Sequencing and expression of the second allele of the interleukin-1β1 gene in rainbow trout (Oncorhynchus mykiss): Identification of a novel SINE in the third intron

Fish and Shellfish Immunology

Volumn 16, Issue 3, 2004, Pages 335-358

  Wang, Tiehui ^a   Johnson, Niel ^a   Zou, Jim ^a   Bols, Niels ^b   Secombes, Christopher J ^a  

^a UNIVERSITY OF ABERDEEN   (United Kingdom)

^b UNIVERSITY OF WATERLOO   (Canada)

Author keywords

Allele B; Allele formation; Interleukin 1 1; Rainbow trout; Retroposition; SINE

Indexed keywords

INSERTION SEQUENCES; ONCORHYNCHUS; ONCORHYNCHUS MYKISS; SALMONIDAE;

EID: 1642365802     PISSN: 10504648     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1050-4648(03)00114-1     Document Type: Article

References (88)

1. Dinarello CA. Interleukin-1. In: Thomson A, editor. The Cytokine Handbook 3rd edn London (England): Academic Press; 1998a, pp. 35-72.
2. Dinarello CA. Interleukin-1, interleukin-1 receptors and interleukin-1 receptor antagonist. International Review of Immunology 1998b;16:457-99.
3. Sporri B, Bickel M, Dobbelaere D, Machado J Jr, Lottaz D. Soluble interleukin-1 receptor-reverse signalling in innate immunoregulation. Cytokine & Growth Factor Reviews 2001;12:27-32.
4. Eisenberg SP, Evans RJ, Arend WP, Verderber E, Brewer MT, Hannum CH et al. Primary structure and functional expression from complementary DNA of a human interleukin-1 receptor antagonist. Nature 1990;343:341-6.
5. Hannum CH, Wilcox CJ, Arend WP, Joslin FG, Dripps DJ, Heimdal PL et al. Interleukin-1 receptor antagonist activity of a human interleukin-1 inhibitor. Nature 1990;343:336-40.
6. Colotta F, Dower SK, Sims JE, Mantovani A. The type II "decoy" receptor: a novel regulatory pathway for interleukin 1. Immunology Today 1994;15:562-6.
7. Mantovani A, Locati M, Vecchi A, Sozzani S, Allavena P. Decoy receptors: a strategy to regulate inflammatory cytokines and chemokines. Trends in Immunology 2001;22:328-36.
8. Dinarello CA. Biologic basis for interleukin-1 in disease. Blood 1996;87:2095-147.
9. McDowell TL, Symons JA, Ploski R, Forre O, Duff GW. A genetic association between juvenile rheumatoid arthritis and a novel interleukin-1 alpha polymorphism. Arthritis and Rheumatism 1995;38:221-8.
10. Jouvenne P, Chaudhary A, Buchs N, Giovine FS, Duff GW, Miossec P. Possible genetic association between interleukin-1alpha gene polymorphism and the severity of chronic polyarthritis. European Cytokine Network 1999;10:33-6.
11. Bailly S, di Giovine FS, Duff GW. Polymorphic tandem repeat region in interleukin-1 alpha intron 6. Human Genetics 1993;91:85-6.
12. Bailly S, Israel N, Fay M, Gougerot-Pocidalo MA, Duff GW. An intronic polymorphic repeat sequence modulates interleukin-1 alpha gene regulation. Molecular Immunology 1996;33:999-1006.
13. di Giovine FS, Takhsh E, Blakemore AI, Duff GW. Single base polymorphism at-511 in the human interleukin-1 beta gene (IL1 beta). Human Molecular Genetics 1992;1:450.
14. Meisenzahl EM, Rujescu D, Kirner A, Giegling I, Kathmann N, Leinsinger G et al. Association of an interleukin-1beta genetic polymorphism with altered brain structure in patients with schizophrenia. American Journal of Psychiatry 2001;158:1316-9.
15. Bioque G, Crusius JB, Koutroubakis I, Bouma G, Kostense PJ, Meuwissen SG et al. Allelic polymorphism in IL-1 beta and IL-1 receptor antagonist (IL-1Ra) genes in inflammatory bowel disease. Clinical Experimental Immunology 1995;102:379-83.
16. Gore EA, Sanders JJ, Pandey JP, Palesch Y, Galbraith GM. Interleukin-1beta+3953 allele 2: association with disease status in adult periodontitis. Journal of Clinical Periodontology 1998;25:781-5.
17. Steinkasserer A, Koelble K, Sim RB. Length variation within intron 2 of the human IL-1 receptor antagonist protein gene (IL1RN). Nucleic Acids Research 1991;19:5095.
18. Tarlow JK, Blakemore AI, Lennard A, Solari R, Hughes HN, Steinkasserer A et al. Polymorphism in human IL-1 receptor antagonist gene intron 2 is caused by variable numbers of an 86-bp tandem repeat. Human Genetics 1993;91:403-4.
19. Danis VA, Millington M, Hyland VJ, Grennan D. Cytokine production by normal human monocytes: inter-subject variation and relationship to an IL-1 receptor antagonist (IL-1Ra) gene polymorphism. Clinical and Experimental Immunology 1995;99:303-10.
20. Weining KC, Sick C, Kaspers B, Staeheli P. A chicken homolog of mammalian interleukin-1 beta: cDNA cloning and purification of active recombinant protein. European Journal of Biochemistry 1998;258:994-1000.
21. Zou J, Bird S, Minter R, Horton J, Cunningham C, Secombes CJ. Molecular cloning of the gene for interleukin-1beta from Xenopus laevis and analysis of expression in vivo and in vitro. Immunogenetics 2000;51:332-8.
22. Zou J, Grabowski PS, Cunningham C, Secombes CJ. Molecular cloning of interleukin 1beta from rainbow trout Oncorhynchus mykiss reveals no evidence of an ice cut site. Cytokine 1999;11:552-60.
23. Bird S, Wang T, Zou J, Secombes CJ. Interleukin-1 beta in dogfish (Scyliorhinus canicula): cloning the first cartilaginous fish cytokine gene. Journal of Immunology 2002;168:3329-40.
24. Secombes C, Zou J, Daniels G, Cunningham C, Koussounadis A, Kemp G. Rainbow trout cytokine and cytokine receptor genes. Immunological Reviews 1998;166:333-40.
25. Pleguezuelos O, Zou J, Cunningham C, Secombes CJ. Cloning, sequencing, and analysis of expression of a second IL-1beta gene in rainbow trout (Oncorhynchus mykiss). Immunogenetics 2000;51:1002-11.
26. Fujiki K, Shin DH, Nakao M, Yano T. Molecular cloning and expression analysis of carp (Cyprinus carpio) interleukin-1 beta, high affinity immunoglobulin E Fc receptor gamma subunit and serum amyloid A. Fish & Shellfish Immunology 2000;10:229-42.
27. Engelsma MY, Stet RJM, Verburg-van Kemenade LBM. Cloning and sequencing of two carp interleukin 1 beta 2 complementary DNAs. EMBL accession number: AJ401030, 2000.
28. Bird S. Molecular evolution of IL-1β within vertebrates. PhD Thesis, University of Aberdeen, UK, 2002.
29. Engelsma MY, Stet RJM, Schipper H, Verburg-van Kemenade BML. Regulation of interleukin 1 beta RNA expression in the common carp, Cyprinus carpio L. Developmental and Comparative Immunology 2001;25:195-203.
30. Wang T, Bird S, Zou J, Secombes CJ. Sequencing, gene organisation and differential expression of two goldfish IL-1 beta genes. EMBL accession number: AJ419848, 2001a.
31. Wang T, Bird S, Zou J, Secombes CJ. Sequencing, gene organisation and differential expression of two goldfish IL-1 beta genes. EMBL accession number: AJ4I9849, 2001b.
32. Nikaido M, Okada N. CetSINEs and AREs are not SINEs but are parts of cetartiodactyl L1 Mamm. Genome 2000;11:1123-6.
33. Ogiwara I, Miya M, Ohshima K, Okada N. Retropositional parasitism of SINEs on LINEs: identification of SINEs and LINEs in elasmobranchs. Molecular Biology Evolution 1999;16:1238-50.
34. Roy AM, West NC, Rao A, Adhikari P, Aleman C, Barnes AP, Deininger PL. Upstream flanking sequences and transcription of SINEs. Journal of Molecular Biology 2000;302:17-25.
35. Okada N, Hamada M. The 3′ ends of tRNA-derived SINEs originated from the 3′ ends of LINEs: a new example from the bovine genome. Journal of Molecular Evolution 1997;44(Supplement 1):S52-6.
36. Kido Y, Saitoh M, Murata S, Okada N. Evolution of the active sequences of the HpaI short interspersed elements. Journal of Molecular Evolution 1995;41:986-95.
37. Kido Y, Aono M, Yamaki T, Matsumoto K, Murata S, Saneyoshi M et al. Shaping and reshaping of salmonid genomes by amplification of tRNA-derived retroposons during evolution. Proceedings of the National Academy of Sciences in United States of America 1991;88:2326-30.
38. Hamada M, Kido Y, Himberg M, Reist JD, Ying C, Hasegawa M et al. A newly isolated family of short interspersed repetitive elements (SINEs) in coregonid fishes (whitefish) with sequences that are almost identical to those of the Smal family of repeats: possible evidence for the horizontal transfer of SINEs. Genetics 1997;146:355-67.
39. Hamada M, Takasaki N, Reist JD, DeCicco AL, Goto A, Okada N. Detection of the ongoing sorting of ancestrally polymorphic SINEs toward fixation or loss in populations of two species of charr during speciation. Genetics 1998;150:301-11.
40. Murata S, Takasaki N, Saitoh M, Okada N. Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution. Proceedings of the National Academy of Sciences in United States of America 1993;90:6995-9.
41. Murata S, Takasaki N, Saitoh M, Tachida H, Okada N. Details of retropositional genome dynamics that provide a rationale for a generic division: the distinct branching of all the pacific salmon and trout (Oncorhynchus) from the Atlantic salmon and trout (Salmo). Genetics 1996;142:915-26.
42. Wolf K, Quimby MC. Established eurythermic line of fish cells in vitro. Science, New York 1962;135:1065-6.
43. Ganassin RC, Bols NC. Development of a monocyte/macrophage-like cell line, RTS11, from Rainbow trout spleen. Fish & Shellfish Immunology 1998;8:457-76.
44. Hong S, Zou J, Crampe M, Peddie S, Scapigliati G, Bols N et al. The production and bioactivity of rainbow trout (Oncorhynchus mykiss) recombinant IL-1 beta. Veterinary Immunology and Immunopathology 2001;81:1-14.
45. Wang T, Ward M, Grabowski P, Secombes CJ. Molecular cloning, gene organisation and expression of rainbow trout (Oncorhynchus mykiss) inducible nitric oxide synthase (iNOS) gene. Biochemical Journal 2001c;358:747-55.
46. Zou J, Cunningham C, Secombes CJ. The rainbow trout Oncorhynchus mykiss interleukin-1 beta gene has a different organization to mammals and undergoes incomplete splicing. European Journal of Biochemistry 1999;259:901-8.
47. Sambrook J, Fritsch EF, Maniatis T. Molecular cloning. A laboratory manual. 2nd edn London (England): Cold Spring Harbour Laboratory Press, 1989.
48. Wang T, Zou J, Cunningham C, Secombes CJ. Cloning and functional characterisation of the interleukin-1β1 promoter of rainbow trout. Biochimica Biophysica Acta 2002;1575:108-16.
49. Huang X, Miller W. A time-efficient, linear-space local similarity algorithm. Advanced Applied Mathematics 1991;12:337-57.
50. Quandt K, Frech K, Karas H, Wingender E, Werner T. MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Research 1995;23:4878-84.
51. Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V et al. TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Research 2000;28:316-9.
52. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research 1994;22:4673-80.
53. Pearson WR, Lipman DI. Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences in United States of America 1988;85:2444-8.
54. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 1997;25:3389-402.
55. Altschul SF, Gish W, Miller W, Myers E, Lipman DJ. Best local alignment search tool. Journal of Molecular Biology 1990;215:403-10.
56. Secombes CJ, Bird S, Cunningham C, Zou J. Interleukin-1 in fish. Fish & Shellfish Immunology 1999;9:335-43.
57. Hiscott J, Marois J, Garoufalis J et al. Characterization of a functional NF-kappa B site in the human interleukin 1 beta promoter: evidence for a positive autoregulatory loop. Molecular Cell Biology 1993;13:6231-40.
58. Cogswell JP, Godlevski MM, Wisely GB, Clay WC, Leesnitzer LM, Ways JP et al. NF-kappa B regulates IL-1 beta transcription through a consensus NF-kappa B binding site and a nonconsensus CRE-like site. Journal of Immunology 1994;153:712-23.
59. Goto M, Katayama KI, Shirakawa F, Tanaka I. Involvement of NF-kappaB p50/p65 heterodimer in activation of the human pro-interleukin-1beta gene at two subregions of the upstream enhancer element. Cytokine 1999;11:16-28.
60. Jeon YJ, Han SH, Lee YW, Lee M, Yang KH, Kim HM. Dexamethasone inhibits IL-1 beta gene expression in LPS-stimulated RAW 264.7 cells by blocking NF-kappa B/Rel and AP-1 activation. Immunopharmacology 2000;48:173-83.
61. Husmann M, Jehnichen P, Jahn B, Schlosshan D, Romahn E, Marx J. A novel SP-1 site in the human interleukin-1 beta promoter confers preferential transcriptional activity in keratinocytes. European Journal of Immunology 1996;26:3008-14.
62. Yang Z, Wara-Aswapati N, Chen C, Tsukada J, Auron PE. NF-IL6 (C/EBPbeta) vigorously activates IL-1β gene expression via a Spi-1 (PU.1) protein-protein tether. Journal of Biological Chemistry 2000;275:21272-7.
63. Ubeda M, Wang XZ, Zinszner H, Wu I, Habener JF, Ron D. Stress-induced binding of the transcriptional factor CHOP to a novel DNA control element. Molecular Cell Biology 1996;16:1479-89.
64. Zweidler-Mckay PA, Grimes HL, Flubacher MM, Tsichlis PN. Gfi-1 encodes a nuclear zinc finger protein that binds DNA and functions as a transcriptional repressor. Molecular and Cell Biology 1996;16:4024-34.
65. Brubacher JL, Secombes CJ, Zou J, Bols NC. Constitutive and LPS-induced gene expression in a macrophage-like cell line from the rainbow trout (Oncorhynchus mykiss). Developmental and Comparative Immunology 2000;24:565-74.
66. Takasaki N, Park L, Kaeriyama M, Gharrett AJ, Okada N. Characterization of species-specifically amplified SINEs in three salmonid species-chum salmon, pink salmon, and kokanee: the local environment of the genome may be important for the generation of a dominant source gene at a newly retroposed locus. Journal of Molecular Evolution 1996;42:103.
67. Von Schalburg KR, Sherwood NM. Regulation and expression of gonadotropin-releasing hormone gene differs in brain and gonads in rainbow trout. Endocrinology 1999;140:3012-24.
68. Gilbert N, Labuda D. CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs. Proceedings of the National Academy of Sciences in United States of America 1999;96:2869-74.
69. Lowe TM, Eddy SR. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 1997;25:955-64.
70. Wang AM, Doyle MV, Mark DF. Quantitation of mRNA by the polymerase chain reaction. Proceedings of the National Academy of Sciences in United States of America 1989;86:9717-21.
71. McCulloch RK, Choong CS, Hurley DM. An evaluation of competitor type and size for use in the determination of mRNA by competitive PCR. PCR Methods Applications 1995;4:219-26.
72. Alvarez MJ, Depino AM, Podhajcer OL, Pitossi FJ. Bias in estimations of DNA content by competitive polymerase chain reaction. Analytical Biochemistry 2000;287:87-94.
73. Burch JB, Davis DL, Haas NB. Chicken repeat 1 elements contain a pol-like open reading frame and belong to the non-long terminal repeat class of retrotransposons. Proceedings of the National Academy of Sciences in United States of America 1993;90:8199-203.
74. Brosius J. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 1999;238:115-34.
75. Takahashi K, Terai Y, Nishida M, Okada N. A novel family of short interspersed repetitive elements (SINEs) from cichlids: the patterns of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichlid fishes in Lake Tanganyika. Molecular Biological Evolution 1998;15:391-407.
76. Cantrell MA, Filanoski BJ, Ingermann AR, Olsson K, DiLuglio N, Lister Z et al. An ancient retrovirus-like element contains hot spots for SINE insertion. Genetics 2001;158:769-77.
77. Huleihel M, Lunenfeld E, Horowitz S, Levy A, Potashnik G, Glezerman M. Production of interleukin-1-like molecules by human sperm cells. Fertilisation and Sterilisation 2000;73:1132-7.
78. Soder O, Sultana T, Jonsson C, Wahlgren A, Petersen C, Holst M. The interleukin-1 system in the testis. Andrologia 2000;32:52-5.
79. Matsumi H, Yano T, Koji T, Ogura T, Tsutsumi O, Taketani Y et al. Expression and localization of inducible nitric oxide synthase in the rat ovary: a possible involvement of nitric oxide in the follicular development. Biochemical and Biophysical Research Communications 1998;243:67-72.
80. O'Bryan MK, Schlatt S, Gerdprasert O, Phillipsde DJ, Kretser DM, Hedger MP. Inducible nitric oxide synthase in the rat testis: evidence for potential roles in both normal function and inflammation-mediated infertility. Biology of Reproduction 2000;63:1285-93.
81. Geiduschek EP, Kassavetis GA. The RNA polymerase III transcription apparatus. Journal of Molecular Biology 2001;310:1-26.
82. Paule MR, White RJ. Survey and summary: transcription by RNA polymerases I and III. Nucleic Acids Research 2000;28:1283-98.
83. Johnson KR, Wright JE Jr, May B. Linkage relationships reflecting ancestral tetraploidy in salmonid fish. Genetics 1987;116:579-91.
84. Hordvik I. The impact of ancestral tetraploidy on antibody heterogeneity in salmonid fishes. Immunological Reviews 1998;166:153-7.
85. Andersson E, Peixoto B, Tormanen V, Matsunaga T. Evolution of the immunoglobulin M constant region genes of salmonid fish, rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus): implications concerning divergence time of species. Immunogenetics 1995;41:312-5.
86. Laing KJ, Wang T, Zou J, Holland J, Hong S, Bols N et al. Cloning and expression analysis of rainbow trout Oncorhynchus mykiss tumour necrosis factor-alpha. European Journal of Biochemistry 2001;268:1315-22.
87. Zou J, Wang T, Hirono I et al. Differential expression of two tumor necrosis factor genes in rainbow trout, Oncorhynchus mykiss. Developmental and Comparative Immunology 2002;26:161-72.
88. Gilbert N, Labuda D. Evolutionary inventions and continuity of CORE-SINEs in mammals. Journal of Molecular Biology 2000;298:365-77.