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Shimizu K, Negishi L, Kurumizaka H, Suzuki M. Diversification of von Willebrand Factor A and Chitin-Binding Domains in Pif/BMSPs Among Mollusks. J Mol Evol 2024; 92:415-431. [PMID: 38864871 PMCID: PMC11291548 DOI: 10.1007/s00239-024-10180-1] [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: 10/27/2023] [Accepted: 05/23/2024] [Indexed: 06/13/2024]
Abstract
Pif is a shell matrix protein (SMP) identified in the nacreous layer of Pinctada fucata (Pfu) comprised two proteins, Pif97 and Pif 80. Pif97 contains a von Willebrand factor A (VWA) and chitin-binding domains, whereas Pif80 can bind calcium carbonate crystals. The VWA domain is conserved in the SMPs of various mollusk species; however, their phylogenetic relationship remains obscure. Furthermore, although the VWA domain participates in protein-protein interactions, its role in shell formation has not been established. Accordingly, in the current study, we investigate the phylogenetic relationship between PfuPif and other VWA domain-containing proteins in major mollusk species. The shell-related proteins containing VWA domains formed a large clade (the Pif/BMSP family) and were classified into eight subfamilies with unique sequential features, expression patterns, and taxa diversity. Furthermore, a pull-down assay using recombinant proteins containing the VWA domain of PfuPif 97 revealed that the VWA domain interacts with five nacreous layer-related SMPs of P. fucata, including Pif 80 and nacrein. Collectively, these results suggest that the VWA domain is important in the formation of organic complexes and participates in shell mineralisation.
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Affiliation(s)
- Keisuke Shimizu
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-Cho, Yokosuka, Kanagawa, 237-0061, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan.
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2
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Sleight VA. Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation. Brief Funct Genomics 2023; 22:509-516. [PMID: 37592885 PMCID: PMC10658180 DOI: 10.1093/bfgp/elad033] [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: 05/21/2023] [Revised: 07/10/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
Biomineralisation is the process by which living organisms produce hard structures such as shells and bone. There are multiple independent origins of biomineralised skeletons across the tree of life. This review gives a glimpse into the diversity of spiralian biominerals and what they can teach us about the evolution of novelty. It discusses different levels of biological organisation that may be informative to understand the evolution of biomineralisation and considers the relationship between skeletal and non-skeletal biominerals. More specifically, this review explores if cell type and gene regulatory network approaches could enhance our understanding of the evolutionary origins of biomineralisation.
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Affiliation(s)
- Victoria A Sleight
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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3
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Ruiz-Puerta EJ, Keighley X, Desjardins SPA, Gotfredsen AB, Pan SE, Star B, Boessenkool S, Barrett JH, McCarthy ML, Andersen LW, Born EW, Howse LR, Szpak P, Pálsson S, Malmquist HJ, Rufolo S, Jordan PD, Olsen MT. Holocene deglaciation drove rapid genetic diversification of Atlantic walrus. Proc Biol Sci 2023; 290:20231349. [PMID: 37752842 PMCID: PMC10523089 DOI: 10.1098/rspb.2023.1349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/27/2023] [Indexed: 09/28/2023] Open
Abstract
Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus' response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations was initially shaped by the last glacial maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat.
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Affiliation(s)
- Emily J. Ruiz-Puerta
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- Arctic Centre & Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, PO Box 716, 9700 AS Groningen, The Netherlands
| | - Xénia Keighley
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- The Bureau of Meteorology, The Treasury Building, Parkes Place West, Parkes, Australian Capital Territory 2600, Australia
| | - Sean P. A. Desjardins
- Arctic Centre & Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, PO Box 716, 9700 AS Groningen, The Netherlands
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Anne Birgitte Gotfredsen
- Section for GeoGenetics, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen Kobenhavn, Denmark
| | - Shyong En Pan
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway
| | - James H. Barrett
- Department of Archaeology and Cultural History, NTNU University Museum, 7491 Trondheim, Norway
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Morgan L. McCarthy
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
| | - Liselotte W. Andersen
- Department of Ecoscience, Aarhus University, CF Møllers Allé 4-8, build. 1110, 8000 Aarhus C, Denmark
| | - Erik W. Born
- Greenland Institute of Natural Resources, PO Box 570, 3900 Nuuk, Greenland
| | - Lesley R. Howse
- Archaeology Centre, University of Toronto, 19 Ursula Franklin Street, Toronto, Ontario Canada M5S 2S2
| | - Paul Szpak
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, Ontario, Canada K9L 0G2
| | - Snæbjörn Pálsson
- Faculty of Life and Environmental Sciences, University of Iceland, Askja, Sturlugata 7, 101 Reykjavik, Iceland
| | - Hilmar J. Malmquist
- Icelandic Museum of Natural History, Suðurlandsbraut 24, 108 Reykjavík, Iceland
| | - Scott Rufolo
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Peter D. Jordan
- Department of Archaeology and Ancient History, Lund University, Helgonavägen 3, 223 62 Lund, Sweden
- Global Station for Indigenous Studies and Cultural Diversity (GSI), GI-CoRE, HokkaidoUniversity, Japan
| | - Morten Tange Olsen
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- Natural History Museum of Denmark, University of Copenhagen, Denmark
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4
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Khurshid B, Jackson DJ, Engilberge S, Motreuil S, Broussard C, Thomas J, Immel F, Harrington MJ, Crowley PB, Vielzeuf D, Perrin J, Marin F. Molecular characterization of accripin11, a soluble shell protein with an acidic C-terminus, identified in the prismatic layer of the Mediterranean fan mussel Pinna nobilis (Bivalvia, Pteriomorphia). FEBS Open Bio 2022; 13:10-25. [PMID: 36219517 PMCID: PMC9808598 DOI: 10.1002/2211-5463.13497] [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: 06/13/2022] [Revised: 08/23/2022] [Accepted: 10/10/2022] [Indexed: 01/07/2023] Open
Abstract
We have identified a novel shell protein, accripin11, as a major soluble component of the calcitic prisms of the fan mussel Pinna nobilis. Initially retrieved from a cDNA library, its full sequence is confirmed here by transcriptomic and proteomic approaches. The sequence of the mature protein is 103 residues with a theoretical molecular weight of 11 kDa and is moderately acidic (pI 6.74) except for its C-terminus which is highly enriched in aspartic acid. The protein exhibits a peculiar cysteine pattern in its central domain. The full sequence shares similarity with six other uncharacterized molluscan shell proteins from the orders Ostreida, Pteriida and Mytilida, all of which are pteriomorphids and produce a phylogenetically restricted pattern of nacro-prismatic shell microstructures. This suggests that accripin11 is a member of a family of clade-specific shell proteins. A 3D model of accripin11 was predicted with AlphaFold2, indicating that it possesses three short alpha helices and a disordered C-terminus. Recombinant accripin11 was tested in vitro for its ability to influence the crystallization of CaCO3 , while a polyclonal antibody was able to locate accripin11 to prismatic extracts, particularly in the acetic acid-soluble matrix. The putative functions of accripin11 are further discussed in relation to shell biomineralization.
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Affiliation(s)
- Benazir Khurshid
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance,Synchrotron SOLEILBeamline ANATOMIXGif‐sur‐YvetteFrance
| | | | - Sylvain Engilberge
- Structural Biology GroupEuropean Synchrotron Radiation FacilityGrenobleFrance
| | - Sébastien Motreuil
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance
| | | | - Jérôme Thomas
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance
| | - Françoise Immel
- Chrono‐Environnement, UMR 6249 CNRSUniversité de Bourgogne Franche‐ComtéBesançonFrance
| | | | - Peter B. Crowley
- School of Biological and Chemical SciencesNational University of IrelandGalwayIreland
| | | | | | - Frédéric Marin
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance
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5
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Cavallo A, Clark MS, Peck LS, Harper EM, Sleight VA. Evolutionary conservation and divergence of the transcriptional regulation of bivalve shell secretion across life-history stages. ROYAL SOCIETY OPEN SCIENCE 2022; 9:221022. [PMID: 36569229 PMCID: PMC9768464 DOI: 10.1098/rsos.221022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/13/2022] [Indexed: 06/17/2023]
Abstract
Adult molluscs produce shells with diverse morphologies and ornamentations, different colour patterns and microstructures. The larval shell, however, is a phenotypically more conserved structure. How do developmental and evolutionary processes generate varying diversity at different life-history stages within a species? Using live imaging, histology, scanning electron microscopy and transcriptomic profiling, we have described shell development in a heteroconchian bivalve, the Antarctic clam, Laternula elliptica, and compared it to adult shell secretion processes in the same species. Adult downstream shell genes, such as those encoding extracellular matrix proteins and biomineralization enzymes, were largely not expressed during shell development. Instead, a development-specific downstream gene repertoire was expressed. Upstream regulatory genes such as transcription factors and signalling molecules were largely conserved between developmental and adult shell secretion. Comparing heteroconchian data with recently reported pteriomorphian larval shell development data suggests that, despite being phenotypically more conserved, the downstream effectors constituting the larval shell 'tool-kit' may be as diverse as that of adults. Overall, our new data suggest that a larval shell formed using development-specific downstream effector genes is a conserved and ancestral feature of the bivalve lineage, and possibly more broadly across the molluscs.
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Affiliation(s)
- Alessandro Cavallo
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge CB3 0ET, UK
| | - Melody S. Clark
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge CB3 0ET, UK
| | - Lloyd S. Peck
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge CB3 0ET, UK
| | - Elizabeth M. Harper
- Department of Earth Sciences, University of Cambridge, Cambridge CB2 1TN, UK
| | - Victoria A. Sleight
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge CB3 0ET, UK
- Department of Zoology, University of Cambridge, Cambridge CB2 1TN, UK
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK
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6
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Gouveia N, Oliveira AJLA, Yokota Harayashiki CA, Souza JC, Longo E, Cano NF, Maltez HF, Lourenço RA, Turpo-Huahuasoncco KV, Castro ÍB. Chemical contamination in coastal areas alters shape, resistance and composition of carnivorous gastropod shells. CHEMOSPHERE 2022; 307:135926. [PMID: 35934096 DOI: 10.1016/j.chemosphere.2022.135926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/28/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Morphological, structural and compositional alterations in shells of molluscs have been proposed as putative biomarkers of chemical contamination in coastal zones. Despite this, few studies were carried out using top predator gastropods which tend to be more susceptible to contamination exposure. Thus, the present study assessed disturbances on shells of Stramonita brasiliensis considering compression resistance and organic and mineralogical matrix composition, related to morphometric alterations. Results showed reductions in compression resistance and organic matrix content associated with higher contaminated sites. In addition, a predominance of calcite polymorphs was seen in shells obtained in polluted areas. Such outputs were consistent with local contamination levels which may have induced the observed alterations. Thus, changes in mollusc shells showed good performance as potential biomarkers of coastal contamination, being probably observed in other species of carnivorous gastropods around the world.
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Affiliation(s)
- Nayara Gouveia
- Instituto do Mar, Universidade Federal de São Paulo (IMAR-UNIFESP), Santos, Brazil
| | | | | | - Josiane Carneiro Souza
- Centro de Desenvolvimento de Materiais Funcionais (CDMF), Departamento de Química, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Elson Longo
- Centro de Desenvolvimento de Materiais Funcionais (CDMF), Departamento de Química, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Nilo F Cano
- Instituto do Mar, Universidade Federal de São Paulo (IMAR-UNIFESP), Santos, Brazil
| | - Heloisa França Maltez
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Rafael André Lourenço
- Instituto Oceanográfico, Universidade de São Paulo (IO-USP), Cidade Universitária, São Paulo, 05508-120, Brazil
| | - Klinton V Turpo-Huahuasoncco
- Escuela Profesional de Física, Facultad de Ciencias Naturales y Formales, Universidad Nacional de San Agustín de Arequipa (UNSA), Arequipa, Peru
| | - Ítalo Braga Castro
- Instituto do Mar, Universidade Federal de São Paulo (IMAR-UNIFESP), Santos, Brazil.
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7
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Yuan J, Zhang X, Li S, Liu C, Yu Y, Zhang X, Xiang J, Li F. Convergent evolution of barnacles and molluscs sheds lights in origin and diversification of calcareous shell and sessile lifestyle. Proc Biol Sci 2022; 289:20221535. [PMID: 36100022 PMCID: PMC9470267 DOI: 10.1098/rspb.2022.1535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 08/22/2022] [Indexed: 11/12/2022] Open
Abstract
The calcareous shell and sessile lifestyle are the representative phenotypes of many molluscs, which happen to be present in barnacles, a group of unique crustaceans. The origin of these phenotypes is unclear, but it may be embodied in the convergent genetics of such distant groups (interphylum). Herein, we perform comprehensive comparative genomics analysis in barnacles and molluscs, and reveal a genome-wide strong convergent molecular evolution between them, including coexpansion of biomineralization and organic matrix genes for shell formation, and origination of lineage-specific orphan genes for settlement. Notably, the expanded biomineralization gene encoding alkaline phosphatase evolves a novel, highly conserved motif that may trigger the origin of barnacle shell formation. Unlike molluscs, barnacles adopt novel organic matrices and cement proteins for shell formation and settlement, respectively, and their calcareous shells have potentially originated from the cuticle system of crustaceans. Therefore, our study corroborates the idea that selection pressures driving convergent evolution may strongly act in organisms inhabiting similar environments regardless of phylogenetic distance. The convergence signatures shed light on the origin of the shell and sessile lifestyle of barnacles and molluscs. In addition, notable non-convergence signatures are also present and may contribute to morphological and functional specificities.
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Affiliation(s)
- Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, 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, 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
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, 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
| | - Chengzhang Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, 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
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, 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
| | - Xiaoxi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, 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, 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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8
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Schwaner C, Farhat S, Haley J, Pales Espinosa E, Allam B. Transcriptomic, Proteomic, and Functional Assays Underline the Dual Role of Extrapallial Hemocytes in Immunity and Biomineralization in the Hard Clam Mercenaria mercenaria. Front Immunol 2022; 13:838530. [PMID: 35273613 PMCID: PMC8902148 DOI: 10.3389/fimmu.2022.838530] [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: 12/17/2021] [Accepted: 01/28/2022] [Indexed: 12/13/2022] Open
Abstract
Circulating hemocytes in the hemolymph represent the backbone of innate immunity in bivalves. Hemocytes are also found in the extrapallial fluid (EPF), the space delimited between the shell and the mantle, which is the site of shell biomineralization. This study investigated the transcriptome, proteome, and function of EPF and hemolymph in the hard clam Mercenaria mercenaria. Total and differential hemocyte counts were similar between EPF and hemolymph. Overexpressed genes in the EPF were found to have domains previously identified as being part of the "biomineralization toolkit" and involved in bivalve shell formation. Biomineralization related genes included chitin-metabolism genes, carbonic anhydrase, perlucin, and insoluble shell matrix protein genes. Overexpressed genes in the EPF encoded proteins present at higher abundances in the EPF proteome, specifically those related to shell formation such as carbonic anhydrase and insoluble shell matrix proteins. Genes coding for bicarbonate and ion transporters were also overexpressed, suggesting that EPF hemocytes are involved in regulating the availability of ions critical for biomineralization. Functional assays also showed that Ca2+ content of hemocytes in the EPF were significantly higher than those in hemolymph, supporting the idea that hemocytes serve as a source of Ca2+ during biomineralization. Overexpressed genes and proteins also contained domains such as C1q that have dual functions in biomineralization and immune response. The percent of phagocytic granulocytes was not significantly different between EPF and hemolymph. Together, these findings suggest that hemocytes in EPF play a central role in both biomineralization and immunity.
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Affiliation(s)
- Caroline Schwaner
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Sarah Farhat
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - John Haley
- Stony Brook University Biological Mass Spectrometry Center, Stony Brook Medicine, Stony Brook, NY, United States
| | | | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
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9
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First Insights into the Repertoire of Secretory Lectins in Rotifers. Mar Drugs 2022; 20:md20020130. [PMID: 35200659 PMCID: PMC8878817 DOI: 10.3390/md20020130] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 02/06/2023] Open
Abstract
Due to their high biodiversity and adaptation to a mutable and challenging environment, aquatic lophotrochozoan animals are regarded as a virtually unlimited source of bioactive molecules. Among these, lectins, i.e., proteins with remarkable carbohydrate-recognition properties involved in immunity, reproduction, self/nonself recognition and several other biological processes, are particularly attractive targets for biotechnological research. To date, lectin research in the Lophotrochozoa has been restricted to the most widespread phyla, which are the usual targets of comparative immunology studies, such as Mollusca and Annelida. Here we provide the first overview of the repertoire of the secretory lectin-like molecules encoded by the genomes of six target rotifer species: Brachionus calyciflorus, Brachionus plicatilis, Proales similis (class Monogononta), Adineta ricciae, Didymodactylos carnosus and Rotaria sordida (class Bdelloidea). Overall, while rotifer secretory lectins display a high molecular diversity and belong to nine different structural classes, their total number is significantly lower than for other groups of lophotrochozoans, with no evidence of lineage-specific expansion events. Considering the high evolutionary divergence between rotifers and the other major sister phyla, their widespread distribution in aquatic environments and the ease of their collection and rearing in laboratory conditions, these organisms may represent interesting targets for glycobiological studies, which may allow the identification of novel carbohydrate-binding proteins with peculiar biological properties.
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10
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Setiamarga DHE, Hirota K, Yoshida MA, Takeda Y, Kito K, Ishikawa M, Shimizu K, Isowa Y, Ikeo K, Sasaki T, Endo K. Hydrophilic Shell Matrix Proteins of Nautilus pompilius and the Identification of a Core Set of Conchiferan Domains. Genes (Basel) 2021; 12:genes12121925. [PMID: 34946873 PMCID: PMC8700984 DOI: 10.3390/genes12121925] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 02/05/2023] Open
Abstract
Despite being a member of the shelled mollusks (Conchiferans), most members of extant cephalopods have lost their external biomineralized shells, except for the basally diverging Nautilids. Here, we report the result of our study to identify major Shell Matrix Proteins and their domains in the Nautilid Nautilus pompilius, in order to gain a general insight into the evolution of Conchiferan Shell Matrix Proteins. In order to do so, we performed a multiomics study on the shell of N. pompilius, by conducting transcriptomics of its mantle tissue and proteomics of its shell matrix. Analyses of obtained data identified 61 distinct shell-specific sequences. Of the successfully annotated 27 sequences, protein domains were predicted in 19. Comparative analysis of Nautilus sequences with four Conchiferans for which Shell Matrix Protein data were available (the pacific oyster, the pearl oyster, the limpet and the Euhadra snail) revealed that three proteins and six protein domains were conserved in all Conchiferans. Interestingly, when the terrestrial Euhadra snail was excluded, another five proteins and six protein domains were found to be shared among the four marine Conchiferans. Phylogenetic analyses indicated that most of these proteins and domains were probably present in the ancestral Conchiferan, but employed in shell formation later and independently in most clades. Even though further studies utilizing deeper sequencing techniques to obtain genome and full-length sequences, and functional analyses, must be carried out in the future, our results here provide important pieces of information for the elucidation of the evolution of Conchiferan shells at the molecular level.
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Affiliation(s)
- Davin H. E. Setiamarga
- Department of Applied Chemistry and Biochemistry, National Institute of Technology (KOSEN), Wakayama College, Gobo 644-0023, Japan;
- Graduate School of Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; (M.I.); (K.S.); (Y.I.); (K.E.)
- The University Museum, The University of Tokyo, Tokyo 113-0033, Japan; (Y.T.); (T.S.)
- Correspondence:
| | - Kazuki Hirota
- Department of Applied Chemistry and Biochemistry, National Institute of Technology (KOSEN), Wakayama College, Gobo 644-0023, Japan;
- Graduate School of Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; (M.I.); (K.S.); (Y.I.); (K.E.)
| | - Masa-aki Yoshida
- Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Science, Shimane University, Unnan 685-0024, Japan;
| | - Yusuke Takeda
- The University Museum, The University of Tokyo, Tokyo 113-0033, Japan; (Y.T.); (T.S.)
- Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Keiji Kito
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan;
| | - Makiko Ishikawa
- Graduate School of Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; (M.I.); (K.S.); (Y.I.); (K.E.)
- Faculty of Animal Health Technology, Yamazaki University of Animal Health Technology, Hachiouji 192-0364, Japan
| | - Keisuke Shimizu
- Graduate School of Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; (M.I.); (K.S.); (Y.I.); (K.E.)
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Yayoi, Tokyo 113-8657, Japan
| | - Yukinobu Isowa
- Graduate School of Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; (M.I.); (K.S.); (Y.I.); (K.E.)
- Shimoda Marine Research Center, University of Tsukuba, Shimoda 415-0025, Japan
| | - Kazuho Ikeo
- Center for Information Biology, National Institute of Genetics, Mishima 411-8540, Japan;
| | - Takenori Sasaki
- The University Museum, The University of Tokyo, Tokyo 113-0033, Japan; (Y.T.); (T.S.)
| | - Kazuyoshi Endo
- Graduate School of Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; (M.I.); (K.S.); (Y.I.); (K.E.)
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11
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Chandra Rajan K, Meng Y, Yu Z, Roberts SB, Vengatesen T. Oyster biomineralization under ocean acidification: From genes to shell. GLOBAL CHANGE BIOLOGY 2021; 27:3779-3797. [PMID: 33964098 DOI: 10.1111/gcb.15675] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/02/2021] [Indexed: 05/27/2023]
Abstract
Biomineralization is one of the key processes that is notably affected in marine calcifiers such as oysters under ocean acidification (OA). Understanding molecular changes in the biomineralization process under OA and its heritability, therefore, is key to developing conservation strategies for protecting ecologically and economically important oyster species. To do this, in this study, we have explicitly chosen the tissue involved in biomineralization (mantle) of an estuarine commercial oyster species, Crassostrea hongkongensis. The primary aim of this study is to understand the influence of DNA methylation over gene expression of mantle tissue under decreased ~pH 7.4, a proxy of OA, and to extrapolate if these molecular changes can be observed in the product of biomineralization-the shell. We grew early juvenile C. hongkongensis, under decreased ~pH 7.4 and control ~pH 8.0 over 4.5 months and studied OA-induced DNA methylation and gene expression patterns along with shell properties such as microstructure, crystal orientation and hardness. The population of oysters used in this study was found to be moderately resilient to OA at the end of the experiment. The expression of key biomineralization-related genes such as carbonic anhydrase and alkaline phosphatase remained unaffected; thus, the mechanical properties of the shell (shell growth rate, hardness and crystal orientation) were also maintained without any significant difference between control and OA conditions with signs of severe dissolution. In addition, this study makes three major conclusions: (1) higher expression of Ca2+ binding/signalling-related genes in the mantle plays a key role in maintaining biomineralization under OA; (2) DNA methylation changes occur in response to OA; however, these methylation changes do not directly control gene expression; and (3) OA would be more of a 'dissolution problem' rather than a 'biomineralization problem' for resilient species that maintain calcification rate with normal shell growth and mechanical properties.
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Affiliation(s)
- Kanmani Chandra Rajan
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Yuan Meng
- State Key Laboratory of Respiratory Disease, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ziniu Yu
- South China Sea Institute of Oceanology, Guangzhou, China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Thiyagarajan Vengatesen
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
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12
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Takeuchi T, Fujie M, Koyanagi R, Plasseraud L, Ziegler-Devin I, Brosse N, Broussard C, Satoh N, Marin F. The 'Shellome' of the Crocus Clam Tridacna crocea Emphasizes Essential Components of Mollusk Shell Biomineralization. Front Genet 2021; 12:674539. [PMID: 34168677 PMCID: PMC8217771 DOI: 10.3389/fgene.2021.674539] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/13/2021] [Indexed: 01/31/2023] Open
Abstract
Molluscan shells are among the most fascinating research objects because of their diverse morphologies and textures. The formation of these delicate biomineralized structures is a matrix-mediated process. A question that arises is what are the essential components required to build these exoskeletons. In order to understand the molecular mechanisms of molluscan shell formation, it is crucial to identify organic macromolecules in different shells from diverse taxa. In the case of bivalves, however, taxon sampling in previous shell proteomics studies are focused predominantly on representatives of the class Pteriomorphia such as pearl oysters, edible oysters and mussels. In this study, we have characterized the shell organic matrix from the crocus clam, Tridacna crocea, (Heterodonta) using various biochemical techniques, including SDS-PAGE, FT-IR, monosaccharide analysis, and enzyme-linked lectin assay (ELLA). Furthermore, we have identified a number of shell matrix proteins (SMPs) using a comprehensive proteomics approach combined to RNA-seq. The biochemical studies confirmed the presence of proteins, polysaccharides, and sulfates in the T. crocea shell organic matrix. Proteomics analysis revealed that the majority of the T. crocea SMPs are novel and dissimilar to known SMPs identified from the other bivalve species. Meanwhile, the SMP repertoire of the crocus clam also includes proteins with conserved functional domains such as chitin-binding domain, VWA domain, and protease inhibitor domain. We also identified BMSP (Blue Mussel Shell Protein, originally reported from Mytilus), which is widely distributed among molluscan shell matrix proteins. Tridacna SMPs also include low-complexity regions (LCRs) that are absent in the other molluscan genomes, indicating that these genes may have evolved in specific lineage. These results highlight the diversity of the organic molecules – in particular proteins – that are essential for molluscan shell formation.
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Affiliation(s)
- Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Ryo Koyanagi
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Laurent Plasseraud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, UMR CNRS 6302, Faculté des Sciences Mirande, Université de Bourgogne - Franche-Comté (UBFC), Dijon, France
| | - Isabelle Ziegler-Devin
- LERMAB, Faculté des Sciences et Technologies - Campus Aiguillettes, Université de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Nicolas Brosse
- LERMAB, Faculté des Sciences et Technologies - Campus Aiguillettes, Université de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Cédric Broussard
- 3P5 Proteomic Platform, Cochin Institute, University of Paris, INSERM U1016, CNRS UMR 8104, Paris, France
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Frédéric Marin
- UMR CNRS 6282 Biogéosciences, Bâtiment des Sciences Gabriel, Université de Bourgogne - Franche-Comté (UBFC), Dijon, France
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13
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Abstract
Mollusc shells are a result of the deposition of crystalline and amorphous calcite catalysed by enzymes and shell matrix proteins. Developing a detailed understanding of bivalve mollusc biomineralization pathways is complicated not only by the multiplicity of shell forms and microstructures in this class, but also by the evolution of associated proteins by domain co-option and domain shuffling. In spite of this, a minimal biomineralization toolbox comprising proteins and protein domains critical for shell production across species has been identified. Using a matched pair design to reduce experimental noise from inter-individual variation, combined with damage-repair experiments and a database of biomineralization shell matrix proteins (SMP) derived from published works, proteins were identified that are likely to be involved in shell calcification. Eighteen new, shared proteins likely to be involved in the processes related to the calcification of shells were identified by analysis of genes expressed during repair in Crassostrea gigas, Mytilus edulis and Pecten maximus. Genes involved in ion transport were also identified as potentially involved in calcification either via the maintenance of cell acid-base balance or transport of critical ions to the extrapallial space, the site of shell assembly. These data expand the number of candidate biomineralization proteins in bivalve molluscs for future functional studies and define a minimal functional protein domain set required to produce solid microstructures from soluble calcium carbonate. This is important for understanding molluscan shell evolution, the likely impacts of environmental change on biomineralization processes, materials science, and biomimicry research.
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Affiliation(s)
- Tejaswi Yarra
- University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK.,British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Mark Blaxter
- Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
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14
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F-Type Lectins: Structure, Function, and Evolution. Methods Mol Biol 2021. [PMID: 32306331 DOI: 10.1007/978-1-0716-0430-4_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
F-type lectins (FTLs) are characterized by a fucose recognition domain (F-type lectin domain; FTLD) that displays a novel jellyroll fold ("F-type" fold) and unique carbohydrate- and calcium-binding sequence motifs. This novel lectin family comprises widely distributed proteins exhibiting single, double, or greater multiples of the FTLD, either tandemly arrayed or combined with other structurally and functionally distinct domains. Further, differences in carbohydrate specificity among tandemly arrayed FTLDs present in any FTL polypeptide subunit, together with the expression of multiple FTL isoforms in a single individual supports a striking diversity in ligand recognition. Functions of FTLs in self/nonself recognition include innate immunity, fertilization, microbial adhesion, and pathogenesis, among others, revealing an extensive structural/functional diversification. The taxonomic distribution of FTLDs is surprisingly discontinuous, suggesting that this lectin family has been subject to secondary loss, lateral transfer, and functional co-option along evolutionary lineages.
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15
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Liu C, Zhang R. Biomineral proteomics: A tool for multiple disciplinary studies. J Proteomics 2021; 238:104171. [PMID: 33652138 DOI: 10.1016/j.jprot.2021.104171] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/06/2021] [Accepted: 02/21/2021] [Indexed: 12/11/2022]
Abstract
The hard tissues of animals, such as skeletons and teeth, are constructed by a biologically controlled process called biomineralization. In invertebrate animals, biominerals are considered important for their evolutionary success. These biominerals are hieratical biocomposites with excellent mechanical properties, and their formation has intrigued researchers for decades. Although proteins account for ~5 wt% of biominerals, they are critical players in biomineralization. With the development of high-throughput analysis methods, such as proteomics, biomineral protein data are rapidly accumulating, thus necessitating a refined model for biomineralization. This review focuses on biomineral proteomics in invertebrate animals to highlight the diversity of biomineral proteins (generally 40-80 proteins), and the results indicate that biomineralization includes thermodynamic crystal growth as well as intense extracellular matrix activity and/or vesicle transport. Biominerals have multiple functions linked to biological immunity and antipathogen activity. A comparison of proteomes across species and biomineral types showed that von Willebrand factor type A and epidermal growth factor, which frequently couple with other extracellular domains, are the most common domains. Combined with species-specific repetitive low complexity domains, shell matrix proteins can be employed to predict biomineral types. Furthermore, this review discusses the applications of biomineral proteomics in diverse fields, such as tissue regeneration, developmental biology, archeology, environmental science, and material science.
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Affiliation(s)
- Chuang Liu
- College of Oceanography, Hohai University, Xikang Road, Nanjing, Jiangsu 210098, China.
| | - Rongqing Zhang
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, 705 Yatai Road, Jiaxing 314006, PR China; College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China.
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16
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McDougall C, Aguilera F, Shokoohmand A, Moase P, Degnan BM. Pearl Sac Gene Expression Profiles Associated With Pearl Attributes in the Silver-Lip Pearl Oyster, Pinctada maxima. Front Genet 2021; 11:597459. [PMID: 33488672 PMCID: PMC7820862 DOI: 10.3389/fgene.2020.597459] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/07/2020] [Indexed: 11/21/2022] Open
Abstract
Pearls are highly prized biomineralized gemstones produced by molluscs. The appearance and mineralogy of cultured pearls can vary markedly, greatly affecting their commercial value. To begin to understand the role of pearl sacs—organs that form in host oysters from explanted mantle tissues that surround and synthesize pearls—we undertook transcriptomic analyses to identify genes that are differentially expressed in sacs producing pearls with different surface and structural characteristics. Our results indicate that gene expression profiles correlate with different pearl defects, suggesting that gene regulation in the pearl sac contributes to pearl appearance and quality. For instance, pearl sacs that produced pearls with surface non-lustrous calcification significantly down-regulate genes associated with cilia and microtubule function compared to pearl sacs giving rise to lustrous pearls. These results suggest that gene expression profiling can advance our understanding of processes that control biomineralization, which may be of direct value to the pearl industry, particularly in relation to defects that result in low value pearls.
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Affiliation(s)
- Carmel McDougall
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia.,Australian Rivers Institute, Griffith University, Nathan, QLD, Australia
| | - Felipe Aguilera
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Ali Shokoohmand
- Australian Rivers Institute, Griffith University, Nathan, QLD, Australia
| | - Patrick Moase
- Clipper Pearls and Autore Pearling, Broome, WA, Australia
| | - Bernard M Degnan
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
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17
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Harayashiki CAY, Márquez F, Cariou E, Castro ÍB. Mollusk shell alterations resulting from coastal contamination and other environmental factors. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114881. [PMID: 32505962 DOI: 10.1016/j.envpol.2020.114881] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/13/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Effects of contamination on aquatic organisms have been investigated and employed as biomarkers in environmental quality assessment for years. A commonly referenced aquatic organism, mollusks represent a group of major interest in toxicological studies. Both gastropods and bivalves have external mineral shells that protects their soft tissue from predation and desiccation. These structures are composed of an organic matrix and an inorganic matrix, both of which are affected by environmental changes, including exposure to hazardous chemicals. This literature review evaluates studies that propose mollusk shell alterations as biomarkers of aquatic system quality. The studies included herein show that changes to natural variables such as salinity, temperature, food availability, hydrodynamics, desiccation, predatory pressure, and substrate type may influence the form, structure, and composition of mollusk shells. However, in the spatial and temporal studies performed in coastal waters around the world, shells of organisms sampled from multi-impacted areas were found to differ in the form and composition of both organic and inorganic matrices relative to shells from less contaminated areas. Though these findings are useful, the toxicological studies were often performed in the field and were not able to attribute shell alterations to a specific molecule. It is known that the organic matrix of shells regulates the biomineralization process; proteomic analyses of shells may therefore elucidate how different contaminants affect shell biomineralization. Further research using approaches that allow a clearer distinction between shell alterations caused by natural variations and those caused by anthropogenic influence, as well as studies to identify which molecule is responsible for such alterations or to determine the ecological implications of shell alterations, are needed before any responses can be applied universally.
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Affiliation(s)
- Cyntia Ayumi Yokota Harayashiki
- Departamento de Ciências do Mar, Universidade Federal de São Paulo (UNIFESP), Rua Carvalho de Mendonça 144, CEP, 11070-100, Santos, Brazil.
| | - Federico Márquez
- LARBIM - IBIOMAR. CCT CONICET-CENPAT, Bvd. Brown 2915, U9120ACV, Puerto Madryn, Chubut, Argentina; Facultad de Ciencias Naturales, Universidad Nacional de La Patagonia San Juan Bosco (UNPSJB), Bvd. Brown 3051, U9120ACV, Puerto Madryn, Chubut, Argentina
| | - Elsa Cariou
- Observatory of Universe Sciences of Nantes-Atlantique, University of Nantes, Campus Lombarderie, 2 Rue de La Houssinière, 44322, Nantes, France
| | - Ítalo Braga Castro
- Departamento de Ciências do Mar, Universidade Federal de São Paulo (UNIFESP), Rua Carvalho de Mendonça 144, CEP, 11070-100, Santos, Brazil
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18
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Marin F. Mollusc shellomes: Past, present and future. J Struct Biol 2020; 212:107583. [PMID: 32721585 DOI: 10.1016/j.jsb.2020.107583] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/19/2020] [Accepted: 07/21/2020] [Indexed: 01/31/2023]
Abstract
In molluscs, the shell fabrication requires a large array of secreted macromolecules including proteins and polysaccharides. Some of them are occluded in the shell during mineralization process and constitute the shell repertoire. The protein moieties, also called shell proteomes or, more simply, 'shellomes', are nowadays analyzed via high-throughput approaches. These latter, applied so far on about thirty genera, have evidenced the huge diversity of shellomes from model to model. They also pinpoint the recurrent presence of functional domains of diverse natures. Shell proteins are not only involved in guiding the mineral deposition, but also in enzymatic and immunity-related functions, in signaling or in coping with many extracellular molecules such as saccharides. Many shell proteins exhibit low complexity domains, the function of which remains unclear. Shellomes appear as self-organizing systems that must be approached from the point of view of complex systems biology: at supramolecular level, they generate emergent properties, i.e., microstructures that cannot be simply explained by the sum of their parts. A conceptual scheme is developed here that reconciles the plasticity of the shellome, its evolvability and the constrained frame of microstructures. Other perspectives arising from the study of shellomes are briefly discussed, including the macroevolution of shell repertoires, their maturation and their transformation through time.
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Affiliation(s)
- Frédéric Marin
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne - Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France
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19
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Ishikawa A, Shimizu K, Isowa Y, Takeuchi T, Zhao R, Kito K, Fujie M, Satoh N, Endo K. Functional shell matrix proteins tentatively identified by asymmetric snail shell morphology. Sci Rep 2020; 10:9768. [PMID: 32555253 PMCID: PMC7299971 DOI: 10.1038/s41598-020-66021-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 05/13/2020] [Indexed: 12/21/2022] Open
Abstract
Molluscan shell matrix proteins (SMPs) are essential in biomineralization. Here, we identify potentially important SMPs by exploiting the asymmetric shell growth in snail, Lymnaea stagnalis. Asymmetric shells require bilaterally asymmetric expression of SMP genes. We examined expression levels of 35,951 transcripts expressed in the left and right sides of mantle tissue of the pond snail, Lymnaea stagnalis. This transcriptome dataset was used to identify 207 SMPs by LC-MS/MS. 32 of the 207 SMP genes show asymmetric expression patterns, which were further verified for 4 of the 32 SMPs using quantitative PCR analysis. Among asymmetrically expressed SMPs in dextral snails, those that are more highly expressed on the left side than the right side are 3 times more abundant than those that are more highly expressed on the right than the left, suggesting potentially inhibitory roles of SMPs in shell formation. The 32 SMPs thus identified have distinctive features, such as conserved domains and low complexity regions, which may be essential in biomineralization.
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Affiliation(s)
- Akito Ishikawa
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan.
| | - Keisuke Shimizu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Yukinobu Isowa
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, 429-63 Sugashima, Toba, Mie, 517-0004, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Ran Zhao
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Keiji Kito
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama, Kawasaki, Kanagawa, 214-8571, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Kazuyoshi Endo
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan.
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20
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Sun Q, Jiang Y, Fan M, Zhang X, Xu H, Liao Z. Characterization of a novel shell matrix protein with vWA domain from Mytilus coruscus. Biosci Biotechnol Biochem 2020; 84:1629-1644. [PMID: 32314940 DOI: 10.1080/09168451.2020.1756735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Mollusk shell is a product of biomineralization with excellent mechanical properties, and the shell matrix proteins (SMPs) have important functions in shell formation. A vWA domain-containing protein (VDCP) was identified from the shell of Mytilus coruscus as a novel shell matrix protein. The VDCP gene is expressed at a high level in specific locations in the mantle and adductor muscle. Recombinant VDCP (rVDCP) showed abilities to alter the morphology of both calcite and aragonite, induce the polymorph change of calcite, bind calcite, and decrease the crystallization rate of calcite. In addition, immunohistochemistry analyses revealed the specific location of VDCP in the mantle, the adductor muscle, and the myostracum layer of the shell. Furthermore, a pull-down analysis revealed eight protein interaction partners of VDCP in shell matrices and provided a possible protein-protein interaction network of VDCP in the shell.
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Affiliation(s)
- Qi Sun
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University , Zhoushan City, Zhejiang, China
| | - Yuting Jiang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University , Zhoushan City, Zhejiang, China
| | - Meihua Fan
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University , Zhoushan City, Zhejiang, China
| | - Xiaolin Zhang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University , Zhoushan City, Zhejiang, China
| | - Huanzhi Xu
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University , Zhoushan City, Zhejiang, China
| | - Zhi Liao
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University , Zhoushan City, Zhejiang, China
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21
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Zheng Z, Li W, Xu J, Xie B, Yang M, Huang H, Li H, Wang Q. LncMSEN1, a mantle-specific LncRNA participating in nacre formation and response to polyI:C stimulation in pearl oyster Pinctada fucata martensii. FISH & SHELLFISH IMMUNOLOGY 2020; 96:330-335. [PMID: 31830566 DOI: 10.1016/j.fsi.2019.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/02/2019] [Accepted: 12/08/2019] [Indexed: 06/10/2023]
Abstract
Long noncoding RNA (LncRNA) regulates various life processes, including biomineralization and innate immune response through complex mechanisms. In this research, we identified a LncRNA named LncMSEN1 from pearl oyster Pinctada fucata martensii. LncMSEN1 sequence was validated by PCR, and its expression was high in mantle tissues according to qRT-PCR. LncMSEN1 was co-located with the nacre matrix protein N-U8 and fibrinogen domain-containing protein. And LncMSEN1 and N-U8 expression levels in the mantle were positively correlated. RNA interference was used to detect its effect on nacre formation in shells. Results showed that the decreased LncMSEN1 expression in mantle can cause the disordered growth of crystals on the inner surface of nacre in the shells, as well as the decrease expression of N-U8. In addition, the LncMSEN1 expression level significantly increased at 24 h after polyI:C stimulation in the mantle (P < 0.05). These findings suggested the involvement of LncMSEN1 in the formation of nacre in shells and related to innate immune response in pearl oyster, which provided additional insights into the roles of LncRNAs in pearl oysters.
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Affiliation(s)
- Zhe Zheng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Wenhui Li
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Jiehua Xu
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Bingyi Xie
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Modong Yang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Huajie Huang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Huishan Li
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Qingheng Wang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China.
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Feng D, Li Q, Yu H. RNA Interference by Ingested dsRNA-Expressing Bacteria to Study Shell Biosynthesis and Pigmentation in Crassostrea gigas. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:526-536. [PMID: 31093810 DOI: 10.1007/s10126-019-09900-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/16/2019] [Indexed: 06/09/2023]
Abstract
RNA interference (RNAi) is an important molecular tool for analysis of gene function in vivo. Although the Pacific oyster Crassostrea gigas is an economically important species with fully sequenced genome, very few mechanistic studies have been carried out due to the lack of molecular techniques to alter gene expression without inducing stress. In this present study, we used unicellular alga Platymonas subcordiformis and Nitzschia closterium f. minutissima as a vector to feed oysters with Escherichia coli strain HT115 engineered to express double-stranded RNAs (dsRNAs) targeting specific genes involved in shell pigmentation. A C. gigas strain with black shell was used to target tyrosinase or peroxidase gene expression by RNAi using the above-mentioned approach. The results showed that feeding oyster with dsRNA of tyrosinase could knock down the expression of corresponding tyrosinase and hinder the developed shell growth. Feeding oyster with dsRNA of peroxidase could knock down the expression of the corresponding peroxidase and result in reduced black pigmentation in the newly developed shell. This non-invasive RNAi study demonstrated that tyrosinase played a vital role in the assembly and maturation of shell matrices and peroxidase was essential for black pigmentation in the shell. Moreover, the RNA interference by ingested dsRNA-expressing bacteria is a relatively simple and effective method for knockdown of a gene expression in adult oysters, thus further advances the use of C. gigas as model organism in functional genomic studies.
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Affiliation(s)
- Dandan Feng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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Liao Z, Jiang YT, Sun Q, Fan MH, Wang JX, Liang HY. Microstructure and in-depth proteomic analysis of Perna viridis shell. PLoS One 2019; 14:e0219699. [PMID: 31323046 PMCID: PMC6641155 DOI: 10.1371/journal.pone.0219699] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/28/2019] [Indexed: 12/20/2022] Open
Abstract
For understanding the structural characteristics and the proteome of Perna shell, the microstructure, polymorph, and protein composition of the adult Perna viridis shell were investigated. The P. viridis shell have two distinct mineral layers, myostracum and nacre, with the same calcium carbonate polymorph of aragonite, determined by scanning electron microscope, Fourier transform infrared spectroscopy, and x-ray crystalline diffraction. Using Illumina sequencing, the mantle transcriptome of P. viridis was investigated and a total of 69,859 unigenes was generated. Using a combined proteomic/transcriptomic approach, a total of 378 shell proteins from P. viridis shell were identified, in which, 132 shell proteins identified with more than two matched unique peptides. Of the 132 shell proteins, 69 are exclusive to the nacre, 12 to the myostracum, and 51 are shared by both. The Myosin-tail domain containing proteins, Filament-like proteins, and Chitin-binding domain containing proteins represent the most abundant molecules. In addition, the shell matrix proteins (SMPs) containing biomineralization-related domains, such as Kunitz, A2M, WAP, EF-hand, PDZ, VWA, Collagen domain, and low complexity regions with abundant certain amino acids, were also identified from P. viridis shell. Collagenase and chitinase degradation can significantly change the morphology of the shell, indicating the important roles of collagen and chitin in the shell formation and the muscle-shell attachment. Our results present for the first time the proteome of P. viridis shell and increase the knowledge of SMPs in this genus.
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Affiliation(s)
- Zhi Liao
- Laboratory of Marine Biological Source and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, Zhejiang, P.R. China
| | - Yu-ting Jiang
- Laboratory of Marine Biological Source and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, Zhejiang, P.R. China
| | - Qi Sun
- Laboratory of Marine Biological Source and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, Zhejiang, P.R. China
| | - Mei-hua Fan
- Laboratory of Marine Biological Source and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, Zhejiang, P.R. China
| | - Jian-xin Wang
- Laboratory of Marine Biological Source and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, Zhejiang, P.R. China
| | - Hai-ying Liang
- Fisheries College, Guangdong Ocean University, Zhanjiang, Guangdong, P.R. China
- * E-mail:
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Shimizu K, Kimura K, Isowa Y, Oshima K, Ishikawa M, Kagi H, Kito K, Hattori M, Chiba S, Endo K. Insights into the Evolution of Shells and Love Darts of Land Snails Revealed from Their Matrix Proteins. Genome Biol Evol 2019; 11:380-397. [PMID: 30388206 PMCID: PMC6368272 DOI: 10.1093/gbe/evy242] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2018] [Indexed: 12/14/2022] Open
Abstract
Over the past decade, many skeletal matrix proteins that are possibly related to calcification have been reported in various calcifying animals. Molluscs are among the most diverse calcifying animals and some gastropods have adapted to terrestrial ecological niches. Although many shell matrix proteins (SMPs) have already been reported in molluscs, most reports have focused on marine molluscs, and the SMPs of terrestrial snails remain unclear. In addition, some terrestrial stylommatophoran snails have evolved an additional unique calcified character, called a "love dart," used for mating behavior. We identified 54 SMPs in the terrestrial snail Euhadra quaesita, and found that they contain specific domains that are widely conserved in molluscan SMPs. However, our results also suggest that some of them possibly have evolved independently by domain shuffling, domain recruitment, or gene co-option. We then identified four dart matrix proteins, and found that two of them are the same proteins as those identified as SMPs. Our results suggest that some dart matrix proteins possibly have evolved by independent gene co-option from SMPs during dart evolution events. These results provide a new perspective on the evolution of SMPs and "love darts" in land snails.
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Affiliation(s)
- Keisuke Shimizu
- Department of Earth and Planetary Science, The University of Tokyo, Hongo, Japan
- College of Life and Environmental Sciences, University of Exeter, United Kingdom
| | - Kazuki Kimura
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
- Research Institute for Ulleungdo and Dokdo Islands, Kyungpook National University, Bukgu, Daegu, Korea
| | - Yukinobu Isowa
- Organization for the Strategic Coordination of Research and Intellectual Properties, Meiji University, Kawasaki, Kanagawa, Japan
| | - Kenshiro Oshima
- Center for Omics and Bioinformatics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Makiko Ishikawa
- Department of Earth and Planetary Science, The University of Tokyo, Hongo, Japan
- Faculty of Animal Health Technology, Yamazaki University of Animal Health Technology, Hachioji, Tokyo, Japan
| | - Hiroyuki Kagi
- Geochemical Research Center, Graduate School of Science, The University of Tokyo, Hongo, Japan
| | - Keiji Kito
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Masahira Hattori
- Center for Omics and Bioinformatics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
- Cooperative Major of Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Japan
| | - Satoshi Chiba
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Kazuyoshi Endo
- Department of Earth and Planetary Science, The University of Tokyo, Hongo, Japan
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Malachowicz M, Wenne R. Mantle transcriptome sequencing of Mytilus spp. and identification of putative biomineralization genes. PeerJ 2019; 6:e6245. [PMID: 30723611 PMCID: PMC6359903 DOI: 10.7717/peerj.6245] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 12/09/2018] [Indexed: 12/16/2022] Open
Abstract
In molluscs, the shell secreted by mantle tissue during the biomineralization process is the first barrier against predators and mechanical damage. Changing environmental conditions, such as ocean acidification, influence shell strength and thus protection of the soft body within. Mussels are marine bivalves with important commercial and ecological value worldwide. Despite this importance, the proteins involved in the biomineralization and pigmentation processes in Mytilus spp. remain unclear, as does taxonomy of Mytilus taxa, though there have been many molecular studies. To further understanding in these areas, this study aimed to characterize and compare mantle transcriptomes of four mussel taxa using next generation sequencing. Mussels representing four taxa, were collected from several localities and RNA from mantle tissue was extracted. RNA sequences obtained were assembled, annotated and potential molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were identified. Candidate contigs putatively related to biomineralization and pigmentation processes were then selected and several transcripts were chosen for phylogenetic analyses from the Bivalvia class. Transcriptome comparisons between Mytilus taxa, including gene ontology (GO) enrichment analysis and orthologues identification were performed. Of assembled contigs, 46.57%, 37.28% and 17.53% were annotated using NCBI NR, GO and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Potential SSRs (483) and SNPs (1,497) were identified. Results presented a total of 1,292 contigs putatively involved in biomineralization and melanogenesis. Phylogenetic analyses of α-carbonic anhydrase, chitinase and tyrosinase revealed complex evolutionary history and diversity of these genes, which may be a result of duplication events or adaptation to different environments in mussels and other bivalves. Enrichment analyses revealed GO terms associated with pH and thermal response in Mytilus edulis from the North Sea and M. galloprovincialis from the Mediterranean Sea. The phylogenetic analysis within the genus Mytilus revealed M. californianus and M. coruscus to be genetically more distant from the other taxa: M. trossulus, M. edulis, M. chilensis and M. galloprovincialis. This work represents the first mantle transcriptome comparison between Mytilus taxa and provides contigs putatively involved in biomineralization.
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Affiliation(s)
| | - Roman Wenne
- Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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Mahajan S, Ramya TNC. F-type Lectin Domains: Provenance, Prevalence, Properties, Peculiarities, and Potential. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1112:345-363. [DOI: 10.1007/978-981-13-3065-0_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Sleight VA, Peck LS, Dyrynda EA, Smith VJ, Clark MS. Cellular stress responses to chronic heat shock and shell damage in temperate Mya truncata. Cell Stress Chaperones 2018; 23:1003-1017. [PMID: 29754331 PMCID: PMC6111077 DOI: 10.1007/s12192-018-0910-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/06/2018] [Accepted: 05/01/2018] [Indexed: 12/21/2022] Open
Abstract
Acclimation, via phenotypic flexibility, is a potential means for a fast response to climate change. Understanding the molecular mechanisms underpinning phenotypic flexibility can provide a fine-scale cellular understanding of how organisms acclimate. In the last 30 years, Mya truncata populations around the UK have faced an average increase in sea surface temperature of 0.7 °C and further warming of between 1.5 and 4 °C, in all marine regions adjacent to the UK, is predicted by the end of the century. Hence, data are required on the ability of M. truncata to acclimate to physiological stresses, and most notably, chronic increases in temperature. Animals in the present study were exposed to chronic heat-stress for 2 months prior to shell damage and subsequently, only 3, out of 20 damaged individuals, were able to repair their shells within 2 weeks. Differentially expressed genes (between control and damaged animals) were functionally enriched with processes relating to cellular stress, the immune response and biomineralisation. Comparative transcriptomics highlighted genes, and more broadly molecular mechanisms, that are likely to be pivotal in this lack of acclimation. This study demonstrates that discovery-led transcriptomic profiling of animals during stress-response experiments can shed light on the complexity of biological processes and changes within organisms that can be more difficult to detect at higher levels of biological organisation.
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Affiliation(s)
- Victoria A Sleight
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.
- British Antarctic Survey, Natural Environment Research Council (NERC), High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council (NERC), High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Elisabeth A Dyrynda
- Centre for Marine Biodiversity & Biotechnology, Institute of Life & Earth Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Valerie J Smith
- Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council (NERC), High Cross, Madingley Road, Cambridge, CB3 0ET, UK
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Mann K, Cerveau N, Gummich M, Fritz M, Mann M, Jackson DJ. In-depth proteomic analyses of Haliotis laevigata (greenlip abalone) nacre and prismatic organic shell matrix. Proteome Sci 2018; 16:11. [PMID: 29983641 PMCID: PMC6003135 DOI: 10.1186/s12953-018-0139-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/25/2018] [Indexed: 01/12/2023] Open
Abstract
Background The shells of various Haliotis species have served as models of invertebrate biomineralization and physical shell properties for more than 20 years. A focus of this research has been the nacreous inner layer of the shell with its conspicuous arrangement of aragonite platelets, resembling in cross-section a brick-and-mortar wall. In comparison, the outer, less stable, calcitic prismatic layer has received much less attention. One of the first molluscan shell proteins to be characterized at the molecular level was Lustrin A, a component of the nacreous organic matrix of Haliotis rufescens. This was soon followed by the C-type lectin perlucin and the growth factor-binding perlustrin, both isolated from H. laevigata nacre, and the crystal growth-modulating AP7 and AP24, isolated from H. rufescens nacre. Mass spectrometry-based proteomics was subsequently applied to to Haliotis biomineralization research with the analysis of the H. asinina shell matrix and yielded 14 different shell-associated proteins. That study was the most comprehensive for a Haliotis species to date. Methods The shell proteomes of nacre and prismatic layer of the marine gastropod Haliotis laevigata were analyzed combining mass spectrometry-based proteomics and next generation sequencing. Results We identified 297 proteins from the nacreous shell layer and 350 proteins from the prismatic shell layer from the green lip abalone H. laevigata. Considering the overlap between the two sets we identified a total of 448 proteins. Fifty-one nacre proteins and 43 prismatic layer proteins were defined as major proteins based on their abundance at more than 0.2% of the total. The remaining proteins occurred at low abundance and may not play any significant role in shell fabrication. The overlap of major proteins between the two shell layers was 17, amounting to a total of 77 major proteins. Conclusions The H. laevigata shell proteome shares moderate sequence similarity at the protein level with other gastropod, bivalve and more distantly related invertebrate biomineralising proteomes. Features conserved in H. laevigata and other molluscan shell proteomes include short repetitive sequences of low complexity predicted to lack intrinsic three-dimensional structure, and domains such as tyrosinase, chitin-binding, and carbonic anhydrase. This catalogue of H. laevigata shell proteins represents the most comprehensive for a haliotid and should support future efforts to elucidate the molecular mechanisms of shell assembly. Electronic supplementary material The online version of this article (10.1186/s12953-018-0139-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karlheinz Mann
- 1Abteilung Proteomics und Signaltransduktion, Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Nicolas Cerveau
- 2Department of Geobiology, Georg-August University of Göttingen, Goldschmidstr. 3, 37077 Göttingen, Germany
| | - Meike Gummich
- 3Universität Bremen, Institut für Biophysik, Otto Hahn Allee NW1, D-28334 Bremen, Germany
| | - Monika Fritz
- 3Universität Bremen, Institut für Biophysik, Otto Hahn Allee NW1, D-28334 Bremen, Germany
| | - Matthias Mann
- 1Abteilung Proteomics und Signaltransduktion, Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Daniel J Jackson
- 2Department of Geobiology, Georg-August University of Göttingen, Goldschmidstr. 3, 37077 Göttingen, Germany
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Herlitze I, Marie B, Marin F, Jackson DJ. Molecular modularity and asymmetry of the molluscan mantle revealed by a gene expression atlas. Gigascience 2018; 7:4997018. [PMID: 29788257 PMCID: PMC6007483 DOI: 10.1093/gigascience/giy056] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/09/2018] [Indexed: 12/31/2022] Open
Abstract
Background Conchiferan molluscs construct a biocalcified shell that likely supported much of their evolutionary success. However, beyond broad proteomic and transcriptomic surveys of molluscan shells and the shell-forming mantle tissue, little is known of the spatial and ontogenetic regulation of shell fabrication. In addition, most efforts have been focused on species that deposit nacre, which is at odds with the majority of conchiferan species that fabricate shells using a crossed-lamellar microstructure, sensu lato. Results By combining proteomic and transcriptomic sequencing with in situ hybridization we have identified a suite of gene products associated with the production of the crossed-lamellar shell in Lymnaea stagnalis. With this spatial expression data we are able to generate novel hypotheses of how the adult mantle tissue coordinates the deposition of the calcified shell. These hypotheses include functional roles for unusual and otherwise difficult-to-study proteins such as those containing repetitive low-complexity domains. The spatial expression readouts of shell-forming genes also reveal cryptic patterns of asymmetry and modularity in the shell-forming cells of larvae and adult mantle tissue. Conclusions This molecular modularity of the shell-forming mantle tissue hints at intimate associations between structure, function, and evolvability and may provide an elegant explanation for the evolutionary success of the second largest phylum among the Metazoa.
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Affiliation(s)
- Ines Herlitze
- Department of Geobiology, Georg-August University of Göttingen, Goldschmidtstrasse 3, 37077 Göttingen, Germany
| | - Benjamin Marie
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Département Aviv, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Frédéric Marin
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne - Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France
| | - Daniel J Jackson
- Department of Geobiology, Georg-August University of Göttingen, Goldschmidtstrasse 3, 37077 Göttingen, Germany
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Vasta GR, Amzel LM, Bianchet MA, Cammarata M, Feng C, Saito K. F-Type Lectins: A Highly Diversified Family of Fucose-Binding Proteins with a Unique Sequence Motif and Structural Fold, Involved in Self/Non-Self-Recognition. Front Immunol 2017; 8:1648. [PMID: 29238345 PMCID: PMC5712786 DOI: 10.3389/fimmu.2017.01648] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/10/2017] [Indexed: 12/25/2022] Open
Abstract
The F-type lectin (FTL) family is one of the most recent to be identified and structurally characterized. Members of the FTL family are characterized by a fucose recognition domain [F-type lectin domain (FTLD)] that displays a novel jellyroll fold ("F-type" fold) and unique carbohydrate- and calcium-binding sequence motifs. This novel lectin family comprises widely distributed proteins exhibiting single, double, or greater multiples of the FTLD, either tandemly arrayed or combined with other structurally and functionally distinct domains, yielding lectin subunits of pleiotropic properties even within a single species. Furthermore, the extraordinary variability of FTL sequences (isoforms) that are expressed in a single individual has revealed genetic mechanisms of diversification in ligand recognition that are unique to FTLs. Functions of FTLs in self/non-self-recognition include innate immunity, fertilization, microbial adhesion, and pathogenesis, among others. In addition, although the F-type fold is distinctive for FTLs, a structure-based search revealed apparently unrelated proteins with minor sequence similarity to FTLs that displayed the FTLD fold. In general, the phylogenetic analysis of FTLD sequences from viruses to mammals reveals clades that are consistent with the currently accepted taxonomy of extant species. However, the surprisingly discontinuous distribution of FTLDs within each taxonomic category suggests not only an extensive structural/functional diversification of the FTLs along evolutionary lineages but also that this intriguing lectin family has been subject to frequent gene duplication, secondary loss, lateral transfer, and functional co-option.
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Affiliation(s)
- Gerardo R. Vasta
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Mario A. Bianchet
- Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Matteo Cammarata
- Department of Earth and Marine Sciences, University of Palermo, Palermo, Italy
| | - Chiguang Feng
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Keiko Saito
- Department of Marine Biotechnology, Institute of Marine and Environmental Technology, University of Maryland Baltimore County, Baltimore, MD, United States
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Marie B, Arivalagan J, Mathéron L, Bolbach G, Berland S, Marie A, Marin F. Deep conservation of bivalve nacre proteins highlighted by shell matrix proteomics of the Unionoida Elliptio complanata and Villosa lienosa. J R Soc Interface 2017; 14:rsif.2016.0846. [PMID: 28123096 DOI: 10.1098/rsif.2016.0846] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/20/2016] [Indexed: 01/12/2023] Open
Abstract
The formation of the molluscan shell nacre is regulated to a large extent by a matrix of extracellular macromolecules that are secreted by the shell-forming tissue, the mantle. This so-called 'calcifying matrix' is a complex mixture of proteins, glycoproteins and polysaccharides that is assembled and occluded within the mineral phase during the calcification process. Better molecular-level characterization of the substances that regulate nacre formation is still required. Notable advances in expressed tag sequencing of freshwater mussels, such as Elliptio complanata and Villosa lienosa, provide a pre-requisite to further characterize bivalve nacre proteins by a proteomic approach. In this study, we have identified a total of 48 different proteins from the insoluble matrices of the nacre, 31 of which are common to both E. complanata and V. lienosa A few of these proteins, such as PIF, MSI60, CA, shematrin-like, Kunitz-like, LamG, chitin-binding-containing proteins, together with A-, D-, G-, M- and Q-rich proteins, appear to be analogues, if not true homologues, of proteins previously described from the pearl oyster or the edible mussel nacre matrices, thus forming a remarkable list of deeply conserved nacre proteins. This work constitutes a comprehensive nacre proteomic study of non-pteriomorphid bivalves that has enabled us to describe the molecular basis of a deeply conserved biomineralization toolkit among nacreous shell-bearing bivalves, with regard to proteins associated with other shell microstructures, with those of other mollusc classes (gastropods, cephalopods) and, finally, with other lophotrochozoans (brachiopods).
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Affiliation(s)
- Benjamin Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris, France
| | - Jaison Arivalagan
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris, France
| | - Lucrèce Mathéron
- UMR 7203 CNRS/UPMC/ENS/INSERM Laboratoire des Biomolécules, Institut de Biologie Paris Seine, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | - Gérard Bolbach
- UMR 7203 CNRS/UPMC/ENS/INSERM Laboratoire des Biomolécules, Institut de Biologie Paris Seine, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | - Sophie Berland
- UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris, France
| | - Arul Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris, France
| | - Frédéric Marin
- UMR 6282 CNRS/uB Biogéosciences, Université de Bourgogne Franche-Comté (UB-FC), Dijon, France
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32
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Feng D, Li Q, Yu H, Kong L, Du S. Identification of conserved proteins from diverse shell matrix proteome in Crassostrea gigas: characterization of genetic bases regulating shell formation. Sci Rep 2017; 7:45754. [PMID: 28374770 PMCID: PMC5379566 DOI: 10.1038/srep45754] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/06/2017] [Indexed: 12/21/2022] Open
Abstract
The calcifying shell is an excellent model for studying biomineralization and evolution. However, the molecular mechanisms of shell formation are only beginning to be elucidated in Mollusca. It is known that shell matrix proteins (SMPs) play important roles in shell formation. With increasing data of shell matrix proteomes from various species, we carried out a BLASTp bioinformatics analysis using the shell matrix proteome from Crassostrea gigas against 443 SMPs from nine other species. The highly conserved tyrosinase and chitin related proteins were identified in bivalve. In addition, the relatively conserved proteins containing domains of carbonic anhydrase, Sushi, Von Willebrand factor type A, and chitin binding, were identified from all the ten species. Moreover, 25 genes encoding SMPs were annotated and characterized that are involved in CaCO3 crystallization and represent chitin related or ECM related proteins. Together, data from these analyses provide new knowledge underlying the molecular mechanism of shell formation in C.gigas, supporting a refined shell formation model including chitin and ECM-related proteins.
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Affiliation(s)
- Dandan Feng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shaojun Du
- Institute of Marine and Environmental Technology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, United States
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33
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Guan Y, He M, Wu H. Differential mantle transcriptomics and characterization of growth-related genes in the diploid and triploid pearl oyster Pinctada fucata. Mar Genomics 2017; 33:31-38. [PMID: 28188115 DOI: 10.1016/j.margen.2017.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 12/13/2022]
Abstract
To explore the molecular mechanism of triploidy effect in the pearl oyster Pinctada fucata, two RNA-seq libraries were constructed from the mantle tissue of diploids and triploids by Roche-454 massive parallel pyrosequencing. The identification of differential expressed genes (DEGs) between diploid and triploid may reveal the molecular mechanism of triploidy effect. In this study, 230 down-regulated and 259 up-regulated DEGs were obtained by comparison between diploid and triploid libraries. The gene ontology and KEGG pathway analysis revealed more functional activation in triploids and it may due to the duplicated gene expression in transcriptional level during whole genome duplication (WGD). To confirm the sequencing data, a set of 11 up-regulated genes related to growth and development control and regulation were analyzed by RT-qPCR in independent experiment. According to the validation and annotation of these genes, it is hypothesized that the set of up-regulated expressed genes had the correlated expression pattern involved in shell building or other interactive probable functions during triploidization. The up- regulation of growth-related genes may support the classic hypotheses of 'energy redistribution' from early research. The results provide valuable resources to understand the molecular mechanism of triploidy effect in both shell building and producing high-quality seawater pearls.
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Affiliation(s)
- Yunyan Guan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China, Guangzhou 510301, China.
| | - Maoxian He
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China, Guangzhou 510301, China
| | - Houbo Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China, Guangzhou 510301, China.
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Arivalagan J, Yarra T, Marie B, Sleight VA, Duvernois-Berthet E, Clark MS, Marie A, Berland S. Insights from the Shell Proteome: Biomineralization to Adaptation. Mol Biol Evol 2017; 34:66-77. [PMID: 27744410 PMCID: PMC5854119 DOI: 10.1093/molbev/msw219] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bivalves have evolved a range of complex shell forming mechanisms that are reflected by their incredible diversity in shell mineralogy and microstructures. A suite of proteins exported to the shell matrix space plays a significant role in controlling these features, in addition to underpinning some of the physical properties of the shell itself. Although, there is a general consensus that a minimum basic protein tool kit is required for shell construction, to date, this remains undefined. In this study, the shell matrix proteins (SMPs) of four highly divergent bivalves (The Pacific oyster, Crassostrea gigas; the blue mussel, Mytilus edulis; the clam, Mya truncata, and the king scallop, Pecten maximus) were analyzed in an identical fashion using proteomics pipeline. This enabled us to identify the critical elements of a "basic tool kit" for calcification processes, which were conserved across the taxa irrespective of the shell morphology and arrangement of the crystal surfaces. In addition, protein domains controlling the crystal layers specific to aragonite and calcite were also identified. Intriguingly, a significant number of the identified SMPs contained domains related to immune functions. These were often are unique to each species implying their involvement not only in immunity, but also environmental adaptation. This suggests that the SMPs are selectively exported in a complex mix to endow the shell with both mechanical protection and biochemical defense.
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Affiliation(s)
- Jaison Arivalagan
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
- UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Tejaswi Yarra
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, United Kingdom
- University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, United Kingdom
| | - Benjamin Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Victoria A Sleight
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, United Kingdom
| | - Evelyne Duvernois-Berthet
- UMR 7221 CNRS/MNHN Evolution des Régulations Endocriniennes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, United Kingdom
| | - Arul Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Sophie Berland
- UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
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35
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Deterioration of eggshell quality is related to calbindin in laying hens infected with velogenic genotype VIId Newcastle disease virus. Theriogenology 2016; 91:62-68. [PMID: 28215687 DOI: 10.1016/j.theriogenology.2016.12.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 12/18/2022]
Abstract
The aim of this study was to determine the mechanism by which Newcastle disease virus (NDV) affects eggshell quality. Thirty-week-old specific pathogen free (SPF) egg-laying hens were inoculated with the velogenic genotype VIId NDV strain (infected group) or with inoculating media without virus (control group) by combined intraocular and intranasal routes. The levels of CaBP-D28k mRNA expression in the uterus, a gene related to eggshell quality, were examined by quantitative reverse transcriptase polymerase chain reaction (RT-PCR). The quality of eggshells was analyzed by scanning electron microscopy (SEM). The infected group showed a marked decline in egg production when compared to the control group. The NDV antigen was found more abundantly in the glandular epithelium of the infected hens' uteri from 1 to 15 d post-inoculation (dpi). The levels of CaBP-D28k mRNA expression in the uteri of infected hens were significantly lower than in the control hens from 3 to 15 dpi (P < 0.05). The changes in the Ca concentrations in the eggshells were consistent with the expression of CaBP-D28k mRNA in the infected hens. Ultrastructural examination of eggshells showed significantly reduced shell thickness in the infected hens from 1 to 15 dpi (P < 0.05). Furthermore, obvious changes in the structure of the external shell surface and shell membrane were detected in the infected hens compared with the control hens. In conclusion, the current study confirmed that velogenic genotype VIId NDV infection is associated with the deterioration of the eggshell quality of the laying hens.
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Gardères J, Domart-Coulon I, Marie A, Hamer B, Batel R, Müller WEG, Bourguet-Kondracki ML. Purification and partial characterization of a lectin protein complex, the clathrilectin, from the calcareous sponge Clathrina clathrus. Comp Biochem Physiol B Biochem Mol Biol 2016; 200:17-27. [PMID: 27113336 DOI: 10.1016/j.cbpb.2016.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/14/2016] [Accepted: 04/20/2016] [Indexed: 11/26/2022]
Abstract
Carbohydrate-binding proteins were purified from the marine calcareous sponge Clathrina clathrus via affinity chromatography on lactose and N-acetyl glucosamine-agarose resins. Proteomic analysis of acrylamide gel separated protein subunits obtained in reducing conditions pointed out several candidates for lectins. Based on amino-acid sequence similarity, two peptides displayed homology with the jack bean lectin Concanavalin A, including a conserved domain shared by proteins in the L-type lectin superfamily. An N-acetyl glucosamine - binding protein complex, named clathrilectin, was further purified via gel filtration chromatography, bioguided with a diagnostic rabbit erythrocyte haemagglutination assay, and its activity was found to be calcium dependent. Clathrilectin, a protein complex of 3200kDa estimated by gel filtration, is composed of monomers with apparent molecular masses of 208 and 180kDa estimated on 10% SDS-PAGE. Nine internal peptides were identified using proteomic analyses, and compared to protein libraries from the demosponge Amphimedon queenslandica and a calcareous sponge Sycon sp. from the Adriatic Sea. The clathrilectin is the first lectin isolated from a calcareous sponge and displays homologies with predicted sponge proteins potentially involved in cell aggregation and interaction with bacteria.
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Affiliation(s)
- Johan Gardères
- Unité Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 54, 57 rue Cuvier, 75005 Paris, France; Laboratory for Marine Molecular Biology, Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia
| | - Isabelle Domart-Coulon
- Unité Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Arul Marie
- Unité Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Bojan Hamer
- Laboratory for Marine Molecular Biology, Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia
| | - Renato Batel
- Laboratory for Marine Molecular Biology, Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia
| | - Werner E G Müller
- ERC Advanced Investigator Grant Research Group at Institute for Physiological Chemistry, University Medical Center of Johannes Gutenberg University Mainz, Duesbergweg 6, 55128 Mainz, Germany
| | - Marie-Lise Bourguet-Kondracki
- Unité Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 54, 57 rue Cuvier, 75005 Paris, France.
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37
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Morris JP, Wang Y, Backeljau T, Chapelle G. Biomimetic and bio-inspired uses of mollusc shells. Mar Genomics 2016; 27:85-90. [PMID: 27083864 DOI: 10.1016/j.margen.2016.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/30/2016] [Accepted: 04/06/2016] [Indexed: 10/21/2022]
Abstract
Climate change and ocean acidification are likely to have a profound effect on marine molluscs, which are of great ecological and economic importance. One process particularly sensitive to climate change is the formation of biominerals in mollusc shells. Fundamental research is broadening our understanding of the biomineralization process, as well as providing more informed predictions on the effects of climate change on marine molluscs. Such studies are important in their own right, but their value also extends to applied sciences. Biominerals, organic/inorganic hybrid materials with many remarkable physical and chemical properties, have been studied for decades, and the possibilities for future improved use of such materials for society are widely recognised. This article highlights the potential use of our understanding of the shell biomineralization process in novel bio-inspired and biomimetic applications. It also highlights the potential for the valorisation of shells produced as a by-product of the aquaculture industry. Studying shells and the formation of biominerals will inspire novel functional hybrid materials. It may also provide sustainable, ecologically- and economically-viable solutions to some of the problems created by current human resource exploitation.
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Affiliation(s)
- J P Morris
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000 Brussels, Belgium.
| | - Y Wang
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000 Brussels, Belgium.
| | - T Backeljau
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000 Brussels, Belgium; Evolutionary Ecology Group, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - G Chapelle
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000 Brussels, Belgium; Rue Alphonse Renard 29, 1050 Brussels, Belgium
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38
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Sleight VA, Thorne MAS, Peck LS, Arivalagan J, Berland S, Marie A, Clark MS. Characterisation of the mantle transcriptome and biomineralisation genes in the blunt-gaper clam, Mya truncata. Mar Genomics 2016; 27:47-55. [PMID: 26777791 DOI: 10.1016/j.margen.2016.01.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/28/2015] [Accepted: 01/07/2016] [Indexed: 12/16/2022]
Abstract
Members of the Myidae family are ecologically and economically important, but there is currently very little molecular data on these species. The present study sequenced and assembled the mantle transcriptome of Mya truncata from the North West coast of Scotland and identified candidate biomineralisation genes. RNA-Seq reads were assembled to create 20,106 contigs in a de novo transciptome, 18.81% of which were assigned putative functions using BLAST sequence similarity searching (cuttoff E-value 1E-10). The most highly expressed genes were compared to the Antarctic clam (Laternula elliptica) and showed that many of the dominant biological functions (muscle contraction, energy production, biomineralisation) in the mantle were conserved. There were however, differences in the constitutive expression of heat shock proteins, which were possibly due to the M. truncata sampling location being at a relatively low latitude, and hence relatively warm, in terms of the global distribution of the species. Phylogenetic analyses of the Tyrosinase proteins from M. truncata showed a gene expansion which was absent in L. elliptica. The tissue distribution expression patterns of putative biomineralisation genes were investigated using quantitative PCR, all genes showed a mantle specific expression pattern supporting their hypothesised role in shell secretion. The present study provides some preliminary insights into how clams from different environments - temperate versus polar - build their shells. In addition, the transcriptome data provides a valuable resource for future comparative studies investigating biomineralisation.
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Affiliation(s)
- Victoria A Sleight
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK.
| | - Michael A S Thorne
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Jaison Arivalagan
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris 75005, France; UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Sophie Berland
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Arul Marie
- UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
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