The basis for haplotype complexity in VCBPs, an immune-type receptor in amphioxus

Immunogenetics

Volumn 62, Issue 9, 2010, Pages 623-631

  Dishaw, Larry J ^a,b   Ota, Tatsuya ^c   Mueller, M Gail ^a   Cannon, John P ^b,d   Haire, Robert N ^d   Gwatney, Natasha R ^d   Litman, Ronda T ^d   Litman, Gary W ^a,b,d  

^a JOHNS HOPKINS ALL CHILDREN S HOSPITAL   (United States)

^b H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

^c GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^d UNIVERSITY OF SOUTH FLORIDA   (United States)

Author keywords

Evolution; Innate immunity; Variable immunoglobulin polymorphism; Variable region containing chitin binding protein

Indexed keywords

BINDING PROTEIN; COMPLEMENTARY DNA; UNCLASSIFIED DRUG; VARIABLE REGION CONTAINING CHITIN BINDING PROTEIN 2; VARIABLE REGION CONTAINING CHITIN BINDING PROTEIN 5;

AMINO TERMINAL SEQUENCE; ARTICLE; BRANCHIOSTOMA FLORIDAE; COPY NUMBER VARIATION; DNA POLYMORPHISM; DNA SEQUENCE; GENE CLUSTER; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME; HAPLOTYPE; IMMUNOGLOBULIN GENE; INNATE IMMUNITY; INVERTEBRATE CHORDATA; MULTIGENE FAMILY; NONHUMAN; PRIORITY JOURNAL;

AMINO ACID SEQUENCE; ANIMALS; CHITIN; CHORDATA, NONVERTEBRATE; DNA, COMPLEMENTARY; EVOLUTION, MOLECULAR; GENOME; HAPLOTYPES; IMMUNOGLOBULIN VARIABLE REGION; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, GENETIC; RECEPTORS, IMMUNOLOGIC; SEQUENCE HOMOLOGY, AMINO ACID;

ANIMALIA; BRANCHIOSTOMA FLORIDAE; BRANCHIOSTOMA LANCEOLATUM; INVERTEBRATA; VERTEBRATA;

EID: 77957556787     PISSN: 00937711     EISSN: 14321211     Source Type: Journal    
DOI: 10.1007/s00251-010-0464-x     Document Type: Article

References (39)

1. SF Altschul W Gish W Miller EW Myers DJ Lipman 1990 Basic local alignment search tool J Mol Biol 215 403 410 1:CAS:528:DyaK3MXitVGmsA%3D%3D 2231712
2. M Brudno R Steinkamp B Morgenstern 2004 The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences Nucleic Acids Res 32 W41 W44 1:CAS:528:DC%2BD2cXlvFKns7w%3D 10.1093/nar/gkh361 15215346 (Pubitemid 38997296)
3. JP Cannon RN Haire GW Litman 2002 Identification of diversified genes that contain immunoglobulin-like variable regions in a protochordate Nat Immunol 3 1200 1207 1:CAS:528:DC%2BD38XovFChsb8%3D 10.1038/ni849 12415263 (Pubitemid 35469705)
4. JP Cannon RN Haire JP Rast GW Litman 2004 The phylogenetic origins of the antigen binding receptors and somatic diversification mechanisms Immunol Rev 200 12 22 1:CAS:528:DC%2BD2cXmvVGqtrc%3D 10.1111/j.0105-2896.2004.00166.x 15242392 (Pubitemid 38998189)
5. JP Cannon RN Haire N Schnitker MG Mueller GW Litman 2004 Individual protochordates possess unique immune-type receptor repertoires Curr Biol 14 R465 R466 1:CAS:528:DC%2BD2cXltVOgt7s%3D 10.1016/j.cub.2004.06.009 15203016 (Pubitemid 38791577)
6. F Delsuc H Brinkmann D Chourrout H Philippe 2006 Tunicates and not cephalochordates are the closest living relatives of vertebrates Nature 439 965 968 1:CAS:528:DC%2BD28Xhs1KjsLY%3D 10.1038/nature04336 16495997 (Pubitemid 43292413)
7. NM Dheilly SV Nair LC Smith DA Raftos 2009 Highly variable immune-response proteins (185/333) from the sea urchin, Strongylocentrotus purpuratus: proteomic analysis identifies diversity within and between individuals J Immunol 182 2203 2212 1:CAS:528:DC%2BD1MXhsFKrsro%3D 10.4049/jimmunol.07012766 19201874
8. LJ Dishaw MG Mueller N Gwatney JP Cannon RN Haire RT Litman CT Amemiya T Ota L Rowen G Glusman GW Litman 2008 Genomic complexity of the variable region-containing chitin-binding proteins in amphioxus BMC Genomics 9 78 10.1186/1471-2164-9-78 (Pubitemid 351344691)
9. Y Dong HE Taylor G Dimopoulos 2006 AgDscam, a hypervariable immunoglobulin domain-containing receptor of the Anopheles gambiae innate immune system PLoS Biol 4 1137 1146 1:CAS:528:DC%2BD28Xntlequ7o%3D 10.1371/journal.pbio.0040229 (Pubitemid 44049612)
10. DD Dudley J Chaudhuri CH Bassing FW Alt 2005 Mechanism and control of V(D)J recombination versus class switch recombination: similarities and differences Adv Immunol 86 43 112 1:CAS:528:DC%2BD2MXksFGnur0%3D 10.1016/S0065-2776(04)86002-4 15705419 (Pubitemid 40215690)
11. AR Friedman BJ Baker 2007 The evolution of resistance genes in multi-protein plant resistance systems Curr Opin Genet Dev 17 493 499 1:CAS:528:DC%2BD2sXhsVWisbzM 10.1016/j.gde.2007.08.014 17942300 (Pubitemid 350184307)
12. P Guo M Hirano BR Herrin J Li C Yu A Sadlonova MD Cooper 2009 Dual nature of the adaptive immune system in lampreys Nature 459 796 801 1:CAS:528:DC%2BD1MXmsVGgtrc%3D 10.1038/nature08068 19474790
13. JA Hernandez Prada RN Haire M Allaire J Jakoncic N Stojanovic JP Cannon GW Litman DA Ostrov 2006 Ancient evolutionary origin of diversified variable regions revealed by crystal structures of an immune-type receptor in amphioxus Nat Immunol 7 875 10.1038/ni1359 16799561 (Pubitemid 44084095)
14. LZ Holland V Laudet M Schubert 2004 The chordate amphioxus: an emerging model organism for developmental biology Cell Mol Life Sci 61 2290 2308 1:CAS:528:DC%2BD2cXhtVWlu7nM 10.1007/s00018-004-4075-2 15378201 (Pubitemid 39382022)
15. LZ Holland R Albalat K Azumi E Benito-Gutierrez MJ Blow M Bronner-Fraser F Brunet T Butts S Candiani LJ Dishaw DE Ferrier J Garcia-Fernandez JJ Gibson-Brown C Gissi A Godzik F Hallbook D Hirose K Hosomichi T Ikuta H Inoko M Kasahara J Kasamatsu T Kawashima A Kimura M Kobayashi Z Kozmik K Kubokawa V Laudet GW Litman AC McHardy D Meulemans M Nonaka RP Olinski Z Pancer LA Pennacchio M Pestarino JP Rast I Rigoutsos M Robinson-Rechavi G Roch H Saiga Y Sasakura M Satake Y Satou M Schubert N Sherwood T Shiina N Takatori J Tello P Vopalensky S Wada A Xu Y Ye K Yoshida F Yoshizaki JK Yu Q Zhang CM Zmasek PJ de Jong K Osoegawa NH Putnam DS Rokhsar N Satoh PW Holland 2008 The amphioxus genome illuminates vertebrate origins and cephalochordate biology Genome Res 18 1100 1111 1:CAS:528:DC%2BD1cXotlKmtr8%3D 10.1101/gr.073676.107 18562680 (Pubitemid 351931161)
16. KC Hsu S Chida DE Geraghty B Dupont 2002 The killer cell immunoglobulin-like receptor (KIR) genomic region: gene-order, haplotypes and allelic polymorphism Immunol Rev 190 40 52 1:CAS:528:DC%2BD3sXnt12luw%3D%3D 10.1034/j.1600-065X.2002.19004.x 12493005 (Pubitemid 36071925)
17. SI Khakoo R Rajalingam BP Shum K Weidenbach L Flodin DG Muir F Canavez SL Cooper NM Valiante LL Lanier P Parham 2000 Rapid evolution of NK cell receptor systems demonstrated by comparison of chimpanzees and humans Immunity 12 687 698 1:CAS:528:DC%2BD3cXkslagtbc%3D 10.1016/S1074-7613(00)80219-8 10894168
18. S Kurata 2006 Recognition and elimination of diversified pathogens in insect defense systems Mol Divers 10 599 605 1:CAS:528:DC%2BD28Xht1Ohsb3O 10.1007/s11030-006-9032-6 16969720 (Pubitemid 44885236)
19. J Kurtz SA Armitage 2006 Alternative adaptive immunity in invertebrates Trends Immunol 27 493 496 1:CAS:528:DC%2BD28XhtVGju7zI 10.1016/j.it.2006.09.001 16979938 (Pubitemid 44499157)
20. GW Litman MD Cooper 2007 Commentary: why study the evolution of immunity? Nat Immunol 8 547 548 1:CAS:528:DC%2BD2sXlsVSku7c%3D 10.1038/ni0607-547 17514203 (Pubitemid 46785114)
21. GW Litman JP Cannon LJ Dishaw 2005 Reconstructing immune phylogeny: new perspectives Nat Rev Immunol 5 866 879 1:CAS:528:DC%2BD2MXhtFKls7jI 10.1038/nri1712 16261174 (Pubitemid 41581668)
22. GW Litman LJ Dishaw JP Cannon RN Haire JP Rast 2007 Alternative mechanisms of immune receptor diversity Curr Opin Biol 19 526 534 1:CAS:528:DC%2BD2sXhtFSmu7vL
23. C Messier-Solek KM Buckley JP Rast 2010 Highly diversified innate receptor systems and new forms of animal immunity Semin Immunol 22 39 47 1:CAS:528:DC%2BC3cXitVKjtb8%3D 10.1016/j.smim.2009.11.007 20022762
24. M Mondragon-Palomino BS Gaut 2005 Gene conversion and the evolution of three leucine-rich repeat gene families in Arabidopsis thaliana Mol Biol Evol 22 2444 2456 1:CAS:528:DC%2BD2MXht1KgtLnE 10.1093/molbev/msi241 16120808 (Pubitemid 41661381)
25. F Nagawa N Kishihita K Shimizu S Hirose M Miyoshi J Nezu T Nishimura H Nishizumi Y Takahashi S Hashimoto M Takeuchi A Miyajima T Takemori AJ Otsuka H Sakano 2007 Antigen-receptor genes of the agnathan lamprey are assembled by a process involving copy choice Nat Immunol 8 206 213 1:CAS:528: DC%2BD2sXnt1Kisw%3D%3D 10.1038/ni1419 17187071 (Pubitemid 46152652)
26. M Nei T Gojobori 1986 Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions Mol Biol Evol 3 418 426 1:CAS:528:DyaL28Xmt1aisbs%3D 3444411
27. PJ Norman L Abi-Rached K Gendzekhadze JA Hammond AK Moesta D Sharma T Graef KL McQueen LA Guethlein CV Carrington D Chandanayingyong YH Chang C Crespi G Saruhan-Direskeneli K Hameed G Kamkamidze KA Koram Z Layrisse N Matamoros J Mila MH Park RM Pitchappan DD Ramdath MY Shiau HA Stephens S Struik D Tyan DH Verity RW Vaughan RW Davis PA Fraser EM Riley M Ronaghi P Parham 2009 Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes Genome Res 19 757 769 1:CAS:528:DC%2BD1MXlsFykuro%3D 10.1101/gr.085738.108 19411600
28. Z Pancer CT Amemiya RA Ehrhardt J Ceitlin GL Gartland MD Cooper 2004 Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey Nature 430 174 180 1:CAS:528:DC%2BD2cXlsVGjtrw%3D 10.1038/nature02740 15241406 (Pubitemid 38902420)
29. M Parniske KE Hammond-Kosack C Golstein CM Thomas DA Jones K Harrison BB Wulff JD Jones 1997 Novel disease resistance specificities result from sequence exchange between tandemly repeated genes at the Cf-4/9 locus of tomato Cell 91 821 832 1:CAS:528:DyaK2sXotV2itbY%3D 10.1016/S0092-8674(00)80470-5 9413991 (Pubitemid 28007738)
30. NH Putnam T Butts DE Ferrier RF Furlong U Hellsten T Kawashima M Robinson-Rechavi E Shoguchi A Terry JK Yu EL Benito-Gutierrez I Dubchak J Garcia-Fernandez JJ Gibson-Brown IV Grigoriev AC Horton PJ de Jong J Jurka VV Kapitonov Y Kohara E Lindquist S Lucas K Osoegawa LA Pennacchio AA Salamov Y Satou T Sauka-Spengler J Schmutz I Shin A Toyoda M Bronner-Fraser A Fujiyama LZ Holland PW Holland N Satoh DS Rokhsar 2008 The amphioxus genome and the evolution of the chordate karyotype Nature 453 1064 1071 1:CAS:528: DC%2BD1cXntlGjtb4%3D 10.1038/nature06967 18563158 (Pubitemid 351888243)
31. JP Rast LC Smith M Loza-Coll T Hibino GW Litman 2006 Genomic insights into the immune system of the sea urchin Science 314 952 956 1:CAS:528:DC%2BD28XhtFyqtLbO 10.1126/science.1134301 17095692 (Pubitemid 44749931)
32. P Rice I Longden A Bleasby 2000 EMBOSS: the European Molecular Biology Open Software Suite Trends Genet 16 276 277 1:CAS:528:DC%2BD3cXjvVygsbs%3D 10.1016/S0168-9525(00)02024-2 10827456
33. H Schulenburg C Boehnisch NK Michiels 2007 How do invertebrates generate a highly specific innate immune response? Mol Immunol 44 3338 3344 1:CAS:528:DC%2BD2sXkvFWntrw%3D 10.1016/j.molimm.2007.02.019 17391764 (Pubitemid 46678200)
34. HG Shilling LA Guethlein NW Cheng CM Gardiner R Rodriguez D Tyan P Parham 2002 Allelic polymorphism synergizes with variable gene content to individualize human KIR genotype J Immunol 168 2307 2315 1:CAS:528: DC%2BD38XhvVegs7w%3D 11859120
35. P Stothard 2000 The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences Biotechniques 28 1102 1104 1:CAS:528:DC%2BD3cXktF2ks7w%3D 10868275
36. K Tamura J Dudley M Nei S Kumar 2007 MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 Mol Biol Evol 24 1596 1599 1:CAS:528:DC%2BD2sXpsVGrsL8%3D 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
37. S Tasumi CA Velikovsky G Xu SA Gai KD Wittrup MF Flajnik RA Mariuzza Z Pancer 2009 High-affinity lamprey VLRA and VLRB monoclonal antibodies Proc Natl Acad Sci USA 106 12891 12896 1:CAS:528:DC%2BD1MXhtVKlt73M 10.1073/pnas. 0904443106 19625627
38. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins 1997 The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 25 4876 4882 1:CAS:528:DyaK1cXntFyntQ%3D%3D 10.1093/nar/25.24.4876 9396791 (Pubitemid 28022245)
39. S Yuan S Huang W Zhang T Wu M Dong Y Yu T Liu K Wu H Liu M Yang H Zhang A Xu 2009 An amphioxus TLR with dynamic embryonic expression pattern responses to pathogens and activates NF-kappaB pathway via MyD88 Mol Immunol 46 2348 2356 1:CAS:528:DC%2BD1MXntFynsLw%3D 10.1016/j.molimm.2009.03.022 19394698