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

Overview

Journal J Mol Evol

Specialty Biochemistry

Date 2003 Sep 10

PMID 12962304

Citations 1

Authors

Mun-Kit Choy

Maude E Phipps

Affiliations

Soon will be listed here.

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 alpha3 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.

Citing Articles

Association between MICA polymorphisms, s-MICA levels, and pancreatic cancer risk in a population-based case-control study.

Onyeaghala G, Lane J, Pankratz N, Nelson H, Thyagarajan B, Walcheck B PLoS One. 2019; 14(6):e0217868.

PMID: 31166958 PMC: 6550421. DOI: 10.1371/journal.pone.0217868.

References

Martinez A, Fernandez-Arquero M, Balsa A, Rubio A, Alves H, Pascual-Salcedo D . Primary association of a MICA allele with protection against rheumatoid arthritis. Arthritis Rheum. 2001; 44(6):1261-5. DOI: 10.1002/1529-0131(200106)44:6<1261::AID-ART217>3.0.CO;2-L. View

Bahram S, Bresnahan M, Geraghty D, Spies T . A second lineage of mammalian major histocompatibility complex class I genes. Proc Natl Acad Sci U S A. 1994; 91(14):6259-63. PMC: 44180. DOI: 10.1073/pnas.91.14.6259. View

Ota M, Katsuyama Y, Mizuki N, Ando H, Furihata K, Ono S . Trinucleotide 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. 1997; 49(5):448-54. DOI: 10.1111/j.1399-0039.1997.tb02778.x. View

Visser C, Tilanus M, SCHAEFFER V, Tatari Z, Tamouza R, Janin A . Sequencing-based typing reveals six novel MHC class I chain-related gene B (MICB) alleles. Tissue Antigens. 1998; 51(6):649-52. DOI: 10.1111/j.1399-0039.1998.tb03008.x. View

Bahram S . MIC genes: from genetics to biology. Adv Immunol. 2000; 76:1-60. DOI: 10.1016/s0065-2776(01)76018-x. View

Robinson J, Waller M, Parham P, Bodmer J, Marsh S . IMGT/HLA Database--a sequence database for the human major histocompatibility complex. Nucleic Acids Res. 2000; 29(1):210-3. PMC: 29780. DOI: 10.1093/nar/29.1.210. View

Singal D, Li J, Zhang G . Microsatellite polymorphism of the MICA gene and susceptibility to rheumatoid arthritis. Clin Exp Rheumatol. 2001; 19(4):451-2. View

Xiao C, Zhang S, Cheng L, Jing H, Hou Y, Chu J . [Studies on the polymorphism of MICA gene in four Chinese populations]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2000; 17(6):424-8. View

Thompson J, Gibson T, Plewniak F, Jeanmougin F, Higgins D . The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1998; 25(24):4876-82. PMC: 147148. DOI: 10.1093/nar/25.24.4876. View

10.

Lopez-Vazquez A, Rodrigo L, Fuentes D, Riestra S, Bousono C, Garcia-Fernandez S . MICA-A5.1 allele is associated with atypical forms of celiac disease in HLA-DQ2-negative patients. Immunogenetics. 2002; 53(10-11):989-91. DOI: 10.1007/s00251-001-0413-9. View

11.

Collins R, Stephens H, Clare M, Vaughan R . High resolution molecular phototyping of MICA and MICB alleles using sequence specific primers. Hum Immunol. 2002; 63(9):783-94. DOI: 10.1016/s0198-8859(02)00425-1. View

12.

Leelayuwat C, Townend D, Degli-Esposti M, Abraham L, Dawkins R . A new polymorphic and multicopy MHC gene family related to nonmammalian class I. Immunogenetics. 1994; 40(5):339-51. DOI: 10.1007/BF01246675. View

13.

Kimura M . A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980; 16(2):111-20. DOI: 10.1007/BF01731581. View

14.

Dunn D, Williamson J, Cattley S, Tay G, Gaudieri S, Leelayuwat C . Coevolution of HLA-B and PERB11.1 (MICA): significance of independent triplet expansion within the transmembrane region of PERB11.1 (MICA). J Mol Evol. 2000; 50(4):359-65. DOI: 10.1007/s002399910039. View

15.

Kulski J, Gaudieri S, Martin A, Dawkins R . Coevolution of PERB11 (MIC) and HLA class I genes with HERV-16 and retroelements by extended genomic duplication. J Mol Evol. 1999; 49(1):84-97. DOI: 10.1007/pl00006537. View

16.

Kumar S, Tamura K, Jakobsen I, Nei M . MEGA2: molecular evolutionary genetics analysis software. Bioinformatics. 2001; 17(12):1244-5. DOI: 10.1093/bioinformatics/17.12.1244. View

17.

Zhang Y, Lazaro A, Lavingia B, Stastny P . Typing for all known MICA alleles by group-specific PCR and SSOP. Hum Immunol. 2001; 62(6):620-31. DOI: 10.1016/s0198-8859(01)00241-5. View

18.

Cattley S, Longman N, Dawkins R, Gaudieri S, Kulski J, Leelayuwat C . Phylogenetic 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. 1999; 26(2-3):233-8. DOI: 10.1046/j.1365-2370.1999.00154.x. View

19.

Katsuyama Y, Ota M, Ando H, Saito S, Mizuki N, Kera J . Sequencing based typing for genetic polymorphisms in exons, 2, 3 and 4 of the MICA gene. Tissue Antigens. 1999; 54(2):178-84. DOI: 10.1034/j.1399-0039.1999.540209.x. View

20.

Fernandez L, Fernandez-Arquero M, Gual L, Lazaro F, Maluenda C, Polanco I . Triplet repeat polymorphism in the transmembrane region of the MICA gene in celiac disease. Tissue Antigens. 2002; 59(3):219-22. DOI: 10.1034/j.1399-0039.2002.590307.x. View