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Cloning and Comparative Analyses of the Zebrafish Ugt Repertoire Reveal Its Evolutionary Diversity  [PDF]
Haiyan Huang,Qiang Wu
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0009144
Abstract: UDP-glucuronosyltransferases (Ugts) are a supergene family of phase II drug-metabolizing enzymes that catalyze the conjugation of numerous hydrophobic small molecules with the UDP-glucuronic acid, converting them into hydrophilic molecules. Here, we report the identification and cloning of the complete zebrafish Ugt gene repertoire. We found that the zebrafish genome contains 45 Ugt genes that can be divided into three families: Ugt1, Ugt2, and Ugt5. Both Ugt1 and Ugt2 have two unlinked clusters: a and b. The Ugt1a, Ugt1b, Ugt2a, and Ugt2b clusters each contain variable and constant regions, similar to that of the protocadherin (Pcdh), immunoglobulin (Ig), and T-cell receptor (Tcr) clusters. Cloning the full-length coding sequences confirmed that each of the variable exons is separately spliced to the set of constant exons within each zebrafish Ugt cluster. Comparative analyses showed that both a and b clusters of the zebrafish Ugt1 and Ugt2 genes have orthologs in other teleosts, suggesting that they may be resulted from the “fish-specific” whole-genome duplication event. The Ugt5 genes are a novel family of Ugt genes that exist in teleosts and amphibians. Their entire open reading frames are encoded by single large exons. The zebrafish Ugt1, Ugt2, and Ugt5 genes can generate additional transcript diversity through alternative splicing. Based on phylogenetic analyses, we propose that the ancestral tetrapod and teleost Ugt1 clusters contained multiple Ugt1 paralogs. After speciation, these ancestral Ugt1 clusters underwent lineage-specific gene loss and duplication. The ancestral vertebrate Ugt2 cluster also underwent lineage-specific duplication. The intronless Ugt5 open reading frames may be derived from retrotransposition followed by gene duplication. They have been expanded dramatically in teleosts and have become the most abundant Ugt family in these lineages. These findings have interesting implications regarding the molecular evolution of genes with diversified variable exons in vertebrates.
The evolution of farnesoid X, vitamin D, and pregnane X receptors: insights from the green-spotted pufferfish (Tetraodon nigriviridis) and other non-mammalian species
Matthew D Krasowski, Ni Ai, Lee R Hagey, Erin M Kollitz, Seth W Kullman, Erica J Reschly, Sean Ekins
BMC Biochemistry , 2011, DOI: 10.1186/1471-2091-12-5
Abstract: Tetraodon FXR has a ligand selectivity profile very similar to human FXR, with strong activation by the synthetic ligand GW4064 and by the primary bile acid chenodeoxycholic acid. Homology modelling and docking studies suggest a ligand-binding pocket architecture more similar to human and rat FXRs than to lamprey or zebrafish FXRs. Tetraodon PXR was activated by a variety of bile acids and steroids, although not by the larger synthetic ligands that activate human PXR such as rifampicin. Homology modelling predicts a larger ligand-binding cavity than zebrafish PXR. We also demonstrate that VDRs from the pufferfish and Japanese medaka were activated by small secondary bile acids such as lithocholic acid, whereas the African clawed frog VDR was not.Our studies provide further evidence of the relationship between both FXR, PXR, and VDR ligand selectivity and cross-species variation in bile salt profiles. Zebrafish and green-spotted pufferfish provide a clear contrast in having markedly different primary bile salt profiles (planar bile alcohols for zebrafish and sterically bent bile acids for the pufferfish) and receptor selectivity that matches these differences in endogenous ligands. Our observations to date present an integrated picture of the co-evolution of bile salt structure and changes in the binding pockets of three nuclear hormone receptors across the species studied.Nuclear hormone receptors (NHRs) are transcription factors that work in concert with co-activators and co-repressors to regulate gene expression [1,2]. Most of the NHRs in vertebrates are ligand-activated, although some NHRs function in a ligand-independent manner. Examples of ligands for NHRs include a range of endogenous compounds such as bile acids, retinoids, steroid hormones, thyroid hormone, and vitamin D. A few NHRs, such as the pair of xenobiotic sensors, pregnane X receptor (PXR; NR1I2; also known as steroid and xenobiotic receptor or SXR) and constitutive androstane receptor (CAR; NR1I3),
Power to the pufferfish  [cached]
Jonathan B Weitzman
Genome Biology , 2002, DOI: 10.1186/gb-spotlight-20020726-01
Abstract: The Consortium chose a whole-genome shotgun sequencing approach that involved assembling over 3.7 million sequencing reads into large scaffolds covering more than 80% of the 365-megabase genome. Using homology-searching programs, the authors found 31,059 predicted gene loci, similar to the number of certified human genes. Gene loci represent about one third of the genome, with clear variation in gene density. Comparative genome analysis allowed the Consortium to identify almost one thousand novel putative gene loci in the human genome.Repetitive sequences account for 2.7% of the Fugu genome, an order of magnitude less than in mammals. But there are at least 40 different families of transposable elements, many more than in the human genome. The authors suggest that the pufferfish genome has experienced rapid deletion of non-functional sequences. The compactness of the genome is also reflected in the small size of introns, three-quarters of which are less than 425 nucleotides long. Careful analysis revealed the existence of several "giant genes" with extended introns that are spread over very large distances, significantly greater than their human homologs. The Consortium found little evidence for large tandem duplications, but did find fish-specific segmental duplications of certain loci.The similarities and the differences between the Fugu and human genomes are enlightening. Around a quarter of human proteins have no homology match within the Fugu genome. These include genes encoding inflammatory cytokines and immune system components. The Fugu genome has an excess of potassium channel subunits and kinases, whereas the human genome contains more zinc-finger proteins and novel receptor families.The Consortium estimates the cost of sequencing the pufferfish genome at around $12 million, two orders of magnitude less than for the human genome. This cost-effective project has generated a key resource for comparing vertebrate genomes, and for gaining insights into the evo
The zebrafish genome encodes the largest vertebrate repertoire of functional aquaporins with dual paralogy and substrate specificities similar to mammals
Angèle Tingaud-Sequeira, Magdalena Calusinska, Roderick N Finn, Fran?ois Chauvigné, Juanjo Lozano, Joan Cerdà
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-38
Abstract: The screening and isolation of transcripts from the zebrafish (Danio rerio) genome revealed eighteen sequences structurally related to the four subfamilies of tetrapod aquaporins, i.e., aquaporins (AQP0, -1 and -4), water and glycerol transporters or aquaglyceroporins (Glps; AQP3 and AQP7-10), a water and urea transporter (AQP8), and two unorthodox aquaporins (AQP11 and -12). Phylogenetic analyses of nucleotide and deduced amino acid sequences demonstrated dual paralogy between teleost and human aquaporins. Three of the duplicated zebrafish isoforms have unlinked loci, two have linked loci, while DrAqp8 was found in triplicate across two chromosomes. Genomic sequencing, structural analysis, and maximum likelihood reconstruction, further revealed the presence of a putative pseudogene that displays hybrid exons similar to tetrapod AQP5 and -1. Ectopic expression of the cloned transcripts in Xenopus laevis oocytes demonstrated that zebrafish aquaporins and Glps transport water or water, glycerol and urea, respectively, whereas DrAqp11b and -12 were not functional in oocytes. Contrary to humans and some rodents, intrachromosomal duplicates of zebrafish AQP8 were water and urea permeable, while the genomic duplicate only transported water. All aquaporin transcripts were expressed in adult tissues and found to have divergent expression patterns. In some tissues, however, redundant expression of transcripts encoding two duplicated paralogs seems to occur.The zebrafish genome encodes the largest repertoire of functional vertebrate aquaporins with dual paralogy to human isoforms. Our data reveal an early and specific diversification of these integral membrane proteins at the root of the crown-clade of Teleostei. Despite the increase in gene copy number, zebrafish aquaporins mostly retain the substrate specificity characteristic of the tetrapod counterparts. Based upon the integration of phylogenetic, genomic and functional data we propose a new classification for the piscine
The repertoire of olfactory C family G protein-coupled receptors in zebrafish: candidate chemosensory receptors for amino acids
Tyler S Alioto, John Ngai
BMC Genomics , 2006, DOI: 10.1186/1471-2164-7-309
Abstract: Using genome database mining and other informatics approaches, we identified and characterized the repertoire of 54 intact "V2R-like" olfactory C family GPCRs in the zebrafish. Phylogenetic analysis – which also included a set of 34 C family GPCRs from fugu – places the fish olfactory receptors in three major groups, which are related to but clearly distinct from other C family GPCRs, including the calcium sensing receptor, metabotropic glutamate receptors, GABA-B receptor, T1R taste receptors, and the major group of V2R vomeronasal receptor families. Interestingly, an analysis of sequence conservation and selective pressure in the zebrafish receptors revealed the retention of a conserved sequence motif previously shown to be required for ligand binding in other amino acid receptors.Based on our findings, we propose that the repertoire of zebrafish olfactory C family GPCRs has evolved to allow the detection and discrimination of a spectrum of amino acid and/or amino acid-based compounds, which are potent olfactory cues in fish. Furthermore, as the major groups of fish receptors and mammalian V2R receptors appear to have diverged significantly from a common ancestral gene(s), these receptors likely mediate chemosensation of different classes of chemical structures by their respective organisms.The vertebrate olfactory system receives and decodes sensory information from a myriad chemical cues. The first step in this process is the recognition of these cues by receptors expressed by the primary sensory neurons in the olfactory epithelium (reviewed in refs. [1,2]). Receptor-mediated activity within the population of olfactory sensory neurons is then interpreted by the brain to identify the molecular nature of the odorant stimulus. A large multigene family thought to encode odorant receptors was initially identified in the rat [3] and belong to what is now referred to as the "OR" superfamily of odorant receptors (reviewed in [4]). The predicted structure of these recept
Study of Sylvilagus rabbit TRIM5α species-specific domain: how ancient endoviruses could have shaped the antiviral repertoire in Lagomorpha
Ana Lemos de Matos, Wessel van der Loo, Helena Areal, Dennis K Lanning, Pedro J Esteves
BMC Evolutionary Biology , 2011, DOI: 10.1186/1471-2148-11-294
Abstract: The deduced protein sequence of Iberian hare TRIM5α was 89% identical to European rabbit TRIM5α, although high divergence was observed at the PRYSPRY v1 region between rabbit and the identified alleles from this hare species (allele 1: 50% divergence; allele 2: 53% divergence). A high identity was expected between the Sylvilagus and Oryctolagus TRIM5α proteins and, in fact, the Sylvilagus TRIM5α was 91% identical to the Oryctolagus protein. Nevertheless, the PRYSPRY v1 region was only 50% similar between these genera. Selection analysis of Lagomorpha TRIM5α proteins identified 25 positively-selected codons, 11 of which are located in the PRYSPRY v1 region, responsible for species specific differences in viral capsid recognition.By extending Lagomorpha TRIM5α studies to an additional genus known to bear RELIK, we verified that the divergent species-specific pattern observed between the Oryctolagus and Lepus PRYSPRY-domains is also present in Sylvilagus TRIM5α. This work is one of the first known studies that compare the evolution of the antiretroviral restriction factor TRIM5α in different mammalian groups, Lagomorpha and Primates.Retroviruses are RNA viruses that, when infecting a host cell, produce a viral reverse transcriptase and a viral integrase that make a DNA copy of the viral genome and integrate it into the host genome, respectively [1]. The family Retroviridae comprises a diverse range of animal viruses, including the viral genus Lentivirus. Lentiviruses have been isolated from primates, domestic and wild felids, and a variety of domestic ungulates (goat, sheep, cattle and horse) [2]. Until recently, all known lentiviruses were classified as exogenous (transmitted horizontally from host to host) [3]. However, in 2007, Katzourakis and colleagues [4] reported the first endogenous lentivirus identified in any species, the rabbit endogenous lentivirus type K (RELIK), present in the genome of the European rabbit (Oryctolagus cuniculus). RELIK has subsequently b
The Early ANTP Gene Repertoire: Insights from the Placozoan Genome  [PDF]
Bernd Schierwater, Kai Kamm, Mansi Srivastava, Daniel Rokhsar, Rafael D. Rosengarten, Stephen L. Dellaporta
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002457
Abstract: The evolution of ANTP genes in the Metazoa has been the subject of conflicting hypotheses derived from full or partial gene sequences and genomic organization in higher animals. Whole genome sequences have recently filled in some crucial gaps for the basal metazoan phyla Cnidaria and Porifera. Here we analyze the complete genome of Trichoplax adhaerens, representing the basal metazoan phylum Placozoa, for its set of ANTP class genes. The Trichoplax genome encodes representatives of Hox/ParaHox-like, NKL, and extended Hox genes. This repertoire possibly mirrors the condition of a hypothetical cnidarian-bilaterian ancestor. The evolution of the cnidarian and bilaterian ANTP gene repertoires can be deduced by a limited number of cis-duplications of NKL and “extended Hox” genes and the presence of a single ancestral “ProtoHox” gene.
A Fish-Specific Transposable Element Shapes the Repertoire of p53 Target Genes in Zebrafish  [PDF]
Lucia Micale, Maria Nicla Loviglio, Marta Manzoni, Carmela Fusco, Bartolomeo Augello, Eugenia Migliavacca, Grazia Cotugno, Eugenio Monti, Giuseppe Borsani, Alexandre Reymond, Giuseppe Merla
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0046642
Abstract: Transposable elements, as major components of most eukaryotic organisms' genomes, define their structural organization and plasticity. They supply host genomes with functional elements, for example, binding sites of the pleiotropic master transcription factor p53 were identified in LINE1, Alu and LTR repeats in the human genome. Similarly, in this report we reveal the role of zebrafish (Danio rerio) EnSpmN6_DR non-autonomous DNA transposon in shaping the repertoire of the p53 target genes. The multiple copies of EnSpmN6_DR and their embedded p53 responsive elements drive in several instances p53-dependent transcriptional modulation of the adjacent gene, whose human orthologs were frequently previously annotated as p53 targets. These transposons define predominantly a set of target genes whose human orthologs contribute to neuronal morphogenesis, axonogenesis, synaptic transmission and the regulation of programmed cell death. Consistent with these biological functions the orthologs of the EnSpmN6_DR-colonized loci are enriched for genes expressed in the amygdala, the hippocampus and the brain cortex. Our data pinpoint a remarkable example of convergent evolution: the exaptation of lineage-specific transposons to shape p53-regulated neuronal morphogenesis-related pathways in both a hominid and a teleost fish.
Myelopoiesis and Myeloid Leukaemogenesis in the Zebrafish  [PDF]
A. Michael Forrester,Jason N. Berman,Elspeth M. Payne
Advances in Hematology , 2012, DOI: 10.1155/2012/358518
Abstract: Over the past ten years, studies using the zebrafish model have contributed to our understanding of vertebrate haematopoiesis, myelopoiesis, and myeloid leukaemogenesis. Novel insights into the conservation of haematopoietic lineages and improvements in our capacity to identify, isolate, and culture such haematopoietic cells continue to enhance our ability to use this simple organism to address disease biology. Coupled with the strengths of the zebrafish embryo to dissect developmental myelopoiesis and the continually expanding repertoire of models of myeloid malignancies, this versatile organism has established its niche as a valuable tool to address key questions in the field of myelopoiesis and myeloid leukaemogenesis. In this paper, we address the recent advances and future directions in the field of myelopoiesis and leukaemogenesis using the zebrafish system. 1. Introduction The zebrafish is emerging as a powerful model system in which to study haematopoiesis and leukaemogenesis. In addition to the benefits afforded by scale and simplicity of this versatile genetic model system for studying developmental aspects of haematopoiesis, the last decade has seen an explosion of molecular methods and models to facilitate studies informing on haematopoietic disease biology, particularly leukaemogenesis and cancer. At its inception as a cancer model, proliferation and angiogenesis were proposed as phenotypic attributes as readouts relevant to cancer pathogenesis [1]. However, it was the generation of a transgenic zebrafish expressing the C-myc oncogene under the control of the rag2 promoter that went on to develop T-cell acute lymphoblastic leukaemia (ALL), which really revolutionized the view of the scientific world on this small organism as a cancer disease model [2]. In the ensuing 10 years, many models of oncogene induced cancer have been generated in zebrafish along with mutagenesis strategies to identify novel tumour suppressor genes or chromosome instability loci [3–5]. The utility of such models to answer key biological questions continues to grow. In this paper, we focus on developments in the field of myelopoiesis in the zebrafish, cancer models affecting the myeloid lineages, and how these have instructed our knowledge on the biology of these diseases. 2. Zebrafish Myeloid Development Zebrafish haematopoiesis occurs in two waves in the developing embryo, termed primitive and definitive [6]. In contrast to human and murine haematopoiesis (where primitive haematopoiesis initiates with the development of primitive erythroid cells in the blood islands
Evolution and origin of vomeronasal-type odorant receptor gene repertoire in fishes
Yasuyuki Hashiguchi, Mutsumi Nishida
BMC Evolutionary Biology , 2006, DOI: 10.1186/1471-2148-6-76
Abstract: To understand the evolutionary dynamics of V2R genes in fishes, V2R sequences in zebrafish, medaka, fugu, and spotted green pufferfish were identified from their draft genome sequences. There were remarkable differences in the number of intact V2R genes in different species. Most V2R genes in these fishes were tightly clustered in one or two specific chromosomal regions. Phylogenetic analysis revealed that the fish V2R family could be subdivided into 16 subfamilies that had diverged before the separation of the four fishes. Genes in two subfamilies in zebrafish and another subfamily in medaka increased in their number independently, suggesting species-specific evolution in olfaction. Interestingly, the arrangements of V2R genes in the gene clusters were highly conserved among species in the subfamily level. A genomic region of tetrapods corresponding to the region in fishes that contains the V2R cluster was found to have no V2R gene in any species.Our results have indicated that the evolutionary dynamics of fish V2Rs are characterized by rapid gene turnover and lineage-specific phylogenetic clustering. In addition, the present phylogenetic and comparative genome analyses have shown that the fish V2Rs have expanded after the divergence between teleost and tetrapod lineages. The present identification of the entire V2R repertoire in fishes would provide useful foundation to the future functional and evolutionary studies of fish V2R gene family.Olfaction is a sense for recognizing environmental chemicals. In many animals, olfaction plays crucial roles in various activities, such as foraging, migration, and mating. In vertebrates, odor chemicals are perceived by three evolutionary distinct groups of seven-transmembrane G protein-coupled receptors (GPCRs). Genes encoding the main odorant receptors (ORs) form the largest multigene family in vertebrates. For example, over 1,000 distinct OR copies have been identified in the mouse genome [1,2]. In addition to ORs, vertebrat
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