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PubMed2001

Functional analysis of zebrafish GDNF.

We have identified zebrafish orthologues of glial cell line-derived neurotrophic factor (GDNF) and the ligand-binding component of its receptor GFRalpha1. We examined the mRNA expression pattern of these genes in the developing spinal cord primary motor neurons (PMN), kidney, and enteric nervous systems (ENS) and have identified areas of correlated expression of the ligand and the receptor that suggest functional significance. Many aspects of zebrafish GDNF expression appear conserved with those reported in mouse, rat, and avian systems. In the zebrafish PMN, GFRalpha1 is only expressed in the CaP motor neuron while GDNF is expressed in the ventral somitic muscle that it innervates. To test the functional significance of this correlated expression pattern, we ectopically overexpressed GDNF in somitic muscle during the period of motor axon outgrowth and found specific perturbations in the pattern of CaP axon growth. We also depleted GDNF protein in zebrafish embryos using morpholino antisense oligos and found that GDNF protein is critical for the development of the zebrafish ENS but appears dispensable for the development of the kidney and PMN.

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PubMed2002

Inhibition of BMP activity by the FGF signal promotes posterior neural development in zebrafish.

The expression patterns of region-specific neuroectodermal genes and fate-map analyses in zebrafish gastrulae suggest that posterior neural development is initiated by nonaxial signals, distinct from organizer-derived secreted bone morphogenetic protein (BMP) antagonists. This notion is further supported by the misexpression of a constitutively active form of zebrafish BMP type IA receptor (CA-BRIA) in the zebrafish embryos. It effectively suppressed the anterior neural marker, otx2, but not the posterior marker, hoxb1b. Furthermore, we demonstrated that the cells in the presumptive posterior neural region lose their neural fate only when CA-BRIA and Xenopus dominant-negative fibroblast growth factor (FGF) receptors (XFD) are coexpressed. The indications are that FGF signaling is involved in the formation of the posterior neural region, counteracting the BMP signaling pathway within the target cells. We then examined the functions of Fgf3 in posterior neural development. Zebrafish fgf3 is expressed in the correct place (dorsolateral margin) and at the correct time (late blastula to early gastrula stages), the same point that the most precocious posterior neural marker, hoxb1b, is first activated. Unlike other members of the FGF family, Fgf3 had little mesoderm-inducing activity. When ectopically expressed, Fgf3 expands the neural region with suppression of anterior neural fate. However, this effect was mediated by Chordino (zebrafish Chordin), because Fgf3 induces chordino expression in the epiblast and Fgf3-induced neural expansion was substantially suppressed in dino mutants with mutated chordino genes. The results obtained in the present study reveal multiple actions of the FGF signal on neural development: it antagonizes BMP signaling within posterior neural cells, induces the expression of secreted BMP antagonists, and suppresses anterior neural fate.

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PubMed2003

The evolutionary relationships of zebrafish genes tbx6, tbx16/spadetail and mga.

The T-box (Tbx) genes encode a family of transcription factors required for development of vertebrate embryos. In an attempt to discover human orthologues of the zebrafish (Danio rerio) tbx6 and tbx16/spadetail genes, we found that the most similar human (Homo sapiens) gene is the orthologue of mouse (Mus musculus) Mga (MAX gene associated). We have identified the zebrafish orthologue of Mga using analyses of sequence similarity and the orthologies of syntenic genes. Zebrafish mga maps close to dtk (developmental receptor tyrosine kinase), the orthologue of human TYRO3 (TYRO3 protein tyrosine kinase). Like its human and mouse orthologues, zebrafish mga lacks the three conserved introns within the T-box coding sequences that are characteristic of the vertebrate T-box gene family. This suggests that these genes are derived from an ancient reverse transcription event. The human genome does not appear to possess orthologues of zebrafish tbx6 or tbx16/spadetail.

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PubMed1998

Characterization of the zebrafish tbx16 gene and evolution of the vertebrate T-box family.

We report on a new zebrafish T-box-containing gene, tbx16. It encodes a message that is first detected throughout the blastoderm soon after the initiation of zygotic gene expression. Following gastrulation, expression becomes restricted to paraxial mesoderm and later primarily to the developing tail bud. To gain an evolutionary prospective on the potential function of this gene, we have analyzed its phylogenetic relationships to known T-box genes from other species. Zebrafish tbx16 is likely orthologous to the chicken Tbx6L and Xenopus Xombi/Antipodean/Brat/VegT genes. Our analysis also shows that zebrafish tbx6 and mouse Tbx6 genes are paralogous to zebrafish tbx16. We present evidence which argues, that despite the same name and similar expression, zebrafish tbx6 and mouse Tbx6 genes are not orthologous to each other but instead represent relatively distant paralogs. The expression patterns of all genes are discussed in the light of their evolutionary relationships.

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PubMed2004

Artemin-like immunoreactivity in the zebrafish, Danio rerio.

Artemin is a member of the glial cell line-derived neurotrophic factor (GDNF) family. It is a neurotrophic factor that supports neurite migration and outgrowth and survival of the sympathetic and sensory nervous system. Artemin has been studied in human and murine tissues, but no study has been devoted to nonmammalian species. Zebrafish is a teleost fish belonging to the family Ciprinidae, which is becoming an important model species for genetic and developmental studies. Thus, the aim of the present investigation was to evaluate, by immunochemical and immunocytochemical analyses, the tissue distribution pattern of artemin in zebrafish. Different isoforms of artemin with corresponding different molecular weights were detected in the brain, muscle, testis, ovary, kidney, gut, and gills of zebrafish by Western blot analysis. Immunocytochemical analysis showed artemin-like immunoreactivity in different cell types: in glial cells and rare neurons of the central nervous system, taste buds, retina, neuromasts of the lateral line, dorsal root ganglia, sympathetic ganglia, gill epithelium, tubular kidney epithelium, gut epithelium and ganglia, pancreas, thyroid, hypothalamus, testis, and ovary. These results indicate a wide distribution of artemin-like immunoreactivity in adult zebrafish, related to the presence of different forms of artemin. These findings might suggest a complex maturation pattern of artemin, whose forms could also exert different roles in zebrafish tissues.

Animals↗

PubMed2005

Identification of keratins and analysis of their expression in carp and goldfish: comparison with the zebrafish and trout keratin catalog.

With more than 50 genes in human, keratins make up a large gene family, but the evolutionary pressure leading to their diversity remains largely unclear. Nevertheless, this diversity offers a means to examine the evolutionary relationships among organisms that express keratins. Here, we report the analysis of keratins expressed in two cyprinid fishes, goldfish and carp, by two-dimensional polyacrylamide gel electrophoresis, complementary keratin blot binding assay, and immunoblotting. We further explore the expression of keratins by immunofluorescence microscopy. Comparison is made with the keratin expression and catalogs of zebrafish and rainbow trout. The keratins among these fishes exhibit a similar range of molecular weights and isoelectric points, with a similar overall pattern on two-dimensional gels. In addition, immunofluorescence microscopy studies of goldfish and carp tissues have revealed the expression of keratins in both epithelial and mesenchymally derived tissues, as reported previously for zebrafish and trout. We conclude that keratin expression is qualitatively similar among these fishes, with goldfish and carp patterns being more similar to each other than to zebrafish, and the cyprinid fishes being more similar to each other than to the salmonid trout. Because of the detected similarity of keratin expression among the cyprinid fishes, we propose that, for certain experiments, they are interchangeable. Although the zebrafish distinguishes itself as being a developmental and genetic/genomic model organism, we have found that the goldfish, in particular, is a more suitable model for both biochemical and histological studies of the cytoskeleton, especially since goldfish cytoskeletal preparations seem to be more resistant to degradation than those from carp or zebrafish.

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PubMed2004

Histological analysis of acute toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in zebrafish.

Previous studies have demonstrated that acute exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) by injection leads to inhibition of caudal fin regeneration in zebrafish. Since the TCDD exposure in these studies is systemic, it is possible that pathology in organs other than the fin could result in inhibition of fin regeneration. Therefore, histopathology of adult zebrafish (Danio rerio) organs was characterized following abdominal cavity injection of a TCDD dose (70ng/g). The most pronounced histopathologic changes 5 days post-injection included lipidosis and hypertrophy of liver hepatocytes and hypertrophy of gill lamellae. Effects of TCDD exposure on immunolocalization of the zebrafish aryl hydrocarbon receptor nuclear translocator (ARNT2), the heterodimer partner of the aryl hydrocarbon receptor (AHR2), and an AHR regulated gene cytochrome P450 1A (CYP1A) was also determined. ARNT2 was immunolocalized to the gastrointestinal tract, gill lamellae, kidney, ventricle of the heart, caudal fin, brain and liver of zebrafish. TCDD exposure had no measurable effect on ARNT2 abundance or localization. CYP1A was immunolocalized in TCDD exposed fish as a biomarker for cells with an activated AHR pathway. CYP1A was not detected in any tissue from vehicle exposed fish. Significant TCDD-dependent induction of CYP1A was detected in the proximal tubules of the kidney, in liver hepatocytes and in the gastrointestinal tract of TCDD exposed fish. Significant but lower TCDD-dependent CYP1A expression was evident in the gill, caudal fin and ventricle of the heart. Overall, TCDD exposure in adult zebrafish leads to histopathology similar to that reported in other fish species, and it appears unlikely that the histopathology in these organs completely explains the inhibition of fin regeneration.

Animals↗

PubMed2004

Molecular cloning, characterization, and expression in brain and gonad of Dmrt5 of zebrafish.

The DM domain gene family has at least eight members with conserved DNA-binding DM domain, which encodes putative transcription factors related to the sexual regulator Dsx of Drosophila and Mab-3 of Caenorhabditis elegans. Although some of the DM genes are involved in sexual development, the function of most of these genes remains unclear. There is also few structural and functional analysis concerning DM domain genes of the model fish, zebrafish. We report here molecular cloning, sequence, and expression of zebrafish Dmrt5, which consists of two exons, and encodes a 440-amino acid protein with conserved DMA and DMB domains in addition to DM domain. Phylogenetic analysis shows that zebrafish Dmrt5 fits within the Dmrt5 clade of fish and mammals. Zebrafish Dmrt5 was expressed in early gastrula period, subsequently increased to a high level in late stage of gastrula period (bud stage) and lower until the hatch period. In situ hybridization analysis showed its expression in developing central nervous system of embryos, especially in mid-brain and mid-hind brain boundary. In adult, its expression was restricted in brain and developing germ cells, especially in spermatogonia, spermatocytes, spermatids, and sperm cells, and in developing oocytes, including early perinucleolus stage oocyte, late yolk vesicle stage oocyte, and oil drop stage oocyte. These data suggest that zebrafish Dmrt5 have potentially important roles in gonadal development and may have contributed to the functional endocrine axis.

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PubMed2004

Identification of a novel splicing form of zebrafish p73 having a strong transcriptional activity.

p73 is a transcriptional activator related to tumor suppressor p53 and regulates differentiation, cell-cycle arrest, and apoptosis. Recently, zebrafish p73 (zp73alpha) was isolated and shown to be required for zebrafish embryogenesis. In this study, we isolated a novel splicing-variant of zp73 mRNA, which was generated by the use of an alternative splicing acceptor site, and designated it as zp73theta;. The zp73theta; mRNA encoded a carboxy-terminal structure distinct from that of zp73alpha. Whereas the expression level of zp73theta; mRNA was much lower than that of zp73alpha in zebrafish adult tissues, it was relatively high and fluctuated during embryogenesis. Using Saos-2 cells for a transient reporter assay, we found that zp73theta;, but not zp73alpha, had strong transcriptional activity when the experiments were performed at 34 degrees C. In addition, zp73theta; had the ability to suppress the growth of Saos-2 cells and to cause the developmental defects in zebrafish. These data indicated that zp73theta; could work as a transcriptional activator in zebrafish.

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PubMed2005

Transcription regulation of the vegf gene by the BMP/Smad pathway in the angioblast of zebrafish embryos.

Vascular endothelial growth factor (VEGF) is a mitogen that is critically involved in vasculogenesis, angiogenesis, and hematopoiesis. However, what and how transcription factors participate in the regulation of vegf gene expression are not fully understood. Here we report the cloning and sequencing of the zebrafish vegf promoter which revealed that the promoter contains a number of bone morphogenetic protein (BMP)-activated Smad binding elements (SBE), implicating Smad1 and Smad5 in the regulation of BMP-induced expression of vegf. Electrophoretic mobility shift assays of adding recombinant Smad proteins to the SBE-containing DNA oligonucleotides that represent portions of zebrafish vegf promoter resulted in mobility shift of the oligonucleotides. These changes demonstrate potential interactions between Smad1/5 and the vegf promoter. Reporter activity assays using the wild-type or SBE-deleted vegf promoters to drive the luciferase reporter gene expression revealed that Smad1 stimulated while Smad5 repressed the vegf promoter activity in zebrafish embryos. These data indicate that the BMP/Smad signaling pathway is involved in the regulation of zebrafish vegf transcription. In addition, we demonstrate that transgenic expression of human BMP4 in zebrafish embryos induced an expansion of the posterior intermediate cell mass (ICM, also commonly called blood island), a population of cells containing endothelial and hematopoietic precursors. In the expanded ICM, vegf and VEGF receptor 2 (flk-1) were ectopically co-expressed, suggesting that an autocrine/paracrine regulation of vegf expression may exist and contribute to the BMP-induced hemangiogenic cell proliferation.

Animals↗

PubMed2005

Expression and characterization of a brain-specific protein kinase BSK146 from zebrafish.

We have previously identified a novel protein kinase, pk146, in the brain of Tetraodon. In the present study, we cloned the homologous protein kinase gene encoding a protein of 385 amino acid residues from zebrafish. The overall amino acid sequence and the kinase domain of zebrafish BSK146 shows 48% and 69% identity to that of rat sbk, a SH3-containing serine/threonine protein kinase. By whole-mount in situ hybridization and RT-PCR, the expression of bsk146 mRNA was mainly in the brain. To explore the in vivo function of BSK146 during zebrafish development, we used morpholino knockdown approach and found that BSK146 morphants displayed enlarged hindbrain ventricle and smaller eyes. Whole-mount in situ hybridization was further performed to analyze the brain defects in BSK146-MO-injected embryos. The expression of brain-specific markers, such as otx2, pax2.1, and krox20, was found normal in morphant embryos at 24hpf, while expression of pax2.1 exerted changes in midbrain-hindbrain boundary and hindbrain in morphant embryos at 48hpf. These data suggest that BSK146 may play an important role in later ventricle expansion in zebrafish brain development. Although the recombinant BSK146 protein produced in insect cells was active and could phosphorylate both histone H1 and histone 2B, the endogenous substrate of BSK146 in the embryonic brain of zebrafish is not clear at the present time and needs further investigation.

Amino Acid Sequence↗

PubMed2006

Zebrafish DJ-1 is evolutionarily conserved and expressed in dopaminergic neurons.

Loss-of-function mutations in the human PARK7 gene, encoding DJ-1, are a rare cause of autosomal recessive Parkinson's disease (ARPD). To facilitate generation of a novel vertebrate model, in which to examine the biochemical functions of DJ-1 in vivo, we cloned and characterized the zebrafish orthologue of DJ-1 (zDJ-1). The 0.95 kb zDJ-1 mRNA is expressed in adult zebrafish brain, muscle and gut, and in the embryo from 24 h post-fertilization. The zDJ-1 transcript encodes a 19.8 kDa, 189 amino acid protein, which is 83% identical to human DJ-1. Residues thought to be functionally important sites of post-translational modification in human DJ-1, and critical positions affected by pathogenic missense mutations in ARPD patients, are conserved in zDJ-1. The 14 kb zDJ-1 gene contains six exons and is located on zebrafish chromosome 8; the structure of the gene is highly homologous to human DJ-1, except that there are no alternatively spliced non-coding 5' exons. The single zDJ-1 first exon shows 5' end heterogeneity, reflecting multiple transcription start sites. In the adult zebrafish brain, zDJ-1 immunoreactivity was prominent in the cytoplasm of most neurons, and in the neuropil, but was less evident within white matter tracts, consistent with neuronal somatic and dendritic localization. Dopaminergic neurons in each of the major forebrain and diencephalic TH-positive cell groups expressed zDJ-1. These studies show that zDJ-1 is very similar to human DJ-1 and delineate essential resources, allowing further examination of the function and regulation of DJ-1, using the zebrafish as a model.

Animals↗

PubMed2004

Sequence, linkage mapping and early developmental expression of the intestinal-type fatty acid-binding protein gene (fabp2) from zebrafish (Danio rerio).

The intestinal fatty acid-binding protein (I-FABP) shows binding specificity for long-chain fatty acids and is proposed to be involved in uptake of dietary fatty acids and their intracellular transport. We have determined the sequence of the gene encoding I-FABP in zebrafish. The zebrafish I-FABP gene contains four exons interrupted by three introns. Radiation hybrid mapping assigned the I-FABP gene to linkage group 1. A 924 bp sequence 5' upstream of the initiation codon in the I-FABP gene contained several putative cis-acting regulatory elements. In adult zebrafish, reverse transcription-polymerase chain reaction (RT-PCR) detected I-FABP mRNA in intestine, brain, liver, muscle and testis. Quantitative RT-PCR demonstrated that I-FABP mRNA was most abundant in intestine, followed by brain. I-FABP mRNA levels were very low in muscle, testis, heart, liver, skin and ovary. RT-PCR using total RNA extracted from zebrafish embryos detected I-FABP mRNA as early as 12 h post-fertilization. Whole-mount in situ hybridization to zebrafish embryos detected I-FABP mRNA in the yolk syncytial layer (YSL) at early somitogenesis. Later during embryonic development the I-FABP mRNA was detected in the intestinal bulb, liver and pancreas primordium. Expression in YSL, liver or pancreas has not been previously reported for fish or mammalian I-FABP genes and may be related to specific physiological differences between fishes and mammals.

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PubMed2005

Non-sense mutations in the dihydropyridine receptor beta1 gene, CACNB1, paralyze zebrafish relaxed mutants.

Contractions by skeletal muscle require proper excitation-contraction (EC) coupling, whereby depolarization of the muscle membrane leads to an increase in cytosolic Ca(2+) and contraction. Changes in membrane voltage are detected by dihydropyridine receptors (DHPR) that directly interact with and activate ryanodine receptors to release Ca(2+) from the sarcoplasmic reticulum into the cytosol. A genetic screen for motility mutations isolated a new allele of the immotile zebrafish mutant relaxed. Muscles in relaxed embryos do not contract in response to potassium chloride (KCl) thus appear unresponsive to membrane depolarization, but do contract when stimulated by caffeine, an agonist of ryanodine receptors. This suggests that relaxed mutant muscles are defective in EC coupling. Indeed, immunohistochemical analysis demonstrated that mutants lack DHPRs in skeletal muscles. The mutant phenotype results from non-sense mutations in the zebrafish CACNB1 gene that encodes the DHPR beta1 subunit. The zebrafish CACNB1 gene is expressed in skeletal muscles, PNS and CNS. Electrophysiological recordings showed no obvious abnormalities in the motor output of relaxed mutants, presumably due to redundancy provided by other beta subunits. The structural and functional homology of CACNB1 in zebrafish and mammals, suggests that zebrafish can be useful for studying EC coupling and potential neuronal function of CACNB1.

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PubMed2004

Cloning and characterization of an Mx gene and its corresponding promoter from the zebrafish, Danio rerio.

Type I interferons (IFNs) represent a crucial component of the innate immune response to viruses. An important downstream effector of IFN is the Mx gene, which is activated solely through this pathway. Mx proteins are characterized by a tripartite GTP-binding domain, dynamin family signature, and leucine zipper motif. Mx genes are transcribed upon activation of an interferon-stimulated response element (ISRE) located in the Mx promoter region. In this article, we describe the cloning and analysis of an Mx gene and its corresponding promoter from the zebrafish (Danio rerio). The deduced amino acid sequence of zebrafish Mx contains the conserved GTP-binding domain, dynamin family signature, and leucine zipper motif common to Mx proteins, and shows a 50% identity to human MxA and 69% identity both to rainbow trout and to Atlantic salmon. Zebrafish liver cells produced high levels of Mx mRNA in response to induction by the known IFN-inducer polyinosinic-polycytidylic acid (Poly[I:C]). The zebrafish Mx promoter contains two ISREs homologous to those found in the promoter regions of many IFN-inducible genes, and was able to drive transcription of a luciferase reporter gene when induced by either purified zebrafish IFN or Poly[I:C].

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PubMed2006

Structural and functional characterization of the zebrafish lamin B receptor.

The lamin B receptor (LBR) is an integral membrane protein of the inner nuclear membrane that is interacting with B-type lamins, chromatin and DNA. The complete loss of the protein in mouse mutants causes a reduced viability of embryos, and viable animals develop abnormalities of the skeleton. Here, we present the molecular characterization of the zebrafish LBR (zLBR) gene and the functional analysis of LBR during zebrafish embryogenesis. We found that the coding region of the LBR mRNA of zebrafish as well as of mammals is contained in 13 exons. At the protein level, human and zebrafish LBR exhibit a high sequence identity (57% and higher) in 8 of the 13 exons. Knockdown of zLBR by microinjection of 0.5-1.0 mM morpholino antisense oligonucleotides (MO) into 1- to 2-cell stage embryos reduced the amount of endogenous zLBR protein to approximately 10-20%. The viability of MO-injected embryos within 24 h was reduced to 70-77%. Surviving 1-day-old embryos exhibited morphological alterations including reduced growth of head structures, retardation of tail growth and a bent backbone and tail. Expression analysis of the transcription factors no tail (ntl) and goosecoid (gsc) by in situ hybridization suggests that these malformations are caused by altered cell migration during gastrulation. Our data indicate that the LBR of zebrafish and mammals are both required for correct development.

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PubMed2004

Genomic organization and transcripts of the zebrafish Protocadherin genes.

We have examined the protocadherin (Pcdh) gene clusters of the zebrafish (Danio rerio). At least three sets of the Pcdh gene cluster were found in the zebrafish genome. Here, we describe the complete organization of the DrPcdh2 gene clusters. Classification by phylogenetic and transcript analyses revealed 7 DrPcdh2omicron, 20 DrPcdh2alphaa, 12 DrPcdh2alphab, and 1 DrPcdh2alphac variable exons upstream of the DrPcdh2alpha constant region exons in the DrPcdh2 gene cluster. The constant regions of the DrPcdh1alpha and DrPcdh2alpha genes in zebrafish were orthologs of those of the mammalian Pcdhalpha. These exons all encoded plural PXXP motifs in their cytoplasmic tails. The sequences of the variable exons were highly conserved within each family: DrPcdh2omicron, DrPcdh2alphaa, and DrPcdh2alphab. Transcript analysis revealed that zebrafish Pcdhs had alternatively spliced variants in the constant region that were not found in mammals. More gene clusters, more variable exons, and more alternative splicing variants were found in zebrafish than in mammals. Thus, although the Pcdhalpha families were common to diverse vertebrates, their gene number, structure, and transcripts were different between teleosts and mammals.

Alternative Splicing↗

PubMed2006

Phylogenetic relationships and gene expression pattern of three different cathepsin L (Ctsl) isoforms in zebrafish: Ctsla is the putative yolk processing enzyme.

Certain cysteine proteases, such as cathepsin L (Ctsl), have been involved in yolk processing mechanisms in oocytes and embryos of lower vertebrates. In zebrafish (Danio rerio), three different ctsl genes, ctsla, ctslb and ctslc, have been found in the genome, but their pattern of expression, as well as information on which the encoded enzymes are potentially involved in yolk absorption during embryogenesis, is unknown. Here, phylogenetic and gene structure analysis revealed that zebrafish ctsla and ctslb genes are similar, showing a highly conserved structure in comparison with human ctsl, while ctslc presents different exon organization together with an earlier evolution. Thus, ctslc appears to be evolved from a common ancestral ctsl-like gene, possibly through an early duplication event, whereas ctsla and ctslb may be originated from a second duplication mechanism. Zebrafish ctsla, ctslb and ctslc also showed different patterns of mRNA expression during embryogenesis and in adult tissues. While Ctsla transcripts were accumulated in embryos throughout development and in the adult ovary, those encoding Ctslb were detected only in embryos around the time of hatching as previously reported, and those for Ctslc appeared only in larvae and in some adult tissues, but not in the ovary. In zebrafish and killifish (Fundulus heteroclitus) embryos, Ctsla mRNA was first detected in blastomers, and later in development it was localized in cells of the yolk syncytial layer, an embryonic structure involved in yolk absorption. These data therefore suggested that Ctsla is most likely the putative protease involved in yolk processing in fish embryos, while Ctslc seems not to be required during early embryogenesis in zebrafish.

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