Analysis of the dopamine receptor family in the compact genome of the puffer fish Fugu rubripes

First identification of dopamine receptors in pikeperch, Sander lucioperca, during the pre-ovulatory period

Dopamine (DA) is a ubiquitous neurotransmitter exerting a range of pleiotropic actions through two DA receptor families, the D1 and the D2. To date in vertebrates, a maximum of four receptor subtypes have been identified within the D1 family, D₁ (former D_1A), D₅ (former D_1B), D₆ (former D_1C and D_1D) and D₇ (former D_1E), while the D2 family encloses five subtypes, D₂, D₃, D₄, D₈ (former D_2like or D_2l) and D₉ (former D_{4-related sequence} or D_4-rs). In teleosts, no study has investigated in parallel all the DA receptors to identify and localize the whole receptor repertoire from both families. In pikeperch, Sander lucioperca, a species of interest for aquaculture development, the existence, number and location of the DA receptors are totally unknown. To address these questions, RNA-seq with de novo transcriptome reconstruction, functional annotation and phylogenetic analysis were performed to characterize the transcript repertoire of DA receptors in the brain of female pikeperch at the pre-ovulatory period. Ten different cDNA were identified and showed to belong to the D1 family: two D₁, one D_5a, one D_6a and one D_6b and to the D2 family: two spliced variants of D₂, one D₃, one D₈ and one D_9. Unlike zebrafish, the subtypes D₄ and D₇ have not yet been isolated in pikeperch. As expected D₁, D₃, D₈ and D₉ are mostly expressed in brain parts except for the cerebellum (D₁ and D₃). The inter-species differences in the number of DA receptors and the inter-organ differences in the gene expression of all receptors support the complexity of the dopaminergic actions in vertebrate.

Genomic strategies for the identification of dopamine receptor genes in zebrafish

In this chapter, we describe the identification and cloning of D2-like dopamine receptor (DR) genes in zebrafish, a vertebrate model genetic organism. To identify DR genes, we performed searches of the zebrafish genomic sequence database that yielded contig segments of several D2-like DR genes. From these sequences, we amplified full-length cDNAs encoding three D2, one D3, and three D4 DR receptor subtypes via RT-PCR. The predicted proteins displayed 57-72% amino acid identity when compared to their human DR counterparts. To validate the identity of zebrafish DR genes, each of the genes was mapped by using the T51 radiation hybrid panel. With the exception of drd2b and drd4b, each of the zebrafish DR genes mapped to chromosomal positions that were syntenic with regions of human chromosomes containing orthologs of the zebrafish DR genes. To further validate the identity of the D2-like DR genes in zebrafish, we conducted phylogenetic analysis which supported the predicted identities of the cloned DR receptor cDNAs.

Regulation of dopamine D2 receptor expression in grass carp pituitary cells: a possible mechanism for dopaminergic modification of luteinizing hormone synthesis

In many fishes, dopamine (DA) strongly inhibits luteinizing hormone (LH) release by direct action at the pituitary level. In this study, the effect of DA on LH synthesis was examined by detecting its β-subunit mRNA level in immature grass carp pituitary cells. Results showed that DA inhibited LHβ mRNA expression and its inhibition was antagonized by a DA D2 receptor (DRD2) antagonist, sulpiride, suggesting that DA inhibited LH synthesis via DRD2. This notion was further supported by the finding that the grass carp DRD2 (gcDRD2) immunoreactivity was observed in the proximal pars distalis of the pituitary in which gonadotrophs are distributed. Accordingly, a full-length cDNA for DRD2 was cloned from grass carp pituitary and it showed closer phylogenetic relationships to the DA D2 receptors compared with the D3 and D4 or D1-like receptors in other vertebrates. Besides brain, the expression of this receptor in pituitary was revealed by tissue distribution assay, implying the pituitary function of gcDRD2 in immature grass carp. In grass carp pituitary cells, gcDRD2 transcript level was stimulated by DA and this stimulation was blocked by sulpiride. However, hCG, a functional homolog of grass carp LH, was found to inhibit gcDRD2 mRNA expression, indicating an intrapituitary negative feedback of LH on gcDRD2 expression. In view of our observation that the DRD2 mediated the dopaminergic inhibition of LH synthesis, we speculate that the DA stimulation and LH suppression on gcDRD2 may reinforce or attenuate the DA inhibition on LH synthesis, respectively and this regulation of gcDRD2 may at least partially contribute to the steady state levels of LH mRNA in prepubertal grass carp.

Dopamine receptors in a songbird brain

Dopamine is a key neuromodulatory transmitter in the brain. It acts through dopamine receptors to affect changes in neural activity, gene expression, and behavior. In songbirds, dopamine is released into the striatal song nucleus Area X, and the levels depend on social contexts of undirected and directed singing. This differential release is associated with differential expression of activity-dependent genes, such as egr1 (avian zenk), which in mammalian brain are modulated by dopamine receptors. Here we cloned from zebra finch brain cDNAs of all avian dopamine receptors: the D1 (D1A, D1B, D1D) and D2 (D2, D3, D4) families. Comparative sequence analyses of predicted proteins revealed expected phylogenetic relationships, in which the D1 family exists as single exon and the D2 family exists as spliced exon genes. In both zebra finch and chicken, the D1A, D1B, and D2 receptors were highly expressed in the striatum, the D1D and D3 throughout the pallium and within the mesopallium, respectively, and the D4 mainly in the cerebellum. Furthermore, within the zebra finch, all receptors, except for D4, showed differential expression in song nuclei relative to the surrounding regions and developmentally regulated expression that decreased for most receptors during the sensory acquisition and sensorimotor phases of song learning. Within Area X, half of the cells expressed both D1A and D2 receptors, and a higher proportion of the D1A-only-containing neurons expressed egr1 during undirected but not during directed singing. Our findings are consistent with hypotheses that dopamine receptors may be involved in song development and social context-dependent behaviors. J. Comp. Neurol. 518:741–769, 2010. © 2009 Wiley-Liss, Inc.

Neuroendocrine control by dopamine of teleost reproduction

While gonadotropin-releasing hormone (GnRH) is considered as the major hypothalamic factor controlling pituitary gonadotrophins in mammals and most other vertebrates, its stimulatory actions may be opposed by the potent inhibitory actions of dopamine (DA) in teleosts. This dual neuroendocrine control of reproduction by GnRH and DA has been demonstrated in various, but not all, adult teleosts, where DA participates in an inhibitory role in the neuroendocrine regulation of the last steps of gametogenesis (final oocyte maturation and ovulation in females and spermiation in males). This has major implications for inducing spawning in aquaculture. In addition, DA may also play an inhibitory role during the early steps of gametogenesis in some teleost species, and thus interact with GnRH in the control of puberty. Various neuroanatomical investigations have shown that DA neurones responsible for the inhibitory control of reproduction originate in a specific nucleus of the preoptic area (NPOav) and project directly to the region of the pituitary where gonadotrophic cells are located. Pharmacological studies showed that the inhibitory effects of DA on pituitary gonadotrophin production are mediated by DA-D2 type receptors. DA-D2 receptors have now been sequenced in several teleosts, and the coexistence of several DA-D2 subtypes has been demonstrated in a few species. Hypophysiotropic DA activity varies with development and reproductive cycle and probably is controlled by environmental cues as well as endogenous signals. Sex steroids have been shown to regulate dopaminergic systems in several teleost species, affecting both DA synthesis and DA-D2 receptor expression. This demonstrates that sex steroid feedbacks target DA hypophysiotropic system, as well as the other components of the brain-pituitary gonadotrophic axis, GnRH and gonadotrophins. Recent studies have revealed that melatonin modulates the activity of DA systems in some teleosts, making the melatonin-DA pathway a prominent relay between environmental cues and control of reproduction. The recruitment of DA neurons for the neuroendocrine control of reproduction provides an additional brain pathway for the integration of various internal and environmental cues. The plasticity of the DA neuroendocrine role observed in teleosts may have contributed to their large diversity of reproductive cycles.

Dopaminergic system in birdsong learning and maintenance

Dopamine function in birdsong has been studied extensively in recent years. Several song and auditory nuclei are innervated by midbrain dopaminergic fibers and contain neurons with various dopamine receptors. During sexually motivated singing, activity of midbrain dopaminergic neurons in the ventral tegmental area and dopamine release in the striatal Area X, involved in song learning and maintenance, are higher. In this review we provide an overview of the dopaminergic system and neurotransmission in songbirds and the outline of possible involvement of dopamine in control of song learning, production, and maintenance. Based on both behavioral and computational biology data, we describe several models of song learning and the proposed role of dopamine in them. Special attention is given to possible role of dopamine in incentive salience (wanting) and reward prediction error signaling during song learning and maintenance, as well as the role of dopamine-mediated synaptic plasticity in reward processing. Finally, the role of dopamine in determination of personality traits in relation to birdsong is discussed.

Kinetics and pharmacology of the D1- and D2-like dopamine receptors in Japanese quail brain

Although the avian brain dopamine system and its functions have been studied much less than the mammalian one, there is an increasing interest in the role of dopamine and its receptors in a wide variety of motor, cognitive and emotional functions in birds with implications for basic research, medicine or agriculture. Pharmacological characterisation of the avian dopamine receptors has had little attention. In this paper we characterise the two classes of dopamine receptors in Japanese quail brain by radioligand binding techniques using [(3)H]SCH 23390 (D(1)) and [(3)H]spiperone (D(2)). Association, dissociation and saturation analyses showed that the binding of both radioligands is time- and concentration-dependent, saturable and reversible. Apparent dissociation constants determined for [(3)H]SCH 23390 and [(3)H]spiperone from concentration isotherms were 1.07 and 0.302 nM and the maximum binding capacities were 89.3 and 389.3 fmol per mg of protein, respectively. Using competitive binding studies with a spectrum of dopamine and other neurotransmitter receptor agonists/antagonists, the [(3)H]SCH 23390 and [(3)H]spiperone binding sites were characterised pharmacologically. Pharmacological profiles of quail dopamine receptors showed a high degree of pharmacological homology with other vertebrate dopamine receptors. The data presented extend the knowledge of kinetics and pharmacology of D(1)- and D(2)-like dopamine receptors in birds, provide data for avian psychopharmacological and comparative studies and represent an important complement to studies using cell expression systems.

The goldfish (Carassius auratus) as a model for neuroendocrine signaling

Goldfish (Carassius auratus) are excellent model organisms for the neuroendocrine signaling and the regulation of reproduction in vertebrates. Goldfish also serve as useful model organisms in numerous other fields. In contrast to mammals, teleost fish do not have a median eminence; the anterior pituitary is innervated by numerous neuronal cell types and thus, pituitary hormone release is directly regulated. Here we briefly describe the neuroendocrine control of luteinizing hormone. Stimulation by gonadotropin-releasing hormone and a multitude of classical neurotransmitters and neuropeptides is opposed by the potent inhibitory actions of dopamine. The stimulatory actions of gamma-aminobutyric acid and serotonin are also discussed. We will focus on the development of a cDNA microarray composed of carp and goldfish sequences which has allowed us to examine neurotransmitter-regulated gene expression in the neuroendocrine brain and to investigate potential genomic interactions between these key neurotransmitter systems. We observed that isotocin (fish homologue of oxytocin) and activins are regulated by multiple neurotransmitters, which is discussed in light of their roles in reproduction in other species. We have also found that many novel and uncharacterized goldfish expressed sequence tags in the brain are also regulated by neurotransmitters. Their sites of production and whether they play a role in neuroendocrine signaling and control of reproduction remain to be determined. The transcriptomic tools developed to study reproduction could also be used to advance our understanding of neuroendocrine-immune interactions and the relationship between growth and food intake in fish.

Neuroendocrine regulation of puberty in fish: insights from the grey mullet (Mugil cephalus) model

We investigated the molecular regulation of pubertal development in the grey mullet, Mugil cephalus, a relatively late-maturing teleost fish. We have isolated and characterized the cDNAs of key reproductive genes along the brain-pituitary-gonadal (BPG) axis as well as the promoters of genes that modulate the axis at multiple levels. Together with relevant findings from other model species, we propose a conceptual model of the neuroendocrine regulation of puberty in the female grey mullet. Research areas that warrant further investigation are identified in the model.

Isolation of dopamine D(2) receptor (D (2)R) promoters in Mugil cephalus

This paper reports the isolation of two putative D(2)R promoters from grey mullet, one 5'flanking and the other an intronic sequence immediately upstream of the first coding exon. Promoter activity of the intronic sequence was confirmed in vitro through functional analysis using luciferase as reporter gene. The functional characteristics of the region flanking the 5'UTR is currently under investigation.

Growth hormone-induced stimulation of swimming and feeding behaviour of rainbow trout is abolished by the D1 dopamine antagonist SCH23390

The effects of GH on various types of behaviour in fish are well documented although the underlying mechanisms are not fully understood. In rainbow trout, an involvement of the brain dopaminergic system in mediating the behavioural effects of GH has been indicated, as GH can alter the brain dopaminergic activity. To further examine the role of the dopaminergic system in the mediation of GH effects on locomotion and foraging, GH- and sham-implanted juvenile rainbow trout were injected with the selective D1 dopamine antagonist SCH23390 or vehicle. Swimming and feeding activity was then studied by direct observation. Brains were thereafter sampled and analysed for the content of serotonin, dopamine and their metabolites in the hypothalamus, optic tectum, cerebellum, telencephalon, and brain stem. GH increased swimming activity as well as feed intake, effects which were abolished by SCH23390. By itself, the antagonist did not affect behaviour, nor did it affect the brain monoamines. In contrast, treatment with GH, with or without SCH23390, decreased the content of the dopamine metabolite homovanillic acid (HVA) in the optic tectum and the cerebellum, as well as the serotonin content (5-HT) in the optic tectum. It is concluded that the D1 dopamine receptor of the dopaminergic system appears to be of importance in the mediation of the effects of GH on behaviour.

Evolution and expression of D2 and D3 dopamine receptor genes in zebrafish

We mined the zebrafish genomic sequence database and identified contigs containing segments of several dopamine receptor genes. By using a polymerase chain reaction amplification strategy, we generated full-length cDNAs encoding a single dopamine D3 receptor and three distinct D2 receptor subtypes. Zebrafish dopamine receptor genes were mapped by using the T51 radiation hybrid panel. The D3 receptor gene (drd3) mapped to linkage group (LG) 24. The three D2 receptor genes were localized to LG 15 (drd2a), LG 16, (drd2b), and LG 5 (drd2c). With the exception of the drd2b gene, each of these map positions was syntenic with regions of human chromosomes containing orthologs of the zebrafish dopamine receptor genes. Whole-mount in situ hybridization was used to investigate expression of the D2 and D3 receptor genes. Expression of the drd3 gene was first detected at mid-somitogenesis and was particularly prominent in somites. Thereafter, the drd3 gene was expressed diffusely throughout the brain and spinal cord. The three D2 receptor genes were expressed throughout the central nervous system (CNS) in distinct but overlapping patterns. In early embryos, the drd2a gene was expressed exclusively in the epiphysis, whereas the drd2c gene was localized to the notochord. After 24 hpf, the drd2a, drd2b, and drd2c genes were differentially expressed throughout the CNS. The identification of dopamine receptor genes in zebrafish should allow us to use the power of zebrafish genetics to analyze the functional properties of this important class of neurotransmitter receptors.

Comparative analysis of vertebrate dystrophin loci indicate intron gigantism as a common feature

The human DMD gene is the largest known to date, spanning > 2000 kb on the X chromosome. The gene size is mainly accounted for by huge intronic regions. We sequenced 190 kb of Fugu rubripes (pufferfish) genomic DNA corresponding to the complete dystrophin gene (FrDMD) and provide the first report of gene structure and sequence comparison among dystrophin genomic sequences from different vertebrate organisms. Almost all intron positions and phases are conserved between FrDMD and its mammalian counterparts, and the predicted protein product of the Fugu gene displays 55% identity and 71% similarity to human dystrophin. In analogy to the human gene, FrDMD presents several-fold longer than average intronic regions. Analysis of intron sequences of the human and murine genes revealed that they are extremely conserved in size and that a similar fraction of total intron length is represented by repetitive elements; moreover, our data indicate that intron expansion through repeat accumulation in the two orthologs is the result of independent insertional events. The hypothesis that intron length might be functionally relevant to the DMD gene regulation is proposed and substantiated by the finding that dystrophin intron gigantism is common to the three vertebrate genes.

Distribution of dopamine D2 receptor mRNAs in the brain and the pituitary of female rainbow trout: an in situ hybridization study

The distribution of D(2)R (dopamine D(2) receptor) mRNAs was studied in the forebrain of maturing female rainbow trout by means of in situ hybridization using a (35)S-labeled riboprobe (810 bp) spanning the third intracytoplasmic loop. A hybridization signal was consistently obtained in the olfactory epithelium, the internal cell layer of the olfactory bulbs, the ventral and dorsal subdivisions of the ventral telencephalon, and most preoptic subdivisions, with the notable exception of the magnocellular preoptic nucleus, and the periventricular regions of the mediobasal hypothalamus, including the posterior tuberculum. In the pituitary, the signal was higher in the pars intermedia than in the proximal and the rostral pars distalis, but no obvious correspondence with a given cell type could be assigned. Labeled cells were also located in the thalamic region, some pretectal nuclei, the optic tectum, and the torus semicircularis. These results provide a morphologic basis for a better understanding on the functions and evolution of the dopaminergic systems in lower vertebrates.

Fugu: a compact vertebrate reference genome

At 400 Mb, the Japanese pufferfish, Fugu rubripes, has the smallest vertebrate genome but has a similar gene repertoire to other vertebrates. Its genes are densely packed with short intergenic and intronic sequences devoid of repetitive elements. It likely has a mutational bias towards DNA elimination and is probably close to a 'minimal' vertebrate genome. As such it is a useful reference genome for gene discovery and gene validation in other vertebrates. Its usefulness in the discovery of conserved regulatory elements has already been demonstrated. The Fugu genome sequence is a good complement to genetic studies in other vertebrates.

Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning

We have generated and analyzed >50,000 shotgun clones from 1059 Fugu cosmid clones. All sequences have been minimally edited and searched against protein and DNA databases. These data are all displayed on a searchable, publicly available web site at. With an average of 50 reads per cosmid, this is virtually nonredundant sequence skimming, covering 30%-50% of each clone. This essentially random data set covers nearly 25 Mb (>6%) of the Fugu genome and forms the basis of a series of whole genome analyses which address questions regarding gene density and distribution in the Fugu genome and the similarity between Fugu and mammalian genes. The Fugu genome, with eight times less DNA but a similar gene repertoire, is ideally suited to this type of study because most cosmids contain more than one identifiable gene. General features of the genome are also discussed. We have made some estimation of the syntenic relationship between mammals and Fugu and looked at the efficacy of ORF prediction from short, unedited Fugu genomic sequences. Comparative DNA sequence analyses are an essential tool in the functional interpretation of complex vertebrate genomes. This project highlights the utility of using the Fugu genome in this kind of study.

Molecular cloning of EDG-3 and N-Shc genes from the puffer fish, Fugu rubripes, and conservation of synteny with the human genome

EDG-3 is a receptor for sphingosine-1-phosphate mapped on human chromosome 9q22.1-q22.2. We used the compact Fugu genome for its linkage analysis. The Fugu EDG-3 was composed of one intron and two exons, encoding a 384 amino acid protein that has 56.9% homology with the human EDG-3. Approximately 3 kb apart, a neuronal Shc (N-Shc) gene was identified. It spans 7 kb containing 12 coding exons, and has an overall 53.4% similarity with the human protein. We mapped the human N-Shc gene to chromosome 9q21.3-q22.2. This is the first report of the genomic structure and the linkage of these two genes conserved between Fugu and human.

Molecular cloning and tissue distribution of an avian D2 dopamine receptor mRNA from the domestic turkey (Maleagris gallopavo)

The reverse transcriptase-polymerase chain reaction (RT-PCR), in combination with 5' and 3' rapid amplification of cDNA ends (RACE), was used to clone a G protein-coupled receptor from turkey brain mRNA. This cDNA clone has an open reading frame of 1,311 base pairs encoding a 436-residue protein with seven transmembrane-spanning domains and exhibits high homology with previously cloned mammalian D2 dopamine receptors. Northern blot analysis of turkey brain mRNA detected an approximate 2.4-kb transcript. RT-PCR and subsequent nucleotide sequence analysis of turkey brain and peripheral tissue mRNA also demonstrated the presence of an alternatively spliced mRNA corresponding to the predicted D2 short isoform. RT-PCR experiments demonstrated a widespread distribution of alternatively spliced D2 dopamine receptor transcripts throughout the turkey brain and in select peripheral tissues as well. In situ hybridization experiments detected strong autoradiographic signals over much of the turkey telencephalon, diencephalon, mesencephalon, cerebellum, pituitary, and pineal gland. Dopamine has several important functions as a neurotransmitter and hormone in mammals and may have similar actions in avian species. The cloning and tissue distribution of the D2 receptor subtype should enable the investigation of any functional role dopamine and dopamine receptors exert on the physiology and behavior of birds.

Genomic Structure and Comparative Analysis of Nine Fugu Genes: Conservation of Synteny with Human Chromosome Xp22.2–p22.1

The pufferfish Fugu rubripes has a compact 400-Mb genome that is ∼7.5 times smaller than the human genome but contains a similar number of genes. Focusing on the distal short arm of the human X chromosome, we have studied the evolutionary conservation of gene orders in Fugu and man. Sequencing of 68 kb of Fugugenomic DNA identified nine genes in the following order: (SCML2)-STK9, XLRS1, PPEF-1, KELCH2, KELCH1, PHKA2, AP19, and U2AF1-RS2. Apart from an evolutionary inversion separatingAP19 and U2AF1-RS2 from PHKA2, gene orders are identical in Fugu and man, and all nine human homologs map to the Xp22 band. All Fugu genes were found to be smaller than their human counterparts, but gene structures were mostly identical. These data suggest that genomic sequencing in Fugu is a powerful and economical strategy to predict gene orders in the human genome and to elucidate the structure of human genes.

[Sequence data for this article were deposited with the EMBL/GenBank data libraries under accession nos. AJ011381 and AF094327.]

The aryl hydrocarbon receptor: a comparative perspective

The aryl hydrocarbon receptor (Ah receptor or AHR) is a ligand-activated transcription factor involved in the regulation of several genes, including those for xenobiotic-metabolizing enzymes such as cytochrome P450 1A and 1B forms. Ligands for the AHR include a variety of aromatic hydrocarbons, including the chlorinated dioxins and related halogenated aromatic hydrocarbons whose toxicity occurs through activation of the AHR. The AHR and its dimerization partner ARNT are members of the emerging bHLH-PAS family of transcriptional regulatory proteins. In this review, our current understanding of the AHR signal transduction pathway in non-mammalian and other non-traditional species is summarized, with an emphasis on similarities and differences in comparison to the AHR pathway in rodents and humans. Evidence and prospects for the presence of a functional AHR in early vertebrates and invertebrates are also examined. An overview of the bHLH-PAS family is presented in relation to the diversity of bHLH-PAS proteins and the functional and evolutionary relationships of the AHR and ARNT to the other members of this family. Finally, some of the most promising directions for future research on the comparative biochemistry and molecular biology of the AHR and ARNT are discussed.

Isolation and genomic characterization of the TUPLE1/HIRA gene of the pufferfish Fugu rubripes

In an effort to obtain a small genomic construct for the generation of a HIRA transgenic mouse, we have isolated and sequenced the Fugu TUPLE1/HIRA gene. We have compared the gene organization and the proteins encoded in pufferfish and human and also searched for conserved DNA sequences that might be important in gene regulation. The pufferfish gene spans approx. 9 kb, which is approx. 11 times smaller than the human gene, owing to the reduced size of the introns. Like its human counterpart, it is organized into 25 exons. The majority of the splice sites are in identical positions to those found in the human gene, however, for three internal exons the positions of the splice sites are not directly comparable. The coding regions are almost identical in size and show a high degree of similarity, especially at the amino and carboxy termini. Comparisons of 5' and 3' sequences failed to detect similarities or sequences involved in regulation.

The pufferfish SLP-1 gene, a new member of the SCL/TAL-1 family of transcription factors

The SCL/TAL-1 gene encodes a basic helix-loop-helix (bHLH) transcription factor essential for the development of all hemopoietic lineages and also acts as a T-cell oncogene. Four related genes have been described in mammals (LYL-1, TAL-2, NSCL1, and NSCL2), all of which exhibit a high degree of sequence similarity to SCL/TAL-1 in the bHLH domain and two of which (LYL-1 and TAL-2) have also been implicated in the pathogenesis of T-cell acute lymphoblastic leukemia. In this study we describe the identification and characterization of a pufferfish gene termed SLP-1, which represents a new member of this gene family. The genomic structure and sequence of SLP-1 suggests that it forms a subfamily with SCL/TAL-1 and LYL-1 and is most closely related to SCL/TAL-1. However, unlike SCL/TAL-1, SLP-1 is widely expressed. Sequence analysis of a whole cosmid containing SLP-1 shows that SLP-1 is flanked upstream by a zinc finger gene and a fork-head-domain gene and downstream by a heme-oxygenase and a RING finger gene.

Neurobiology of retinal dopamine in relation to degenerative states of the tissue

Neurobiology of retinal dopamine is reviewed and discussed in relation to degenerative states of the tissue. The Introduction deals with the basic physiological actions of dopamine on the different neurons in vertebrate retinae with an emphasis upon mammals. The intimate relationship between the dopamine and melatonin systems is also covered. Recent advances in the molecular biology of dopamine receptors is reviewed in some detail. As degenerative states of the retina, three examples are highlighted: Parkinson's disease; ageing; and retinal dystrophy (retinitis pigmentosa). As visual functions controlled, at least in part, by dopamine, absolute sensitivity, spatial contrast sensitivity, temporal (including flicker) sensitivity and colour vision are reviewed. Possible cellular and synaptic bases of the visual dysfunctions observed during retinal degenerations are discussed in relation to dopaminergic control. It is concluded that impairment of the dopamine system during retinal degenerations could give rise to many of the visual abnormalities observed. In particular, the involvement of dopamine in controlling the coupling of horizontal and amacrine cell lateral systems appears to be central to the visual defects seen.

Aberrant processing of the Fugu HD (FrHD) mRNA in mouse cells and in transgenic mice

The puffer fish ( Fugu rubripes ) has a compact genome of 400 Mbp which is approximately 7.5-fold smaller than the human genome. It contains a similar number of genes but is deficient in intergenic, intronic and dispersed repetitive sequences. Fugu is becoming established as the model vertebrate genome for the identification and characterisation of novel human genes and conserved regulatory sequences. It has also been proposed that Fugu genes may provide natural mini-genes for the production of transgenic mice. We have used the Fugu homologue of the Huntington's disease (HD) gene to test this possibility. The human and Fugu HD genes cover 170 kb and 23 kb respectively and have previously been sequenced in their entirety. In Fugu tissue, the Fugu HD gene was found to be expressed as predicted from the gene sequence but three differentially spliced forms were also detected. Despite the absence of conserved promoter sequences, the Fugu promoter was found to be functional in mouse cells. We have generated mice transgenic for the Fugu HD gene and conducted a detailed expression analysis across the entire 10 kb transcript. This revealed the presence of many aberrant splice forms which would be incompatible with the production of the Fugu huntingtin protein. The Fugu HD gene is incorrectly processed in mouse cells both in vitro and in vivo which sheds doubt on the usefulness of Fugu genes for transgenesis.

Towards a reconciliation of the introns early or late views: triosephosphate isomerase genes from insects

The gene encoding the glycolytic enzyme, triosephosphate isomerase (TPI; EC 5.3.1.1), is a favourite model for molecular evolutionists who either subscribe to the theory that introns co-evolved with the ancestral gene, the introns early view, or alternatively, that introns are more recent immigrants. The discovery of an intron in the TPI gene of Culex mosquitoes at a site which was predicted by proponents of the intron early school supported that theory. More recently, the discovery of additional intron sites in several eukaryotes was presented as evidence supporting the introns late school. We have found the 'Culex intron' in two closely related mosquitoes, but not in two more evolutionary primitive Dipterans, suggesting that, if it is an 'ancient intron', loss may be more frequent than that supposed by the intron late school. In addition, we have found that three introns punctuating the TPI gene from the Lepidopteran, Heliothis, appear to be ancestrally related and may be the result of transposable element insertion, 50-90 million years ago. It is argued that both opposing schools in the intron debate be reconciled -- some introns may have been early and certainly others have arrived subsequent to the appearance of the TPI gene.

Molecular cloning of 5-hydroxytryptamine (5-HT) type 1 receptor genes from the Japanese puffer fish, Fugu rubripes

To characterize the structure of Fugu G-protein coupled receptor family and its evolutionary divergence, we have cloned and sequenced the Fugu 5-HT type 1 receptor genes by Polymerase Chain Reaction (PCR) with degenerate primers followed by phage library screening. The analysis of the deduced amino acid sequences showed that F1A alpha and F1A beta have the highest homology to the human 5-HT1A receptor (71.5% and 63.7%, respectively). Another clone, F1D, showed highest (70.5%) homology to the human type 1D receptor. The amino acid residues that are important for ligand binding have been conserved in these Fugu genes. The phylogenetic tree analysis suggests that the duplication event of the Fugu type 1A receptor may have occurred after the divergence of Fugu and the tetrapod lineage.

Early emergence of three dopamine D1 receptor subtypes in vertebrates. Molecular phylogenetic, pharmacological, and functional criteria defining D1A, D1B, and D1C receptors in European eel Anguilla anguilla

The existence of dopamine D1C and D1D receptors in Xenopus and chicken, respectively, challenged the established duality (D1A and D1B) of the dopamine D1 receptor class in vertebrates. To ascertain the molecular diversity of this gene family in early diverging vertebrates, we isolated four receptor-encoding sequences from the European eel Anguilla anguilla. Molecular phylogeny assigned two receptor sequences (D1A1 and D1A2) to the D1A subtype, and a third receptor to the D1B subtype. Additional sequence was orthologous to the Xenopus D1C receptor and to several other previously unclassified fish D1-like receptors. When expressed in COS-7 cells, eel D1A and D1B receptors display affinity profiles for dopaminergic ligands similar to those of other known vertebrate homologues. The D1C receptor exhibits pharmacological characteristics virtually identical to its Xenopus homologue. Functionally, while all eel D1 receptors stimulate adenylate cyclase, the eel D1B receptor exhibits greater constitutive activity than either D1A or D1C receptors. Semiquantitative reverse transcription-polymerase chain reaction reveals the differential distribution of D1A1, D1A2, D1B, and D1C receptor mRNA within the hypothalamic-pituitary axis of the eel brain. Taken together, these data suggest that the D1A, D1B, and D1C receptors arose prior to the evolutionary divergence of fish and tetrapods and exhibit molecular, pharmacological, and functional attributes that unambiguously allow for their classification as distinct D1 receptor subtypes in the vertebrate phylum.

G protein alpha subunit multigene family in the Japanese puffer fish Fugu rubripes: PCR from a compact vertebrate genome

We compare the complexity and organization of the G protein alpha subunit multigene family in the vertebrate genomes of mammals and the Japanese puffer fish Fugu rubripes. Fourteen Fugu G alpha genes were identified of the 16 genes characterized previously in mammals, including Fugu genes from the four classes of alpha subunits Gs, Gi, Gq, and G12. Fugu and mammalian G alpha coding sequences are highly homologous, and the intron/exon structure of the fish and mammalian orthologs is identical throughout the coding regions. A novel G alpha gene, G alpha p1, was also identified in Fugu rubripes and two other species of puffer fish. The complete sequence of Gnaz and the tandemly duplicated genes Gnai2 and Gnat1 were obtained from a Fugu genomic cosmid library. Introns in the puffer fish G alpha genes lacked repeat DNA sequences, other than simple sequence length repeats, and most introns were significantly shorter in Fugu than in mammalian orthologs. The compact genome of puffer fish provides a unique vertebrate model for characterizing multigene families and identifying novel genes directly from genomic DNA by PCR amplification with degenerate primers. The fact that Fugu encodes most, if not all, of the G protein alpha subunits identified in mammals strongly supports Fugu as a model organism for vertebrate genome research.

Fugu intron oversize reveals the presence of U15 snoRNA coding sequences in some introns of the ribosomal protein S3 gene

We present here the analysis of the genomic organization of the Fugu gene coding for ribosomal protein S3 and its intron encoded U15 RNA, and compare it with the homologous human and Xenopus genes. Only two of the six Fugu S3 gene introns do not contain the U15 sequence and are in fact shorter than 100 nucleotides, as most Fugu introns. The other four introns are somewhat longer and contain sequences homologous to U15 RNA; two of these represent functional copies, as shown by microinjections of Fugu transcripts into Xenopus oocytes, whereas the other two appear to be nonfunctional pseudocopies. Thus Fugu turns out to be ideal for the study of intron encoded snoRNAs, partly because of the reduced cloning and sequencing workload, and partly because the intron length per se can be an indication of the presence of a snoRNA coding sequence.

Quality not quantity: the pufferfish genome

The genome of the pufferfish, Fugu rubripes (Fugu) is compact. With a similar gene complement to mammals and a genome size of just 400 Mb, gene density is high averaging one every 6-7 kb. Initial characterization of this genome has shown that although genes are much smaller and more densely spaced, their intron/exon structure is conserved with the resulting introns being small. There is little repetitive DNA in the genome and this greatly facilitates comparative genomic studies. The coding content of genes is highly conserved as are critical regulatory elements of some genes. Other DNA is not, however, and this allows the identification of homologous coding sequence between Fugu and mammalian genes. Although the genome of Fugu is 7.5 times smaller than the human genome, not all genes are reduced proportionately. Some regions of the genome show conserved synteny with mammalian genomes, although at the present time only short physical distances have been examined. The structure of the genome is also being studied. Initial data suggest that this may be different to that found in mammals. It is not clear that the same kind of isochore structure is present in this early vertebrate genome. Patterns of methylation may be different resulting in a different distribution of CpG islands. An attempt is being made to centralize both resources and data from the genome of Fugu so that everything may be integrated into a single, publicly accessible database which in turn, may be integrated with databases from other organisms.

A functional role for some Fugu introns larger than the typical short ones: the example of the gene coding for ribosomal protein S7 and snoRNA U17

The compact genome of Fugu rubripes, with its very small introns, appears to be particularly suitable to study intron-encoded functions. We have analyzed the Fugu gene for ribosomal protein S7 (formerly S8, see Note), whose Xenopus homolog contains in its introns the coding sequences for the small nucleolar RNA U17. Except for intron length, the organization of the Fugu S7 gene is very similar to that of the Xenopus counterpart. The total length of the Fugu S7 gene is 3930 bp, compared with 12691 bp for Xenopus. This length difference is uniquely due to smaller introns. Although short, the six introns are longer than the approximately 100 bp size of most Fugu introns, as they host U17 RNA coding sequences. While four of the six U17 sequences are 'canonical', the remaining two represent diverged U17 pseudocopies. In fact, microinjection in Xenopus oocytes of in vitro synthesized Fugu transcripts containing the 'canonical' U17f sequence results in efficient production of mature U17 RNA, while injection of a transcript containing the U17 psi b sequence does not.

Small is beautiful: comparative genomics with the pufferfish (Fugu rubripes)

As the Human Genome Project advances, it is clear that the emphasis will switch from accumulation of data to their interpretation. Comparative genomics provides a powerful way in which to analyse sequence data. Indeed, there is already a long list of 'model' organisms, which allow comparative analyses in a variety of ways. The very small vertebrate genome of the pufferfish provides a simple and economical way of comparing sequence data from mammals and fish, representing a large evolutionary divergence and so permitting the identification of essential elements that are still present in both species. These elements include genes and the associated machinery that controls their expression; elements that, in many cases, have survived the test of time.

Cloning and sequencing of the chaperonin-encoding Cctd gene from Fugu rubripes rubripes

CCT, a chaperonin containing t-complex polypeptide 1 (TCP-1), is a cytosolic molecular chaperone involved in the folding of proteins. We have isolated the Cctd gene from a Fugu rubripes rubripes (Frr) genomic library using a rat Ccta cDNA as a probe, and cloned its cDNA by reverse transcription-polymerase chain reaction (RT-PCR) using a pair of oligodeoxyribonucleotides corresponding to the 5' and 3' non-coding regions of Frr Cctd. Cctd spans a region of 4.7 kb and consists of at least 13 exons with small introns of about 144 bp on average. The Cctd cDNA sequence revealed a deduced polypeptide of 536 amino acids sharing a high degree of homology with that of the mouse Cctd cDNA (88%). Cctd is present as a single-copy gene, as shown by genomic Southern blot analysis, and can be used for evolutionary and classification analyses of Fugu species.

Mutation of a new sodium channel gene, Scn8a, in the mouse mutant 'motor endplate disease'

The mouse neurological mutant 'motor endplate disease' (med) is characterized by early onset progressive paralysis of the hind limbs, severe muscle atrophy, degeneration of Purkinje cells and juvenile lethality. We have isolated a voltage-gated sodium channel gene, Scn8a, from the flanking region of a transgene-induced allele of med. Scn8a is expressed in brain and spinal cord but not in skeletal muscle or heart, and encodes a predicted protein of 1,732 amino acids. An intragenic deletion at the transgene insertion site results in loss of expression. Scn8a is closely related to other sodium channel alpha subunits, with greatest similarity to a brain transcript from the pufferfish Fugu rubripes. The human homologue, SCN8A, maps to chromosome 12q13 and is a candidate gene for inherited neurodegenerative disease.