1
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Thompson AW, Wojtas H, Davoll M, Braasch I. Genome of the Rio Pearlfish (Nematolebias whitei), a bi-annual killifish model for Eco-Evo-Devo in extreme environments. G3 (BETHESDA, MD.) 2022; 12:6533448. [PMID: 35188191 PMCID: PMC8982402 DOI: 10.1093/g3journal/jkac045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/11/2022] [Indexed: 12/13/2022]
Abstract
The Rio Pearlfish, Nematolebias whitei, is a bi-annual killifish species inhabiting seasonal pools in the Rio de Janeiro region of Brazil that dry twice per year. Embryos enter dormant diapause stages in the soil, waiting for the inundation of the habitat which triggers hatching and commencement of a new life cycle. Rio Pearlfish represents a convergent, independent origin of annualism from other emerging killifish model species. While some transcriptomic datasets are available for Rio Pearlfish, thus far, a sequenced genome has been unavailable. Here, we present a high quality, 1.2 Gb chromosome-level genome assembly, genome annotations, and a comparative genomic investigation of the Rio Pearlfish as representative of a vertebrate clade that evolved environmentally cued hatching. We show conservation of 3D genome structure across teleost fish evolution, developmental stages, tissues, and cell types. Our analysis of mobile DNA shows that Rio Pearlfish, like other annual killifishes, possesses an expanded transposable element profile with implications for rapid aging and adaptation to harsh conditions. We use the Rio Pearlfish genome to identify its hatching enzyme gene repertoire and the location of the hatching gland, a key first step in understanding the developmental genetic control of hatching. The Rio Pearlfish genome expands the comparative genomic toolkit available to study convergent origins of seasonal life histories, diapause, and rapid aging phenotypes. We present the first set of genomic resources for this emerging model organism, critical for future functional genetic, and multiomic explorations of “Eco-Evo-Devo” phenotypes of resilience and adaptation to extreme environments.
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Affiliation(s)
- Andrew W Thompson
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Ecology, Evolution & Behavior (EEB) Program, Michigan State University, East Lansing, MI 48824, USA
| | - Harrison Wojtas
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Myles Davoll
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Ecology, Evolution & Behavior (EEB) Program, Michigan State University, East Lansing, MI 48824, USA
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2
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Nagasawa T, Kawaguchi M, Nishi K, Yasumasu S. Molecular evolution of hatching enzymes and their paralogous genes in vertebrates. BMC Ecol Evol 2022; 22:9. [PMID: 35109790 PMCID: PMC8812170 DOI: 10.1186/s12862-022-01966-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hatching is identified as one of the most important events in the reproduction of oviparous vertebrates. The genes for hatching enzymes, which are vital in the hatching process, are conserved among vertebrates. However, especially in teleost, it is difficult to trace their molecular evolution in detail due to the presence of other C6astacins, which are the subfamily to which the genes for hatching enzymes belong and are highly diverged. In particular, the hatching enzyme genes are diversified with frequent genome translocations due to retrocopy. RESULTS In this study, we took advantage of the rapid expansion of whole-genome data in recent years to examine the molecular evolutionary process of these genes in vertebrates. The phylogenetic analysis and the genomic synteny analysis revealed C6astacin genes other than the hatching enzyme genes, which was previously considered to be retained only in teleosts, was also retained in the genomes of basal ray-finned fishes, coelacanths, and cartilaginous fishes. These results suggest that the common ancestor of these genes can be traced back to at least the common ancestor of the Gnathostomata. Moreover, we also found that many of the C6astacin genes underwent multiple gene duplications during vertebrate evolution, and the results of gene expression analysis in frogs implied that genes derived from hatching enzyme genes underwent neo-functionalization. CONCLUSIONS In this study, we describe in detail the molecular evolution of the C6astacin gene in vertebrates, which has not been summarized previously. The results revealed the presence of the previously unknown C6astacin gene in the basal-lineage of jawed vertebrates and large-scale gene duplication of hatching enzyme genes in amphibians. The comprehensive investigation reported in this study will be an important basis for studying the molecular evolution of the vertebrate C6astacin genes, hatching enzyme, and its paralogous genes and for identifying these genes without the need for gene expression and functional analysis.
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Affiliation(s)
- Tatsuki Nagasawa
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, 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
| | - Kohki Nishi
- 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.
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3
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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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4
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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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5
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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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6
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Cohen KL, Piacentino ML, Warkentin KM. Two types of hatching gland cells facilitate escape-hatching at different developmental stages in red-eyed treefrogs, Agalychnis callidryas (Anura: Phyllomedusidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly214] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
| | | | - Karen M Warkentin
- Department of Biology, Boston University, Boston, MA, USA
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
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7
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Zhang Y, Zhang R, Sun H, Chen Q, Yu X, Zhang T, Yi M, Liu JX. Copper inhibits hatching of fish embryos via inducing reactive oxygen species and down-regulating Wnt signaling. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 205:156-164. [PMID: 30388615 DOI: 10.1016/j.aquatox.2018.10.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 05/26/2023]
Abstract
The copper ion (Cu2+) has been reported to suppress the hatching of fish. However, little is known about the underlying mechanism. In this study, copper nanoparticles (CuNPs) and Cu2+ were shown to significantly suppress hatching of zebrafish in a dosage-dependent manner, and reactive oxygen species (ROS) scavengers NAC (N-acetylcysteine) & GSH (reduced glutathione) and Wnt signaling agonist BIO (6-bromoindirubin-3'-oxime) significantly alleviated the suppressing effects of Cu2+ and CuNPs on egg hatching. Mechanistically, NAC, GSH, and BIO recovered the egg hatching in copper-treated group via increasing the embryonic motility rather than stimulating the expression and secretion of hatching enzymes before hatching. Additionally, no significant difference in egg hatching was observed between the control and Cu2+-treated group at 72 hpf (hours post fertilization) in cox17 mutant embryos, in which little ROS was producd after copper stimulation. This may be the first report that Cu2+ and CuNPs suppress embryonic motility and the subsequent hatching via inducing ROS and at the same time down-regulating Wnt signaling in fish embryos.
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Affiliation(s)
- YanJun Zhang
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - RuiTao Zhang
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - HaoJie Sun
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qi Chen
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - XueDong Yu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ting Zhang
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ming Yi
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jing-Xia Liu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China; Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Hunan, Changde, 415000, China.
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8
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Zhao L, Si J, Wei Y, Li S, Jiang Y, Zhou R, Liu B, Zhang H. Toxicity of porcelain-fused-to-metal substrate to zebrafish ( Danio rerio ) embryos and larvae. Life Sci 2018; 203:66-71. [DOI: 10.1016/j.lfs.2018.04.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 03/27/2018] [Accepted: 04/12/2018] [Indexed: 10/17/2022]
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9
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Uhrig RG, Moorhead G. AtSLP2 is an intronless protein phosphatase that co-expresses with intronless mitochondrial pentatricopeptide repeat (PPR) and tetratricopeptide (TPR) protein encoding genes. PLANT SIGNALING & BEHAVIOR 2017; 12:e1307493. [PMID: 28350216 PMCID: PMC5437834 DOI: 10.1080/15592324.2017.1307493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 03/11/2017] [Accepted: 03/13/2017] [Indexed: 06/06/2023]
Abstract
Shewanella-like PPP family phosphatases (SLPs) are a unique lineage of eukaryote PPP-family phosphatases of bacterial origin which are not found in metazoans. 1,2 Their absence in metazoans is marked by their ancient bacterial origins and presence in plants. 1 Recently, we found that the SLP2 phosphatase ortholog of Arabidopsis thaliana localized to the mitochondrial intermembrane space (IMS) where it was determined to be activated by mitochondrial intermembrane space protein 40 (MIA40) to regulate seed germination. 3 Through examination of atslp2 knockout (accelerated germination) and 35S::AtSLP2 over-expressing (delayed germination) plants it was found that AtSLP2 influences Arabidopsis thaliana germination rates via gibberellic acid (GA) biosynthesis. 3 However, the exact mechanism by which this occurs remains unresolved. To identify potential partners of AtSLP2 in regulating germination through GA, we undertook a gene co-expression network analysis using RNA-sequencing data available through Genevestigator ( https://genevestigator.com/gv/ ).
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Affiliation(s)
- R. Glen Uhrig
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Group of Plant Biotechnology, Department of Biology, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Greg Moorhead
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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10
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Nagasawa T, Kawaguchi M, Yano T, Sano K, Okabe M, Yasumasu S. Evolutionary Changes in the Developmental Origin of Hatching Gland Cells in Basal Ray-Finned Fishes. Zoolog Sci 2016; 33:272-81. [PMID: 27268981 DOI: 10.2108/zs150183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Hatching gland cells (HGCs) originate from different germ layers between frogs and teleosts, although the hatching enzyme genes are orthologous. Teleostei HGCs differentiate in the mesoendodermal cells at the anterior end of the involved hypoblast layer (known as the polster) in late gastrula embryos. Conversely, frog HGCs differentiate in the epidermal cells at the neural plate border in early neurula embryos. To infer the transition in the developmental origin of HGCs, we studied two basal ray-finned fishes, bichir (Polypterus) and sturgeon. We observed expression patterns of their hatching enzyme (HE) and that of three transcription factors that are critical for HGC differentiation: KLF17 is common to both teleosts and frogs; whereas FoxA3 and Pax3 are specific to teleosts and frogs, respectively. We then inferred the transition in the developmental origin of HGCs. In sturgeon, the KLF17, FoxA3, and HE genes were expressed during the tailbud stage in the cell mass at the anterior region of the body axis, a region corresponding to the polster in teleost embryos. In contrast, the bichir was suggested to possess both teleost- and amphibian-type HGCs, i.e. the KLF17 and FoxA3 genes were expressed in the anterior cell mass corresponding to the polster, and the KLF17, Pax3 and HE genes were expressed in dorsal epidermal layer of the head. The change in developmental origin is thought to have occurred during the evolution of basal ray-finned fish, because bichir has two HGCs, while sturgeon only has the teleost-type.
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Affiliation(s)
- Tatsuki Nagasawa
- 1 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
- 1 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
- 2 Department of Anatomy, The Jikei University School of Medicine, 3-25-8 Nishishinbasi, Minato-ku, Tokyo 105-8461, Japan
| | - Kaori Sano
- 3 Department of Chemistry, Faculty of Science, Josai University, 1-1 Keyakidai, Sakado, Saitama 350-0295, Japan
| | - Masataka Okabe
- 2 Department of Anatomy, The Jikei University School of Medicine, 3-25-8 Nishishinbasi, Minato-ku, Tokyo 105-8461, Japan
| | - Shigeki Yasumasu
- 1 Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan
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11
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Nagasawa T, Kawaguchi M, Sano K, Yasumasu S. Sturgeon hatching enzyme and the mechanism of egg envelope digestion: Insight into changes in the mechanism of egg envelope digestion during the evolution of ray-finned fish. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:720-32. [DOI: 10.1002/jez.b.22660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 10/13/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Tatsuki Nagasawa
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo; Japan
| | - Mari Kawaguchi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo; Japan
| | - Kaori Sano
- Department of Chemistry, Faculty of Science, Josai University, 1-1 Keyakidai, Sakado, Saitama; Japan
| | - Shigeki Yasumasu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo; Japan
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12
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Kawaguchi M, Sano K, Yoshizaki N, Shimizu D, Fujinami Y, Noda T, Yasumasu S. Comparison of Hatching Mode in Pelagic and Demersal Eggs of Two Closely Related Species in the Order Pleuronectiformes. Zoolog Sci 2014; 31:709-15. [DOI: 10.2108/zs140018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- 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
| | - Kaori Sano
- Department of Chemistry, Faculty of Science, Josai University, Saitama 350-0295, Japan
| | - Norio Yoshizaki
- Department of Agricultural Science, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Daisuke Shimizu
- Stock Enhancement and Aquaculture Division, Tohoku National Fisheries Research Institute, Fisheries Research Agency, Miyako, Iwate 027-0097, Japan
| | - Yuichiro Fujinami
- Stock Enhancement and Aquaculture Division, Tohoku National Fisheries Research Institute, Fisheries Research Agency, Miyako, Iwate 027-0097, Japan
| | - Tsutomu Noda
- Stock Enhancement and Aquaculture Division, Seikai National Fisheries Research Institute, Fisheries Research Agency, Goto, Nagasaki 853-0508, 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
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13
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Atractaspis aterrima toxins: the first insight into the molecular evolution of venom in side-stabbers. Toxins (Basel) 2013; 5:1948-64. [PMID: 24169588 PMCID: PMC3847709 DOI: 10.3390/toxins5111948] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/19/2013] [Accepted: 10/22/2013] [Indexed: 12/13/2022] Open
Abstract
Although snake venoms have been the subject of intense research, primarily because of their tremendous potential as a bioresource for design and development of therapeutic compounds, some specific groups of snakes, such as the genus Atractaspis, have been completely neglected. To date only limited number of toxins, such as sarafotoxins have been well characterized from this lineage. In order to investigate the molecular diversity of venom from Atractaspis aterrima—the slender burrowing asp, we utilized a high-throughput transcriptomic approach completed with an original bioinformatics analysis pipeline. Surprisingly, we found that Sarafotoxins do not constitute the major ingredient of the transcriptomic cocktail; rather a large number of previously well-characterized snake venom-components were identified. Notably, we recovered a large diversity of three-finger toxins (3FTxs), which were found to have evolved under the significant influence of positive selection. From the normalized and non-normalized transcriptome libraries, we were able to evaluate the relative abundance of the different toxin groups, uncover rare transcripts, and gain new insight into the transcriptomic machinery. In addition to previously characterized toxin families, we were able to detect numerous highly-transcribed compounds that possess all the key features of venom-components and may constitute new classes of toxins.
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14
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Kawaguchi M, Inoue K, Iuchi I, Nishida M, Yasumasu S. Molecular co-evolution of a protease and its substrate elucidated by analysis of the activity of predicted ancestral hatching enzyme. BMC Evol Biol 2013; 13:231. [PMID: 24161109 PMCID: PMC3819744 DOI: 10.1186/1471-2148-13-231] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 10/23/2013] [Indexed: 02/08/2023] Open
Abstract
Background Hatching enzyme is a protease that digests the egg envelope, enabling hatching of the embryo. We have comprehensively studied the molecular mechanisms of the enzyme action to its substrate egg envelope, and determined the gene/protein structure and phylogenetic relationships. Because the hatching enzyme must have evolved while maintaining its ability to digest the egg envelope, the hatching enzyme-egg envelope protein pair is a good model for studying molecular co-evolution of a protease and its substrate. Results Hatching enzymes from medaka (Oryzias latipes) and killifish (Fundulus heteroclitus) showed species-specific egg envelope digestion. We found that by introducing four medaka-type residue amino acid substitutions into recombinant killifish hatching enzyme, the mutant killifish hatching enzyme could digest medaka egg envelope. Further, we studied the participation of the cleavage site of the substrate in the species-specificity of hatching enzyme. A P2-site single amino acid substitution was responsible for the species-specificity. Estimation of the activity of the predicted ancestral enzymes towards various types of cleavage sites along with prediction of the evolutionary timing of substitutions allowed prediction of a possible evolutionary pathway, as follows: ancestral hatching enzyme, which had relatively strict substrate specificity, developed broader specificity as a result of four amino acid substitutions in the active site cleft of the enzyme. Subsequently, a single substitution occurred within the cleavage site of the substrate, and the recent feature of species-specificity was established in the hatching enzyme-egg envelope system. Conclusions The present study clearly provides an ideal model for protease-substrate co-evolution. The evolutionary process giving rise to species-specific egg envelope digestion of hatching enzyme was initiated by amino acid substitutions in the enzyme, resulting in altered substrate specificity, which later allowed an amino acid substitution in the substrate.
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Affiliation(s)
| | | | | | | | - 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.
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Tingaud-Sequeira A, Lozano JJ, Zapater C, Otero D, Kube M, Reinhardt R, Cerdà J. A rapid transcriptome response is associated with desiccation resistance in aerially-exposed killifish embryos. PLoS One 2013; 8:e64410. [PMID: 23741328 PMCID: PMC3669298 DOI: 10.1371/journal.pone.0064410] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 04/12/2013] [Indexed: 11/21/2022] Open
Abstract
Delayed hatching is a form of dormancy evolved in some amphibian and fish embryos to cope with environmental conditions transiently hostile to the survival of hatchlings or larvae. While diapause and cryptobiosis have been extensively studied in several animals, very little is known concerning the molecular mechanisms involved in the sensing and response of fish embryos to environmental cues. Embryos of the euryhaline killifish Fundulus heteroclitus advance dvelopment when exposed to air but hatching is suspended until flooding with seawater. Here, we investigated how transcriptome regulation underpins this adaptive response by examining changes in gene expression profiles of aerially incubated killifish embryos at ∼100% relative humidity, compared to embryos continuously flooded in water. The results confirm that mid-gastrula embryos are able to stimulate development in response to aerial incubation, which is accompanied by the differential expression of at least 806 distinct genes during a 24 h period. Most of these genes (∼70%) appear to be differentially expressed within 3 h of aerial exposure, suggesting a broad and rapid transcriptomic response. This response seems to include an early sensing phase, which overlaps with a tissue remodeling and activation of embryonic development phase involving many regulatory and metabolic pathways. Interestingly, we found fast (0.5–1 h) transcriptional differences in representatives of classical “stress” proteins, such as some molecular chaperones, members of signalling pathways typically involved in the transduction of sensor signals to stress response genes, and oxidative stress-related proteins, similar to that described in other animals undergoing dormancy, diapause or desiccation. To our knowledge, these data represent the first transcriptional profiling of molecular processes associated with desiccation resistance during delayed hatching in non-mammalian vertebrates. The exceptional transcriptomic plasticity observed in killifish embryos provides an important insight as to how the embryos are able to rapidly adapt to non-lethal desiccation conditions.
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Affiliation(s)
- Angèle Tingaud-Sequeira
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA)-Institut de Ciències del Mar, CSIC, Barcelona, Spain
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16
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Kawaguchi M, Takahashi H, Takehana Y, Naruse K, Nishida M, Yasumasu S. Sub-Functionalization of Duplicated Genes in the Evolution of Nine-Spined Stickleback Hatching Enzyme. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:140-50. [DOI: 10.1002/jez.b.22490] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 01/16/2013] [Accepted: 01/22/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Mari Kawaguchi
- Department of Materials and Life Sciences; Faculty of Science and Technology, Sophia University; Chiyoda-ku; Tokyo; Japan
| | - Hiroshi Takahashi
- Department of Applied Aquabiology; National Fisheries University; Yamaguchi; Japan
| | - Yusuke Takehana
- Laboratory of Bioresources; National Institute for Basic Biology; Okazaki, Aichi; Japan
| | - Kiyoshi Naruse
- Laboratory of Bioresources; National Institute for Basic Biology; Okazaki, Aichi; Japan
| | - Mutsumi Nishida
- Atmosphere and Ocean Research Institute; The University of Tokyo; Kashiwa; Chiba; Japan
| | - Shigeki Yasumasu
- Department of Materials and Life Sciences; Faculty of Science and Technology, Sophia University; Chiyoda-ku; Tokyo; Japan
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Kawaguchi M, Yasumasu S, Shimizu A, Kudo N, Sano K, Iuchi I, Nishida M. Adaptive evolution of fish hatching enzyme: one amino acid substitution results in differential salt dependency of the enzyme. J Exp Biol 2013; 216:1609-15. [DOI: 10.1242/jeb.069716] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Summary
Embryos of medaka Oryzias latipes hatch in freshwater, while those of killifish Fundulus heteroclitus hatch in brackish water. Medaka and Fundulus possess two kinds of hatching enzymes, high choriolytic enzyme (HCE) and low choriolytic enzyme (LCE), which cooperatively digest their egg envelope at the time of hatching. Optimal salinity of medaka HCE was found to be in 0 M NaCl, and the activity was decreased with increased salt concentrations. One of the two Fundulus HCEs, FHCE1, showed the highest activity in 0 M NaCl, the other FHCE2 did in 0.125 M NaCl. The results suggest that the salt dependencies of HCEs are well adapted to each salinity at the time of hatching. Different from HCE, LCEs of both species maintained the activity sufficient for egg envelope digestion in various salinities. The difference of amino acid sequence between FHCE1 and FHCE2 was found in only a single site at position 36 (Gly/Arg), suggesting that this single substitution causes the different salt dependency between the two enzymes. Superimposition of FHCE1 and FHCE2 with the 3D-structure model of medaka HCE revealed that position 36 was located on the surface of HCE molecule, far from its active site cleft. The results suggest a hypothesis that position 36 influences salt dependent activity of HCE not with recognition of primary structure around the cleavage site but with recognition of higher ordered structure of egg envelope protein.
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Keow JY, Pond ED, Cisar JS, Cravatt BF, Crawford BD. Activity-based labeling of matrix metalloproteinases in living vertebrate embryos. PLoS One 2012; 7:e43434. [PMID: 22952682 PMCID: PMC3429480 DOI: 10.1371/journal.pone.0043434] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Accepted: 07/23/2012] [Indexed: 12/25/2022] Open
Abstract
Extracellular matrix (ECM) remodeling is a physiologically and developmentally essential process mediated by a family of zinc-dependent extracellular proteases called matrix metalloproteinases (MMPs). In addition to complex transcriptional control, MMPs are subject to extensive post-translational regulation. Because of this, classical biochemical, molecular and histological techniques that detect the expression of specific gene products provide useful but limited data regarding the biologically relevant activity of MMPs. Using benzophenone-bearing hydroxamate-based probes that interact with the catalytic zinc ion in MMPs, active proteases can be covalently ‘tagged’ by UV cross-linking. This approach has been successfully used to tag MMP-2 in vitro in tissue culture supernatants, and we show here that this probe tags proteins with mobilities consistent with known MMPs and detectable gelatinolytic activity in homogenates of zebrafish embryos. Furthermore, because of the transparency of the zebrafish embryo, UV-photocroslinking can be accomplished in vivo, and rhodamated benzophenone probe is detected in striking spatial patterns consistent with known distributions of active matrix remodeling in embryos. Finally, in metamorphosing Xenopus tadpoles, this probe can be used to biotinylate active MMP-2 by injecting it and cross-linking it in vivo, allowing the protein to be subsequently extracted and biochemically identified.
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Affiliation(s)
- Jonathan Y. Keow
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Eric D. Pond
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Justin S. Cisar
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Benjamin F. Cravatt
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Bryan D. Crawford
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
- * E-mail:
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Molecular cloning and characterization of hatching enzyme-like geneII (BmHELII) in the silkworm, Bombyx mori. Biochem Biophys Res Commun 2012; 419:194-9. [PMID: 22342669 DOI: 10.1016/j.bbrc.2012.01.144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 01/30/2012] [Indexed: 11/23/2022]
Abstract
Hatching enzyme (HE) is an enzyme that digests an egg envelop at the time of embryo hatching. Previously, we have reported a kind of Bombyx mori hatching enzyme-like gene (BmHEL). In this paper, the full length of another BmHEL cDNA sequence (BmHELII, GenBank ID: JN627443) was cloned from bluish-silkworm-eggs. The cDNA was 977 bp in length with an open reading frame of 885 bp which encodes a polypeptide of 294 amino acids including a putative signal peptide of 16 amino acid residues and a mature protein of 278 amino acids. The deduced BmHELII had a predicted molecular mass of 33.62 kDa, isoelectric point of 5.44 and two conserved signature sequences of astacin family. Bioinformatic analysis results showed that the deduced protease domain amino acid sequence of BmHELII had 29.5-87.0% identities to that of HE identified in the other species. The BmHELII gene structure was 6-exon-5-intron, and the promoter region harbored some basal promoter elements and some embryo development related transcription factor binding sites. Semi-quantitative RT-PCR analysis revealed that the relative level of BmHELII transcripts at different stages during egg incubation increased with the development of embryos and reached to a maximum just before hatching, hence declined gradually after hatching. The spatio-temporal expression pattern of BmHELII basically resembled that of hatching enzyme gene. Moreover, the BmHELII transcript was detected in testis of the silkworm, and semi-quantitative RT-PCR analysis showed that it kept at the high level in testis of silkworm from larvae to moth, which suggested that BmHELII might take part in the development of sperm. These results will be helpful to provide a molecular basis for understanding the mechanism underlying silkworm hatching as well as spermatogenesis.
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Sano K, Kawaguchi M, Yoshikawa M, Kaneko T, Tanaka T, Iuchi I, Yasumasu S. Hatching enzyme of Japanese eel Anguilla japonica and the possible evolution of the egg envelope digestion mechanism. FEBS J 2011; 278:3711-23. [DOI: 10.1111/j.1742-4658.2011.08289.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Martin K, Bailey K, Moravek C, Carlson K. Taking the plunge: California Grunion embryos emerge rapidly with environmentally cued hatching. Integr Comp Biol 2011; 51:26-37. [PMID: 21665921 DOI: 10.1093/icb/icr037] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The process of hatching has been well studied in some model species of teleosts: the medaka Oryzias latipes, the mummichog Fundulus heteroclitus, and the zebrafish Danio rerio. These models are compared to the California Grunion, Leuresthes tenuis that has some unique features of reproduction related to tidal synchrony of spawning and environmentally cued hatching (ECH). During oviposition at spring tides, this marine teleost spawns out of water to bury its clutches on sandy beaches in the high intertidal zone. After embryos of L. tenuis reach hatching competence, hatching can be triggered at any time. Incubation above the water line inhibits hatching until ECH is triggered by rising tides during the following lunar phase, and hatching occurs within a few seconds. We review the embryo's response to environmental cues at hatching and the effects of the surrounding medium on the chorionase and chorion for this form of ECH. Leuresthes tenuis shares some similarities as well as some important differences with the model species. Comparison of hatching across teleostean taxa indicates great variability in stage at hatching and in duration of incubation that suggest hatching plasticity in response to environmental cues may be more widespread than currently appreciated.
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Affiliation(s)
- Karen Martin
- Department of Biology, Pepperdine University, Malibu, CA 90263-4321, USA
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22
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Kawaguchi M, Yasumasu S, Shimizu A, Sano K, Iuchi I, Nishida M. Conservation of the egg envelope digestion mechanism of hatching enzyme in euteleostean fishes. FEBS J 2010; 277:4973-87. [PMID: 21070609 DOI: 10.1111/j.1742-4658.2010.07907.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We purified two hatching enzymes, namely high choriolytic enzyme (HCE; EC 3.4.24.67) and low choriolytic enzyme (LCE; EC 3.4.24.66), from the hatching liquid of Fundulus heteroclitus, which were named Fundulus HCE (FHCE) and Fundulus LCE (FLCE). FHCE swelled the inner layer of egg envelope, and FLCE completely digested the FHCE-swollen envelope. In addition, we cloned three Fundulus cDNAs orthologous to cDNAs for the medaka precursors of egg envelope subunit proteins (i.e. choriogenins H, H minor and L) from the female liver. Cleavage sites of FHCE and FLCE on egg envelope subunit proteins were determined by comparing the N-terminal amino acid sequences of digests with the sequences deduced from the cDNAs for egg envelope subunit proteins. FHCE and FLCE cleaved different sites of the subunit proteins. FHCE efficiently cleaved the Pro-X-Y repeat regions into tripeptides to dodecapeptides to swell the envelope, whereas FLCE cleaved the inside of the zona pellucida domain, the core structure of egg envelope subunit protein, to completely digest the FHCE-swollen envelope. A comparison showed that the positions of hatching enzyme cleavage sites on egg envelope subunit proteins were strictly conserved between Fundulus and medaka. Finally, we extended such a comparison to three other euteleosts (i.e. three-spined stickleback, spotted halibut and rainbow trout) and found that the egg envelope digestion mechanism was well conserved among them. During evolution, the egg envelope digestion by HCE and LCE orthologs was established in the lineage of euteleosts, and the mechanism is suggested to be conserved.
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Affiliation(s)
- Mari Kawaguchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
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Kawaguchi M, Hiroi J, Miya M, Nishida M, Iuchi I, Yasumasu S. Intron-loss evolution of hatching enzyme genes in Teleostei. BMC Evol Biol 2010; 10:260. [PMID: 20796321 PMCID: PMC2939575 DOI: 10.1186/1471-2148-10-260] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 08/27/2010] [Indexed: 11/29/2022] Open
Abstract
Background Hatching enzyme, belonging to the astacin metallo-protease family, digests egg envelope at embryo hatching. Orthologous genes of the enzyme are found in all vertebrate genomes. Recently, we found that exon-intron structures of the genes were conserved among tetrapods, while the genes of teleosts frequently lost their introns. Occurrence of such intron losses in teleostean hatching enzyme genes is an uncommon evolutionary event, as most eukaryotic genes are generally known to be interrupted by introns and the intron insertion sites are conserved from species to species. Here, we report on extensive studies of the exon-intron structures of teleostean hatching enzyme genes for insight into how and why introns were lost during evolution. Results We investigated the evolutionary pathway of intron-losses in hatching enzyme genes of 27 species of Teleostei. Hatching enzyme genes of basal teleosts are of only one type, which conserves the 9-exon-8-intron structure of an assumed ancestor. On the other hand, otocephalans and euteleosts possess two types of hatching enzyme genes, suggesting a gene duplication event in the common ancestor of otocephalans and euteleosts. The duplicated genes were classified into two clades, clades I and II, based on phylogenetic analysis. In otocephalans and euteleosts, clade I genes developed a phylogeny-specific structure, such as an 8-exon-7-intron, 5-exon-4-intron, 4-exon-3-intron or intron-less structure. In contrast to the clade I genes, the structures of clade II genes were relatively stable in their configuration, and were similar to that of the ancestral genes. Expression analyses revealed that hatching enzyme genes were high-expression genes, when compared to that of housekeeping genes. When expression levels were compared between clade I and II genes, clade I genes tends to be expressed more highly than clade II genes. Conclusions Hatching enzyme genes evolved to lose their introns, and the intron-loss events occurred at the specific points of teleostean phylogeny. We propose that the high-expression hatching enzyme genes frequently lost their introns during the evolution of teleosts, while the low-expression genes maintained the exon-intron structure of the ancestral gene.
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Affiliation(s)
- Mari Kawaguchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
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Okada A, Sano K, Nagata K, Yasumasu S, Ohtsuka J, Yamamura A, Kubota K, Iuchi I, Tanokura M. Crystal structure of zebrafish hatching enzyme 1 from the zebrafish Danio rerio. J Mol Biol 2010; 402:865-78. [PMID: 20727360 DOI: 10.1016/j.jmb.2010.08.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2010] [Revised: 08/05/2010] [Accepted: 08/11/2010] [Indexed: 10/19/2022]
Abstract
Fish hatching enzymes are zinc metalloproteases that digest the egg envelope (chorion) at the time of hatching. The crystal structure of zebrafish hatching enzyme 1 (ZHE1) has been solved at 1.10 Å resolution. ZHE1 is monomeric, is mitten shaped, and has a cleft at the center of the molecule. ZHE1 consists of three 3(10)-helices, three α-helices, and two β-sheets. The central cleft represents the active site of the enzyme that is crucial for substrate recognition and catalysis. Alanine-scanning mutagenesis of the two substrate peptides has shown that AspP1' contributes the most and that the residues at P4-P2' also contribute to the recognition of the major substrate peptide by ZHE1, whereas GluP3' and the hydrophobic residues at P4-P2, P2', and P5' contribute significantly to the recognition of the minor substrate peptide by ZHE1. Molecular models of these two substrate peptides bound to ZHE1 have been built based on the crystal structure of a transition-state analog inhibitor bound to astacin. In substrate-recognition models, the AspP1' in the major substrate peptide forms a salt bridge with Arg182 of ZHE1, while the GluP3' in the minor substrate peptide instead forms a salt bridge with Arg182. Thus, these two substrate peptides would be differently recognized by ZHE1. The shapes and electrostatic potentials of the substrate-binding clefts of ZHE1 and the structurally similar proteins astacin and bone morphogenetic protein 1 are significantly dissimilar due to different side chains, which would confer their distinctive substrate preferences.
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Affiliation(s)
- Akitoshi Okada
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Okada A, Nagata K, Sano K, Yasumasu S, Kubota K, Ohtsuka J, Iuchi I, Tanokura M. Crystallization and preliminary X-ray analysis of ZHE1, a hatching enzyme from the zebrafish Danio rerio. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1018-20. [PMID: 19851011 DOI: 10.1107/s1744309109033016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 08/19/2009] [Indexed: 11/10/2022]
Abstract
The hatching enzyme of the zebrafish, ZHE1 (29.3 kDa), is a zinc metalloprotease that catalyzes digestion of the egg envelope (chorion). ZHE1 was heterologously expressed in Escherichia coli, purified and crystallized by the hanging-drop vapour-diffusion method using PEG 3350 as the precipitant. Two diffraction data sets with resolution ranges 50.0-1.80 and 50.0-1.14 A were independently collected from two crystals and were merged to give a highly complete data set over the full resolution range 50.0-1.14 A. The space group was assigned as primitive orthorhombic P2(1)2(1)2(1), with unit-cell parameters a = 32.9, b = 62.5, c = 87.4 A. The crystal contained one ZHE1 molecule in the asymmetric unit.
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Affiliation(s)
- Akitoshi Okada
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Kawaguchi M, Fujita H, Yoshizaki N, Hiroi J, Okouchi H, Nagakura Y, Noda T, Watanabe S, Katayama S, Iwamuro S, Nishida M, Iuchi I, Yasumasu S. Different hatching strategies in embryos of two species, pacific herring Clupea pallasii and Japanese anchovy Engraulis japonicus, that belong to the same order Clupeiformes, and their environmental adaptation. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2009; 312:95-107. [PMID: 19025965 DOI: 10.1002/jez.b.21247] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Pacific herring Clupea pallasii and Japanese anchovy Engraulis japonicus, which belong to the same order Clupeiformes, spawn different types of eggs: demersal adherent eggs and pelagic eggs, respectively. We cloned three cDNAs for Pacific herring hatching enzyme and five for Japanese anchovy. Each of them was divided into two groups (group A and B) by phylogenetic analysis. They were expressed specifically in hatching gland cells (HGCs), which differentiated from the pillow and migrated to the edge of the head in both species. HGCs of Japanese anchovy stopped migration at that place, whereas those of Pacific herring continued to migrate dorsally and distributed widely all over the head region. During evolution, the program for the HGC migration would be varied to adapt to different hatching timing. Analysis of the gene expression revealed that Pacific herring embryos synthesized a large amount of hatching enzyme when compared with Japanese anchovy. Chorion of Pacific herring embryo was about 7.5 times thicker than that of Japanese anchovy embryo. Thus, the difference in their gene expression levels between two species is correlated with the difference in the thickness of chorion. These results suggest that the hatching system of each fish adapted to its respective hatching environment. Finally, hatching enzyme genes were cloned from each genomic DNA. The exon-intron structure of group B genes basically conserved that of the ancestral gene, whereas group A genes lost one intron. Several gene-specific changes of the exon-intron structure owing to nucleotide insertion and/or duplication were found in Japanese anchovy genes.
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Affiliation(s)
- Mari Kawaguchi
- Ocean Research Institute, The University of Tokyo, Minamidai, Nakano-ku, Tokyo, Japan
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Lu FH, Tang SM, Shen XJ, Wang N, Zhao QL, Zhang GZ, Guo XJ. Molecular cloning and characterization of hatching enzyme-like gene in the silkworm, Bombyx mori. Mol Biol Rep 2009; 37:1175-82. [PMID: 19253029 DOI: 10.1007/s11033-009-9483-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 02/19/2009] [Indexed: 01/30/2023]
Abstract
Hatching is the important process for the life of the metazoan, in which hatching enzyme (HE) plays a key role. In this paper, we cloned the full-length sequence of hatching enzyme-like cDNA from bluish-silkworm-eggs of Bombyx mori (BmHEL) by the method of in silico cloning, SMART cDNA synthesis and RACE-PCR technique. The BmHEL is 974 bp in length, and contains an ORF of 885 bp, encoding 294 amino acids residues. The deduced amino acid sequence of BmHEL has 30.3-47.1% identities to that of HE identified in the other species. Two similar signature sequences of HE gene family harbor in the BmHEL. The BmHEL gene structure is 6-exon-5-intron, and a promoter region with high scores has been predicted, which harbors some basal elements and some embryo-development related transcription factor binding sites. In the silkworm eggs at different developmental stages during incubation, the BmHEL transcripts can be detected and keep at a low level during the early stages, increase dramatically since 7th day of incubation, and reach to the maximum on 9th day. Change of BmHEL transcripts is in accordance with the process of embryo development and hatching, indicated that it plays an important role in these processes. Moreover, BmHEL transcript can be detected in the midgut and testis at larval stage, suggested that BmHEL may have other biological functions. To the best of our knowledge, this is the first report on HE gene in the Lepidoptera insects and will be helpful to provide a molecular basis for understanding the complicated mechanism underlying silkworm hatching.
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Affiliation(s)
- Fu-hao Lu
- College of Biotechnology and Environmental Engineering, Jiangsu University of Science and Technology, Zhenjiang, People's Republic China
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Sano K, Inohaya K, Kawaguchi M, Yoshizaki N, Iuchi I, Yasumasu S. Purification and characterization of zebrafish hatching enzyme - an evolutionary aspect of the mechanism of egg envelope digestion. FEBS J 2009; 275:5934-46. [PMID: 19021768 DOI: 10.1111/j.1742-4658.2008.06722.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
There are two hatching enzyme homologues in the zebrafish genome: zebrafish hatching enzyme ZHE1 and ZHE2. Northern blot and RT-PCR analysis revealed that ZHE1 was mainly expressed in pre-hatching embryos, whereas ZHE2 was rarely expressed. This was consistent with the results obtained in an experiment conducted at the protein level, which demonstrated that one kind of hatching enzyme, ZHE1, was able to be purified from the hatching liquid. Therefore, the hatching of zebrafish embryo is performed by a single enzyme, different from the finding that the medaka hatching enzyme is an enzyme system composed of two enzymes, medaka high choriolytic enzyme (MHCE) and medaka low choriolytic enzyme (MLCE), which cooperatively digest the egg envelope. The six ZHE1-cleaving sites were located in the N-terminal regions of egg envelope subunit proteins, ZP2 and ZP3, but not in the internal regions, such as the ZP domains. The digestion manner of ZHE1 appears to be highly analogous to that of MHCE, which partially digests the egg envelope and swells the envelope. The cross-species digestion using enzymes and substrates of zebrafish and medaka revealed that both ZHE1 and MHCE cleaved the same sites of the egg envelope proteins of two species, suggesting that the substrate specificity of ZHE1 is quite similar to that of MHCE. However, MLCE did not show such similarity. Because HCE and LCE are the result of gene duplication in the evolutionary pathway of Teleostei, the present study suggests that ZHE1 and MHCE maintain the character of an ancestral hatching enzyme, and that MLCE acquires a new function, such as promoting the complete digestion of the egg envelope swollen by MHCE.
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Affiliation(s)
- Kaori Sano
- Graduate Program of Biological Science, Graduate School of Science and Technology, Sophia University, Tokyo, Japan
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Kawaguchi M, Nakagawa M, Noda T, Yoshizaki N, Hiroi J, Nishida M, Iuchi I, Yasumasu S. Hatching enzyme of the ovoviviparous black rockfish Sebastes schlegelii- environmental adaptation of the hatching enzyme and evolutionary aspects of formation of the pseudogene. FEBS J 2008; 275:2884-98. [DOI: 10.1111/j.1742-4658.2008.06427.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Recent papers on zebrafish and other aquarium fish models. Zebrafish 2008; 2:215-24. [PMID: 18248196 DOI: 10.1089/zeb.2005.2.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Kawaguchi M, Yasumasu S, Hiroi J, Naruse K, Suzuki T, Iuchi I. Analysis of the exon–intron structures of fish, amphibian, bird and mammalian hatching enzyme genes, with special reference to the intron loss evolution of hatching enzyme genes in Teleostei. Gene 2007; 392:77-88. [PMID: 17222522 DOI: 10.1016/j.gene.2006.11.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 11/17/2006] [Accepted: 11/17/2006] [Indexed: 11/26/2022]
Abstract
Using gene cloning and in silico cloning, we analyzed the structures of hatching enzyme gene orthologs of vertebrates. Comparison led to a hypothesis that hatching enzyme genes of Japanese eel conserve an ancestral structure of the genes of fishes, amphibians, birds and mammals. However, the exon-intron structure of the genes was different from species to species in Teleostei: Japanese eel hatching enzyme genes were 9-exon-8-intron genes, and zebrafish genes were 5-exon-4-intron genes. In the present study, we further analyzed the gene structures of fishes belonging to Acanthopterygii. In the species of Teleostei we examined, diversification of hatching enzyme gene into two paralogous genes for HCE (high choriolytic enzyme) and LCE (low choriolytic enzyme) was found only in the acanthopterygian fishes such as medaka Oryzias latipes, Fundulus heteroclitus, Takifugu rubripes and Tetraodon nigroviridis. In addition, the HCE gene had no intron, while the LCE gene consisted of 8 exons and 7 introns. Phylogenetic analysis revealed that HCE and LCE genes were paralogous to each other, and diverged during the evolutionary lineage to Acanthopterygii. Analysis of gene synteny and cluster structure showed that the syntenic genes around the HCE and LCE genes were highly conserved between medaka and Teraodon, but such synteny was not found around the zebrafish hatching enzyme genes. We hypothesize that the zebrafish hatching enzyme genes were translocated from chromosome to chromosome, and lost some of their introns during evolution.
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Affiliation(s)
- Mari Kawaguchi
- Life Science Institute, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan
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Xiong X, Chen L, Li Y, Xie L, Zhang R. Pf-ALMP, a novel astacin-like metalloproteinase with cysteine arrays, is abundant in hemocytes of pearl oyster Pinctada fucata. ACTA ACUST UNITED AC 2006; 1759:526-34. [PMID: 17207871 DOI: 10.1016/j.bbaexp.2006.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 09/28/2006] [Accepted: 09/28/2006] [Indexed: 10/24/2022]
Abstract
The astacin family metalloproteinase is a family of zinc-dependent endopeptidases which play crucial roles in embryonic development, bone growth and morphogenesis. A cDNA clone encoding a putative astacin-like metalloproteinase (pf-ALMP) was isolated from hemocytes of pearl oyster, Pinctada fucata. The novel metalloproteinase presents a molecular organization close to the astacins, but has a novel C-terminal domain with cysteine arrays. RT-PCR analysis revealed that pf-ALMP was expressed dramatically high in hemocytes, which was affected by lipopolysaccharides (LPS) challenge. High expression of pf-ALMP was also found in gill, gonad and digestion gland, and in situ hybridization demonstrated that pf-ALMP was expressed in the epithelia cells of these tissues. Substrate analysis studies indicated that the recombinant pf-ALMP catalytic domain could digest gelatin. Interestingly, the pf-ALMP also could be involved in cell proliferation processes and the cysteine arrays were necessary for the proliferative activity. Taken together, these studies also help to further understand the functions of astacins which may be related to the processes of molluscan inflammatory response, embryo development, proliferation and shell formation.
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Affiliation(s)
- Xunhao Xiong
- Institute of Marine Biotechnology, Department of Biological Science and Biotechnology, Tsinghua University, Beijing, 100084, China
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Kawaguchi M, Yasumasu S, Hiroi J, Naruse K, Inoue M, Iuchi I. Evolution of teleostean hatching enzyme genes and their paralogous genes. Dev Genes Evol 2006; 216:769-84. [PMID: 17016731 DOI: 10.1007/s00427-006-0104-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Accepted: 07/14/2006] [Indexed: 01/26/2023]
Abstract
We isolated genes for hatching enzymes and their paralogs having two cysteine residues at their N-terminal regions in addition to four cysteines conserved in all the astacin family proteases. Genes for such six-cysteine-containing astacin proteases (C6AST) were searched out in the medaka genome database. Five genes for MC6AST1 to 5 were found in addition to embryo-specific hatching enzyme genes. RT-PCR and whole-mount in situ hybridization evidenced that MC6AST1 was expressed in embryos and epidermis of almost all adult tissues examined, while MC6AST2 and 3 were in mesenterium, intestine, and testis. MC6AST4 and 5 were specifically expressed in jaw. In addition, we cloned C6AST cDNA homologs from zebrafish, ayu, and fugu. The MC6AST1 to 5 genes were classified into three groups in the phylogenetic positions, and the expression patterns and hatching enzymes were clearly discriminated from other C6ASTs. Analysis of the exon-intron structures clarified that genes for hatching enzymes MHCE and MAHCE were intron-less, while other MC6AST genes were basically the same as the gene for another hatching enzyme MLCE. In the basal Teleost, the C6AST genes having the ancestral exon-intron structure (nine exon/eight intron structure) first appeared by duplication and chromosomal translocation. Thereafter, maintaining such ancestral exon-intron structure, the LCE gene was newly diversified in Euteleostei, and the MC6AST1 to 5 gene orthologs were duplicated and diversified independently in respective fish lineages. The HCE gene lost all introns in Euteleostei, whereas in the lineage to zebrafish, it was translocated from chromosome to chromosome and lost some of its introns.
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Affiliation(s)
- Mari Kawaguchi
- Life Science Institute, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan
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