Abstract
During the development of B and T lymphocytes, Ig and TCR variable region genes are assembled from germline V, D, and J gene segments by a site-specific recombination reaction known as V(D)J recombination. The process of somatic V(D)J recombination, mediated by the recombination-activating gene (RAG) products, is the most significant characteristic of adaptive immunity in jawed vertebrates. Flounder (Paralichthys olivaceus) RAG1 and RAG2 were isolated by Genome Walker and RT-PCR, and their expression patterns were analysed by RT-PCR and in situ hybridization on sections. RAG1 spans over 7.0 kb, containing 4 exons and 3 introns, and the full-length ORF is 3207 bp, encoding a peptide of 1068 amino acids. The first exon lies in the 5′-UTR, which is an alternative exon. RAG2 full-length ORF is 1062 bp, encodes a peptide of 533 amino acids, and lacks introns in the coding region. In 6-month-old flounders, the expression of RAG1 and RAG2 was essentially restricted to the pronephros (head kidney) and mesonephros (truck kidney). Additionally, both of them were mainly expressed in the thymus. These results revealed that the thymus and kidney most likely serve as the primary lymphoid tissues in the flounder.
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Aidinis V, Dias DC, Gomez CA, Bhattacharyya D, Spanopoulou E and Santagata S 2000 Definition of minimal domains of interaction within the recombination-activating genes 1 and 2 recombinase complex. J. Immunol. 164 5826–5832
Arbuckle JL, Fauss LA, Simpson R, Ptaszek LM and Rodgers KK 2001 Identification of two topologically independent domains in RAG1 and their role in macromolecular interactions relevant to V(D)J recombination. J. Biol. Chem. 276 37093–37101
Bain G, Maandag EC, Izon DJ, Amsen D, Kruisbeek AM, Weintraub BC, Krop I, Schlissel MS, et al. 1994 E2A proteins are required for proper B cell development and initiation of immunoglobulin gene rearrangements. Cell 79 885–892
Bernstein RM, Schluter SF, Bernstein H and Marchalonis JJ 1996 Primordial emergence of the recombination activating gene 1 (RAG1): sequence of the complete shark gene indicates homology to microbial integrases. Proc. Natl. Acad. Sci. USA 93 9454–9459
Bertrand FE 3rd, Olson SL, Martin DA and Wu GE 1998a Sequence analysis of the mouse RAG locus intergenic region. Dev. Immunol. 5 215–222
Bertrand FE 3rd, Olson SL, Willett CE and Wu GE 1998b Sequence of the RAG1 and RAG2 intergenic region in zebrafish (Danio rerio). Dev. Immunol. 5 211–214
Boehm T, Gonzalez-Sarmiento R, Kennedy M and Rabbitts TH 1991 A simple technique for generating probes for RNA in situ hybridization: an adjunct to genome mapping exemplified by the RAG-1/RAG-2 gene cluster. Proc. Natl. Acad. Sci. USA 88 3927–3931
Carlson LM, Oettinger MA, Schatz DG, Masteller EL, Hurley EA, McCormack WT, Baltimore D and Thompson CB 1991 Selective expression of RAG-2 in chicken B cells undergoing immunoglobulin gene conversion. Cell 64 201–208
Chun JJ, Schatz DG, Oettinger MA, Jaenisch R and Baltimore D 1991 The recombination activating gene-1 (RAG1) transcript is present in the murine central nervous system. Cell 64 189–200
Corripio-Miyar Y, Bird S, Treasurer JW and Secombes CJ 2007 RAG-1 and IgM genes, markers for early development of the immune system in the gadoid haddock, Melanogrammus aeglefinus, L. Fish Shellfish Immunol. 23 71–85
Covello JM, Bird S, Morrison RN, Bridle AR, Battaglene SC, Secombes CJ and Nowak BF 2013 Isolation of RAG-1 and IgM transcripts from the striped trumpeter (Latris lineata), and their expression as markers for development of the adaptive immune response. Fish Shellfish Immunol. 34 778–788
Danilova N, Hohman VS, Sacher F, Ota T, Willett CE and Steiner LA 2004 T cells and the thymus in developing zebrafish. Dev. Comp. Immunol. 28 755–767
De P and Rodgers KK 2004 Putting the pieces together: identification and characterization of structural domains in the V(D)J recombination protein RAG1. Immunol. Rev. 200 70–82
Du Pasquier L 1992 Origin and evolution of the vertebrate immune system. APMIS 100 383–392
Fitzsimmons D, Hodsdon W, Wheat W, Maira SM, Wasylyk B and Hagman J 1996 Pax-5 (BSAP) recruits Ets proto-oncogene family proteins to form functional ternary complexes on a B-cell-specific promoter. Genes Dev. 10 2198–2211
Fugmann SD, Villey IJ, Ptaszek LM and Schatz DG 2000 Identification of two catalytic residues in RAG1 that define a single active site within the RAG1/RAG2 protein complex. Mol. Cell 5 97–107
Grawunder U, West RB and Lieber MR 1998 Antigen receptor gene rearrangement. Curr. Opin. Immunol. 10 172–180
Greenhalgh P and Steiner LA 1995 Recombination activating gene (RAG 1) in zebrafish and shark. Immunogenetics 41 54–55
Greenhalgh P, Olesen CE and Steiner LA 1993 Characterization and expression of recombination activating genes (RAG-1 and RAG-2) in Xenopus laevis. J. Immunol. 151 3100–3110
Groth JG and Barrowclough GF 1999 Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Mol. Phylogenet. Evol. 12 115–123
Gwyn LM, Peak MM, De P, Rahman NS and Rodgers KK 2009 A zinc site in the C-terminal domain of RAG1 is essential for DNA cleavage activity. J. Mol. Biol. 390 863–878
Hansen JD and Kaattari SL 1995 The recombination activation gene 1 (RAG1) of rainbow trout (Oncorhynchus mykiss): cloning, expression, and phylogenetic analysis. Immunogenetics 42 188–195
Hansen JD and Zapata AG 1998 Lymphocyte development in fish and amphibians. Immunol. Rev. 166 199e220
Hansen JD 1997 Inspection of the 3' UTR genomic region for RAG1 and RAG2 in rainbow trout (Oncorhynchus mykiss) reveals potential regulatory motifs. Dev. Immunol. 5 129–131
Hansen JD and Kaattari SL 1996 The recombination activating gene 2 (RAG2) of the rainbow trout (Oncorhynchus mykiss). Immunogenetics 44 203–211
Hsu LY, Lauring J, Liang HE, Greenbaum S, Cado D, Zhuang Y and Schlissel MS 2003 A conserved transcriptional enhancer regulates RAG gene expression in developing B cells. Immunity 19 105–117
Ichihara Y, Hirai M and Kurosawa Y 1992 Sequence and chromosome assignment to the 11p13-p12 of human RAG genes. Immunol. Lett. 33 277–284
Ikuta K, Uchida N, Friedman J and Weissman IL 1992 Lymphocyte development from stem cells. Annu. Rev. Immunol. 10 759–783
Josefsson S and Tatner MF 1993 Histogenesis of the lymphoid organs in sea bream, Sparus auratus L. Fish Shellfish Immunol. 3 35e50
Kim DR, Dai Y, Mundy CL, Yang W and Oettinger MA 1999 Mutations of acidic residues in RAG1 define the active site of the V(D)J recombinase. Genes Dev. 13 3070–3080
Kuo TC and Schlissel MS 2009 Mechanisms controlling expression of the RAG locus during lymphocyte development. Curr. Opin. Immunol. 21 173–178
Lam SH, Chua HL, Gong Z, Lam TJ and Sin YM 2004 Development and maturation of the immune system in zebrafish, Danio rerio: a gene expression profiling, in situ hybridization and immunological study. Dev. Comp. Immunol. 28 9–28
Lam SH, Chua HL, Gong Z, Wen Z, Lam TJ and Sin YM 2002 Morphologic transformation of the thymus in developing zebrafish. Dev. Dyn. 225 87–94
Landree MA, Wibbenmeyer JA and Roth DB 1999 Mutational analysis of RAG1 and RAG2 identifies three catalytic amino acids in RAG1 critical for both cleavage steps of V(D)J recombination. Genes Dev. 13 3059–3069
Lin WC and Desiderio S 1994 Cell cycle regulation of V(D)J recombination-activating protein RAG-2. Proc. Natl. Acad. Sci. USA 91 2733–2737
Martin AP 1999 Substitution rates of organelle and nuclear genes in sharks: implicating metabolic rate (again). Mol. Biol. Evol. 16 996–1002
Matthews AG and Oettinger MA 2009 RAG: a recombinase diversified. Nat. Immunol. 10 817–821
Mombaerts P, Iacomini J, Johnson RS, Herrup K, Tonegawa S and Papaioannou VE 1992 RAG-1-deficient mice have no mature B and T lymphocytes. Cell 68 869–877
Oettinger MA, Schatz DG, Gorka C and Baltimore D 1990 RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248 1517–1523
Padrós F and Crespo S 1996 Ontogeny of the lymphoid organs in the turbot Scophtalmus maximus: a light and electron microscope study. Aquaculture 144 1e16
Paton TA, Baker AJ, Groth JG and Barrowclough GF 2003 RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds. Mol. Phylogenet. Evol. 29 268–278
Peixoto BR, Mikawa Y and Brenner S 2000 Characterization of the recombinase activating gene-1 and 2 locus in the Japanese pufferfish, Fugu rubripes. Gene 246 275–283
Pulsford A, Tomlinson MG, Lemaire-Gony S and Glynn PJ 1994 Development and immunocompetence of juvenile flounders, Platichthys flesus L. Fish Shellfish Immunol. 4 63e78
Rodgers KK, Bu Z, Fleming KG, Schatz DG, Engelman DM and Coleman JE 1996 A zinc-binding domain involved in the dimerization of RAG1. J. Mol. Biol. 260 70–84
Romano N, Fanelli M, Maria Del Papa G, Scapigliati G and Mastrolia L 1999 Histological and cytological studies on the developing thymus of sharpsnout seabream, Diplodus puntazzo. J. Anat. 194 39e50
Saitou N and Nei M 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 406–425
San Mauro D, Gower DJ, Oommen OV, Wilkinson M and Zardoya R 2004 Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1. Mol. Phylogenet. Evol. 33 413–427
Sato JJ and Suzuki H 2004 Phylogenetic relationships and divergence times of the genus Tokudaia within Murinae (Muridae; Rodentia) inferred from the nucleotide sequences encoding the Cytb gene, RAG 1, and IRBP. Can. J. Zool. 82 1343–1351
Schatz DG, Oettinger MA and Baltimore D 1989 The V(D)J recombination activating gene, RAG-1. Cell 59 1035–1048
Schatz DG, Oettinger MA and Schlissel SM 1992 V(D)J recombination: molecular biology and regulation. Annu. Rev. Immunol. 10 359–383
Schatz DG 2004 V(D)J recombination. Immunol. Rev. 200 5–11
Schlissel M, Voronova A and Baltimore D 1991 Helix-loop-helix transcription factor E47 activates germ-line immunoglobulin heavy-chain gene transcription and rearrangement in a pre-T-cell line. Genes Dev. 5 1367–1376
Shinkai Y, Rathbun G, Lam KP, Oltz EM, Stewart V, Mendelsohn M, Charron J, Datta M, et al. 1992 RAG-2-deficient mice lack mature lymphocytes owing to inability to initiate V(D)J rearrangement. Cell 68 855–867
Shlyakhtenko LS, Gilmore J, Kriatchko AN, Kumar S, Swanson PC and Lyubchenko YL 2009 Molecular mechanism underlying RAG1/RAG2 synaptic complex formation. J. Biol. Chem. 284 20956–20965
Tamura K, Stecher G, Peterson D, Filipski A and Kumar S 2013 MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30 2725–2729
Valbuena-Ureña E, Amat F and Carranza S 2013 Integrative phylogeography of calotriton newts (Amphibia, Salamandridae), with special remarks on the conservation of the endangered Montseny brook newt (Calotriton arnoldi). PLoS ONE 8 e62542
Verkoczy L, Ait-Azzouzene D, Skog P, Martensson A, Lang J, Duong B and Nemazee D 2005 A role for nuclear factor kappa B/rel transcription factors in the regulation of the recombinase activator genes. Immunity 22 519–531
Wang X, Tan X, Zhang P and Xu Y 2012 Construction and expression of a prokaryotic vector of recombinant olive flounder RAG2. Mar. Sci. (Chinese) 36 59–63
Wei XC, Kishi H, Jin ZX, Zhao WP, Kondo S, Matsuda T, Saito S and Muraguchi A 2002 Characterization of chromatin structure and enhancer elements for murine recombination activating gene-2. J. Immunol. 169 873–881
Willett CE, Cherry JJ and Steiner LA 1997 Characterization and expression of the recombination activating genes (rag1 and rag2) of zebrafish. Immunogenetics 45 394–404
Zapata A, Diez B, Cejalvo T, Gutiérrez-de Frías C and Cortés A 2006 Ontogeny of the immune system of fish. Fish Shellfish Immunol. 20 126–136
Zhang XL, Lu YS, Jian JC and Wu ZH 2012 Cloning and expression analysis of recombination activating genes (RAG1/2) in red snapper (Lutjanus sanguineus). Fish Shellfish Immunol. 32 534–543
Zhang Y, Tan X, Zhang PJ and Xu Y 2006 Characterization of muscle-regulatory gene, MyoD, from flounder (Paralichthys olivaceus) and analysis of its expression patterns during embryogenesis. Mar. Biotechnol. (NY) 8 139–148
Zuckerkandl E and Pauling L 1965 Evolutionary divergence and convergence in proteins; in Evolving genes and proteins (eds) V Bryson and HJ Vogel (New York: Academic Press) pp 97–166
Acknowledgements
This work was supported by the National High Technology Research and Development Program of China (863 Program, 2012AA092203), the National Key Basic Program of Science and Technology of China-Platforms of Aquaculture Stock Resources and National & Local Joint Engineering Laboratory of Ecological Mariculture. We would like to thank Lijing Zhang of the Yellow Sea Fisheries Research Institute for the paraffin sections.
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[Wang X, Tan X, Zhang P-J, Zhang Y and Xu P 2014 Recombination-activating gene 1 and 2 (RAG1 and RAG2) in flounder (Paralichthys olivaceus). J. Biosci. 39 1–10] DOI 10.1007/s12038-014-9469-1
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Wang, X., Tan, X., Zhang, PJ. et al. Recombination-activating gene 1 and 2 (RAG1 and RAG2) in flounder (Paralichthys olivaceus). J Biosci 39, 849–858 (2014). https://doi.org/10.1007/s12038-014-9469-1
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DOI: https://doi.org/10.1007/s12038-014-9469-1