Characterization of arrangement and expression of the T cell receptor γ locus in the sandbar shark

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 21, 2009, Pages 8591-8596

  Chen, Hao ^a   Kshirsagar, Sarika ^a   Jensen, Ingvill ^a   Lau, Kevin ^a   Covarrubias, Roman ^a   Schluter, Samuel F ^a   Marchalonis, John J ^a  

^a UNIVERSITY OF ARIZONA COLLEGE OF MEDICINE   (United States)

Author keywords

Diversity; Translocon

Indexed keywords

T CELL RECEPTOR GAMMA; T LYMPHOCYTE RECEPTOR; UNCLASSIFIED DRUG;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; GENOME ANALYSIS; GERM LINE; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN STRUCTURE; SHARK; UNINDEXED SEQUENCE;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CLONING, MOLECULAR; CONSERVED SEQUENCE; DNA, COMPLEMENTARY; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RECEPTORS, ANTIGEN, T-CELL, GAMMA-DELTA; SEQUENCE ALIGNMENT; SHARKS;

CARCHARHINUS PLUMBEUS; CHONDRICHTHYES; TELEOSTEI; TETRAPODA;

EID: 66649097841     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0811283106     Document Type: Article

References (51)

1. Bernstein RM, Schluter SF, Bernstein H, Marchalonis JJ (1996) Primordial emergence of the recombination activating gene 1 (RAG1): Sequence of the complete shark gene indicates homology to microbial integrases. Proc Natl Acad Sci USA 93:9454-9459. (Pubitemid 26296629)
2. Marchalonis JJ, Schluter SF, Bernstein RM, Shen S, Edmundson AB (1998) Phylogenetic emergence and molecular evolution of the immunoglobulin family. Adv Immunol 70:417-506. (Pubitemid 128678842)
3. Hohman VS, Schluter SF, Marchalonis JJ (1995) Diversity of Ig light chain clusters in the sandbar shark (Carcharhinus plumbeus). J Immunol 155:3922-3928.
4. Hohman VS, Schuchman DB, Schluter SF, Marchalonis JJ (1993) Genomic clone for sandbar shark lambda light chain: Generation of diversity in the absence of gene rearrangement. Proc Natl Acad Sci USA 90:9882-9886. (Pubitemid 23328214)
5. Rast JP, et al. (1994) Immunoglobulin light chain class multiplicity and alternative organizational forms in early vertebrate phylogeny. Immunogenetics 40:83-99. (Pubitemid 24193957)
6. Rast JP, Amemiya CT, Litman RT, Strong SJ, Litman GW (1998) Distinct patterns of IgH structure and organization in a divergent lineage of chrondrichthyan fishes. Immunogenetics 47:234-245. (Pubitemid 28059526)
7. Rumfelt LL, et al. (2001) A shark antibody heavy chain encoded by a nonsomatically rearranged VDJ is preferentially expressed in early development and is convergent with mammalian IgG. Proc Natl Acad Sci USA 98:1775-1780. (Pubitemid 32165574)
8. Vazquez M, Mizuki N, Flajnik MF, McKinney EC, Kasahara M (1992) Nucleotide sequence of a nurse shark immunoglobulin heavy chain cDNA clone. Mol Immunol 29:1157-1158.
9. Hunkapiller T, Hood L (1989) Diversity of the immunoglobulin gene superfamily. Adv Immunol 44:1-63. (Pubitemid 19090835)
10. Rast JP, et al. (1997) alpha, beta, gamma, and delta T cell antigen receptor genes arose early in vertebrate phylogeny. Immunity 6:1-11. (Pubitemid 27130210)
11. Rast JP, Litman GW (1994) T-cell receptor gene homologs are present in the most primitive jawed vertebrates. Proc Natl Acad Sci USA 91:9248-9252. (Pubitemid 24297891)
12. Hawke NA, Rast JP, Litman GW (1996) Extensive diversity of transcribed TCR-beta in phylogenetically primitive vertebrate. J Immunol 156:2458-2464. (Pubitemid 26091571)
13. Cheynier R, Henrichwark S, Wain-Hobson S (1998) Somatic hypermutation of the T cell receptor V beta gene in microdissected splenic white pulps from HIV-1-positive patients. Eur J Immunol 28:1604-1610. (Pubitemid 28221164)
14. Zheng B, Xue W, Kelsoe G (1994) Locus-specific somatic hypermutation in germinal centre T cells. Nature 372:556-559. (Pubitemid 24368538)
15. Marshall B, Schulz R, Zhou M, Mellor A (1999) Alternative splicing and hypermutation of a nonproductively rearranged TCR alpha-chain in a T cell hybridoma. J Immunol 162:871-877. (Pubitemid 29035411)
16. Tonegawa S (1983) Somatic generation of antibody diversity. Nature 302:575-581.
17. Cowell LG, Davila M, Kepler TB, Kelsoe G (2002) Identification and utilization of arbitrary correlations in models of recombination signal sequences. Genome Biol, 10.1186/gb-2002-3-12-research0072.
18. Lee V, et al. (2008) The evolution of multiple isotypic IgM heavy chain genes in the shark. J Immunol 180:7461-7470.
19. Rock EP, Sibbald PR, Davis MM, Chien YH (1994) CDR3 length in antigen-specific immune receptors. J Exp Med 179:323-328. (Pubitemid 24012999)
20. Lee SS, Tranchina D, Ohta Y, Flajnik MF, Hsu E (2002) Hypermutation in shark immunoglobulin light chain genes results in contiguous substitutions. Immunity 16:571-582. (Pubitemid 34442581)
21. Diaz M, Velez J, Singh M, Cerny J, Flajnik MF (1999) Mutational pattern of the nurse shark antigen receptor gene (NAR) is similar to that of mammalian Ig genes and to spontaneous mutations in evolution: The translesion synthesis model of somatic hypermutation. Int Immunol 11:825-833. (Pubitemid 29237773)
22. Greenberg AS, et al. (1995) A new antigen receptor gene family that undergoes rearrangement and extensive somatic diversification in sharks. Nature 374:168-173.
23. Shamblott MJ, Litman GW (1989) Genomic organization and sequences of immunoglobulin light chain genes in a primitive vertebrate suggest coevolution of immunoglobulin gene organization. EMBO J 8:3733-3739. (Pubitemid 20016053)
24. Daggfeldt A, Bengten E, Pilstrom L (1993) A cluster type organization of the loci of the immunoglobulin light chain in Atlantic cod (Gadus morhua L.) and rainbow trout (Oncorhynchus mykiss Walbaum) indicated by nucleotide sequences of cDNAs and hybridization analysis. Immunogenetics 38:199-209. (Pubitemid 23219220)
25. Selsing E, Miller J, Wilson R, Storb U (1982) Evolution of mouse immunoglobulin lambda genes. Proc Natl Acad Sci USA 79:4681-4685.
26. Chang H, et al. (1986) Identification of three new Ig lambda-like genes in man. J Exp Med 163:425-435. (Pubitemid 16113077)
27. Lefranc MP, et al. (1989) Molecular mapping of the human T cell receptor gamma (TRG) genes and linkage of the variable and constant regions. Eur J Immunol 19:989-994. (Pubitemid 19181148)
28. Toyonaga B, Yoshikai Y, Vadasz V, Chin B, Mak TW (1985) Organization and sequences of the diversity, joining, and constant region genes of the human T-cell receptor beta chain. Proc Natl Acad Sci USA 82:8624-8628. (Pubitemid 16105115)
29. Tunnacliffe A, Kefford R, Milstein C, Forster A, Rabbitts TH (1985) Sequence and evolution of the human T-cell antigen receptor beta-chain genes. Proc Natl Acad Sci USA 82:5068-5072. (Pubitemid 15249945)
30. Chien YH, Jores R, Crowley MP (1996) Recognition by gamma/delta T cells. Annu Rev Immunol 14:511-532.
31. Carding SR, Egan PJ (2002) Gammadelta T cells: Functional plasticity and heterogeneity. Nat Rev Immunol 2:336-345. (Pubitemid 37328756)
32. Hein WR, Dudler L (1997) TCR gamma delta+ cells are prominent in normal bovine skin and express a diverse repertoire of antigen receptors. Immunology 91:58-64. (Pubitemid 27196000)
33. Vaccarelli G, et al. (2005) Genomic organization of the sheep TRG1@ locus and comparative analyses of Bovidae and human variable genes. Gene 357:103-114. (Pubitemid 41297576)
34. Herzig C, Blumerman S, Lefranc MP, Baldwin C (2006) Bovine T cell receptor gamma variable and constant genes: Combinatorial usage by circulating gammadelta T cells. Immunogenetics 58:138-151. (Pubitemid 44343148)
35. Yazawa R, et al. (2008) Functional adaptive diversity of the Atlantic salmon T-cell receptor gamma locus. Mol Immunol 45:2150-2157. (Pubitemid 350180071)
36. Malecek K, et al. (2008) Immunoglobulin heavy chain exclusion in the shark. PLoS Biol, 10.1371/journal.pbio.0060157.
37. Chang YF, Imam JS, Wilkinson MF (2007) The nonsense-mediated decay RNA surveillance pathway. Annu Rev Biochem 76:51-74.
38. Richards MH, Nelson JL (2000) The evolution of vertebrate antigen receptors: A phylogenetic approach. Mol Biol Evol 17:146-155. (Pubitemid 30057000)
39. Chien YH, Bonneville M (2006) Gamma delta T cell receptors. Cell Mol Life Sci 63:2089-2094. (Pubitemid 44465683)
40. Wilson IA, Stanfield RL (2001) Unraveling the mysteries of gammadelta T cell recognition. Nat Immunol 2:579-581. (Pubitemid 32677622)
41. Pancer Z, Cooper MD (2006) The evolution of adaptive immunity. Annu Rev Immunol 24:497-518.
42. Alder MN, et al. (2005) Diversity and function of adaptive immunereceptors in a jawless vertebrate. Science 310:1970-1973. (Pubitemid 43005993)
43. Pancer Z, et al. (2005) Variable lymphocyte receptors in hagfish. Proc Natl Acad Sci USA 102:9224-9229. (Pubitemid 40923545)
44. Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059-3066.
45. Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33:511-518. (Pubitemid 40360980)
46. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680. (Pubitemid 24354800)
47. Larkin MA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948. (Pubitemid 350162903)
48. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599. (Pubitemid 47236692)
49. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783-795. (Pubitemid 38829638)
50. Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
51. Lefranc MP, et al. (2005) IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev Comp Immunol 29:185-203. (Pubitemid 39575119)