Abstract
The round-spotted pufferfishTetraodon fluviatilis has a genome size of 380 Mb which is slightly smaller than that of another pufferfish,Fugu rubripes rubripes (Fugu). Due to their compact genome and small introns, both pufferfishes have been proposed as model organisms for genome studies. In this study, we have used genomic DNA as template to perform PCR to screen for protein kinase (pk) genes. Forty-oneT. fluviatilis pk genes encoding 7 receptor tyrosine kinases, 14 nonreceptor tyrosine kinases, 16 serine/threonine kinases, 1 dual kinase and 3 novel kinases have been identified. The success of this approach depends on the size and location of the introns. Most of the identifiedpk gene fragments contain introns, ranging from 71 to 300 bp, with an average of 120 bp. It is noteworthy that the intron/exon boundaries of certain genes which belong to the same family are identical. We also analyzed by specific RT-PCR primers the expression profile of those 3 novel genes as well as some selectedpk genes in a variety of tissues. We found thaterbB3,pku α, mrk, CaMK I,CaMKIIγ, and two novel kinase genes (133 and 3–26) are expressed in all tissues examined. However, the novel clone 146 is strongly expressed in the brain and weakly in the intestine, kidney and heart.
Similar content being viewed by others
References
Abe S, Yagi T, Ishiyama S, Hiroe M, Marumo F, Ikawa Y. Molecular cloning of a novel serine/threonine kinase, MRK, possibly involved in cardiac development. Oncogene 11:2187–2195;1995.
Abraham N, Miceli MC, Parnes JR, Veillette A. Enhancement of T-cell responsiveness by the lymphocyte-specific tyrosine protein kinase p56lck. Nature 350:62–66;1991.
Breathnach R, Chambon P. Organization and expression of eukaryotic split genes coding for proteins. Annu Rev Biochem 50:349–383;1981.
Brenner S, Elgar G, Sandford R, Macrae A, Venkatesh B, Aparicio S. Characterization of the pufferfish(Fugu) genome as a compact model vertebrate genome. Nature 366:567–571;1993.
Cantley LC, Auger KR, Carpenter C, Duckworth B, Graziani A, Kapeller R, Soltoff S. Oncogenes and signal transduction. Cell 64:281–302;1991.
Chang CM, Shu HK, Kung HJ. Disease specificity of kinase domains: thesrc-encoded catalytic domain convertserbB into a sarcoma oncogene. Proc Natl Acad Sci USA 92:3928–3932;1995.
Chang MS, Leu JH, Yao CW, Huang FL, Huang CJ. Genomic structure of c-fos gene of the round-spotted pufferfish(Tetraodon fluviatilis). Zool Stud 36:159–169;1997.
Crnogorac-Jurcevic T, Brown JR, Lehrach H, Schalkwyk LC.Tetraodon fluviatilis, a new puffer fish model for genome studies. Genomics 41:177–181;1997.
Davidson D, Chow LM, Veillette A. Chk, a Csk family tyrosine protein kinase, exhibits Csklike activity in fibroblasts, but not in an antigen-specific T-cell line. J Biol Chem 272:1355–1362;1997.
Edelman AM, Blumenthal DK, Krebs KG. Protein serine/threonine kinases. Annu Rev Biochem 56:567–613;1987.
Elgar G, Sandford R, Aparicio S, Macrae A, Venkatesh B, Brenner S. Small is beautiful: Comparative genomics with the pufferfish(Fugu rubripes). Trends Genet 12:145–150;1996.
Ershler MA, Nagorskaya TV, Visser JWM, Belyavsky AV. Novel CDC2-related protein kinases produced in murine hematopoietic stem cells. Gene 124:305–306;1993.
Flenniken AM, Gale NW, Yancopoulos GD, Wilkinson DG. Dinstinct and overlap** expression patterns of ligands for EPH-related receptor tyrosine kinase during mouse embryogenesis. Dev Biol 179:382–401;1996.
Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG. Life with 6000 genes. Science 274:546–567;1996.
Gross T, Lutzelberger M, Weigmann H, Klingenhoff A, Shenoy S, Kaufer NF. Functional analysis of the fission yeast Prp4 protein kinase involved in pre-mRNA splicing and isolation of a putative mammalian homologue. Nucleic Acids Res 25:1028–1035;1997.
Hanks SK, Hunter T. The eukaryotic protein kinase superfamily: Kinase (catalytic) domain structure and classification. FASEB J 9:576–596;1995.
Hanks SK, Quinn AM, Hunter T. The protein kinase family: Conserved features and deduced phylogeny of the catalytic domains. Science 241:42–52;1988.
Hanks SK, Quinn AM. Protein kinase catalytic domain sequences database: Identification of conserved features of primary structure and classification of family members. Methods Enzymol 200:38–62;1991.
Hinegardner R, Rosen DE. Cellular DNA content and the evolution of teleostean fishes. Am Naturalist 106:621–644;1972.
Hunter T, Cooper JA. Protein-tyrosine kinases. Annu Rev Biochem 54:897–930;1985.
Hunter T, Plowman GD. The protein kinase of budding yeast: Six score and more. Trends Biochem Sci 22:18–22;1997.
Hunter T. 1001 protein kinases redux — towards 2000. Semin Cell Biol 5:367–376;1994.
Johnson JD, Edman JC, Rutter WJ. A receptor tyrosine kinase found in breast carcinoma cells has an extracellular discoidin I-like domain. Proc Natl Acad Sci USA 90:5677–5681;1993.
Kawakami Y, Yao L, Tashiro M, Gibson S, Mills BG, Kawakami T. Activation and interaction with protein kinase C of a cytoplasmic tyrosine kinase, Itk/Tsk/Emt, on Fc epsilon RI cross-linking on mast cells. J Immunol 155:3556–3562;1995.
Kentrup H, Becker W, Heukelbach J, Wilmes A, Schurmann A, Huppertz C, Kainulainen H, Joost HG. Dyrk, a dual specificity protein kinase with unique structural features whose activity is dependent on tyrosine residues between subdomains VII and VIII. J Biol Chem 271:3488–3495;1996.
Kraus MH, Issing W, Miki T, Popescu NC, Aaronson SA. Isolation and characterization of ERBB3, a third member of the ERBB/EGFR family: Evidence for overexpression in a subset of human mammary tumors. Proc Natl Acad Sci USA 86:9193–9197;1989.
Lee J, Wang Z, Luoh SM, Wood WI, Scadden DT. Cloning of FRK, a novel human intracellular Src-like tyrosine kinase-encoding gene. Gene 138:247–251;1994.
Lev S, Moreno H, Martinez R, Canoll P, Peles E, Musacchio JM, Plowman GD, Rudy B, Schlessinger J. Protein tyrosine kinase PYK2 involved in Ca2+-induced regulation of ion channel and MAP kinase functions. Nature 376:737–745;1995.
Muller R, Mumberg D, Lucibello FC. Signals and genes in the control of cell-cycle progression. Biochim Biophys Acta 1155:151–179;1993.
Ngiehm P, Saati SM, Martens CL, Gardner P, Schulman H. Cloning and analysis of two isoforms of multifunctional Ca2+/calmodulin-dependent protein kinase. Expression in multiple human tissues. J Biol Chem 268:5471–5479;1993.
Ohno S, Kawasaki H, Imajoh S, Suzuki K, Inagaki M, Yokokura H, Sakoh T, Hidaka H. Tissue-specific expression of three distinct types of rabbit protein kinase C. Nature 325:161–165;1987.
Pasini B, Ceccherini I, Romeo G. RET mutations in human disease. Trends Genet 12:138–144;1996.
Patel M, Leevers SJ, Brickell PM. Structure of the complete human c-fgr protooncogene and identification of multiple transcriptional start sites. Oncogene 5:201–206;1990.
Preat T, Therond P, Lamour-Isnard C, Limbourg-Bouchon B, Tricoire H, Erk I, Mairol MC, Busson D. A putative serine/threonine protein kinase encoded by the segment-polarityfused gene ofDrosophila. Nature 347:87–89;1990.
Richardson A, Parsons T. A mechanism for regulation of the adhesion-associated protein tyrosine kinase pp125FAK. Nature 380:538–540;1996.
Robinson D, He F, Pretlow T, Kung HJ. A tyrosine kinase profile of prostate carcinoma. Proc Natl Acad Sci USA 93:5958–5962;1996.
Roe JL, Rivin CJ, Sessions RA, Feldmann KA, Zambryski PC. The Tousled gene inA. thaliana encodes a protein kinase homologue that is required for leaf and flower development. Cell 75:939–950;1993.
Rosnet O, Marchetto S, Delapeyriere O, Birnbaum D. Murine Flt3, a gene encoding a novel tyrosine kinase receptor of the PDGFR/CSFR1 family. Oncogene 6:1641–1650;1991.
Rouer E, Huynh TV, Lavareda de Souza S, Lang MC, Fischer S, Bernarous R. Structure of the humanlck gene: Differences in genomic organization withsrc-related genes affect only N-terminal exons. Gene 14:4335–4341;1989.
Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467;1977.
Schindler C, Darnell JE Jr. Transcriptional responses to polypeptide ligands: The JAK-STAT pathway. Annu Rev Biochem 64:621–651;1995.
Schultz SJ, Nigg EA. Identification of 21 novel human protein kinases, including 3 members of a family related to the cell cycle regulator nima ofAspergillus nidulans. Cell Growth Differ 4:821–830;1993.
Seger R, Krebs EG. The MAPK signaling cascade. FASEB J 9:726–735;1995.
Tanaka A, Gibbs CP, Arthur RR, Anderson SK, Kung HJ, Fujita DJ. DNA sequence encoding the amino-terminal region of the human c-src protein: Implications of sequence divergence among src-type kinase oncogenes. Mol Cell Biol 7:1978–1983;1987.
Wilks AF. Two putative protein-tyrosine kinases identified by application of the polymerase chain reaction. Proc Natl Acad Sci USA 86:1603–1607;1989.
Ziegler SF, Pleiman CM, Perlmutter RM. Structure and expression of the murinehck gene. Oncogene 6:283–288;1991.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Chou, CM., Lin, Wc., Leu, JH. et al. Isolation and identification of novel protein kinase genes from the round-spotted pufferfish(Tetraodon fluviatilis) genomic DNA. J Biomed Sci 5, 127–134 (1998). https://doi.org/10.1007/BF02258366
Issue Date:
DOI: https://doi.org/10.1007/BF02258366