Comprehensive transcriptome profiling and functional analysis of the frog (Bombina maxima) immune system

DNA Research

Volumn 21, Issue 1, 2014, Pages 1-13

  Zhao, Feng ^a,b   Yan, Chao ^a,b   Wang, Xuan ^a,b   Yang, Yang ^a,b   Wang, Guangyin ^a,b   Lee, Wenhui ^a   Xiang, Yang ^a   Zhang, Yun ^a  

^a KUNMING INSTITUTE OF ZOOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

frog; immune system; non coding RNAs; tissue specific genes; transcriptome

Indexed keywords

FROG; IMMUNE SYSTEM; NON-CODING RNAS; TISSUE-SPECIFIC GENES; TRANSCRIPTOME;

ADAPTIVE IMMUNITY; ANIMALS; ANURA; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; IMMUNE SYSTEM; IMMUNITY, INNATE; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84894594866     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dst035     Document Type: Article

References (51)

1. Pollet, N. andMazabraud, A. 2006, Insights fromXenopus genomes, Genome Dyn., 2, 138-53.
2. Yergeau, D.A. and Mead, P.E. 2007, Manipulating the Xenopus genome with transposable elements, Genome Biol., 8(Suppl 1), S11.
3. Morin, R.D., Chang, E., Petrescu,A., et al. 2006, Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals posttetraploidization transcriptome remodeling, Genome Res., 16, 796-803.
4. Hellsten, U., Harland, R.M., Gilchrist, M.J., et al. 2010, The genome of the Western clawed frog Xenopus tropicalis, Science, 328, 633-36.
5. Rockman, M.V. and Kruglyak, L. 2006, Genetics of global gene expression, Nat. Rev. Genet., 7, 862-72.
6. Zhang, J., Zhang, Y., Wan, S.G., Wei, S.S. and Lee, W.H. 2005, Bm-TFF2, a trefoil factor protein with platelet activation activity from frog Bombina maxima skin secretions, Biochem. Biophys. Res. Commun., 330, 1027-33.
7. Lee, W.H., Li, Y., Lai, R., Li, S., Zhang, Y. and Wang, W. 2005, Variety of antimicrobial peptides in the Bombina maxima toad and evidence of their rapid diversification, Eur. J. Immunol., 35, 1220-9.
8. Xiang, Y., Gao, Q., Su, W., et al. 2012, Establishment, characterization and immortalization of a fibroblast cell line from the Chinese red belly toad Bombina maxima skin, Cytotechnology, 64, 95-105.
9. Liu, S.B., He, Y.Y., Zhang, Y., et al. 2008, A novel non-lens betagamma-crystallin and trefoil factor complex from amphibian skin and its functional implications, PLoS One, 3, e1770.
10. Xu, Y., Tao, X., Shen, B., et al. 2000, Structural basis for signal transduction by the Toll/interleukin-1 receptor domains, Nature, 408, 111-5.
11. Robert, J. and Cohen, N. 2011, The genus Xenopus as a multispecies model for evolutionary and comparative immunobiology of the 21st century, Dev. Comp. Immunol., 35, 916-23.
12. Wiesner, J. and Vilcinskas, A. 2010, Antimicrobial peptides: the ancient arm of the human immune system, Virulence, 1, 440-64.
13. Yang, X., Lee, W.H. and Zhang, Y. 2012, Extremely abundant antimicrobial peptides existed in the skins of nine kinds of Chinese odorous frogs, J. Proteome Res., 11, 306-19.
14. Du Pasquier, L., Schwager, J. and Flajnik, M.F. 1989, The immune system of Xenopus, Annu. Rev. Immunol., 7, 251-75.
15. Blackburn, D.C., Bickford, D.P., Diesmos, A.C., Iskandar, D.T. and Brown, R.M. 2010, An ancient origin for the enigmatic flat-headed frogs (Bombinatoridae: Barbourula) from the islands of Southeast Asia, PloS One, 5, e12090.
16. Shendure, J. and Ji, H. 2008, Next-generation DNA sequencing, Nat. Biotechnol., 26, 1135-45.
17. Tan, M.H., Au, K.F., Yablonovitch, A.L., et al. 2013, RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development, Genome Res., 23, 201-16.
18. Pfaffl, M.W. 2001, A new mathematical model for relative quantification in real-time RT-PCR, Nucleic Acids Res., 29, e45.
19. Coppe, A., Pujolar, J.M., Maes, G.E., et al. 2010, Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel, BMC Genomics, 11, 635.
20. Ma, K., Qiu, G., Feng, J. and Li, J. 2012, Transcriptome analysis of the oriental river prawn, Macrobrachium nipponense using 454 pyrosequencing for discovery of genes and markers, PloS One, 7, e39727.
21. Fu, B. and He, S. 2012, Transcriptome analysis of silver carp (Hypophthalmichthys molitrix) by paired-end RNA sequencing, DNA Res., 19, 131-42.
22. Nie, Q., Fang, M., Jia, X., et al. 2011, Analysis of muscle and ovary transcriptome of Sus scrofa: assembly, annotation and marker discovery, DNA Res., 18, 343-51.
23. Procaccini, C., Galgani, M., De Rosa, V. and Matarese, G. 2012, Intracellular metabolic pathways control immune tolerance, Trends Immunol., 33, 1-7.
24. Font, J. and Mackay, J.P. 2010, Beyond DNA: zinc finger domains as RNA-binding modules, Methods Mol. Biol., 649, 479-91.
25. Jung, H., Lyons, R.E.,Dinh, H.,Hurwood, D.A.,McWilliam, S. and Mather, P.B. 2011, Transcriptomics of a giant freshwater prawn (Macrobrachium rosenbergii): de novo assembly, annotation and marker discovery, PLoS One, 6, e27938.
26. Ravasi, T., Huber, T., Zavolan, M., et al. 2003, Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome, Genome Res., 13, 1430-42.
27. Ohta, Y. and Flajnik, M. 2006, IgD, like IgM, is a primordial immunoglobulin class perpetuated in most jawed vertebrates, Proc. Natl Acad. Sci. USA, 103, 10723-28.
28. Iliev, D.B., Roach, J.C., Mackenzie, S., Planas, J.V. and Goetz, F.W. 2005, Endotoxin recognition: in fish or not in fish? FEBS Lett., 579, 6519-28.
29. Nikolaeva, S., Bachteeva, V., Fock, E., et al. 2012, Frog urinary bladder epithelial cells express TLR4 and respond to bacterial LPS by increase of iNOS expression and L-arginine uptake. Am. J. Physiol. Regul. Integr. Comp. Physiol., 303, R1042-52.
30. Chow, J.C., Young, D.W., Golenbock, D.T., Christ, W.J. and Gusovsky, F.1999,Toll-likereceptor-4mediates lipopolysaccharide-induced signal transduction, J. Biol. Chem., 274, 10689-92.
31. Fitzgerald, K.A., Palsson-McDermott, E.M., Bowie, A.G., et al. 2001, Mal (MyD88-adapter-like) is required for Toll-like receptor-4 signal transduction, Nature, 413, 78-83.
32. Prothmann, C., Armstrong, N.J. and Rupp, R.A. 2000, The Toll/IL-1 receptor binding protein MyD88 is required for Xenopus axis formation, Mech. Develop., 97, 85-92.
33. Li, D. and Roberts, R. 2001, WD-repeat proteins: structure characteristics, biological function,andtheir involvement in human diseases, Cell. Mol. Life Sci., 58, 2085-97.
34. Oshiumi, H., Suzuki, Y., Matsumoto, M. and Seya, T. 2009, Regulator of complement activation (RCA) gene cluster in Xenopus tropicalis, Immunogenetics, 61, 371-84.
35. Del Rio-Tsonis, K., Tsonis, P.A., Zarkadis, I.K., Tsagas, A.G. and Lambris, J.D. 1998, Expression of the third component of complement, C3, in regenerating limb blastema cells of urodeles, J. Immunol., 161, 6819-24.
36. Huising, M.O., Stet, R.J., Savelkoul, H.F. and Verburg-van Kemenade, B.M. 2004, The molecular evolution of the interleukin-1 family of cytokines; IL-18 in teleost fish, Dev. Comp. Immunol., 28, 395-413.
37. Wargnier, A. and Lagrange, P.H. 1993, [Bactericidal activity of cells of the immune system], Pathol. Biol., 41, 887-96.
38. Calandra, T. and Roger, T. 2003, Macrophage migration inhibitory factor: a regulator of innate immunity, Nat. Rev. Immunol., 3, 791-800.
39. Taylor, G.A., Feng, C.G. and Sher, A. 2004, p47 GTPases: regulators of immunity to intracellular pathogens, Nat. Rev. Immunol., 4, 100-9.
40. Klamp, T., Boehm, U., Schenk, D., Pfeffer, K. and Howard, J.C. 2003, A giant GTPase, very large inducible GTPase-1, is inducible by IFNs, J. Immunol., 171, 1255-65.
41. Martinon, F.,Mayor, A. and Tschopp, J. 2009, The inflammasomes: guardians of the body, Annu. Rev. Immunol.,27, 229-65.
42. Schluter, S.F., Bernstein, R.M., Bernstein, H. and Marchalonis, J.J. 1999, 'Big Bang' emergence of the combinatorial immune system, Dev. Comp. Immunol., 23, 107-11.
43. Flajnik, M.F. and Kasahara, M. 2010, Origin and evolution of the adaptive immune system: genetic events and selective pressures, Nat. Rev. Genet., 11, 47-59.
44. Flajnik, M.F. 2002, Comparative analyses of immunoglobulin genes: surprises and portents, Nat. Rev. Immunol., 2, 688-98.
45. Warr, G.W., Magor, K.E. and Higgins, D.A. 1995, IgY: clues to the origins of modern antibodies, Immunol. Today, 16, 392-8.
46. Kasahara, M. 1999, Genome dynamics of the major histocompatibility complex: insights fromgenome paralogy, Immunogenetics, 50, 134-45.
47. Kiemnec-Tyburczy, K.M., Richmond, J.Q., Savage, A.E., Lips, K.R. and Zamudio, K.R. 2012, Genetic diversity of MHC class I loci in six non-model frogs is shaped by positive selectionandgeneduplication, Heredity (Edinb),109, 146-55.
48. McConnell, T.J., Godwin, U.B. and Cuthbertson, B.J. 1998, Expressedmajorhistocompatibilitycomplex class II loci in fishes, Immunol Rev., 166, 294-300.
49. Flajnik, M.F., Canel, C., Kramer, J. and Kasahara, M. 1991, Evolution of the major histocompatibility complex: molecular cloning of major histocompatibility complex class I from the amphibian Xenopus, Proc. Natl Acad. Sci. USA, 88, 537-41.
50. Panopoulou, G. and Poustka, A.J. 2005, Timing and mechanism of ancient vertebrate genome duplications-the adventure of a hypothesis, Trends Genet., 21, 559-67.
51. Flajnik, M.F., Kasahara, M., Shum, B.P., Salter-Cid, L., Taylor, E. and Du Pasquier, L. 1993, A novel type of class I gene organization in vertebrates: a large family of non-MHC-linked class I genes is expressed at the RNA level in the amphibian Xenopus, EMBO J., 12, 4385-96.