Organization of lamprey variable lymphocyte receptor C locus and repertoire development

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

Volumn 110, Issue 15, 2013, Pages 6043-6048

  Das, Sabyasachi ^a   Hirano, Masayuki ^a   Aghaallaei, Narges ^b   Bajoghli, Baubak ^b   Boehm, Thomas ^b   Cooper, Max D ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b MAX PLANCK INSTITUTE OF IMMUNOBIOLOGY AND EPIGENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

LYMPHOCYTE RECEPTOR;

ARTICLE; DNA FLANKING REGION; EXON; GENE CASSETTE; GENE LOCUS; GENE SEQUENCE; GERM LINE; LAMPREY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

AMINO ACID SEQUENCE; ANIMALS; EVOLUTION, MOLECULAR; GENE REARRANGEMENT; GENOME; GENOMICS; MOLECULAR SEQUENCE DATA; PETROMYZON; PHYLOGENY; RECEPTORS, ANTIGEN; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID;

HAGFISH; LAMPETRA PLANERI; LETHENTERON JAPONICUM; PETROMYZON MARINUS; PETROMYZONTIDAE; VERTEBRATA;

EID: 84876016474     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1302500110     Document Type: Article

References (41)

1. Litman GW, Anderson MK, Rast JP (1999) Evolution of antigen binding receptors. Annu Rev Immunol 17:109-147.
2. Hirano M, Das S, Guo P, Cooper MD (2011) The evolution of adaptive immunity in vertebrates. Adv Immunol 109:125-157.
3. Dudley DD, Chaudhuri J, Bassing CH, Alt FW (2005) Mechanism and control of V (D) J recombination versus class switch recombination: Similarities and differences. Adv Immunol 86:43-112.
4. Pancer Z, et al. (2004) Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature 430(6996):174-180.
5. Boehm T, et al. (2012) VLR-based adaptive immunity. Annu Rev Immunol 30:203-220.
6. Rogozin IB, et al. (2007) Evolution and diversification of lamprey antigen receptors: Evidence for involvement of an AID-APOBEC family cytosine deaminase. Nat Immunol 8(6):647-656.
7. Kasamatsu J, et al. (2010) Identification of a third variable lymphocyte receptor in the lamprey. Proc Natl Acad Sci USA 107(32):14304-14308.
8. Pancer Z, et al. (2005) Variable lymphocyte receptors in hagfish. Proc Natl Acad Sci USA 102(26):9224-9229.
9. Guo P, et al. (2009) Dual nature of the adaptive immune system in lampreys. Nature 459(7248):796-801.
10. Alder MN, et al. (2005) Diversity and function of adaptive immune receptors in a jawless vertebrate. Science 310(5756):1970-1973.
11. Alder MN, et al. (2008) Antibody responses of variable lymphocyte receptors in the lamprey. Nat Immunol 9(3):319-327.
12. Herrin BR, et al. (2008) Structure and specificity of lamprey monoclonal antibodies. Proc Natl Acad Sci USA 105(6):2040-2045.
13. Bajoghli B, et al. (2011) A thymus candidate in lampreys. Nature 470(7332):90-94.
14. Nagawa F, et al. (2007) Antigen-receptor genes of the agnathan lamprey are assembled by a process involving copy choice. Nat Immunol 8(2):206-213.
15. Han BW, Herrin BR, Cooper MD, Wilson IA (2008) Antigen recognition by variable lymphocyte receptors. Science 321(5897):1834-1837.
16. Velikovsky CA, et al. (2009) Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen. Nat Struct Mol Biol 16(7):725-730.
17. Deng L, et al. (2010) A structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey. Proc Natl Acad Sci USA 107(30):13408-13413.
18. Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406-425.
19. Felsenstein J (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17(6):368-376.
20. Das S, Nozawa M, Klein J, Nei M (2008) Evolutionary dynamics of the immunoglobulin heavy chain variable region genes in vertebrates. Immunogenetics 60(1):47-55.
21. Das S (2009) Evolutionary origin and genomic organization of micro-RNA genes in immunoglobulin lambda variable region gene family. Mol Biol Evol 26(5):1179-1189.
22. Parra ZE, et al. (2008) Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica. BMC Genomics 9:111.
23. Malynn BA, Yancopoulos GD, Barth JE, Bona CA, Alt FW (1990) Biased expression of JH-proximal VH genes occurs in the newly generated repertoire of neonatal and adult mice. J Exp Med 171(3):843-859.
24. Kraj P, et al. (1997) The human heavy chain Ig V region gene repertoire is biased at all stages of B cell ontogeny, including early pre-B cells. J Immunol 158(12):5824-5832.
25. Day EB, et al. (2011) Structural basis for enabling T-cell receptor diversity within biased virus-specific CD8+ T-cell responses. Proc Natl Acad Sci USA 108(23):9536-9541.
26. Butler JE, Wertz N, Sun J, Sacco RE (2005) Comparison of the expressed porcine Vbeta and Jbeta repertoire of thymocytes and peripheral T cells. Immunology 114(2):184-193.
27. Kirchdoerfer RN, et al. (2012) Variable lymphocyte receptor recognition of the immunodominant glycoprotein of Bacillus anthracis spores. Structure 20(3):479-486.
28. Nei M, Rogozin IB, Piontkivska H (2000) Purifying selection and birth-and-death evolution in the ubiquitin gene family. Proc Natl Acad Sci USA 97(20):10866-10871.
29. Das S, Nikolaidis N, Klein J, Nei M (2008) Evolutionary redefinition of immunoglobulin light chain isotypes in tetrapods using molecular markers. Proc Natl Acad Sci USA 105(43):16647-16652.
30. Nikolaidis N, Nei M (2004) Concerted and nonconcerted evolution of the Hsp70 gene superfamily in two sibling species of nematodes. Mol Biol Evol 21(3):498-505.
31. Schultz J, Milpetz F, Bork P, Ponting CP (1998) SMART, a simple modular architecture research tool: Identification of signaling domains. Proc Natl Acad Sci USA 95(11):5857-5864.
32. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673-4680.
33. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: A sequence logo generator. Genome Res 14(6):1188-1190.
34. Tamura K, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731-2739.
35. Nei M, Kumar S (2000) Molecular Evolution and Phylogenetics (Oxford Univ Press, Oxford).
36. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10(3):512-526.
37. Milanesi L, Muselli M, Arrigo P (1996) Hamming-clustering method for signals prediction in 5' and 3' regions of eukaryotic genes. Comput Appl Biosci 12(5):399-404.
38. Hiller K, Grote A, Scheer M, Münch R, Jahn D (2004) PrediSi: Prediction of signal peptides and their cleavage positions. Nucleic Acids Res 32(Web Server issue):W375-9.
39. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340(4):783-795.
40. Gomi M, Sonoyama M, Mitaku S (2004) High-performance system for signal peptide prediction: SOSUIsignal. Chem Bio Inform J 4:142-147.
41. Kohany O, Gentles AJ, Hankus L, Jurka J (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7:474.