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Parey E, Ortega-Martinez O, Delroisse J, Piovani L, Czarkwiani A, Dylus D, Arya S, Dupont S, Thorndyke M, Larsson T, Johannesson K, Buckley KM, Martinez P, Oliveri P, Marlétaz F. The brittle star genome illuminates the genetic basis of animal appendage regeneration. Nat Ecol Evol 2024:10.1038/s41559-024-02456-y. [PMID: 39030276 DOI: 10.1038/s41559-024-02456-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/29/2024] [Indexed: 07/21/2024]
Abstract
Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars are a species-rich class of echinoderms with outstanding regenerative abilities, but investigations into the genetic bases of regeneration in this group have been hindered by the limited genomic resources. Here we report a chromosome-scale genome assembly for the brittle star Amphiura filiformis. We show that the brittle star genome is the most rearranged among echinoderms sequenced so far, featuring a reorganized Hox cluster reminiscent of the rearrangements observed in sea urchins. In addition, we performed an extensive profiling of gene expression during brittle star adult arm regeneration and identified sequential waves of gene expression governing wound healing, proliferation and differentiation. We conducted comparative transcriptomic analyses with other invertebrate and vertebrate models for appendage regeneration and uncovered hundreds of genes with conserved expression dynamics, particularly during the proliferative phase of regeneration. Our findings emphasize the crucial importance of echinoderms to detect long-range expression conservation between vertebrates and classical invertebrate regeneration model systems.
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Affiliation(s)
- Elise Parey
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Olga Ortega-Martinez
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Jérôme Delroisse
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Laura Piovani
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Anna Czarkwiani
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Technische Universität Dresden, Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany
| | - David Dylus
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Roche Pharmaceutical Research and Early Development (pRED), Cardiovascular and Metabolism, Immunology, Infectious Disease, and Ophthalmology (CMI2O), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Srishti Arya
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK
| | - Samuel Dupont
- Department of Biology and Environmental Science, University of Gothenburg, Kristineberg Marine Research Station, Fiskebäckskil, Sweden
- IAEA Marine Environment Laboratories, Radioecology Laboratory, Quai Antoine 1er, Monaco
| | - Michael Thorndyke
- Department of Biology and Environmental Science, University of Gothenburg, Kristineberg Marine Research Station, Fiskebäckskil, Sweden
| | - Tomas Larsson
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kerstin Johannesson
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | | | - Pedro Martinez
- Departament de Genètica, Microbiologia, i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Paola Oliveri
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Ferdinand Marlétaz
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
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2
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Silchenko AS, Kalinovsky AI, Avilov SA, Popov RS, Chingizova EA, Menchinskaya ES, Zelepuga EA, Tabakmakher KM, Stepanov VG, Kalinin VI. The Composition of Triterpene Glycosides in the Sea Cucumber Psolus peronii: Anticancer Activity of the Glycosides against Three Human Breast Cancer Cell Lines and Quantitative Structure-Activity Relationships (QSAR). Mar Drugs 2024; 22:292. [PMID: 39057402 DOI: 10.3390/md22070292] [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: 05/27/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Eight sulfated triterpene glycosides, peronioside A (1) and psolusosides A (2), B (3), G (4), I (5), L (6), N (7) and P (8), were isolated from the sea cucumber Psolus peronii. Peronioside A (1) is a new glycoside, while compounds 2-8 were found previously in Psolus fabricii, indicating the phylogenetic and systematic closeness of these species of sea cucumbers. The activity of 1-8 against human erythrocytes and their cytotoxicity against the breast cancer cell lines MCF-7, T-47D and triple-negative MDA-MB-231 were tested. The most active against cancer cell compounds, psolusosides A (2) and L (6), which were not cytotoxic to the non-transformed cells of the mammary gland, were chosen to study the inhibition of the migration, formation and growth of colonies of the cancer cell lines. Glycoside 2 effectively inhibited the growth of colonies and the migration of the MDA-MB-231 cell line. Compound 6 blocked the growth of colonies of T-47D cells and showed a pronounced antimigration effect on MDA-MB-231 cells. The quantitative structure-activity relationships (QSAR) indicated the strong impact on the activity of the form and size of the molecules, which is connected to the length and architecture of the carbohydrate chain, the distribution of charge on the molecules' surface and various aspects of hydrogen bond formation, depending on the quantity and positions of the sulfate groups. The QSAR calculations were in good accordance with the observed SAR tendencies.
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Affiliation(s)
- Alexandra Sergeevna Silchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia
| | - Anatoly Ivanovich Kalinovsky
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia
| | - Sergey Anatolievich Avilov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia
| | - Roman Sergeevich Popov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia
| | - Ekaterina Alexandrovna Chingizova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia
| | - Ekaterina Sergeevna Menchinskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia
| | - Elena Alexandrovna Zelepuga
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia
| | - Kseniya Mikhailovna Tabakmakher
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia
| | - Vadim Georgievich Stepanov
- Kamchatka Branch of Pacific Institute of Geography, Far Eastern Branch of the Russian Academy of Sciences, Partizanskaya st. 6, 683000 Petropavlovsk-Kamchatsky, Russia
| | - Vladimir Ivanovich Kalinin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia
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3
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Yu H, Li Y, Han W, Bao L, Liu F, Ma Y, Pu Z, Zeng Q, Zhang L, Bao Z, Wang S. Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach. Nat Protoc 2024; 19:1623-1678. [PMID: 38514839 DOI: 10.1038/s41596-024-00966-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 12/20/2023] [Indexed: 03/23/2024]
Abstract
The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, ( https://github.com/yhw320/PanSyn ), the most comprehensive and up-to-date genome synteny pipeline, providing step-by-step instructions and application examples to demonstrate its usage. PanSyn inherits both basic and advanced functions from existing popular tools, offering a user-friendly, highly customized approach for genome macrosynteny analysis and integrated pan-evolutionary and regulatory analysis of genome architecture, which are not yet available in public synteny software or tools. The advantages of PanSyn include: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis, including the inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny for pan-evolutionary profiling of genome architecture and regulatory blocks, as well as integration with external functional genomics datasets from three- or four-dimensional genome and ENCODE projects. PanSyn requires basic knowledge of the Linux environment and Perl programming language and the ability to access a computer cluster, especially for large-scale genomic comparisons. Our protocol can be easily implemented by a competent graduate student or postdoc and takes several days to weeks to execute for dozens to hundreds of genomes. PanSyn provides yet the most comprehensive and powerful tool for integrated evolutionary and functional genomics.
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Affiliation(s)
- Hongwei Yu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
| | - Wentao Han
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Fuyun Liu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuanting Ma
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lingling Zhang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Zhenmin Bao
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
- Laboratory for Marine Fisheries and Aquaculture, Laoshan Laboratory, Qingdao, China
| | - Shi Wang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
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4
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Perillo M, Sepe RM, Paganos P, Toscano A, Annunziata R. Sea cucumbers: an emerging system in evo-devo. EvoDevo 2024; 15:3. [PMID: 38368336 PMCID: PMC10874539 DOI: 10.1186/s13227-023-00220-0] [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: 05/29/2023] [Accepted: 12/24/2023] [Indexed: 02/19/2024] Open
Abstract
A challenge for evolutionary developmental (evo-devo) biology is to expand the breadth of research organisms used to investigate how animal diversity has evolved through changes in embryonic development. New experimental systems should couple a relevant phylogenetic position with available molecular tools and genomic resources. As a phylum of the sister group to chordates, echinoderms extensively contributed to our knowledge of embryonic patterning, organ development and cell-type evolution. Echinoderms display a variety of larval forms with diverse shapes, making them a suitable group to compare the evolution of embryonic developmental strategies. However, because of the laboratory accessibility and the already available techniques, most studies focus on sea urchins and sea stars mainly. As a comparative approach, the field would benefit from including information on other members of this group, like the sea cucumbers (holothuroids), for which little is known on the molecular basis of their development. Here, we review the spawning and culture methods, the available morphological and molecular information, and the current state of genomic and transcriptomic resources on sea cucumbers. With the goal of making this system accessible to the broader community, we discuss how sea cucumber embryos and larvae can be a powerful system to address the open questions in evo-devo, including understanding the origins of bilaterian structures.
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Affiliation(s)
- Margherita Perillo
- Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA, 02543, USA.
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Rosa Maria Sepe
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Periklis Paganos
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Alfonso Toscano
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
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5
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Huang Y, Liu H, Zhou Y, Lu Z, Pu Y, Zhang H. Cloning and functional characterization of the oxidative squalene cyclase gene in the deep-sea holothurian Chiridota sp. Gene 2024; 894:147971. [PMID: 37949417 DOI: 10.1016/j.gene.2023.147971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Saponins derived from holothurians have high potential medicinal value. However, the de novo synthesis of the derivatization of triterpenes is still unclear. Oxidative squalene cyclase (OSC) can catalyze 2,3-Oxidosqualene into diverse products that serve as important precursors for triterpene synthesis. However, the function of theOSCgene in Chiridotasp. hasnot been elucidated. In this study, an OSCgenederived from the deep-sea holothurianChiridota sp. was cloned and characterized functionally in a yeast system. The open reading frame of the OSC gene was 2086 bp, which encoded 695 amino acids. The Chiridota sp. OSC gene has a similarity of 66.89 % to the OSC of other holothurian species and 63.51 % to that of Acanthaster planci. The phylogenetic tree showed that the echinozoan OSCsclustered together, and then they formeda sister group to fungi and plant homologs. Chiridota sp. OSC catalyzed 2,3-Oxidosqualene into parkeol.Under high pressure, the relative enzymatic activity and stability of cyclase inChiridota sp. was higher than that in the shallow-sea holothurianStichopus horrens. The newly cloned OSC of Chiridota sp.provideskey information for the interpretation of the saponin synthesis pathway in deep-sea holothurians.
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Affiliation(s)
- Yanan Huang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Helu Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Yang Zhou
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Zaiqing Lu
- Ocean University of China, Qingdao 266100, China
| | - Yujin Pu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
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6
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Ye Z, Wei Y, Zhang G, Ge L, Wu C, Ren Y, Wang J, Xu X, Yang J, Wang T. Circadian rhythm regulation in the sea cucumber Apostichopus japonicus: Insights into clock gene expression, photoperiod susceptibility, and neurohormone signaling. Comp Biochem Physiol B Biochem Mol Biol 2024; 270:110930. [PMID: 38065309 DOI: 10.1016/j.cbpb.2023.110930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/03/2023] [Accepted: 12/03/2023] [Indexed: 01/10/2024]
Abstract
Sea cucumber Apostichopus japonicus displays the typical circadian rhythms. This present study investigated the molecular regulation of clock genes, as well as monoamines and melatonin, in multiple tissues of A. japonicus, responding to the photoperiod. In order to determine their pivotal role in circadian rhythms, the crucial clock genes, namely AjClock, AjArnt1, AjCry1, and AjTimeless, were identified and a comprehensive analysis of their expressions across various tissues in adult A. japonicus was conducted, revealing the potential existence of central and peripheral oscillators. Results demonstrated that the tissues of polian vesicle and nerve ring exhibited significant clock gene expression associated with the orchestration of circadian regulation, and that environmental light fluctuations exerted influence on the expression of these clock genes. However, a number of genes, such as AjArnt1 and AjCry1, maintained their circadian rhythmicity even under continuous light conditions. Moreover, we further investigated the circadian patterns of melatonin (MT), serotonin (5-HT), and dopamine (DA) secretion in A. japonicus, data that underscored the tissue-specific regulatory differences and the inherent adaptability to dynamic light environments. Collectively, these findings will provide the molecular mechanisms controlling the circadian rhythm in echinoderms and the candidate tissues playing the role of central oscillators in sea cucumbers.
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Affiliation(s)
- Zhiqing Ye
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Ying Wei
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Guangbo Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Lifei Ge
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Chenqian Wu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Yucheng Ren
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Jixiu Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Xiuwen Xu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Jingwen Yang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Tianming Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China.
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7
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Silchenko AS, Kalinovsky AI, Avilov SA, Popov RS, Chingizova EA, Menchinskaya ES, Zelepuga EA, Panina EG, Stepanov VG, Kalinin VI, Dmitrenok PS. Sulfated Triterpene Glycosides from the Far Eastern Sea Cucumber Cucumaria djakonovi: Djakonoviosides C 1, D 1, E 1, and F 1; Cytotoxicity against Human Breast Cancer Cell Lines; Quantitative Structure-Activity Relationships. Mar Drugs 2023; 21:602. [PMID: 38132923 PMCID: PMC10744391 DOI: 10.3390/md21120602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Four new mono- and trisulfated triterpene penta- and tetraosides, djakonoviosides C1 (1), D1 (2), E1 (3), and F1 (4) were isolated from the Far Eastern sea cucumber Cucumaria djakonovi (Cucumariidae, Dendrochirotida), along with six known glycosides found earlier in other Cucumaria species. The structures of unreported compounds were established on the basis of extensive analysis of 1D and 2D NMR spectra as well as by HR-ESI-MS data. The set of compounds contains six different types of carbohydrate chains including two new ones. Thus, djakonovioside C1 (1) is characterized by xylose as the second residue, that was a branchpoint in the pentasaccharide chain. Meanwhile, only quinovose and rarely glucose have been found earlier in pentasaccharide chains branched at C-2 of the second sugar unit. Djakonovioside E1 (3) is characterized by a tetrasaccharide trisulfated chain, with glucose as the second residue. So, in the series of isolated glycosides, three types of sugars in the second position were presented: the most common, quinovose-in six compounds; glucose-in three substances; and the rare xylose-in one glycoside. The set of aglycones was composed of holostane- and non-holostane-type polycyclic systems; the latter comprised normal and reduced side chains. Noticeably, isokoreoside A (9), isolated from C. djakonovi, was a single glycoside having a 9(11)-double bond, indicating two oxidosqualenecyclases are operating in the process of the biosynthesis of aglycones. Some of the glycosides from C. djakonovi, which were characterized by pentasaccharide branched chains containing one to three sulfate groups, are chemotaxonomic features of the representatives of the genus Cucumaria. The assortment of sugar parts of Cucumaria's glycosides was broadened with previously undescribed penta- and tetrasaccharide moieties. The metabolic network of sugar parts and aglycones is constructed based on biogenetic relationships. The cytotoxic action of compounds 1-10, isolated from C. djakonovi, against human breast cancer cell lines was investigated along with the hemolytic activity. Erythrocytes were, as usual, more sensitive to the membranolytic action of the glycosides than cancer cells. The triple-negative breast cancer MDA-MB-231 cell line was more vulnerable to the action of glycosides in comparison with the other tested cancer cells, while the MCF-7 cell line was less susceptible to cytotoxic action. Djakonovioside E1 (3) demonstrated selective action against ER-positive MCF-7 and triple-negative MDA-MB-231 cell lines, while the toxic effect in relation to normal mammary epithelial cells (MCF-10A) was absent. Cucumarioside A2-5 (6) inhibited the formation and growth of colonies of cancer cells to 44% and tumor cell migration to 85% of the control. Quantitative structure-activity relationships (QSAR) were calculated on the basis of the correlational analysis of the physicochemical properties and structural features of the glycosidic molecules and their membranolytic activity. QSAR revealed the extremely complex nature of such relationships, but these calculations correlated well with the observed SAR.
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Affiliation(s)
- Alexandra S. Silchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (A.I.K.); (S.A.A.); (R.S.P.); (E.A.C.); (E.S.M.); (E.A.Z.); (V.I.K.)
| | - Anatoly I. Kalinovsky
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (A.I.K.); (S.A.A.); (R.S.P.); (E.A.C.); (E.S.M.); (E.A.Z.); (V.I.K.)
| | - Sergey A. Avilov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (A.I.K.); (S.A.A.); (R.S.P.); (E.A.C.); (E.S.M.); (E.A.Z.); (V.I.K.)
| | - Roman S. Popov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (A.I.K.); (S.A.A.); (R.S.P.); (E.A.C.); (E.S.M.); (E.A.Z.); (V.I.K.)
| | - Ekaterina A. Chingizova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (A.I.K.); (S.A.A.); (R.S.P.); (E.A.C.); (E.S.M.); (E.A.Z.); (V.I.K.)
| | - Ekaterina S. Menchinskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (A.I.K.); (S.A.A.); (R.S.P.); (E.A.C.); (E.S.M.); (E.A.Z.); (V.I.K.)
| | - Elena A. Zelepuga
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (A.I.K.); (S.A.A.); (R.S.P.); (E.A.C.); (E.S.M.); (E.A.Z.); (V.I.K.)
| | - Elena G. Panina
- Kamchatka Branch of Pacific Institute of Geography, Far Eastern Branch of the Russian Academy of Sciences, Partizanskaya st. 6, 683000 Petropavlovsk-Kamchatsky, Russia; (E.G.P.); (V.G.S.)
| | - Vadim G. Stepanov
- Kamchatka Branch of Pacific Institute of Geography, Far Eastern Branch of the Russian Academy of Sciences, Partizanskaya st. 6, 683000 Petropavlovsk-Kamchatsky, Russia; (E.G.P.); (V.G.S.)
| | - Vladimir I. Kalinin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (A.I.K.); (S.A.A.); (R.S.P.); (E.A.C.); (E.S.M.); (E.A.Z.); (V.I.K.)
| | - Pavel S. Dmitrenok
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (A.I.K.); (S.A.A.); (R.S.P.); (E.A.C.); (E.S.M.); (E.A.Z.); (V.I.K.)
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8
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Jiang C, Storey KB, Yang H, Sun L. Aestivation in Nature: Physiological Strategies and Evolutionary Adaptations in Hypometabolic States. Int J Mol Sci 2023; 24:14093. [PMID: 37762394 PMCID: PMC10531719 DOI: 10.3390/ijms241814093] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Aestivation is considered to be one of the "purest" hypometabolic states in nature, as it involves aerobic dormancy that can be induced and sustained without complex factors. Animals that undergo aestivation to protect themselves from environmental stressors such as high temperatures, droughts, and food shortages. However, this shift in body metabolism presents new challenges for survival, including oxidative stress upon awakening from aestivation, accumulation of toxic metabolites, changes in energy sources, adjustments to immune status, muscle atrophy due to prolonged immobility, and degeneration of internal organs due to prolonged food deprivation. In this review, we summarize the physiological and metabolic strategies, key regulatory factors, and networks utilized by aestivating animals to address the aforementioned components of aestivation. Furthermore, we present a comprehensive overview of the advancements made in aestivation research across major species, including amphibians, fish, reptiles, annelids, mollusks, and echinoderms, categorized according to their respective evolutionary positions. This approach offers a distinct perspective for comparative analysis, facilitating an understanding of the shared traits and unique features of aestivation across different groups of organisms.
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Affiliation(s)
- Chunxi Jiang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences & Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (C.J.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science & Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences & Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (C.J.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science & Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences & Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (C.J.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science & Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Sun L, Jiang C, Su F, Cui W, Yang H. Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus. Sci Data 2023; 10:454. [PMID: 37443361 PMCID: PMC10344927 DOI: 10.1038/s41597-023-02368-9] [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: 03/08/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Sea cucumber is a morphologically diverse and ecologically important clade of echinoderms. The sea cucumber Apostichopus japonicus is the most economically valuable species of sea cucumber. The initial assembly of the A. japonicus genome was released in 2017. However, this genome assembly is fragmented and lacks relative position information of genes on chromosomes. In this study, we produced a high-quality chromosome-level genome of A. japonicus using Pacbio HiFi long-reads and Hi-C sequencing data. The assembled A. japonicus genome spanned 671.60 Mb with a contig N50 size of 17.20 Mb and scaffold N50 size of 29.65 Mb. A total of 99.9% of the assembly was anchored to 23 chromosomes. In total, 19,828 genes were annotated, and 97.2% of BUSCO genes were fully represented. This high-quality genome of A. japonicus will not only aid in the development of sustainable aquaculture practices, but also lay a foundation for a deeper understanding of their genetic makeup, evolutionary history, and ecological adaptation.
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Affiliation(s)
- Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chunxi Jiang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Su
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Cui
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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10
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Zhao Z, Wang X, Jiang J, Dong Y, Pan Y, Guan X, Wang B, Gao S, Chen Z, Zhou Z. Adverse effects of polystyrene nanoplastics on sea cucumber Apostichopus japonicus and their association with gut microbiota dysbiosis. CHEMOSPHERE 2023; 330:138568. [PMID: 37019397 DOI: 10.1016/j.chemosphere.2023.138568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/22/2023] [Accepted: 03/31/2023] [Indexed: 05/14/2023]
Abstract
The mariculture environment is a sink of microplastics (MPs) due to its enclosed nature and mass use of plastics. Nanoplastics (NPs) are MPs with a diameter <1 μm that have a more toxic effect on aquatic organisms than other MPs. However, little is known about the underlying mechanisms of NP toxicity on mariculture species. Here, we performed a multi-omics investigation to explore gut microbiota dysbiosis and associated health problems induced by NPs in juvenile sea cucumber Apostichopus japonicus, a commercially and ecologically important marine invertebrate. We observed significant differences in gut microbiota composition after 21 days of NP exposure. Ingestion of NPs significantly increased core gut microbes, especially Rhodobacteraceae and Flavobacteriaceae families. Additionally, gut gene expression profiles were altered by NPs, especially those related to neurological diseases and movement disorders. Correlation and network analyses indicated close relationships between transcriptome changes and gut microbiota variation. Furthermore, NPs induced oxidative stress in sea cucumber intestines, which may be associated with intraspecies variation in Rhodobacteraceae in the gut microbiota. The results suggested that NPs were harmful to the health of sea cucumbers, and they highlighted the importance of the gut microbiota in the responses to NP toxicity in marine invertebrates.
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Affiliation(s)
- Zelong Zhao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Xuda Wang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Jingwei Jiang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China.
| | - Ying Dong
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Yongjia Pan
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Xiaoyan Guan
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Bai Wang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Shan Gao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zhong Chen
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zunchun Zhou
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China.
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11
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Zhang F, Wang Y, Yue J, Zhang R, Hu YE, Huang R, Ji AJ, Hess BA, Liu Z, Duan L, Wu R. Discovering a uniform functional trade-off of the CBC-type 2,3-oxidosqualene cyclases and deciphering its chemical logic. SCIENCE ADVANCES 2023; 9:eadh1418. [PMID: 37285431 DOI: 10.1126/sciadv.adh1418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/01/2023] [Indexed: 06/09/2023]
Abstract
Many functionally promiscuous plant 2,3-oxidosqualene cyclases (OSCs) have been found, but complete functional reshaping is rarely reported. In this study, we have identified two new plant OSCs: a unique protostadienol synthase (AoPDS) and a common cycloartenol synthase (AoCAS) from Alisma orientale (Sam.) Juzep. Multiscale simulations and mutagenesis experiments revealed that threonine-727 is an essential residue responsible for protosta-13 (17),24-dienol biosynthesis in AoPDS and that the F726T mutant completely reshapes the native function of AoCAS into a PDS function to yield almost exclusively protosta-13 (17),24-dienol. Unexpectedly, various native functions were uniformly reshaped into a PDS function by introducing the phenylalanine → threonine substitution at this conserved position in other plant and non-plant chair-boat-chair-type OSCs. Further computational modeling elaborated the trade-off mechanisms of the phenylalanine → threonine substitution that leads to the PDS activity. This study demonstrates a general strategy for functional reshaping by using a plastic residue based on the decipherment of the catalytic mechanism.
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Affiliation(s)
- Fan Zhang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, P. R. China
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Yunpeng Wang
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Jingyang Yue
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Rongrong Zhang
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Yong-Er Hu
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Ruoshi Huang
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Ai-Jia Ji
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - B Andes Hess
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Zhongqiu Liu
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Lixin Duan
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, P. R. China
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12
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Yuan J, Yang J, Xu X, Wang Z, Jiang Z, Ye Z, Ren Y, Wang Q, Wang T. Bisphenol A (BPA) Directly Activates the G Protein-Coupled Estrogen Receptor 1 and Triggers the Metabolic Disruption in the Gonadal Tissue of Apostichopus japonicus. BIOLOGY 2023; 12:798. [PMID: 37372083 DOI: 10.3390/biology12060798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023]
Abstract
The sea cucumber, Apostichopus japonicus, is a marine benthic organism that feeds on small benthic particulate matter and is easily affected by pollutants. Bisphenol A (BPA, 4,4'-isopropylidenediphenol) has been identified as an endocrine disruptor. It is ubiquitously detectable in oceans and affects a variety of marine animals. It functions as an estrogen analog and typically causes reproductive toxicity by interfering with the endocrine system. To comparatively analyze the reproductive effects of estradiol (E2) and BPA on sea cucumbers, we identified a G protein-coupled estrogen receptor 1 (GPER1) in A. japonicus and investigated its effects on reproduction. The results showed that BPA and E2 exposure activated A. japonicus AjGPER1, thereby mediating the mitogen-activated protein kinase signaling pathways. High-level expression of AjGPER1 in the ovarian tissue was confirmed by qPCR. Furthermore, metabolic changes were induced by 100 nM (22.83 μg/L) BPA exposure in the ovarian tissue, leading to a notable increase in the activities of trehalase and phosphofructokinase. Overall, our findings suggest that AjGPER1 is directly activated by BPA and affects sea cucumber reproduction by disrupting ovarian tissue metabolism, suggesting that marine pollutants pose a threat to the conservation of sea cucumber resources.
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Affiliation(s)
- Jieyi Yuan
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jingwen Yang
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Xiuwen Xu
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zexianghua Wang
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhijing Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhiqing Ye
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yucheng Ren
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Qing Wang
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Tianming Wang
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China
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13
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Zhong S, Ma X, Jiang Y, Liu X, Zeng M, Zhao L, Huang L, Huang G, Zhao Y, Qiao Y, Chen X. The draft genome of the tropical sea cucumber Stichopus monotuberculatus (Echinodermata, Stichopodidae) reveals critical genes in fucosylated chondroitin sulfates biosynthetic pathway. Front Genet 2023; 14:1182002. [PMID: 37252657 PMCID: PMC10213396 DOI: 10.3389/fgene.2023.1182002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023] Open
Affiliation(s)
- Shengping Zhong
- Guangxi Key Laboratory of Marine Drugs, Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, China
| | - Xiaowan Ma
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Yan Jiang
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, China
| | - Xujia Liu
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, China
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, China
| | - Mengqing Zeng
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, China
| | - Longyan Zhao
- Guangxi Key Laboratory of Marine Drugs, Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Lianghua Huang
- Guangxi Key Laboratory of Marine Drugs, Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Guoqiang Huang
- Guangxi Key Laboratory of Marine Drugs, Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Ying Qiao
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
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14
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Chen T, Ren C, Wong NK, Yan A, Sun C, Fan D, Luo P, Jiang X, Zhang L, Ruan Y, Li J, Wu X, Huo D, Huang J, Li X, Wu F, E Z, Cheng C, Zhang X, Wang Y, Hu C. The Holothuria leucospilota genome elucidates sacrificial organ expulsion and bioadhesive trap enriched with amyloid-patterned proteins. Proc Natl Acad Sci U S A 2023; 120:e2213512120. [PMID: 37036994 PMCID: PMC10120082 DOI: 10.1073/pnas.2213512120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 02/04/2023] [Indexed: 04/12/2023] Open
Abstract
Some tropical sea cucumbers of the family Holothuriidae can efficiently repel or even fatally ensnare predators by sacrificially ejecting a bioadhesive matrix termed the Cuvierian organ (CO), so named by the French zoologist Georges Cuvier who first described it in 1831. Still, the precise mechanisms for how adhesiveness genetically arose in CO and how sea cucumbers perceive and transduce danger signals for CO expulsion during defense have remained unclear. Here, we report the first high-quality, chromosome-level genome assembly of Holothuria leucospilota, an ecologically significant sea cucumber with prototypical CO. The H. leucospilota genome reveals characteristic long-repeat signatures in CO-specific outer-layer proteins, analogous to fibrous proteins of disparate species origins, including spider spidroin and silkworm fibroin. Intriguingly, several CO-specific proteins occur with amyloid-like patterns featuring extensive intramolecular cross-β structures readily stainable by amyloid indicator dyes. Distinct proteins within the CO connective tissue and outer surface cooperate to give the expelled matrix its apparent tenacity and adhesiveness, respectively. Genomic evidence offers further hints that H. leucospilota directly transduces predator-induced mechanical pressure onto the CO surface through mediation by transient receptor potential channels, which culminates in acetylcholine-triggered CO expulsion in part or in entirety. Evolutionarily, innovative events in two distinct regions of the H. leucospilota genome have apparently spurred CO's differentiation from the respiratory tree to a lethal defensive organ against predators.
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Affiliation(s)
- Ting Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Chunhua Ren
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Nai-Kei Wong
- Clinical Pharmacology Section, Department of Pharmacology, Shantou University Medical College, Shantou515041, China
| | - Aifen Yan
- School of Medicine, Foshan University, Foshan528225, China
| | - Caiyun Sun
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou510275, China
- Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou510275, China
| | - Dingding Fan
- EasyATGC Limited Liability Company, Shenzhen518081, China
| | - Peng Luo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Xiao Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Lvping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Yao Ruan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Jiaxi Li
- School of Medicine, Foshan University, Foshan528225, China
| | - Xiaofen Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Da Huo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Jiasheng Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Xiaomin Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Feifei Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Zixuan E
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Chuhang Cheng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning530007, China
| | - Xin Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Yanhong Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Chaoqun Hu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning530007, China
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15
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Zhao J, Chen J, Tian X, Jiang L, Cui Q, Sun Y, Wu N, Liu G, Ding Y, Wang J, Liu Y, Han D, Xu Y. Amantadine Toxicity in Apostichopus japonicus Revealed by Proteomics. TOXICS 2023; 11:226. [PMID: 36976991 PMCID: PMC10053536 DOI: 10.3390/toxics11030226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Amantadine exposure can alter biological processes in sea cucumbers, which are an economically important seafood in China. In this study, amantadine toxicity in Apostichopus japonicus was analyzed by oxidative stress and histopathological methods. Quantitative tandem mass tag labeling was used to examine changes in protein contents and metabolic pathways in A. japonicus intestinal tissues after exposure to 100 µg/L amantadine for 96 h. Catalase activity significantly increased from days 1 to 3 of exposure, but it decreased on day 4. Superoxide dismutase and glutathione activities were inhibited throughout the exposure period. Malondialdehyde contents increased on days 1 and 4 but decreased on days 2 and 3. Proteomics analysis revealed 111 differentially expressed proteins in the intestines of A. japonicus after amantadine exposure compared with the control group. An analysis of the involved metabolic pathways showed that the glycolytic and glycogenic pathways may have increased energy production and conversion in A. japonicus after amantadine exposure. The NF-κB, TNF, and IL-17 pathways were likely induced by amantadine exposure, thereby activating NF-κB and triggering intestinal inflammation and apoptosis. Amino acid metabolism analysis showed that the leucine and isoleucine degradation pathways and the phenylalanine metabolic pathway inhibited protein synthesis and growth in A. japonicus. This study investigated the regulatory response mechanisms in A. japonicus intestinal tissues after exposure to amantadine, providing a theoretical basis for further research on amantadine toxicity.
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Affiliation(s)
- Junqiang Zhao
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
- School of Food, Shanghai Ocean University, Shanghai 200120, China
| | - Jianqiang Chen
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Xiuhui Tian
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Lisheng Jiang
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Qingkui Cui
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Yanqing Sun
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Ningning Wu
- Qingdao Ocean Management Security Center, Qingdao 266000, China
| | - Ge Liu
- Laizhou Marine Development and Fisheries Service Center, Yantai 261499, China
| | - Yuzhu Ding
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Jing Wang
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Yongchun Liu
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Dianfeng Han
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Yingjiang Xu
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
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16
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Gut Microbiota and Metabolites May Play a Crucial Role in Sea Cucumber Apostichopus japonicus Aestivation. Microorganisms 2023; 11:microorganisms11020416. [PMID: 36838381 PMCID: PMC9961660 DOI: 10.3390/microorganisms11020416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
The constant increase in temperatures under global warming has led to a prolonged aestivation period for Apostichopus japonicus, resulting in considerable losses in production and economic benefits. However, the specific mechanism of aestivation has not been fully elucidated. In this study, we first tried to illustrate the biological mechanisms of aestivation from the perspective of the gut microbiota and metabolites. Significant differences were found in the gut microbiota of aestivating adult A. japonicus (AAJSD group) compared with nonaestivating adult A. japonicus (AAJRT group) and young A. japonicus (YAJRT and YAJSD groups) based on 16S rRNA gene high-throughput sequencing analysis. The abundances of Desulfobacterota, Myxococcota, Bdellovibrionota, and Firmicutes (4 phyla) in the AAJSD group significantly increased. Moreover, the levels of Pseudoalteromonas, Fusibacter, Labilibacter, Litorilituus, Flammeovirga, Polaribacter, Ferrimonas, PB19, and Blfdi19 genera were significantly higher in the AAJSD group than in the other three groups. Further analysis of the LDA effect size showed that species with significant variation in abundance in the AAJSD group, including the phylum Firmicutes and the genera Litorilituus, Fusibacter, and Abilibacter, might be important biomarkers for aestivating adult A. japonicus. In addition, the results of metabolomics analysis showed that there were three distinct metabolic pathways, namely biosynthesis of secondary metabolites, tryptophan metabolism, and sesquiterpenoid and triterpenoid biosynthesis in the AAJSD group compared with the other three groups. Notably, 5-hydroxytryptophan was significantly upregulated in the AAJSD group in the tryptophan metabolism pathway. Moreover, the genera Labilibacter, Litorilituus, Ferrimonas, Flammeovirga, Blfdi19, Fusibacter, Pseudoalteromonas, and PB19 with high abundance in the gut of aestivating adult A. japonicus were positively correlated with the metabolite 5-HTP. These findings suggest that there may be potential biological associations among the gut microbiota, metabolites, and aestivation in A. japonicus. This work may provide a new perspective for further understanding the aestivation mechanism of A. japonicus.
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Liu BZ, Cong JJ, Su WY, Hao ZL, Sun ZH, Chang YQ. Identification and functional analysis of Dmrt1 gene and the SoxE gene in the sexual development of sea cucumber, Apostichopus japonicus. Front Genet 2023; 14:1097825. [PMID: 36741310 PMCID: PMC9894652 DOI: 10.3389/fgene.2023.1097825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/06/2023] [Indexed: 01/20/2023] Open
Abstract
Members of the Doublesex and Mab-3-related transcription factor (Dmrt) gene family handle various vital functions in several biological processes, including sex determination/differentiation and gonad development. Dmrt1 and Sox9 (SoxE in invertebrates) exhibit a very conserved interaction function during testis formation in vertebrates. However, the dynamic expression pattern and functional roles of the Dmrt gene family and SoxE have not yet been identified in any echinoderm species. Herein, five members of the Dmrt gene family (Dmrt1, 2, 3a, 3b and 5) and the ancestor SoxE gene were identified from the genome of Apostichopus japonicus. Expression studies of Dmrt family genes and SoxE in different tissues of adult males and females revealed different expression patterns of each gene. Transcription of Dmrt2, Dmrt3a and Dmrt3b was higher expressed in the tube feet and coelomocytes instead of in gonadal tissues. The expression of Dmrt1 was found to be sustained throughout spermatogenesis. Knocking-down of Dmrt1 by means of RNA interference (RNAi) led to the downregulation of SoxE and upregulation of the ovarian regulator foxl2 in the testes. This indicates that Dmrt1 may be a positive regulator of SoxE and may play a role in the development of the testes in the sea cucumber. The expression level of SoxE was higher in the ovaries than in the testes, and knocking down of SoxE by RNAi reduced SoxE and Dmrt1 expression but conversely increased the expression of foxl2 in the testes. In summary, this study indicates that Dmrt1 and SoxE are indispensable for testicular differentiation, and SoxE might play a functional role during ovary differentiation in the sea cucumber.
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18
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Draghici GA, Dehelean CA, Moaca AE, Moise ML, Pinzaru I, Vladut VN, Banatean-Dunea I, Nica D. Cadmium nitrate and DNA methylation in gastropods: comparison between ovotestis and hepatopancreas. PeerJ 2023; 11:e15032. [PMID: 37073276 PMCID: PMC10106083 DOI: 10.7717/peerj.15032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/19/2023] [Indexed: 04/20/2023] Open
Abstract
Dietary ingestion is the main route of exposure to hazardous contaminants in land animals. Cadmium, a high-profile toxic metal, affects living systems at different organismal levels, including major storage organs (liver, kidneys), key organs for species survival (gonads), and epigenetic networks regulating gene expression. 5-methylcytosine (5mC) is the most common and best-characterized epigenetic mark among different modified nucleosides in DNA. This important player in methylation-driven gene expression is impacted by cadmium in sentinel terrestrial vertebrates. However, limited information exists regarding its impact on macroinvertebrates, especially land snails commonly used as (eco)toxicological models. We first investigate the methylomic effects of dietary cadmium given as cadmium nitrate on terrestrial mollusks. Mature specimens of the common brown garden snail, Cornu aspersum, were continuously exposed for four weeks to environmentally-relevant cadmium levels. We determined global genomic DNA methylation in hepatopancreas and ovotestis, as well as changes in the methylation status of CG pairs at the 5' region close to the transcription site of gene encoding the Cd-selective metallothionein (Cd-MT). Weight gain/loss, hypometabolism tendency, and survival rates were also assessed. Although this exposure event did not adversely affect survival, gastropods exposed to the highest Cd dose revealed a significant reduction in body weight and a significant increase in hypometabolic behavior. The hepatopancreas, but not the ovotestis, displayed significant hypermethylation, but only for the aforementioned specimens. We also found that the 5' end of the Cd-MT gene was unmethylated in both organs and its methylation status was insensitive to cadmium exposure. Our results are important since they provide scientists, for the first time, with quantitative data on DNA methylation in gastropod ovotestis and refine our understanding of Cd epigenetic effects on terrestrial mollusks.
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Affiliation(s)
- George A. Draghici
- Department of Toxicology and Drug Industry, Faculty of Pharmacy, University of Medicine and Pharmacy of Timisoara, Timisoara, Timis, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, University of Medicine and Pharmacy of Timisoara, Timisoara, Timis, Romania
| | - Cristina A. Dehelean
- Department of Toxicology and Drug Industry, Faculty of Pharmacy, University of Medicine and Pharmacy of Timisoara, Timisoara, Timis, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, University of Medicine and Pharmacy of Timisoara, Timisoara, Timis, Romania
| | - Alina E. Moaca
- Department of Toxicology and Drug Industry, Faculty of Pharmacy, University of Medicine and Pharmacy of Timisoara, Timisoara, Timis, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, University of Medicine and Pharmacy of Timisoara, Timisoara, Timis, Romania
| | - Marius L. Moise
- Premiere Hospital, Regina Maria Health Network, Timisoara, Timis, Romania
| | - Iulia Pinzaru
- Department of Toxicology and Drug Industry, Faculty of Pharmacy, University of Medicine and Pharmacy of Timisoara, Timisoara, Timis, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, University of Medicine and Pharmacy of Timisoara, Timisoara, Timis, Romania
| | - Valentin N. Vladut
- The National Institute of Research –Development for Machines and Installations Designed for Agriculture and Food Industry, Bucharest, Romania
| | - Ioan Banatean-Dunea
- Faculty of Agriculture, University of Life Sciences “King Mihai I” from Timişoara, Timisoara, Timis, Romania
| | - Dragos Nica
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, University of Medicine and Pharmacy of Timisoara, Timisoara, Timis, Romania
- The National Institute of Research –Development for Machines and Installations Designed for Agriculture and Food Industry, Bucharest, Romania
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Silchenko AS, Avilov SA, Andrijaschenko PV, Popov RS, Chingizova EA, Grebnev BB, Rasin AB, Kalinin VI. The Isolation, Structure Elucidation and Bioactivity Study of Chilensosides A, A1, B, C, and D, Holostane Triterpene Di-, Tri- and Tetrasulfated Pentaosides from the Sea Cucumber Paracaudina chilensis (Caudinidae, Molpadida). Molecules 2022; 27:molecules27217655. [PMID: 36364484 PMCID: PMC9658831 DOI: 10.3390/molecules27217655] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Five new triterpene (4,4,14-trimethylsterol) di-, tri- and tetrasulfated pentaosides, chilensosides A (1), A1 (2), B (3), C (4), and D (5) were isolated from the Far-Eastern sea cucumber Paracaudina chilensis. The structures were established on the basis of extensive analysis of 1D and 2D NMR spectra and confirmed by HR-ESI-MS data. The structural variability of the glycosides concerned the pentasaccharide chains. Their architecture was characterized by the upper semi-chain consisting of three sugar units and the bottom semi-chain of two sugars. Carbohydrate chains of compounds 2–5 differed in the quantity and positions of sulfate groups. The interesting structural features of the glycosides were: the presence of two sulfate groups at C-4 and C-6 of the same glucose residue in the upper semi-chain of 1, 2, 4, and 5 and the sulfation at C-3 of terminal glucose residue in the bottom semi-chain of 4 that makes its further elongation impossible. Chilensoside D (5) was the sixth tetrasulfated glycoside found in sea cucumbers. The architecture of the sugar chains of chilensosides A–D (1–5), the positions of sulfation, the quantity of sulfate groups, as well as the aglycone structures, demonstrate their similarity to the glycosides of the representatives of the order Dendrochirotida, confirming the phylogenetic closeness of the orders Molpadida and Dendrochirotida. The cytotoxic activities of the compounds 1–5 against human erythrocytes and some cancer cell lines are presented. Disulfated chilensosides A1 (2) and B (3) and trisulfated chilensoside C (4) showed significant cytotoxic activity against human cancer cells.
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Jiang P, Gao S, Chen Z, Sun H, Li P, Yue D, Pan Y, Wang X, Mi R, Dong Y, Jiang J, Zhou Z. Cloning and characterization of a phosphomevalonate kinase gene that is involved in saponin biosynthesis in the sea cucumber Apostichopus japonicus. FISH & SHELLFISH IMMUNOLOGY 2022; 128:67-73. [PMID: 35921931 DOI: 10.1016/j.fsi.2022.07.073] [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: 05/24/2022] [Revised: 07/18/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
The sea cucumber Apostichopus japonicus is one of the most dominant and economically important aquaculture species in China. Saponin, which possesses notable biological and pharmacological properties, is a key determinant of the nutritional and health value of A. japonicus. In the present study, we amplified the full-length cDNA of a phosphomevalonate kinase (PMK) gene (named AjPMK) using rapid amplification of cDNA ends (RACE). Subsequently, we engineered a recombinant AjPMK (rAjPMK) protein and assessed its enzymatic activity by enzyme-linked immunosorbent assay (ELISA). Proteins that interact with rAjPMK were screened and identified via pull-down assay combined with liquid chromatography with tandem mass spectrometry (LC-MS/MS). We found that the full-length cDNA of AjPMK contained 1354 bp and an open reading frame (ORF) of 612 bp. The AjPMK protein was predicted not to contain a signal peptide but to contain a phosphonolate kinase domain seen in higher eukaryotes and a P-loop with a relatively conserved nucleoside triphosphate hydrolase domain. The molecular weight of the AjPMK protein was estimated to be 23.81 kDa, and its isoelectric point was predicted to be 8.72. Phylogenetic analysis showed that AjPMK had a closer evolutionary relationship with genes from starfish than with those of other selected species. Besides, we found that rAjPMK synthesized mevalonate-5-diphosphate, interacted either directly or indirectly with crucial pattern recognition receptors (PRRs) and was regulated by immune-related processes, including antioxidative reactions, stress resistance responses and enzyme hydrolysis. Moreover, AjPMK also interacted with farnesyl pyrophosphate synthase, an enzyme reported to be involved in saponin biosynthesis. Together, our findings implied that AjPMK may be directly involved in saponin biosynthesis and the regulation of various innate immune processes.
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Affiliation(s)
- Pingzhe Jiang
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Shan Gao
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Zhong Chen
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Hongjuan Sun
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Peipei Li
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Dongmei Yue
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Yongjia Pan
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Xuda Wang
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Rui Mi
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Ying Dong
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Jingwei Jiang
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China.
| | - Zunchun Zhou
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China.
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Lertphadungkit P, Qiao X, Ye M, Bunsupa S. Characterization of oxidosqualene cyclases from Trichosanthes cucumerina L. reveals key amino acids responsible for substrate specificity of isomultiflorenol synthase. PLANTA 2022; 256:58. [PMID: 35980476 DOI: 10.1007/s00425-022-03972-6] [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: 01/26/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Two key amino acids of isomultiflorenol synthase, Y125 and M254, were first proposed. They could be associated with the production of isomultiflorenol. Oxidosqualene cyclases (OSCs) are the first committed enzymes in the triterpenoid biosynthesis by converting 2,3-oxidosqualene to specific triterpenoid backbones. Thus, these enzymes are potential targets for developing plant-active compounds through the study of triterpenoid biosynthesis. We applied transcriptome information and metabolite profiling from Trichosanthes cucumerina L. to define the diversity of triterpenoids in this plant through OSCs. Isomultiflorenol synthase and cucurbitadienol synthase were previously identified in this plant. Here, three new OSCs, TcBAS, TcLAS, and TcCAS, were cloned and functionally characterized as β-amyrin synthase, lanosterol synthase, and cycloartenol synthase activities, respectively. We also took advantage of the multiple sequence alignment and molecular docking of OSCs exhibiting in this plant and other plant OSCs to identify key residues associated with isomultiflorenol synthase specificity. Two novel key amino acids, referred to the Y125 and M254, were first discovered. These results provide information on a possible catalytic mechanism for plant OSCs that produce specific products.
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Affiliation(s)
- Pornpatsorn Lertphadungkit
- Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayutthaya Road, Bangkok, 10400, Thailand
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Somnuk Bunsupa
- Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayutthaya Road, Bangkok, 10400, Thailand.
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22
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Lv J, Wang Y, Ni P, Lin P, Hou H, Ding J, Chang Y, Hu J, Wang S, Bao Z. Development of a high-throughput SNP array for sea cucumber (Apostichopus japonicus) and its application in genomic selection with MCP regularized deep neural networks. Genomics 2022; 114:110426. [PMID: 35820495 DOI: 10.1016/j.ygeno.2022.110426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/23/2022] [Accepted: 06/30/2022] [Indexed: 12/22/2022]
Abstract
High-throughput single nucleotide polymorphism (SNP) genotyping assays are powerful tools for genetic studies and genomic breeding applications for many species. Though large numbers of SNPs have been identified in sea cucumber (Apostichopus japonicus), but, as yet, no high-throughput genotyping platform is available for this species. In this study, we designed and developed a high-throughput 24 K SNP genotyping array named HaishenSNP24K for A. japonicus, based on the multi-objective-local optimization (MOLO) algorithm and HD-Marker genotyping method. The SNP array exhibited a relatively high genotyping call rate (> 96%), genotyping accuracy (>95%) and exhibited highly polymorphic in sea cucumber populations. In addition, we also assessed its application in genomic selection (GS). Deep neural networks (DNN) that can capture the complicated interactions of genes have been proposed as a promising tool in GS for SNP-based genomic prediction of complex traits in animal breeding. To overcome the problem of over-fitting when using the HaishenSNP24K array as high-dimensional DNN input, we developed minmax concave penalty (MCP) regularization for sparse deep neural networks (DNN-MCP) that finds an optimal sparse structure of a DNN by minimizing the square error subject to the non-convex penalty MCP on the parameters (weights and biases). Compared to two linear models, namely RR-GBLUP and Bayes B, and the nonlinear model DNN, DNN-MCP has greatly improved the genomic prediction ability for three quantitative traits (e.g., wet weight, dry weight and survival time) in the sea cucumber population. To the best of our knowledge, this is the first work to develop a high-throughput SNP array for A. japonicus and a new model DNN-MCP for genomic prediction of complex traits in GS. The present results provide evidence that supports the HaishenSNP24K array with DNN-MCP will be valuable for genetic studies and molecular breeding in A. japonicus.
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Affiliation(s)
- Jia Lv
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yangfan Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Ping Ni
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Ping Lin
- Division of Mathematics, University of Dundee, Dundee DD1 4HN, UK
| | - Hu Hou
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Jun Ding
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China.
| | - Yaqing Chang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China.
| | - Jingjie Hu
- Ocean University China, Sanya Oceanog Inst, Lab Trop Marine Germplasm Res & Breeding Engn, Sanya 572000, China.
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
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23
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Biosynthesis of saponin defensive compounds in sea cucumbers. Nat Chem Biol 2022; 18:774-781. [PMID: 35761075 PMCID: PMC9236903 DOI: 10.1038/s41589-022-01054-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 05/09/2022] [Indexed: 12/03/2022]
Abstract
Soft-bodied slow-moving sea creatures such as sea stars and sea cucumbers lack an adaptive immune system and have instead evolved the ability to make specialized protective chemicals (glycosylated steroids and triterpenes) as part of their innate immune system. This raises the intriguing question of how these biosynthetic pathways have evolved. Sea star saponins are steroidal, while those of the sea cucumber are triterpenoid. Sterol biosynthesis in animals involves cyclization of 2,3-oxidosqualene to lanosterol by the oxidosqualene cyclase (OSC) enzyme lanosterol synthase (LSS). Here we show that sea cucumbers lack LSS and instead have two divergent OSCs that produce triterpene saponins and that are likely to have evolved from an ancestral LSS by gene duplication and neofunctionalization. We further show that sea cucumbers make alternate sterols that confer protection against self-poisoning by their own saponins. Collectively, these events have enabled sea cucumbers to evolve the ability to produce saponins and saponin-resistant sterols concomitantly. ![]()
Sea stars and sea cucumbers biosynthesize protective glycosylated steroids and triterpenes via divergent oxidosqualene cyclases (OSCs) that produce these distinct saponins in different species as well as in different tissues of a single species.
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Silchenko AS, Avilov SA, Andrijaschenko PV, Popov RS, Chingizova EA, Dmitrenok PS, Kalinovsky AI, Rasin AB, Kalinin VI. Structures and Biologic Activity of Chitonoidosides I, J, K, K1 and L-Triterpene Di-, Tri- and Tetrasulfated Hexaosides from the Sea Cucumber Psolus chitonoides. Mar Drugs 2022; 20:md20060369. [PMID: 35736172 PMCID: PMC9228963 DOI: 10.3390/md20060369] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023] Open
Abstract
Five new triterpene di-, tri- and tetrasulfated hexaosides (chitonoidosides I (1), J (2), K (3), K1 (4) and L (5)) were isolated from the Far-Eastern sea cucumber Psolus chitonoides, collected near Bering Island (Commander Islands) from a depth of 100–150 m. The structural variability of the glycosides concerned both the aglycones (with 7(8)- or 9(11)-double bonds) and carbohydrate chains differing from each other by the third sugar residue (Xyl or sulfated by C-6 Glc) and/or by the fourth—terminal in the bottom semi-chain—residue (Glc or sulfated by C-6 MeGlc) as well as by the positions of a sulfate group at C-4 or C-6 in the sixth—terminal in the upper semi-chain—residue (MeGlc). Hemolytic activities of these compounds 1–5 against human erythrocytes as well as cytotoxicity against human cancer cell lines, HeLa, DLD-1 and HL-60, were studied. The hexaosides, chitonoidosides K (3) and L (5) with four sulfate groups, were the most active against tumor cells in all the tests. Noticeably, the sulfate group at C-4 of MeGlc6 did not decrease the membranolytic effect of 5 as compared with 3, having the sulfate group at C-6 of MeGlc6. Erythrocytes were, as usual, more sensitive to the action of the studied glycosides than cancer cells, although the sensitivity of leukemia promyeloblast HL-60 cells was higher than that of other tumor cells. The glycosides 1 and 2 demonstrated some weaker action in relation to DLD-1 cells than against other tumor cell lines. Chitonoidoside K1 (4) with a hydroxyl at C 25 of the aglycone was not active in all the tests. The metabolic network formed by the carbohydrate chains of all the glycosides isolated from P. chitonoides as well as the aglycones biosynthetic transformations during their biosynthesis are discussed and illustrated with schemes.
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Wang Y, Yang Y, Li Y, Chen M. Identification of sex determination locus in sea cucumber Apostichopus japonicus using genome-wide association study. BMC Genomics 2022; 23:391. [PMID: 35606723 PMCID: PMC9128100 DOI: 10.1186/s12864-022-08632-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/12/2022] [Indexed: 12/26/2022] Open
Abstract
Background Sex determination mechanisms are complicated and diverse across taxonomic categories. Sea cucumber Apostichopus japonicus is a benthic echinoderm, which is the closest group of invertebrates to chordate, and important economic and ecologically aquaculture species in China. A. japonicus is dioecious, and no phenotypic differences between males and females can be detected before sexual maturation. Identification of sex determination locus will broaden knowledge about sex-determination mechanism in echinoderms, which allows for the identification of sex-linked markers and increases the efficiency of sea cucumber breeding industry. Results Here, we integrated assembly of a novel chromosome-level genome and resequencing of female and male populations to investigate the sex determination mechanisms of A. japonicus. We built a chromosome-level genome assembly AJH1.0 using Hi-C technology. The assembly AJH1.0 consists of 23 chromosomes ranging from 22.4 to 60.4 Mb. To identify the sex-determination locus of A. japonicus, we conducted genome-wide association study (GWAS) and analyses of distribution characteristics of sex-specific SNPs and fixation index FST. The GWAS analysis showed that multiple sex-associated loci were located on several chromosomes, including chromosome 4 (24.8%), followed by chromosome 9 (10.7%), chromosome 17 (10.4%), and chromosome 18 (14.1%). Furthermore, analyzing the homozygous and heterozygous genotypes of plenty of sex-specific SNPs in females and males confirmed that A. japonicus might have a XX/XY sex determination system. As a physical region of 10 Mb on chromosome 4 included the highest number of sex-specific SNPs and higher FST values, this region was considered as the candidate sex determination region (SDR) in A. japonicus. Conclusions In the present study, we integrated genome-wide association study and analyses of sex-specific variations to investigate sex determination mechanisms. This will bring novel insights into gene regulation during primitive gonadogenesis and differentiation and identification of master sex determination gene in sea cucumber. In the sea cucumber industry, investigation of molecular mechanisms of sex determination will be helpful for artificial fertilization and precise breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08632-3.
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Affiliation(s)
- Yixin Wang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yujia Yang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China.
| | - Yulong Li
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences (CAS), Chinese Academy of Sciences (CAS), Qingdao, China
| | - Muyan Chen
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China.
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Sea Cucumber Body Vesicular Syndrome Is Driven by the Pond Water Microbiome via an Altered Gut Microbiota. mSystems 2022; 7:e0135721. [PMID: 35418244 PMCID: PMC9239130 DOI: 10.1128/msystems.01357-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Apostichopus japonicus (sea cucumber) is one of the most valuable aquaculture species in China; however, different diseases can limit its economic development. Recently, a novel disease, body vesicular syndrome (BVS), was observed in A. japonicus aquaculture. Diseased animals displayed no obvious phenotypic characteristics; however, after boiling at the postharvest stage, blisters, lysis, and body ruptures appeared. In this study, a multiomics strategy incorporating analysis of the gut microbiota, the pond microbiome, and A. japonicus genotype was established to investigate BVS. Detailed analyses of differentially expressed proteins (DEPs) and metabolites suggested that changes in cell adhesion structures, caused by disordered fatty acid β-oxidation mediated by vitamin B5 deficiency, could be a putative BVS mechanism. Furthermore, intestinal dysbacteriosis due to microbiome variations in pond water was considered a potential reason for vitamin B5 deficiency. Our BVS index, based on biomarkers identified from the A. japonicus gut microbiota, was a useful tool for BVS diagnosis. Finally, vitamin B5 supplementation was successfully used to treat BVS, suggesting an association with BVS etiology. IMPORTANCE Body vesicular syndrome (BVS) is a novel disease in sea cucumber aquaculture. As no phenotypic features are visible, BVS is difficult to confirm during aquaculture and postharvest activities, until animals are boiled. Therefore, BVS could lead to severe economic losses compared with other diseases in sea cucumber aquaculture. In this study, for the first time, we systematically investigated BVS pathogenesis and proposed an effective treatment for the condition. Moreover, based on the gut microbiota, we established a noninvasive diagnostic method for BVS in sea cucumber.
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Zhao Z, Jiang J, Zheng J, Pan Y, Dong Y, Chen Z, Gao S, Xiao Y, Jiang P, Wang X, Zhang G, Wang B, Yu D, Fu Z, Guan X, Sun H, Zhou Z. Exploiting the gut microbiota to predict the origins and quality traits of cultured sea cucumbers. Environ Microbiol 2022; 24:3882-3897. [PMID: 35297145 DOI: 10.1111/1462-2920.15972] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/07/2022] [Indexed: 01/09/2023]
Abstract
Nowadays, the true economic and nutritional value of food is underpinned by both origin and quality traits, more often expressed as increased quality benefits derived from the origin source. Gut microbiota contribute to food metabolism and host health, therefore, it may be suitable as a qualifying indicator of origin and quality of economic species. Here, we investigated relationships between the gut microbiota of the sea cucumber (Apostichopus japonicus), a valuable aquaculture species in Asia, with their origins and quality metrics. Based on data from 287 intestinal samples, we generated the first biogeographical patterns for A. japonicus gut microbiota from origins across China. Importantly, A. japonicus origins were predicted using the random forest model that was constructed using 20 key gut bacterial genera, with 97.6% accuracy. Furthermore, quality traits such as saponin, fat and taurine were also successfully predicted by random forest models based on gut microbiota, with approximately 80% consistency between predicted and true values. We showed that substantial variations existed in the gut microbiota and quality variables in A. japonicus across different origins, and we also demonstrated the great potential of gut microbiota to track A. japonicus origins and predict their quality traits.
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Affiliation(s)
- Zelong Zhao
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Jingwei Jiang
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Jie Zheng
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Yongjia Pan
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Ying Dong
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Zhong Chen
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Shan Gao
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Yao Xiao
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Pingzhe Jiang
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Xuda Wang
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Gaohua Zhang
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Bai Wang
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Di Yu
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Zhiyu Fu
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Xiaoyan Guan
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Hongjuan Sun
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
| | - Zunchun Zhou
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
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Zhang L, He J, Tan P, Gong Z, Qian S, Miao Y, Zhang HY, Tu G, Chen Q, Zhong Q, Han G, He J, Wang M. The genome of an apodid holothuroid (Chiridota heheva) provides insights into its adaptation to a deep-sea reducing environment. Commun Biol 2022; 5:224. [PMID: 35273345 PMCID: PMC8913654 DOI: 10.1038/s42003-022-03176-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/16/2022] [Indexed: 11/09/2022] Open
Abstract
Cold seeps and hydrothermal vents are deep-sea reducing environments that are characterized by lacking oxygen and photosynthesis-derived nutrients. Most animals acquire nutrition in cold seeps or hydrothermal vents by maintaining epi- or endosymbiotic relationship with chemoautotrophic microorganisms. Although several seep- and vent-dwelling animals hosting symbiotic microbes have been well-studied, the genomic basis of adaptation to deep-sea reducing environment in nonsymbiotic animals is still lacking. Here, we report a high-quality genome of Chiridota heheva Pawson & Vance, 2004, which thrives by extracting organic components from sediment detritus and suspended material, as a reference for nonsymbiotic animal's adaptation to deep-sea reducing environments. The expansion of the aerolysin-like protein family in C. heheva compared with other echinoderms might be involved in the disintegration of microbes during digestion. Moreover, several hypoxia-related genes (Pyruvate Kinase M2, PKM2; Phospholysine Phosphohistidine Inorganic Pyrophosphate Phosphatase, LHPP; Poly(A)-specific Ribonuclease Subunit PAN2, PAN2; and Ribosomal RNA Processing 9, RRP9) were subject to positive selection in the genome of C. heheva, which contributes to their adaptation to hypoxic environments.
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Affiliation(s)
- Long Zhang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Jian He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Peipei Tan
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Zhen Gong
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shiyu Qian
- School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Yuanyuan Miao
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Han-Yu Zhang
- Hainan Key Laboratory of Marine Georesource and Prospecting, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Guangxian Tu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Qi Chen
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Qiqi Zhong
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Guanzhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jianguo He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China. .,Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, 525435, China.
| | - Muhua Wang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China. .,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, 525435, China.
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Shao Y, Wang Z, Chen K, Li D, Lv Z, Zhang C, Zhang W, Li C. Xenophagy of invasive bacteria is differentially activated and modulated via a TLR-TRAF6-Beclin1 axis in echinoderms. J Biol Chem 2022; 298:101667. [PMID: 35120925 PMCID: PMC8902612 DOI: 10.1016/j.jbc.2022.101667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022] Open
Abstract
In marine environments, organisms are confronted with numerous microbial challenges, although the differential regulation of xenophagy in response to different pathogenic bacterial species remains relatively unknown. Here, we addressed this issue using Apostichopus japonicus as a model. We identified 39 conserved autophagy-related genes by genome-wide screening, which provided a molecular basis for autophagy regulation in sea cucumbers. Furthermore, xenophagy of two Gram-negative bacteria, Vibrio splendidus and Escherichia coli, but not a Gram-positive bacteria, Micrococcus luteus, was observed in different autophagy assays. Surprisingly, a significantly higher autophagy capacity was found in the E. coli–challenged group than in the V. splendidus–challenged group. To confirm these findings, two different lipopolysaccharides, LPSV. splendidus and LPSE. coli, were isolated; we found that these LPS species differentially activated coelomocyte xenophagy. To explore the molecular mechanism mediating differential levels of xenophagy, we used an siRNA knockdown assay and confirmed that LPSV. splendidus-mediated xenophagy was dependent on an AjTLR3-mediated pathway, whereas LPSE. coli-mediated xenophagy was dependent on AjToll. Moreover, the activation of different AjTLRs resulted in AjTRAF6 ubiquitination and subsequent activation of K63-linked ubiquitination of AjBeclin1. Inversely, the LPSV. splendidus-induced AjTLR3 pathway simultaneously activated the expression of AjA20, which reduced the extent of K63-linked ubiquitination of AjBeclin1 and impaired the induction of autophagy; however, this finding was no t evident with LPSE. coli. Our present results provide the first evidence showing that xenophagy could be differentially induced by different bacterial species to yield differential autophagy levels in echinoderms.
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Affiliation(s)
- Yina Shao
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, PR China
| | - Zhenhui Wang
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, PR China
| | - Kaiyu Chen
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, PR China
| | - Dongdong Li
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, PR China
| | - Zhimeng Lv
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, PR China
| | - Chundan Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, PR China
| | - Weiwei Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, PR China
| | - Chenghua Li
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China; State-Province Joint Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo 315211, China.
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30
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Zhao Z, Li S, Pan Y, Jiang P, Dong Y, Yang H, Wang X, Guan X, Zhou Z. Proteomics reveals gender differences in physiological characteristics of the gonads and tube feet of the sea cucumber, Apostichopus japonicus. J Proteomics 2022; 251:104396. [PMID: 34673268 DOI: 10.1016/j.jprot.2021.104396] [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: 12/22/2020] [Revised: 04/29/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022]
Abstract
The sea cucumber Apostichopus japonicus is an important aquaculture species in China because of its high nutritional and medicinal values. Gender, as a factor affecting the physiology of organisms, is always considered when improving the breeding efficiency of economically important animals. In the present study, protein expression profiles of the gonads and tube feet of male and female A. japonicus were investigated using a comparative proteomics approach. A set of 7499 proteins were identified, which covered a broad range of functions based on function annotations. A significant difference in protein expression profiles was observed between the gonads and tube feet of A. japonicus; gonads showed more apparent gender differences than tube feet. Moreover, the findings revealed that male A. japonicus had more specific functions and most of these functions were associated with energy consumption. Further analyses suggested that the regulation of ERK activity and the capacity of tyrosine production and virus immunity might be more powerful in male and female A. japonicus, respectively. Some candidate proteins were also recognized as potential targets for gender identification of A. japonicus. Overall, our study provides new insights into the understanding of molecular mechanisms underlying gender-based physiological differences in A. japonicus. SIGNIFICANCE: The current study aimed to reveal gender differences in the physiological characteristics of gonads and tube feet of the sea cucumber A. japonicus. To the best of our knowledge, this is the first proteomics study to analyze the differences in the protein expression profiles of external organs between male and female A. japonicus. The analysis revealed gender differences in the protein expression profiles of both gonads and tube feet of A. japonicus, and the gender differences in gonads were quite apparent. Moreover, according to the recognition of differentially expressed proteins and the enrichment analyses based on Kyoto Encyclopedia of Genes and Genomes, a draft view of how the physiological functions of A. japonicus were affected by gender was obtained. Male A. japonicus could have more specific functions related to energy consumption than females. The regulation of ERK activity and virus immunity might be more robust in male and female A. japonicus, respectively. Some candidate proteins were also recognized as potential targets for gender identification of A. japonicus. The findings presented here will improve the understanding of researchers about the molecular mechanisms underlying gender-based differences in A. japonicus and contribute to the meticulous breeding of A. japonicus.
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Affiliation(s)
- Zelong Zhao
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Shilei Li
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Yongjia Pan
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Pingzhe Jiang
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Ying Dong
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Huihua Yang
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Xuda Wang
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Xiaoyan Guan
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zunchun Zhou
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China.
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Effects of Cadmium Sulfate on the Brown Garden Snail Cornu aspersum: Implications for DNA Methylation. TOXICS 2021; 9:toxics9110306. [PMID: 34822697 PMCID: PMC8619149 DOI: 10.3390/toxics9110306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/01/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022]
Abstract
An extensive literature exists regarding the cellular, physiological, and genetic effects of cadmium (Cd)—A highly toxic, but commonly used trace metal in modern industry. However, limited data are available on its epigenetic effects, especially for terrestrial sentinel invertebrates. We determined Cd retention, total DNA methylation, and the methylation status of 5′ end of the Cd-MT gene in the hepatopancreas of the brown garden snail, Cornu aspersum, fed Cd sulfate for four weeks. Bodyweight changes and survival were also measured. Hepatopancreas cadmium increased in a dose-dependent manner from the third-lowest dose onward, with very large amounts being found for the highest treatment group. However, no mortalities occurred, irrespective of dietary Cd dose. We identified significant genome-wide hypermethylation in specimens given the highest dose, which overlapped with a significant bodyweight decrease. The Cd-MT gene showed an unmethylated 5′ end of the Cd-MT gene and this status was not affected by cadmium exposure. Hepatopancreas DNA methylation is as sensitive as bodyweight to non-lethal concentrations of dietary Cd given as cadmium sulfate but less responsive than tissue accumulation. Such an exposure event, by contrast, does not affect the methylation status of the Cd-MT gene 5′ end.
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Liu C, Yuan J, Zhang X, Jin S, Li F, Xiang J. tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis. Open Biol 2021; 11:210190. [PMID: 34753322 PMCID: PMC8580430 DOI: 10.1098/rsob.210190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Using the sea cucumber Apostichopus japonicus as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic non-coding RNAs, transfer RNAs (tRNAs) tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence, which might be a compromise between functionality and translation efficiency for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of A. japonicus was positively correlated with amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitates their saponin synthesis and survival using food resources with low nutrient content.
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Affiliation(s)
- Chengzhang Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Songjun Jin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
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Progress in the Studies of Triterpene Glycosides From Sea Cucumbers (Holothuroidea, Echinodermata) Between 2017 and 2021. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211053934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Structural diversity of triterpene glycosides produced by sea cucumbers or holothurians (Holothuroidea, Echinodermata) is extremely high, although all of them are either lanostane derivatives or, rarely, products of their molecular rearrangements. The majority of them are holostane derivatives possessing an 18(20)-lanostane lactone as aglycone. They contain carbohydrate chains consisting of one to six monosaccharide units including sulfated ones. The glycosides demonstrate interesting biological activities, mainly caused by membranolytic action, namely cytotoxic, ichthyotoxic, antifungal, and hemolytic properties, as well as a series of additional effects at sub-toxic doses, including immunomodulatory, and cancer preventive. This review summarizes the literature data concerning structures and biological activities of all the new triterpene glycosides isolated from sea cucumbers during 2017 to 2021.
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Rinkevich B, Ballarin L, Martinez P, Somorjai I, Ben-Hamo O, Borisenko I, Berezikov E, Ereskovsky A, Gazave E, Khnykin D, Manni L, Petukhova O, Rosner A, Röttinger E, Spagnuolo A, Sugni M, Tiozzo S, Hobmayer B. A pan-metazoan concept for adult stem cells: the wobbling Penrose landscape. Biol Rev Camb Philos Soc 2021; 97:299-325. [PMID: 34617397 PMCID: PMC9292022 DOI: 10.1111/brv.12801] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022]
Abstract
Adult stem cells (ASCs) in vertebrates and model invertebrates (e.g. Drosophila melanogaster) are typically long‐lived, lineage‐restricted, clonogenic and quiescent cells with somatic descendants and tissue/organ‐restricted activities. Such ASCs are mostly rare, morphologically undifferentiated, and undergo asymmetric cell division. Characterized by ‘stemness’ gene expression, they can regulate tissue/organ homeostasis, repair and regeneration. By contrast, analysis of other animal phyla shows that ASCs emerge at different life stages, present both differentiated and undifferentiated phenotypes, and may possess amoeboid movement. Usually pluri/totipotent, they may express germ‐cell markers, but often lack germ‐line sequestering, and typically do not reside in discrete niches. ASCs may constitute up to 40% of animal cells, and participate in a range of biological phenomena, from whole‐body regeneration, dormancy, and agametic asexual reproduction, to indeterminate growth. They are considered legitimate units of selection. Conceptualizing this divergence, we present an alternative stemness metaphor to the Waddington landscape: the ‘wobbling Penrose’ landscape. Here, totipotent ASCs adopt ascending/descending courses of an ‘Escherian stairwell’, in a lifelong totipotency pathway. ASCs may also travel along lower stemness echelons to reach fully differentiated states. However, from any starting state, cells can change their stemness status, underscoring their dynamic cellular potencies. Thus, vertebrate ASCs may reflect just one metazoan ASC archetype.
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Affiliation(s)
- Baruch Rinkevich
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Loriano Ballarin
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35121, Italy
| | - Pedro Martinez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain.,Institut Català de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, 08010, Spain
| | - Ildiko Somorjai
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Oshrat Ben-Hamo
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Ilya Borisenko
- Department of Embryology, Faculty of Biology, Saint-Petersburg State University, University Embankment, 7/9, Saint-Petersburg, 199034, Russia
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Alexander Ereskovsky
- Department of Embryology, Faculty of Biology, Saint-Petersburg State University, University Embankment, 7/9, Saint-Petersburg, 199034, Russia.,Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), Aix Marseille University, CNRS, IRD, Avignon University, Jardin du Pharo, 58 Boulevard Charles Livon, Marseille, 13007, France.,Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Ulitsa Vavilova, 26, Moscow, 119334, Russia
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques Monod, Paris, F-75006, France
| | - Denis Khnykin
- Department of Pathology, Oslo University Hospital, Bygg 19, Gaustad Sykehus, Sognsvannsveien 21, Oslo, 0188, Norway
| | - Lucia Manni
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35121, Italy
| | - Olga Petukhova
- Collection of Vertebrate Cell Cultures, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - Amalia Rosner
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, 06107, France.,Université Côte d'Azur, Federative Research Institute - Marine Resources (IFR MARRES), 28 Avenue de Valrose, Nice, 06103, France
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy (ESP), Università degli Studi di Milano, Via Celoria 26, Milan, 20133, Italy
| | - Stefano Tiozzo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06234 Villefranche-sur-Mer, Villefranche sur Mer, Cedex, France
| | - Bert Hobmayer
- Institute of Zoology and Center for Molecular Biosciences, University of Innsbruck, Technikerstr, Innsbruck, 256020, Austria
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Wang J, Guo Y, Yin X, Wang X, Qi X, Xue Z. Diverse triterpene skeletons are derived from the expansion and divergent evolution of 2,3-oxidosqualene cyclases in plants. Crit Rev Biochem Mol Biol 2021; 57:113-132. [PMID: 34601979 DOI: 10.1080/10409238.2021.1979458] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Triterpenoids are one of the largest groups of secondary metabolites and exhibit diverse structures, which are derived from C30 skeletons that are biosynthesized via the isoprenoid pathway by cyclization of 2,3-oxidosqualene. Triterpenoids have a wide range of biological activities, and are used in functional foods, drugs, and as industrial materials. Due to the low content levels in their native plants and limited feasibility and efficiency of chemical synthesis, heterologous biosynthesis of triterpenoids is the most promising strategy. Herein, we classified 121 triterpene alcohols/ketones according to their conformation and ring numbers, among which 51 skeletons have been experimentally characterized as the products of oxidosqualene cyclases (OSCs). Interestingly, 24 skeletons that have not been reported from nature source were generated by OSCs in heterologous expression. Comprehensive evolutionary analysis of the identified 152 OSCs from 75 species in 25 plant orders show that several pentacyclic triterpene synthases repeatedly originated in multiple plant lineages. Comparative analysis of OSC catalytic reaction revealed that stabilization of intermediate cations, steric hindrance, and conformation of active center amino acid residues are primary factors affecting triterpene formation. Optimization of OSC could be achieved by changing of side-chain orientations of key residues. Recently, methods, such as rationally design of pathways, regulation of metabolic flow, compartmentalization engineering, etc., were introduced in improving chassis for the biosynthesis of triterpenoids. We expect that extensive study of natural variation of large number of OSCs and catalytical mechanism will provide basis for production of high level of triterpenoids by application of synthetic biology strategies.
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Affiliation(s)
- Jing Wang
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.,Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China.,Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, PR China
| | - Yanhong Guo
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.,Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Xue Yin
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.,Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Xiaoning Wang
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, PR China
| | - Zheyong Xue
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.,Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
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36
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Liu C, Yuan J, Zhang X, Jin S, Li F, Xiang J. Clustering genomic organization of sea cucumber miRNAs impacts their evolution and expression. Genomics 2021; 113:3544-3555. [PMID: 34371099 DOI: 10.1016/j.ygeno.2021.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 07/08/2021] [Accepted: 08/03/2021] [Indexed: 12/31/2022]
Abstract
Echinoderms are marine deuterostomes with fascinating adaptation features such as aestivation and organ regeneration. However, post-transcriptional gene regulation by microRNAs (miRNAs) underlying these features are largely unexplored. Here, using homology-based and de novo approaches supported by expression data, we provided a comprehensive annotation of miRNA genes in the sea cucumber Apostichopus japonicus. By linkage and phylogenic analyses, we characterized miRNA genomic organization, evolutionary history and expression regulation. The results showed that sea cucumbers evolved a large number of new miRNAs, which tended to form polycistronic clusters via tandem duplication that had been especially active in the echinoderms. Most new miRNAs were weakly expressed, but miRNA clustering increased the expression level of clustered new miRNAs. The most abundantly expressed new miRNAs were organized in a single tandem cluster (cluster n2), which was activated during aestivation and intestine regeneration. Overall, our analyses suggest that clustering of miRNAs is important for their evolutionary origin, expression control, and functional cooperation.
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Affiliation(s)
- Chengzhang Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jianbo Yuan
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaojun Zhang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Songjun Jin
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Fuhua Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jianhai Xiang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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Li C, Zhao W, Qin C, Yu G, Ma Z, Guo Y, Pan W, Fu Z, Huang X, Chen J. Comparative transcriptome analysis reveals changes in gene expression in sea cucumber (Holothuria leucospilota) in response to acute temperature stress. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100883. [PMID: 34303260 DOI: 10.1016/j.cbd.2021.100883] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022]
Abstract
Ambient temperature is an important abiotic factor that influences growth performance and physiological functions in sea cucumbers. To understand the molecular responses of the sea cucumber Holothuria leucospilota to acute temperature stress, we performed a de novo transcriptome analysis of body wall tissue from H. leucospilota exposed to 2 hoursh of acute heat (35 ± 1 °C) and cold stress (15 ± 1 °C). A total of 99,015 unigenes were obtained after assembly of the sequenced reads. Compared with a control group maintained at 25.0 ± 1 °C, 1169 differentially expressed unigenes (DEGs) were identified after heat stress, 781 were up-regulated and 388 were down-regulated. After cold stress, 1464 DEGs were identified; 900 were up-regulated and 564 were down-regulated. The annotation of DEGs revealed that heat shock proteins play important roles in protecting H. leucospilota from high temperature stress. Furthermore, KEGG pathway enrichment analysis showed that the categories: "Ribosome" and "Protein processing in endoplasmic reticulum" were strongly affected by heat stress. These two pathways are associated with biosynthesis and processing of proteins, and refolding of misfolded proteins. The lipid metabolism pathways "Sphingolipid metabolism" and "Ether lipid metabolism", were affected by cold stress. The RNA-Seq results for eight selected DEGs were verified the expression by quantitative real-time PCR analysis. Our results will improve the understanding of the molecular response mechanisms of H. leucospilota to ambient temperature stress.
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Affiliation(s)
- Changlin Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China
| | - Wang Zhao
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China; Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Chuanxin Qin
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China.
| | - Gang Yu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China.
| | - Zhenhua Ma
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China
| | - Yu Guo
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China
| | - Wanni Pan
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China
| | - Zhengyi Fu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China; Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Xingmei Huang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China; Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Jisheng Chen
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China
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38
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Silchenko AS, Kalinovsky AI, Avilov SA, Andrijaschenko PV, Popov RS, Dmitrenok PS, Chingizova EA, Kalinin VI. Triterpene Glycosides from the Far Eastern Sea Cucumber Thyonidium (=Duasmodactyla) kurilensis (Levin): The Structures, Cytotoxicities, and Biogenesis of Kurilosides A 3, D 1, G, H, I, I 1, J, K, and K 1. Mar Drugs 2021; 19:md19040187. [PMID: 33801633 PMCID: PMC8066294 DOI: 10.3390/md19040187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/16/2021] [Accepted: 03/24/2021] [Indexed: 12/17/2022] Open
Abstract
Nine new mono-, di-, and trisulfated triterpene penta- and hexaosides, kurilosides A3 (1), D1 (2), G (3), H (4), I (5), I1 (6), J (7), K (8), and K1 (9) and two desulfated derivatives, DS-kuriloside L (10), having a trisaccharide branched chain, and DS-kuriloside M (11), having hexa-nor-lanostane aglycone with a 7(8)-double bond, have been isolated from the Far-Eastern deep-water sea cucumber Thyonidium (=Duasmodactyla) kurilensis (Levin) and their structures were elucidated based on 2D NMR spectroscopy and HR-ESI mass-spectrometry. Five earlier unknown carbohydrate chains and two aglycones (having a 16β,(20S)-dihydroxy-fragment and a 16β-acetoxy,(20S)-hydroxy fragment) were found in these glycosides. All the glycosides 1–9 have a sulfate group at C-6 Glc, attached to C-4 Xyl1, while the positions of the other sulfate groups vary in different groups of kurilosides. The analysis of the structural features of the aglycones and the carbohydrate chains of all the glycosides of T. kurilensis showed their biogenetic relationships. Cytotoxic activities of the compounds 1–9 against mouse neuroblastoma Neuro 2a, normal epithelial JB-6 cells, and erythrocytes were studied. The highest cytotoxicity in the series was demonstrated by trisulfated hexaoside kuriloside H (4), having acetoxy-groups at C(16) and C(20), the latter one obviously compensated the absence of a side chain, essential for the membranolytic action of the glycosides. Kuriloside I1 (6), differing from 4 in the lacking of a terminal glucose residue in the bottom semi-chain, was slightly less active. The compounds 1–3, 5, and 8 did not demonstrate cytotoxic activity due to the presence of hydroxyl groups in their aglycones.
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Tedeschi LO, Muir JP, Naumann HD, Norris AB, Ramírez-Restrepo CA, Mertens-Talcott SU. Nutritional Aspects of Ecologically Relevant Phytochemicals in Ruminant Production. Front Vet Sci 2021; 8:628445. [PMID: 33748210 PMCID: PMC7973208 DOI: 10.3389/fvets.2021.628445] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/04/2021] [Indexed: 12/14/2022] Open
Abstract
This review provides an update of ecologically relevant phytochemicals for ruminant production, focusing on their contribution to advancing nutrition. Phytochemicals embody a broad spectrum of chemical components that influence resource competence and biological advantage in determining plant species' distribution and density in different ecosystems. These natural compounds also often act as plant defensive chemicals against predatorial microbes, insects, and herbivores. They may modulate or exacerbate microbial transactions in the gastrointestinal tract and physiological responses in ruminant microbiomes. To harness their production-enhancing characteristics, phytochemicals have been actively researched as feed additives to manipulate ruminal fermentation and establish other phytochemoprophylactic (prevent animal diseases) and phytochemotherapeutic (treat animal diseases) roles. However, phytochemical-host interactions, the exact mechanism of action, and their effects require more profound elucidation to provide definitive recommendations for ruminant production. The majority of phytochemicals of nutritional and pharmacological interest are typically classified as flavonoids (9%), terpenoids (55%), and alkaloids (36%). Within flavonoids, polyphenolics (e.g., hydrolyzable and condensed tannins) have many benefits to ruminants, including reducing methane (CH4) emission, gastrointestinal nematode parasitism, and ruminal proteolysis. Within terpenoids, saponins and essential oils also mitigate CH4 emission, but triterpenoid saponins have rich biochemical structures with many clinical benefits in humans. The anti-methanogenic property in ruminants is variable because of the simultaneous targeting of several physiological pathways. This may explain saponin-containing forages' relative safety for long-term use and describe associated molecular interactions on all ruminant metabolism phases. Alkaloids are N-containing compounds with vast pharmacological properties currently used to treat humans, but their phytochemical usage as feed additives in ruminants has yet to be exploited as they may act as ghost compounds alongside other phytochemicals of known importance. We discussed strategic recommendations for phytochemicals to support sustainable ruminant production, such as replacements for antibiotics and anthelmintics. Topics that merit further examination are discussed and include the role of fresh forages vis-à-vis processed feeds in confined ruminant operations. Applications and benefits of phytochemicals to humankind are yet to be fully understood or utilized. Scientific explorations have provided promising results, pending thorough vetting before primetime use, such that academic and commercial interests in the technology are fully adopted.
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Affiliation(s)
- Luis O. Tedeschi
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - James P. Muir
- Texas A&M AgriLife Research, Stephenville, TX, United States
| | - Harley D. Naumann
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Aaron B. Norris
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX, United States
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Abstract
This review covers the literature published between January and December in 2018 for marine natural products (MNPs), with 717 citations (706 for the period January to December 2018) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1554 in 469 papers for 2018), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. The proportion of MNPs assigned absolute configuration over the last decade is also surveyed.
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Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. and Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia and School of Environment and Science, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Michèle R Prinsep
- Chemistry, School of Science, University of Waikato, Hamilton, New Zealand
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Comparative metabolomic analysis of the body wall from four varieties of the sea cucumber Apostichopus japonicus. Food Chem 2021; 352:129339. [PMID: 33667918 DOI: 10.1016/j.foodchem.2021.129339] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/20/2021] [Accepted: 02/06/2021] [Indexed: 11/23/2022]
Abstract
The sea cucumber, Apostichopus japonicas, is an important economic species with high nutritive value. In recent years, driven by significant market demand, the sea cucumber breeding industry has developed rapidly. Body color and number of papillae are important factors that determine the value and price of sea cucumbers. In this study, metabolite profiling of four sea cucumber varieties (green, white, purple and spiny) was performed using ultra-performance liquid chromatography-quadrupole-time-of-flight-mass spectrometry (UPLC-QTOF-MS) combined with multivariate analysis. Orthogonal partial least-squares discriminant analysis (OPLS-DA) clearly discriminated the body wall metabolites of four sea cucumber varieties. Differential metabolites included fatty acids, phospholipids, and sugars. KEGG metabolic pathway analysis revealed that carbohydrate, protein, and phospholipid metabolism were highly conserved among the varieties. These results provide a comprehensive insight into differences in the metabolite profile of four A. japonicus varieties and a deeper understanding of sea cucumber varieties breeding.
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42
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Huang B, Lv Z, Li Y, Li C. Identification and functional characterization of natural resistance-associated macrophage protein 2 from sea cucumber Apostichopus japonicus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 114:103835. [PMID: 32841622 DOI: 10.1016/j.dci.2020.103835] [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: 07/19/2020] [Revised: 08/15/2020] [Accepted: 08/15/2020] [Indexed: 06/11/2023]
Abstract
As a member of natural resistance-associated macrophage protein (Nramp) family, Nramp2 conservatively exists in the cell membrane across species and is essential for normal iron homeostasis in an H+-dependent manner. Withholding available iron represents an important host defense strategy. However, the function of Nramp2 in response to invading pathogens is largely unknown in invertebrates. In this study, a unique echinoderm Nramp2 was identified from sea cucumber Apostichopus japonicus (designated as AjNramp2). The cDNA sequence of AjNramp2 was 2360 bp, with a putative open reading frame of 1713 bp, encoding a typical Nramp domain containing protein with 570 amino acid residues. Structural analysis revealed that AjNramp2 consisted of highly conserved helix regions similar with the human Nramp2. Spatial expression analysis revealed that AjNramp2 was ubiquitously expressed in all examined tissues, with the highest level found in the intestine. Immunohistochemistry assay showed that AjNramp2 was mainly located in the cellular membrane in coelomocytes. Vibrio splendidus challenge and lipopolysaccharide (LPS) stimulation could significantly promote the expression of AjNramp2, which was consistent with the cellular iron level in coelomocytes. Moreover, when the expression of AjNramp2 was knocked down by siRNA-AjNramp2, the cellular iron level was coordinately decreased in coelomocytes under LPS stimulation. Taken together, results indicated that AjNramp2 serves as an iron transport receptor to withhold available iron and may contribute to the nutritional immunity defense system of sea cucumber.
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Affiliation(s)
- Bowen Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, PR China
| | - Zhimeng Lv
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, PR China
| | - Yanan Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, PR China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China.
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Yang Y, Zheng Y, Sun L, Chen M. Genome-Wide DNA Methylation Signatures of Sea Cucumber Apostichopus japonicus during Environmental Induced Aestivation. Genes (Basel) 2020; 11:genes11091020. [PMID: 32877994 PMCID: PMC7565549 DOI: 10.3390/genes11091020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/21/2020] [Accepted: 08/28/2020] [Indexed: 02/07/2023] Open
Abstract
Organisms respond to severe environmental changes by entering into hypometabolic states, minimizing their metabolic rates, suspending development and reproduction, and surviving critical ecological changes. They come back to an active lifestyle once the environmental conditions are conducive. Marine invertebrates live in the aquatic environment and adapt to environmental changes in their whole life. Sea cucumbers and sponges are only two recently known types of marine organisms that aestivate in response to temperature change. Sea cucumber has become an excellent model organism for studies of environmentally-induced aestivation by marine invertebrates. DNA methylation, the most widely considered epigenetic marks, has been reported to contribute to phenotypic plasticity in response to environmental stress in aquatic organisms. Most of methylation-related enzymes, including DNA methyltransferases, Methyl-CpG binding domain proteins, and DNA demethylases, were up-regulated during aestivation. We conducted high-resolution whole-genome bisulfite sequencing of the intestine from sea cucumber at non-aestivation and deep-aestivation stages. Further DNA methylation profile analysis was also conducted across the distinct genomic features and entire transcriptional units. A different elevation in methylation level at internal exons was observed with clear demarcation of intron/exon boundaries during transcriptional unit scanning. The lowest methylation level occurs in the first exons, followed by the last exons and the internal exons. A significant increase in non-CpG methylation (CHG and CHH) was observed within the intron and mRNA regions in aestivation groups. A total of 1393 genes were annotated within hypermethylated DMRs (differentially methylated regions), and 749 genes were annotated within hypomethylated DMRs. Differentially methylated genes were enriched in the mRNA surveillance pathway, metabolic pathway, and RNA transport. Then, 24 hypermethylated genes and 15 hypomethylated genes were Retrovirus-related Pol polyprotein from transposon (RPPT) genes. This study provides further understanding of epigenetic control on environmental induced hypometabolism in aquatic organisms.
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Affiliation(s)
- Yujia Yang
- Laboratory for Evolution and Development, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China;
| | - Yingqiu Zheng
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266071, China;
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences (CAS), Qingdao 266003, China
- Correspondence: (L.S.); (M.C.)
| | - Muyan Chen
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266071, China;
- Correspondence: (L.S.); (M.C.)
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Chen Y, Li Y, Zhan Y, Hu W, Sun J, Zhang W, Song J, Li D, Chang Y. Identification of molecular markers for superior quantitative traits in a novel sea cucumber strain by comparative microRNA-mRNA expression profiling. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100686. [PMID: 32413829 DOI: 10.1016/j.cbd.2020.100686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/14/2020] [Accepted: 04/21/2020] [Indexed: 01/21/2023]
Abstract
To investigate the adaptability of Apostichopus japonicus (A. japonicus) strain "Anyuan No. 1" in the South China Sea, field monitoring and microRNA-mRNA integrated analyses were conducted between "Anyuan No. 1" and a regular A. japonicus population from Wendeng (Shandong Province, as a control) in the Xiapu farming area in Fujian Province, China. The results showed that "Anyuan No. 1" exhibited greater body weight increase and a higher number of papillae compared to the control during two and a half months of field monitoring. Comparative microRNA (miRNA) and mRNA transcriptome analyses identified 12 differentially expressed miRNAs (DEMs) and 165 differentially expressed genes (DEGs) in "Anyuan No. 1" compared to the control. Long-chain specific acyl-CoA dehydrogenase (ACADL), transmembrane protein 251 (TMEM251), dehydrogenase/reductase SDR family protein 7-like (Dhrs7), insulin-like growth factor-binding protein 7 (IGFBP-7), CDK5 regulatory subunit-associated protein 1 (CDK5RAP1), visual pigment-like receptor peropsin, 39S ribosomal protein, miR-10, miR-153, miR-7, and miR-3529 were identified as gene and miRNA candidates correlated with superior economic traits in "Anyuan No. 1". Collectively, "Anyuan No. 1" is suitable for large-scale cultivation extension due to its better adaptability to the South China Sea area. Furthermore, we identified "miR10-ACADL" as a potential module for further molecular marker-assisted selective breeding of A. japonicus.
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Affiliation(s)
- Yang Chen
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yingying Li
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yaoyao Zhan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China.
| | - Wanbin Hu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Jingxian Sun
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Weijie Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Jian Song
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Dantong Li
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China.
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Wu X, Chen T, Huo D, Yu Z, Ruan Y, Cheng C, Jiang X, Ren C. Transcriptomic analysis of sea cucumber (Holothuria leucospilota) coelomocytes revealed the echinoderm cytokine response during immune challenge. BMC Genomics 2020; 21:306. [PMID: 32299355 PMCID: PMC7161275 DOI: 10.1186/s12864-020-6698-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 03/24/2020] [Indexed: 12/18/2022] Open
Abstract
Background The sea cucumber Holothuria leucospilota belongs to echinoderm, which is evolutionally the most primitive group of deuterostomes. Sea cucumber has a cavity between its digestive tract and the body wall that is filled with fluid and suspended coelomic cells similar to blood cells. The humoral immune response of the sea cucumber is based on the secretion of various immune factors from coelomocytes into the coelomic cavity. The aim of this study is to lay out a foundation for the immune mechanisms in echinoderms and their origins in chordates by using RNA-seq. Results Sea cucumber primary coelomocytes were isolated from healthy H. leucospilota and incubated with lipopolysaccharide (LPS, 10 μg/ml), polyinosinic-polycytidylic acid [Poly (I:C), 10 μg/ml] and heat-inactived Vibrio harveyi (107 cell/ml) for 24 h, respectively. After high-throughput mRNA sequencing on an Illumina HiSeq2500, a de novo transcriptome was assembled and the Unigenes were annotated. Thirteen differentially expressed genes (DEGs) were selected randomly from our data and subsequently verified by using RT-qPCR. The results of RT-qPCR were consistent with those of the RNA-seq (R2 = 0.61). The top 10 significantly enriched signaling pathways and immune-related pathways of the common and unique DEGs were screened from the transcriptome data. Twenty-one cytokine candidate DEGs were identified, which belong to 4 cytokine families, namely, BCL/CLL, EPRF1, IL-17 and TSP/TPO. Gene expression in response to LPS dose-increased treatment (0, 10, 20 and 50 μg/ml) showed that IL-17 family cytokines were significantly upregulated after 10 μg/ml LPS challenge for 24 h. Conclusion A de novo transcriptome was sequenced and assembled to generate the gene expression profiling across the sea cucumber coelomocytes treated with LPS, Poly (I:C) and V. harveyi. The cytokine genes identified in DEGs could be classified into 4 cytokine families, in which the expression of IL-17 family cytokines was most significantly induced after 10 μg/ml LPS challenge for 24 h. Our findings have laid the foundation not only for the research of molecular mechanisms related to the immune response in echinoderms but also for their origins in chordates, particularly in higher vertebrates.
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Affiliation(s)
- Xiaofen Wu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Ting Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.,Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, PR China
| | - Da Huo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.,Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510301, People's Republic of China
| | - Zonghe Yu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.,Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510301, People's Republic of China
| | - Yao Ruan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Chuhang Cheng
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xiao Jiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.,Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510301, People's Republic of China
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China. .,Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, PR China. .,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510301, People's Republic of China.
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Wang J, Zhang L, Lian S, Qin Z, Zhu X, Dai X, Huang Z, Ke C, Zhou Z, Wei J, Liu P, Hu N, Zeng Q, Dong B, Dong Y, Kong D, Zhang Z, Liu S, Xia Y, Li Y, Zhao L, Xing Q, Huang X, Hu X, Bao Z, Wang S. Evolutionary transcriptomics of metazoan biphasic life cycle supports a single intercalation origin of metazoan larvae. Nat Ecol Evol 2020; 4:725-736. [PMID: 32203475 DOI: 10.1038/s41559-020-1138-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 02/06/2020] [Indexed: 12/16/2022]
Abstract
The transient larva-bearing biphasic life cycle is the hallmark of many metazoan phyla, but how metazoan larvae originated remains a major enigma in animal evolution. There are two hypotheses for larval origin. The 'larva-first' hypothesis suggests that the first metazoans were similar to extant larvae, with later evolution of the adult-added biphasic life cycle; the 'adult-first' hypothesis suggests that the first metazoans were adult forms, with the biphasic life cycle arising later via larval intercalation. Here, we investigate the evolutionary origin of primary larvae by conducting ontogenetic transcriptome profiling for Mollusca-the largest marine phylum characterized by a trochophore larval stage and highly variable adult forms. We reveal that trochophore larvae exhibit rapid transcriptome evolution with extraordinary incorporation of novel genes (potentially contributing to adult shell evolution), and that cell signalling/communication genes (for example, caveolin and innexin) are probably crucial for larval evolution. Transcriptome age analysis of eight metazoan species reveals the wide presence of young larval transcriptomes in both trochozoans and other major metazoan lineages, therefore arguing against the prevailing larva-first hypothesis. Our findings support an adult-first evolutionary scenario with a single metazoan larval intercalation, and suggest that the first appearance of proto-larva probably occurred after the divergence of direct-developing Ctenophora from a metazoan ancestor.
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Affiliation(s)
- Jing Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shanshan Lian
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenkui Qin
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xuan Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Dai
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Jiankai Wei
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Pingping Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Naina Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Bo Dong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Dong
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Dexu Kong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhifeng Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Sinuo Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yu Xia
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yangping Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Liang Zhao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China. .,The Sars-Fang Centre, Ocean University of China, Qingdao, China.
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Suzuki A, Aikawa Y, Ito R, Hoshino T. Oryza sativa
Parkeol Cyclase: Changes in the Substrate‐Folding Conformation and the Deprotonation Sites on Mutation at Tyr257: Importance of the Hydroxy Group and Steric Bulk. Chembiochem 2019; 20:2862-2875. [DOI: 10.1002/cbic.201900314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Asuka Suzuki
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2-8050 Nishi-ku Niigata 950–2181 Japan
| | - Yuko Aikawa
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2-8050 Nishi-ku Niigata 950–2181 Japan
| | - Ryousuke Ito
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2-8050 Nishi-ku Niigata 950–2181 Japan
| | - Tsutomu Hoshino
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2-8050 Nishi-ku Niigata 950–2181 Japan
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Jiang J, Zhao Z, Pan Y, Dong Y, Gao S, Li S, Wang C, Yang H, Lin S, Zhou Z. Gender specific differences of immune competence in the sea cucumber Apostichopus japonicus before and after spawning. FISH & SHELLFISH IMMUNOLOGY 2019; 90:73-79. [PMID: 31022452 DOI: 10.1016/j.fsi.2019.04.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/14/2019] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
The gender differences of immunity have been elucidated in many vertebrates and invertebrates. However, the information of this difference was still not clear in the sea cucumber Apostichopus japonicus, which is one of the most valuable aquaculture species and susceptible to diseases caused by pathogen infection. In the present study, the transcriptome of coelomocytes from female and male A. japonicus before and after spawning was obtained by RNA-sequencing technology. A total of 4,538 and 8,248 differentially expressed genes were identified between female and male A. japonicus before and after spawning, respectively, indicating that the gender differences of gene expression profiles in A. japonicus were more remarkable after spawning. Further KEGG enrichment analyses were conducted for both male and female up-regulated genes before and after spawning. The results revealed that the capacity to kill pathogens in female A. japonicus might be more powerful than that in males no matter before and after spawning; the antioxidant ability in male A. japonicus was probably stronger than that in females after spawning; the complement system in male A. japonicus might be more effective than that in females after spawning; and the apoptosis was likely to be more serious in male A. japonicus before spawning. Moreover, we speculated that the fatty acid composition might be one of the inducements for gender specific immune differences of A. japonicus. Overall, the results of our study illustrated the global gender specific immune differences of A. japonicus and contributed to understanding of the molecular mechanisms underlying sea cucumber immune regulation.
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Affiliation(s)
- Jingwei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Zelong Zhao
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Yongjia Pan
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Ying Dong
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Shan Gao
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Shilei Li
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Chao Wang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Huihua Yang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Shanshan Lin
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China.
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49
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Chen M, Talarovicova A, Zheng Y, Storey KB, Elphick MR. Neuropeptide precursors and neuropeptides in the sea cucumber Apostichopus japonicus: a genomic, transcriptomic and proteomic analysis. Sci Rep 2019; 9:8829. [PMID: 31222106 PMCID: PMC6586643 DOI: 10.1038/s41598-019-45271-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/04/2019] [Indexed: 02/07/2023] Open
Abstract
The sea cucumber Apostichopus japonicus is a foodstuff with very high economic value in China, Japan and other countries in south-east Asia. It is at the heart of a multibillion-dollar industry and to meet demand for this product, aquaculture methods and facilities have been established. However, there are challenges associated with optimization of reproduction, feeding and growth in non-natural environments. Therefore, we need to learn more about the biology of A. japonicus, including processes such as aestivation, evisceration, regeneration and albinism. One of the major classes of molecules that regulate physiology and behaviour in animals are neuropeptides, and a few bioactive peptides have already been identified in A. japonicus. To facilitate more comprehensive investigations of neuropeptide function in A. japonicus, here we have analysed genomic and transcriptomic sequence data and proteomic data to identify neuropeptide precursors and neuropeptides in this species. We identified 44 transcripts encoding neuropeptide precursors or putative neuropeptide precursors, and in some instances neuropeptides derived from these precursors were confirmed by mass spectrometry. Furthermore, analysis of genomic sequence data enabled identification of the location of neuropeptide precursor genes on genomic scaffolds and linkage groups (chromosomes) and determination of gene structure. Many of the precursors identified contain homologs of neuropeptides that have been identified in other bilaterian animals. Precursors of neuropeptides that have thus far only been identified in echinoderms were identified, including L- and F-type SALMFamides, AN peptides and others. Precursors of several peptides that act as modulators of neuromuscular activity in A. japonicus were also identified. The discovery of a large repertoire of neuropeptide precursors and neuropeptides provides a basis for experimental studies that investigate the physiological roles of neuropeptide signaling systems in A. japonicus. Looking ahead, some of these neuropeptides may have effects that could be harnessed to enable improvements in the aquaculture of this economically important species.
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Affiliation(s)
- Muyan Chen
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, PR, China.
| | - Alzbeta Talarovicova
- School of Biological & Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Yingqiu Zheng
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, PR, China
| | - Kenneth B Storey
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Maurice R Elphick
- School of Biological & Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
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50
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Claereboudt EJS, Caulier G, Decroo C, Colson E, Gerbaux P, Claereboudt MR, Schaller H, Flammang P, Deleu M, Eeckhaut I. Triterpenoids in Echinoderms: Fundamental Differences in Diversity and Biosynthetic Pathways. Mar Drugs 2019; 17:E352. [PMID: 31200494 PMCID: PMC6627624 DOI: 10.3390/md17060352] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/30/2019] [Accepted: 06/04/2019] [Indexed: 02/03/2023] Open
Abstract
Echinoderms form a remarkable phylum of marine invertebrates that present specific chemical signatures unique in the animal kingdom. It is particularly the case for essential triterpenoids that evolved separately in each of the five echinoderm classes. Indeed, while most animals have Δ5-sterols, sea cucumbers (Holothuroidea) and sea stars (Asteroidea) also possess Δ7 and Δ9(11)-sterols, a characteristic not shared with brittle stars (Ophiuroidea), sea urchins (Echinoidea), and crinoids (Crinoidea). These particular Δ7 and Δ9(11) sterols emerged as a self-protection against membranolytic saponins that only sea cucumbers and sea stars produce as a defense mechanism. The diversity of saponins is large; several hundred molecules have been described in the two classes of these saponins (i.e., triterpenoid or steroid saponins). This review aims to highlight the diversity of triterpenoids in echinoderms by focusing on sterols and triterpenoid glycosides, but more importantly to provide an updated view of the biosynthesis of these molecules in echinoderms.
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Affiliation(s)
- Emily J S Claereboudt
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons-UMONS, 7000 Mons, Belgium.
- Laboratory of molecular biophysics of interfaces, Gembloux Agro-Bio Tech, University of Liege, 5030 Gembloux, Belgium.
| | - Guillaume Caulier
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons-UMONS, 7000 Mons, Belgium.
| | - Corentin Decroo
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons-UMONS, 7000 Mons, Belgium.
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry, Research Institute for Biosciences, University of Mons-UMONS, 7000 Mons, Belgium.
| | - Emmanuel Colson
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons-UMONS, 7000 Mons, Belgium.
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry, Research Institute for Biosciences, University of Mons-UMONS, 7000 Mons, Belgium.
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry, Research Institute for Biosciences, University of Mons-UMONS, 7000 Mons, Belgium.
| | - Michel R Claereboudt
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, 123 Al-Khod, Oman.
| | - Hubert Schaller
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 67084 Strasbourg Cedex, France.
| | - Patrick Flammang
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons-UMONS, 7000 Mons, Belgium.
| | - Magali Deleu
- Laboratory of molecular biophysics of interfaces, Gembloux Agro-Bio Tech, University of Liege, 5030 Gembloux, Belgium.
| | - Igor Eeckhaut
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons-UMONS, 7000 Mons, Belgium.
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