Single nucleotide polymorphism discovery in the avian Tapasin gene

Poultry Science

Volumn 85, Issue 4, 2006, Pages 606-612

  Sironi, L ^a   Lazzari, B ^a   Ramelli, P ^a   Gorni, C ^a   Mariani, P ^a  

^a PARCO TECNOLOGICO PADANO   (Italy)

Author keywords

Amino acid comparison; Major histocompatibility complex; Sequence homology; Single nucleotide polymorphism; Tapasin

Indexed keywords

AVES;

ANTIPORTER; CARRIER PROTEIN; IMMUNOGLOBULIN; TAPASIN;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; GALLIFORMES; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE;

AMINO ACID SEQUENCE; ANIMALS; ANTIPORTERS; BASE SEQUENCE; GALLIFORMES; IMMUNOGLOBULINS; MEMBRANE TRANSPORT PROTEINS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; SPECIES SPECIFICITY;

EID: 33646949224     PISSN: 00325791     EISSN: 15253171     Source Type: Journal    
DOI: 10.1093/ps/85.4.606     Document Type: Article

References (34)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSIBLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. Antoniou, A. N., S. J. Powis, and T. Elliott. 2003. Assembly and export of MHC class I peptide ligands. Curr. Opin. Immunol. 15:75-81.
4. Barnden, M. J., A. W. Purcell, J. J. Gorman, and J. McCluskey. 2000. Tapasin-mediated retention and optimization of peptide ligands during the assembly of class I molecules. J. Immunol. 165:322-330.
5. Beck, S., and J. Trowsdale. 2000. The human major histocompatibility complex: Lessons from the DNA sequence. Annu. Rev. Genomics Hum. Genet. 1:117-137.
6. Boardman, P. E., J. Sanz-Ezquerro, I. M. Overton, D. W. Burt, E. Bosch, W. T. Fong, C. Tickle, W. R. Brown, S. A. Wilson, and S. J. Hubbard. 2002. A comprehensive collection of chicken cDNAs. Curr. Biol. 12:1965-1969.
7. Bouvier, M. 2003. Accessory proteins and the assembly of human class I MHC molecules: A molecular and structural perspective. Mol. Immunol. 39:697-706.
8. Brocke, P., N. Garbi, F. Momburg, and G. J. Hammerling. 2002. HLA-DM, HLA-DO and tapasin: Functional similarities and differences. Curr. Opin. Immunol. 14:22-29.
9. Ewing, B., and P. Green. 1998. Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186-194.
10. Ewing, B., L. Hillier, M. Wendl, and P. Green. 1998. Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.
11. Frangoulis, B., I. Park, F. Guillemot, V. Severac, C. Auffray, and R. Zoorob. 1999. Identification of the Tapasin gene in the chicken major histocompatibility complex. Immunogenetics 49:328-337.
12. Garbi, N., N. Tiwari, F. Momburg, and G. J. Hammerling. 2003. A major role for tapasin as a stabilizer of the TAP peptide transporter and consequences for MHC class I expression. Eur. J. Immunol. 33:264-273.
13. Gordon, D. 2004. Viewing and editing assembled sequences using consed. In Current Protocols in Bioinformatics. A. D. Baxevanis and D. B. Davison, ed. John Wiley & Co., New York, NY.
14. Grandea, A. G., III, and L. Van Kaer. 2001. Tapasin: An ER chaperone that controls MHC class I assembly with peptide. Trends Immunol. 22:194-199.
15. Hall, T. A. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids. Symp. Ser. 41:95-98.
16. Herberg, J. A., J. Sgouros, T. Jones, J. Copeman, S. J. Humphray, D. Sheer, P. Cresswell, S. Beck, and J. Trowsdale. 1998. Genomic analysis of the Tapasin gene, located close to the TAP loci in the MHC. Eur. J. Immunol. 28:459-467.
17. Huang, X. 1994. On global sequence alignment. Comput. Appl. Biosci. 10:227-235.
18. Huang, X., and A. Madan. 1999. CAP3: A DNA sequence assembly program. Genome Res. 9:868-877.
19. Jacob, J. P., S. Milne, S. Beck, and J. Kaufman. 2000. The major and the minor class II β-chain (B-LB) gene flank the Tapasin gene in the B-F/B-L region of the chicken major histocompatibility complex. Immunogenetics 51:138-147.
20. Kaufman, J. 1999. Co-evolving genes in MHC haplotypes: The "rule" for nonmammalian vertebrates? Immunogenetics 50:228-236.
21. Kaufman, J., S. Milne, T. W. Gobel, B. A. Walker, J. P. Jacob, C. Auffray, R. Zoorob, and S. Beck. 1999. The chicken B locus is a minimal essential major histocompatibility complex. Nature 401:923-925.
22. Kaufman, J., H. Volk, and H. J. Wallny. 1995. A "Minimal Essential MHC" and an "Unrecognized MHC:" Two extremes in selection for polymorphism. Immunol. Rev. 143:63-68.
23. Lehner, P. J., M. J. Surman, and P. Cresswell. 1998. Soluble tapasin restores MHC class I expression and function in the tapasin-negative cell line .220. Immunity 8:221-231.
24. Li, S., K. M. Paulsson, S. Chen, H. O. Sjogren, and P. Wang. 2000. Tapasin is required for efficient peptide binding to transporter associated with antigen processing. J. Biol. Chem. 275:1581-1586.
25. Marchler-Bauer, A., and S. H. Bryant. 2004. CD-Search: Protein domain annotations on the fly. Nucleic Acids Res. 32:327-331.
26. Marth, G. T., I. Korf, M. D. Yandell, R. T. Yeh, Z. Gu, H. Zakeri, N. O. Stitziel, L. D. Hillier, P. Y. Kwok, and W. R. Gish. 1999. A general approach to single-nucleotide polymorphism discovery. Nat. Genet. 23:452-456.
27. Mayer, W. E., and J. Klein. 2001. Is tapasin a modified MHC class I molecule? Immunogenetics 53:719-723.
28. Ortmann, B., J. Copeman, P. J. Lehner, B. Sadasivan, J. A. Herberg, A. G. Grandea, S. R. Riddell, R. Tampè, T. Spies, J. Trowsdale, and P. Cresswell. 1997. A critical role for tapasin in the assembly and function of multimeric MHC class I-TAP complexes. Science 277:1306-1309.
29. Pamer, E., and P. Cresswell. 1998. Mechanism of MHC class I-restricted antigen processing. Annu. Rev. Immunol. 16:323-358.
30. Purcell, W. A., J. J. Gorman, M. Garcia-Peydrò, A. Paradela, S. R. Burrows, G. H. Talbo, N. Laham, C. A. Peh, E. C. Reynolds, J. A. Lopez de Castro, and J. McCluskey. 2001. Quantitative and qualitative influences of tapasin on the class I peptide repertoire. J. Immunol. 166:1016-1027.
31. Raghuraman, G., P. E. Lapinski, and M. Raghavan. 2002. Tapasin interacts with the membrane-spanning domains of both TAP subunits and enhances the structural stability of TAP1-TAP2 complexes. J. Biol. Chem. 277:41786-41794.
32. Sadasivan, B., P. J. Lehner, B. Ortmann, T. Spies, and P. Cresswell. 1996. Roles for calreticulin and a novel glycoprotein, tapasin, in the interaction of MHC class I molecules with TAP. Immunity 5:103-114.
33. The MHC sequencing consortium. 1999. Complete sequence and gene map of a human major histocompatibilty complex. Nature 401:921-923.
34. Zarling, A. L., C. J. Luckey, J. A. Marto, F. M. White, C. J. Brame, A. M. Evans, P. J. Lehner, P. Cresswell, J. Shabanowitz, D. F. Hunt, and V. H. Engelhard. 2003. Tapasin is a facilitator, not an editor, of class I MHC peptide binding. J. Immunol. 171:5287-5295.