tonukari NJ, Yamage M, Glew EJ, de Villiers EP, Shah T, Bishop R, Abuya E, Awino E, Gachanja J, Luyai AE, Mbwika F, Muthiani AM, Ndegwa DM, Njahira M, Nyanjui JK, Onono FO, Osaso J, Saya RM, Wildmann C, Fraser CM, Maudlin I, Gardner MJ, Morzaria SP, Loosmore S, Gilbert SC, Audonnet JC, van der Bruggen P, Nene V, Taracha EL (2006) Theileria parva candidate vaccine antigens recognized by immune bovine cytotoxic T lymphocytes. Proc Natl Acad Sci U S A 103(9):3286–3291CrossRefPubMedPubMedCentralGoogle Scholar
  16. Graham S, Honda Y, Pelle R, Mwangi DM, Glew EJ, DeVilliers EP, Shah T, Bishop R, van der Bruggen P, Nene V, Taracha ELN (2007) A novel strategy for the identification of antigens that are recognised by Bovine MHC class I restricted cytotoxic T cells in a protozoan infection using reverse vaccinology. Immunome Res 3:2CrossRefPubMedPubMedCentralGoogle Scholar
  17. Graham SP, Pellé R, Yamage M, Mwangi DM, Honda Y, Mwakubambanya RS, de Villiers EP, Abuya E, Awino E, Gachanja J, Mbwika F, Muthiani AM, Muriuki C, Nyanjui JK, Onono FO, Osaso J, Riitho V, Saya RM, Ellis SA, McKeever DJ, MacHugh ND, Gilbert SC, Audonnet JC, Morrison WI, van der Bruggen P, Taracha EL (2008) Characterization of the fine specificity of bovine CD8 T-cell responses to defined antigens from the protozoan parasite Theileria parva. Infect Immun 76(2):685–694CrossRefPubMedPubMedCentralGoogle Scholar
  18. Hansen AM, Rasmussen M, Svitek N, Harndahl M, Golde WT, Barlow J, Nene V, Buus S, Nielsen M (2014) Characterization of binding specificities of bovine leucocyte class I molecules: impacts for rational epitope discovery. Immunogenetics 66(12):705–718CrossRefPubMedPubMedCentralGoogle Scholar
  19. Harndahl M, Justesen S, Lamberth K, Roder G, Nielsen M, Buus S (2009) Peptide binding to HLA class I molecules: homogenous, high-throughput screening, and affinity assays. J Biomol Screen 14:173–180CrossRefPubMedGoogle Scholar
  20. Holmes EC, Roberts AF, Staines KA, Ellis SA (2003) Evolution of major histocompatibility complex class I genes in Cetartiodactyls. Immunogenetics 55(4):193–202CrossRefPubMedGoogle Scholar
  21. Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, Lund O, Buus S, Nielsen M (2009) NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics 61(1):1–13CrossRefPubMedPubMedCentralGoogle Scholar
  22. Janetzki S, Price L, Schroeder H, Britten CM, Welters MJ, Hoos A (2015) Guidelines for the automated evaluation of Elispot assays. Nat Protoc 10(7):1098–1115CrossRefPubMedGoogle Scholar
  23. Katende J, Morzaria S, Toye P, Skilton R, Nene V, Nkonge C, Musoke A (1998) An enzyme-linked immunosorbent assay for detection of Theileria parva antibodies in cattle using a recombinant polymorphic immunodominant molecule. Parasitol Res 84(5):408–416CrossRefPubMedGoogle Scholar
  24. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772–780CrossRefPubMedPubMedCentralGoogle Scholar
  25. MacHugh DE, Shriver MD, Loftus RT, Cunningham P, Bradley DG (1997) Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus). Genetics 146(3):1071–1086PubMedPubMedCentralGoogle Scholar
  26. McKeever DJ, Taracha EL, Innes EL, MacHugh ND, Awino E, Goddeeris BM, Morrison WI (1994) Adoptive transfer of immunity to Theileria parva in the CD8+ fraction of responding efferent lymph. Proc Natl Acad Sci U S A 91(5):1959–1963CrossRefPubMedPubMedCentralGoogle Scholar
  27. Musoke AJ, Nantulya VM, Buscher G, Masake RA, Otim B (1982) Bovine immune response to Theileria parva: neutralizing antibodies to sporozoites. Immunology 45:663–668PubMedPubMedCentralGoogle Scholar
  28. Nene V, Gobright E, Bishop R, Morzaria S, Musoke A (1999) Linear peptide specificity of bovine antibody responses to p67 of Theileria parva and sequence diversity of sporozoite-neutralizing epitopes: implications for a vaccine. Infect Immun 67:1261–1266PubMedPubMedCentralGoogle Scholar
  29. Nene V, Svitek N, Toye P, Golde WT, Barlow J, Harndahl M, Buus S, Nielsen M (2012) Designing bovine T cell vaccines via reverse immunology. Ticks Tick Borne Dis 3(3):188–192CrossRefPubMedGoogle Scholar
  30. Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Røder G, Peters B, Sette A, Lund O, Buus S (2007) NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS One 2(8):e796CrossRefPubMedPubMedCentralGoogle Scholar
  31. Norval RAI, Perry BD, Young AS (1992) The epidemiology of Theileria in Africa. Academic, LondonGoogle Scholar
  32. Obara I, Ulrike S, Musoke T, Spooner PR, Jabbar A, Odongo D, Kemp S, Silva JC, Bishop RP (2015) Molecular evolution of a central region containing B cell epitopes in the gene encoding the p67 sporozoite antigen within a field population of Theileria parva. Parasitol Res 114(5):1729–1737CrossRefPubMedPubMedCentralGoogle Scholar
  33. O’Leary CE, Wiseman RW, Karl JA, Bimber BN, Lank SM, Tuscher JJ, O’Connor DH (2009) Identification of novel MHC class I sequences in pig-tailed macaques by amplicon pyrosequencing and full-length cDNA cloning and sequencing. Immunogenetics 61(10):689–701CrossRefPubMedPubMedCentralGoogle Scholar
  34. Paling RW, Mpangala C, Luttikhuizen B, Sibomana G (1991) Exposure of Ankole and crossbred cattle to Theileriosis in Rwanda. Trop Anim Health Prod 23(4):203–214CrossRefPubMedGoogle Scholar
  35. Pandya M, Rasmussen M, Hansen A, Nielsen M, Buus S, Golde W, Barlow J (2015) A modern approach for epitope prediction: identification of foot-and-mouth disease virus peptides binding bovine leukocyte antigen (BoLA) class I molecules. Immunogenetics 67(11):691–703Google Scholar
  36. Pedersen LE, Harndahl M, Rasmussen M, Lamberth K, Golde WT, Lund O, Nielsen M, Buus S (2011) Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities. Immunogenetics 63(12):821–834CrossRefPubMedPubMedCentralGoogle Scholar
  37. Radley DE, Brown CGD, Burridge MJ, Cunningham MP, Kirimi IM, Purnell RE, Young AS (1975) Chemoprophylactic immunisation of cattle against Theileria parva (Muguga) and five Theileria strains. Vet Parasitol 1:35–41CrossRefGoogle Scholar
  38. Robinson J, Halliwell JA, McWilliam H, Lopez R, Marsh SG (2013) IPD—the immuno polymorphism database. Nucleic Acids Res 41(Database issue):D1234–D1240CrossRefPubMedPubMedCentralGoogle Scholar
  39. Sette A, Sidney J (1999) Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism. Immunogenetics 50(3–4):201–212CrossRefPubMedGoogle Scholar
  40. Sommer S, Courtiol A, Mazzoni CJ (2013) MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout. BMC Genomics 14:542CrossRefPubMedPubMedCentralGoogle Scholar
  41. Steinaa L, Saya R, Awino E, Toye P (2012) Cytotoxic T lymphocytes from cattle immunized against Theileria parva exhibit pronounced cross-reactivity among different strain-specific epitopes of the Tp1 antigen. Vet Immunol Immunopathol 145(3–4):571–581CrossRefPubMedGoogle Scholar
  42. Svitek N, Hansen AM, Steinaa L, Saya R, Awino E, Nielsen M, Buus S, Nene V (2014) Use of ‘one-pot, mix-and-read’ peptide-MHC class I tetramers and predictive algorithms to improve detection of cytotoxic T lymphocyte responses in cattle. Vet Res 45:50CrossRefPubMedPubMedCentralGoogle Scholar
  43. Swofford DL (2002) PAUP: phylogenetic analysis using parsimony and other methods. Version 4. Sinauer Associates, SunderlandGoogle Scholar
  44. Thomsen M, Lundegaard C, Buus S, Lund O, Nielsen M (2013) MHCcluster, a method for functional clustering of MHC molecules. Immunogenetics 65(9):655–665CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Isaiah Obara
    • 1
    Email author
  • Morten Nielsen
    • 2
    • 3
  • Marie Jeschek
    • 4
  • Ard Nijhof
    • 1
  • Camila J. Mazzoni
    • 4
    • 5
  • Nicholas Svitek
    • 6
  • Lucilla Steinaa
    • 6
  • Elias Awino
    • 6
  • Cassandra Olds
    • 6
  • Ahmed Jabbar
    • 1
  • Peter-Henning Clausen
    • 1
  • Richard P. Bishop
    • 6
  1. 1.Institute for Parasitology and Tropical Veterinary MedicineFreie Universität BerlinBerlinGermany
  2. 2.Center for Biological Sequence Analysis (CBS), Department of Systems BiologyThe Technical University of DenmarkLyngbyDenmark
  3. 3.Instituto de Investigaciones BiotecnológicasUniversidad Nacional de San MartínSan MartínArgentina
  4. 4.Berlin Center for Genomics in Biodiversity Research (BeGenDiv)BerlinGermany
  5. 5.Leibniz-Institute for Zoo and Wildlife Research (IZW)Evolutionary GeneticsBerlinGermany
  6. 6.International Livestock Research Institute (ILRI)NairobiKenya

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