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Cardoso JCR, Félix RC, Costa C, Palma PFS, Canário AVM, Power DM. Evolution of the glucagon-like system across fish. Gen Comp Endocrinol 2018; 264:113-130. [PMID: 29056448 DOI: 10.1016/j.ygcen.2017.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/04/2017] [Accepted: 10/10/2017] [Indexed: 12/25/2022]
Abstract
In fishes, including the jawless lampreys, the most ancient lineage of extant vertebrates, plasma glucose levels are highly variable and regulation is more relaxed than in mammals. The regulation of glucose and lipid in fishes in common with mammals involves members of the glucagon (GCG)-like family of gastrointestinal peptides. In mammals, four peptides GCG, glucagon-like peptide 1 and 2 (GLP1 and GLP2) and glucose-dependent insulinotropic peptide (GIP) that activate four specific receptors exist. However, in lamprey and other fishes the glucagon-like family evolved differently and they retained additional gene family members (glucagon-related peptide, gcrp and its receptor, gcrpr) that are absent from mammals. In the present study, we analysed the evolution of the glucagon-like system in fish and characterized gene expression of the family members in the European sea bass (Dicentrarchus labrax) a teleost fish. Phylogenetic analysis revealed that multiple receptors and peptides of the glucagon-like family emerged early during the vertebrate radiation and evolved via lineage specific events. Synteny analysis suggested that family member gene loss is likely to be the result of a single gene deletion event. Lamprey was the only fish where a putative glp1r persisted and the presence of the receptor gene in the genomes of the elephant shark and coelacanth remains unresolved. In the coelacanth and elephant shark, unique proglucagon genes were acquired which in the former only encoded Gcg and Glp2 and in the latter, shared a similar structure to the teleost proglucagon gene but possessed an extra exon coding for Glp-like peptide that was most similar to Glp2. The variable tissue distribution of the gene transcripts encoding the ligands and receptors of the glucagon-like system in an advanced teleost, the European sea bass, suggested that, as occurs in mammals, they have acquired distinct functions. Statistically significant (p < .05) down-regulation of teleost proglucagon a in sea bass with modified plasma glucose levels confirmed the link between these peptides and metabolism. The tissue distribution of members of the glucagon-like system in sea bass and human suggests that evolution of the brain-gut-peptide regulatory loop diverged between teleosts and mammals despite the overall conservation and similarity of glucagon-like family members.
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Affiliation(s)
- João C R Cardoso
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
| | - Rute C Félix
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
| | - Carina Costa
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Pedro F S Palma
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
| | - Adelino V M Canário
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
| | - Deborah M Power
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
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Irwin DM, Mojsov S. Diversification of the functions of proglucagon and glucagon receptor genes in fish. Gen Comp Endocrinol 2018; 261:148-165. [PMID: 29510149 DOI: 10.1016/j.ygcen.2018.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/05/2018] [Accepted: 03/02/2018] [Indexed: 01/30/2023]
Abstract
The teleost fish-specific genome duplication gave rise to a great number of species inhabiting diverse environments with different access to nutrients and life histories. This event produced duplicated gcg genes, gcga and gcgb, for proglucagon-derived peptides, glucagon and GLP-1 and duplicated gcgr receptor genes, gcgra and gcgrb, which play key roles connecting the consumption of nutrients with glucose metabolism. We conducted a systematic survey of the genomes from 28 species of fish (24 bony (Superclass Osteichthyes), 1 lobe-finned (Class Sarcoperygii), 1 cartilaginous (Superclass Chondrichthyes), and 2 jawless (Superclass Agnatha)) and find that almost all surveyed ray-finned fish contain gcga and gcgb genes with different coding potential and duplicated gcgr genes, gcgra and gcgrb that form two separate clades in the phylogenetic tree consistent with the accepted species phylogeny. All gcgb genes encoded only glucagon and GLP-1 and gcga genes encoded glucagon, GLP-1, and GLP-2, indicating that gcga was subfunctionalized to produce GLP-2. We find a single glp2r, but no glp1r suggesting that duplicated gcgrb was neofunctionalized to bind GLP-1, as demonstrated for the zebrafish gcgrb (Oren et al., 2016). In functional experiments with zebrafish gcgrb and GLP-1 from diverse fish we find that anglerfish GLP-1a, encoded by gcga, is less biologically active than the gcgb anglerfish GLP-1b paralog. But some other fish (zebrafish, salmon, and catfish) gcga GLP-1a display similar biological activities, indicating that the regulation of glucose metabolism by GLP-1 in ray-finned fish is species-specific. Searches of genomes in cartilaginous fish identified a proglucagon gene that encodes a novel GLP-3 peptide in addition to glucagon, GLP-1, and GLP-2, as well as a single gcgr, glp2r, and a new glucagon receptor-like receptor whose identity still needs to be confirmed. The sequence of the shark GLP-1 contained an N-terminal mammalian-like extension that in mammals undergoes a proteolytic cleavage to release biologically active GLP-1. Our results indicate that early in vertebrate evolution diverse regulatory mechanisms emerged for the control of glucose metabolism by proglucagon-derived peptides and their receptors and that in ray-finned fish they included subfunctionalization and neofunctionalization of these genes.
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Affiliation(s)
- David M Irwin
- Department of Laboratory Medicine and Pathobiology, Banting and Best Diabetes Centre, University of Toronto, Toronto, Ont M5S 1A8, Canada.
| | - Svetlana Mojsov
- The Rockefeller University, New York, NY 10065, United States
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Zhang Y, Qin C, Yang L, Lu R, Zhao X, Nie G. A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals. BMC Genomics 2018; 19:246. [PMID: 29642853 PMCID: PMC5896114 DOI: 10.1186/s12864-018-4647-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 04/03/2018] [Indexed: 12/31/2022] Open
Abstract
Background Glucose plays a key role as an energy source in most mammals, but its importance in fish appears to be limited that so far seemed to belong to diabetic humans only. Several laboratories worldwide have made important efforts in order to better understand this strange phenotype observed in fish. However, the mechanism of carbohydrate/glucose metabolism is astonishingly complex. Why basal glycaemia is different between fish and mammals and how carbohydrate metabolism is different amongst organisms is largely uncharted territory. The utilization of comparative systems biology with model vertebrates to explore fish metabolism has become an essential approach to unravelling hidden in vivo mechanisms. Results In this study, we first built a database containing 791, 593, 523, 666 and 698 carbohydrate/glucose metabolic genes from the genomes of Danio rerio, Xenopus tropicalis, Gallus gallus, Mus musculus and Homo sapiens, respectively, and most of these genes in our database are predicted to encode specific enzymes that play roles in defined reactions; over 57% of these genes are related to human type 2 diabetes. Then, we systematically compared these genes and found that more than 70% of the carbohydrate/glucose metabolic genes are conserved in the five species. Interestingly, there are 4 zebrafish-specific genes (si:ch211-167b20.8, CABZ01043017.1, socs9 and eif4e1c) and 1 human-specific gene (CALML6) that may alter glucose utilization in their corresponding species. Interestingly, these 5 genes are all carbohydrate regulation factors, but the enzymes themselves are involved in insulin regulation pathways. Lastly, in order to facilitate the use of our data sets, we constructed a glucose metabolism database platform (http://101.200.43.1:10000/). Conclusions This study provides the first systematic genomic insights into carbohydrate/glucose metabolism. After exhaustive analysis, we found that most metabolic genes are conserved in vertebrates. This work may resolve some of the complexities of carbohydrate/glucose metabolic heterogeneity amongst different vertebrates and may provide a reference for the treatment of diabetes and for applications in the aquaculture industry. Electronic supplementary material The online version of this article (10.1186/s12864-018-4647-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuru Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China.,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Chaobin Qin
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China.,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Liping Yang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China.,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Ronghua Lu
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China.,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Xiaoyan Zhao
- School of Computer and Information Engineering, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Guoxing Nie
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China. .,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China.
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Hu CK, Southey BR, Romanova EV, Maruska KP, Sweedler JV, Fernald RD. Identification of prohormones and pituitary neuropeptides in the African cichlid, Astatotilapia burtoni. BMC Genomics 2016; 17:660. [PMID: 27543050 PMCID: PMC4992253 DOI: 10.1186/s12864-016-2914-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 07/06/2016] [Indexed: 12/14/2022] Open
Abstract
Background Cichlid fishes have evolved remarkably diverse reproductive, social, and feeding behaviors. Cell-to-cell signaling molecules, notably neuropeptides and peptide hormones, are known to regulate these behaviors across vertebrates. This class of signaling molecules derives from prohormone genes that have undergone multiple duplications and losses in fishes. Whether and how subfunctionalization, neofunctionalization, or losses of neuropeptides and peptide hormones have contributed to fish behavioral diversity is largely unknown. Information on fish prohormones has been limited and is complicated by the whole genome duplication of the teleost ancestor. We combined bioinformatics, mass spectrometry-enabled peptidomics, and molecular techniques to identify the suite of neuropeptide prohormones and pituitary peptide products in Astatotilapia burtoni, a well-studied member of the diverse African cichlid clade. Results Utilizing the A. burtoni genome, we identified 148 prohormone genes, with 21 identified as a single copy and 39 with at least 2 duplicated copies. Retention of prohormone duplicates was therefore 41 %, which is markedly above previous reports for the genome-wide average in teleosts. Beyond the expected whole genome duplication, differences between cichlids and mammals can be attributed to gene loss in tetrapods and additional duplication after divergence. Mass spectrometric analysis of the pituitary identified 620 unique peptide sequences that were matched to 120 unique proteins. Finally, we used in situ hybridization to localize the expression of galanin, a prohormone with exceptional sequence divergence in cichlids, as well as the expression of a proopiomelanocortin, prohormone that has undergone an additional duplication in some bony fish lineages. Conclusion We characterized the A. burtoni prohormone complement. Two thirds of prohormone families contain duplications either from the teleost whole genome duplication or a more recent duplication. Our bioinformatic and mass spectrometric findings provide information on a major vertebrate clade that will further our understanding of the functional ramifications of these prohormone losses, duplications, and sequence changes across vertebrate evolution. In the context of the cichlid radiation, these findings will also facilitate the exploration of neuropeptide and peptide hormone function in behavioral diversity both within A. burtoni and across cichlid and other fish species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2914-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Caroline K Hu
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.,Present address: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Elena V Romanova
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Karen P Maruska
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Russell D Fernald
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
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AlMomin S, Kumar V, Al-Amad S, Al-Hussaini M, Dashti T, Al-Enezi K, Akbar A. Draft genome sequence of the silver pomfret fish, Pampus argenteus. Genome 2015; 59:51-8. [PMID: 26692342 DOI: 10.1139/gen-2015-0056] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Silver pomfret, Pampus argenteus, is a fish species from coastal waters. Despite its high commercial value, this edible fish has not been sequenced. Hence, its genetic and genomic studies have been limited. We report the first draft genome sequence of the silver pomfret obtained using a Next Generation Sequencing (NGS) technology. We assembled 38.7 Gb of nucleotides into scaffolds of 350 Mb with N50 of about 1.5 kb, using high quality paired end reads. These scaffolds represent 63.7% of the estimated silver pomfret genome length. The newly sequenced and assembled genome has 11.06% repetitive DNA regions, and this percentage is comparable to that of the tilapia genome. The genome analysis predicted 16 322 genes. About 91% of these genes showed homology with known proteins. Many gene clusters were annotated to protein and fatty-acid metabolism pathways that may be important in the context of the meat texture and immune system developmental processes. The reference genome can pave the way for the identification of many other genomic features that could improve breeding and population-management strategies, and it can also help characterize the genetic diversity of P. argenteus.
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Affiliation(s)
- Sabah AlMomin
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Vinod Kumar
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Sami Al-Amad
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Mohsen Al-Hussaini
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Talal Dashti
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Khaznah Al-Enezi
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Abrar Akbar
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
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Cardoso JCR, Félix RC, Martins RST, Trindade M, Fonseca VG, Fuentes J, Power DM. PACAP system evolution and its role in melanophore function in teleost fish skin. Mol Cell Endocrinol 2015; 411:130-45. [PMID: 25933704 DOI: 10.1016/j.mce.2015.04.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 01/12/2023]
Abstract
Pituitary adenylate cyclase-activating polypeptide (PACAP) administered to tilapia melanophores ex-vivo causes significant pigment aggregation and this is a newly identified function for this peptide in fish. The G-protein coupled receptors (GPCRs), adcyap1r1a (encoding Pac1a) and vipr2a (encoding Vpac2a), are the only receptors in melanophores with appreciable levels of expression and are significantly (p < 0.05) down-regulated in the absence of light. Vpac2a is activated exclusively by peptide histidine isoleucine (PHI), which suggests that Pac1a mediates the melanin aggregating effect of PACAP on melanophores. Paradoxically activation of Pac1a with PACAP caused a rise in cAMP, which in fish melanophores is associated with melanin dispersion. We hypothesise that the duplicate adcyap1ra and vipr2a genes in teleosts have acquired a specific role in skin and that the melanin aggregating effect of PACAP results from the interaction of Pac1a with Ramp that attenuates cAMP-dependent PKA activity and favours the Ca(2+)/Calmodulin dependent pathway.
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Affiliation(s)
- João C R Cardoso
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
| | - Rute C Félix
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Rute S T Martins
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Marlene Trindade
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Vera G Fonseca
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Juan Fuentes
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Deborah M Power
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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