A new human transporter associated with antigen processing alleles encodes a large C-terminal protein domain

 Springer-Verlag 1997

Immunogenetics (1997) 45: 280 – 281

SEQUENCE REGISTER Maya M. Cesari ? Sophie J. Dulay ? Henri Caillens Christine Robert ? Claude Rouch ? Fre´de´ric Cadet Michel Pabion

A new human transporter associated with antigen processing alleles encodes a large C-terminal protein domain

Received: 27 June 1996 / Revised: 7 October 1996

The transporter associated with antigen processing (TAP) translocates peptides from the cytosol into the lumen of the endoplasmic reticulum. Five nucleotide variation sites that induce a change in amino acid residues were identified in the TAP2 gene, and seven alleles derived from the combination of these dimorphic sites have been described (Bahram et al. 1991; Colona et al. 1992; Moins-Teisserenc et al. 1994; Szaffer et al. 1994; see Table 1). In the present study, TAP2 typing was performed by amplification refractory mutation system (ARMS) polymerase chain reaction (PCR) as previously described (Powis et al. 1993). Oligonucleotide primers used for this typing are shown in Table 2. A group of 78 families living on Reunion Island, consisting of 82 insulin-dependent diabetes mellitus (IDDM) patients and most of their first-degree relatives (i. e., 154 parents and full sibling subjects), were studied.

Seventeen of the 236 persons analyzed (seven IDDM patients and ten parental controls) showed a new combination of nucleotides located at polymorphic sites, allowing the definition of a new allele. This new allele, TAP2 G (see Table 1), was characterized by the presence of amino acid residues Thr on position 665 and Gln on position 687. No exception to the previously detected association between 655 Ala and 687 Gln or 665 Thr and 687 Stop has been described in Caucasians (Martinez-Laso et al. 1994; Szaffer et al. 1994). This linkage disequilibrium which was considered absolute in Caucasians (IDDM patients and control) is not recovered in the Reunion Island population, which is highly crossbred (including Caucasians, Africans, Indians, and Chinese). Sequence analysis of cDNA PCR amplified fragment, coming from the homozygous immortalized B-cell line Reu-M4-1, has confirmed the existence of this allele.

Table 1mAllelic variations in TAP2. Presentation of TAP2 alleles showing the amino acid (AA) positions which vary in the different alleles and the nucleotidic sequence that encodes for these amino acids. The variant nucleotide (Nt) in each codon is underlined Polymorphic sites WHO name

Local name

Nt 1231

AA 379

Nt 1789

AA 565

Nt 2047

AA 651

Nt 2089

AA 665

Nt 2155

AA 687

Nt 2187

TAP2 0101 Tap2 0201

TAP2 A TAP2 B TAP2 C TAP2 D TAP2 E TAP2 F TAP2 G

GTA GTA ATA ATA GTA GTA GTA ATA

Val Val Ile Ile Val Val Val Ile

GCT GCT GCT ACT ACT GCT GCT GCT

Ala Ala Ala Thr Thr Ala Ala Ala

CGT CGT CGT CGT CGT TGT CGT CGT

Arg Arg Arg Arg Arg Cys Arg Arg

ACA GCA ACA ACA ACA ACA ACA GCA

Thr Ala Thr Thr Thr Thr Thr Ala

TAG CAG TAG TAG TAG TAG CAG CAG

Stop Gln Stop Stop Stop Stop Gln Gln

G T

TAP2 0102 TAP2 0103a TAP2 0202b a b

G G T

Allele previously described by Cano and co-workers (1995) Allele previously described by Bahram and co-workers (1991)

M. M. Cesari ? C. Robert ? C. Rouch ? F. Cadet? M. Pabion ( ) Laboratoire de Biochimie, Faculte´ des Sciences Universite´ de la Re´union, 15 Av. Rene´ Cassin. B. P. 7151, 97715 Saint Denis Messag Cedex 9, Re´union France-DOM S. J. Dulay

?

H. Caillens

Finally, the new allele TAP2 G should be considered a long version of TAP2 A (see Table 1). The new polymorphism corresponding to 665 Thr together with 687 Gln, never shown in Caucasians, may increase the potential combinations of amino acids at polymorphic sites and thus the numbers of TAP2 allele in African, Chinese, or Indian populations.

M. M. Cesari et al.: A new human TAP2 allele encodes a large C terminal protein domain

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Table 2mOligonucleotide primers used for ARMS PCR typing of TAP2 Sequence 59 → 39

Polymorphic sites

Name

Codon 379 Nucleotide 1231

ARMS ARMS ARMS ARMS

1 2 3 4

TTG GAG ACA ACA

GAG ACC ACC TAG

GGC TGG ACT CTC

TGC AAC CTG CCC

AGA GCG GTA ACG

CCG CCT TCT CTC

TTC TGT TAC TCC

GCA ACC CCT TGG

GTT TGC CCT TAG

TTG GCG GAT ATC

Codon 565 Nucleotide 1789

ARMS ARMS ARMS ARMS

5 6 7 8

CTC TGT ATC GGA

ACA TCT ATC GCA

GTA CCG TTC AGC

TGA GTT GCA TTA

ACA CTG GCT CAA

CTG TGA CTG TTT

CTA GGA CAG GTA

CCT ACA CCC GAA

GCA ACA ATA GAT

CAG GTA AAC ACC

Codon 651 Nucleotide 2047

ARMS ARMS ARMS ARMS

9 12 17 18

TTG TCA CAC AGC

GGG GCC CCC AAT

AAT GCT TTC CAC

GGA GCT AGC CAG

ATC GCA TGC CAC

CGG CCA AGG TGT

TGG GGC ACT GCG

TGT GGG GGA ATC

GAG AAT ATT CCC

GGC AGA CTC ATA

Codon 665 Nucleotide 2089

ARMS ARMS ARMS ARMS

13 14 15 16

TCC AGG CAG CAA

AGC GCA GCG AAG

TGT AGC GGA CAC

GGC TGC ATA ACA

AGT AGA GAG GTG

ACA AGC GTC TCC

GCC TTG CTG AAA

GGG CCC TCC TCT

AGA AGC CTC CCA

GAA CCT ATG TCG

Codon 687 Nucleotide 2155

ARMS ARMS ARMS ARMS

9 10 11 12

TTG CAG CAC TCA

GGG TGC CAG GCC

AAT TGG GAT GCT

GGA TGA CTG GCT

ATC TTG GTG GCA

CGG CTC GGC CCA

TGG ACA GCG GGC

TGT GGC CTG GGG

GAG TGC AAC AAT

GGC AAA TAC AGA

ARMS PCR was performed according to the method previously described (Powis et al. 1993) modified as follows: genomic DNA (0.1 µg) was amplified in 25 µl reaction mixture containing 0.03 µg of

each primer and 1.5 mM MgCl2. Reaction conditions were: 94 °C for 7 min followed by 40 cycles of 58 °C, 1 min; 72 °C, 45 s; 94 °C, 1 min

AcknowledgmentsmThis work was supported in part by a grant from le Ministe`re de l’Education Nationale de l’Enseignement Supe´rieur et de la Recherche, le Conseil Re´gional de La Re´union, le Conseil Ge´ne´ral de La Re´union, and l’INSERM.

Colona, M., Bresnaham, M., Bahram, S., Strominger, J. L., and Spies, T. Allelic variants of the human putative transporter involved in antigen processing. Proc Natl Acad Sci USA 89: 3932 – 3936, 1992 Martinez-Laso, J., Martin-Villa, J. M., Alvarez, M., Martinez-Quiles, N., Liedo, G., and Arnaiz-Villena, A. Susceptibility to insulindependent diabetes mellitus and short cytoplasmic ATP-binding domain TAP2 0201 alleles. Tissue Antigens 44: 184 – 188, 1994 Moins-Teisserenc, H., Bobrynina, V., Loiseau, P., and Charron, D. New polymorphism within the human TAP1 and TAP2 coding region. Immunogenetics 40: 242, 1994 Powis, S. H., Tonks, S., Mockridge, I., Kelly, A. P., Bodmer, J. G., and Trowsdale, J., Allele and haplotypes of the MHC-encoded ABC transporters TAP1 and TAP2. Immunogenetics 37: 373 – 380, 1993 Szaffer, F., Oksenberg, J. R., and Stienman, L. New allelic polymorphism in TAP genes. Immunogenetics 39: 374, 1994

References Bahram, S., Arnold, D., Bresnaham, M., Strominger, J. L., and Spies, T. Two putative subunits of a peptide pump encoded in the human major histocompatibility complex class II region. Proc Natl Acad Sci USA 88: 10094 – 10098, 1991 Cano, P. and Baxter-Iowe, L. A. Novel human TAP2 103 allele shows further polymorphism in the ATP-binding domain. Tissue Antigens 45: 139 – 142, 1995