Systematic classification of vertebrate chemokines based on conserved synteny and evolutionary history

Genes to Cells

Volumn 18, Issue 1, 2013, Pages 1-16

  Nomiyama, Hisayuki ^a   Osada, Naoki ^b   Yoshie, Osamu ^c  

^a KUMAMOTO UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c KINKI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CCL25A CHEMOKINE; CCL25B CHEMOKINE; CCR8 CHEMOKINE; CHEMOKINE; CHEMOKINE RECEPTOR CX3CR1; CXCL10G CHEMOKINE; CXCL11G CHEMOKINE; CXCL12G CHEMOKINE; CXCL13G CHEMOKINE; CXCL14G CHEMOKINE; CXCL15G CHEMOKINE; CXCL16G CHEMOKINE; CXCL17G CHEMOKINE; CXCL18G CHEMOKINE; CXCL1G CHEMOKINE; CXCL2G CHEMOKINE; CXCL3G CHEMOKINE; CXCL4G CHEMOKINE; CXCL5G CHEMOKINE; CXCL6G CHEMOKINE; CXCL7G CHEMOKINE; CXCL8G CHEMOKINE; CXCL9G CHEMOKINE; CXCR3 CHEMOKINE; EOTAXIN 3; MONOCYTE CHEMOTACTIC PROTEIN 2; MONOCYTE CHEMOTACTIC PROTEIN 5; UNCLASSIFIED DRUG;

CELL MIGRATION; CHROMOSOME; EVOLUTION; GENE CLUSTER; GENETIC ANALYSIS; GENOME; HISTORY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; REVIEW; SYNTENY; VERTEBRATE;

ANIMALS; CHEMOKINES; EVOLUTION, MOLECULAR; GENOME, HUMAN; HUMANS; MULTIGENE FAMILY; PHYLOGENY; RECEPTORS, CHEMOKINE; SYNTENY;

VERTEBRATA;

EID: 84871616815     PISSN: 13569597     EISSN: 13652443     Source Type: Journal    
DOI: 10.1111/gtc.12013     Document Type: Review

References (62)

1. Bajoghli, B., Aghaallaei, N., Hess, I., Rode, I., Netuschil, N., Tay, B.H., Venkatesh, B., Yu, J.K., Kaltenbach, S.L., Holland, N.D., Diekhoff, D., Happe, C., Schorpp, M. & Boehm, T. (2009) Evolution of genetic networks underlying the emergence of thymopoiesis in vertebrates. Cell 138, 186-197.
2. Braasch, I. & Postlethwait, J.H. (2011) The teleost agouti-related protein 2 gene is an ohnolog gone missing from the tetrapod genome. Proc. Natl Acad. Sci. USA 108, E47-E48.
3. Catchen, J.M., Braasch, I. & Postlethwait, J.H. (2011) Conserved synteny and the zebrafish genome. Methods Cell Biol. 104, 259-285.
4. Catchen, J.M., Conery, J.S. & Postlethwait, J.H. (2009) Automated identification of conserved synteny after whole-genome duplication. Genome Res. 19, 1497-1505.
5. Coelho, A.L., Hogaboam, C.M. & Kunkel, S.L. (2005) Chemokines provide the sustained inflammatory bridge between innate and acquired immunity. Cytokine Growth Factor Rev. 16, 553-560.
6. Colobran, R., Pedrosa, E., Carretero-Iglesia, L. & Juan, M. (2010) Copy number variation in chemokine superfamily: the complex scene of CCL3L-CCL4L genes in health and disease. Clin. Exp. Immunol. 162, 41-52.
7. Colobran, R., Pujol-Borrell, R., Armengol, M.P. & Juan, M. (2007) The chemokine network. I. How the genomic organization of chemokines contains clues for deciphering their functional complexity. Clin. Exp. Immunol. 148, 208-217.
8. Cooper, M.D. & Alder, M.N. (2006) The evolution of adaptive immune systems. Cell 124, 815-822.
9. Dalloul, R.A., Long, J.A. & Zimin, A.V. et al. (2010) Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol. 8, e1000475.
10. David, N.B., Sapede, D., Saint-Etienne, L., Thisse, C., Thisse, B., Dambly-Chaudiere, C., Rosa, F.M. & Ghysen, A. (2002) Molecular basis of cell migration in the fish lateral line: role of the chemokine receptor CXCR4 and of its ligand, SDF1. Proc. Natl Acad. Sci. U S A 99, 16297-16302.
11. Dehal, P. & Boore, J.L. (2005) Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 3, e314.
12. Delsuc, F., Brinkmann, H., Chourrout, D. & Philippe, H. (2006) Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439, 965-968.
13. DeVries, M.E., Kelvin, A.A., Xu, L., Ran, L., Robinson, J. & Kelvin, D.J. (2006) Defining the origins and evolution of the chemokine/chemokine receptor system. J. Immunol. 176, 401-415.
14. Doitsidou, M., Reichman-Fried, M., Stebler, J., Koprunner, M., Dorries, J., Meyer, D., Esguerra, C.V., Leung, T. & Raz, E. (2002) Guidance of primordial germ cell migration by the chemokine SDF-1. Cell 111, 647-659.
15. Graham, G.J. (2009) D6 and the atypical chemokine receptor family: novel regulators of immune and inflammatory processes. Eur. J. Immunol. 39, 342-351.
16. Hedges, S.B. & Kumar, S. (2003) Genomic clocks and evolutionary timescales. Trends Genet. 19, 200-206.
17. Hoegg, S. & Meyer, A. (2005) Hox clusters as models for vertebrate genome evolution. Trends Genet. 21, 421-424.
18. Islam, S.A., Chang, D.S., Colvin, R.A., Byrne, M.H., McCully, M.L., Moser, B., Lira, S.A., Charo, I.F. & Luster, A.D. (2011) Mouse CCL8, a CCR8 agonist, promotes atopic dermatitis by recruiting IL-5+ T(H)2 cells. Nat. Immunol. 12, 167-177.
19. Jaillon, O., Aury, J.M., Brunet, F., et al. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431, 946-957.
20. Kasahara, M. (2007) The 2R hypothesis: an update. Curr. Opin. Immunol. 19, 547-552.
21. Kasahara, M., Naruse, K., Sasaki, S., et al. (2007) The medaka draft genome and insights into vertebrate genome evolution. Nature 447, 714-719.
22. Knaut, H., Werz, C., Geisler, R. & Nusslein-Volhard, C. (2003) A zebrafish homologue of the chemokine receptor Cxcr4 is a germ-cell guidance receptor. Nature 421, 279-282.
23. Kuraku, S., Meyer, A. & Kuratani, S. (2009) Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after? Mol. Biol. Evol. 26, 47-59.
24. Laisney, J.A., Braasch, I., Walter, R.B., Meierjohann, S. & Schartl, M. (2010) Lineage-specific co-evolution of the Egf receptor/ligand signaling system. BMC Evol. Biol. 10, 27.
25. Lalani, A.S., Barrett, J.W. & McFadden, G. (2000) Modulating chemokines: more lessons from viruses. Immunol. Today 21, 100-106.
26. Leick, M., Catusse, J., Follo, M., Nibbs, R.J., Hartmann, T.N., Veelken, H. & Burger, M. (2010) CCL19 is a specific ligand of the constitutively recycling atypical human chemokine receptor CRAM-B. Immunology 129, 536-546.
27. Lim, J.K., Glass, W.G., McDermott, D.H. & Murphy, P.M. (2006) CCR5: no longer a "good for nothing" gene-chemokine control of West Nile virus infection. Trends Immunol. 27, 308-312.
28. Lim, J.K., Obara, C.J., Rivollier, A., Pletnev, A.G., Kelsall, B.L. & Murphy, P.M. (2011) Chemokine receptor Ccr2 is critical for monocyte accumulation and survival in West Nile virus encephalitis. J. Immunol. 186, 471-478.
29. Luster, A.D. (2002) The role of chemokines in linking innate and adaptive immunity. Curr. Opin. Immunol. 14, 129-135.
30. Luttichau, H.R., Johnsen, A.H., Jurlander, J., Rosenkilde, M.M. & Schwartz, T.W. (2007) Kaposi sarcoma-associated herpes virus targets the lymphotactin receptor with both a broad spectrum antagonist vCCL2 and a highly selective and potent agonist vCCL3. J. Biol. Chem. 282, 17794-17805.
31. Mantovani, A. (1999) The chemokine system: redundancy for robust outputs. Immunol. Today 20, 254-257.
32. Mantovani, A., Bonecchi, R. & Locati, M. (2006) Tuning inflammation and immunity by chemokine sequestration: decoys and more. Nat. Rev. Immunol. 6, 907-918.
33. Meyer, A. & Van de Peer, Y. (2005) From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). BioEssays 27, 937-945.
34. Mortier, A., Van Damme, J. & Proost, P. (2008) Regulation of chemokine activity by posttranslational modification. Pharmacol. Ther. 120, 197-217.
35. Moser, B., Wolf, M., Walz, A. & Loetscher, P. (2004) Chemokines: multiple levels of leukocyte migration control. Trends Immunol. 25, 75-84.
36. Murphy, P.M. (1993) Molecular mimicry and the generation of host defense protein diversity. Cell 72, 823-826.
37. Murphy, P.M., Baggiolini, M., Charo, I.F., Hebert, C.A., Horuk, R., Matsushima, K., Miller, L.H., Oppenheim, J.J. & Power, C.A. (2000) International union of pharmacology. XXII. Nomenclature for chemokine receptors. Pharmacol. Rev. 52, 145-176.
38. Nagasawa, T., Hirota, S., Tachibana, K., Takakura, N., Nishikawa, S., Kitamura, Y., Yoshida, N., Kikutani, H. & Kishimoto, T. (1996) Defects of B-cell lymphopoiesis and bone-marrow myelopoiesis in mice lacking the CXC chemokine PBSF/SDF-1. Nature 382, 635-638.
39. Nair, S. & Schilling, T.F. (2008) Chemokine signaling controls endodermal migration during zebrafish gastrulation. Science 322, 89-92.
40. Nakatani, Y., Takeda, H., Kohara, Y. & Morishita, S. (2007) Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res. 17, 1254-1265.
41. Nakayama, T., Watanabe, Y., Oiso, N., Higuchi, T., Shigeta, A., Mizuguchi, N., Katou, F., Hashimoto, K., Kawada, A. & Yoshie, O. (2010) Eotaxin-3/CC chemokine ligand 26 is a functional ligand for CX3CR1. J. Immunol. 185, 6472-6479.
42. Naumann, U., Cameroni, E., Pruenster, M., Mahabaleshwar, H., Raz, E., Zerwes, H.G., Rot, A. & Thelen, M. (2010) CXCR7 functions as a scavenger for CXCL12 and CXCL11. PLoS ONE 5, e9175.
43. Nei, M. & Rooney, A.P. (2005) Concerted and birth-and-death evolution of multigene families. Annu. Rev. Genet. 39, 121-152.
44. Nomiyama, H., Egami, K., Tanase, S., Miura, R., Hirakawa, H., Kuhara, S., Ogasawara, J., Morishita, S., Yoshie, O., Kusuda, J. & Hashimoto, K. (2003) Comparative DNA sequence analysis of mouse and human CC chemokine gene clusters. J. Interferon Cytokine Res. 23, 37-45.
45. Nomiyama, H., Hieshima, K., Osada, N., Kato-Unoki, Y., Otsuka-Ono, K., Takegawa, S., Izawa, T., Yoshizawa, A., Kikuchi, Y., Tanase, S., Miura, R., Kusuda, J., Nakao, M. & Yoshie, O. (2008) Extensive expansion and diversification of the chemokine gene family in zebrafish: identification of a novel chemokine subfamily CX. BMC Genomics 9, 222.
46. Nomiyama, H., Osada, N. & Yoshie, O. (2010) The evolution of mammalian chemokine genes. Cytokine Growth Factor Rev. 21, 253-262.
47. Nomiyama, H., Osada, N. & Yoshie, O. (2011) A family tree of vertebrate chemokine receptors for a unified nomenclature. Dev. Comp. Immunol. 35, 705-715.
48. Oppenheim, J.J., Zachariae, C.O., Mukaida, N. & Matsushima, K. (1991) Properties of the novel proinflammatory supergene "intercrine" cytokine family. Annu. Rev. Immunol. 9, 617-648.
49. Peatman, E. & Liu, Z. (2007) Evolution of CC chemokines in teleost fish: a case study in gene duplication and implications for immune diversity. Immunogenetics 59, 613-623.
50. Raz, E. & Mahabaleshwar, H. (2009) Chemokine signaling in embryonic cell migration: a fisheye view. Development 136, 1223-1229.
51. Sarafi, M.N., Garcia-Zepeda, E.A., MacLean, J.A., Charo, I.F. & Luster, A.D. (1997) Murine monocyte chemoattractant protein (MCP)-5: a novel CC chemokine that is a structural and functional homologue of human MCP-1. J. Exp. Med. 185, 99-109.
52. Shields, D.C. (2000) Gene conversion among chemokine receptors. Gene 246, 239-245.
53. Soto, H., Wang, W., Strieter, R.M., Copeland, N.G., Gilbert, D.J., Jenkins, N.A., Hedrick, J. & Zlotnik, A. (1998) The CC chemokine 6Ckine binds the CXC chemokine receptor CXCR3. Proc. Natl Acad. Sci. USA 95, 8205-8210.
54. Vazquez-Salat, N., Yuhki, N., Beck, T., O'Brien, S.J. & Murphy, W.J. (2007) Gene conversion between mammalian CCR2 and CCR5 chemokine receptor genes: a potential mechanism for receptor dimerization. Genomics 90, 213-224.
55. Vicari, A.P., Figueroa, D.J., Hedrick, J.A., Foster, J.S., Singh, K.P., Menon, S., Copeland, N.G., Gilbert, D.J., Jenkins, N.A., Bacon, K.B. & Zlotnik, A. (1997) TECK: a novel CC chemokine specifically expressed by thymic dendritic cells and potentially involved in T cell development. Immunity 7, 291-301.
56. Wolfe, K. (2000) Robustness-it's not where you think it is. Nat. Genet. 25, 3-4.
57. Wurbel, M.A., Malissen, M., Guy-Grand, D., Malissen, B. & Campbell, J.J. (2007) Impaired accumulation of antigen-specific CD8 lymphocytes in chemokine CCL25-deficient intestinal epithelium and lamina propria. J. Immunol. 178, 7598-7606.
58. Yoshie, O., Imai, T. & Nomiyama, H. (2001) Chemokines in immunity. Adv. Immunol. 78, 57-110.
59. Zlotnik, A., Burkhardt, A.M. & Homey, B. (2011) Homeostatic chemokine receptors and organ-specific metastasis. Nat. Rev. Immunol. 11, 597-606.
60. Zlotnik, A. & Yoshie, O. (2000) Chemokines: a new classification system and their role in immunity. Immunity 12, 121-127.
61. Zlotnik, A. & Yoshie, O. (2012) The chemokine superfamily revisited. Immunity 36, 705-716.
62. Zlotnik, A., Yoshie, O. & Nomiyama, H. (2006) The chemokine and chemokine receptor superfamilies and their molecular evolution. Genome Biol. 7, 243.