Tyrosine kinases have significant roles in cell growth, apoptosis, development, and disease. To explore the use of zebrafish as a vertebrate model for tyrosine kinase signaling and to better understand their roles, we have identified all of the tyrosine kinases encoded in the zebrafish genome and quantified RNA expression of selected tyrosine kinases during early development. Using profile hidden Markov model analysis, we identified 122 zebrafish tyrosine kinase genes and proposed unambiguous gene names where needed. We found them to be organized into 39 nonreceptor and 83 receptor type, and 30 families consistent with human tyrosine kinase family assignments. We found five human tyrosine kinase genes (epha1, bmx, fgr, srm, and insrr) with no identifiable zebrafish ortholog, and one zebrafish gene (yrk) with no identifiable human ortholog. We also found that receptor tyrosine kinase genes were duplicated more often than nonreceptor tyrosine kinase genes in zebrafish. We profiled expression levels of 30 tyrosine kinases representing all families using direct digital detection at different stages during the first 24 hours of development. The profiling experiments clearly indicate regulated expression of tyrosine kinases in the zebrafish, suggesting their role during early embryonic development. In summary, our study has resulted in the first comprehensive description of the zebrafish tyrosine kinome.
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References
1.
EckhartW, HutchinsonMA, HunterT. An activity phosphorylating tyrosine in polyoma T antigen immunoprecipitates. Cell, 1979; 18:925–933.
2.
HunterT, EckhartW. The discovery of tyrosine phosphorylation: It's all in the buffer!Cell, 2004; 116:S35–91 p following S48.
3.
SeftonBM, HunterT, BeemonK. Product of in vitro translation of the Rous sarcoma virus src gene has protein kinase activity. J Virol, 1979; 30:311–318.
4.
CollettMS, PurchioAF, EriksonRL. Avian sarcoma virus-transforming protein, pp60src shows protein kinase activity specific for tyrosine. Nature, 1980; 285:167–169.
5.
LevinsonAD, OppermannH, VarmusHE, BishopJM. The purified product of the transforming gene of avian sarcoma virus phosphorylates tyrosine. J Biol Chem, 1980; 255:11973–11980.
6.
SeftonBM, HunterT, BeemonK, EckhartW. Evidence that the phosphorylation of tyrosine is essential for cellular transformation by Rous sarcoma virus. Cell, 1980; 20:807–816.
7.
Ben-BassatH. Biological activity of tyrosine kinase inhibitors: Novel agents for psoriasis therapy. Curr Opin Investig Drugs, 2001; 2:1539–1545.
8.
WongWS, LeongKP. Tyrosine kinase inhibitors: A new approach for asthma. Biochim Biophys Acta, 2004; 1697:53–69.
9.
TibesR, TrentJ, KurzrockR. Tyrosine kinase inhibitors and the dawn of molecular cancer therapeutics. Ann Rev Pharmacol Therap, 2005; 45:357–384.
10.
HunterT. Tyrosine phosphorylation: Thirty years and counting. Curr Opin Cell Biol, 2009; 21:140–146.
11.
HubbardSR. Crystal structure of the activated insulin receptor tyrosine kinase in complex with peptide substrate and ATP analog. EMBO J, 1997; 16:5572–5581.
12.
SicheriF, MoarefiI, KuriyanJ. Crystal structure of the Src family tyrosine kinase Hck. Nature, 1997; 385:602–609.
13.
FuttererK, WongJ, GruczaRA, ChanAC, WaksmanG. Structural basis for Syk tyrosine kinase ubiquity in signal transduction pathways revealed by the crystal structure of its regulatory SH2 domains bound to a dually phosphorylated ITAM peptide. J Mol Biol, 1998; 281:523–537.
14.
BrdickaT, KadlecekTA, RooseJP, PastuszakAW, WeissA. Intramolecular regulatory switch in ZAP-70: Analogy with receptor tyrosine kinases. Mol Cell Biol, 2005; 25:4924–4933.
15.
HartmannJT, HaapM, KoppHG, LippHP. Tyrosine kinase inhibitors. A review on pharmacology, metabolism and side effects. Curr Drug Metab, 2009; 10:470–481.
16.
VerkhivkerGM. Exploring sequence-structure relationships in the tyrosine kinome space: Functional classification of the binding specificity mechanisms for cancer therapeutics. Bioinformatics, 2007; 23:1919–1926.
17.
LiW, YoungSL, KingN, MillerWT. Signaling properties of a non-metazoan Src kinase and the evolutionary history of Src negative regulation. J Biol Chem, 2008; 283:15491–15501.
18.
ManningG, YoungSL, MillerWT, ZhaiY. The protist, Monosiga brevicollis, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan. Proc Natl Acad Sci USA, 2008; 105:9674–9679.
19.
BudiEH, PattersonLB, ParichyDM. Embryonic requirements for ErbB signaling in neural crest development and adult pigment pattern formation. Development, 2008; 135:2603–2614.
Rojas-MunozA, RajadhykshaS, GilmourD, van BebberF, AntosC, Rodriguez EstebanCet al.ErbB2 and ErbB3 regulate amputation-induced proliferation and migration during vertebrate regeneration. Dev Biol, 2009; 327:177–190.
22.
BarriosA, PooleRJ, DurbinL, BrennanC, HolderN. Wilson SW. Eph/Ephrin signaling regulates the mesenchymal-to-epithelial transition of the paraxial mesoderm during somite morphogenesis. Curr Biol, 2003; 13:1571–1582.
23.
JulichD, MouldAP, KoperE, HolleySA. Control of extracellular matrix assembly along tissue boundaries via Integrin and Eph/Ephrin signaling. Development, 2009; 136:2913–2921.
24.
OatesAC, LackmannM, PowerMA, BrennanC, DownLM, DoCet al.An early developmental role for eph-ephrin interaction during vertebrate gastrulation. Mech Dev, 1999; 83:77–94.
25.
WagleM, GrunewaldB, SubburajuS, BarzaghiC, Le GuyaderS, ChanJet al.EphrinB2a in the zebrafish retinotectal system. J Neurobiol, 2004; 59:57–65.
26.
SharmaD, KinseyWH. Fertilization triggers localized activation of Src-family protein kinases in the zebrafish egg. Dev Biol, 2006; 295:604–614.
27.
CrawfordBD, HenryCA, ClasonTA, BeckerAL, HilleMB. Activity and distribution of paxillin, focal adhesion kinase, and cadherin indicate cooperative roles during zebrafish morphogenesis. Mol Biol Cell, 2003; 14:3065–3081.
28.
HenryCA, CrawfordBD, YanYL, PostlethwaitJ, CooperMS, HilleMB. Roles for zebrafish focal adhesion kinase in notochord and somite morphogenesis. Dev Biol, 2001; 240:474–487.
29.
ElsenGE, ChoiLY, PrinceVE, HoRK. The autism susceptibility gene met regulates zebrafish cerebellar development and facial motor neuron migration. Dev Biol, 2009; 335:78–92.
30.
LatimerAJ, JessenJR. Hgf/c-met expression and functional analysis during zebrafish embryogenesis. Dev Dyn, 2008; 237:3904–3915.
31.
TallafussA, EisenJS. The Met receptor tyrosine kinase prevents zebrafish primary motoneurons from expressing an incorrect neurotransmitter. Neural Dev, 2008; 3:18.
LumT, HuynhG, HeinrichG. Brain-derived neurotrophic factor and TrkB tyrosine kinase receptor gene expression in zebrafish embryo and larva. Int J Dev Neurosci, 2001; 19:569–587.
34.
JingL, GordonLR, ShtibinE, GranatoM. Temporal and spatial requirements of unplugged/MuSK function during zebrafish neuromuscular development. PLoS One, 5:e8843.
35.
GolubkovVS, ChekanovAV, CieplakP, AleshinAE, ChernovAV, ZhuWet al.The Wnt/planar cell polarity protein-tyrosine kinase-7 (PTK7) is a highly efficient proteolytic target of membrane type-1 matrix metalloproteinase: Implications in cancer and embryogenesis. J Biol Chem, 2010; 285:35740–35749.
ChanJ, BaylissPE, WoodJM, RobertsTM. Dissection of angiogenic signaling in zebrafish using a chemical genetic approach. Cancer Cell, 2002; 1:257–267.
38.
BuchananCM, ShihJH, AstinJW, RewcastleGW, FlanaganJU, CrosierPSet al.DMXAA (Vadimezan, ASA404) is a multi-kinase inhibitor targetting VEGF-R2 in particular. Clin Sci (Lond), 2012; 122:449–457.
39.
HusonDH, RichterDC, RauschC, DezulianT, FranzM, RuppR. Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformat, 2007; 8:460.
40.
GjiniE, HekkingLH, KuchlerA, SaharinenP, WienholdsE, PostJAet al.Zebrafish Tie-2 shares a redundant role with Tie-1 in heart development and regulates vessel integrity. Dis Model Mech, 2011; 4:57–66.
41.
OatesAC, BrownlieA, PrattSJ, IrvineDV, LiaoEC, PawBHet al.Gene duplication of zebrafish JAK2 homologs is accompanied by divergent embryonic expression patterns: Only jak2a is expressed during erythropoiesis. Blood, 1999; 94:2622–2636.
42.
ChristieTL, CarterA, RollinsEL, ChildsSJ. Syk and Zap-70 function redundantly to promote angioblast migration. Dev Biol, 2010; 340:22–29.
43.
MellgrenEM, JohnsonSL. The evolution of morphological complexity in zebrafish stripes. Trends Genet, 2002; 18:128–134.
SchlueterPJ, RoyerT, FarahMH, LaserB, ChanSJ, SteinerDFet al.Gene duplication and functional divergence of the zebrafish insulin-like growth factor 1 receptors. FASEB J, 2006; 20:1230–1232.
46.
LemeerS, JoplingC, NajiF, RuijtenbeekR, SlijperM, HeckAJet al.Protein-tyrosine kinase activity profiling in knock down zebrafish embryos. PLoS One, 2007; 2:e581.
47.
LemeerS, PinkseMW, MohammedS, van BreukelenB, den HertogJ, SlijperMet al.Online automated in vivo zebrafish phosphoproteomics: From large-scale analysis down to a single embryo. J Proteome Res, 2008; 7:1555–1564.
PruittKD, TatusovaT, MaglottDR. NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res, 2007; 35:D61–65.
50.
EddySR. A new generation of homology search tools based on probabilistic inference. Genome Inform, 2009; 23:205–211.
51.
Marchler-BauerA, AndersonJB, ChitsazF, DerbyshireMK, DeWeese-ScottC, FongJHet al.CDD: Specific functional annotation with the Conserved Domain Database. Nucleic Acids Res, 2009; 37:D205–210.
52.
EdgarRC. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res, 2004; 32:1792–1797.
53.
KimmelCB, BallardWW, KimmelSR, UllmannB, SchillingTF. Stages of embryonic development of the zebrafish. Dev Dyn, 1995; 203:253–310.
54.
GeissGK, BumgarnerRE, BirdittB, DahlT, DowidarN, DunawayDLet al.Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol, 2008; 26:317–325.
55.
SatoY, HashiguchiY, NishidaM. Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication. BMC Evol Biol, 2009; 9:127.
56.
SugaH, DacreM, de MendozaA, Shalchian-TabriziK, ManningG, Ruiz-TrilloI. Genomic survey of premetazoans shows deep conservation of cytoplasmic tyrosine kinases and multiple radiations of receptor tyrosine kinases. Sci Signal, 2012; 5:ra35.
57.
AlbertsB. Redefining cancer research. Science, 2009; 325:1319.
58.
EtchinJ, KankiJP, LookAT. Zebrafish as a model for the study of human cancer. Methods Cell Biol, 2011; 105:309–337.
59.
ZhaoC, WangX, ZhaoY, LiZ, LinS, WeiYet al.A novel xenograft model in zebrafish for high-resolution investigating dynamics of neovascularization in tumors. PLoS ONE, 2011; 6:e21768.
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