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Iguchi A, Hayashi M, Yorifuji M, Nishijima M, Gibu K, Kunishima T, Bell T, Suzuki A, Ono T. Whole transcriptome analysis of demersal fish eggs reveals complex responses to ocean deoxygenation and acidification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:169484. [PMID: 38302347 DOI: 10.1016/j.scitotenv.2023.169484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 11/20/2023] [Accepted: 12/16/2023] [Indexed: 02/03/2024]
Abstract
Ocean acidification and deoxygenation co-occur in marine environments, causing deterioration of marine ecosystems. However, effects of compound stresses on marine organisms and their physiological coping mechanisms are largely unknown. Here, we show how high pCO2 and low dissolved oxygen (DO) cause transcriptomic changes in eggs of a demersal fish (Sillago japonica), which are fully exposed to such stresses in natural environment. Overall gene expression was affected more strongly by low DO than by high pCO2. Enrichment analysis detected significant stress responses such as glycolytic processes in response to low DO. Increased expression of a group of glycolytic genes under low DO conditions is presumably because oxygen depletion disables the electron transfer pathway, complementing ATP production in the glycolytic pathway. Contrary to expectations, apparent mitigation of gene expression changes was dominant under combined stress conditions, and may represent an innate fish adaptive trait for severe environments.
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Affiliation(s)
- Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan; Research Laboratory on Environmentally-conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan.
| | - Masahiro Hayashi
- Demonstration Laboratory, Marine Ecology Research Institute, 4-7-17 Arahama, Kashiwazaki, Niigata 945-0017, Japan
| | - Makiko Yorifuji
- Demonstration Laboratory, Marine Ecology Research Institute, 4-7-17 Arahama, Kashiwazaki, Niigata 945-0017, Japan
| | - Miyuki Nishijima
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Kodai Gibu
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Taiga Kunishima
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan; Laboratory of Marine Biology, Division of Applied Biological Science, Faculty of Agriculture, Setsunan University, Hirakata, Japan
| | - Tomoko Bell
- Division of Science and Mathmatics, Newman University, Wichita 67213, KS, USA
| | - Atsushi Suzuki
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan; Research Laboratory on Environmentally-conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan
| | - Tsuneo Ono
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
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Clark B, Kuwalekar M, Fischer B, Woltering J, Biran J, Juntti S, Kratochwil CF, Santos ME, Almeida MV. Genome editing in East African cichlids and tilapias: state-of-the-art and future directions. Open Biol 2023; 13:230257. [PMID: 38018094 PMCID: PMC10685126 DOI: 10.1098/rsob.230257] [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: 08/02/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023] Open
Abstract
African cichlid fishes of the Cichlidae family are a group of teleosts important for aquaculture and research. A thriving research community is particularly interested in the cichlid radiations of the East African Great Lakes. One key goal is to pinpoint genetic variation underlying phenotypic diversification, but the lack of genetic tools has precluded thorough dissection of the genetic basis of relevant traits in cichlids. Genome editing technologies are well established in teleost models like zebrafish and medaka. However, this is not the case for emerging model organisms, such as East African cichlids, where these technologies remain inaccessible to most laboratories, due in part to limited exchange of knowledge and expertise. The Cichlid Science 2022 meeting (Cambridge, UK) hosted for the first time a Genome Editing Workshop, where the community discussed recent advances in genome editing, with an emphasis on CRISPR/Cas9 technologies. Based on the workshop findings and discussions, in this review we define the state-of-the-art of cichlid genome editing, share resources and protocols, and propose new possible avenues to further expand the cichlid genome editing toolkit.
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Affiliation(s)
- Bethan Clark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Muktai Kuwalekar
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Uusimaa 00014, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Uusimaa 00014, Finland
| | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Joost Woltering
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg 78457, Germany
| | - Jakob Biran
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
| | - Scott Juntti
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Claudius F. Kratochwil
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Uusimaa 00014, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Uusimaa 00014, Finland
| | | | - Miguel Vasconcelos Almeida
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
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Yokokawa R, Watanabe K, Kanda S, Nishino Y, Yasumasu S, Sano K. Egg envelope formation of medaka Oryzias latipes requires ZP proteins originating from both the liver and ovary. J Biol Chem 2023; 299:104600. [PMID: 36906145 PMCID: PMC10140178 DOI: 10.1016/j.jbc.2023.104600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/12/2023] Open
Abstract
Teleost oocytes are surrounded by a structure, called chorion or egg envelopes, which is composed of zona pellucida (ZP) proteins. As a result of the gene duplication in teleost, the expression site of the zp genes, coding the major component protein of egg envelopes, changed from the ovary to the maternal liver. In Euteleostei, there are three liver-expressed zp genes, named choriogenin (chg) h, chg hm, and chg l, and the composition of the egg envelope is mostly made up of these Chgs. In addition, ovary-expressed zp genes are also conserved in the medaka genomes, and their proteins have also been found to be minor components of the egg envelopes. However, the specific role of liver-expressed versus ovary-expressed zp genes was unclear. In the present study, we showed that ovary-synthesized ZP proteins first form the base layer of the egg envelope, and then Chgs polymerize inwardly to thicken the egg envelope. To analyze the effects of dysfunction of the chg gene, we generated some chg knockout medaka. All knockout females failed to produce normally fertilized eggs by the natural spawning. The egg envelopes lacking Chgs were significantly thinner, but layers formed by ZP proteins synthesized in the ovary were found in the thin egg envelope of knockout as well as wild-type eggs. These results suggest that the ovary-expressed zp gene is well conserved in all teleosts, including those species in which liver-derived ZP proteins are the major component, because it is essential for the initiation of egg envelope formation.
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Affiliation(s)
- Reo Yokokawa
- Department of Materials Science, Graduate School of Science, Josai University, Sakado, Japan
| | - Kana Watanabe
- Graduate School of Pharmaceutical Sciences, Josai University, Sakado, Japan
| | - Shinji Kanda
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Yoshihide Nishino
- Department of Materials and Lifesciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Shigeki Yasumasu
- Department of Materials and Lifesciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan.
| | - Kaori Sano
- Department of Materials Science, Graduate School of Science, Josai University, Sakado, Japan; Department of Chemistry, Faculty of Science, Josai University, Sakado, Japan.
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Chen F, Wang Y, He J, Chen L, Xue G, Zhao Y, Peng Y, Smith C, Zhang J, Chen J, Xie P. Molecular Mechanisms of Spawning Habits for the Adaptive Radiation of Endemic East Asian Cyprinid Fishes. Research (Wash D C) 2022; 2022:9827986. [PMID: 36204246 PMCID: PMC9513835 DOI: 10.34133/2022/9827986] [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: 05/24/2022] [Accepted: 08/15/2022] [Indexed: 11/06/2022] Open
Abstract
Despite the widespread recognition of adaptive radiation as a driver of speciation, the mechanisms by which natural selection generates new species are incompletely understood. The evolutionary radiation of endemic East Asian cyprinids has been proposed as evolving through a change in spawning habits, involving a transition from semibuoyant eggs to adhesive eggs in response to crosslinked river-lake system formation. Here, we investigated the molecular mechanisms that underpin this radiation, associated with egg hydration and adhesiveness. We demonstrated that semibuoyant eggs enhance hydration by increasing the degradation of yolk protein and accumulation of Ca2+ and Mg2+ ions, while adhesive eggs improve adhesiveness and hardness of the egg envelope by producing an adhesive layer and a unique 4th layer to the egg envelope. Based on multiomics analyses and verification tests, we showed that during the process of adaptive radiation, adhesive eggs downregulated the “vitellogenin degradation pathway,” “zinc metalloprotease pathway,” and “ubiquitin-proteasome pathway” and the pathways of Ca2+ and Mg2+ active transport to reduce their hydration. At the same time, adhesive eggs upregulated the crosslinks of microfilament-associated proteins and adhesive-related proteins, the hardening-related proteins of the egg envelope, and the biosynthesis of glycosaminoglycan in the ovary to generate adhesiveness. These findings illustrate the novel molecular mechanisms associated with hydration and adhesiveness of freshwater fish eggs and identify critical molecular mechanisms involved in the adaptive radiation of endemic East Asian cyprinids. We propose that these key egg attributes may function as “magic traits” in this adaptive radiation.
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Affiliation(s)
- Feng Chen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yeke Wang
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun He
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Liang Chen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Ge Xue
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Zhao
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanghui Peng
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Carl Smith
- Department of Ecology and Vertebrate Zoology, University of Łódź, Łódź, Poland
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Jia Zhang
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Chen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Ping Xie
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Institute of Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environment, Yunnan University, Kunming 650500, China
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5
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Gazo I, Naraine R, Lebeda I, Tomčala A, Dietrich M, Franěk R, Pšenička M, Šindelka R. Transcriptome and Proteome Analyses Reveal Stage-Specific DNA Damage Response in Embryos of Sturgeon ( Acipenser ruthenus). Int J Mol Sci 2022; 23:ijms23126392. [PMID: 35742841 PMCID: PMC9223696 DOI: 10.3390/ijms23126392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/27/2022] Open
Abstract
DNA damage during early life stages may have a negative effect on embryo development, inducing mortality and malformations that have long-lasting effects during adult life. Therefore, in the current study, we analyzed the effect of DNA damage induced by genotoxicants (camptothecin (CPT) and olaparib) at different stages of embryo development. The survival, DNA fragmentation, transcriptome, and proteome of the endangered sturgeon Acipenser ruthenus were analyzed. Sturgeons are non-model fish species that can provide new insights into the DNA damage response and embryo development. The transcriptomic and proteomic patterns changed significantly after exposure to genotoxicants in a stage-dependent manner. The results of this study indicate a correlation between phenotype formation and changes in transcriptomic and proteomic profiles. CPT and olaparib downregulated oxidative phosphorylation and metabolic pathways, and upregulated pathways involved in nucleotide excision repair, base excision repair, and homologous recombination. We observed the upregulated expression of zona pellucida sperm-binding proteins in all treatment groups, as well as the upregulation of several glycolytic enzymes. The analysis of gene expression revealed several markers of DNA damage response and adaptive stress response, which could be applied in toxicological studies on fish embryos. This study is the first complex analysis of the DNA damage response in endangered sturgeons.
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Affiliation(s)
- Ievgeniia Gazo
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25 Vodňany, Czech Republic; (I.L.); (R.F.); (M.P.)
- Correspondence: ; Tel.: +420-38777-4607
| | - Ravindra Naraine
- Laboratory of Gene Expression, Institute of Biotechnology—Biocev, Academy of Science of Czech Republic, 252 50 Vestec, Czech Republic; (R.N.); (R.Š.)
| | - Ievgen Lebeda
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25 Vodňany, Czech Republic; (I.L.); (R.F.); (M.P.)
| | - Aleš Tomčala
- Institute of Aquaculture and Protection of Waters, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Husova tř. 458/102, 370 05 České Budějovice, Czech Republic;
| | - Mariola Dietrich
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland;
| | - Roman Franěk
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25 Vodňany, Czech Republic; (I.L.); (R.F.); (M.P.)
| | - Martin Pšenička
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25 Vodňany, Czech Republic; (I.L.); (R.F.); (M.P.)
| | - Radek Šindelka
- Laboratory of Gene Expression, Institute of Biotechnology—Biocev, Academy of Science of Czech Republic, 252 50 Vestec, Czech Republic; (R.N.); (R.Š.)
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6
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Killingbeck EE, Wilburn DB, Merrihew GE, MacCoss MJ, Swanson WJ. Proteomics support the threespine stickleback egg coat as a protective oocyte envelope. Mol Reprod Dev 2021; 88:500-515. [PMID: 34148267 PMCID: PMC8362008 DOI: 10.1002/mrd.23517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 05/20/2021] [Accepted: 05/22/2021] [Indexed: 12/20/2022]
Abstract
Ancestrally marine threespine stickleback fish (Gasterosteus aculeatus) have undergone an adaptive radiation into freshwater environments throughout the Northern Hemisphere, creating an excellent model system for studying molecular adaptation and speciation. Ecological and behavioral factors have been suggested to underlie stickleback reproductive isolation and incipient speciation, but reproductive proteins mediating gamete recognition during fertilization have so far remained unexplored. To begin to investigate the contribution of reproductive proteins to stickleback reproductive isolation, we have characterized the stickleback egg coat proteome. We find that stickleback egg coats are comprised of homologs to the zona pellucida (ZP) proteins ZP1 and ZP3, as in other teleost fish. Our molecular evolutionary analyses indicate that across teleosts, ZP3 but not ZP1 has experienced positive Darwinian selection. Mammalian ZP3 is also rapidly evolving, and surprisingly some residues under selection in stickleback and mammalian ZP3 directly align. Despite broad homology, however, we find differences between mammalian and stickleback ZP proteins with respect to glycosylation, disulfide bonding, and sites of synthesis. Taken together, the changes we observe in stickleback ZP protein architecture suggest that the egg coats of stickleback fish, and perhaps fish more generally, have evolved to fulfill a more protective functional role than their mammalian counterparts.
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Affiliation(s)
- Emily E Killingbeck
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Damien B Wilburn
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Gennifer E Merrihew
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Willie J Swanson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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7
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Zhang H, Zhang B, Kawaguchi M, Lin Q. Effects of hatching enzymes on egg envelope digestion in the male-brooding seahorse. Mol Reprod Dev 2021; 88:459-470. [PMID: 33960059 DOI: 10.1002/mrd.23474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/08/2021] [Accepted: 04/26/2021] [Indexed: 11/11/2022]
Abstract
In the present study, we aimed to evaluate the effects of hatching enzymes on the egg envelope digestion during the hatching period in the male brooding seahorse. The complementary DNAs encoding two hatching-enzyme genes, high choriolytic enzyme (HCE) and low choriolytic enzyme (LCE), were cloned and functionally characterized from the lined seahorse (Hippocampus erectus). The genomic-synteny analysis confirmed that teleosts shared LCE gene synteny. In contrast, the genomic location of HCE was found to be conserved with pipefish, but not other teleosts, suggesting that translocation into a novel genomic location occurred. Whole-mount in situ hybridization showed that HCE and LCE mRNAs were expressed in hatching gland cells. To determine the digestion mechanisms of HCE and LCE in hatching, recombinant HCE and LCE were generated and their enzyme activities were examined using fertilized egg envelopes and synthetic peptides. Seahorse HCE and LCE independently digested and softened the egg envelopes of the lined seahorse. Although the egg envelope was digested more following HCE and LCE co-treatment, envelope solubilization was not observed. Indeed, both HCE and LCE showed similar substrate specificities toward four different synthetic peptides designed from the cleavage sites of egg envelope proteins. HCE and LCE proteins from other euteleostean fishes showed different specificities, and the egg envelope was solubilized by the cooperative action of HCE and LCE. These results suggest that the function of LCE was degenerated in the lined seahorse. Our results imply a digestion mechanism for evolutionary adaptation in ovoviviparous fish with male pregnancy.
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Affiliation(s)
- Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bo Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Mari Kawaguchi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
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Wang Y, Chen F, He J, Xue G, Chen J, Xie P. Cellular and molecular modification of egg envelope hardening in fertilization. Biochimie 2020; 181:134-144. [PMID: 33333173 DOI: 10.1016/j.biochi.2020.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/07/2020] [Accepted: 12/13/2020] [Indexed: 11/30/2022]
Abstract
Fertilization is an essential process that fundamentally impacts fitness. An egg changes dramatically after fertilization mediating the beginning of life, which mainly includes the transformation of the egg envelope via hardening, which is thought to be due to complex reactions involved in the conversion of cellular and molecular. This review highlights the mechanisms of egg envelope hardening in teleost fish. We conclude that the egg envelope hardening might be carried out in two steps. (a) A metalloprotease (alveolin) hydrolyzes the N-terminal proline-glutamine (Pro-Gln) region of zona pellucida (ZP) 1 and (b) triggers intermolecular cross-linking to ZP3 catalyzed by transglutaminase (TGase). The post-fertilization hardening of the egg envelope is an evolutionarily conserved phenomenon across species. We discuss the biochemical function and interaction of some factors reported to be essential to egg envelope hardening in mammalian and nonmammalian species, including metalloprotease, TGase, peroxidase/ovoperoxidase, and other factors (carbohydrate moieties, zinc and Larp6 proteins), and the relevant data suggest that egg envelope hardening is crucial to block polyspermy in internal fertilization, in addition to protecting the developing embryo from mechanical shock and preventing bacterial infection in external fertilization. Increased knowledge of the processes of egg envelope hardening and fertilization is likely to make a remarkable contribution to reproduction and aquaculture.
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Affiliation(s)
- Yeke Wang
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Feng Chen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun He
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ge Xue
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Chen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ping Xie
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; Institute of Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environment, Yunnan University, Kunming, 650500, PR China.
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9
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Vijay P, Sehgal N. Structural analysis and characterization of egg-envelope in the Indian freshwater murrel, Channa punctatus. FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:1847-1856. [PMID: 32535727 DOI: 10.1007/s10695-020-00834-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Egg-envelope, an acellular coat, surrounds the egg and is essential for vitellogenin incorporation. It also plays a pivotal role during fertilization and provides protection to the developing embryo. In the present study, scanning electron microscopy was used to elucidate the structural details of isolated egg-envelopes from the Indian freshwater murrel, Channa punctatus. Several pores and single micropyle were observed on outer surface, whereas inner layer indicated deposition of proteinaceous material. The constituent proteins of egg-envelope were further characterized by Fourier transform infrared (FT-IR) spectroscopy, and electrophoresis and mass-spectrometry (MALDI-TOF-MS/MS). The secondary structure of egg-envelope proteins showed the presence of antiparallel ß-pleated sheets and aromatic amino acids. These proteins resolved into two peptides (130 kDa and 68 kDa) under denaturing conditions, which exhibited glycoprotein nature. The peptide band with low molecular mass showed significant similarity with transmembrane protein, whereas peptide band with high molecular mass matched with choriogenin protein of other fishes. These results confirm that chorion is derived from precursor protein, Choriogenin, in murrel. Chemical composition of egg-envelope supports that chorion is responsible exchange material and chemical defence during embryogenesis.
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Affiliation(s)
- Pooja Vijay
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Neeta Sehgal
- Department of Zoology, University of Delhi, Delhi, 110007, India.
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10
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The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Nat Ecol Evol 2020; 4:841-852. [PMID: 32231327 PMCID: PMC7269910 DOI: 10.1038/s41559-020-1166-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 02/27/2020] [Indexed: 12/20/2022]
Abstract
Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it in a key phylogenetic position at the base of the ~30,000 modern teleost fish species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities to investigate the evolution of polyploid genomes. We assembled a high-quality chromosome-level reference genome for the sterlet, Acipenser ruthenus. Our analysis revealed a very low protein evolution rate that is at least as slow as in other deep branches of the vertebrate tree, such as that of the coelacanth. We uncovered a whole-genome duplication that occurred in the Jurassic, early in the evolution of the entire sturgeon lineage. Following this polyploidization, the rediploidization of the genome included the loss of whole chromosomes in a segmental deduplication process. While known adaptive processes helped conserve a high degree of structural and functional tetraploidy over more than 180 million years, the reduction of redundancy of the polyploid genome seems to have been remarkably random. A genome assembly of the sterlet, Acipenser ruthenus, reveals a whole-genome duplication early in the evolution of the entire sturgeon lineage and provides details about the rediploidization of the genome.
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Sano K, Yokoyama R, Kitano T, Takegaki T, Kitazawa N, Kaneko T, Nishino Y, Yasumasu S, Kawaguchi M. Male parental assistance in embryo hatching of barred‐chin blenny
Rhabdoblennius nitidus. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:81-91. [DOI: 10.1002/jez.b.22854] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/08/2019] [Accepted: 03/20/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Kaori Sano
- Department of Chemistry, Faculty of ScienceJosai UniversitySakado Saitama Japan
| | - Risa Yokoyama
- Department of Chemistry, Faculty of ScienceJosai UniversitySakado Saitama Japan
| | - Takako Kitano
- Faculty of FisheriesNagasaki UniversityNagasaki Japan
| | - Takeshi Takegaki
- Graduate School of Fisheries and Environmental SciencesNagasaki UniversityNagasaki Japan
| | - Nobumasa Kitazawa
- Department of Chemistry, Faculty of ScienceJosai UniversitySakado Saitama Japan
| | - Toyoji Kaneko
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyo Japan
| | - Yoshihide Nishino
- Department of Materials and Life Sciences, Faculty of Science and TechnologySophia UniversityTokyo Japan
| | - Shigeki Yasumasu
- Department of Materials and Life Sciences, Faculty of Science and TechnologySophia UniversityTokyo Japan
| | - Mari Kawaguchi
- Department of Materials and Life Sciences, Faculty of Science and TechnologySophia UniversityTokyo Japan
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Kim BM, Amores A, Kang S, Ahn DH, Kim JH, Kim IC, Lee JH, Lee SG, Lee H, Lee J, Kim HW, Desvignes T, Batzel P, Sydes J, Titus T, Wilson CA, Catchen JM, Warren WC, Schartl M, Detrich HW, Postlethwait JH, Park H. Antarctic blackfin icefish genome reveals adaptations to extreme environments. Nat Ecol Evol 2019; 3:469-478. [PMID: 30804520 PMCID: PMC7307600 DOI: 10.1038/s41559-019-0812-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 01/15/2019] [Indexed: 11/09/2022]
Abstract
Icefishes (suborder Notothenioidei; family Channichthyidae) are the only vertebrates that lack functional haemoglobin genes and red blood cells. Here, we report a high-quality genome assembly and linkage map for the Antarctic blackfin icefish Chaenocephalus aceratus, highlighting evolved genomic features for its unique physiology. Phylogenomic analysis revealed that Antarctic fish of the teleost suborder Notothenioidei, including icefishes, diverged from the stickleback lineage about 77 million years ago and subsequently evolved cold-adapted phenotypes as the Southern Ocean cooled to sub-zero temperatures. Our results show that genes involved in protection from ice damage, including genes encoding antifreeze glycoprotein and zona pellucida proteins, are highly expanded in the icefish genome. Furthermore, genes that encode enzymes that help to control cellular redox state, including members of the sod3 and nqo1 gene families, are expanded, probably as evolutionary adaptations to the relatively high concentration of oxygen dissolved in cold Antarctic waters. In contrast, some crucial regulators of circadian homeostasis (cry and per genes) are absent from the icefish genome, suggesting compromised control of biological rhythms in the polar light environment. The availability of the icefish genome sequence will accelerate our understanding of adaptation to extreme Antarctic environments.
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Affiliation(s)
- Bo-Mi Kim
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Seunghyun Kang
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea
| | - Do-Hwan Ahn
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea
| | - Jin-Hyoung Kim
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea
| | - Il-Chan Kim
- Department of Polar Life Science, Korea Polar Research Institute, Incheon, Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea.,Polar Science, University of Science and Technology, Daejeon, Korea
| | - Sung Gu Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea.,Polar Science, University of Science and Technology, Daejeon, Korea
| | - Hyoungseok Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea.,Polar Science, University of Science and Technology, Daejeon, Korea
| | - Jungeun Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea.,Polar Science, University of Science and Technology, Daejeon, Korea
| | - Han-Woo Kim
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea.,Polar Science, University of Science and Technology, Daejeon, Korea
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Tom Titus
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | | | - Julian M Catchen
- Department of Animal Biology, University of Illinois, Champaign, IL, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Manfred Schartl
- Department of Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany. .,Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, USA. .,Department of Biology, Texas A&M University, College Station, TX, USA.
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA.
| | | | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea. .,Polar Science, University of Science and Technology, Daejeon, Korea.
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Nagasawa T, Kawaguchi M, Yano T, Isoyama S, Yasumasu S, Okabe M. Translocation of promoter-conserved hatching enzyme genes with intron-loss provides a new insight in the role of retrocopy during teleostean evolution. Sci Rep 2019; 9:2448. [PMID: 30792427 PMCID: PMC6385490 DOI: 10.1038/s41598-019-38693-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 12/17/2018] [Indexed: 11/12/2022] Open
Abstract
The hatcing enzyme gene (HE) encodes a protease that is indispensable for the hatching process and is conserved during vertebrate evolution. During teleostean evolution, it is known that HE experienced a drastic transfiguration of gene structure, namely, losing all of its introns. However, these facts are contradiction with each other, since intron-less genes typically lose their original promoter because of duplication via mature mRNA, called retrocopy. Here, using a comparative genomic assay, we showed that HEs have changed their genomic location several times, with the evolutionary timings of these translocations being identical to those of intron-loss. We further showed that HEs maintain the promoter sequence upstream of them after translocation. Therefore, teleostean HEs are unique genes which have changed intra- (exon-intron) and extra-genomic structure (genomic loci) several times, although their indispensability for the reproductive process of hatching implies that HE genes are translocated by retrocopy with their promoter sequence.
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Affiliation(s)
- Tatsuki Nagasawa
- Department of Anatomy, The Jikei University School of Medicine, 3-25-8 Nishishimbashi, Minato-ku, Tokyo, 105-8461, Japan.,Research Fellow of the Japan Society for the Promotion of Science (JSPS), Tokyo, 102-0083, Japan.,Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Mari Kawaguchi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Tohru Yano
- Department of Anatomy, The Jikei University School of Medicine, 3-25-8 Nishishimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Sho Isoyama
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Shigeki Yasumasu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan.
| | - Masataka Okabe
- Department of Anatomy, The Jikei University School of Medicine, 3-25-8 Nishishimbashi, Minato-ku, Tokyo, 105-8461, Japan
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Nishio S, Okumura H, Matsuda T. Egg-Coat and Zona Pellucida Proteins of Chicken as a Typical Species of Aves. Curr Top Dev Biol 2018; 130:307-329. [PMID: 29853181 DOI: 10.1016/bs.ctdb.2018.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Birds are oviparous vertebrates in terrestrial animals. Birds' eggs accumulate mass of egg yolk during the egg development and are accordingly much larger than the eggs of viviparous vertebrates. Despite such difference in size and contents, the birds' eggs are surrounded with the egg-coat morphologically and compositionally resembling the mammalian egg-coat, zona pellucida. On the other hand, there are some differences in part between the two egg-coats, though relationships of such structural differences to any biological roles specific for the extracellular matrix of birds' eggs are not fully understood. In birds, unlike mammals, ZP proteins constituting the egg-coat are highly conserved and therefore those of chicken are described as a representative of birds. The egg-coat ZP proteins, ZP1, ZP3, and ZPD as the majors, accumulate and form the matrix by self-assembly around the egg rapidly growing in the ovarian follicle, in which ZP1 is from liver and both ZP3 and ZPD are from follicular granulosa cells. Although details of the egg-coat-sperm interaction on fertilization remain to be investigated, the lytic degradation process of egg-coat matrix for the sperm penetration has become to be clarified gradually. ZP1 is the primary target of sperm acrosin, and the limited cleavage in the specific region leading to the loss of intermolecular cross-linkages is crucial for the lysis of egg-coat matrix. Possible roles of the ZP1 with the additional sequence characteristic to birds are discussed from a viewpoint of giving both robustness and elastomeric nature to the egg-coat matrix for the birds' eggs.
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Affiliation(s)
- Shunsuke Nishio
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | | | - Tsukasa Matsuda
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.
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