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Stennette KA, Godwin JR. Estrogenic influences on agonistic behavior in teleost fishes. Horm Behav 2024; 161:105519. [PMID: 38452611 DOI: 10.1016/j.yhbeh.2024.105519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024]
Abstract
Teleost fishes show an extraordinary diversity of sexual patterns, social structures, and sociosexual behaviors. Sex steroid hormones are key modulators of social behaviors in teleosts as in other vertebrates and act on sex steroid receptor-containing brain nuclei that form the evolutionarily conserved vertebrate social behavior network (SBN). Fishes also display important differences relative to tetrapod vertebrates that make them particularly well-suited to study the physiological mechanisms modulating social behavior. Specifically, fishes exhibit high levels of brain aromatization and have what has been proposed to be a lifelong, steroid hormone dependent plasticity in the neural substrates mediating sociosexual behavior. In this review, we examine how estrogenic signaling modulates sociosexual behaviors in teleosts with a particular focus on agonistic behavior. Estrogens have been shown to mediate agonistic behaviors in a broad range of fishes, from sexually monomorphic gonochoristic species to highly dimorphic sex changers with alternate reproductive phenotypes. These similarities across such diverse taxa contribute to a growing body of evidence that estrogens play a crucial role in the modulation of aggression in vertebrates. As analytical techniques and genomic tools rapidly advance, methods such as LC-MS/MS, snRNAseq, and CRISPR-based mutagenesis show great promise to further elucidate the mechanistic basis of estrogenic effects on social behavior in the diverse teleost lineage.
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Affiliation(s)
- Katherine A Stennette
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - John R Godwin
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA.
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Guo C, Zhang K, Li C, Xing R, Xu S, Wang D, Wang X. Cyp19a1a Promotes Ovarian Maturation through Regulating E2 Synthesis with Estrogen Receptor 2a in Pampus argenteus (Euphrasen, 1788). Int J Mol Sci 2024; 25:1583. [PMID: 38338860 PMCID: PMC10855460 DOI: 10.3390/ijms25031583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
In the artificial breeding of Pampus argenteus (Euphrasen, 1788), female fish spawn before male release sperm, which indicates rapid ovarian development. In fish, aromatase is responsible for converting androgens into estrogens and estrogen plays a crucial role in ovarian development. In this study, we aimed to investigate the potential role of brain-type and ovarian-type aromatase to study the rapid ovarian development mechanism. The results showed that cyp19a1a was mainly expressed in the ovary and could be classified as the ovarian type, whereas cyp19a1b could be considered as the brain type for its expression was mainly in the brain. During ovarian development, the expression of cyp19a1a in the ovary significantly increased from stage IV to stage V and Cyp19a1a signals were present in the follicle cells, while cyp19a1b expression in the pituitary gland decreased from stage IV to stage V. To further investigate the function of Cyp19a1a, recombinant Cyp19a1a (rCyp19a1a) was produced and specific anti-Cyp19a1a antiserum was obtained. The expressions of cyp19a1a, estrogen receptors 2 alpha (esr2a), and androgen receptor alpha (arα) were significantly upregulated in the presence of rCyp19a1a. Meanwhile, cyp19a1a was expressed significantly after E2 treatment in both ovarian and testicular tissue culture. Taken together, we found two forms of aromatase in silver pomfret. The ovarian-type aromatase might play an important role in ovarian differentiation and maturation, and participate in E2 synthesis through co-regulation with esr2a. The brain-type aromatase cyp19a1b might be involved in the regulation of both brain and gonadal development.
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Affiliation(s)
- Chunyang Guo
- College of Marine Science, Ningbo University, Ningbo 315211, China; (C.G.); (K.Z.); (C.L.); (R.X.); (S.X.); (D.W.)
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo 315211, China
| | - Kai Zhang
- College of Marine Science, Ningbo University, Ningbo 315211, China; (C.G.); (K.Z.); (C.L.); (R.X.); (S.X.); (D.W.)
| | - Chang Li
- College of Marine Science, Ningbo University, Ningbo 315211, China; (C.G.); (K.Z.); (C.L.); (R.X.); (S.X.); (D.W.)
| | - Ruixue Xing
- College of Marine Science, Ningbo University, Ningbo 315211, China; (C.G.); (K.Z.); (C.L.); (R.X.); (S.X.); (D.W.)
| | - Shanliang Xu
- College of Marine Science, Ningbo University, Ningbo 315211, China; (C.G.); (K.Z.); (C.L.); (R.X.); (S.X.); (D.W.)
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo 315211, China
| | - Danli Wang
- College of Marine Science, Ningbo University, Ningbo 315211, China; (C.G.); (K.Z.); (C.L.); (R.X.); (S.X.); (D.W.)
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo 315211, China
| | - Xubo Wang
- College of Marine Science, Ningbo University, Ningbo 315211, China; (C.G.); (K.Z.); (C.L.); (R.X.); (S.X.); (D.W.)
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo 315211, China
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Zhi F, Jiang DN, Mustapha UF, Li SX, Shi HJ, Li GL, Zhu CH. Expression and regulation of 42Sp50 in spotted scat (Scatophagus argus). Front Genet 2022; 13:964150. [PMID: 36035129 PMCID: PMC9403048 DOI: 10.3389/fgene.2022.964150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
42Sp50 is an isoform of the eukaryotic translation elongation factor 1 A (eEF1A) and is vital for fish ovarian development. Spotted scat (Scatophagus argus) is a popular marine cultured fish species in Southern Asia and China, and its artificial reproduction is complicated, with a relatively low success ratio in practice. In this study, the 42Sp50 gene was cloned from spotted scat. Tissue distribution analysis showed that 42Sp50 was mainly expressed in the ovary. qRT-PCR showed that 42Sp50 expression levels gradually decreased insignificantly in the ovaries from phase II to IV. Western blot analysis showed that 42Sp50 was highly expressed in the ovary, while it was almost undetectable in the testis. Immunohistochemistry analysis stained 42Sp50 mainly in the cytoplasm of the previtellogenic oocytes in ovaries of normal XX-female and sex-reversed XY-female. Aside from fish and amphibians, 42Sp50 was also identified in some reptile species using genomic database searching. Analyses of the transcriptome data from four different fish species (Hainan medaka (Oryzias curvinotus), silver sillago (Sillago sihama), Nile tilapia (Oreochromis niloticus), and Hong Kong catfish (Clarias fuscus)) revealed ovaries biased expression of 42Sp50 in all, similar to spotted scat. While the neighbor genes of 42Sp50 did not show ovary biased expression in the fish species analyzed. Bisulfite Sequencing PCR (BSP) results showed that the DNA methylation level of 42Sp50 promoter was low in ovaries, testes, and muscles. The luciferase reporter assay demonstrated that Dmrt4 activated 42Sp50 expression in the presence of Sf1 or Foxh1. These results suggest that 42Sp50 may be involved in regulating the early phase oocytes development of spotted scat.
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The First Genome Survey and De Novo Assembly of the Short Mackerel (Rastrelliger brachysoma) and Indian Mackerel (Rastrelliger kanagurta). Animals (Basel) 2022; 12:ani12141769. [PMID: 35883316 PMCID: PMC9312166 DOI: 10.3390/ani12141769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/29/2022] [Accepted: 07/08/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Mackerel species are commercially important marine species in Southeast Asia, especially short mackerel and Indian mackerel. However, genomic information about them is still limited. Genome survey of these two mackerel species was reported in this study. Next-generation sequencing and comprehensive bioinformatics were performed to obtain the genetic information. The estimated genome size of both species is around 680 Mbp. The heterozygosity of these species was very similar, while the repeat content for Indian mackerel was slightly higher than for short mackerel. Functional annotation also was reported in this study. This is the first reported genome survey and assembly of species in the genus Rastrelliger and could be useful for future comparative genomic studies. Abstract Rastrelliger brachysoma (short mackerel) and Rastrelliger kanagurta (Indian mackerel) are commercially important marine species in Southeast Asia. In recent years, numbers of these two species have been decreasing in the wild, and genomic information about them is still limited. We conducted a genome survey of these two mackerel species to acquire essential genomic information using next-generation sequencing data. To obtain this genetic information, comprehensive bioinformatics analyses were performed, including de novo assembly, gene prediction, functional annotation, and phylogenetic analysis. The estimated genome sizes were around 680.14 Mbp (R. brachysoma) and 688.82 Mbp (R. kanagurta). The heterozygosity of these species was very similar (≈0.81), while the repeat content for R. kanagurta (9.30%) was slightly higher than for R. brachysoma (8.30%). Functional annotation indicated that most of the genes predicted in these two species shared very close average amino acid identities (94.06%). The phylogenetic analysis revealed close phylogenetic relationships between these two species and other scombrids. This is the first reported genome survey and assembly of species in the genus Rastrelliger and could be useful for future comparative genomic studies.
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Boonekamp FJ, Knibbe E, Vieira-Lara MA, Wijsman M, Luttik MAH, van Eunen K, Ridder MD, Bron R, Almonacid Suarez AM, van Rijn P, Wolters JC, Pabst M, Daran JM, Bakker BM, Daran-Lapujade P. Full humanization of the glycolytic pathway in Saccharomyces cerevisiae. Cell Rep 2022; 39:111010. [PMID: 35767960 DOI: 10.1016/j.celrep.2022.111010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/03/2022] [Accepted: 06/07/2022] [Indexed: 12/22/2022] Open
Abstract
Although transplantation of single genes in yeast plays a key role in elucidating gene functionality in metazoans, technical challenges hamper humanization of full pathways and processes. Empowered by advances in synthetic biology, this study demonstrates the feasibility and implementation of full humanization of glycolysis in yeast. Single gene and full pathway transplantation revealed the remarkable conservation of glycolytic and moonlighting functions and, combined with evolutionary strategies, brought to light context-dependent responses. Human hexokinase 1 and 2, but not 4, required mutations in their catalytic or allosteric sites for functionality in yeast, whereas hexokinase 3 was unable to complement its yeast ortholog. Comparison with human tissues cultures showed preservation of turnover numbers of human glycolytic enzymes in yeast and human cell cultures. This demonstration of transplantation of an entire essential pathway paves the way for establishment of species-, tissue-, and disease-specific metazoan models.
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Affiliation(s)
- Francine J Boonekamp
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Ewout Knibbe
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Marcel A Vieira-Lara
- Laboratory of Pediatrics, Section Systems Medicine and Metabolic Signalling, Center for Liver, Digestive and Metabolic Disease, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Melanie Wijsman
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Karen van Eunen
- Laboratory of Pediatrics, Section Systems Medicine and Metabolic Signalling, Center for Liver, Digestive and Metabolic Disease, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Maxime den Ridder
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Reinier Bron
- Department of Biomedical Engineering-FB40, W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ana Maria Almonacid Suarez
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Patrick van Rijn
- Department of Biomedical Engineering-FB40, W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Justina C Wolters
- Laboratory of Pediatrics, Section Systems Medicine and Metabolic Signalling, Center for Liver, Digestive and Metabolic Disease, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Barbara M Bakker
- Laboratory of Pediatrics, Section Systems Medicine and Metabolic Signalling, Center for Liver, Digestive and Metabolic Disease, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands.
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Liang Y, Grauvogl M, Meyer A, Kratochwil CF. Functional conservation and divergence of color‐pattern‐related agouti family genes in teleost fishes. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:443-450. [DOI: 10.1002/jez.b.23041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/31/2021] [Accepted: 02/27/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Yipeng Liang
- Department of Biology, Chair in Zoology and Evolutionary Biology University of Konstanz Konstanz Germany
| | - Maximilian Grauvogl
- Department of Biology, Chair in Zoology and Evolutionary Biology University of Konstanz Konstanz Germany
| | - Axel Meyer
- Department of Biology, Chair in Zoology and Evolutionary Biology University of Konstanz Konstanz Germany
| | - Claudius F. Kratochwil
- Department of Biology, Chair in Zoology and Evolutionary Biology University of Konstanz Konstanz Germany
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Cellular Mechanisms Participating in Brain Repair of Adult Zebrafish and Mammals after Injury. Cells 2021; 10:cells10020391. [PMID: 33672842 PMCID: PMC7917790 DOI: 10.3390/cells10020391] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open
Abstract
Adult neurogenesis is an evolutionary conserved process occurring in all vertebrates. However, striking differences are observed between the taxa, considering the number of neurogenic niches, the neural stem cell (NSC) identity, and brain plasticity under constitutive and injury-induced conditions. Zebrafish has become a popular model for the investigation of the molecular and cellular mechanisms involved in adult neurogenesis. Compared to mammals, the adult zebrafish displays a high number of neurogenic niches distributed throughout the brain. Furthermore, it exhibits a strong regenerative capacity without scar formation or any obvious disabilities. In this review, we will first discuss the similarities and differences regarding (i) the distribution of neurogenic niches in the brain of adult zebrafish and mammals (mainly mouse) and (ii) the nature of the neural stem cells within the main telencephalic niches. In the second part, we will describe the cascade of cellular events occurring after telencephalic injury in zebrafish and mouse. Our study clearly shows that most early events happening right after the brain injury are shared between zebrafish and mouse including cell death, microglia, and oligodendrocyte recruitment, as well as injury-induced neurogenesis. In mammals, one of the consequences following an injury is the formation of a glial scar that is persistent. This is not the case in zebrafish, which may be one of the main reasons that zebrafish display a higher regenerative capacity.
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Fontaine R, Royan MR, von Krogh K, Weltzien FA, Baker DM. Direct and Indirect Effects of Sex Steroids on Gonadotrope Cell Plasticity in the Teleost Fish Pituitary. Front Endocrinol (Lausanne) 2020; 11:605068. [PMID: 33365013 PMCID: PMC7750530 DOI: 10.3389/fendo.2020.605068] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/12/2020] [Indexed: 12/26/2022] Open
Abstract
The pituitary gland controls many important physiological processes in vertebrates, including growth, homeostasis, and reproduction. As in mammals, the teleost pituitary exhibits a high degree of plasticity. This plasticity permits changes in hormone production and secretion necessary to meet the fluctuating demands over the life of an animal. Pituitary plasticity is achieved at both cellular and population levels. At the cellular level, hormone synthesis and release can be regulated via changes in cell composition to modulate both sensitivity and response to different signals. At the cell population level, the number of cells producing a given hormone can change due to proliferation, differentiation of progenitor cells, or transdifferentiation of specific cell types. Gonadotropes, which play an important role in the control of reproduction, have been intensively investigated during the last decades and found to display plasticity. To ensure appropriate endocrine function, gonadotropes rely on external and internal signals integrated at the brain level or by the gonadotropes themselves. One important group of internal signals is the sex steroids, produced mainly by the gonadal steroidogenic cells. Sex steroids have been shown to exert complex effects on the teleost pituitary, with differential effects depending on the species investigated, physiological status or sex of the animal, and dose or method of administration. This review summarizes current knowledge of the effects of sex steroids (androgens and estrogens) on gonadotrope cell plasticity in teleost anterior pituitary, discriminating direct from indirect effects.
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Affiliation(s)
- Romain Fontaine
- Physiology Unit, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Muhammad Rahmad Royan
- Physiology Unit, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Kristine von Krogh
- Physiology Unit, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Finn-Arne Weltzien
- Physiology Unit, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Dianne M. Baker
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, VA, United States
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9
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Hou ZS, Xin YR, Zeng C, Zhao HK, Tian Y, Li JF, Wen HS. GHRH-SST-GH-IGF axis regulates crosstalk between growth and immunity in rainbow trout (Oncorhynchus mykiss) infected with Vibrio anguillarum. FISH & SHELLFISH IMMUNOLOGY 2020; 106:887-897. [PMID: 32866610 DOI: 10.1016/j.fsi.2020.08.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/15/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
An energy trade-off is existed between immunological competence and growth. The axis of growth hormone releasing hormone, somatostatin, growth hormone, insulin-like growth factor (GHRH-SST-GH-IGF axis) regulates growth performances and immune competences in rainbow trout (Oncorhynchus mykiss). The salmonid-specific whole genome duplication event is known to result in duplicated copies of several key genes in GHRH-SST-GH-IGF axis. In this study, we evaluated the physiological functions of GHRH-SST-GH-IGF axis in regulating crosstalk between growth and immunity. Based on principal components analysis (PCA), we observed the overall expression profiles of GHRH-SST-GH-IGF axis were significantly altered by Vibrio anguillarum infection. Trout challenged with Vibrio anguillarum showed down-regulated igf1s subtypes and up-regulated igfbp1a1. The brain sst genes (sst1a, sst1b, sst3b and sst5) and igfpbs genes (igfbp4s and igfbp5b2) were significantly affected by V. anguillarum infection, while the igfbp4s, igfbp5s, igfbp6s and igf2bps genes showed significant changes in peripheral immune tissues in response to V. anguillarum infection. Gene enrichment analyses showed functional and signaling pathways associated with apoptosis (such as p53, HIF-1 or FoxO signaling) were activated. We further proposed a possible model that describes the IGF and IGFBPs-regulated interaction between cell growth and programmed death. Our study provided new insights into the physiological functions and potentially regulatory mechanisms of the GHRH-SST-GH-IGF axis, indicating the pleiotropic effects of GHRH-SST-GH-IGF axis in regulating crosstalk between growth and immunity in trout.
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Affiliation(s)
- Zhi-Shuai Hou
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education (KLMME), Qingdao, China.
| | - Yuan-Ru Xin
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education (KLMME), Qingdao, China
| | - Chu Zeng
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education (KLMME), Qingdao, China
| | - Hong-Kui Zhao
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education (KLMME), Qingdao, China
| | - Yuan Tian
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education (KLMME), Qingdao, China
| | - Ji-Fang Li
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education (KLMME), Qingdao, China
| | - Hai-Shen Wen
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education (KLMME), Qingdao, China.
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Conant GC. The lasting after-effects of an ancient polyploidy on the genomes of teleosts. PLoS One 2020; 15:e0231356. [PMID: 32298330 PMCID: PMC7161988 DOI: 10.1371/journal.pone.0231356] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/20/2020] [Indexed: 12/20/2022] Open
Abstract
The ancestor of most teleost fishes underwent a whole-genome duplication event three hundred million years ago. Despite its antiquity, the effects of this event are evident both in the structure of teleost genomes and in how the surviving duplicated genes still operate to drive form and function. I inferred a set of shared syntenic regions that survive from the teleost genome duplication (TGD) using eight teleost genomes and the outgroup gar genome (which lacks the TGD). I then phylogenetically modeled the TGD's resolution via shared and independent gene losses and applied a new simulation-based statistical test for the presence of bias toward the preservation of genes from one parental subgenome. On the basis of that test, I argue that the TGD was likely an allopolyploidy. I find that duplicate genes surviving from this duplication in zebrafish are less likely to function in early embryo development than are genes that have returned to single copy at some point in this species' history. The tissues these ohnologs are expressed in, as well as their biological functions, lend support to recent suggestions that the TGD was the source of a morphological innovation in the structure of the teleost retina. Surviving duplicates also appear less likely to be essential than singletons, despite the fact that their single-copy orthologs in mouse are no less essential than other genes.
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Affiliation(s)
- Gavin C. Conant
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America
- Program in Genetics, North Carolina State University, Raleigh, NC, United States of America
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States of America
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Wang XS, Zhang S, Xu Z, Zheng SQ, Long J, Wang DS. Genome-wide identification, evolution of ATF/CREB family and their expression in Nile tilapia. Comp Biochem Physiol B Biochem Mol Biol 2019; 237:110324. [DOI: 10.1016/j.cbpb.2019.110324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/09/2019] [Accepted: 08/22/2019] [Indexed: 01/06/2023]
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12
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Cartography of rhodopsin-like G protein-coupled receptors across vertebrate genomes. Sci Rep 2019; 9:7058. [PMID: 31064998 PMCID: PMC6504862 DOI: 10.1038/s41598-018-33120-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 09/17/2018] [Indexed: 12/26/2022] Open
Abstract
We conduct a cartography of rhodopsin-like non-olfactory G protein-coupled receptors in the Ensembl database. The most recent genomic data (releases 90–92, 90 vertebrate genomes) are analyzed through the online interface and receptors mapped on phylogenetic guide trees that were constructed based on a set of ~14.000 amino acid sequences. This snapshot of genomic data suggest vertebrate genomes to harbour 142 clades of GPCRs without human orthologues. Among those, 69 have not to our knowledge been mentioned or studied previously in the literature, of which 28 are distant from existing receptors and likely new orphans. These newly identified receptors are candidates for more focused evolutionary studies such as chromosomal mapping as well for in-depth pharmacological characterization. Interestingly, we also show that 37 of the 72 human orphan (or recently deorphanized) receptors included in this study cluster into nineteen closely related groups, which implies that there are less ligands to be identified than previously anticipated. Altogether, this work has significant implications when discussing nomenclature issues for GPCRs.
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Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes. Proc Natl Acad Sci U S A 2019; 116:2165-2174. [PMID: 30674676 PMCID: PMC6369804 DOI: 10.1073/pnas.1801757116] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Studying the organization of genes within genomes across broad evolutionary timescales can advance our understanding of the evolution of traits and clades. We have used a network approach to investigate genome dynamics of mammals and angiosperms. In general, genome organization and gene microcollinearity is much more conserved in mammals than in flowering plants. We then identified the genomic outliers or “rebel genes,” within each clade. Genes that have moved are unusual for mammals, whereas highly conserved single-copy genes are exceptional for plants. How conservation and changes in synteny or fundamental differences in genome organization have contributed to the evolution of lineages could be a new scientific frontier. A comprehensive analysis of relative gene order, or microsynteny, can provide valuable information for understanding the evolutionary history of genes and genomes, and ultimately traits and species, across broad phylogenetic groups and divergence times. We have used our network-based phylogenomic synteny analysis pipeline to first analyze the overall patterns and major differences between 87 mammalian and 107 angiosperm genomes. These two important groups have both evolved and radiated over the last ∼170 MYR. Secondly, we identified the genomic outliers or “rebel genes” within each clade. We theorize that rebel genes potentially have influenced trait and lineage evolution. Microsynteny networks use genes as nodes and syntenic relationships between genes as edges. Networks were decomposed into clusters using the Infomap algorithm, followed by phylogenomic copy-number profiling of each cluster. The differences in syntenic properties of all annotated gene families, including BUSCO genes, between the two clades are striking: most genes are single copy and syntenic across mammalian genomes, whereas most genes are multicopy and/or have lineage-specific distributions for angiosperms. We propose microsynteny scores as an alternative and complementary metric to BUSCO for assessing genome assemblies. We further found that the rebel genes are different between the two groups: lineage-specific gene transpositions are unusual in mammals, whereas single-copy highly syntenic genes are rare for flowering plants. We illustrate several examples of mammalian transpositions, such as brain-development genes in primates, and syntenic conservation across angiosperms, such as single-copy genes related to photosynthesis. Future experimental work can test if these are indeed rebels with a cause.
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Weger M, Diotel N, Weger BD, Beil T, Zaucker A, Eachus HL, Oakes JA, do Rego JL, Storbeck KH, Gut P, Strähle U, Rastegar S, Müller F, Krone N. Expression and activity profiling of the steroidogenic enzymes of glucocorticoid biosynthesis and the fdx1 co-factors in zebrafish. J Neuroendocrinol 2018; 30:e12586. [PMID: 29486070 DOI: 10.1111/jne.12586] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/06/2018] [Accepted: 02/22/2018] [Indexed: 01/23/2023]
Abstract
The spatial and temporal expression of steroidogenic genes in zebrafish has not been fully characterised. Because zebrafish are increasingly employed in endocrine and stress research, a better characterisation of steroidogenic pathways is required to target specific steps in the biosynthetic pathways. In the present study, we have systematically defined the temporal and spatial expression of steroidogenic enzymes involved in glucocorticoid biosynthesis (cyp21a2, cyp11c1, cyp11a1, cyp11a2, cyp17a1, cyp17a2, hsd3b1, hsd3b2), as well as the mitochondrial electron-providing ferredoxin co-factors (fdx1, fdx1b), during zebrafish development. Our studies showed an early expression of all these genes during embryogenesis. In larvae, expression of cyp11a2, cyp11c1, cyp17a2, cyp21a2, hsd3b1 and fdx1b can be detected in the interrenal gland, which is the zebrafish counterpart of the mammalian adrenal gland, whereas the fdx1 transcript is mainly found in the digestive system. Gene expression studies using quantitative reverse transcriptase-PCR and whole-mount in situ hybridisation in the adult zebrafish brain revealed a wide expression of these genes throughout the encephalon, including neurogenic regions. Using ultra-high-performance liquid chromatography tandem mass spectrometry, we were able to demonstrate the presence of the glucocorticoid cortisol in the adult zebrafish brain. Moreover, we demonstrate de novo biosynthesis of cortisol and the neurosteroid tetrahydrodeoxycorticosterone in the adult zebrafish brain from radiolabelled pregnenolone. Taken together, the present study comprises a comprehensive characterisation of the steroidogenic genes and the fdx co-factors facilitating glucocorticoid biosynthesis in zebrafish. Furthermore, we provide additional evidence of de novo neurosteroid biosynthesising in the brain of adult zebrafish facilitated by enzymes involved in glucocorticoid biosynthesis. Our study provides a valuable source for establishing the zebrafish as a translational model with respect to understanding the roles of the genes for glucocorticoid biosynthesis and fdx co-factors during embryonic development and stress, as well as in brain homeostasis and function.
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Affiliation(s)
- M Weger
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - N Diotel
- INSERM, UMR 1188, Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Université de La Réunion, Saint-Denis de La Réunion, France
| | - B D Weger
- Nestlé Institute of Health Sciences SA, Lausanne, Switzerland
| | - T Beil
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - A Zaucker
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - H L Eachus
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
- Department of Biomedical Science, The Bateson Centre, Sheffield, UK
| | - J A Oakes
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
- Department of Biomedical Science, The Bateson Centre, Sheffield, UK
| | - J L do Rego
- Plateforme d'Analyse Comportementale (SCAC), Institut de Recherche et d'Innovation Biomédicale, Inserm U1234, Université de Rouen, Rouen Cedex, France
| | - K-H Storbeck
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - P Gut
- Nestlé Institute of Health Sciences SA, Lausanne, Switzerland
| | - U Strähle
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - S Rastegar
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - F Müller
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - N Krone
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
- Department of Biomedical Science, The Bateson Centre, Sheffield, UK
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15
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Seasonal variation of pituitary gonadotropin subunit, brain-type aromatase and sex steroid receptor mRNAs, and plasma steroids during gametogenesis in wild sablefish. Comp Biochem Physiol A Mol Integr Physiol 2018; 219-220:48-57. [PMID: 29496550 DOI: 10.1016/j.cbpa.2018.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/19/2018] [Accepted: 02/20/2018] [Indexed: 11/22/2022]
Abstract
Pituitary-hormone signaling plays critical roles in the onset and progression of gametogenesis in vertebrates. This study characterized expression patterns of pituitary gonadotropin beta-subunits (fshb and lhb), brain-type aromatase (cyp19a1b), androgen (ar1, ar2) and estrogen receptors (esr1, esr2a, esr2b), and changes in plasma steroid levels by liquid chromatography/tandem mass spectrometry in wild sablefish (Anoplopoma fimbria, order Scorpaeniformes) during a complete reproductive cycle. Transcripts for fshb increased during early gametogenesis and peaked in late vitellogenic females and late recrudescent males, while expression of lhb reached maximum levels in periovulatory and spermiating fish. Pituitary levels of cyp19a1b and ar1 were strongly correlated with those of lhb in females and males, increasing during gametogenesis and reaching maximum levels prior to spawning. By contrast, expression of ar2, and the three estrogen receptors differed between female and male sablefish. 17β-estradiol (E2) was the dominant steroid in females during vitellogenesis, while a range of at least 6 steroids (11β-hydroxyandrostenedione, testosterone [T], E2, 11-ketotestosterone [11KT], 11-deoxycortisol, and 17α,20β,21-trihydroxyprogesterone) were detected at similar levels in males during testicular development. Prior to spawning, a marked increase in 4-androstenedione, T, 11KT and E2 was found in both periovulatory females and spermiating males. In conclusion, the concomitant changes in plasma androgen levels and pituitary ar1 expression during gametogenesis suggest a specific role for androgens in pituitary hormone regulation of reproduction in sablefish. Further, our data highlight the importance of E2 during final stages of maturation in this species, which may regulate the transcription of pituitary lhb in a paracrine fashion.
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Marandel L, Panserat S, Plagnes-Juan E, Arbenoits E, Soengas JL, Bobe J. Evolutionary history of glucose-6-phosphatase encoding genes in vertebrate lineages: towards a better understanding of the functions of multiple duplicates. BMC Genomics 2017; 18:342. [PMID: 28464795 PMCID: PMC5414149 DOI: 10.1186/s12864-017-3727-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 04/26/2017] [Indexed: 12/20/2022] Open
Abstract
Background Glucose-6-phosphate (G6pc) is a key enzyme involved in the regulation of the glucose homeostasis. The present study aims at revisiting and clarifying the evolutionary history of g6pc genes in vertebrates. Results g6pc duplications happened by successive rounds of whole genome duplication that occurred during vertebrate evolution. g6pc duplicated before or around Osteichthyes/Chondrichthyes radiation, giving rise to g6pca and g6pcb as a consequence of the second vertebrate whole genome duplication. g6pca was lost after this duplication in Sarcopterygii whereas both g6pca and g6pcb then duplicated as a consequence of the teleost-specific whole genome duplication. One g6pca duplicate was lost after this duplication in teleosts. Similarly one g6pcb2 duplicate was lost at least in the ancestor of percomorpha. The analysis of the evolution of spatial expression patterns of g6pc genes in vertebrates showed that all g6pc were mainly expressed in intestine and liver whereas teleost-specific g6pcb2 genes were mainly and surprisingly expressed in brain and heart. g6pcb2b, one gene previously hypothesised to be involved in the glucose intolerant phenotype in trout, was unexpectedly up-regulated (as it was in liver) by carbohydrates in trout telencephalon without showing significant changes in other brain regions. This up-regulation is in striking contrast with expected glucosensing mechanisms suggesting that its positive response to glucose relates to specific unknown processes in this brain area. Conclusions Our results suggested that the fixation and the divergence of g6pc duplicated genes during vertebrates’ evolution may lead to adaptive novelty and probably to the emergence of novel phenotypes related to glucose homeostasis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3727-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lucie Marandel
- INRA, UPPA, UMR 1419 Nutrition, Metabolism, Aquaculture, F-64310, Saint Pée sur Nivelle, France.
| | - Stéphane Panserat
- INRA, UPPA, UMR 1419 Nutrition, Metabolism, Aquaculture, F-64310, Saint Pée sur Nivelle, France
| | - Elisabeth Plagnes-Juan
- INRA, UPPA, UMR 1419 Nutrition, Metabolism, Aquaculture, F-64310, Saint Pée sur Nivelle, France
| | - Eva Arbenoits
- INRA, UPPA, UMR 1419 Nutrition, Metabolism, Aquaculture, F-64310, Saint Pée sur Nivelle, France
| | - José Luis Soengas
- Departamento de Bioloxía Funcional e Ciencias da Saúde, Laboratorio de Fisioloxía Animal, Facultade de Bioloxía, Universidade de Vigo, E-36310, Vigo, Spain
| | - Julien Bobe
- INRA, UR1037 LPGP, Campus de Beaulieu, F-35000, Rennes, France
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17
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Nonaka MI, Terado T, Kimura H, Nonaka M. Evolutionary analysis of two complement C4 genes: Ancient duplication and conservation during jawed vertebrate evolution. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 68:1-11. [PMID: 27840295 DOI: 10.1016/j.dci.2016.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/05/2016] [Accepted: 11/05/2016] [Indexed: 06/06/2023]
Abstract
The complement C4 is a thioester-containing protein, and a histidine (H) residue catalyzes the cleavage of the thioester to allow covalent binding to carbohydrates on target cells. Some mammalian and teleost species possess an additional isotype where the catalytic H is replaced by an aspartic acid (D), which binds preferentially to proteins. We found the two C4 isotypes in many other jawed vertebrates, including sharks and birds/reptiles. Phylogenetic analysis suggested that C4 gene duplication occurred in the early days of the jawed vertebrate evolution. The D-type C4 of bony fish except for mammals formed a cluster, termed D-lineage. The D-lineage genes were located in a syntenic region outside MHC, and evolved conservatively. Mammals lost the D-lineage before speciation, but D-type C4 was regenerated by recent gene duplication in some mammalian species or groups. Dual C4 molecules with different substrate specificities would have contributed to development of the antibody-dependent classical pathway.
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Affiliation(s)
- Mayumi I Nonaka
- Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Tokio Terado
- Department of Molecular Genetics in Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Hiroshi Kimura
- Department of Molecular Genetics in Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Masaru Nonaka
- Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Identification of genes in the hypothalamus-pituitary-gonad axis in the brain of Amur sturgeons (Acipenser schrenckii) by comparative transcriptome analysis in relation to kisspeptin treatment. Gene 2016; 595:53-61. [DOI: 10.1016/j.gene.2016.09.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/31/2016] [Accepted: 09/16/2016] [Indexed: 11/22/2022]
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Kuang MC, Hutchins PD, Russell JD, Coon JJ, Hittinger CT. Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network. eLife 2016; 5:e19027. [PMID: 27690225 PMCID: PMC5089864 DOI: 10.7554/elife.19027] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/28/2016] [Indexed: 12/23/2022] Open
Abstract
The evolutionary mechanisms leading to duplicate gene retention are well understood, but the long-term impacts of paralog differentiation on the regulation of metabolism remain underappreciated. Here we experimentally dissect the functions of two pairs of ancient paralogs of the GALactose sugar utilization network in two yeast species. We show that the Saccharomyces uvarum network is more active, even as over-induction is prevented by a second co-repressor that the model yeast Saccharomyces cerevisiae lacks. Surprisingly, removal of this repression system leads to a strong growth arrest, likely due to overly rapid galactose catabolism and metabolic overload. Alternative sugars, such as fructose, circumvent metabolic control systems and exacerbate this phenotype. We further show that S. cerevisiae experiences homologous metabolic constraints that are subtler due to how the paralogs have diversified. These results show how the functional differentiation of paralogs continues to shape regulatory network architectures and metabolic strategies long after initial preservation.
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Affiliation(s)
- Meihua Christina Kuang
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, United States
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, United States
- JF Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Madison, United States
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States
| | - Paul D Hutchins
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States
| | - Jason D Russell
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States
- Metabolism Research Group, Morgridge Institute for Research, Madison, United States
| | - Joshua J Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States
- Metabolism Research Group, Morgridge Institute for Research, Madison, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States
| | - Chris Todd Hittinger
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, United States
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, United States
- JF Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Madison, United States
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States
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Pellegrini E, Diotel N, Vaillant-Capitaine C, Pérez Maria R, Gueguen MM, Nasri A, Cano Nicolau J, Kah O. Steroid modulation of neurogenesis: Focus on radial glial cells in zebrafish. J Steroid Biochem Mol Biol 2016; 160:27-36. [PMID: 26151741 DOI: 10.1016/j.jsbmb.2015.06.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/01/2015] [Accepted: 06/16/2015] [Indexed: 10/23/2022]
Abstract
Estrogens are known as steroid hormones affecting the brain in many different ways and a wealth of data now document effects on neurogenesis. Estrogens are provided by the periphery but can also be locally produced within the brain itself due to local aromatization of circulating androgens. Adult neurogenesis is described in all vertebrate species examined so far, but comparative investigations have brought to light differences between vertebrate groups. In teleost fishes, the neurogenic activity is spectacular and adult stem cells maintain their mitogenic activity in many proliferative areas within the brain. Fish are also quite unique because brain aromatase expression is limited to radial glia cells, the progenitor cells of adult fish brain. The zebrafish has emerged as an interesting vertebrate model to elucidate the cellular and molecular mechanisms of adult neurogenesis, and notably its modulation by steroids. The main objective of this review is to summarize data related to the functional link between estrogens production in the brain and neurogenesis in fish. First, we will demonstrate that the brain of zebrafish is an endogenous source of steroids and is directly targeted by local and/or peripheral steroids. Then, we will present data demonstrating the progenitor nature of radial glial cells in the brain of adult fish. Next, we will emphasize the role of estrogens in constitutive neurogenesis and its potential contribution to the regenerative neurogenesis. Finally, the negative impacts on neurogenesis of synthetic hormones used in contraceptive pills production and released in the aquatic environment will be discussed.
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Affiliation(s)
- Elisabeth Pellegrini
- Inserm U1085, Université de Rennes 1, Research Institute in Health, Environment and Occupation, 35000 Rennes, France.
| | - Nicolas Diotel
- Inserm U1085, Université de Rennes 1, Research Institute in Health, Environment and Occupation, 35000 Rennes, France; Inserm UMR 1188, Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), plateforme CYROI, Sainte-Clotilde F-97490, France; Université de La Réunion, UMR 1188, Sainte-Clotilde F-97490, France
| | - Colette Vaillant-Capitaine
- Inserm U1085, Université de Rennes 1, Research Institute in Health, Environment and Occupation, 35000 Rennes, France
| | - Rita Pérez Maria
- Inserm U1085, Université de Rennes 1, Research Institute in Health, Environment and Occupation, 35000 Rennes, France; Laboratorio de Ictiología, Instituto Nacional de Limnología (INALI. CONICET-UNL), Paraje El Pozo, Ciudad Universitaria UNL, 3000 Santa Fe, Argentina
| | - Marie-Madeleine Gueguen
- Inserm U1085, Université de Rennes 1, Research Institute in Health, Environment and Occupation, 35000 Rennes, France
| | - Ahmed Nasri
- Inserm U1085, Université de Rennes 1, Research Institute in Health, Environment and Occupation, 35000 Rennes, France; Laboratoire de Biosurveillance de l'Environnement, Unité d'Ecologie côtière et d'Ecotoxicologie, Faculté des Sciences de Bizerte, Zarzouna 7021, Tunisia
| | - Joel Cano Nicolau
- Inserm U1085, Université de Rennes 1, Research Institute in Health, Environment and Occupation, 35000 Rennes, France
| | - Olivier Kah
- Inserm U1085, Université de Rennes 1, Research Institute in Health, Environment and Occupation, 35000 Rennes, France
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Mapping of brain lipid binding protein (Blbp) in the brain of adult zebrafish, co-expression with aromatase B and links with proliferation. Gene Expr Patterns 2016; 20:42-54. [DOI: 10.1016/j.gep.2015.11.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/25/2015] [Accepted: 11/10/2015] [Indexed: 01/05/2023]
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22
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Solis-Escalante D, Kuijpers NGA, Barrajon-Simancas N, van den Broek M, Pronk JT, Daran JM, Daran-Lapujade P. A Minimal Set of Glycolytic Genes Reveals Strong Redundancies in Saccharomyces cerevisiae Central Metabolism. EUKARYOTIC CELL 2015; 14:804-16. [PMID: 26071034 PMCID: PMC4519752 DOI: 10.1128/ec.00064-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 05/26/2015] [Indexed: 01/13/2023]
Abstract
As a result of ancestral whole-genome and small-scale duplication events, the genomes of Saccharomyces cerevisiae and many eukaryotes still contain a substantial fraction of duplicated genes. In all investigated organisms, metabolic pathways, and more particularly glycolysis, are specifically enriched for functionally redundant paralogs. In ancestors of the Saccharomyces lineage, the duplication of glycolytic genes is purported to have played an important role leading to S. cerevisiae's current lifestyle favoring fermentative metabolism even in the presence of oxygen and characterized by a high glycolytic capacity. In modern S. cerevisiae strains, the 12 glycolytic reactions leading to the biochemical conversion from glucose to ethanol are encoded by 27 paralogs. In order to experimentally explore the physiological role of this genetic redundancy, a yeast strain with a minimal set of 14 paralogs was constructed (the "minimal glycolysis" [MG] strain). Remarkably, a combination of a quantitative systems approach and semiquantitative analysis in a wide array of growth environments revealed the absence of a phenotypic response to the cumulative deletion of 13 glycolytic paralogs. This observation indicates that duplication of glycolytic genes is not a prerequisite for achieving the high glycolytic fluxes and fermentative capacities that are characteristic of S. cerevisiae and essential for many of its industrial applications and argues against gene dosage effects as a means of fixing minor glycolytic paralogs in the yeast genome. The MG strain was carefully designed and constructed to provide a robust prototrophic platform for quantitative studies and has been made available to the scientific community.
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Affiliation(s)
| | - Niels G A Kuijpers
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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Molina-Luzón MJ, Hermida M, Navajas-Pérez R, Robles F, Navas JI, Ruiz-Rejón C, Bouza C, Martínez P, de la Herrán R. First haploid genetic map based on microsatellite markers in Senegalese sole (Solea senegalensis, Kaup 1858). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:8-22. [PMID: 25107689 DOI: 10.1007/s10126-014-9589-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 07/12/2014] [Indexed: 06/03/2023]
Abstract
The Senegalese sole (Solea senegalensis, Kaup 1858) is a flatfish species of great value for aquaculture. In this study, we develop the first linkage map in this species based on microsatellite markers characterized from genomic DNA libraries and EST databases of Senegalese sole and from other flatfish species. Three reference gynogenetic families were obtained by chromosome-manipulation techniques: two haploid gynogenetics, used to assign and order microsatellites to linkage groups and another diploid gynogenetic family, used for estimating marker-centromere distances. The consensus map consists of 129 microsatellites distributed in 27 linkage groups (LG), with an average density of 4.7 markers per LG and comprising 1,004 centimorgans (cM). Additionally, 15 markers remained unlinked. Through half-tetrad analysis, we were able to estimate the centromere distance for 81 markers belonging to 24 LG, representing an average of 3 markers per LG. Comparative mapping was performed between flatfish species LG and model fish species chromosomes (stickleback, Tetraodon, medaka, fugu and zebrafish). The usefulness of microsatellite markers and the genetic map as tools for comparative mapping and evolution studies is discussed.
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Affiliation(s)
- Ma Jesús Molina-Luzón
- Facultad de Ciencias, Departamento de Genética, Universidad de Granada, 18071, Granada, Spain
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Kang JH, Manousaki T, Franchini P, Kneitz S, Schartl M, Meyer A. Transcriptomics of two evolutionary novelties: how to make a sperm-transfer organ out of an anal fin and a sexually selected "sword" out of a caudal fin. Ecol Evol 2015; 5:848-64. [PMID: 25750712 PMCID: PMC4338968 DOI: 10.1002/ece3.1390] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/10/2014] [Accepted: 12/12/2014] [Indexed: 01/09/2023] Open
Abstract
Swords are exaggerated male ornaments of swordtail fishes that have been of great interest to evolutionary biologists ever since Darwin described them in the Descent of Man (1871). They are a novel sexually selected trait derived from modified ventral caudal fin rays and are only found in the genus Xiphophorus. Another phylogenetically more widespread and older male trait is the gonopodium, an intromittent organ found in all poeciliid fishes, that is derived from a modified anal fin. Despite many evolutionary and behavioral studies on both traits, little is known so far about the molecular mechanisms underlying their development. By investigating transcriptomic changes (utilizing a RNA-Seq approach) in response to testosterone treatment in the swordtail fish, Xiphophorus hellerii, we aimed to better understand the architecture of the gene regulatory networks underpinning the development of these two evolutionary novelties. Large numbers of genes with tissue-specific expression patterns were identified. Among the "sword genes" those involved in embryonic organ development, sexual character development and coloration were highly expressed, while in the gonopodium rather more morphogenesis-related genes were found. Interestingly, many genes and genetic pathways are shared between both developing novel traits derived from median fins: the sword and the gonopodium. Our analyses show that a larger set of gene networks was co-opted during the development and evolution of the "older" gonopodium than in the "younger," and morphologically less complex trait, the sword. We provide a catalog of candidate genes for future efforts to dissect the development of those sexually selected exaggerated male traits in swordtails.
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Affiliation(s)
- Ji Hyoun Kang
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of KonstanzKonstanz, Germany
| | - Tereza Manousaki
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine ResearchHeraklion, Greece
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of WürzburgAm Hubland, Würzburg, Germany
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of WürzburgAm Hubland, Würzburg, Germany
- Comprehensive Cancer Center, University Clinic WürzburgJosef Schneider Straβe 6, 97074, Würzburg, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of KonstanzKonstanz, Germany
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25
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Luckenbach T, Fischer S, Sturm A. Current advances on ABC drug transporters in fish. Comp Biochem Physiol C Toxicol Pharmacol 2014; 165:28-52. [PMID: 24858718 DOI: 10.1016/j.cbpc.2014.05.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 01/14/2023]
Abstract
Most members of the large ATP-binding cassette (ABC) gene family are transporters involved in substrate translocation across biological membranes. In eukaryotes, ABC proteins functioning as drug transporters are located in the plasma membrane and mediate the cellular efflux of a wide range of organic chemicals, with some transporters also transporting certain metals. As the enhanced expression of ABC drug transporters can confer multidrug resistance (MDR) to cancers and multixenobiotic resistance (MXR) to organisms from polluted habitats, these ABC family members are also referred to as MDR or MXR proteins. In mammals, ABC drug transporters show predominant expression in tissues involved in excretion or constituting internal or external body boundaries, where they facilitate the excretion of chemicals and their metabolites, and limit chemical uptake and penetration into "sanctuary" sites of the body. Available knowledge about ABC proteins is still limited in teleost fish, a large vertebrate group of high ecological and economic importance. Using transport activity measurements and immunochemical approaches, early studies demonstrated similarities in the tissue distribution of ABC drug transporters between teleosts and mammals, suggesting conserved roles of the transporters in the biochemical defence against toxicants. Recently, the availability of teleost genome assemblies has stimulated studies of the ABC family in this taxon. This review summarises the current knowledge regarding the genetics, functional properties, physiological function, and ecotoxicological relevance of teleostean ABC transporters. The available literature is reviewed with emphasis on recent studies addressing the tissue distribution, substrate spectrum, regulation, physiological function and phylogenetic origin of teleostean ABC transporters.
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Affiliation(s)
- Till Luckenbach
- Department of Bioanalytical Ecotoxicology, UFZ-Helmholtz Centre for Environmental Research, 04318 Leipzig, Germany
| | - Stephan Fischer
- Department of Environmental Toxicology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; Department of Environmental Systems Sciences, ETH Zürich, Institute of Biogeochemistry and Pollutant Dynamics, 8092 Zürich, Switzerland
| | - Armin Sturm
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK.
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Findeisen P, Mühlhausen S, Dempewolf S, Hertzog J, Zietlow A, Carlomagno T, Kollmar M. Six subgroups and extensive recent duplications characterize the evolution of the eukaryotic tubulin protein family. Genome Biol Evol 2014; 6:2274-88. [PMID: 25169981 PMCID: PMC4202323 DOI: 10.1093/gbe/evu187] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Tubulins belong to the most abundant proteins in eukaryotes providing the backbone for many cellular substructures like the mitotic and meiotic spindles, the intracellular cytoskeletal network, and the axonemes of cilia and flagella. Homologs have even been reported for archaea and bacteria. However, a taxonomically broad and whole-genome-based analysis of the tubulin protein family has never been performed, and thus, the number of subfamilies, their taxonomic distribution, and the exact grouping of the supposed archaeal and bacterial homologs are unknown. Here, we present the analysis of 3,524 tubulins from 504 species. The tubulins formed six major subfamilies, α to ζ. Species of all major kingdoms of the eukaryotes encode members of these subfamilies implying that they must have already been present in the last common eukaryotic ancestor. The proposed archaeal homologs grouped together with the bacterial TubZ proteins as sister clade to the FtsZ proteins indicating that tubulins are unique to eukaryotes. Most species contained α- and/or β-tubulin gene duplicates resulting from recent branch- and species-specific duplication events. This shows that tubulins cannot be used for constructing species phylogenies without resolving their ortholog–paralog relationships. The many gene duplicates and also the independent loss of the δ-, ε-, or ζ-tubulins, which have been shown to be part of the triplet microtubules in basal bodies, suggest that tubulins can functionally substitute each other.
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Affiliation(s)
- Peggy Findeisen
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefanie Mühlhausen
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Silke Dempewolf
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jonny Hertzog
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexander Zietlow
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Teresa Carlomagno
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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Jiang Y, Xu P, Liu Z. Generation of physical map contig-specific sequences. Front Genet 2014; 5:243. [PMID: 25101119 PMCID: PMC4105628 DOI: 10.3389/fgene.2014.00243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 07/07/2014] [Indexed: 12/13/2022] Open
Abstract
Rapid advances of the next-generation sequencing technologies have allowed whole genome sequencing of many species. However, with the current sequencing technologies, the whole genome sequence assemblies often fall in short in one of the four quality measurements: accuracy, contiguity, connectivity, and completeness. In particular, small-sized contigs and scaffolds limit the applicability of whole genome sequences for genetic analysis. To enhance the quality of whole genome sequence assemblies, particularly the scaffolding capabilities, additional genomic resources are required. Among these, sequences derived from known physical locations offer great powers for scaffolding. In this mini-review, we will describe the principles, procedures and applications of physical-map-derived sequences, with the focus on physical map contig-specific sequences.
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Affiliation(s)
- Yanliang Jiang
- Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences Beijing, China
| | - Peng Xu
- Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences Beijing, China
| | - Zhanjiang Liu
- Aquatic Genomics Unit, The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University AL, USA
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Aromatase, estrogen receptors and brain development in fish and amphibians. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:152-62. [PMID: 25038582 DOI: 10.1016/j.bbagrm.2014.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/19/2014] [Accepted: 07/07/2014] [Indexed: 12/20/2022]
Abstract
Estrogens affect brain development of vertebrates, not only by impacting activity and morphology of existing circuits, but also by modulating embryonic and adult neurogenesis. The issue is complex as estrogens can not only originate from peripheral tissues, but also be locally produced within the brain itself due to local aromatization of androgens. In this respect, teleost fishes are quite unique because aromatase is expressed exclusively in radial glial cells, which represent pluripotent cells in the brain of all vertebrates. Expression of aromatase in the brain of fish is also strongly stimulated by estrogens and some androgens. This creates a very intriguing positive auto-regulatory loop leading to dramatic aromatase expression in sexually mature fish with elevated levels of circulating steroids. Looking at the effects of estrogens or anti-estrogens in the brain of adult zebrafish showed that estrogens inhibit rather than stimulate cell proliferation and newborn cell migration. The functional meaning of these observations is still unclear, but these data suggest that the brain of fish is experiencing constant remodeling under the influence of circulating steroids and brain-derived neurosteroids, possibly permitting a diversification of sexual strategies, notably hermaphroditism. Recent data in frogs indicate that aromatase expression is limited to neurons and do not concern radial glial cells. Thus, until now, there is no other example of vertebrates in which radial progenitors express aromatase. This raises the question of when and why these new features were gained and what are their adaptive benefits. This article is part of a Special Issue entitled: Nuclear receptors in animal development.
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Molecular characterization and transcriptional regulation of the Na +/K+ ATPase α subunit isoforms during development and salinity challenge in a teleost fish, the Senegalese sole (Solea senegalensis). Comp Biochem Physiol B Biochem Mol Biol 2014; 175:23-38. [PMID: 24947209 DOI: 10.1016/j.cbpb.2014.06.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/28/2014] [Accepted: 06/06/2014] [Indexed: 01/12/2023]
Abstract
In the present work, five genes encoding different Na(+),K(+) ATPase (NKA) α-isoforms in the teleost Solea senegalensis are described for the first time. Sequence analysis of predicted polypeptides revealed a high degree of conservation across teleosts and mammals. Phylogenetic analysis clustered the five genes into three main clades: α1 (designated atp1a1a and atp1a1b), α2 (designated atp1a2) and α3 (designated atp1a3a and atp1a3b) isoforms. Transcriptional analysis in larvae showed distinct expression profiles during development. In juvenile tissues, the atp1a1a gene was highly expressed in osmoregulatory organs, atp1a2 in skeletal muscle, atp1a1b in brain and heart and atp1a3a and atp1a3b mainly in brain. Quantification of mRNA abundance after a salinity challenge showed that atp1a1a transcript levels increased significantly in the gill of soles transferred to high salinity water (60 ppt). In contrast, atp1a3a transcripts increased at low salinity (5 ppt). In situ hybridization (ISH) analysis revealed that the number of ionocytes expressing atp1a1a transcripts in the primary gill filaments was higher at 35 and 60 ppt than at 5 ppt and remained undetectable or at very low levels in the lamellae at 5 and 35 ppt but increased at 60 ppt. Immunohistochemistry showed a higher number of positive cells in the lamellae. Whole-mount analysis of atp1a1a mRNA in young sole larvae revealed that it was localized in gut, pronephric tubule, gill, otic vesicle, yolk sac ionocytes and chordacentrum. Moreover, atp1a1a mRNAs increased at mouth opening (3 DPH) in larvae incubated at 36 ppt with a greater signal in gills.
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Abstract
In mammals, secretin is a 27-amino acid peptide that was first studied in 1902 by Bayliss and Starling from the extracts of the jejunal mucosa for its ability to stimulate pancreatic secretion. To date, secretin has only been identified in tetrapods, with the earliest diverged secretin found in frogs. Despite being the first hormone discovered, secretin's evolutionary origin remains enigmatic, it shows moderate sequence identity in nonmammalian tetrapods but is highly conserved in mammals. Current hypotheses suggest that although secretin has already emerged before the divergence of osteichthyans, it was lost in fish and retained only in land vertebrates. Nevertheless, the cognate receptor of secretin has been identified in both actinopterygian fish (zebrafish) and sarcopterygian fish (lungfish). However, the zebrafish secretin receptor was shown to be nonbioactive. Based on the present information that the earliest diverged bioactive secretin receptor was found in lungfish, and its ability to interact with both vasoactive intestinal peptide and pituitary adenylate cyclase-activating polypeptide potently suggested that secretin receptor was descended from a VPAC-like receptor gene before the Actinopterygii-Sarcopterygii split in the vertebrate lineage. Hence, secretin and secretin receptor have gone through independent evolutionary trajectories despite their concurrent emergence post-2R. A functional secretin-secretin receptor axis has probably emerged in the amphibians. Although the pleiotropic actions of secretin are well documented in the literature, only limited information of its physiological functions in nonmammalian tetrapods have been reported. To decipher the structural and functional divergence of secretin and secretin receptor, functional characterization of the ligand-receptor pair in nonmammals would be the next perspective for investigation.
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Affiliation(s)
- Janice K V Tam
- School of Biological SciencesThe University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Leo T O Lee
- School of Biological SciencesThe University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Jun Jin
- School of Biological SciencesThe University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Billy K C Chow
- School of Biological SciencesThe University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
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Hartmann AM, Tesch D, Nothwang HG, Bininda-Emonds OR. Evolution of the Cation Chloride Cotransporter Family: Ancient Origins, Gene Losses, and Subfunctionalization through Duplication. Mol Biol Evol 2013; 31:434-47. [DOI: 10.1093/molbev/mst225] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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32
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Jiang Y, Ninwichian P, Liu S, Zhang J, Kucuktas H, Sun F, Kaltenboeck L, Sun L, Bao L, Liu Z. Generation of physical map contig-specific sequences useful for whole genome sequence scaffolding. PLoS One 2013; 8:e78872. [PMID: 24205335 PMCID: PMC3811975 DOI: 10.1371/journal.pone.0078872] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 09/16/2013] [Indexed: 11/29/2022] Open
Abstract
Along with the rapid advances of the nextgen sequencing technologies, more and more species are added to the list of organisms whose whole genomes are sequenced. However, the assembled draft genome of many organisms consists of numerous small contigs, due to the short length of the reads generated by nextgen sequencing platforms. In order to improve the assembly and bring the genome contigs together, more genome resources are needed. In this study, we developed a strategy to generate a valuable genome resource, physical map contig-specific sequences, which are randomly distributed genome sequences in each physical contig. Two-dimensional tagging method was used to create specific tags for 1,824 physical contigs, in which the cost was dramatically reduced. A total of 94,111,841 100-bp reads and 315,277 assembled contigs are identified containing physical map contig-specific tags. The physical map contig-specific sequences along with the currently available BAC end sequences were then used to anchor the catfish draft genome contigs. A total of 156,457 genome contigs (~79% of whole genome sequencing assembly) were anchored and grouped into 1,824 pools, in which 16,680 unique genes were annotated. The physical map contig-specific sequences are valuable resources to link physical map, genetic linkage map and draft whole genome sequences, consequently have the capability to improve the whole genome sequences assembly and scaffolding, and improve the genome-wide comparative analysis as well. The strategy developed in this study could also be adopted in other species whose whole genome assembly is still facing a challenge.
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Affiliation(s)
- Yanliang Jiang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Parichart Ninwichian
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Jiaren Zhang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Huseyin Kucuktas
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Fanyue Sun
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Ludmilla Kaltenboeck
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Luyang Sun
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Lisui Bao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
- * E-mail:
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Bernardi G. Speciation in fishes. Mol Ecol 2013; 22:5487-502. [PMID: 24118417 DOI: 10.1111/mec.12494] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/08/2013] [Accepted: 08/14/2013] [Indexed: 12/27/2022]
Abstract
The field of speciation has seen much renewed interest in the past few years, with theoretical and empirical advances that have moved it from a descriptive field to a predictive and testable one. The goal of this review is to provide a general background on research on speciation as it pertains to fishes. Three major components to the question are first discussed: the spatial, ecological and sexual factors that influence speciation mechanisms. We then move to the latest developments in the field of speciation genomics. Affordable and rapidly available, massively parallel sequencing data allow speciation studies to converge into a single comprehensive line of investigation, where the focus has shifted to the search for speciation genes and genomic islands of speciation. We argue that fish present a very diverse array of scenarios, making them an ideal model to study speciation processes.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 100 Shaffer Road, Santa Cruz, CA, 95076, USA
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34
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Mechaly AS, Viñas J, Piferrer F. The kisspeptin system genes in teleost fish, their structure and regulation, with particular attention to the situation in Pleuronectiformes. Gen Comp Endocrinol 2013; 188:258-68. [PMID: 23624122 DOI: 10.1016/j.ygcen.2013.04.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 04/16/2013] [Indexed: 10/26/2022]
Abstract
It is well established that Kisspeptin regulates the onset of puberty in vertebrates through stimulation of the secretion of gonadotropin-releasing hormones. However, the function of kisspeptin in peripheral tissues and in other functions is still poorly understood. Recently, the evolution and distribution of kisspeptin genes in vertebrates has been clarified. In contrast to placental mammals, which have a single gene for the ligand (Kiss) and for the receptor (Kissr), fish may have up to three Kiss genes and up to four Kissr genes because of genome duplications. However, information on the genomic structure of the piscine kiss and kissr genes is still scarce. Furthermore, when data from several species is taken together, interspecific differences in the expression of kiss and kissr during the reproductive cycle are found. Here, we discuss data gathered from several fish species, but mainly from two flatfishes, the Senegalese sole and the Atlantic halibut, to address general questions on kiss gene structure, regulation and function. Flatfish are among the most derived fish species and the two species referred to above have only one ligand and one receptor, probably because of the genome reduction observed in Pleuronectiformes. However, gene analysis shows that both species have an alternative splicing mechanism based on intron retention, but the functions of the alternative isoforms are unclear. In the Senegalese sole, sex-related differences in the temporal and spatial expression of kiss and kissr were observed during a whole reproductive cycle. In addition, recent studies suggested that kisspeptin system gene expression is correlated to energy balance and reproduction. This suggests that kisspeptin signaling may involve different sources of information to synchronize important biological functions in vertebrates, including reproduction. We propose a set of criteria to facilitate the comparison of kiss and kissr gene expression data across species.
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Affiliation(s)
- Alejandro S Mechaly
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.
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Li R, Wang T, Bird S, Zou J, Dooley H, Secombes CJ. B cell receptor accessory molecule CD79α: characterisation and expression analysis in a cartilaginous fish, the spiny dogfish (Squalus acanthias). FISH & SHELLFISH IMMUNOLOGY 2013; 34:1404-15. [PMID: 23454429 PMCID: PMC4034164 DOI: 10.1016/j.fsi.2013.02.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 02/08/2013] [Accepted: 02/18/2013] [Indexed: 05/16/2023]
Abstract
CD79α (also known as Igα) is a component of the B cell antigen receptor complex and plays an important role in B cell signalling. The CD79α protein is present on the surface of B cells throughout their life cycle, and is absent on all other healthy cells, making it a highly reliable marker for B cells in mammals. In this study the spiny dogfish (Squalus acanthias) CD79α (SaCD79α) is described and its expression studied under constitutive and stimulated conditions. The spiny dogfish CD79α cDNA contains an open reading frame of 618 bp, encoding a protein of 205 amino acids. Comparison of the SaCD79α gene with that of other species shows that the gross structure (number of exons, exon/intron boundaries, etc.) is highly conserved across phylogeny. Additionally, analysis of the 5' flanking region shows SaCD79α lacks a TATA box and possesses binding sites for multiple transcription factors implicated in its B cell-specific gene transcription in other species. Spiny dogfish CD79α is most highly expressed in immune tissues, such as spleen, epigonal and Leydig organ, and its transcript level significantly correlates with those of spiny dogfish immunoglobulin heavy chains. Additionally, CD79α transcription is up-regulated, to a small but significant degree, in peripheral blood cells following stimulation with pokeweed mitogen. These results strongly indicate that, as in mammals, spiny dogfish CD79α is expressed by shark B cells where it associates with surface-bound immunoglobulin to form a fully functional BCR, and thus may serve as a pan-B cell marker in future shark immunological studies.
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Affiliation(s)
- Ronggai Li
- Scottish Fish Immunology Research Centre, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
| | - Tiehui Wang
- Scottish Fish Immunology Research Centre, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
| | - Steve Bird
- Department of Biological Sciences, School of Science and Engineering, University of Waikato, New Zealand
| | - Jun Zou
- Scottish Fish Immunology Research Centre, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
| | - Helen Dooley
- Scottish Fish Immunology Research Centre, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
| | - Christopher J. Secombes
- Scottish Fish Immunology Research Centre, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
- Corresponding author. Tel.: +44 1224 278272; fax: +44 (0)1224 272396.
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Watt WB, Hudson RR, Wang B, Wang E. A genetic polymorphism evolving in parallel in two cell compartments and in two clades. BMC Evol Biol 2013; 13:9. [PMID: 23311980 PMCID: PMC3556304 DOI: 10.1186/1471-2148-13-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 12/12/2012] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The enzyme phosphoenolpyruvate carboxykinase, PEPCK, occurs in its guanosine-nucleotide-using form in animals and a few prokaryotes. We study its natural genetic variation in Colias (Lepidoptera, Pieridae). PEPCK offers a route, alternative to pyruvate kinase, for carbon skeletons to move between cytosolic glycolysis and mitochondrial Krebs cycle reactions. RESULTS PEPCK is expressed in both cytosol and mitochondrion, but differently in diverse animal clades. In vertebrates and independently in Drosophila, compartment-specific paralogous genes occur. In a contrasting expression strategy, compartment-specific PEPCKs of Colias and of the silkmoth, Bombyx, differ only in their first, 5', exons; these are alternatively spliced onto a common series of following exons. In two Colias species from distinct clades, PEPCK sequence is highly variable at nonsynonymous and synonymous sites, mainly in its common exons. Three major amino acid polymorphisms, Gly 335 ↔ Ser, Asp 503 ↔ Glu, and Ile 629 ↔ Val occur in both species, and in the first two cases are similar in frequency between species. Homology-based structural modelling shows that the variants can alter hydrogen bonding, salt bridging, or van der Waals interactions of amino acid side chains, locally or at one another's sites which are distant in PEPCK's structure, and thus may affect its enzyme function. We ask, using coalescent simulations, if these polymorphisms' cross-species similarities are compatible with neutral evolution by genetic drift, but find the probability of this null hypothesis is 0.001 ≤ P ≤ 0.006 under differing scenarios. CONCLUSION Our results make the null hypothesis of neutrality of these PEPCK polymorphisms quite unlikely, but support an alternative hypothesis that they are maintained by natural selection in parallel in the two species. This alternative can now be justifiably tested further via studies of PEPCK genotypes' effects on function, organismal performance, and fitness. This case emphasizes the importance, for evolutionary insight, of studying gene-specific mechanisms affected by natural genetic variation as an essential complement to surveys of such variation.
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Affiliation(s)
- Ward B Watt
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO 81224, USA
| | - Richard R Hudson
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Baiqing Wang
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Eddie Wang
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
- Present address: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 0213, USA
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38
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Jeng SR, Yueh WS, Pen YT, Gueguen MM, Pasquier J, Dufour S, Chang CF, Kah O. Expression of aromatase in radial glial cells in the brain of the Japanese eel provides insight into the evolution of the cyp191a gene in Actinopterygians. PLoS One 2012; 7:e44750. [PMID: 22957105 PMCID: PMC3434150 DOI: 10.1371/journal.pone.0044750] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 08/06/2012] [Indexed: 11/23/2022] Open
Abstract
The cyp19a1 gene that encodes aromatase, the only enzyme permitting conversion of C19 aromatizable androgens into estrogens, is present as a single copy in the genome of most vertebrate species, except in teleosts in which it has been duplicated. This study aimed at investigating the brain expression of a cyp19a1 gene expressed in both gonad and brain of Japanese eel, a basal teleost. By means of immunohistochemistry and in situ hybridization, we show that cyp19a1 is expressed only in radial glial cells of the brain and in pituitary cells. Treatments with salmon pituitary homogenates (female) or human chorionic gonadotrophin (male), known to turn on steroid production in immature eels, strongly stimulated cyp19a1 messenger and protein expression in radial glial cells and pituitary cells. Using double staining studies, we also showed that aromatase-expressing radial glial cells exhibit proliferative activity in both the brain and the pituitary. Altogether, these data indicate that brain and pituitary expression of Japanese eel cyp19a1 exhibits characteristics similar to those reported for the brain specific cyp19a1b gene in teleosts having duplicated cyp19a1 genes. This supports the hypothesis that, despite the fact that eels also underwent the teleost specific genome duplication, they have a single cyp19a1 expressed in both brain and gonad. Such data also suggest that the intriguing features of brain aromatase expression in teleost fishes were not gained after the whole genome duplication and may reflect properties of the cyp19a1 gene of ancestral Actinopterygians.
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Affiliation(s)
- Shan-Ru Jeng
- Department of Aquaculture, National Kaohsiung Marine University, Kaohsiung, Taiwan
- Team NEED, Institut de Recherche en Santé, Environnement et Travail, INSERM U1085, IFR140, Université de Rennes 1, Rennes, France
| | - Wen-Shiun Yueh
- Department of Aquaculture, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - Yi-Ting Pen
- Department of Aquaculture, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - Marie-Madeleine Gueguen
- Team NEED, Institut de Recherche en Santé, Environnement et Travail, INSERM U1085, IFR140, Université de Rennes 1, Rennes, France
| | - Jérémy Pasquier
- Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS 7208/IRD 207/UPMC, Muséum National d'Histoire Naturelle, Paris, France
| | - Sylvie Dufour
- Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS 7208/IRD 207/UPMC, Muséum National d'Histoire Naturelle, Paris, France
| | - Ching-Fong Chang
- Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS 7208/IRD 207/UPMC, Muséum National d'Histoire Naturelle, Paris, France
- Department of Aquaculture, Center of Excellence for Marine Bioenvironment and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Olivier Kah
- Team NEED, Institut de Recherche en Santé, Environnement et Travail, INSERM U1085, IFR140, Université de Rennes 1, Rennes, France
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Kollmar M, Lbik D, Enge S. Evolution of the eukaryotic ARP2/3 activators of the WASP family: WASP, WAVE, WASH, and WHAMM, and the proposed new family members WAWH and WAML. BMC Res Notes 2012; 5:88. [PMID: 22316129 PMCID: PMC3298513 DOI: 10.1186/1756-0500-5-88] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 02/08/2012] [Indexed: 12/14/2022] Open
Abstract
Background WASP family proteins stimulate the actin-nucleating activity of the ARP2/3 complex. They include members of the well-known WASP and WAVE/Scar proteins, and the recently identified WASH and WHAMM proteins. WASP family proteins contain family specific N-terminal domains followed by proline-rich regions and C-terminal VCA domains that harbour the ARP2/3-activating regions. Results To reveal the evolution of ARP2/3 activation by WASP family proteins we performed a "holistic" analysis by manually assembling and annotating all homologs in most of the eukaryotic genomes available. We have identified two new families: the WAML proteins (WASP and MIM like), which combine the membrane-deforming and actin bundling functions of the IMD domains with the ARP2/3-activating VCA regions, and the WAWH protein (WASP without WH1 domain) that have been identified in amoebae, Apusozoa, and the anole lizard. Surprisingly, with one exception we did not identify any alternative splice forms for WASP family proteins, which is in strong contrast to other actin-binding proteins like Ena/VASP, MIM, or NHS proteins that share domains with WASP proteins. Conclusions Our analysis showed that the last common ancestor of the eukaryotes must have contained a homolog of WASP, WAVE, and WASH. Specific families have subsequently been lost in many taxa like the WASPs in plants, algae, Stramenopiles, and Euglenozoa, and the WASH proteins in fungi. The WHAMM proteins are metazoa specific and have most probably been invented by the Eumetazoa. The diversity of WASP family proteins has strongly been increased by many species- and taxon-specific gene duplications and multimerisations. All data is freely accessible via http://www.cymobase.org.
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Affiliation(s)
- Martin Kollmar
- Abteilung NMR basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany.
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40
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Marzban H, Hawkes R. On the architecture of the posterior zone of the cerebellum. THE CEREBELLUM 2012; 10:422-34. [PMID: 20838950 DOI: 10.1007/s12311-010-0208-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mammalian cerebellum is histologically uniform. However, underlying the simple laminar architecture is a complex arrangement of parasagittal stripes and transverse zones that can be revealed by the expression of many molecules, in particular, zebrin II/aldolase C. By using a combination of Purkinje cell antigenic markers and afferent tracing, four transverse zones have been identified: in mouse, these are the anterior zone (∼lobules I-V), the central zone (∼lobules VI-VII), the posterior zone (PZ: ∼lobules VIII-dorsal IX), and the nodular zone (∼ventral lobule IX + lobule X). A fifth transverse zone-the lingular zone (∼lobule I)-is found in birds and bats. Within the anterior and posterior zones, parasagittal stripes of Purkinje cells expressing zebrin II alternate with those that do not. To explore this model further and to broaden our understanding of the evolution of cerebellar patterning, stripes in the PZ have been compared in multiple mammalian species. We conclude that a posterior zone with a conserved stripe organization is a common feature of the mammalian and avian cerebellar vermis and that zonal boundaries are independent of cerebellar lobulation.
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Affiliation(s)
- Hassan Marzban
- Department of Cell Biology & Anatomy, Faculty of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
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41
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Diotel N, Do Rego JL, Anglade I, Vaillant C, Pellegrini E, Vaudry H, Kah O. The brain of teleost fish, a source, and a target of sexual steroids. Front Neurosci 2011; 5:137. [PMID: 22194715 PMCID: PMC3242406 DOI: 10.3389/fnins.2011.00137] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 11/30/2011] [Indexed: 11/13/2022] Open
Abstract
Neurosteroids are defined as steroids de novo synthesized in the central nervous system. While the production of neurosteroids is well documented in mammals and amphibians, there is less information about teleosts, the largest group of fish. Teleosts have long been known for their high brain aromatase and 5α-reductase activities, but recent data now document the capacity of the fish brain to produce a large variety of sex steroids. This article aims at reviewing the available information regarding expression and/or activity of the main steroidogenic enzymes in the brain of fish. In addition, the distribution of estrogen, androgen, and progesterone nuclear receptors is documented in relation with the potential sites of production of neurosteroids. Interestingly, radial glial cells acting as neuronal progenitors, appear to be a potential source of neurosteroids, but also a target for centrally and/or peripherally produced steroids.
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Affiliation(s)
- Nicolas Diotel
- Neurogenesis and Œstrogens, UMR CNRS 6026, IFR 140, Université de Rennes 1 Rennes, France
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Sarropoulou E, Nousdili D, Kotoulas G, Magoulas A. Functional divergences of GAPDH isoforms during early development in two perciform fish species. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:1115-1124. [PMID: 21559871 DOI: 10.1007/s10126-011-9375-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 03/29/2011] [Indexed: 05/30/2023]
Abstract
Glyceraldehyde-3-phospate dehydrogenase (GAPDH) is involved in basic cell catabolic processes and, as it is thought to be continuously expressed, belongs to the group of housekeeping genes. Thus, it is frequently used as an internal control in quantitative gene expression studies. However, the evidence of different expression patterns in a broad range of organisms and tissues, as well as the occurrence of different isoforms, shows that GAPDH has to be reevaluated as an internal control in qPCR studies, and its annotation has to be enriched. GAPDH has been shown to be involved in the pathway of energy and carbon molecule supply as well as in transcription and apoptosis. In the present study, we isolated the two isoforms, GAPDH-1 and GAPDH-2, of the gilthead sea bream (Sparus aurata) and the European sea bass (Dicentrarchus labrax). We inferred the phylogenetic relationships to ten other fish species and gave the gene structure of both genes. We further investigated gene expression analysis in both species for different developmental stages showing divergent gene expression of the two isoforms and the possible function of GAPDH-1 as a maternal gene.
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Affiliation(s)
- Elena Sarropoulou
- Institute of Marine Biology and Genetics (I.M.B.G.), Hellenic Centre for Marine Research Crete, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece.
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FTZ-F1 and FOXL2 up-regulate catfish brain aromatase gene transcription by specific binding to the promoter motifs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:57-66. [PMID: 22019437 DOI: 10.1016/j.bbagrm.2011.10.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 10/06/2011] [Accepted: 10/08/2011] [Indexed: 11/23/2022]
Abstract
Cytochrome P450 aromatase (cyp19) catalyzes the conversion of androgens into estrogens. Teleosts have distinct, ovarian specific (cyp19a1a) and brain specific (cyp19a1b) cyp19 genes. Previous studies in teleosts demonstrated regulation of cyp19a1a expression by the NR5A nuclear receptor subfamily as well as a fork head transcription factor, FOXL2. In the present study, we investigated the involvement of fushi tarazu factor 1, FTZ-F1, a NR5A subfamily member, and FOXL2 in the regulation of cyp19a1b expression in brain of the air-breathing catfish, Clarias gariepinus. Based on the synchronous expression pattern of cyp19a1b, FTZ-F1 and FOXL2 in the brain, we isolated the 5' upstream region of cyp19a1b to analyse regulatory motifs. Promoter motif analysis revealed FTZ-F1/NR5A1 and FOXL2 binding nucleotide sequences. Transient transfection studies showed that FTZ-F1 and FOXL2 together enhanced the transcriptional activity of cyp19a1b gene in mammalian cell lines. Mutation in either of their putative binding sites within the cyp19a1b promoter abolished this effect. Electrophoretic gel mobility shift experiments indicated that FTZ-F1 and FOXL2 proteins bind to the synthesized radio-labelled oligomers used as probes and mobility shifted upon addition of their respective antibodies. Chromatin immunoprecipitation assay confirmed the binding of both these transcription factors to their corresponding cis-acting elements in the upstream region of cyp19a1b. To our knowledge, this study is the first report on the transcriptional regulation of cyp19a1b by FTZ-F1 and FOXL2 in a teleost fish.
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44
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A holistic phylogeny of the coronin gene family reveals an ancient origin of the tandem-coronin, defines a new subfamily, and predicts protein function. BMC Evol Biol 2011; 11:268. [PMID: 21943019 PMCID: PMC3203266 DOI: 10.1186/1471-2148-11-268] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 09/25/2011] [Indexed: 01/11/2023] Open
Abstract
Background Coronins belong to the superfamily of the eukaryotic-specific WD40-repeat proteins and play a role in several actin-dependent processes like cytokinesis, cell motility, phagocytosis, and vesicular trafficking. Two major types of coronins are known: First, the short coronins consisting of an N-terminal coronin domain, a unique region and a short coiled-coil region, and secondly the tandem coronins comprising two coronin domains. Results 723 coronin proteins from 358 species have been identified by analyzing the whole-genome assemblies of all available sequenced eukaryotes (March 2011). The organisms analyzed represent most eukaryotic kingdoms but also cover every taxon several times to provide a better statistical sampling. The phylogenetic tree of the coronin domains based on the Bayesian method is in accordance with the most recent grouping of the major kingdoms of the eukaryotes and also with the grouping of more recently separated branches. Based on this "holistic" approach the coronins group into four classes: class-1 (Type I) and class-2 (Type II) are metazoan/choanoflagellate specific classes, class-3 contains the tandem-coronins (Type III), and the new class-4 represents the coronins fused to villin (Type IV). Short coronins from non-metazoans are equally related to class-1 and class-2 coronins and thus remain unclassified. Conclusions The coronin class distribution suggests that the last common eukaryotic ancestor possessed a single and a tandem-coronin, and most probably a class-4 coronin of which homologs have been identified in Excavata and Opisthokonts although most of these species subsequently lost the class-4 homolog. The most ancient short coronin already contained the trimerization motif in the coiled-coil domain.
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45
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Kuravsky ML, Aleshin VV, Frishman D, Muronetz VI. Testis-specific glyceraldehyde-3-phosphate dehydrogenase: origin and evolution. BMC Evol Biol 2011; 11:160. [PMID: 21663662 PMCID: PMC3224139 DOI: 10.1186/1471-2148-11-160] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 06/10/2011] [Indexed: 11/25/2022] Open
Abstract
Background Glyceraldehyde-3-phosphate dehydrogenase (GAPD) catalyses one of the glycolytic reactions and is also involved in a number of non-glycolytic processes, such as endocytosis, DNA excision repair, and induction of apoptosis. Mammals are known to possess two homologous GAPD isoenzymes: GAPD-1, a well-studied protein found in all somatic cells, and GAPD-2, which is expressed solely in testis. GAPD-2 supplies energy required for the movement of spermatozoa and is tightly bound to the sperm tail cytoskeleton by the additional N-terminal proline-rich domain absent in GAPD-1. In this study we investigate the evolutionary history of GAPD and gain some insights into specialization of GAPD-2 as a testis-specific protein. Results A dataset of GAPD sequences was assembled from public databases and used for phylogeny reconstruction by means of the Bayesian method. Since resolution in some clades of the obtained tree was too low, syntenic analysis was carried out to define the evolutionary history of GAPD more precisely. The performed selection tests showed that selective pressure varies across lineages and isoenzymes, as well as across different regions of the same sequences. Conclusions The obtained results suggest that GAPD-1 and GAPD-2 emerged after duplication during the early evolution of chordates. GAPD-2 was subsequently lost by most lineages except lizards, mammals, as well as cartilaginous and bony fishes. In reptilians and mammals, GAPD-2 specialized to a testis-specific protein and acquired the novel N-terminal proline-rich domain anchoring the protein in the sperm tail cytoskeleton. This domain is likely to have originated by exonization of a microsatellite genomic region. Recognition of the proline-rich domain by cytoskeletal proteins seems to be unspecific. Besides testis, GAPD-2 of lizards was also found in some regenerating tissues, but it lacks the proline-rich domain due to tissue-specific alternative splicing.
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Affiliation(s)
- Mikhail L Kuravsky
- Faculty of Bioengineering and Bioinformatics, MV Lomonosov Moscow State University, Moscow, Russian Federation
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Ainali C, Simon M, Freilich S, Espinosa O, Hazelwood L, Tsoka S, Ouzounis CA, Hancock JM. Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins. BMC Evol Biol 2011; 11:142. [PMID: 21612628 PMCID: PMC3112093 DOI: 10.1186/1471-2148-11-142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 05/25/2011] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Cellular ATP levels are generated by glucose-stimulated mitochondrial metabolism and determine metabolic responses, such as glucose-stimulated insulin secretion (GSIS) from the β-cells of pancreatic islets. We describe an analysis of the evolutionary processes affecting the core enzymes involved in glucose-stimulated insulin secretion in mammals. The proteins involved in this system belong to ancient enzymatic pathways: glycolysis, the TCA cycle and oxidative phosphorylation. RESULTS We identify two sets of proteins, or protein coalitions, in this group of 77 enzymes with distinct evolutionary patterns. Members of the glycolysis, TCA cycle, metabolite transport, pyruvate and NADH shuttles have low rates of protein sequence evolution, as inferred from a human-mouse comparison, and relatively high rates of evolutionary gene duplication. Respiratory chain and glutathione pathway proteins evolve faster, exhibiting lower rates of gene duplication. A small number of proteins in the system evolve significantly faster than co-pathway members and may serve as rapidly evolving adapters, linking groups of co-evolving genes. CONCLUSIONS Our results provide insights into the evolution of the involved proteins. We find evidence for two coalitions of proteins and the role of co-adaptation in protein evolution is identified and could be used in future research within a functional context.
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Affiliation(s)
- Chrysanthi Ainali
- Centre for Bioinformatics, Department of Informatics, School of Natural and Mathematical Sciences, King's College London, Strand, UK
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Infante C, Ponce M, Manchado M. Duplication of calsequestrin genes in teleosts: Molecular characterization in the Senegalese sole (Solea senegalensis). Comp Biochem Physiol B Biochem Mol Biol 2011; 158:304-14. [PMID: 21256971 DOI: 10.1016/j.cbpb.2011.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 01/16/2011] [Accepted: 01/17/2011] [Indexed: 01/20/2023]
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Bekaert M, Conant GC. Copy number alterations among mammalian enzymes cluster in the metabolic network. Mol Biol Evol 2010; 28:1111-21. [PMID: 21051442 DOI: 10.1093/molbev/msq296] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Using two high-quality human metabolic networks, we employed comparative genomics techniques to infer metabolic network structures for seven other mammals. We then studied copy number alterations (CNAs) in these networks. Using a graph-theoretic approach, we show that the pattern of CNAs is distinctly different from the random distributions expected under genetic drift. Instead, we find that changes in copy number are most common among transporter genes and that the CNAs differ depending on the mammalian lineage in question. Thus, we find an excess of transporter genes in cattle involved in the milk production, secretion, and regulation. These results suggest a potential role for dosage selection in the evolution of mammalian metabolic networks.
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Affiliation(s)
- Michaël Bekaert
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA.
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49
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On the architecture of the posterior zone of the cerebellum. CEREBELLUM (LONDON, ENGLAND) 2010. [PMID: 20838950 DOI: 10.1007/s12311‐010‐0208‐3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
The mammalian cerebellum is histologically uniform. However, underlying the simple laminar architecture is a complex arrangement of parasagittal stripes and transverse zones that can be revealed by the expression of many molecules, in particular, zebrin II/aldolase C. By using a combination of Purkinje cell antigenic markers and afferent tracing, four transverse zones have been identified: in mouse, these are the anterior zone (∼lobules I-V), the central zone (∼lobules VI-VII), the posterior zone (PZ: ∼lobules VIII-dorsal IX), and the nodular zone (∼ventral lobule IX + lobule X). A fifth transverse zone-the lingular zone (∼lobule I)-is found in birds and bats. Within the anterior and posterior zones, parasagittal stripes of Purkinje cells expressing zebrin II alternate with those that do not. To explore this model further and to broaden our understanding of the evolution of cerebellar patterning, stripes in the PZ have been compared in multiple mammalian species. We conclude that a posterior zone with a conserved stripe organization is a common feature of the mammalian and avian cerebellar vermis and that zonal boundaries are independent of cerebellar lobulation.
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50
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Ponce M, Infante C, Manchado M. Molecular characterization and gene expression of thyrotropin receptor (TSHR) and a truncated TSHR-like in Senegalese sole. Gen Comp Endocrinol 2010; 168:431-9. [PMID: 20685365 DOI: 10.1016/j.ygcen.2010.05.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 05/26/2010] [Accepted: 05/27/2010] [Indexed: 01/31/2023]
Abstract
Thyroid hormones (THs) play a key role in larval development, growth and metamorphosis in flatfish. Their synthesis is tightly regulated by the hypothalamic-pituitary-thyroid axis. Thyroid-stimulating hormone receptor (TSHR) is a key protein in the control of thyroid function stimulating TH synthesis after binding its ligand, the thyrotropin. In teleost fish, numerous reports have associated the TSHR with gametogenesis. However, little information about its role during larval development is available. In this study, we report the cloning of two different cDNAs with high similarity to TSHR. Phylogenetic analysis clustered both cDNAs separately. One of them (referred to TSHR) grouped with TSHR orthologs in tetrapods and teleost fish and possessed the three typical conserved domains and regulatory motifs. The second receptor (referred to as TSHRtr-like) represented a novel truncated cDNA bearing the extracellular and part of the transmembrane domain. TSHRtr-like orthologs were only found in teleosts, which suggests that it could have appeared after fish-specific 3R genome duplication. Expression profiles of both genes are analyzed in juvenile tissues and during larval development using a real-time PCR approach. In juvenile fish, TSHR and TSHRtr-like are expressed ubiquitously although transcript levels varied between organs. In both cases, the highest mRNAs levels are detected in brain. During larval development, both genes are expressed to a high level during the first stages (2-3days after hatching) reducing progressively their abundance in the whole larvae during metamorphosis. This reduction in mRNA abundance is more accentuated for the TSHRtr-like gene. To evaluate the possible regulation of both receptors by T4 during sole metamorphosis, larvae are exposed to the goitrogen thiourea (TU). Only TSHRtr-like modifies its expression, increasing its transcripts at 11days after treatment. Moreover, adding exogenous T4 hormone to TU-treated larvae restores the TSHRtr-like steady-state levels similar to the untreated control. Overall, these results demonstrate the existence of two thyrotropin receptors differentially regulated by THs in teleosts.
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Affiliation(s)
- Marian Ponce
- IFAPA Centro El Toruño, Junta de Andalucía, 11500 El Puerto de Santa María, Cádiz, Spain
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