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Diversity and evolution of MHII β genes in a non-model percid species—The Eurasian perch (Perca fluviatilis L.). Mol Immunol 2009; 46:3399-410. [DOI: 10.1016/j.molimm.2009.07.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 07/14/2009] [Accepted: 07/16/2009] [Indexed: 11/20/2022]
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52
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Cloning and transcription of nuclear receptors and other toxicologically relevant genes, and exposure biomarkers in European hake (Merluccius merluccius) after the Prestige oil spill. Mar Genomics 2009; 2:201-13. [DOI: 10.1016/j.margen.2009.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 10/09/2009] [Accepted: 10/15/2009] [Indexed: 11/21/2022]
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53
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Kassahn KS, Dang VT, Wilkins SJ, Perkins AC, Ragan MA. Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates. Genome Res 2009; 19:1404-18. [PMID: 19439512 DOI: 10.1101/gr.086827.108] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The significance of whole-genome duplications (WGD) for vertebrate evolution remains controversial, in part because the mechanisms by which WGD contributed to functional evolution or speciation are still incompletely characterized. Fish genomes provide an ideal context in which to examine the consequences of WGD, because the teleost lineage experienced an additional WGD soon after divergence from tetrapods and because five teleost genomes are available for comparative analysis. Here we present an integrated approach to characterize these post-duplication genomes based on genome-scale synteny, phylogenetic, temporal, and spatial gene expression and on protein sequence data. A minimum of 3%-4% of protein-coding loci have been retained in two copies in each of the five fish genomes, and many of these duplicates are key developmental genes that function as transcription factors or signaling molecules. Almost all duplicate gene pairs we examined have diverged in spatial and/or temporal expression during embryogenesis. A quarter of duplicate pairs have diverged in function via the acquisition of novel protein domains or via changes in the subcellular localization of their encoded proteins. We compared the spatial expression and protein domain architecture of zebrafish WGD-duplicates to those of their single mouse ortholog and found many examples supporting a model of neofunctionalization. WGD-duplicates have acquired novel protein domains more often than have single-copy genes. Post-WGD changes at the gene regulatory level were more common than changes at the protein level. We conclude that the most significant consequence of WGD for vertebrate evolution has been to enable more-specialized regulatory control of development via the acquisition of novel spatiotemporal expression domains. We find limited evidence that reciprocal gene loss led to reproductive isolation and speciation in this lineage.
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Affiliation(s)
- Karin S Kassahn
- The University of Queensland, Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, QLD, Australia
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54
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Helvik JV, Rødahl E, Drivenes Ø, Haarr L. Identification and characterization of two zebrafish nectin-1 genes that are differentially expressed in the developing eye and brain. Dev Dyn 2009; 238:43-55. [PMID: 19097185 DOI: 10.1002/dvdy.21813] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Nectins are cell adhesion molecules of the immunoglobulin type that play important roles in the development of the nervous system. We have characterized two paralogous zebrafish nectin-1 genes, nectin-1a and nectin-1b, that differ in expression. Nectin-1a expression is first found in the anterior neural keel and later in the optic cup. In the retina, nectin-1a appears in the outer part and extends inwards, while nectin-1b starts in the inner part and spreads outwards. Only nectin-1a was detected in the cornea, the lens, and in the region of photoreceptor cell differentiation in the retina. Both genes were expressed in ganglion cells and inner nuclear neurons. In the brain, nectin-1a was restricted to the epiphysis and a cluster of cells in the posterior hindbrain, whereas nectin-1b was found in several brain areas. Zebrafish may, therefore, be a useful model for identifying different functions of nectin-1 in the developing eye and nervous system.
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Affiliation(s)
- Jon Vidar Helvik
- Department of Biology, University of Bergen, and Department of Ophthalmology, Haukeland University Hospital, Bergen, Norway.
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55
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Raingeard D, Cancio I, Cajaraville MP. Cloning and expression pattern of peroxisome proliferator-activated receptors, estrogen receptor alpha and retinoid X receptor alpha in the thicklip grey mullet Chelon labrosus. Comp Biochem Physiol C Toxicol Pharmacol 2009; 149:26-35. [PMID: 18619562 DOI: 10.1016/j.cbpc.2008.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 06/17/2008] [Accepted: 06/17/2008] [Indexed: 02/07/2023]
Abstract
Aquatic organisms are exposed to diverse xenobiotics that cause peroxisome proliferation and/or endocrine disruption, both modulated in vertebrates by transcription factors of the nuclear receptor (NR) superfamily. Peroxisome proliferators are agonists of peroxisome proliferator-activated receptors (PPARs) that heterodimerize with the retinoid X receptor (RXR). Many xenoestrogens activate the estrogen receptor (ER). Here, 1090 bp of PPARalpha, 1255 bp of PPARgamma, 278 bp of RXRalpha, and 578 bp of ERalpha of thicklip grey mullet Chelon labrosus were cloned. Sequences were highly conserved, although relevant changes with respect to mammalian homologs were identified in PPARgamma and ERalpha. Semi-quantitative RT-PCR was used to determine if these NRs were expressed in different tissues of male, female and undifferentiated mullets captured in January and June. Expression of PPARs was highest in liver and lowest in muscle. RXRalpha expression was homogeneous excepting a low expression in male and female gill in January and brain and heart of undifferentiated fish in January and June. ERalpha expression predominated in liver and female gonad in June. The expression level of PPARs and ERalpha was significantly higher in liver in January than in gills in January or June. The present results show tissue-dependent modulation of expression of NRs in mullets.
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Affiliation(s)
- Damien Raingeard
- Laboratory of Cell Biology and Histology, Department of Zoology and Animal Cell Biology, University of the Basque Country, Bilbao, Basque Country, Spain
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56
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Effects of dietary fatty acid composition on the regulation of carnitine palmitoyltransferase (CPT) I in rainbow trout (Oncorhynchus mykiss). Comp Biochem Physiol B Biochem Mol Biol 2009; 152:85-93. [DOI: 10.1016/j.cbpb.2008.10.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 10/03/2008] [Accepted: 10/03/2008] [Indexed: 01/02/2023]
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57
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Krumschnabel G, Podrabsky JE. Fish as model systems for the study of vertebrate apoptosis. Apoptosis 2008; 14:1-21. [PMID: 19082731 DOI: 10.1007/s10495-008-0281-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 11/17/2008] [Indexed: 01/18/2023]
Abstract
Apoptosis is a process of pivotal importance for multi-cellular organisms and due to its implication in the development of cancer and degenerative disease it is intensively studied in humans and mammalian model systems. Invertebrate models of apoptosis have been well-studied, especially in C. elegans and D. melanogaster, but as these are evolutionarily distant from mammals the relevance of findings for human research is sometimes limited. Presently, a non-mammalian vertebrate model for studying apoptosis is missing. However, in the past few years an increasing number of studies on cell death in fish have been published and thus new model systems may emerge. This review aims at highlighting the most important of these findings, showing similarities and dissimilarities between fish and mammals, and will suggest topics for future research. In addition, the outstanding usefulness of fish as research models will be pointed out, hoping to spark future research on this exciting, often underrated group of vertebrates.
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Affiliation(s)
- Gerhard Krumschnabel
- Division of Developmental Immunology, Biocenter, Innsbruck Medical University, 6020 Innsbruck, Austria.
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58
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Leaver MJ, Bautista JM, Björnsson BT, Jönsson E, Krey G, Tocher DR, Torstensen BE. Towards Fish Lipid Nutrigenomics: Current State and Prospects for Fin-Fish Aquaculture. ACTA ACUST UNITED AC 2008. [DOI: 10.1080/10641260802325278] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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59
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Molecular characterization of peroxisome proliferator-activated receptors (PPARs) and their gene expression in the differentiating adipocytes of red sea bream Pagrus major. Comp Biochem Physiol B Biochem Mol Biol 2008; 151:268-77. [PMID: 18691667 DOI: 10.1016/j.cbpb.2008.07.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 07/13/2008] [Accepted: 07/14/2008] [Indexed: 11/21/2022]
Abstract
To investigate the molecular mechanism of fish adipocyte differentiation, the three subtypes of PPAR genes (alpha, beta and gamma) were characterized in a marine teleost red sea bream (Pagrus major). The primary structures of red sea bream PPARs exhibited high degrees of similarities to their mammalian counterparts, and their gene expression was detected in various tissues including adipose tissue, heart and hepatopancreas. During the differentiation of primary cultured red sea bream adipocytes, three PPARs showed distinct expression patterns: The alpha subtype showed a transient increase and the beta gene expression tended to increase during adipocyte differentiation whereas the gene expression level of PPARgamma did not change. These results suggest that they play distinct roles in adipocyte differentiation in red sea bream. In the differentiating red sea bream adipocytes, mammalian PPAR agonists, 15-deoxy-Delta(12,14)-prostaglandin J(2), ciglitazone and fenofibrate did not show clear effects on the adipogenic gene expression. However, 2-bromopalmitate increased the PPARgamma and related adipogenic gene expression levels, suggesting the gamma subtype plays a central role in red sea bream adipocyte differentiation and in addition, fatty acid metabolites can be used as modulators of adipocyte function. Thus our study highlighted the roles of PPARs in fish adipocyte differentiation and provided information on the molecular mechanisms of fish adipocyte development.
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60
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Rebl A, Høyheim B, Fischer U, Köllner B, Siegl E, Seyfert HM. Tollip, a negative regulator of TLR-signalling, is encoded by twin genes in salmonid fish. FISH & SHELLFISH IMMUNOLOGY 2008; 25:153-162. [PMID: 18502148 DOI: 10.1016/j.fsi.2008.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Revised: 03/28/2008] [Accepted: 04/08/2008] [Indexed: 05/26/2023]
Abstract
The factor Tollip is known to dampen TLR2- and TLR4-mediated signalling in mammals. No negative regulator of the piscine TLR-signalling cascade has been described so far, albeit a sizable collection of factors contributing to this ancient pathogen-sensing system are known from fish to date. We identified two closely related Tollip-encoding genes in Atlantic salmon (Salmo salar) and the respective ortholog mRNA molecules in rainbow trout (Oncorhynchus mykiss). The salmonid Tollip genes are segmented into 6 exons, similar to the human orthologous gene. The protein-encoding sequences are homologous to >97% among the twin factors and also between the species. Both encoded proteins contain a C2 domain and an ubiquitin system component, which are also characteristic features of the mammalian Tollip factor. We analysed the expression of these genes in trout. Both Tollip-encoding genes are ubiquitously and also equally expressed, as indicated by similar mRNA concentrations of both factors in any one tissue. Tollip expression was found to be up-regulated by viral infection. Our data suggest that the Tollip genes were duplicated before salmon and trout were evolutionary separated. Moreover, pathways dampening the activity of the TLR-cascade may have been conserved from lower vertebrates to mammals since Tollip, as a respective key factor has been highly conserved from fish to human.
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Affiliation(s)
- Alexander Rebl
- Research Institute for the Biology of Farm Animals (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
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61
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Intertissue regulation of carnitine palmitoyltransferase I (CPTI): mitochondrial membrane properties and gene expression in rainbow trout (Oncorhynchus mykiss). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:1382-9. [PMID: 18359285 DOI: 10.1016/j.bbamem.2008.02.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 02/19/2008] [Accepted: 02/20/2008] [Indexed: 11/22/2022]
Abstract
Carnitine palmitoyltransferase (CPT) I is regulated by several genetic and non-genetic factors including allosteric inhibition, mitochondrial membrane composition and/or fluidity and transcriptional regulation of enzyme content. To determine the intrinsic differences in these regulating factors that may result in differences between tissues in fatty acid oxidation ability, mitochondria were isolated from red, white and heart muscles and liver tissue from rainbow trout. Maximal activity (V(max)) for beta-oxidation enzymes and citrate synthase per mg tissue protein as well as CPT I in isolated mitochondria followed a pattern across tissues of red muscle>heart>white muscle>liver suggesting both quantitative and qualitative differences in mitochondria. CPT I inhibition showed a similar pattern with the highest malonyl-CoA concentration to inhibit activity by 50% (IC(50)) found in red muscle while liver had the lowest. Tissue malonyl-CoA content was highest in white muscle with no differences between the other tissues. Interestingly, the gene expression profiles did not follow the same pattern as the tissue enzyme activity. CPT I mRNA expression was greatest in heart>red muscle>white muscle>liver. In contrast, PPARalpha mRNA was greatest in the liver>red muscle>heart>white muscle. There were no significant differences in the mRNA expression of PPARbeta between tissues. As well, no significant differences were found in the mitochondrial membrane composition between tissues, however, there was a tendency for red muscle to exhibit higher proportions of PUFAs as well as a decreased PC:PE ratio, both of which would indicate increased membrane fluidity. In fact, there were significant correlations between IC(50) of CPT I for malonyl-CoA and indicators of membrane fluidity across tissues. This supports the notion that sensitivity of CPT I to its allosteric regulator could be modulated by changes in mitochondrial membrane composition and/or fluidity.
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62
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Manzoni M, Colombi P, Papini N, Rubaga L, Tiso N, Preti A, Venerando B, Tettamanti G, Bresciani R, Argenton F, Borsani G, Monti E. Molecular cloning and biochemical characterization of sialidases from zebrafish (Danio rerio). Biochem J 2008; 408:395-406. [PMID: 17708749 PMCID: PMC2267369 DOI: 10.1042/bj20070627] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sialidases remove sialic acid residues from various sialo-derivatives. To gain further insights into the biological roles of sialidases in vertebrates, we exploited zebrafish (Danio rerio) as an animal model. A zebrafish transcriptome- and genome-wide search using the sequences of the human NEU polypeptides as templates revealed the presence of seven different genes related to human sialidases. neu1 and neu4 are the putative orthologues of the mammalian sialidases NEU1 and NEU4 respectively. Interestingly, the remaining genes are organized in clusters located on chromosome 21 and are all more closely related to mammalian sialidase NEU3. They were thus named neu3.1, neu3.2, neu3.3, neu3.4 and neu3.5. Using RT-PCR (reverse transcription-PCR) we detected transcripts for all genes, apart from neu3.4, and whole-mount in situ hybridization experiments show a localized expression pattern in gut and lens for neu3.1 and neu4 respectively. Transfection experiments in COS7 (monkey kidney) cells demonstrate that Neu3.1, Neu3.2, Neu3.3 and Neu4 zebrafish proteins are sialidase enzymes. Neu3.1, Neu3.3 and Neu4 are membrane-associated and show a very acidic pH optimum below 3.0, whereas Neu3.2 is a soluble sialidase with a pH optimum of 5.6. These results were further confirmed by subcellular localization studies carried out using immunofluorescence. Moreover, expression in COS7 cells of these novel zebrafish sialidases (with the exception of Neu3.2) induces a significant modification of the ganglioside pattern, consistent with the results obtained with membrane-associated mammalian sialidases. Overall, the redundancy of sialidases together with their expression profile and their activity exerted on gangliosides of living cells indicate the biological relevance of this class of enzymes in zebrafish.
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Affiliation(s)
- Marta Manzoni
- *Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, viale Europa 11, 25123 Brescia, Italy
| | - Paolo Colombi
- *Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, viale Europa 11, 25123 Brescia, Italy
| | - Nadia Papini
- †Department of Medical Chemistry, Biochemistry and Biotechnology, L.I.T.A. (Laboratorio Interdisciplinare di Tecnologie Avanzate)-Segrate, School of Medicine, University of Milano, via Fratelli Cervi 93, 20090 Segrate, Italy
| | - Luana Rubaga
- *Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, viale Europa 11, 25123 Brescia, Italy
| | - Natascia Tiso
- ‡Department of Biology, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy
| | - Augusto Preti
- *Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, viale Europa 11, 25123 Brescia, Italy
| | - Bruno Venerando
- †Department of Medical Chemistry, Biochemistry and Biotechnology, L.I.T.A. (Laboratorio Interdisciplinare di Tecnologie Avanzate)-Segrate, School of Medicine, University of Milano, via Fratelli Cervi 93, 20090 Segrate, Italy
| | - Guido Tettamanti
- †Department of Medical Chemistry, Biochemistry and Biotechnology, L.I.T.A. (Laboratorio Interdisciplinare di Tecnologie Avanzate)-Segrate, School of Medicine, University of Milano, via Fratelli Cervi 93, 20090 Segrate, Italy
| | - Roberto Bresciani
- *Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, viale Europa 11, 25123 Brescia, Italy
| | - Francesco Argenton
- ‡Department of Biology, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy
| | - Giuseppe Borsani
- *Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, viale Europa 11, 25123 Brescia, Italy
- Correspondence may be addressed to either of these authors (email or )
| | - Eugenio Monti
- *Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, viale Europa 11, 25123 Brescia, Italy
- Correspondence may be addressed to either of these authors (email or )
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63
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Dettaï A, di Prisco G, Lecointre G, Parisi E, Verde C. Inferring evolution of fish proteins: the globin case study. Methods Enzymol 2008; 436:539-70. [PMID: 18237653 DOI: 10.1016/s0076-6879(08)36030-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Because hemoglobins (Hbs) of all animal species have the same heme group, differences in their properties, including oxygen affinity, electrophoretic mobility, and pH sensitivity, must result from the interaction of the prosthetic group with specific amino acid residues in the primary structure. For this reason, fish globins have been the object of extensive studies in the past few years, not only for their structural characteristics but also because they offer the possibility to investigate the evolutionary history of Hbs in marine and freshwater species living in a large variety of environmental conditions. For such a purpose, phylogenetic analysis of globin sequences can be combined with knowledge of the phylogenetic relationships between species. In addition, Type I functional-divergence analysis is aimed toward predicting the amino acid residues that are more likely responsible for biochemical diversification of different Hb families. These residues, mapped on the three-dimensional Hb structure, can provide insights into functional and structural divergence.
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Affiliation(s)
- Agnes Dettaï
- UMR, Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Paris, France
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64
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Fu KY, Chen CY, Lin CT, Chang WM. Molecular cloning and tissue distribution of three estrogen receptors from the cyprinid fish Varicorhinus barbatulus. J Comp Physiol B 2007; 178:189-97. [DOI: 10.1007/s00360-007-0210-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Revised: 08/27/2007] [Accepted: 08/29/2007] [Indexed: 10/22/2022]
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65
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Kondo H, Misaki R, Gelman L, Watabe S. Ligand-dependent transcriptional activities of four torafugu pufferfish Takifugu rubripes peroxisome proliferator-activated receptors. Gen Comp Endocrinol 2007; 154:120-7. [PMID: 17632107 DOI: 10.1016/j.ygcen.2007.05.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Revised: 05/21/2007] [Accepted: 05/26/2007] [Indexed: 10/23/2022]
Abstract
Structural and functional properties were investigated for four peroxisome proliferator-activated receptors (PPARs), PPARalpha1, PPARalpha2, PPARbeta, and PPARgamma, from torafugu pufferfish Takifugu rubripes and determined for their transcriptional activity by the reporter assay using reporter plasmids containing three copies of the acyl-CoA oxidase PPAR response element. Although torafugu PPARs showed a high similarity in the primary structure to other vertebrate counterparts, torafugu PPARalpha2 and gamma contained additional sequences of 21 and 28 amino acids, respectively, as in the case of other teleost fish species when compared with African clawed frog counterparts. The transcriptional activity of torafugu PPARalpha1 was enhanced 4.5- and 11.5-fold by Wy-14643 and 5,8,11,14-eicosatetraynoic acid (ETYA) each at 10 microM, respectively, whereas that of PPARalpha2, 4.5- and 7.3-fold at the same concentration of the respective ligands, respectively. The activities of torafugu PPARalpha1 and alpha2 were also enhanced 5.6- and 6.3-fold by ETYA at 1 microM, respectively, but not by Wy-14643 at this concentration. Furthermore, the activities of the two torafugu PPARalphas were enhanced 4.3- and 7.6-fold by arachidonic acid, 4.4- and 5.2-fold by docosahexaenoic acid, and 6.7- and 8.0-fold by eicosapentaenoic acid each at 50 microM, respectively. On the other hand, the activities of torafugu PPARbeta and gamma were not changed by Wy-14643, ETYA, rosiglitazone, nor PUFAs. These results suggest that the activities of torafugu PPARbeta and gamma require undefined ligands. Alternatively, the molecular mechanisms involved in their activation are different from those of other vertebrates.
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Affiliation(s)
- Hidehiro Kondo
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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66
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Hillegass JM, Villano CM, Cooper KR, White LA. Matrix metalloproteinase-13 is required for zebra fish (Danio rerio) development and is a target for glucocorticoids. Toxicol Sci 2007; 100:168-79. [PMID: 17728286 DOI: 10.1093/toxsci/kfm192] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are endopeptidases that degrade the proteins of the extracellular matrix (ECM). Expression and activity of the MMPs are essential for embryogenesis, where MMPs participate in the normal ECM remodeling that occurs during tissue morphogenesis and development. Studies have demonstrated that MMP gene expression is inhibited by glucocorticoids in mammalian cell culture systems and that exposure to glucocorticoids causes developmental abnormalities in several species. Therefore, we proposed that glucocorticoids impede normal development through alteration of MMP expression. Zebra fish (Danio rerio) were used as a model to study MMP-13 expression both during normal embryogenesis and following acute exposure to two glucocorticoids, dexamethasone, and hydrocortisone. MMP-13 is one of three collagenases identified in vertebrates that catalyzes the degradation of type I collagens at neutral pH. MMP-13 expression varied during zebra fish development, with peak expression at 48 h post-fertilization (hpf). Morpholino knockdown studies showed that MMP-13 expression is necessary for normal zebra fish embryogenesis. Acute exposure to dexamethasone and hydrocortisone resulted in abnormal zebra fish development including craniofacial abnormalities, altered somitogenesis, blood pooling and pericardial and yolk sac edema as well as increased MMP-13 mRNA and activity at 72 hpf. In situ hybridization experiments were used to confirm the increase in MMP-13 expression following glucocorticoid treatment and showed elevated MMP-13 expression in the rostral trunk, brain, eye, heart, and anterior kidney of treated embryos. These data demonstrate that normal zebra fish embryogenesis requires MMP-13 and that dexamethasone and hydrocortisone modulate the expression of this gene, leading to increased activity and potentially contributing to subsequent dysmorphogenesis.
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Affiliation(s)
- Jedd Michael Hillegass
- Joint Graduate Program in Toxicology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
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67
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Li P, Peatman E, Wang S, Feng J, He C, Baoprasertkul P, Xu P, Kucuktas H, Nandi S, Somridhivej B, Serapion J, Simmons M, Turan C, Liu L, Muir W, Dunham R, Brady Y, Grizzle J, Liu Z. Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs. BMC Genomics 2007; 8:177. [PMID: 17577415 PMCID: PMC1906771 DOI: 10.1186/1471-2164-8-177] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Accepted: 06/18/2007] [Indexed: 12/20/2022] Open
Abstract
Background EST sequencing is one of the most efficient means for gene discovery and molecular marker development, and can be additionally utilized in both comparative genome analysis and evaluation of gene duplications. While much progress has been made in catfish genomics, large-scale EST resources have been lacking. The objectives of this project were to construct primary cDNA libraries, to conduct initial EST sequencing to generate catfish EST resources, and to obtain baseline information about highly expressed genes in various catfish organs to provide a guide for the production of normalized and subtracted cDNA libraries for large-scale transcriptome analysis in catfish. Results A total of 17 cDNA libraries were constructed including 12 from channel catfish (Ictalurus punctatus) and 5 from blue catfish (I. furcatus). A total of 31,215 ESTs, with average length of 778 bp, were generated including 20,451 from the channel catfish and 10,764 from blue catfish. Cluster analysis indicated that 73% of channel catfish and 67% of blue catfish ESTs were unique within the project. Over 53% and 50% of the channel catfish and blue catfish ESTs, respectively, had significant similarities to known genes. All ESTs have been deposited in GenBank. Evaluation of the catfish EST resources demonstrated their potential for molecular marker development, comparative genome analysis, and evaluation of ancient and recent gene duplications. Subtraction of abundantly expressed genes in a variety of catfish tissues, identified here, will allow the production of low-redundancy libraries for in-depth sequencing. Conclusion The sequencing of 31,215 ESTs from channel catfish and blue catfish has significantly increased the EST resources in catfish. The EST resources should provide the potential for microarray development, polymorphic marker identification, mapping, and comparative genome analysis.
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Affiliation(s)
- Ping Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Eric Peatman
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Shaolin Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Jinian Feng
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Chongbo He
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Puttharat Baoprasertkul
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Peng Xu
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Huseyin Kucuktas
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Samiran Nandi
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Benjaporn Somridhivej
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Jerry Serapion
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Micah Simmons
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Cemal Turan
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Lei Liu
- The W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - William Muir
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Yolanda Brady
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - John Grizzle
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
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68
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Acerete L, Balasch JC, Castellana B, Redruello B, Roher N, Canario AV, Planas JV, MacKenzie S, Tort L. Cloning of the glucocorticoid receptor (GR) in gilthead seabream (Sparus aurata). Differential expression of GR and immune genes in gilthead seabream after an immune challenge. Comp Biochem Physiol B Biochem Mol Biol 2007; 148:32-43. [PMID: 17544309 DOI: 10.1016/j.cbpb.2007.04.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Revised: 04/19/2007] [Accepted: 04/19/2007] [Indexed: 01/22/2023]
Abstract
In order to determine the cortisol response after an immune challenge in the gilthead seabream (Sparus aurata), a cortisol receptor (GR) was cloned, sequenced and its expression determined after lipopolysaccharide (LPS) treatment. To clone the gilthead seabream GR (sbGR), consecutive PCR amplifications and screening of a pituitary cDNA library were performed. We obtained a clone of 4586 bp encoding a 784aa protein. Northern blot analysis from head kidney, heart and intestine revealed that the full length sbGR mRNA was approximately 6.5 Kb. A LPS treatment, used as an acute stress model, was employed to characterise the expression of sbGR and some selected genes involved in the immune response (IL-1beta, TNF-alpha, Mx protein, cathepsin D and PPAR-gamma). All genes were expressed in all tissues examined and responses were tissue and time dependent revealing differential gene expression profiles after LPS administration. Furthermore, analysis of plasma cortisol levels after LPS injection, showed an acute response to inflammatory stress with a significant increase two and six h after injection, recovering to basal levels 12 h post-stress in all LPS concentrations tested.
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Affiliation(s)
- L Acerete
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Facultat de Ciències, 08193 Bellaterra, Spain.
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69
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McPartland JM, Glass M, Matias I, Norris RW, Kilpatrick CW. A shifted repertoire of endocannabinoid genes in the zebrafish (Danio rerio). Mol Genet Genomics 2007; 277:555-70. [PMID: 17256142 DOI: 10.1007/s00438-007-0207-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Accepted: 01/03/2007] [Indexed: 01/27/2023]
Abstract
The zebrafish has served as a model organism for developmental biology. Sequencing its genome has expanded zebrafish research into physiology and drug-development testing. Several cannabinoid pharmaceuticals are in development, but expression of endocannabinoid receptors and enzymes remains unknown in this species. We conducted a bioinformatics analysis of the zebrafish genome using 17 human endocannabinoid genes as a reference set. Putative zebrafish orthologs were identified in filtered BLAST searches as reciprocal best hits. Orthology was confirmed by three in silico methods: phylogenetic testing, synteny analysis, and functional mapping. Zebrafish expressed orthologs of cannabinoid receptor 1, transient receptor potential channel vanilloid receptor 4, GPR55 receptor, fatty acid amide hydrolase 1, monoacylglycerol lipase, NAPE-selective phospholipase D, abhydrolase domain-containing protein 4, and diacylglycerol lipase alpha and beta; and paired paralogs of cannabinoid receptor 2, fatty acid amide hydrolase 2, peroxisome proliferator-activated receptor alpha, prostaglandin-endoperoxide synthase 2, and transient receptor potential cation channel subtype A1. Functional mapping suggested the orthologs of transient receptor potential vanilloid receptor 1 and peroxisome proliferator-activated receptor gamma lack specific amino acids critical for cannabinoid ligand binding. No orthologs of N-acylethanolamine acid amidase or protein tyrosine phosphatase, non-receptor type 22 were identified. In conclusion, the zebrafish genome expresses a shifted repertoire of endocannabinoid genes. In vitro analyses are warranted before using zebrafish for cannabinoid development testing.
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70
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Rebl A, Siegl E, Köllner B, Fischer U, Seyfert HM. Characterization of twin toll-like receptors from rainbow trout (Oncorhynchus mykiss): evolutionary relationship and induced expression by Aeromonas salmonicida salmonicida. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2007; 31:499-510. [PMID: 17070576 DOI: 10.1016/j.dci.2006.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Revised: 08/23/2006] [Accepted: 08/23/2006] [Indexed: 05/12/2023]
Abstract
Structure and function of factors contributing to the innate immune system of lower vertebrates, including fish are only sparsely characterized. We retrieved with RT-PCR cDNA copies of two closely related Toll-like receptors (TLR) from liver RNA of the rainbow trout (Oncorhynchus mykiss). The cDNA sequences are homologous to 95.6%. The phylogenetic analysis of their deduced amino acid sequences places these twin factors closely to other known TLRs from fish. The twin factors are equally expressed in all tissues analysed, most abundantly in spleen and head kidney and lowest in adipose tissue. Formalin-inactivated Aeromonas salmonicida pathogens induce their expression up to eight-fold in vitro in peripheral blood lymphocytes and in tissues from spleen and head kidney. Our sequence information will be useful to establish expression constructs for these factors necessary to analyse the pathogen specific signal transduction activating the innate immune defence in fish.
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Affiliation(s)
- Alexander Rebl
- Research Institute for the Biology of Farm Animals (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
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71
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Bricaud O, Collazo A. The transcription factor six1 inhibits neuronal and promotes hair cell fate in the developing zebrafish (Danio rerio) inner ear. J Neurosci 2006; 26:10438-51. [PMID: 17035528 PMCID: PMC6674689 DOI: 10.1523/jneurosci.1025-06.2006] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The developmental processes leading to the differentiation of mechanosensory hair cells and statoacoustic ganglion neurons from the early otic epithelium remain unclear. Possible candidates include members of the Pax-Six-Eya-Dach (paired box-sine oculis homeobox-eyes absent-dachshund) gene regulatory network. We cloned zebrafish six1 and studied its function in inner ear development. Gain- and loss-of-function experiments show that six1 has opposing roles in hair cell and neuronal lineages. It promotes hair cell fate and, conversely, inhibits neuronal fate by differentially affecting cell proliferation and cell death in these lineages. By independently targeting hair cells with atoh1a (atonal homolog 1a) knockdown or neurons with neurog1 (neurogenin 1) knockdown, we showed that the remaining cell population, neurons or hair cells, respectively, is still affected by gain or loss of six1 function. six1 interacts with other members of the Pax-Six-Eya-Dach regulatory network, in particular dacha and dachb in the hair cell but not neuronal lineage. Unlike in mouse, six1 does not appear to be dependent on eya1, although it seems to be important for the regulation of eya1 and pax2b expression in the ventral otic epithelium. Furthermore, six1 expression appears to be regulated by pax2b and also by foxi1 (forkhead box I1) as expected for an early inducer of the otic placode. Our results are the first to demonstrate a dual role for a member of the Pax-Six-Eya-Dach regulatory network in inner ear development.
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Affiliation(s)
- Olivier Bricaud
- Leslie and Susan Gonda (Goldschmied) Cell and Molecular Biology Department, House Ear Institute, Los Angeles, California 90057, USA.
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72
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Mank JE, Avise JC. Phylogenetic conservation of chromosome numbers in Actinopterygiian fishes. Genetica 2006; 127:321-7. [PMID: 16850236 DOI: 10.1007/s10709-005-5248-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Accepted: 11/16/2005] [Indexed: 10/24/2022]
Abstract
The genomes of ray-finned fishes (Actinopterygii) are well known for their evolutionary dynamism as reflected by drastic alterations in DNA content often via regional and whole-genome duplications, differential patterns of gene silencing or loss, shifts in the insertion-to-deletion ratios of genomic segments, and major re-patternings of chromosomes via non-homologous recombination. In sharp contrast, chromosome numbers in somatic karyotypes have been highly conserved over vast evolutionary timescales - a histogram of available counts is strongly leptokurtic with more than 50% of surveyed species displaying either 48 or 50 chromosomes. Here we employ comparative phylogenetic analyses to examine the evolutionary history of alterations in fish chromosome numbers. The most parsimonious ancestral state for major actinopterygiian clades is 48 chromosomes. When interpreted in a phylogenetic context, chromosome numbers evidence many recent instances of polyploidization in various lineages but there is no clear indication of a singular polyploidization event that has been hypothesized to have immediately preceded the teleost radiation. After factoring out evident polyploidizations, a correlation between chromosome numbers and genome sizes across the Actinopterygii is marginally statistically significant (p = 0.012) but exceedingly weak (R (2) = 0.0096). Overall, our phylogenetic analysis indicates a mosaic evolutionary pattern in which the forces that govern labile features of fish genomes must operate largely independently of those that operate to conserve chromosome numbers.
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Affiliation(s)
- Judith E Mank
- Department of Genetics, University of Georgia, Life Sciences Building, Athens, GA 30602, USA.
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73
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McClelland GB, Craig PM, Dhekney K, Dipardo S. Temperature- and exercise-induced gene expression and metabolic enzyme changes in skeletal muscle of adult zebrafish (Danio rerio). J Physiol 2006; 577:739-51. [PMID: 16990399 PMCID: PMC1890438 DOI: 10.1113/jphysiol.2006.119032] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Both exercise training and cold acclimatization induce muscle remodelling in vertebrates, producing a more aerobic phenotype. In ectothermic species exercise training and cold-acclimatization represent distinct stimuli. It is currently unclear if these stimuli act through a common mechanism or if different mechanisms lead to a common phenotype. The goal of this study was to survey responses that represent potential mechanisms responsible for contraction- and temperature-induced muscle remodelling, using an ectothermic vertebrate. Separate groups of adult zebrafish (Danio rerio) were either swim trained or cold acclimatized for 4 weeks. We found that the mitochondrial marker enzyme citrate synthase (CS) was increased by 1.5x in cold and by 1.3x with exercise (P<0.05). Cytochrome c oxidase (COx) was increased by 1.2x following exercise training (P<0.05) and 1.2x (P=0.07) with cold acclimatization. However, only cold acclimatization increased beta-hydroxyacyl-CoA dehydrogenase (HOAD) compared to exercise-trained (by 1.3x) and pyruvate kinase (PK) relative to control zebrafish. We assessed the whole-animal performance outcomes of these treatments. Maximum absolute sustained swimming speed (Ucrit) was increased in the exercise trained group but not in the cold acclimatized group. Real-time PCR analysis indicated that increases in CS are primarily transcriptionally regulated with exercise but not with cold treatments. Both treatments showed increases in nuclear respiratory factor (NRF)-1 mRNA which was increased by 2.3x in cold-acclimatized and 4x in exercise-trained zebrafish above controls. In contrast, peroxisome proliferator-activated receptor (PPAR)-alpha mRNA levels were decreased in both experimental groups while PPAR-beta1 declined in exercise training only. Moreover, PPAR-gamma coactivator (PGC)-1alpha mRNA was not changed by either treatment. In zebrafish, both temperature and exercise produce a more aerobic phenotype, but there are stimulus-dependent responses (i.e. HOAD and PK activities). While similar changes in NRF-1 mRNA suggest that common responses might underlie aerobic muscle remodelling there are distinct changes (i.e. CS and PPAR-beta1 mRNA) that contribute to specific temperature- and exercise-induced phenotypes.
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Affiliation(s)
- Grant B McClelland
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
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74
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Peatman E, Liu Z. CC chemokines in zebrafish: Evidence for extensive intrachromosomal gene duplications. Genomics 2006; 88:381-5. [PMID: 16697551 DOI: 10.1016/j.ygeno.2006.03.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Revised: 03/06/2006] [Accepted: 03/23/2006] [Indexed: 11/23/2022]
Abstract
Chemokines are a family of structurally related chemotactic cytokines that regulate the migration of leukocytes. CC chemokines represent the largest subfamily of chemokines, with 28 genes in mammals. In recent studies in channel catfish, Ictalurus punctatus, we identified 26 distinct CC chemokine transcripts and obtained the genomic sequences and structures of 23 CC chemokine genes. However, without the availability of similar sets of CC chemokines in closely related species or a sequenced genome in catfish, it was difficult to make inferences as to the origins and modes of duplication of these molecules or to analyze conserved synteny between teleost and mammalian CC chemokines. Here, we have identified as many as 46 loci in the zebrafish genome that encode putative CC chemokines. The zebrafish CC chemokines are highly clustered on several chromosomes and show evidence of extensive, species-specific intrachromosomal duplications.
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Affiliation(s)
- Eric Peatman
- Fish Molecular Genetics and Biotechnology Laboratory, 203 Swingle Hall, Department of Fisheries and Allied Aquacultures, and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
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75
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Brunet FG, Roest Crollius H, Paris M, Aury JM, Gibert P, Jaillon O, Laudet V, Robinson-Rechavi M. Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. Mol Biol Evol 2006; 23:1808-16. [PMID: 16809621 DOI: 10.1093/molbev/msl049] [Citation(s) in RCA: 281] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Teleost fishes provide the first unambiguous support for ancient whole-genome duplication in an animal lineage. Studies in yeast or plants have shown that the effects of such duplications can be mediated by a complex pattern of gene retention and changes in evolutionary pressure. To explore such patterns in fishes, we have determined by phylogenetic analysis the evolutionary origin of 675 Tetraodon duplicated genes assigned to chromosomes, using additional data from other species of actinopterygian fishes. The subset of genes, which was retained in double after the genome duplication, is enriched in development, signaling, behavior, and regulation functional categories. The evolutionary rate of duplicate fish genes appears to be determined by 3 forces: 1) fish proteins evolve faster than mammalian orthologs; 2) the genes kept in double after genome duplication represent the subset under strongest purifying selection; and 3) following duplication, there is an asymmetric acceleration of evolutionary rate in one of the paralogs. These results show that similar mechanisms are at work in fishes as in yeast or plants and provide a framework for future investigation of the consequences of duplication in fishes and other animals.
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Affiliation(s)
- Frédéric G Brunet
- Laboratoire de Biologie Moléculaire de la Cellule, INRA LA 1237, CNRS UMR5161, IFR 128 BioSciences Lyon-Gerland, Ecole Normale Supérieure de Lyon, Lyon, France
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76
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Takle H, McLeod A, Andersen O. Cloning and characterization of the executioner caspases 3, 6, 7 and Hsp70 in hyperthermic Atlantic salmon (Salmo salar) embryos. Comp Biochem Physiol B Biochem Mol Biol 2006; 144:188-98. [PMID: 16574452 DOI: 10.1016/j.cbpb.2006.02.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2005] [Revised: 01/30/2006] [Accepted: 02/12/2006] [Indexed: 01/20/2023]
Abstract
Hyperthermia during embryogenesis has been reported to induce deformities in Atlantic salmon (Salmo salar). To examine the involvement of executioner caspases in hyperthermia-induced cell-death in a poikilotherm vertebrate species, five genes encoding caspase-3,-6, and -7 were cloned from Atlantic salmon, and the expression was studied in thermal stressed salmon embryos. The salmon genome contained two genetically distinct variants of both salmon caspase-3 and caspase-6 that is likely the result of two independent chromosome or genome duplications. Whereas only partial caspase-3A encoding sequences were isolated, the full-length caspase-3B cDNA encodes the inactive proenzyme of 279 amino acids (aa) consisting of an N-terminal prodomain and the large and the small subunit. The salmon caspase-6A and caspase-6B proenzymes include an additional linker region between the two subunits. The deduced salmon caspase-7 consists of only 245 aa and lacks the prodomain and part of the large subunit similar to the predicted caspase-7 of the puffer fish Tetraodon sp.. Increased apoptotic activity as evidenced by cleavage of nuclear DNA was demonstrated in salmon embryos incubated at 18-20 degrees C for 84 h after acclimatization at 8 degrees C. Hyperthermia-induced activation of the executioner caspases was indicated by the increased mRNA levels of caspase-3B, caspase-6A/B and caspase-7 after 54 h heat exposure as quantified by real-time RT-PCR. The 2-2.5 fold increase in the mRNA expression of the heat shock protein Hsp70 gene coincided with the peak mRNA values of the executioner caspases. Whole-mount in situ hybridization of the salmon embryo identified caspase-7 mRNA in the lens exclusively, while caspase-3B and caspase-6A/B were expressed in multiple tissues of exposed and control embryos. Interestingly, cardiac expression of caspase-6A/B was only identified in heat stressed embryos. Altogether, these results shed light on evolutionary aspects of the executioner caspases in vertebrates and their expression in salmon embryos exposed to hyperthermia. In particular, the heat sensitive caspase-6 expression in the embryonic heart is of interest since cardiac malformations are an emergent problem in salmon aquaculture.
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Affiliation(s)
- Harald Takle
- AKVAFORSK (Institute of Aquaculture Research), Norwegian University of Life Sciences, P.O. Box 5010, N-1432 Aas, Norway.
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77
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Prunet P, Sturm A, Milla S. Multiple corticosteroid receptors in fish: from old ideas to new concepts. Gen Comp Endocrinol 2006; 147:17-23. [PMID: 16545810 DOI: 10.1016/j.ygcen.2006.01.015] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Revised: 12/23/2005] [Accepted: 01/05/2006] [Indexed: 10/24/2022]
Abstract
The effect of corticosteroid hormones in fish are mediated through intracellular receptors that act as ligand-binding transcription factors. Many studies have been devoted to cortisol binding using radiolabeled ligand in fish and allowed characterization of a single class of high affinity binding sites in various tissues. Molecular characterization of cortisol receptors has only been initiated recently by cloning the different receptor forms: Following a isolation of a first glucocorticoid receptor (GR), a mineralocorticoid receptor (MR) was described and the presence of various GR isoforms was recently reported. Sequence comparison and phylogenetic analysis of these sequences confirm that fish possess both GR and MR and that GR gene is duplicated. The importance of these various corticosteroid receptor forms is also illustrated by analysis of their transcriptional activity. When tested in human cell lines, these receptors showed functionally distinct actions on GR-sensitive promotors, thus suggesting a more complicated corticosteroid signaling system than initially anticipated from binding studies. These results also suggest that, whereas cortisol is certainly the physiological ligand for GR, this may not be the case for MR which showed high sensitivity for deoxycorticosterone (DOC) and aldosterone. As this last hormone is probably absent in fish, these results raise the question as to whether DOC could be a physiological ligand for MR in fish. Information on DOC effect in fish is very scarce and clarification of the differential osmoregulatory roles of cortisol and DOC in fish needs ellucidation. This will require analysis of all actors of the corticosteroid signaling system at pre-receptor, receptor, and post-receptor levels.
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Affiliation(s)
- P Prunet
- INRA SCRIBE, IFR 140, Campus de Beaulieu, 35042 Rennes Cedex, France.
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78
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Krushna Padhi B, Akimenko MA, Ekker M. Independent expansion of the keratin gene family in teleostean fish and mammals: An insight from phylogenetic analysis and radiation hybrid mapping of keratin genes in zebrafish. Gene 2006; 368:37-45. [PMID: 16297574 DOI: 10.1016/j.gene.2005.09.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 09/12/2005] [Accepted: 09/29/2005] [Indexed: 12/27/2022]
Abstract
The sequence and chromosomal distribution of keratin genes of zebrafish were compared with that of other fishes and mammals to provide an insight into the evolution of this gene family in vertebrates. By comparative sequence analysis and radiation hybrid mapping, we identified 16 type I and 7 type II keratin genes in the zebrafish genome. This contrasts with mammals, where type I and type II keratin genes are similar in number. The keratin genes are scattered in the fish genome, contrasting with the two clusters of keratin genes in mammalian genomes. Compared to genes from two species of pufferfish, the zebrafish type I keratin genes underwent an expansion by independent tandem duplications. Expression profiles based on EST counts suggest that some of the tandemly duplicated type I keratin genes from zebrafish either underwent sub-functionalization or acquired new expression domains. The chromosomal arrangement of keratins 8, keratin18, and a second type II keratin, as a cluster of three genes, has remained conserved in vertebrate evolution, except for duplication of the three-gene cluster in some teleosts. This contrasts with other members of the keratin gene family, which diverged independently between fish and mammals.
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Affiliation(s)
- Bhaja Krushna Padhi
- Ottawa Health Research Institute, 725 Parkdale Avenue, Ottawa, ON, Canada K1Y 4E9
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79
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Abstract
Duplication of genes, genomes, or morphological structures (or some combination of these) has long been thought to facilitate evolutionary change. Here we focus on studies of the teleost fishes to consider the conceptual similarities in the evolutionary potential of these three different kinds of duplication events. We review recent data that have confirmed the occurrence of a whole-genome duplication event in the ray-finned fish lineage, and discuss whether this event may have fuelled the radiation of teleost fishes. We then consider the fates of individual duplicated genes, from both a theoretical and an experimental viewpoint, focusing on our studies of teleost Hox genes and their functions in patterning the segmented hindbrain. Finally, we consider the duplication of morphological structures, once again drawing on our experimental studies of the hindbrain, which have revealed that experimentally induced duplicated neurons can produce functionally redundant neural circuits. We posit that the availability of duplicated material, independent of its nature, can lead to functional redundancy, which in turn enables evolutionary change.
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Affiliation(s)
- I Hurley
- Department of Organismal Biology and Anatomy, The University of Chicago, 1027 E 57th Street, Chicago, IL 60637, USA
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80
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MANK JUDITHE, PROMISLOW DANIELEL, AVISE JOHNC. Evolution of alternative sex-determining mechanisms in teleost fishes. Biol J Linn Soc Lond 2006. [DOI: 10.1111/j.1095-8312.2006.00558.x] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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81
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Pinto PIS, Passos AL, Martins Deborah M Power RS, Canário AVM. Characterization of estrogen receptor betab in sea bream (Sparus auratus): phylogeny, ligand-binding, and comparative analysis of expression. Gen Comp Endocrinol 2006; 145:197-207. [PMID: 16213504 DOI: 10.1016/j.ygcen.2005.08.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2005] [Revised: 08/08/2005] [Accepted: 08/22/2005] [Indexed: 11/25/2022]
Abstract
Estrogens control many physiological processes in both female and male vertebrates, mostly mediated by specific nuclear estrogen receptors (ER). Two ER subtypes (ERalpha and ERbeta) are present in most vertebrates, including the sea bream (Sparus auratus) a hermaphrodite teleost fish. In the present study several variant cDNAs encoding a second sea bream ERbeta (sbERbetab) is reported. Phylogenetic and Southern blot analysis indicate that sbERbetab and the previously cloned sbERbetaa (formerly sbERbeta) are encoded by different genes, which may have arisen by duplication of an ancestral ERbeta gene. Competitive binding assays show that sbERbetab has high affinity for 17beta-estradiol (K(d) = 1 nM) and specifically binds estrogen agonists (diethylstilbestrol and ethynylestradiol) and antagonists (ICI 182,780). In Northern blot sbERalpha, sbERbetaa, sbERbetab produce several different transcripts in a variety of tissues. RT-PCR showed a partially overlapping but differential tissue distribution in both male and female sea bream.
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Affiliation(s)
- Patrícia I S Pinto
- Centro de Ciências do Mar, CIMAR-Laboratório Associado, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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82
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Mank JE, Avise JC. Cladogenetic correlates of genomic expansions in the recent evolution of actinopterygiian fishes. Proc Biol Sci 2006; 273:33-8. [PMID: 16519231 PMCID: PMC1560015 DOI: 10.1098/rspb.2005.3295] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 08/13/2005] [Indexed: 11/12/2022] Open
Abstract
Genomic expansions via regional gene duplications and polyploidization events have been implicated as catalysts for rapid cladogenetic speciation in some fish taxa, but any general relationships between genome sizes and patterns of evolutionary radiation remain poorly characterized. Here we examine empirical correlations between genome size and species richness (number of extant species within a given clade) both across Actinopterygii (ray-finned fishes) and within several large actinopterygiian clades. We conducted the analyses both without and with correction (by independent contrasts) for phylogenetic effects. Across the full suite of 461 surveyed genera, relatively small but significant positive correlations were present between species richness and evolutionary increases in C-value. Although many variables (including ecological and behavioural factors) clearly can influence speciation rates, the current results are consistent with the notion that genomic architecture may play a role in species proliferation as well.
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Affiliation(s)
- Judith E Mank
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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83
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Cadieux B, Chitramuthu BP, Baranowski D, Bennett HPJ. The zebrafish progranulin gene family and antisense transcripts. BMC Genomics 2005; 6:156. [PMID: 16277664 PMCID: PMC1310530 DOI: 10.1186/1471-2164-6-156] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2005] [Accepted: 11/08/2005] [Indexed: 11/10/2022] Open
Abstract
Background Progranulin is an epithelial tissue growth factor (also known as proepithelin, acrogranin and PC-cell-derived growth factor) that has been implicated in development, wound healing and in the progression of many cancers. The single mammalian progranulin gene encodes a glycoprotein precursor consisting of seven and one half tandemly repeated non-identical copies of the cystine-rich granulin motif. A genome-wide duplication event hypothesized to have occurred at the base of the teleost radiation predicts that mammalian progranulin may be represented by two co-orthologues in zebrafish. Results The cDNAs encoding two zebrafish granulin precursors, progranulins-A and -B, were characterized and found to contain 10 and 9 copies of the granulin motif respectively. The cDNAs and genes encoding the two forms of granulin, progranulins-1 and -2, were also cloned and sequenced. Both latter peptides were found to be encoded by precursors with a simplified architecture consisting of one and one half copies of the granulin motif. A cDNA encoding a chimeric progranulin which likely arises through the mechanism of trans-splicing between grn1 and grn2 was also characterized. A non-coding RNA gene with antisense complementarity to both grn1 and grn2 was identified which may have functional implications with respect to gene dosage, as well as in restricting the formation of the chimeric form of progranulin. Chromosomal localization of the four progranulin (grn) genes reveals syntenic conservation for grna only, suggesting that it is the true orthologue of mammalian grn. RT-PCR and whole-mount in situ hybridization analysis of zebrafish grns during development reveals that combined expression of grna and grnb, but not grn1 and grn2, recapitulate many of the expression patterns observed for the murine counterpart. This includes maternal deposition, widespread central nervous system distribution and specific localization within the epithelial compartments of various organs. Conclusion In support of the duplication-degeneration-complementation model of duplicate gene retention, partitioning of expression between grna and grnb was observed in the intermediate cell mass and yolk syncytial layer, respectively. Taken together these expression patterns suggest that the function of an ancestral grn gene has been devolved upon four paralogues in zebrafish.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Animals
- Blotting, Northern
- Chromatography, High Pressure Liquid
- Chromosome Mapping
- Cloning, Molecular
- DNA, Complementary/metabolism
- Gene Dosage
- Gene Expression Regulation, Developmental
- Gene Library
- Humans
- In Situ Hybridization
- Intercellular Signaling Peptides and Proteins/biosynthesis
- Intercellular Signaling Peptides and Proteins/genetics
- Models, Genetic
- Molecular Sequence Data
- Multigene Family
- Oligonucleotides, Antisense/chemistry
- Oligonucleotides, Antisense/genetics
- Phylogeny
- RNA/metabolism
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Amino Acid
- Tissue Distribution
- Transcription, Genetic
- Zebrafish
- Zebrafish Proteins/biosynthesis
- Zebrafish Proteins/chemistry
- Zebrafish Proteins/genetics
- Zebrafish Proteins/metabolism
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Affiliation(s)
- Benoît Cadieux
- Endocrine Laboratory, Royal Victoria Hospital, McGill University Health Centre, Montreal, Quebec, Canada
- Cancer Research Institute, UCSF, 2340 Sutter Street, N-231 San Francisco, CA 94143, USA
| | - Babykumari P Chitramuthu
- Endocrine Laboratory, Royal Victoria Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | - David Baranowski
- Endocrine Laboratory, Royal Victoria Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | - Hugh PJ Bennett
- Endocrine Laboratory, Royal Victoria Hospital, McGill University Health Centre, Montreal, Quebec, Canada
- Room L2.05, Royal Victoria Hospital, 687 Pine Avenue West, Montreal, Quebec, H3A 1A1, Canada
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84
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Batista-Pinto C, Rodrigues P, Rocha E, Lobo-da-Cunha A. Identification and organ expression of peroxisome proliferator activated receptors in brown trout (Salmo trutta f. fario). ACTA ACUST UNITED AC 2005; 1731:88-94. [PMID: 16229908 DOI: 10.1016/j.bbaexp.2005.09.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Revised: 09/12/2005] [Accepted: 09/14/2005] [Indexed: 11/19/2022]
Abstract
Although widely studied in mammals, little information about fish peroxisome proliferator activated receptors (PPARs) is yet available. As a baseline for future studies, the three PPAR isotypes were identified in brown trout (Salmo trutta f. fario) and their organ distribution pattern was established. The cDNA fragments encoding PPARs alpha, beta and gamma were amplified by PCR, and the deduced sequences of the correspondent peptides were compared with other species sequences. Both the 183 amino acid sequence from PPARalpha and the 103 amino acid sequence from PPARbeta shared high levels of homology with the correspondent peptides of other fishes and terrestrial vertebrates, whereas PPARgamma 108 amino acid sequence showed much less similarity with non-fish PPARgamma. According to both semi-quantitative RT-PCR and real-time RT-PCR, PPARalpha mRNA predominates in white muscle, heart and liver and PPARbeta is more expressed in testis, heart, liver, white muscle and trunk kidney. PPARgamma was only detected in trunk kidney and liver by real-time RT-PCR and also in spleen by semi-quantitative RT-PCR. PPARbeta seems to be the most strongly expressed isotype, whereas PPARgamma shows a much weaker global expression.
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Affiliation(s)
- Carla Batista-Pinto
- Laboratory of Cell Biology, ICBAS-Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal.
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85
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Crow KD, Stadler PF, Lynch VJ, Amemiya C, Wagner GP. The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts. Mol Biol Evol 2005; 23:121-36. [PMID: 16162861 DOI: 10.1093/molbev/msj020] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Hox gene complement of zebrafish, medaka, and fugu differs from that of other gnathostome vertebrates. These fishes have seven to eight Hox clusters compared to the four Hox clusters described in sarcopterygians and shark. The clusters in different teleost lineages are orthologous, implying that a "fish-specific" Hox cluster duplication has occurred in the stem lineage leading to the most recent common ancestor of zebrafish and fugu. The timing of this event, however, is unknown. To address this question, we sequenced four Hox genes from taxa representing basal actinopterygian and teleost lineages and compared them to known sequences from shark, coelacanth, zebrafish, and other teleosts. The resulting gene genealogies suggest that the fish-specific Hox cluster duplication occurred coincident with the origin of crown group teleosts. In addition, we obtained evidence for an independent Hox cluster duplication in the sturgeon lineage (Acipenseriformes). Finally, results from HoxA11 suggest that duplicated Hox genes have experienced diversifying selection immediately after the duplication event. Taken together, these results support the notion that the duplicated Hox genes of teleosts were causally relevant to adaptive evolution during the initial teleost radiation.
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Affiliation(s)
- Karen D Crow
- Department of Ecology and Evolutionary Biology, Yale University, USA.
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86
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Corredor-Adámez M, Welten MCM, Spaink HP, Jeffery JE, Schoon RT, de Bakker MAG, Bagowski CP, Meijer AH, Verbeek FJ, Richardson MK. Genomic annotation and transcriptome analysis of the zebrafish (Danio rerio) hox complex with description of a novel member, hoxb13a. Evol Dev 2005; 7:362-75. [PMID: 16174031 DOI: 10.1111/j.1525-142x.2005.05042.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The zebrafish (Danio rerio) is an important model in evolutionary developmental biology, and its study is being revolutionized by the zebrafish genome project. Sequencing is at an advanced stage, but annotation is largely the result of in silico analyses. We have performed genomic annotation, comparative genomics, and transcriptional analysis using microarrays of the hox homeobox-containing transcription factors. These genes have important roles in specifying the body plan. Candidate sequences were located in version Z v 4 of the Ensembl genome database by TBLASTN searching with Danio and other vertebrate published Hox protein sequences. Homologies were confirmed by alignment with reference sequences, and by the relative position of genes along each cluster. RT-PCR using adult Tübingen cDNA was used to confirm annotations, to check the genomic sequence and to confirm expression in vivo. Our RT-PCR and microarray data show that all 49 hox genes are expressed in adult zebrafish. Significant expression for all known hox genes could be detected in our microarray analysis. We also find significant expression of hox 8 paralogs and hox b 7 a in the anti-sense direction. A novel gene, D. rerio hox b 13 a, was identified, and a preliminary characterization by in situ hybridization showed expression at 24 hpf at the tip of the developing tail. We are currently characterizing this gene at the functional level. We argue that the oligo design for microarrays can be greatly enhanced by the availability of genomic sequences.
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Affiliation(s)
- M Corredor-Adámez
- Institute of Biology, Leiden University, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
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87
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Esbaugh AJ, Perry SF, Bayaa M, Georgalis T, Nickerson J, Tufts BL, Gilmour KM. Cytoplasmic carbonic anhydrase isozymes in rainbow trout Oncorhynchus mykiss: comparative physiology and molecular evolution. ACTA ACUST UNITED AC 2005; 208:1951-61. [PMID: 15879075 DOI: 10.1242/jeb.01551] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
It is well established that the gills of teleost fish contain substantial levels of cytoplasmic carbonic anhydrase (CA), but it is unclear which CA isozyme(s) might be responsible for this activity. The objective of the current study was to determine if branchial CA activity in rainbow trout was the result of a general cytoplasmic CA isozyme, with kinetic properties, tissue distribution and physiological functions distinct from those of the red blood cell (rbc)-specific CA isozyme. Isolation and sequencing of a second trout cytoplasmic CA yielded a 780 bp coding region that was 76% identical with the trout rbc CA (TCAb), although the active sites differed by only 1 amino acid. Interestingly, phylogenetic analyses did not group these two isozymes closely together, suggesting that more fish species may have multiple cytoplasmic CA isozymes. In contrast to TCAb, the second cytoplasmic CA isozyme had a wide tissue distribution with high expression in the gills and brain, and lower expression in many tissues, including the red blood cells. Thus, unlike TCAb, the second isozyme lacks tissue specificity and may be expressed in the cytoplasm of all cells. For this reason, it is referred to hereafter as TCAc (trout cytoplasmic CA). The inhibitor properties of both cytoplasmic isozymes were similar (Ki acetazolamide 1.21+/-0.18 nmol l(-1) and 1.34+/-0.10 nmol l(-1) for TCAc and TCAb, respectively). However, the turnover of TCAb was over three times greater than that of TCAc (30.3+/-5.83 vs 8.90+/-1.95 e4 s(-1), respectively), indicating that the rbc-specific CA isoform was significantly faster than the general cytoplasmic isoform. Induction of anaemia revealed differential expression of the two isozymes in the red blood cell; whereas TCAc mRNA expression was unaffected, TCAb mRNA expression was significantly increased by 30- to 60-fold in anaemic trout.
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Affiliation(s)
- A J Esbaugh
- Department of Biology, Queen's University, Kingston, ON, Canada K7L 3N6.
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88
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Jastroch M, Wuertz S, Kloas W, Klingenspor M. Uncoupling protein 1 in fish uncovers an ancient evolutionary history of mammalian nonshivering thermogenesis. Physiol Genomics 2005; 22:150-6. [PMID: 15886331 DOI: 10.1152/physiolgenomics.00070.2005] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Uncoupling proteins (UCPs) increase proton leakage across the inner mitochondrial membrane. Thereby, UCP1 in brown adipose tissue dissipates proton motive force as heat. This mechanism of nonshivering thermogenesis is considered as a monophyletic trait of endothermic placental mammals that emerged about 140 million years ago and provided a crucial advantage for life in the cold. The paralogues UCP2 and UCP3 are probably not thermogenic proteins but convey mild uncoupling, which may serve to reduce the rate of mitochondrial reactive oxygen species production. Both are present in endotherms (mammals and birds), but so far only UCP2 has been identified in ectothermic vertebrates (fish and amphibia). The evolution of UCPs is of general interest in the search for the origin of mammalian UCP1-mediated nonshivering thermogenesis. We here show the presence of UCP1 and UCP3 in ectothermic teleost fish species using comparative genomics, phylogenetic inference, and gene expression analysis. In the common carp ( Cyprinus carpio), UCP1 is predominantly expressed in the liver and strongly diminished in response to cold exposure, thus contrasting the cold-induced expression of mammalian UCP1 in brown adipose tissue. UCP3 mRNA is only found in carp skeletal muscle with expression levels increased fivefold in response to fasting. Our findings disprove the monophyletic nature of UCP1 in placental mammals and demonstrate that all three members of the core UCP family were already present before the divergence of ray-finned and lobe-finned vertebrate lineages about 420 million years ago.
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Affiliation(s)
- Martin Jastroch
- Department of Animal Physiology, Biology Faculty, Philipps-University Marburg, Germany
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89
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Leaver MJ, Boukouvala E, Antonopoulou E, Diez A, Favre-Krey L, Ezaz MT, Bautista JM, Tocher DR, Krey G. Three peroxisome proliferator-activated receptor isotypes from each of two species of marine fish. Endocrinology 2005; 146:3150-62. [PMID: 15790725 DOI: 10.1210/en.2004-1638] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The cloning and characterization of cDNAs and genes encoding three peroxisome proliferator-activated receptor (PPAR) isotypes from two species of marine fish, the plaice (Pleuronectes platessa) and the gilthead sea bream (Sparus aurata), are reported for the first time. Although differences in the genomic organization of the fish PPAR genes compared with their mammalian counterparts are evident, sequence alignments and phylogenetic comparisons show the fish genes to be homologs of mammalian PPARalpha, PPARbeta/delta, and PPARgamma. Like their mammalian homologs, fish PPARs bind to a variety of natural PPAR response elements (PPREs) present in the promoters of mammalian or piscine genes. In contrast, the mRNA expression pattern of PPARs in the two fish species differs from that observed in other vertebrates. Thus, PPARgamma is expressed more widely in fish tissues than in mammals, whereas PPARalpha and beta are expressed similarly in profile to mammals. Furthermore, nutritional status strongly influences the expression of all three PPAR isotypes in liver, whereas it has no effect on PPAR expression in intestinal and adipose tissues. Fish PPARalpha and beta exhibit an activation profile similar to that of the mammalian PPAR in response to a variety of activators/ligands, whereas PPARgamma is not activated by mammalian PPARgamma-specific ligands. Amino acid residues shown to be critical for ligand binding in mammalian PPARs are not conserved in fish PPARgamma and therefore, together with the distinct tissue expression profile of this receptor, suggest potential differences in the function of PPARgamma in fish compared with mammals.
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Affiliation(s)
- Michael J Leaver
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
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90
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Liu RZ, Sharma MK, Sun Q, Thisse C, Thisse B, Denovan-Wright EM, Wright JM. Retention of the duplicated cellular retinoic acid-binding protein 1 genes (crabp1a and crabp1b) in the zebrafish genome by subfunctionalization of tissue-specific expression. FEBS J 2005; 272:3561-71. [PMID: 16008556 DOI: 10.1111/j.1742-4658.2005.04775.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cellular retinoic acid-binding protein type I (CRABPI) is encoded by a single gene in mammals. We have characterized two crabp1 genes in zebrafish, designated crabp1a and crabp1b. These two crabp1 genes share the same gene structure as the mammalian CRABP1 genes and encode proteins that show the highest amino acid sequence identity to mammalian CRABPIs. The zebrafish crabp1a and crabp1b were assigned to linkage groups 25 and 7, respectively. Both linkage groups show conserved syntenies to a segment of the human chromosome 15 harboring the CRABP1 locus. Phylogenetic analysis suggests that the zebrafish crabp1a and crabp1b are orthologs of the mammalian CRABP1 genes that likely arose from a teleost fish lineage-specific genome duplication. Embryonic whole mount in situ hybridization detected zebrafish crabp1b transcripts in the posterior hindbrain and spinal cord from early stages of embryogenesis. crabp1a mRNA was detected in the forebrain and midbrain at later developmental stages. In adult zebrafish, crabp1a mRNA was localized to the optic tectum, whereas crabp1b mRNA was detected in several tissues by RT-PCR but not by tissue section in situ hybridization. The differential and complementary expression patterns of the zebrafish crabp1a and crabp1b genes imply that subfunctionalization may be the mechanism for the retention of both crabp1 duplicated genes in the zebrafish genome.
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Affiliation(s)
- Rong-Zong Liu
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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91
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Abstract
Teleost fish, which roughly make up half of the extant vertebrate species, exhibit an amazing level of biodiversity affecting their morphology, ecology and behaviour as well as many other aspects of their biology. This huge variability makes fish extremely attractive for the study of many biological questions, particularly of those related to evolution. New insights gained from different teleost species and sequencing projects have recently revealed several peculiar features of fish genomes that might have played a role in fish evolution and speciation. There is now substantial evidence that a round of tetraploidization/rediploidization has taken place during the early evolution of the ray-finned fish lineage, and that hundreds of duplicate pairs generated by this event have been maintained over hundreds of millions of years of evolution. Differential loss or subfunction partitioning of such gene duplicates might have been involved in the generation of fish variability. In contrast to mammalian genomes, teleost genomes also contain multiple families of active transposable elements, which might have played a role in speciation by affecting hybrid sterility and viability. Finally, the amazing diversity of sex determination systems and the plasticity of sex chromosomes observed in teleost might have been involved in both pre- and postmating reproductive isolation. Comparison of data generated by current and future genome projects as well as complementary studies in other species will allow one to approach the molecular and evolutionary mechanisms underlying genome diversity in fish, and will certainly significantly contribute to our understanding of gene evolution and function in humans and other vertebrates.
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Affiliation(s)
- J-N Volff
- BioFuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, am Hubland, D-97074 Würzburg, Germany.
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92
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Boukouvala E, Antonopoulou E, Favre-Krey L, Diez A, Bautista JM, Leaver MJ, Tocher DR, Krey G. Molecular characterization of three peroxisome proliferator-activated receptors from the sea bass (Dicentrarchus labrax). Lipids 2005; 39:1085-92. [PMID: 15726823 DOI: 10.1007/s11745-004-1334-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peroxisome proliferator-activated receptors (PPAR) are nuclear hormone receptors that control the expression of genes involved in lipid homeostasis in mammals. We searched for PPAR in sea bass, a marine fish of particular interest to aquaculture, after hypothesizing that the physiological and molecular processes that regulate lipid metabolism in fish are similar to those in mammals. Here, we report the identification of complementary DNA and corresponding genomic sequences that encode three distinct PPAR from sea bass. The sea bass PPAR are the structural homologs of the mammalian PPAR alpha, beta/delta, and gamma isotypes. As revealed by RNase protection, the tissue expression profile of the fish PPAR appears to be very similar to that of the mammalian PPAR homologs. Thus, PPAR alpha is mainly expressed in the liver, PPAR gamma in adipose tissue, and PPAR beta in all tissues tested, with its highest levels in the liver, where it is also the dominant isotype expressed. Like mammalian PPAR, the sea bass isotypes recognize and bind to PPAR response elements of both mammalian and piscine origin, as heterodimers with the 9-cis retinoic acid receptor. Through the coactivator-dependent receptor ligand assay, we also demonstrated that natural FA and synthetic hypolipidemic compounds can act as ligands of the sea bass PPAR alpha and beta isotypes. This suggests that the sea bass PPAR act through similar mechanisms and perform the same critical lipid metabolism functions as mammalian PPAR.
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Affiliation(s)
- Evridiki Boukouvala
- National Agricultural Research Foundation-Fisheries Research Institute, Nea Peramos, 64007 Kavala, Greece
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93
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Conlon JM, Larhammar D. The evolution of neuroendocrine peptides. Gen Comp Endocrinol 2005; 142:53-9. [PMID: 15862548 DOI: 10.1016/j.ygcen.2004.11.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Revised: 11/23/2004] [Accepted: 11/29/2004] [Indexed: 10/26/2022]
Abstract
The genomes of extant vertebrates have been shaped by a series of whole genome and individual gene duplication events. The 2R hypothesis, which postulates that two whole genome duplications occurred in relatively rapid succession very early in chordate evolution, is gaining increasing acceptance. A further entire genome duplication is believed to have occurred in the ancestral fish lineage approximately 320-350 Myr ago, as well as more recent independent tetraploidization events, mostly but not exclusively, in particular teleost and amphibian lineages. Superimposed upon these whole genome duplications are tandem or segmental duplications of individual genes or groups of genes that have taken place at different rates in the various vertebrate lineages. The majority of duplicated genes become pseudogenes or are deleted but some may evolve to encode components with new functional roles. Genes encoding members of neuropeptide Y- and tachykinin-families are associated with the HOX-bearing chromosomes and these systems provide examples of duplication events that have led to rapid evolution of the duplicated gene which has occasionally produced peptides, such as pancreatic polypeptide, seminalplasmin and hemokinin-1, with new biological functions.
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Affiliation(s)
- J Michael Conlon
- Department of Biochemistry, Faculty of Medicine and Health Sciences, United Arab Emirates University, 17666 Al-Ain, United Arab Emirates.
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94
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Wang XL, Mei J, Sun M, Hong YH, Gui JF. Identification of three duplicated Spin genes in medaka (Oryzias latipes). Gene 2005; 350:99-106. [PMID: 15792533 DOI: 10.1016/j.gene.2005.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2004] [Revised: 01/28/2005] [Accepted: 02/08/2005] [Indexed: 10/25/2022]
Abstract
Gene and genomic duplications are very important and frequent events in fish evolution, and the divergence of duplicated genes in sequences and functions is a focus of research on gene evolution. Here, we report the identification and characterization of three duplicated Spindlin (Spin) genes from medaka (Oryzias latipes): OlSpinA, OlSpinB, and OlSpinC. Molecular cloning, genomic DNA Blast analysis and phylogenetic relationship analysis demonstrated that the three duplicated OlSpin genes should belong to gene duplication. Furthermore, Western blot analysis revealed significant expression differences of the three OlSpins among different tissues and during embryogenesis in medaka, and suggested that sequence and functional divergence might have occurred in evolution among them.
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MESH Headings
- Amino Acid Sequence
- Animals
- Blotting, Western
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- Fish Proteins/genetics
- Fish Proteins/metabolism
- Gene Duplication
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Microtubule-Associated Proteins/genetics
- Microtubule-Associated Proteins/metabolism
- Molecular Sequence Data
- Multigene Family/genetics
- Oryzias/embryology
- Oryzias/genetics
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Phylogeny
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Transcription, Genetic
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Affiliation(s)
- Xiao-Lei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Wuhan Center for Developmental Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate School of Chinese Academy of Sciences, Wuhan 430072, PR China
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95
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Harduin-Lepers A, Mollicone R, Delannoy P, Oriol R. The animal sialyltransferases and sialyltransferase-related genes: a phylogenetic approach. Glycobiology 2005; 15:805-17. [PMID: 15843597 DOI: 10.1093/glycob/cwi063] [Citation(s) in RCA: 213] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The animal sialyltransferases are Golgi type II transmembrane glycosyltransferases. Twenty distinct sialyltransferases have been identified in both human and murine genomes. These enzymes catalyze transfer of sialic acid from CMP-Neu5Ac to the glycan moiety of glycoconjugates. Despite low overall identities, they share four conserved peptide motifs [L (large), S (small), motif III, and motif VS (very small)] that are hallmarks for sialyltransferase identification. We have identified 155 new putative genes in 25 animal species, and we have exploited two lines of evidence: (1) sequence comparisons and (2) exon-intron organization of the genes. An ortholog to the ancestor present before the split of ST6Gal I and II subfamilies was detected in arthropods. An ortholog to the ancestor present before the split of ST6GalNAc III, IV, V, and VI subfamilies was detected in sea urchin. An ortholog to the ancestor present before the split of ST3Gal I and II subfamilies was detected in ciona, and an ortholog to the ancestor of all the ST8Sia was detected in amphioxus. Therefore, single examples of the four families (ST3Gal, ST6Gal, ST6GalNAc, and ST8Sia) have appeared in invertebrates, earlier than previously thought, whereas the four families were all detected in bony fishes, amphibians, birds, and mammals. As previously hypothesized, sequence similarities among sialyltransferases suggest a common genetic origin, by successive duplications of an ancestral gene, followed by divergent evolution. Finally, we propose predictions on these invertebrates sialyltransferase-related activities that have not previously been demonstrated and that will ultimately need to be substantiated by protein expression and enzymatic activity assays.
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Affiliation(s)
- Anne Harduin-Lepers
- Glycobiologie Structurale et Fonctionnelle, UMR CNRS/USTL 8576, Laboratoire de Chimie Biologique, Bâtiment C9, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq cedex, France. [corrected]
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96
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Abstract
Fish offer important advantages for defining the organism-environment interface and responses to natural or anthropogenic stressors. Genomic approaches using fish promise increased investigative power, and have already provided insights into the mechanisms that underlie short-term and long-term environmental adaptations. The range of fish species for which genomic resources are available is increasing, but will require significant further expansion for the optimal application of fish environmental genomics.
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Affiliation(s)
- Andrew R Cossins
- Andrew R. Cossins is at the Liverpool Microarray Facility and Centre for BioArray Innovation, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.
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97
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Wang DS, Senthilkumaran B, Sudhakumari CC, Sakai F, Matsuda M, Kobayashi T, Yoshikuni M, Nagahama Y. Molecular cloning, gene expression and characterization of the third estrogen receptor of the Nile tilapia, Oreochromis niloticus. FISH PHYSIOLOGY AND BIOCHEMISTRY 2005; 31:255-266. [PMID: 20035467 DOI: 10.1007/s10695-006-0033-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Estrogens are essential for many reproductive and non-reproductive functions. In teleosts, it is well-known that several subtypes of estrogen receptors are required for the precise action of estrogens. Present study describes the cloning of the third estrogen receptor, ER- beta2, from the Nile tilapia by EST sequencing coupled microarray. The cloned ER-beta2 showed 77.7% amino acid identity with the reported Atlantic croaker ER-beta. Three ERs, ER-alpha, ER-beta1 and ER-beta2, from the fugu genome were also isolated to analyze their gene structures. Comparison of the intron/exon boundaries and exon numbers of fugu, tilapia, rainbow trout and zebrafish, and phylogenetic analysis of 63 ER sequences revealed that ER-beta probably underwent two successive lineage-specific duplications in teleost. The former took place only in zebrafish lineage, and the latter took place in advanced teleosts without the zebrafish lineage, whereas no duplication of the ER-alpha gene has been detected. Tissue distribution analysis by RT-PCR revealed that tilapia ER-alpha and ER-beta1 were expressed ubiquitously, whereas ER-beta2 is expressed only in the pituitary, liver, intestine, kidney and gonads, with the highest expression in the testis and the lowest level in the ovary. Northern blot analysis detected a single transcript of about 3.4 kb in the testis but not in the ovary mRNAs. In transient transfection assays using human embryonic kidney 293 (HEK293) cells, tilapia ER-beta2 showed estrodiol-17beta dependent transactivation.
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Affiliation(s)
- D S Wang
- Laboratory of Reproductive Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
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Cole NJ, Hall TE, Martin CI, Chapman MA, Kobiyama A, Nihei Y, Watabe S, Johnston IA. Temperature and the expression of myogenic regulatory factors (MRFs) and myosin heavy chain isoforms during embryogenesis in the common carp Cyprinus carpio L. ACTA ACUST UNITED AC 2005; 207:4239-48. [PMID: 15531645 DOI: 10.1242/jeb.01263] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Embryos of the common carp, Cyprinus carpio L., were reared from fertilization of the eggs to inflation of the swim bladder in the larval stage at 18 and 25 degrees C. cRNA probes were used to detect transcripts of the myogenic regulatory factors MyoD, Myf-5 and myogenin, and five myosin heavy chain (MyHC) isoforms during development. The genes encoding Myf-5 and MyoD were switched on first in the unsegmented mesoderm, followed by myogenin as the somites developed. Myf-5 and MyoD transcripts were initially limited to the adaxial cells, but Myf-5 expression spread laterally into the presomitic mesoderm before somite formation. Two distinct bands of staining could be seen corresponding to the cellular fields of the forming somites, but as each furrow delineated, Myf-5 mRNA levels declined. Upon somite formation, MyoD expression spread laterally to encompass the full somite width. Expression of the myogenin gene was also switched on during somite formation, and expression of both transcripts persisted until the somites became chevron-shaped. Expression of MyoD was then downregulated shortly before myogenin. The expression patterns of the carp myogenic regulatory factor (MRF) genes most-closely resembled that seen in the zebrafish rather than the rainbow trout (where expression of MyoD remains restricted to the adaxial domain of the somite for a prolonged period) or the herring (where expression of MyoD persists longer than that of myogenin). Expression of two embryonic forms of MyHC began simultaneously at the 25-30 somite stage and continued until approximately two weeks post-hatch. However, the three adult isoforms of fast muscle MyHC were not detected in any stage examined, emphasizing a developmental gap that must be filled by other, as yet uncharacterised, MyHC isoform(s). No differences in the timing of expression of any mRNA transcripts were seen between temperature groups. A phylogenetic analysis of the MRFs was conducted using all available full-length amino acid sequences. A neighbour-joining tree indicated that all four members evolved from a common ancestral gene, which first duplicated into two lineages, each of which underwent a further duplication to produce Myf-5 and MyoD, and myogenin and MRF4. Parologous copies of MyoD from trout and Xenopus clustered closely together within clades, indicating recent duplications. By contrast, MyoD paralogues from gilthead seabream were more divergent, indicating a more-ancient duplication.
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Affiliation(s)
- Nicholas J Cole
- Division of Cell and Developmental Biology, MSI/WTB Complex, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
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99
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Venkatesh B, Yap WH. Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elements. Bioessays 2005; 27:100-7. [PMID: 15612032 DOI: 10.1002/bies.20134] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
With the imminent completion of the whole genome sequence of humans, increasing attention is being focused on the annotation of cis-regulatory elements in the human genome. Comparative genomics approaches based on evolutionary conservation have proved useful in the detection of conserved cis-regulatory elements. The pufferfish, Fugu rubripes, is an attractive vertebrate model for comparative genomics, by virtue of its compact genome and maximal phylogenetic distance from mammals. Fugu has lost a large proportion of nonessential DNA, and retained single orthologs for many duplicate genes that arose in the fish lineage. Non-coding sequences conserved between fugu and mammals have been shown to be functional cis-regulatory elements. Thus, fugu is a model fish genome of choice for discovering evolutionarily conserved regulatory elements in the human genome. Such evolutionarily conserved elements are likely to be shared by all vertebrates, and related to regulatory interactions fundamental to all vertebrates. The functions of these conserved vertebrate elements can be rapidly assayed in mammalian cell lines or in transgenic systems such as zebrafish/medaka and Xenopus, followed by validation of crucial elements in transgenic rodents.
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Affiliation(s)
- Byrappa Venkatesh
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673.
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100
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Shiina T, Dijkstra JM, Shimizu S, Watanabe A, Yanagiya K, Kiryu I, Fujiwara A, Nishida-Umehara C, Kaba Y, Hirono I, Yoshiura Y, Aoki T, Inoko H, Kulski JK, Ototake M. Interchromosomal duplication of major histocompatibility complex class I regions in rainbow trout (Oncorhynchus mykiss), a species with a presumably recent tetraploid ancestry. Immunogenetics 2005; 56:878-93. [PMID: 15696305 DOI: 10.1007/s00251-004-0755-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Revised: 11/17/2004] [Indexed: 10/25/2022]
Abstract
Salmonid fishes are among the few animal taxa with a probable recent tetraploid ancestor. The present study is the first to compare large (>100 kb) duplicated genomic sequence fragments in such species. Two contiguous stretches with major histocompatibility complex (MHC) class I genes were detected in a rainbow trout BAC library, mapped and sequenced. The MHC class I duplicated regions, mapped by fluorescence in situ hybridization (FISH), were shown to be located on different metaphase chromosomes, Chr 14 and 18. Gene organization in both duplications is similar to that in other fishes, in that the class I loci are tightly linked with the PSMB8, PSMB9, PSMB10 and ABCB3 genes. Whereas one region, Onmy-IA, has a classical MHC class I locus (UBA), Onmy-IB encodes only non-classical class Ib proteins. The nucleotide diversity between the Onmy-IA and Onmy-IB noncoding regions is about 14%. This suggests that the MHC class I duplication event has occurred about 60 mya close to the time of an hypothesized ancestral tetraploid event. The present article is the first convincing report on the co-existence of two closely related MHC class I core regions on two different chromosomes. The interchromosomal duplication and the homology levels are supportive of the tetraploid model.
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Affiliation(s)
- Takashi Shiina
- Department of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan.
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