Evolution of CC chemokines in teleost fish: A case study in gene duplication and implications for immune diversity

Immunogenetics

Volumn 59, Issue 8, 2007, Pages 613-623

  Peatman, Eric ^a   Liu, Zhanjiang ^a  

^a AUBURN UNIVERSITY   (United States)

Author keywords

Catfish; Chemokine; Cytokine; Evolution; Gene duplication; Immunity; Salmon; Trout; Zebrafish

Indexed keywords

BETA CHEMOKINE;

ATLANTIC SALMON; CATFISH; CELL MIGRATION; GENE DUPLICATION; GENETIC VARIABILITY; IMMUNE RESPONSE; INFLAMMATION; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN FUNCTION; RAINBOW TROUT; REVIEW; TELEOST; ZEBRA FISH;

ANIMALS; CHEMOKINES, CC; DATABASES, GENETIC; EVOLUTION, MOLECULAR; FISHES; GENE DUPLICATION; ICTALURIDAE; ONCORHYNCHUS MYKISS; PHYLOGENY; SALMO SALAR; VARIATION (GENETICS); ZEBRAFISH;

DANIO RERIO; MAMMALIA; ONCORHYNCHUS MYKISS; SALMO SALAR; SALMONIDAE; TELEOSTEI; VERTEBRATA;

EID: 34547472948     PISSN: 00937711     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00251-007-0228-4     Document Type: Review

References (44)

1. Bacon K, Baggiolini M, Broxmeyer H, Horuk R, Lindley I, Mantovani A, Matsushima K, Murphy P, Nomiyama H, Oppenheim J, Rot A, Schall T, Tsang M, Thorpe R, Van Damme J, Wadhwa M, Yoshie O, Zlotnik A, Zoon K (2003) Chemokine/chemokine receptor nomenclature. Cytokine 21:48-49
2. Bao B, Peatman E, Peng X, Baoprasertkul P, Wang G, Liu Z (2006) Characterization of 23 CC chemokine genes and analysis of their expression in channel catfish (Ictalurus punctatus). Dev Comp Immunol 30:783-796
3. Davey GC, Caplice NC, Martin SA, Powell R (2001) A survey of genes in the Atlantic salmon (Salmo salar) as identified by expressed sequence tags. Gene 263:121-130
4. DeVries ME, Kelvin AA, Xu L, Ran L, Robinson J, Kelvin DJ (2006) Defining the origins and evolution of the chemokine/chemokine receptor system. J Immunol 176:401-415
5. Dixon B, Shum B, Adams EJ, Magor KE, Hedrick RP, Muir DG, Parham P (1998) CK-1, a putative chemokine of rainbow trout (Oncorhynchus mykiss). Immunol Rev 166:341-348
6. Fujiki K, Shin DH, Nakao M, Yano T (1999) Molecular cloning of carp (Cyprinus carpio) CC chemokine, CXC chemokine receptors, allograft inflammatory factor-1, and natural killer cell enhancing factor by use of suppression subtractive hybridization. Immunogenetics 49:909-914
7. Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, Catano G, Nibbs RJ, Freedman BI, Quinones MP, Bamshad MJ, Murthy KK, Rovin BH, Bradley W, Clark RA, Anderson SA, O'connell RJ, Agan BK, Ahuja SS, Bologna R, Sen L, Dolan MJ, Ahuja SK (2005) The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307:1434-1440
8. Gonzalez SF, Chatziandreou N, Nielsen ME, Li W, Rogers J, Taylor R, Santos Y, Cossins A (2007) Cutaneous immune responses in the common carp detected using transcript analysis. Mol Immunol 44:1664-1679
9. Govoroun M, Le Gac F, Guiguen Y (2006) Generation of a large scale repertoire of Expressed Sequence Tags (ESTs) from normalised rainbow trout cDNA libraries. BMC Genomics 7:196
10. Hagen-Larsen H, Laerdahl JK, Panitz F, Adzhubei A, Hoyheim B (2005) An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar). BMC Genomics 6:171
11. He C, Peatman E, Baoprasertkul P, Kucuktas H, Liu Z (2004) Multiple CC chemokines in channel catfish and blue catfish as revealed by analysis of expressed sequence tags. Immunogenetics 56:379-387
12. Hughes S, Poh TY, Bumstead N, Kaiser P (2007) Re-evaluation of the chicken MIP family of chemokines and their receptors suggests that CCL5 is the prototypic MIP family chemokine, and that different species have developed different repertoires of both the CC chemokines and their receptors. Dev Comp Immunol 31:72-86
13. Khattiya R, Ohira T, Hirono I, Aoki T (2004) Identification of a novel Japanese flounder (Paralichthys olivaceus) CC chemokine gene and an analysis of its function. Immunogenetics 55:763-769
14. Kono T, Kusada R, Kawahara E, Sakai M (2003) The analysis of immune responses of a novel CC-chemokine gene from Japanese flounder Paralichthys olivaceus. Vaccine 21:446-457
15. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics 5:150-163
16. Kuroda N, Uinuk-ool TS, Sato A, Samonte IE, Figueroa F, Mayer WE, Klein J (2003) Identification of chemokines and a chemokine receptor in cichlid fish, shark, and lamprey. Immunogenetics 54:884-895
17. Laing KJ, Secombes CJ (2004a) Chemokines. Dev Comp Immunol 28:443-460
18. Laing KJ, Secombes CJ (2004b) Trout CC chemokines: comparison of their sequences and expression patterns. Mol Immunol 41:793-808
19. Li P, Peatman E, Wang S, Feng J, He C, Baoprasertkul P, Xu P, Kucuktas H, Nandi S, Somridhivej B, Serapion J, Simmons M, Turan C, Liu L, Muir W, Dunham R, Brady Y, Grizzle J, Liu Z (2007) Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs. BMC Genomics (in press)
20. Liu Z, Peatman E (2006) Chemokines in fish: a rapidly expanding repertoire. In: Veskler BA (ed) Focus on immunology research. Nova, NY, pp 121-144
21. Liu L, Fujiki K, Dixon B, Sundick RS (2002) Cloning of a novel rainbow trout (Oncorhynchus mykiss) CC chemokine with a fractalkine-like stalk and a TNF decoy receptor using cDNA fragments containing Au-rich elements. Cytokine 17:71-81
22. Lo J, Lee S, Xu M, Liu F, Ruan H, Eun A, He Y, Ma W, Wang W, Wen Z et al (2003) 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Genome Res 13:455-466
23. Mackenzie S, Liarte C, Iliev D, Planas JV, Tort L, Goetz FW (2004) Characterization of a highly inducible novel CC chemokine from differentiated rainbow trout (Oncorhynchus mykiss) macrophages. Immunogenetics 56:611-615
24. Martin SA, Caplice NC, Davey GC, Powell R (2002) EST-based identification of genes expressed in the liver of adult Atlantic salmon (Salmo salar). Biochem Biophys Res Commun 293:578-585
25. Modi WS, Lautenberger J, An P, Scott K, Goedert JJ, Kirk GD, Buchbinder S, Phair J, Donfield S, O'Brien SJ, Winkler C (2006) Genetic variation in the CCL18-CCL3-CCL4 chemokine gene cluster influences HIV Type 1 transmission and AIDS disease progression. Am J Hum Genet 79:120-128
26. Moser B, Wolf M, Walz A, Loetscher P (2004) Chemokines: multiple levels of leukocyte migration control. Trends Immunol 25:75-85
27. Nibbs RJ, Yang J, Landau NR, Mao JH, Graham GJ (1999) LD78beta, a non-allelic variant of human MIP-1alpha (LD78alpha), has enhanced receptor interactions and potent HIV suppressive activity. J Biol Chem 274:17478-17483
28. Peatman E, Liu Z (2006) CC chemokines in zebrafish: evidence for extensive intrachromosomal gene duplications. Genomics 88:381-385
29. Peatman E, Bao B, Baoprasertkul P, Liu Z (2005) In silico identification and expression analysis of 12 novel CC chemokines in catfish. Immunogenetics 57:409-419
30. Peatman E, Bao B, Peng X, Baoprasertkul P, Brady Y, Liu Z (2006) Catfish CC chemokines: genomic clustering, duplications, and expression after bacterial infection with Edwardsiella ictaluri. Mol Genet Genomics 275:297-309
31. Peatman E, Baoprasertkul P, Terhune J, Xu P, Nandi S, Kucuktas H, Li P, Wang S, Somridhivej B, Dunham R, Liu Z (2007) Expression analysis of the acute phase response in channel catfish (Ictalurus punctatus) after infection with a Gram negative bacterium. Dev Comp Immunol. DOI 10.1016/j.dci.2007.03.003
32. Rexroad CE, 3rd, Lee Y, Keele JW, Karamycheva S, Brown G, Koop B, Gahr SA, Palti Y, Quackenbush J (2003) Sequence analysis of a rainbow trout cDNA library and creation of a gene index. Cytogenet Genome Res 102:347-354
33. Rise ML, von Schalburg KR, Brown GD, Mawer MA, Devlin RH, Kuipers N, Busby M, Beetz-Sargent M, Alberto R, Gibbs AR et al (2004) Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res 14:478-490
34. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
35. Sanchez E, Coll J, Tafalla C (2007) Expression of inducible CC chemokines in rainbow trout (Oncorhynchus mykiss) in response to a viral haemorrhagic septicemia virus (VHSV) DNA vaccine and interleukin 8. Dev Comp Immunol 31(9):916-926
36. Shields DC (2003) Molecular evolution of CXC chemokines and receptors. Trends Immunol 24:355
37. Song HD, Sun XJ, Deng M, Zhang GW, Zhou Y, Wu XY, Sheng Y, Chen Y, Ruan Z, Jiang CL et al (2004) Hematopoietic gene expression profile in zebrafish kidney marrow. Proc Natl Acad Sci USA 101:16240-16245
38. von Schalburg KR, Rise ML, Cooper GA, Brown GD, Gibbs AR, Nelson CC, Davidson WS, Koop BF (2005) Fish and chips: various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics 6:126
39. Wang J, Adelson DL, Yilmaz A, Sze SH, Jin Y, Zhu JJ (2005) Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics. BMC Genomics 6:45
40. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P et al (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562
41. Woods IG, Wilson C, Friedlander B, Chang P, Reyes DK, Nix R, Kelly PD, Chu F, Postlethwait JH, Talbot WS (2005) The zebrafish gene map defines ancestral vertebrate chromosomes. Genome Res 15:1307-1314
42. Yoshie O, Imai T, Nomiyama H (2001) Chemokines in immunity. Adv Immunol 78:57-110
43. Zeng S, Gong Z (2002) Expressed sequence tag analysis of expression profiles of zebrafish testis and ovary. Gene 294:45-53
44. Zlotnik A, Yoshie O, Nomiyama H (2006) The chemokine and chemokine receptor superfamilies and their molecular evolution. Genome Biol 7:243