Skip to main content
SpringerLink
Log in

Possible Polyphyletic Origin of Major Histocompatibility Complex Class I Chain-Related Gene A (MICA) Alleles

  • Published:
Journal of Molecular Evolution Aims and scope Submit manuscript

Abstract

Phylogenetic relationships among 23 nonhuman primate (NHP) major histocompatibility complex class I chain-related gene (MIC) sequences, 54 confirmed human MICA alleles, and 16 human MICE alleles were constructed with methods of sequence analysis. Topology of the phylogenetic tree showed separation between NHP MICs and human MICs. For human MICs, the topology indicated monophyly for the MICB alleles, while MICA alleles were separated into two lineages, LI and LII. Of these, LI MICA alleles shared a common ancestry with gorilla (Ggo) MIC. One conservative amino acid difference and two nonconservative amino acid differences in the α3 domain were found between the MICA lineages. The nonconservative amino acid differences might imply structural and functional differences. Transmembrane (TM) trinucleotide-repeat variants were found to be specific to the MICA lineages such as A4, A9, and A10 to LI and A5 to LII. Variants such as A5.1 and A6 were commonly found in both MICA lineages. Based on these analyses, we postulate a polyphyletic origin for MICA alleles and their division into two lineages, LI and LII. As such, there would be 30 alleles in LI and 24 alleles in LII, thereby reducing the current level of polymorphism that exists, based on a presumed monophyletic origin. The lower degree of polymorphism in MICA would then be in line with the rest of the human major histocompatibility complex nonclassical class I genes.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1

Similar content being viewed by others

References

  1. S Bahram (2001) ArticleTitleMIC genes: From genetics to biology. Adv Immunol 76 1–60

    Google Scholar 

  2. S Bahram M Bresnahan DE Geraghty T Spies (1994) ArticleTitleA second lineage of mammalian major histocompatibility complex class I genes. Proc Natl Acad Sci USA 91 6259–6263 Occurrence Handle1:CAS:528:DyaK2cXlslWrs78%3D Occurrence Handle8022771

    CAS  PubMed  Google Scholar 

  3. SK Cattley N Longman RL Dawkins S Gaudieri JK Kulski C Leelayuwat (1999) ArticleTitlePhylogenetic analysis of primate MIC (PERB11) sequences suggests that the representation of the gene family differs in different primates: Comparison of MIC (PERB11) and C4. Eur J Immunogenet 26 233–238 Occurrence Handle10.1046/j.1365-2370.1999.00154.x Occurrence Handle1:CAS:528:DyaK1MXjtl2js7s%3D Occurrence Handle10331161

    Article  CAS  PubMed  Google Scholar 

  4. RWM Collins HAF Stephens MA Clare RW Vaughan (2002) ArticleTitleHigh-resolution molecular phototyping of MICA and MICB alleles using sequence-specific primers. Hum Immunol 65 IssueID9 783–794 Occurrence Handle10.1016/S0198-8859(02)00425-1

    Article  Google Scholar 

  5. DS Dunn JF Williamson SK Cattley GK Tay S Gaudieri C Leelayuwat RL Dawkins (2000) ArticleTitleCoevolution of HLA-B and PERB11.1 (MICA): Significance of independent triplet expansion within the transmembrane region of PERB11.1 (MICA). J Mol Evol 50 359–365 Occurrence Handle1:CAS:528:DC%2BD3cXivFyjurw%3D Occurrence Handle10795827

    CAS  PubMed  Google Scholar 

  6. L Fernandez M Fernandez-Arquero L Gual F Lazaro C Maluenda I Polanco MA Figueredo EG De La Concha (2002) ArticleTitleTriplet-repeat polymorphism in the transmembrane region of the MICA gene in celiac disease. Tissue Antigens 59 219–222 Occurrence Handle10.1034/j.1399-0039.2002.590307.x Occurrence Handle1:CAS:528:DC%2BD38Xls1ejtbc%3D Occurrence Handle12074713

    Article  CAS  PubMed  Google Scholar 

  7. Y Katsuyama M Ota H Ando S Saito N Mizuki J Kera S Bahram Y Nose H Inoko (1999) ArticleTitleSequencing based typing for genetic polymorphisms in exons 2, 3, and 4 of the MICA gene. Tissue Antigens 54 178–184 Occurrence Handle10.1034/j.1399-0039.1999.540209.x Occurrence Handle1:CAS:528:DyaK1MXmtV2itL0%3D Occurrence Handle10488745

    Article  CAS  PubMed  Google Scholar 

  8. M Kimura (1980) ArticleTitleA simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16 111–120 Occurrence Handle7463489

    PubMed  Google Scholar 

  9. JK Kulski S Gaudieri A Martin RL Dawkins (1999) ArticleTitleCoevolution of PERB11 (MIC) and HLA class 1 genes with HERV-16 and retroelements by extended genomic duplication. J Mol Evol 49 84–97 Occurrence Handle1:CAS:528:DyaK1MXkt1Oktrg%3D Occurrence Handle10368437

    CAS  PubMed  Google Scholar 

  10. S Kumar K Tamura IB Jakobsen M Nei (2001) ArticleTitleMEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 17 1244–1255 Occurrence Handle1:CAS:528:DC%2BD38XmtVCktQ%3D%3D Occurrence Handle11751241

    CAS  PubMed  Google Scholar 

  11. C Leelayuwat DC Townend MA Degli-Esposti LJ Abraham RL Dawkins (1994) ArticleTitleA new polymorphic and multicopy MHC gene family related to non-mammalian class I. Immunogenetics 40 339–351 Occurrence Handle1:CAS:528:DyaK2MXivFSktbw%3D Occurrence Handle7927538

    CAS  PubMed  Google Scholar 

  12. A Martinez M Fernandez-Arquero A Balsa A Rubio H Alves D Pascual-Salcedo E Martin-Mola EG de la Concha (2001) ArticleTitlePrimary association of a MICA allele with protection against rheumatoid arthritis. Arth Rheum 44 1261–1265 Occurrence Handle10.1002/1529-0131(200106)44:6<1261::AID-ART217>3.0.CO;2-L Occurrence Handle1:STN:280:DC%2BD3MzksVOgsw%3D%3D

    Article  CAS  Google Scholar 

  13. A Lopez-Vazquez L Rodrigo D Fuentes S Riestra C Bousono S Garcia-Fernandez J Martinez-Borra S Gonzalez C Lopez-Larrea (2002) ArticleTitleMICA-A5.1 allele is associated with atypical forms of celiac disease in HLA-DQ2-negative patients. Immunogenetics 53 989–991 Occurrence Handle10.1007/s00251-001-0413-9 Occurrence Handle1:CAS:528:DC%2BD38XhsFKksr4%3D Occurrence Handle11862400

    Article  CAS  PubMed  Google Scholar 

  14. M Ota Y Katsuyama N Mizuki H Ando K Furihata S Ono P Pivetti-Pezzi KF Tabbara GD Palimeris B Nikbin F Davatchi H Chams Z Geng S Bahram H Inoko (1997) ArticleTitleTrinucleotide-repeat polymorphism within exon 5 of the MICA gene (MHC class I chain-related gene A): Allele frequency data in the nine population groups Japanese, Northern Han, Hui, Uygur, Kazakhstan, Iranian, Saudi Arabian, Greek, and Italian. Tissue Antigens 49 448–454 Occurrence Handle9174136

    PubMed  Google Scholar 

  15. J Robinson MJ Waller P Parham JG Bodmer SG Marsh (2001) ArticleTitle1MGT/HLA Database—A sequence database for the human major histocompatibility complex. Nucleic Acids Res 29 210–213 Occurrence Handle1:CAS:528:DC%2BD3MXjtlWmsbs%3D Occurrence Handle11125094

    CAS  PubMed  Google Scholar 

  16. DP Singal J Li G Zhang (2001) ArticleTitleMicrosatellite polymorphism of the MICA gene and susceptibility to rheumatoid arthritis. Clin Exp Rheumatol 19 IssueID4 451–452 Occurrence Handle1:STN:280:DC%2BD3MvksV2nug%3D%3D Occurrence Handle11491503

    CAS  PubMed  Google Scholar 

  17. HAF Stephens (2001) ArticleTitleMICA and MICB genes: Can the enigma of their polymorphism be resolved? Trends Immunol 22 378–385 Occurrence Handle1:CAS:528:DC%2BD3MXks1Okt70%3D Occurrence Handle11429322

    CAS  PubMed  Google Scholar 

  18. HAF Stephens RW Vaughan R Collins E Kondeatis J Theron A Payne (1999) ArticleTitleTowards a molecular phototyping system for allelic variants of MICA, encoded by polymorphisms in exons 2, 3, and 4 of MHC class I chain-related genes. Tissue Antigens 53 167–174 Occurrence Handle10.1034/j.1399-0039.1999.530207.x Occurrence Handle1:CAS:528:DyaK1MXhvVSntro%3D Occurrence Handle10090617

    Article  CAS  PubMed  Google Scholar 

  19. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins (1997) ArticleTitleThe ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24 4876–4882 Occurrence Handle10.1093/nar/25.24.4876

    Article  Google Scholar 

  20. CJT Visser MGJ Tilanus V Schaeffer Z Tatari R Tamouza A Janin D Charron (1998) ArticleTitleSequencing-based typing reveals six novel MHC class I chain-related gene B (MICB) alleles. Tissue Antigens 51 649–652 Occurrence Handle1:CAS:528:DyaK1cXks12ks7Y%3D

    CAS  Google Scholar 

  21. C Xiao S Zhang L Cheng H Jing Y Hou J Chu G Zhang J Wu (2000) ArticleTitleStudies on the polymorphism of MICA gene in four Chinese populations. Chin J Med Genet 17 IssueID6 424–428 Occurrence Handle1:CAS:528:DC%2BD3MXktVCrtQ%3D%3D

    CAS  Google Scholar 

  22. Y Zhang AM Lazaro B Lavingia P Stastny (2000) ArticleTitleTyping for all known MICA alleles by group-specific PCR and SSOP. Hum Immunol 62 620–631 Occurrence Handle10.1016/S0198-8859(01)00241-5

    Article  Google Scholar 

Download references

Acknowledgements

We acknowledge C. Leelayuwat and J.K. Kulski for their helpful comments and University of Malaya, Malaysia, for facilities. This research project was supported by the Intensification of Research in Priority Areas (IRPA) Programme (IRPA 06-02-03-0454 and 06-02-03-0718), the Ministry of Science, Technology, and the Environment, Malaysia, and the Postgraduate Scheme, University of Malaya.

Author information

Authors and Affiliations

  1. Allied Health Sciences Department, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia

    Mun-kit Choy & Maude E. Phipps

Authors
  1. Mun-kit Choy
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Maude E. Phipps
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Maude E. Phipps.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Choy, Mk., Phipps, M.E. Possible Polyphyletic Origin of Major Histocompatibility Complex Class I Chain-Related Gene A (MICA) Alleles . J Mol Evol 57, 38–43 (2003). https://doi.org/10.1007/s00239-002-2444-8

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00239-002-2444-8

Keywords

Search

Navigation