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Sun Y, Liu X, Shan X, Wang Y, Zhong C, Lu C, Guan B, Yao S, Huo Y, Sun R, Wei M, Dong Z. Comprehensive investigation of differentially expressed ncRNAs, mRNAs, and their ceRNA networks in the regulation of shell color formation in clam, Cyclina sinensis. Gene 2024; 911:148346. [PMID: 38452877 DOI: 10.1016/j.gene.2024.148346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Noncoding RNAs (ncRNAs) have gained significant attention in recent years due to their crucial roles in various biological processes. However, our understanding of the expression and functions of ncRNAs in Cyclina sinensis, an economically important marine bivalve, remains limited. This study aimed to address this knowledge gap by systematically identifying ncRNAs in the mantles of C. sinensis with purple and white shells. Through our analysis, we identified a differential expression of 1244 mRNAs, 196 lncRNAs, 49 circRNAs, and 23 miRNAs between purple- and white-shell clams. Functional enrichment analysis revealed the involvement of these differentially expressed ncRNAs in biomineralization and pigmentation processes. To gain further insights into the regulatory mechanisms underlying shell color formation, we established competitive endogenous RNA (ceRNA) networks. These networks allowed us to identify targeted differentially expressed miRNAs (DEMis) and genes associated with shell color formation. Based on the ceRNA networks, we obtained an up-down-up lncRNA-miRNA-mRNA network consisting of 13 upregulated lncRNAs and a circRNA-miRNA-mRNA network comprising three upregulated circRNAs (novel_circ_0004787, novel_circ_0001165, novel_circ_0000245). Through these networks, we identified and selected an upregulated novel gene (evm.TU.Hic_asm_7.988) and a downregulated sponge miRNA (hru-miR-1985) as potential contributors to shell color regulation. In summary, the present investigation offers a comprehensive analysis of ncRNA catalogs expressed in the clam mantle of C. sinensis. The findings enhance our comprehension of the molecular mechanisms governing shell coloration and offer new perspectives for selective breeding of C. sinensis in the future.
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Affiliation(s)
- Yuyan Sun
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Xuxiao Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Xin Shan
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Yiwo Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Chongyu Zhong
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Chaofa Lu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Bin Guan
- Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
| | - Shun Yao
- Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
| | - Yujia Huo
- Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
| | - Runkai Sun
- Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
| | - Min Wei
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China.
| | - Zhiguo Dong
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China.
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Li Y, Xue Y, Peng Z, Zhang L. Immune diversity in lophotrochozoans, with a focus on recognition and effector systems. Comput Struct Biotechnol J 2023; 21:2262-2275. [PMID: 37035545 PMCID: PMC10073891 DOI: 10.1016/j.csbj.2023.03.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/11/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
Lophotrochozoa is one of the most species-rich but immunologically poorly explored phyla. Although lack of acquired response in a narrow sense, lophotrochozoans possess various genetic mechanisms that enhance the diversity and specificity of innate immune system. Here, we review the recent advances of comparative immunology studies in lophotrochozoans with focus on immune recognition and effector systems. Haemocytes and coelomocytes are general important yet understudied player. Comparative genomics studies suggest expansion and functional divergence of lophotrochozoan immune reorganization systems is not as "homogeneous and simple" as we thought including the large-scale expansion and molecular divergence of pattern recognition receptors (PRRs) (TLRs, RLRs, lectins, etc.) and signaling adapters (MyD88s etc.), significant domain recombination of immune receptors (RLR, NLRs, lectins, etc.), extensive somatic recombination of fibrinogenrelated proteins (FREPs) in snails. Furthermore, there are repeatedly identified molecular mechanisms that generate immune effector diversity, including high polymorphism of antimicrobial peptides and proteins (AMPs), reactive oxygen and nitrogen species (RONS) and cytokines. Finally, we argue that the next generation omics tools and the recently emerged genome editing technicism will revolutionize our understanding of innate immune system in a comparative immunology perspective.
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Affiliation(s)
- Yongnan Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu Xue
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Agricultural University, Qingdao, China
| | - Zhangjie Peng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Linlin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
- Corresponding author at: CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
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3
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The first high-density genetic map of common cockle (Cerastoderma edule) reveals a major QTL controlling shell color variation. Sci Rep 2022; 12:16971. [PMID: 36216849 PMCID: PMC9551087 DOI: 10.1038/s41598-022-21214-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/23/2022] [Indexed: 12/29/2022] Open
Abstract
Shell color shows broad variation within mollusc species and despite information on the genetic pathways involved in shell construction and color has recently increased, more studies are needed to understand its genetic architecture. The common cockle (Cerastoderma edule) is a valuable species from ecological and commercial perspectives which shows important variation in shell color across Northeast Atlantic. In this study, we constructed a high-density genetic map, as a tool for screening common cockle genome, which was applied to ascertain the genetic basis of color variation in the species. The consensus genetic map comprised 19 linkage groups (LGs) in accordance with the cockle karyotype (2n = 38) and spanned 1073 cM, including 730 markers per LG and an inter-marker distance of 0.13 cM. Five full-sib families showing segregation for several color-associated traits were used for a genome-wide association study and a major QTL on chromosome 13 associated to different color-traits was detected. Mining on this genomic region revealed several candidate genes related to shell construction and color. A genomic region previously reported associated with divergent selection in cockle distribution overlapped with this QTL suggesting its putative role on adaptation.
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4
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Rivera-Pérez C, Arroyo-Loranca RG, Hernández-Saavedra NY. An acidic protein, Hf15, from Haliotis fulgens involved in biomineralization. Comp Biochem Physiol A Mol Integr Physiol 2022; 272:111276. [PMID: 35853523 DOI: 10.1016/j.cbpa.2022.111276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/20/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022]
Abstract
Biomineralization leads to the hardening of mineralized materials, such as the shell of Mollusk, to fulfill a wide range of functions, such as (but not limited to) skeletal support, protection of the soft tissues, navigation, etc. The study of the proteins responsible for this process, shell matrix proteins (SMPs), allows addressing questions related to structure-function relationship and to the mechanism of mineral formation, which is limited in gastropod species. In this study, a low molecular weight protein was isolated from the insoluble fraction after decalcification with acetic acid of the shell of Haliotis fulgens and, named Hf15. The unglycosylated protein has a theoretical molecular weight of 15 kDa, it possesses calcium and chiting binding properties. Hf15 can precipitate calcium carbonate in vitro in presence of different salts. Analysis by LC-MS of the five peptide sequences of Hf15 generated by trypsinization revealed that two peptides displayed homology to an uncharacterized protein 3-like from Haliotis rufescens, Haliotis asinia and H. sorenseni. The results obtained indicated that Hf15 is a novel SMP involved in shell mineralization in Haliotis fulgens.
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Affiliation(s)
| | - Raquel G Arroyo-Loranca
- Fisheries Ecology, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, Mexico
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5
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Evans TG, Bible JM, Maynard A, Griffith KR, Sanford E, Kültz D. Proteomic changes associated with predator-induced morphological defenses in oysters. Mol Ecol 2022; 31:4254-4270. [PMID: 35754098 DOI: 10.1111/mec.16580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/03/2022] [Accepted: 06/20/2022] [Indexed: 11/27/2022]
Abstract
Inducible prey defenses occur when organisms undergo plastic changes in phenotype to reduce predation risk. When predation pressure varies persistently over space or time, such as when predator and prey co-occur over only part of their biogeographic ranges, prey populations can become locally adapted in their inducible defenses. In California estuaries, native Olympia oyster (Ostrea lurida) populations have evolved disparate phenotypic responses to an invasive predator, the Atlantic oyster drill (Urosalpinx cinerea). In this study, oysters from an estuary with drills, and oysters from an estuary without drills, were reared for two generations in a laboratory common garden, and subsequently exposed to cues from Atlantic drills. Comparative proteomics was then used to investigate molecular mechanisms underlying conserved and divergent aspects of their inducible defenses. Both populations developed smaller, thicker, and harder shells after drill exposure, and these changes in shell phenotype were associated with up-regulation of calcium transport proteins that could influence biomineralization. Inducible defenses evolve in part because defended phenotypes incur fitness costs when predation risk is low. Immune proteins were down-regulated by both oyster populations after exposure to drills, implying a trade-off between biomineralization and immune function. Following drill exposure, oysters from the population that co-occurs with drills grew smaller shells than oysters inhabiting the estuary not yet invaded by the predator. Variation in the response to drills between populations was associated with isoform-specific protein expression. This trend suggests that a stronger inducible defense response evolved in oysters that co-occur with drills through modification of an existing mechanism.
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Affiliation(s)
- Tyler G Evans
- Department of Biological Sciences, California State University East Bay, Hayward, CA 94542, USA
| | - Jillian M Bible
- Department of Environmental Science and Studies, Washington College, Chestertown, MD 21620, USA
| | - Ashley Maynard
- Department of Biological Sciences, California State University East Bay, Hayward, CA 94542, USA
| | - Kaylee R Griffith
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA
| | - Eric Sanford
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA
| | - Dietmar Kültz
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
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6
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Huang S, Nishiumi S, Asaduzzaman M, Pan Y, Liu G, Yoshitake K, Maeyama K, Kinoshita S, Nagai K, Watabe S, Yoshida T, Asakawa S. Exosome-derived small non-coding RNAs reveal immune response upon grafting transplantation in Pinctada fucata (Mollusca). Open Biol 2022; 12:210317. [PMID: 35506205 PMCID: PMC9065966 DOI: 10.1098/rsob.210317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Exosomes, a subset of small extracellular vesicles, carry various nucleic acids, proteins, lipids, amino acids and metabolites. They function as a mode of intercellular communication and molecular transfer. Exosome cargo molecules, including small non-coding RNAs (sncRNAs), are involved in the immune response in various organisms. However, the role of exosome-derived sncRNAs in immune responses in molluscs remains unclear. Here, we aimed to reveal the sncRNAs involved in the immune response during grafting transplantation by the pearl oyster Pinctada fucata. Exosomes were successfully extracted from the P. fucata haemolymph during graft transplantation. Abundant microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) were simultaneously discovered in P. fucata exosomes by small RNA sequencing. The expression patterns of the miRNAs and piRNAs at the grafting and initial stages were not substantially different, but varied significantly between the initial and later stages. Target prediction and functional analysis indicate that these miRNAs and piRNAs are related to immune response upon grafting transplantation, whereas piRNAs may also be associated with transposon silencing by targeting with genome transposon elements. This work provides the basis for a functional understanding of exosome-derived sncRNAs and helps to gain further insight into the PIWI/piRNA pathway function outside of germline cells in molluscs.
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Affiliation(s)
- Songqian Huang
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shinya Nishiumi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Md Asaduzzaman
- Department of Marine Bioresources Science, Faculty of Fisheries, Chittagong Veterinary and Animal Sciences University, Khulshi 4225, Chittagong, Bangladesh
| | - Yida Pan
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Guanting Liu
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kaoru Maeyama
- Mikimoto Pharmaceutical Co., Ltd., Kurose 1425, Ise, Mie 516-8581, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kiyohito Nagai
- Pearl Research Laboratory, K. Mikimoto & Co., Ltd., Osaki Hazako 923, Hamajima, Shima, Mie 517-0403, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa 252-0313, Japan
| | - Tetsuhiko Yoshida
- Institute for Advanced Sciences, Toagosei Co., Ltd., Tsukuba, Ibaraki 300-2611, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
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7
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Zeng D, Guo X. Mantle Transcriptome Provides Insights into Biomineralization and Growth Regulation in the Eastern Oyster (Crassostrea virginica). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:82-96. [PMID: 34989931 DOI: 10.1007/s10126-021-10088-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Growth of the eastern oyster Crassostrea virginica, a major aquaculture species in the USA, is highly variable and not well understood at molecular levels. As growth of mollusks is confined in shells constructed by the mantle, mantle transcriptomes of large (fast-growing) and small (slow-growing) eastern oysters were sequenced and compared in this study. Transcription was observed for 31,186 genes, among which 104 genes were differentially expressed between the large and small oysters, including 48 upregulated and 56 downregulated in large oysters. Differentially expressed genes (DEGs) included genes from diverse pathways highlighting the complexity of shell formation and growth regulations. Seventeen of the 48 upregulated DEGs were related to shell matrix formation, most of which were upregulated in large oysters, indicating that large oysters are more active in biomineralization and shell formation. Genomic and transcriptomic analyses identified 22 genes encoding novel polyalanine containing proteins (Pacps) with characteristic motifs for matrix function that are tandemly duplicated on one chromosome, all specifically expressed in mantle and at higher levels in large oysters, suggesting that these expanded Pacps play important roles in shell formation and growth. Analysis of sequence variation identified 244,964 SNPs with 328 associated with growth. This study provides novel candidate genes and markers for shell formation and growth, and suggests that genes related to shell formation are important for the complex regulation of growth in the eastern oyster and possibly other bivalve mollusks. Results of this study show that both transcriptional modulation and functional polymorphism are important in determining growth.
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Affiliation(s)
- Dan Zeng
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, New Jersey, 08349, USA
- College of Life and Environmental Science, Hunan University of Arts and Science, 3150 Dongting Road, Wuling District, Changde, Hunan, 415000, China
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, New Jersey, 08349, USA.
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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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9
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Rivera-Pérez C, Hernández-Saavedra NY. Review: Post-translational modifications of marine shell matrix proteins. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110641. [PMID: 34182126 DOI: 10.1016/j.cbpb.2021.110641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/13/2021] [Accepted: 06/22/2021] [Indexed: 11/18/2022]
Abstract
Shell matrix proteins (SMPs) are key components for the Mollusk shell biomineralization. SMPs function has been hypothesized in several proteins by bioinformatics analysis, and through in vitro crystallization assays. However, studies of the post-translational modifications (PTMs) of SMPs, which contribute to their structure and the function, are limited. This review provides the current status of the SMPs with the most common PTMs described (glycosylation, phosphorylation, and disulfide bond formation) and their role in shell biomineralization. Also, recent studies based on recombinant production of SMPs are discussed. Finally, recommendations for the study of SMPs and their PTMs are provided. The review showed that PTMs are widely distributed in SMPs, and their presence on SMPs may contribute to the modulation of their activity in some SMPs, contributing to the crystal growth formation and differentiation through different mechanisms, however, in a few cases the lack of the PTMs do not alter their inherent function.
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Affiliation(s)
- Crisalejandra Rivera-Pérez
- CONACYT, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, Mexico.
| | - Norma Y Hernández-Saavedra
- Molecular Genetics Laboratory, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23096, Baja California Sur, Mexico
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10
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Ji Y, Yang X, Yang D, Zhang R. PU14, a Novel Matrix Protein, Participates in Pearl Oyster, Pinctada Fucata, Shell Formation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:189-200. [PMID: 33689053 PMCID: PMC8032588 DOI: 10.1007/s10126-020-10014-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/27/2020] [Indexed: 06/12/2023]
Abstract
Biomineralization is a widespread biological process, involved in the formation of shells, teeth, and bones. Shell matrix proteins have been widely studied for their importance during shell formation. In 2015, our group identified 72 unique shell matrix proteins in Pinctada fucata, among which PU14 is a matrix protein detected in the soluble fraction that solely exists in the prismatic layer. However, the function of PU14 is still unclear. In this study, the full-length cDNA sequence of PU14 was obtained and functional analyses of PU14 protein during shell formation were performed. The deduced protein has a molecular mass of 77.8 kDa and an isoelectric point of 11.34. The primary protein structure contains Gln-rich and random repeat units, which are typical characteristics of matrix protein and indicate its potential function during shell formation. In vivo and in vitro experiments indicated PU14 has prismatic layer functions during shell formation. The tissue expression patterns showed that PU14 was mainly expressed in the mantle tissue, which is consistent with prismatic layer formation. Notching experiments suggested that PU14 responded to repair and regenerate the injured shell. After inhibiting gene expression by injecting PU14-specific double-stranded RNA, the inner surface of the prismatic layer changed significantly and became rougher. Further, in vitro experiments showed that recombinant protein rPU14 impacted calcite crystal morphology. Taken together, characterization and functional analyses of a novel matrix protein, PU14, provide new insights about basic matrix proteins and their functions during shell formation.
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Affiliation(s)
- Yinghui Ji
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xue Yang
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Dong Yang
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Rongqing Zhang
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Zhe Jiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, 705 Yatai Road, Jiaxing, 314006, China.
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing, 314001, China.
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11
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Xie B, He Q, Hao R, Zheng Z, Du X. Molecular and functional analysis of PmC1qDC in nacre formation of Pinctada fucata martensii. FISH & SHELLFISH IMMUNOLOGY 2020; 106:621-627. [PMID: 32827655 DOI: 10.1016/j.fsi.2020.08.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 08/05/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
The C1q-domain-containing (C1qDC) proteins are a family of proteins characterized by a globular C1q (gC1q) domain in their C-terminus which hold the potential function in the shell formation as shell matrix proteins. In this study, a C1qDC protein was identified and characterized in pearl oyster (Pinctada fucata martensii) (PmC1qDC) to explore its function in nacre formation. The PmC1qDC-deduced protein sequence carried a typical globular C1q (gC1q) domain that possessed the typical 10-stranded β-sandwich fold with a jelly-roll topology common to all C1qDC family members and shared high homology with other gC1q domains. Homologous analysis of PmC1qDC presented it contained conserved secondary structure and Phe135, Phe155, Tyr166, Phe173, Tyr181, Phe183, and Phe256 amino acid residues. Expression pattern analysis showed that PmC1qDC expressed in all the detected tissues and exhibited a significantly higher expression level in nacre formation-associated tissues. After the shell notching, the expression level of PmC1qDC showed significantly up-regulation after 12 h in the central zone of mantle (MC). PmC1qDC expression significantly decreased in the MC after RNA interference (RNAi). Furthermore, disordered crystals with evident rough surface and irregular crystal tablets were observed in the nacre after RNAi. Results suggested that PmC1qDC affects the shell nacre formation, which is significant to improve the pearl production of pearl oyster.
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Affiliation(s)
- Bingyi Xie
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Qi He
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Ruijuan Hao
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Zhe Zheng
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.
| | - Xiaodong Du
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China.
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12
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Huang S, Jiang H, Zhang L, Gu Q, Wang W, Wen Y, Luo F, Jin W, Cao X. Integrated proteomic and transcriptomic analysis reveals that polymorphic shell colors vary with melanin synthesis in Bellamya purificata snail. J Proteomics 2020; 230:103950. [PMID: 32871245 DOI: 10.1016/j.jprot.2020.103950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
The snail Bellamya purificata is an ecologically and economically important freshwater gastropod species. However, limited genomic resources are available for this snail. In this study, the transcriptome of mantle tissues and proteome of shells of B. purificata with two shell colors (namely light-cyan line (LC) and light-purple line (LP)) were deeply sequenced and characterized. A total of 5.72 million contigs were assembled into 157,015 unigenes, 21,455 (13.66%) of these unigenes were significantly matched to NR, Swiss-Prot, KOG, GO and KEGG database. 1807 differentially expressed genes (DEGs) were identified between the two different shell color lines. These DEGs were significantly enriched in five KEGG pathways including tyrosine metabolism, tryptophan metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, and histidine metabolism, which suggested that the shell color polymorphism in B. purificata was a result of melanin synthesis variation. A total of 1521 proteins were identified in B. purificata here as well. The differentially expressed protein analysis showed that the tyrosinase content in LP was significantly decreased in comparison to LC, which agreed with the transcriptome analysis results. This study provides valuable genomic resources of B. purificata and improves our understanding of molecular mechanisms of biomineralization and shell color polymorphism in snail.
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Affiliation(s)
- Songqian Huang
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, the University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Hanjun Jiang
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Zhang
- College of Marxism, Shanghai University of Finance and Economics, Shanghai 200433, China
| | - Qianhong Gu
- The State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
| | - Weimin Wang
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanhong Wen
- Liuzhou Aquaculture Technology Extending Station, Liuzhou, China
| | - Fuguang Luo
- Liuzhou Aquaculture Technology Extending Station, Liuzhou, China
| | - Wu Jin
- Sino-US Cooperative Laboratory for Germplasm Conservation and Utilization of Freshwater Mollusks, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, Jiangsu, China.
| | - Xiaojuan Cao
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
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13
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A novel matrix protein PfX regulates shell ultrastructure by binding to specific calcium carbonate crystal faces. Int J Biol Macromol 2020; 156:302-313. [PMID: 32289403 DOI: 10.1016/j.ijbiomac.2020.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/02/2020] [Accepted: 04/05/2020] [Indexed: 11/24/2022]
Abstract
Here, we have identified a novel matrix protein, named PfX, from the pearl oyster Pinctada fucada, and investigated the effects of recombinant PfX protein on calcium carbonate crystallization. The expression of PfX was spatially concentrated in the mantle tissue and gill, the former of which is responsible for the formation of shell structures. The shell notching assay showed a PfX expression response during injured shell repair and regeneration, suggesting the potential involvement of this matrix protein in shell biomineralization. Further, an in vitro crystallization assay showed that PfX could alter the CaCO3 morphologies of both calcite and aragonite polymorphs. Correspondingly, a binding assay indicated that PfX has strong binding affinity for CaCO3 crystals, especially aragonite. Further, the protein's calcite binding capacity increased obviously when particular crystal faces were induced. In addition, PfX conjugated with fluorescent dye cyanine-5 (cy5) was preferentially distributed on rough crystal faces instead of the smooth and common (1 0 4) faces of calcite during the crystallization. These results suggest that matrix protein PfX might regulate CaCO3 morphology via selective binding and inhibit the growth of certain crystal faces, providing new clues for understanding biomineralization mechanisms in mollusk.
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14
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Zhu X, Chen Y, Zhang Z, Zhao S, Xie L, Zhang R. A species-specific miRNA participates in biomineralization by targeting CDS regions of Prisilkin-39 and ACCBP in Pinctada fucata. Sci Rep 2020; 10:8971. [PMID: 32488043 PMCID: PMC7265298 DOI: 10.1038/s41598-020-65708-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/20/2020] [Indexed: 12/17/2022] Open
Abstract
Biomineralization is a sophisticated biological process precisely regulated by multiple molecules and pathways. Accumulating miRNAs have been identified in invertebrates but their functions in biomineralization are poorly studied. Here, an oyster species-specific miRNA, novel_miR_1 was found to regulate biomineralization in Pinctada fucata. Target prediction showed that novel_miR_1 could target Prisilkin-39 and ACCBP by binding to their coding sequences (CDS). Tissue distribution analysis revealed that the expression level of novel_miR_1 was highest in the mantle, which was a key tissue participating in biomineralization. Gain-of-function assay in vivo showed that biomineralization-related genes including Prisilkin-39 and ACCBP were down-regulated and shell inner surfaces of both prismatic and nacreous layer were disrupted after the over-expression of novel_miR_1, indicating its dual roles in biomineralization. Furthermore, the shell notching results indicated that novel_miR_1 was involved in shell regeneration. Dual-luciferase reporter assay in vitro demonstrated that novel_miR_1 directly suppressed Prisilkin-39 and ACCBP genes by binding to the CDS regions. Taken together, these results suggest that novel_miR_1 is a direct negative regulator to Prisilkin-39 and ACCBP and plays an indispensable and important role in biomineralization in both prismatic and nacreous layer of P. fucata.
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Affiliation(s)
- Xuejing Zhu
- The Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yan Chen
- The Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhen Zhang
- The 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, China
| | - Shuyan Zhao
- The 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, China
| | - Liping Xie
- The Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Rongqing Zhang
- The 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, China.
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing, 314001, China.
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15
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de la Ballina NR, Villalba A, Cao A. Differences in proteomic profile between two haemocyte types, granulocytes and hyalinocytes, of the flat oyster Ostrea edulis. FISH & SHELLFISH IMMUNOLOGY 2020; 100:456-466. [PMID: 32205190 DOI: 10.1016/j.fsi.2020.03.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/05/2020] [Accepted: 03/17/2020] [Indexed: 06/10/2023]
Abstract
Haemocytes play a dominant role in shellfish immunity, being considered the main defence effector cells in molluscs. These cells are known to be responsible for many functions, including chemotaxis, cellular recognition, attachment, aggregation, shell repair and nutrient transport and digestion. There are two basic cell types of bivalve haemocytes morphologically distinguishable, hyalinocytes and granulocytes; however, functional differences and specific abilities are poorly understood: granulocytes are believed to be more efficient in killing microorganisms, while hyalinocytes are thought to be more specialised in clotting and wound healing. A proteomic approach was implemented to find qualitative differences in the protein profile between granulocytes and hyalinocytes of the European flat oyster, Ostrea edulis, as a way to evaluate functional differences. Oyster haemolymph cells were differentially separated by Percoll® density gradient centrifugation. Granulocyte and hyalinocyte proteins were separated by 2D-PAGE and their protein profiles were analysed and compared with PD Quest software; the protein spots exclusive for each haemocyte type were excised from gels and analysed by MALDI-TOF/TOF with a combination of mass spectrometry (MS) and MS/MS for sequencing and protein identification. A total of 34 proteins were identified, 20 unique to granulocytes and 14 to hyalinocytes. The results suggested differences between the haemocyte types in signal transduction, apoptosis, oxidation reduction processes, cytoskeleton, phagocytosis and pathogen recognition. These results contribute to identify differential roles of each haemocyte type and to better understand the oyster immunity mechanisms, which should help to fight oyster diseases.
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Affiliation(s)
- Nuria R de la Ballina
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620, Vilanova de Arousa, Spain
| | - Antonio Villalba
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620, Vilanova de Arousa, Spain; Departamento de Ciencias de la Vida, Universidad de Alcalá, 28871, Alcalá de Henares, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), 48620, Plentzia, Spain.
| | - Asunción Cao
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620, Vilanova de Arousa, Spain
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16
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Kakinuma M, Yasumoto K, Suzuki M, Kasugai C, Koide M, Mitani K, Shidoji K, Kinoshita S, Hattori F, Maeyama K, Awaji M, Nagai K, Watabe S. Trivalent Iron Is Responsible for the Yellow Color Development in the Nacre of Akoya Pearl Oyster Shells. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:19-30. [PMID: 31728706 DOI: 10.1007/s10126-019-09927-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
The gold and cream colors of cultured Akoya pearls, as well as natural yellow nacre of pearl oyster shells, are thought to arise from intrinsic yellow pigments. While the isolation of the yellow pigments has been attempted using a large amount of gold pearls, the substance concerned is still unknown. We report here on the purification and characterization of yellow pigments from the nacre of Akoya pearl oyster shells. Two yellow components, YC1 and YC2, were isolated from the HCl-methanol (HCl-MeOH) extract from nacreous organic matrices obtained by decalcification of the shells with ethylenediaminetetraacetic acid (EDTA). Energy-dispersive X-ray and infrared spectroscopy analyses suggested that YC1 and YC2 precipitated under basic conditions are composed of Fe-containing inorganic and polyamide-containing organic compounds, respectively. YC1 solubilized under acidic conditions exhibited positive reactions to KSCN and K4[Fe(CN)6] reagents, showing the same ultraviolet-visible absorption spectrum as those of Fe(III)-containing compounds. In addition, X-ray absorption fine structure analysis supported the compound in the form of Fe(III). The total amount of Fe was approximately 2.6 times higher in the yellow than white nacre, and most Fe was fractionated into the EDTA-decalcifying and HCl-MeOH extracts. These results suggest that Fe(III) coordinated to EDTA-soluble and insoluble matrix compounds are mainly associated with yellow color development not only in the Akoya pearl oyster shells but also in the cultured Akoya pearls.
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Affiliation(s)
- Makoto Kakinuma
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan.
| | - Ko Yasumoto
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa, 252-0373, Japan
| | - Michio Suzuki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Chiaki Kasugai
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan
| | - Mirai Koide
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan
| | - Kayo Mitani
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan
| | - Kaho Shidoji
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa, 252-0373, Japan
| | - Shigeharu Kinoshita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Fumihiro Hattori
- Research and Development Department, Mikimoto Pharmaceutical Co., Ltd., 1425 Kurose, Ise, Mie, 516-8581, Japan
| | - Kaoru Maeyama
- Research and Development Department, Mikimoto Pharmaceutical Co., Ltd., 1425 Kurose, Ise, Mie, 516-8581, Japan
| | - Masahiko Awaji
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhamaura, Minami-ise, Mie, 516-0193, Japan
| | - Kiyohito Nagai
- Pearl Research Laboratory, Mikimoto Co., Ltd., 923 Hazako-osaki, Hamajima, Shima, Mie, 517-0403, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa, 252-0373, Japan
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17
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Li H, Bai L, Dong X, Qi X, Liu H, Yu D. SEM observation of early shell formation and expression of biomineralization-related genes during larval development in the pearl oyster Pinctada fucata. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 33:100650. [PMID: 31837590 DOI: 10.1016/j.cbd.2019.100650] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 11/28/2019] [Accepted: 11/28/2019] [Indexed: 11/25/2022]
Abstract
Shell formation of Pinctada fucata in larval development stages plays a crucial role in their survival. Scanning electron microscopy (SEM) was used to observe the morphological changes during larval development. We found that the early shell forms soon after enlargement of the blastopore at the anterior end of the trochophore stage and the complete shell forms in the spats stage, required for metamorphosis of P. fucata. Based on our transcriptome data of trochophore, D-shaped, umbonal, eyespots and spats stages, including the whole process of shell formation, 93 differentially expressed biomineralization-related genes were identified, of which 25 genes were unique to P. fucata, 30 were identical to genes in pacific oyster, and the remaining genes were annotated to other species. Two-dimensional and three-dimensional principal components analysis (PCA) showed that different developmental stages were significantly different, with the early two stages exhibiting a larger difference compared with the next stages. The 93 genes were sorted into 20 trends with three trends being significantly enriched: an initial increase and then a decrease, a monotonic decrease, and a monotonic increase. Gene expression patterns changed with regulatory function during shell formation. Almost all the biomineralization-related genes were up-regulated in the D-shaped stage, but only five genes were up-regulated in that stage but down-regulated in the remaining stages. There were also 11 genes up-regulated in the last three stages, and a total of 24 genes showed high expression level during the last four stages. The 55 genes selected for shell incision experiment sorted into five trends and most genes presented differences in expression between 24 h and other time points. Considering all these results, there is a correlation with the morphological change and the expression of biomineralization-related genes during larval developmental stages, especially of differently expressed genes.
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Affiliation(s)
- Haimei Li
- Weifang Medical University, Weifang 261042, Shandong, China.
| | - Lirong Bai
- Beibu Gulf University, Qinzhou 535011, Guangxi, China
| | - Xiaoyun Dong
- Weifang Medical University, Weifang 261042, Shandong, China
| | - Xiaohui Qi
- Weifang Medical University, Weifang 261042, Shandong, China
| | - Hongying Liu
- Weifang Medical University, Weifang 261042, Shandong, China
| | - Dahui Yu
- Beibu Gulf University, Qinzhou 535011, Guangxi, China.
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18
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Blay C, Planes S, Ky CL. Crossing Phenotype Heritability and Candidate Gene Expression in Grafted Black-Lipped Pearl Oyster Pinctada margaritifera, an Animal Chimera. J Hered 2019; 109:510-519. [PMID: 29584922 DOI: 10.1093/jhered/esy015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 03/23/2018] [Indexed: 12/13/2022] Open
Abstract
Grafting mantle tissue of a donor pearl oyster into the gonad of a recipient oyster results in the formation of a chimera, the pearl sac. The phenotypic variations of this chimera are hypothesized to be the result of interactions between the donor and recipient genomes. In this study, the heritability of phenotypic variation and its association with gene expression were investigated for the first time during Pinctada margaritifera pearl production. Genetic variance was evaluated at different levels, 1) before the graft operation (expression in graft tissue), 2) after grafting (pearl sac tissue expression in chimera), and 3) on the product of the graft (pearl phenotype traits) based on controlled biparental crosses and the F1 generation. Donor-related genetic parameter estimates clearly demonstrate heritability for nacre weight and thickness, darkness and color, and surface defects and grade, which signifies a genetic basis in the donor oyster. In graft relative gene expression, the value of heritability was superior to 0.20 in for almost all genes; whereas in pearl sac, heritability estimates were low (h2 < 0.10; except for CALC1 and Aspein). Pearl sac expression seems to be more influenced by residual variance than the graft, which can be explained by environmental effects that influence pearls sac gene expression and act as a recipient additive genetic component. The interactions between donor and recipient are very complex, and further research is required to understand the role of the recipient oysters on pearl phenotypic and gene expression variances.
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Affiliation(s)
- Carole Blay
- Ifremer, UMR EIO 241, Labex Corail, Centre du Pacifique, Taravao, Tahiti, Polynésie Française.,PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Labex Corail, Université de Perpignan, 52 Avenue Paul Alduy, Perpignan Cedex, France
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Labex Corail, Université de Perpignan, 52 Avenue Paul Alduy, Perpignan Cedex, France
| | - Chin-Long Ky
- Ifremer, UMR EIO 241, Labex Corail, Centre du Pacifique, Taravao, Tahiti, Polynésie Française
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Glycan Binding Profiling of Jacalin-Related Lectins from the Pteria Penguin Pearl Shell. Int J Mol Sci 2019; 20:ijms20184629. [PMID: 31540487 PMCID: PMC6769917 DOI: 10.3390/ijms20184629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/14/2019] [Accepted: 09/15/2019] [Indexed: 11/25/2022] Open
Abstract
We determined the primary structures of jacalin-related lectins termed PPL3s (PPL3A, 3B, and 3C, which are dimers consisting of sequence variants α + α, α + β, β + β, respectively) and PPL4, which is heterodimer consisting of α + β subunits, isolated from mantle secretory fluid of Pteria penguin (Mabe) pearl shell. Their carbohydrate-binding properties were analyzed, in addition to that of PPL2A, which was previously reported as a matrix protein. PPL3s and PPL4 shared only 35–50% homology to PPL2A, respectively; they exhibited significantly different carbohydrate-binding specificities based on the multiple glycan binding profiling data sets from frontal affinity chromatography analysis. The carbohydrate-binding specificity of PPL3s was similar to that of PPL2A, except only for Man3Fuc1Xyl1GlcNAc2 oligosaccharide, while PPL4 showed different carbohydrate-binding specificity compared with PPL2A and PPL3s. PPL2A and PPL3s mainly recognize agalactosylated- and galactosylated-type glycans. On the other hand, PPL4 binds to high-mannose-and hybrid-type N-linked glycans but not agalactosylated- and galactosylated-type glycans.
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21
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Rivera-Perez C, Magallanes-Dominguez C, Dominguez-Beltran RV, Ojeda-Ramirez de Areyano JJ, Hernandez-Saavedra NY. Biochemical and molecular characterization of N66 from the shell of Pinctada mazatlanica. PeerJ 2019; 7:e7212. [PMID: 31293836 PMCID: PMC6599672 DOI: 10.7717/peerj.7212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/30/2019] [Indexed: 11/20/2022] Open
Abstract
Mollusk shell mineralization is a tightly controlled process made by shell matrix proteins (SMPs). However, the study of SMPs has been limited to a few model species. In this study, the N66 mRNA of the pearl oyster Pinctada mazatlanica was cloned and functionally characterized. The full sequence of the N66 mRNA comprises 1,766 base pairs, and encodes one N66 protein. A sequence analysis revealed that N66 contained two carbonic anhydrase (CA) domains, a NG domain and several glycosylation sites. The sequence showed similarity to the CA VII but also with its homolog protein nacrein. The native N66 protein was isolated from the shell and identified by mass spectrometry, the peptide sequence matched to the nucleotide sequence obtained. Native N66 is a glycoprotein with a molecular mass of 60-66 kDa which displays CA activity and calcium carbonate precipitation ability in presence of different salts. Also, a recombinant form of N66 was produced in Escherichia coli, and functionally characterized. The recombinant N66 displayed higher CA activity and crystallization capability than the native N66, suggesting that the lack of posttranslational modifications in the recombinant N66 might modulate its activity.
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Affiliation(s)
- Crisalejandra Rivera-Perez
- Department of Fisheries Ecology, CONACyT-Centro de Investigaciones Biologicas del Noroeste (CIBNOR), La Paz, Baja California Sur, Mexico
| | - Catalina Magallanes-Dominguez
- Department of Fisheries Ecology, Molecular Genetics Laboratory, Centro de Investigaciones Biologicas del Noroeste (CIBNOR), La Paz, Baja California Sur, Mexico
| | | | - Josafat Jehu Ojeda-Ramirez de Areyano
- Department of Fisheries Ecology, Molecular Genetics Laboratory, Centro de Investigaciones Biologicas del Noroeste (CIBNOR), La Paz, Baja California Sur, Mexico
| | - Norma Y. Hernandez-Saavedra
- Department of Fisheries Ecology, Molecular Genetics Laboratory, Centro de Investigaciones Biologicas del Noroeste (CIBNOR), La Paz, Baja California Sur, Mexico
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22
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Huang S, Ichikawa Y, Yoshitake K, Kinoshita S, Igarashi Y, Omori F, Maeyama K, Nagai K, Watabe S, Asakawa S. Identification and Characterization of microRNAs and Their Predicted Functions in Biomineralization in the Pearl Oyster ( Pinctada fucata). BIOLOGY 2019; 8:biology8020047. [PMID: 31212990 PMCID: PMC6627748 DOI: 10.3390/biology8020047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 11/16/2022]
Abstract
The biological process of pearl formation is an ongoing research topic, and a number of genes associated with this process have been identified. However, the involvement of microRNAs (miRNAs) in biomineralization in the pearl oyster, Pinctada fucata, is not well understood. In order to investigate the divergence and function of miRNAs in P. fucata, we performed a transcriptome analysis of small RNA libraries prepared from adductor muscle, gill, ovary, and mantle tissues. We identified 186 known and 42 novel miRNAs in these tissues. Clustering analysis showed that the expression patterns of miRNAs were similar among the somatic tissues, but they differed significantly between the somatic and ovary tissues. To validate the existence of the identified miRNAs, nine known and three novel miRNAs were verified by stem-loop qRT-PCR using U6 snRNA as an internal reference. The expression abundance and target prediction between miRNAs and biomineralization-related genes indicated that miR-1990c-3p, miR-876, miR-9a-3p, and novel-3 may be key factors in the regulatory network that act by controlling the formation of matrix proteins or the differentiation of mineralogenic cells during shell formation in mantle tissue. Our findings serve to further clarify the processes underlying biomineralization in P. fucata.
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Affiliation(s)
- Songqian Huang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Yuki Ichikawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Shigeharu Kinoshita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Yoji Igarashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Fumito Omori
- Mikimoto Pharmaceutical CO., LTD., Kurose 1425, Ise, Mie 516-8581, Japan.
| | - Kaoru Maeyama
- Mikimoto Pharmaceutical CO., LTD., Kurose 1425, Ise, Mie 516-8581, Japan.
| | - Kiyohito Nagai
- Pearl Research Laboratory, K. MIKIMOTO & CO., LTD., Osaki Hazako 923, Hamajima, Shima, Mie 517-0403, Japan.
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa 252-0313, Japan.
| | - Shuichi Asakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
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Ramesh K, Yarra T, Clark MS, John U, Melzner F. Expression of calcification-related ion transporters during blue mussel larval development. Ecol Evol 2019; 9:7157-7172. [PMID: 31380040 PMCID: PMC6662379 DOI: 10.1002/ece3.5287] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 01/03/2023] Open
Abstract
The physiological processes driving the rapid rates of calcification in larval bivalves are poorly understood. Here, we use a calcification substrate-limited approach (low dissolved inorganic carbon, C T) and mRNA sequencing to identify proteins involved in bicarbonate acquisition during shell formation. As a secondary approach, we examined expression of ion transport and shell matrix proteins (SMPs) over the course of larval development and shell formation. We reared four families of Mytilus edulis under ambient (ca. 1865 µmol/kg) and low C T (ca. 941 µmol/kg) conditions and compared expression patterns at six developmental time points. Larvae reared under low C T exhibited a developmental delay, and a small subset of contigs was differentially regulated between ambient and low C T conditions. Of particular note was the identification of one contig encoding an anion transporter (SLC26) which was strongly upregulated (2.3-2.9 fold) under low C T conditions. By analyzing gene expression profiles over the course of larval development, we are able to isolate sequences encoding ion transport and SMPs to enhance our understanding of cellular pathways underlying larval calcification processes. In particular, we observe the differential expression of contigs encoding SLC4 family members (sodium bicarbonate cotransporters, anion exchangers), calcium-transporting ATPases, sodium/calcium exchangers, and SMPs such as nacrein, tyrosinase, and transcripts related to chitin production. With a range of candidate genes, this work identifies ion transport pathways in bivalve larvae and by applying comparative genomics to investigate temporal expression patterns, provides a foundation for further studies to functionally characterize the proteins involved in larval calcification.
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Affiliation(s)
- Kirti Ramesh
- GEOMAR Helmholtz Centre for Ocean ResearchKielGermany
- Department of Biological and Environmental Sciences, Sven Lovén Centre for Marine Infrastructure‐KristinebergUniversity of GothenburgFiskebäckskilSweden
| | - Tejaswi Yarra
- British Antarctic SurveyNatural Environment Research CouncilCambridgeUK
- Ashworth Laboratories, Institute of Evolutionary BiologyUniversity of EdinburghEdinburghUK
| | - Melody S. Clark
- British Antarctic SurveyNatural Environment Research CouncilCambridgeUK
| | - Uwe John
- Ecological ChemistryAlfred‐Wegener‐Institut Helmholtz‐Zentrum für Polar‐und MeeresforschungBremerhavenGermany
- Helmholtz‐Institute for Functional Marine BiodiversityOldenburgGermany
| | - Frank Melzner
- GEOMAR Helmholtz Centre for Ocean ResearchKielGermany
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Electroextraction of Insoluble Proteins from the Organic Matrix of the Nacreous Layer of the Japanese Pearl Oyster, Pinctada fucata. Methods Protoc 2019; 2:mps2020037. [PMID: 31164616 PMCID: PMC6632181 DOI: 10.3390/mps2020037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/02/2019] [Accepted: 05/08/2019] [Indexed: 11/16/2022] Open
Abstract
The nacreous layer of shells and pearls is composed of aragonite crystals arranged in an organic matrix. The organic matrix contains chitin and several proteins that regulate the formation of the nacreous layer. Owing to their strong interactions in the organic matrix, the current method for extraction of insoluble proteins from the pre-powdered nacreous layer involves heating to high temperatures in the presence of a detergent (e.g., sodium dodecyl sulfate, SDS) and reductant (e.g., dithiothreitol, DTT), which is likely to induce protein degradation. Therefore, we have developed an electroextraction method to isolate proteins from the organic matrix of a nacreous organic sheet, that was obtained following the decalcification of shells in their original shape. Our electroextraction method employs milder conditions without heating or detergent. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) patterns of the electro-extracted proteins (EEPs) under non-reduced and reduced conditions revealed that this method yielded a greater number of different proteins compared with the conventional extraction method and the isolated EEPs retained their disulfide bonds. Our method is able to easily extract insoluble proteins from the nacreous layer under mild conditions and will undoubtedly aid future analyses into the functions of the nacreous layer proteins.
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25
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Huang S, Ichikawa Y, Igarashi Y, Yoshitake K, Kinoshita S, Omori F, Maeyama K, Nagai K, Watabe S, Asakawa S. Piwi-interacting RNA (piRNA) expression patterns in pearl oyster (Pinctada fucata) somatic tissues. Sci Rep 2019; 9:247. [PMID: 30670741 PMCID: PMC6342924 DOI: 10.1038/s41598-018-36726-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/19/2018] [Indexed: 12/31/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) belong to a recently discovered class of small non-coding RNAs whose best-understood function is repressing transposable element activity. Most piRNA studies have been conducted on model organisms and little is known about piRNA expression and function in mollusks. We performed high-throughput sequencing of small RNAs extracted from the mantle, adductor muscle, gill, and ovary tissues of the pearl oyster, Pinctada fucata. RNA species with sequences of approximately 30 nt were widely expressed in all tissues. Uridine at the 5' terminal and protection from β-elimination at the 3' terminal suggested that these were putative piRNAs. A total of 18.0 million putative piRNAs were assigned to 2.8 million unique piRNAs, and 35,848 piRNA clusters were identified. Mapping to the reference genome showed that 25% of the unique piRNAs mapped to multiple tandem loci on the scaffold. Expression patterns of the piRNA clusters were similar within the somatic tissues, but differed significantly between the somatic and gonadal tissues. These findings suggest that in pearl oysters piRNAs have important and novel functions beyond those in the germ line.
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Affiliation(s)
- Songqian Huang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yuki Ichikawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoji Igarashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shigeharu Kinoshita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Fumito Omori
- Mikimoto Pharmaceutical CO., LTD., Kurose 1425, Ise, Mie, 516-8581, Japan
| | - Kaoru Maeyama
- Mikimoto Pharmaceutical CO., LTD., Kurose 1425, Ise, Mie, 516-8581, Japan
| | - Kiyohito Nagai
- Pearl Research Laboratory, K. MIKIMOTO & CO., LTD., Osaki Hazako 923, Hamajima, Shima, Mie, 517-0403, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa, 252-0313, Japan
| | - Shuichi Asakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
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Blay C, Planes S, Ky CL. Cultured Pearl Surface Quality Profiling by the Shell Matrix Protein Gene Expression in the Biomineralised Pearl Sac Tissue of Pinctada margaritifera. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:490-501. [PMID: 29663093 DOI: 10.1007/s10126-018-9811-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 03/16/2018] [Indexed: 06/08/2023]
Abstract
Nucleated pearls are produced by molluscs of the Pinctada genus through the biomineralisation activity of the pearl sac tissue within the recipient oyster. The pearl sac originates from graft tissue taken from the donor oyster mantle and its functioning is crucial in determining key factors that impact pearl quality surface characteristics. The specific role of related gene regulation during gem biogenesis was unknown, so we analysed the expression profiles of eight genes encoding nacreous (PIF, MSI60, PERL1) or prismatic (SHEM5, PRISM, ASP, SHEM9) shell matrix proteins or both (CALC1) in the pearl sac (N = 211) of Pinctada margaritifera during pearl biogenesis. The pearls and pearl sacs analysed were from a uniform experimental graft with sequential harvests at 3, 6 and 9 months post-grafting. Quality traits of the corresponding pearls were recorded: surface defects, surface deposits and overall quality grade. Results showed that (1) the first 3 months of culture seem crucial for pearl quality surface determination and (2) all the genes (SHEM5, PRISM, ASP, SHEM9) encoding proteins related to calcite layer formation were over-expressed in the pearl sacs that produced low pearl surface quality. Multivariate regression tree building clearly identified three genes implicated in pearl surface quality, SHEM9, ASP and PIF. SHEM9 and ASP were clearly implicated in low pearl quality, whereas PIF was implicated in high quality. Results could be used as biomarkers for genetic improvement of P. margaritifera pearl quality and constitute a novel perspective to understanding the molecular mechanism of pearl formation.
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Affiliation(s)
- Carole Blay
- Ifremer, UMR EIO241, Labex Corail, Centre du Pacifique, BP 49, 98719, Taravao, Tahiti, French Polynesia
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- Laboratoire d'Excellence "CORAIL", Tahiti, French Polynesia
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- Laboratoire d'Excellence "CORAIL", Tahiti, French Polynesia
| | - Chin-Long Ky
- Ifremer, UMR EIO241, Labex Corail, Centre du Pacifique, BP 49, 98719, Taravao, Tahiti, French Polynesia.
- Laboratoire d'Excellence "CORAIL", Tahiti, French Polynesia.
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Ohmori F, Kinoshita S, Funabara D, Koyama H, Nagai K, Maeyama K, Okamoto K, Asakawa S, Watabe S. Novel Isoforms of N16 and N19 Families Implicated for the Nacreous Layer Formation in the Pearl Oyster Pinctada fucata. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:155-167. [PMID: 29340846 DOI: 10.1007/s10126-017-9793-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 12/28/2017] [Indexed: 06/07/2023]
Abstract
Although a wide variety of proteins and genes possibly related to the shell formation in bivalve have been identified, their functions have been only partially approved. We have recently performed deep sequencing of expressed sequence tags (ESTs) from the pearl oyster Pinctada fucata using a next-generation sequencer, identifying a dozen of novel gene candidates which are possibly associated with the nacreous layer formation. Among the ESTs, we focused on three novel isoforms (N16-6, N16-7, and N19-2) of N16 and N19 families with reference to five known genes in the families and determined the full-length cDNA sequences of these isoforms. Reverse transcription-polymerase chain reaction revealed that N16-6 was expressed in gill, gonad, adductor muscle, and mantle, whereas N16-7 exclusively in mantle. N19-2 was expressed in all tissues examined. In situ hybridization demonstrated their regional expression in mantle and pearl sac, which well corresponded to those shown by EST analysis previously reported. Shells in the pearl oyster injected with dsRNAs of N16-7 and N19-2 showed abnormal surface appearance in the nacreous layer. Taken together, novel isoforms in N16 and N19 families shown in this study are essential to form the nacreous layer.
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Affiliation(s)
- Fumito Ohmori
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shigeharu Kinoshita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Daisuke Funabara
- Graduate School of Bioresources, Mie University, Kurimamachiya 1577, Tsu, Mie, 514-8507, Japan
| | - Hiroki Koyama
- Graduate School of Biosphere Science, Hiroshima University, Hiroshima, 739-8528, Japan
| | - Kiyohito Nagai
- Pearl Research Laboratory, K. Mikimoto & Co., Ltd., Osaki Hazako 923, Hamajima, Shima, Mie, 517-0403, Japan
| | - Kaoru Maeyama
- Mikimoto Pharmaceutical Co., Ltd., Kurose 1425, Ise, Mie, 516-8581, Japan
| | - Kikuhiko Okamoto
- Mikimoto Pharmaceutical Co., Ltd., Kurose 1425, Ise, Mie, 516-8581, Japan
| | - Shuichi Asakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shugo Watabe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa, 252-0313, Japan.
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Abstract
The extracellular matrix (ECM) has central roles in tissue integrity and remodeling throughout the life span of animals. While collagens are the most abundant structural components of ECM in most tissues, tissue-specific molecular complexity is contributed by ECM glycoproteins. The matricellular glycoproteins are categorized primarily according to functional criteria and represented predominantly by the thrombospondin, tenascin, SPARC/osteonectin, and CCN families. These proteins do not self-assemble into ECM fibrils; nevertheless, they shape ECM properties through interactions with structural ECM proteins, growth factors, and cells. Matricellular proteins also promote cell migration or morphological changes through adhesion-modulating or counter-adhesive actions on cell-ECM adhesions, intracellular signaling, and the actin cytoskeleton. Typically, matricellular proteins are most highly expressed during embryonic development. In adult tissues, expression is more limited unless activated by cues for dynamic tissue remodeling and cell motility, such as occur during inflammatory response and wound repair. Many insights in the complex roles of matricellular proteins have been obtained from studies of gene knockout mice. However, with the exception of chordate-specific tenascins, these are highly conserved proteins that are encoded in many animal phyla. This review will consider the increasing body of research on matricellular proteins in nonmammalian animal models. These models provide better access to the very earliest stages of embryonic development and opportunities to study biological processes such as limb and organ regeneration. In aggregate, this research is expanding concepts of the functions and mechanisms of action of matricellular proteins.
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Affiliation(s)
- Josephine C Adams
- School of Biochemistry, University of Bristol, Bristol, United Kingdom.
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29
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Nakae S, Shionyu M, Ogawa T, Shirai T. Structures of jacalin-related lectin PPL3 regulating pearl shell biomineralization. Proteins 2018. [PMID: 29524263 DOI: 10.1002/prot.25491] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The nacreous layer of pearl oysters is one of the major biominerals of commercial and industrial interest. Jacalin-related lectins, including PPL3 isoforms, are known to regulate biomineralization of the Pteria penguin pearl shell, although the molecular mechanisms are largely unknown. The PPL3 crystal structures were determined partly by utilizing microgravity environments for 3 isoforms, namely, PPL3A, PPL3B, and PPL3C. The structures revealed a tail-to-tail dimer structure established by forming a unique inter-subunit disulfide bond at C-termini. The N-terminal residues were found in pyroglutamate form, and this was partly explained by the post-translational modification of PPL3 isoforms implied from the discrepancy between amino acid and gene sequences. The complex structures with trehalose and isomaltose indicated that the novel specificity originated from the unique α-helix of PPL3 isoforms. Docking simulations of PPL3B to various calcite crystal faces suggested the edge of a β-sheet and the carbohydrate-binding site rich in charged residues were the interface to the biomineral, and implied that the isoforms differed in calcite interactions.
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Affiliation(s)
- Setsu Nakae
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga 526-0829, Japan
| | - Masafumi Shionyu
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga 526-0829, Japan
| | - Tomohisa Ogawa
- Department of Biomolecular Science, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Tsuyoshi Shirai
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga 526-0829, Japan
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30
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31
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Li S, Liu Y, Huang J, Zhan A, Xie L, Zhang R. The receptor genes PfBMPR1B and PfBAMBI are involved in regulating shell biomineralization in the pearl oyster Pinctada fucata. Sci Rep 2017; 7:9219. [PMID: 28835628 PMCID: PMC5569090 DOI: 10.1038/s41598-017-10011-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 08/02/2017] [Indexed: 12/15/2022] Open
Abstract
Mounting evidence suggests that TGFβ/BMP signaling pathway is most likely involved in shell biomineralization in molluscs, but the function of pathway receptors is poorly studied. Here, we cloned and identified two homologous BMP receptor genes, PfBMPR1B and PfBAMBI, from the pearl oyster Pinctada fucata. Real-time quantitative PCR and in situ hybridization revealed that these genes were expressed in mantle edge and pallial, specifically located at the outer epithelia. Knockdown of PfBMPR1B by RNA interference (RNAi) significantly decreased the expression levels of matrix protein (MP) genes and induced the abnormal ultrastructure of prismatic and nacreous layers. Conversely, knockdown of PfBAMBI significantly increased the expression levels of a portion of MP genes and induced the overgrowth of nacreous layer crystals. In the RNAi and shell notching experiments, MP gene expressions were competitively regulated by PfBMPR1B and PfBAMBI. In addition, the receptor inhibitor LDN193189 reduced the expression levels of MP genes in mantle primary cells and larvae, and induced abnormal D-shaped shell formation during larval development. Collectively, these results clearly show that PfBMPR1B and PfBAMBI are involved in regulating shell biomineralization in P. fucata. Our study therefore provides the direct evidence that BMP receptors participate in mollusc biomineralization.
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Affiliation(s)
- Shiguo Li
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yangjia Liu
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jingliang Huang
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Liping Xie
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Rongqing Zhang
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, 314006, China.
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32
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Harris J, Böhm CF, Wolf SE. Universal structure motifs in biominerals: a lesson from nature for the efficient design of bioinspired functional materials. Interface Focus 2017. [PMID: 28630670 DOI: 10.1166/jctn.2008.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Biominerals are typically indispensable structures for their host organism in which they serve varying functions, such as mechanical support and protection, mineral storage, detoxification site, or as a sensor or optical guide. In this perspective article, we highlight the occurrence of both structural diversity and uniformity within these biogenic ceramics. For the first time, we demonstrate that the universality-diversity paradigm, which was initially introduced for proteins by Buehler et al. (Cranford & Buehler 2012 Biomateriomics; Cranford et al. 2013 Adv. Mater.25, 802-824 (doi:10.1002/adma.201202553); Ackbarow & Buehler 2008 J. Comput. Theor. Nanosci.5, 1193-1204 (doi:10.1166/jctn.2008.001); Buehler & Yung 2009 Nat. Mater.8, 175-188 (doi:10.1038/nmat2387)), is also valid in the realm of biomineralization. A nanogranular composite structure is shared by most biominerals which rests on a common, non-classical crystal growth mechanism. The nanogranular composite structure affects various properties of the macroscale biogenic ceramic, a phenomenon we attribute to emergence. Emergence, in turn, is typical for hierarchically organized materials. This is a clear call to renew comparative studies of even distantly related biomineralizing organisms to identify further universal design motifs and their associated emergent properties. Such universal motifs with emergent macro-scale properties may represent an unparalleled toolbox for the efficient design of bioinspired functional materials.
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Affiliation(s)
- Joe Harris
- Department of Materials Science and Engineering, Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Martensstrasse 5, 91058 Erlangen, Germany
| | - Corinna F Böhm
- Department of Materials Science and Engineering, Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Martensstrasse 5, 91058 Erlangen, Germany
| | - Stephan E Wolf
- Department of Materials Science and Engineering, Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Martensstrasse 5, 91058 Erlangen, Germany.,Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Haberstrasse 9a, 91058 Erlangen, Germany
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33
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Harris J, Böhm CF, Wolf SE. Universal structure motifs in biominerals: a lesson from nature for the efficient design of bioinspired functional materials. Interface Focus 2017; 7:20160120. [PMID: 28630670 PMCID: PMC5474032 DOI: 10.1098/rsfs.2016.0120] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Biominerals are typically indispensable structures for their host organism in which they serve varying functions, such as mechanical support and protection, mineral storage, detoxification site, or as a sensor or optical guide. In this perspective article, we highlight the occurrence of both structural diversity and uniformity within these biogenic ceramics. For the first time, we demonstrate that the universality-diversity paradigm, which was initially introduced for proteins by Buehler et al. (Cranford & Buehler 2012 Biomateriomics; Cranford et al. 2013 Adv. Mater.25, 802-824 (doi:10.1002/adma.201202553); Ackbarow & Buehler 2008 J. Comput. Theor. Nanosci.5, 1193-1204 (doi:10.1166/jctn.2008.001); Buehler & Yung 2009 Nat. Mater.8, 175-188 (doi:10.1038/nmat2387)), is also valid in the realm of biomineralization. A nanogranular composite structure is shared by most biominerals which rests on a common, non-classical crystal growth mechanism. The nanogranular composite structure affects various properties of the macroscale biogenic ceramic, a phenomenon we attribute to emergence. Emergence, in turn, is typical for hierarchically organized materials. This is a clear call to renew comparative studies of even distantly related biomineralizing organisms to identify further universal design motifs and their associated emergent properties. Such universal motifs with emergent macro-scale properties may represent an unparalleled toolbox for the efficient design of bioinspired functional materials.
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Affiliation(s)
- Joe Harris
- Department of Materials Science and Engineering, Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Martensstrasse 5, 91058 Erlangen, Germany
| | - Corinna F. Böhm
- Department of Materials Science and Engineering, Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Martensstrasse 5, 91058 Erlangen, Germany
| | - Stephan E. Wolf
- Department of Materials Science and Engineering, Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Martensstrasse 5, 91058 Erlangen, Germany
- Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Haberstrasse 9a, 91058 Erlangen, Germany
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Donor and recipient contribution to phenotypic traits and the expression of biomineralisation genes in the pearl oyster model Pinctada margaritifera. Sci Rep 2017; 7:2696. [PMID: 28578397 PMCID: PMC5457395 DOI: 10.1038/s41598-017-02457-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 04/12/2017] [Indexed: 11/08/2022] Open
Abstract
Grafting associates two distinct genotypes, each of which maintains its own genetic identity throughout the life of the grafted organism. Grafting technology is well documented in the plant kingdom, but much less so in animals. The pearl oyster, Pinctada margaritifera, produces valuable pearls as a result of the biomineralisation process of a mantle graft from a donor inserted together with a nucleus into the gonad of a recipient oyster. To explore the respective roles of donor and recipient in pearl formation, a uniform experimental graft was designed using donor and recipient oysters monitored for their growth traits. At the same time, phenotypic parameters corresponding to pearl size and quality traits were recorded. Phenotypic interaction analysis demonstrated: 1) a positive correlation between recipient shell biometric parameters and pearl size, 2) an individual donor effect on cultured pearl quality traits. Furthermore, the expressions of biomineralisation biomarkers encoding proteins in the aragonite or prismatic layer showed: 1) higher gene expression levels of aragonite-related genes in the large donor phenotype in the graft tissue, and 2) correlation of gene expression in the pearl sac tissue with pearl quality traits and recipient biometric parameters. These results emphasize that pearl size is mainly driven by the recipient and that pearl quality traits are mainly driven by the donor.
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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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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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Top-Down Proteomics and Farm Animal and Aquatic Sciences. Proteomes 2016; 4:proteomes4040038. [PMID: 28248248 PMCID: PMC5260971 DOI: 10.3390/proteomes4040038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/25/2016] [Accepted: 12/05/2016] [Indexed: 01/16/2023] Open
Abstract
Proteomics is a field of growing importance in animal and aquatic sciences. Similar to other proteomic approaches, top-down proteomics is slowly making its way within the vast array of proteomic approaches that researchers have access to. This opinion and mini-review article is dedicated to top-down proteomics and how its use can be of importance to animal and aquatic sciences. Herein, we include an overview of the principles of top-down proteomics and how it differs regarding other more commonly used proteomic methods, especially bottom-up proteomics. In addition, we provide relevant sections on how the approach was or can be used as a research tool and conclude with our opinions of future use in animal and aquatic sciences.
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Recombinant production and biochemical characterization of a hypothetical acidic shell matrix protein in Escherichia coli for the preparation of protein-based CaCO3 biominerals. KOREAN J CHEM ENG 2016. [DOI: 10.1007/s11814-016-0091-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Takeuchi T, Yamada L, Shinzato C, Sawada H, Satoh N. Stepwise Evolution of Coral Biomineralization Revealed with Genome-Wide Proteomics and Transcriptomics. PLoS One 2016; 11:e0156424. [PMID: 27253604 PMCID: PMC4890752 DOI: 10.1371/journal.pone.0156424] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/14/2016] [Indexed: 11/19/2022] Open
Abstract
Despite the importance of stony corals in many research fields related to global issues, such as marine ecology, climate change, paleoclimatogy, and metazoan evolution, very little is known about the evolutionary origin of coral skeleton formation. In order to investigate the evolution of coral biomineralization, we have identified skeletal organic matrix proteins (SOMPs) in the skeletal proteome of the scleractinian coral, Acropora digitifera, for which large genomic and transcriptomic datasets are available. Scrupulous gene annotation was conducted based on comparisons of functional domain structures among metazoans. We found that SOMPs include not only coral-specific proteins, but also protein families that are widely conserved among cnidarians and other metazoans. We also identified several conserved transmembrane proteins in the skeletal proteome. Gene expression analysis revealed that expression of these conserved genes continues throughout development. Therefore, these genes are involved not only skeleton formation, but also in basic cellular functions, such as cell-cell interaction and signaling. On the other hand, genes encoding coral-specific proteins, including extracellular matrix domain-containing proteins, galaxins, and acidic proteins, were prominently expressed in post-settlement stages, indicating their role in skeleton formation. Taken together, the process of coral skeleton formation is hypothesized as: 1) formation of initial extracellular matrix between epithelial cells and substrate, employing pre-existing transmembrane proteins; 2) additional extracellular matrix formation using novel proteins that have emerged by domain shuffling and rapid molecular evolution and; 3) calcification controlled by coral-specific SOMPs.
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Affiliation(s)
- Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904–0495, Japan
- * E-mail:
| | - Lixy Yamada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, 517–0004, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904–0495, Japan
| | - Hitoshi Sawada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, 517–0004, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904–0495, Japan
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Bjärnmark NA, Yarra T, Churcher AM, Felix RC, Clark MS, Power DM. Transcriptomics provides insight into Mytilus galloprovincialis (Mollusca: Bivalvia) mantle function and its role in biomineralisation. Mar Genomics 2016; 27:37-45. [PMID: 27037218 DOI: 10.1016/j.margen.2016.03.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 03/03/2016] [Accepted: 03/11/2016] [Indexed: 01/13/2023]
Abstract
The mantle is an organ common to all molluscs and is at the forefront of the biomineralisation process. The present study used the Mediterranean mussel (Mytilus galloprovincialis) as a model species to investigate the structural and functional role of the mantle in shell formation. The transcriptomes of three regions of the mantle edge (umbo to posterior edge) were sequenced using Illumina technology which yielded a total of 61,674,325 reads after adapter trimming and filtering. The raw reads assembled into 179,879 transcripts with an N50 value of 1086bp. A total of 1363 transcripts (321, 223 and 816 in regions 1, 2 and 3, respectively) that differed in abundance in the three mantle regions were identified and putative function was assigned to 54% using BLAST sequence similarity searches (cut-off less than 1e(-10)). Morphological differences detected by histology of the three mantle regions was linked to functional heterogeneity by selecting the top five most abundant Pfam domains in the annotated 1363 differentially abundant transcripts across the three mantle regions. Calcium binding domains dominated region two (middle segment of the mantle edge). Candidate biomineralisation genes were mined and tested by qPCR. This revealed that Flp-like, a penicillin binding protein potentially involved in shell matrix maintenance of the Pacific oyster (Crassostrea gigas), had significantly higher expression in the posterior end of the mantle edge (region one). Our findings are intriguing as they indicate that the mantle edge appears to be a heterogeneous tissue, displaying structural and functional bias.
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Affiliation(s)
- Nadège A Bjärnmark
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal.
| | - T Yarra
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - A M Churcher
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal
| | - R C Felix
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal
| | - M S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - D M Power
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal.
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Williams ST. Molluscan shell colour. Biol Rev Camb Philos Soc 2016; 92:1039-1058. [DOI: 10.1111/brv.12268] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 01/27/2023]
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Takeuchi T, Koyanagi R, Gyoja F, Kanda M, Hisata K, Fujie M, Goto H, Yamasaki S, Nagai K, Morino Y, Miyamoto H, Endo K, Endo H, Nagasawa H, Kinoshita S, Asakawa S, Watabe S, Satoh N, Kawashima T. Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle. ZOOLOGICAL LETTERS 2016; 2:3. [PMID: 26900483 PMCID: PMC4759782 DOI: 10.1186/s40851-016-0039-2] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 02/11/2016] [Indexed: 05/12/2023]
Abstract
INTRODUCTION Bivalve molluscs have flourished in marine environments, and many species constitute important aquatic resources. Recently, whole genome sequences from two bivalves, the pearl oyster, Pinctada fucata, and the Pacific oyster, Crassostrea gigas, have been decoded, making it possible to compare genomic sequences among molluscs, and to explore general and lineage-specific genetic features and trends in bivalves. In order to improve the quality of sequence data for these purposes, we have updated the entire P. fucata genome assembly. RESULTS We present a new genome assembly of the pearl oyster, Pinctada fucata (version 2.0). To update the assembly, we conducted additional sequencing, obtaining accumulated sequence data amounting to 193× the P. fucata genome. Sequence redundancy in contigs that was caused by heterozygosity was removed in silico, which significantly improved subsequent scaffolding. Gene model version 2.0 was generated with the aid of manual gene annotations supplied by the P. fucata research community. Comparison of mollusc and other bilaterian genomes shows that gene arrangements of Hox, ParaHox, and Wnt clusters in the P. fucata genome are similar to those of other molluscs. Like the Pacific oyster, P. fucata possesses many genes involved in environmental responses and in immune defense. Phylogenetic analyses of heat shock protein70 and C1q domain-containing protein families indicate that extensive expansion of genes occurred independently in each lineage. Several gene duplication events prior to the split between the pearl oyster and the Pacific oyster are also evident. In addition, a number of tandem duplications of genes that encode shell matrix proteins are also well characterized in the P. fucata genome. CONCLUSIONS Both the Pinctada and Crassostrea lineages have expanded specific gene families in a lineage-specific manner. Frequent duplication of genes responsible for shell formation in the P. fucata genome explains the diversity of mollusc shell structures. These duplications reveal dynamic genome evolution to forge the complex physiology that enables bivalves to employ a sessile lifestyle in the intertidal zone.
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Affiliation(s)
- Takeshi Takeuchi
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Ryo Koyanagi
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Fuki Gyoja
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Miyuki Kanda
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Kanako Hisata
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Manabu Fujie
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Hiroki Goto
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Shinichi Yamasaki
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Kiyohito Nagai
- />Pearl Research Institute, Mikimoto CO. LTD, Shima, Mie 517-0403 Japan
| | - Yoshiaki Morino
- />Graduate School of Life and Environmental Science, University of Tsukuba, Ibaraki, 305-8572 Japan
| | - Hiroshi Miyamoto
- />Department of Genetic Engineering, Faculty of Biology-Oriented Science and Technology, Kinki University, 930 Nishimitani, Kinokawa, Wakayama 649-6493 Japan
| | - Kazuyoshi Endo
- />Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Hirotoshi Endo
- />Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564 Japan
| | - Hiromichi Nagasawa
- />Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 Japan
- />College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 People’s Republic of China
| | - Shigeharu Kinoshita
- />Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Shuichi Asakawa
- />Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Shugo Watabe
- />Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 Japan
- />Kitasato University School of Marine Bioscience, Sagamihara, Kanagawa 252-0373 Japan
| | - Noriyuki Satoh
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Takeshi Kawashima
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
- />Present Address: Graduate School of Life and Environmental Science, University of Tsukuba, Ibaraki, 305-8572 Japan
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In-depth proteomic analysis of shell matrix proteins of Pinctada fucata. Sci Rep 2015; 5:17269. [PMID: 26608573 PMCID: PMC4660305 DOI: 10.1038/srep17269] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/28/2015] [Indexed: 11/16/2022] Open
Abstract
The shells of pearl oysters, Pinctada fucata, are composed of calcite and aragonite and possess remarkable mechanical properties. These shells are formed under the regulation of macromolecules, especially shell matrix proteins (SMPs). Identification of diverse SMPs will lay a foundation for understanding biomineralization process. Here, we identified 72 unique SMPs using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of proteins extracted from the shells of P. fucata combined with a draft genome. Of 72 SMPs, 17 SMPs are related to both the prismatic and nacreous layers. Moreover, according to the diverse domains found in the SMPs, we hypothesize that in addition to controlling CaCO3 crystallization and crystal organization, these proteins may potentially regulate the extracellular microenvironment and communicate between cells and the extracellular matrix (ECM). Immunohistological localization techniques identify the SMPs in the mantle, shells and synthetic calcite. Together, these proteomic data increase the repertoires of the shell matrix proteins in P. fucata and suggest that shell formation in P. fucata may involve tight regulation of cellular activities and the extracellular microenvironment.
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Bassim S, Chapman RW, Tanguy A, Moraga D, Tremblay R. Predicting growth and mortality of bivalve larvae using gene expression and supervised machine learning. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2015; 16:59-72. [PMID: 26282335 DOI: 10.1016/j.cbd.2015.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 07/13/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022]
Abstract
It is commonly known that the nature of the diet has diverse consequences on larval performance and longevity, however it is still unclear which genes have critical impacts on bivalve development and which pathways are of particular importance in their vulnerability or resistance. First we show that a diet deficient in essential fatty acid (EFA) produces higher larval mortality rates, a reduced shell growth, and lower postlarval performance, all of which are positively correlated with a decline in arachidonic and eicosapentaenoic acids levels, two EFAs known as eicosanoid precursors. Eicosanoids affect the cell inflammatory reactions and are synthesized from long-chain EFAs. Second, we show for the first time that a deficiency in eicosanoid precursors is associated with a network of 29 genes. Their differential regulation can lead to slower growth and higher mortality of Mytilus edulis larvae. Some of these genes are specific to bivalves and others are implicated at the same time in lipid metabolism and defense. Several genes are expressed only during pre-metamorphosis where they are essential for muscle or neurone development and biomineralization, but only in stress-induced larvae. Finally, we discuss how our networks of differentially expressed genes might dynamically alter the development of marine bivalves, especially under dietary influence.
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Affiliation(s)
- Sleiman Bassim
- Institut des Sciences de la mer de Rimouski, Universite du Quebec a Rimouski, 310, allee des Ursulines, Rimouski Quebec G5L 3A1, Canada; Laboratoire des Sciences de l'Environnement Marin, Institut Universitaire Europeen de la Mer, Universite de Bretagne Occidentale, Rue Dumont d'Urville, 29280 Plouzane, France
| | - Robert W Chapman
- Marine Resources Research Institute, South Carolina Department of Natural Resources and Hollings Marine Laboratory, 331 Ft. Johnson Road, Charleston, SC 29412, USA
| | - Arnaud Tanguy
- UPMC Universite Paris 6, UMR 7144, Genetique et Adaptation en Milieu Extreme, Station Biologique de Roscoff, France
| | - Dario Moraga
- Laboratoire des Sciences de l'Environnement Marin, Institut Universitaire Europeen de la Mer, Universite de Bretagne Occidentale, Rue Dumont d'Urville, 29280 Plouzane, France
| | - Rejean Tremblay
- Institut des Sciences de la mer de Rimouski, Universite du Quebec a Rimouski, 310, allee des Ursulines, Rimouski Quebec G5L 3A1, Canada.
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Liu J, Yang D, Liu S, Li S, Xu G, Zheng G, Xie L, Zhang R. Microarray: a global analysis of biomineralization-related gene expression profiles during larval development in the pearl oyster, Pinctada fucata. BMC Genomics 2015; 16:325. [PMID: 25927556 PMCID: PMC4445274 DOI: 10.1186/s12864-015-1524-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/10/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The molluscan Pinctada fucata is an important pearl-culturing organism to study biomineralization mechanisms. Several biomineralization-related genes play important roles regulating shell formation, but most previous work has focused only on their functions in adult oysters. Few studies have investigated biomineralization during larval development, when the shell is initially constructed and formed until the juvenile stage in dissoconch shells. Here, we report, for the first time, a global gene analysis during larval development of P. fucata based on a microarray and reveal the relationships between biomineralization-related genes and the shell formation process. RESULTS Based on the P. fucata mantle transcriptome, 58,940 probes (60 nt), representing 58,623 transcripts, were synthesized. The gene expression profiles of the fertilized egg, trochophore, D-shaped, and umbonal stage larvae, as well as juveniles were analyzed by microarray performance. The expression patterns of the biomineralization-related genes changed corresponding to their regulatory function during shell formation. Matrix proteins chitin synthase and PFMG2 were highly expressed at the D-shaped stage, whereas PFMG6, PFMG8 and PfN23 were significantly up-regulated at the umbonal stage, indicating different roles regulating the formation of either periostracum, Prodissoconch I or Prodissoconch II shells. However, the majority of matrix proteins were expressed at high levels at the juvenile stage, and the shells comprised both an aragonitic nacreous layer and a calcitic prismatic layer as adults. We also identified five new genes that were significantly up-regulated in juveniles. These genes were expressed particularly in the mantle and coded for secreted proteins with tandem-arranged repeat units, as most matrix proteins. RNAi knockdown resulted in disrupted nacreous and prismatic shell layers, indicating their potential roles in shell formation. CONCLUSIONS Our results add a global perspective on larval expression patterns of P. fucata genes and propose a mechanism of how biomineralization-related genes regulate the larval shell formation process. These results increase knowledge about biomineralization-related genes and highlight new aspects of shell formation mechanisms.
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Affiliation(s)
- Jun Liu
- Institute of Marine Biotechnology, Collaborative Innovation Center of Deep Sea Biology, School of Life Science, Tsinghua University, Beijing, 100084, China.
| | - Dong Yang
- Institute of Marine Biotechnology, Collaborative Innovation Center of Deep Sea Biology, School of Life Science, Tsinghua University, Beijing, 100084, China.
| | - Shiting Liu
- Institute of Marine Biotechnology, Collaborative Innovation Center of Deep Sea Biology, School of Life Science, Tsinghua University, Beijing, 100084, China.
| | - Shiguo Li
- Institute of Marine Biotechnology, Collaborative Innovation Center of Deep Sea Biology, School of Life Science, Tsinghua University, Beijing, 100084, China.
| | - Guangrui Xu
- Institute of Marine Biotechnology, Collaborative Innovation Center of Deep Sea Biology, School of Life Science, Tsinghua University, Beijing, 100084, China.
| | - Guilan Zheng
- Institute of Marine Biotechnology, Collaborative Innovation Center of Deep Sea Biology, School of Life Science, Tsinghua University, Beijing, 100084, China.
| | - Liping Xie
- Institute of Marine Biotechnology, Collaborative Innovation Center of Deep Sea Biology, School of Life Science, Tsinghua University, Beijing, 100084, China.
| | - Rongqing Zhang
- Institute of Marine Biotechnology, Collaborative Innovation Center of Deep Sea Biology, School of Life Science, Tsinghua University, Beijing, 100084, China.
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Allam B, Pales Espinosa E, Tanguy A, Jeffroy F, Le Bris C, Paillard C. Transcriptional changes in Manila clam (Ruditapes philippinarum) in response to Brown Ring Disease. FISH & SHELLFISH IMMUNOLOGY 2014; 41:2-11. [PMID: 24882017 DOI: 10.1016/j.fsi.2014.05.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/12/2014] [Accepted: 05/15/2014] [Indexed: 02/05/2023]
Abstract
Brown Ring Disease (BRD) is a bacterial infection affecting the economically-important clam Ruditapes philippinarum. The disease is caused by a bacterium, Vibrio tapetis, that colonizes the edge of the mantle, altering the biomineralization process and normal shell growth. Altered organic shell matrices accumulate on the inner face of the shell leading to the formation of the typical brown ring in the extrapallial space (between the mantle and the shell). Even though structural and functional changes have been described in solid (mantle) and fluid (hemolymph and extrapallial fluids) tissues from infected clams, the underlying molecular alterations and responses remain largely unknown. This study was designed to gather information on clam molecular responses to the disease and to compare focal responses at the site of the infection (mantle and extrapallial fluid) with systemic (hemolymph) responses. To do so, we designed and produced a Manila clam expression oligoarray (15K Agilent) using transcriptomic data available in public databases and used this platform to comparatively assess transcriptomic changes in mantle, hemolymph and extrapallial fluid of infected clams. Results showed significant regulation in diseased clams of molecules involved in pathogen recognition (e.g. lectins, C1q domain-containing proteins) and killing (defensin), apoptosis regulation (death-associated protein, bcl-2) and in biomineralization (shell matrix proteins, perlucin, galaxin, chitin- and calcium-binding proteins). While most changes in response to the disease were tissue-specific, systemic alterations included co-regulation in all 3 tested tissues of molecules involved in microbe recognition and killing (complement-related factors, defensin). These results provide a first glance at molecular alterations and responses caused by BRD and identify targets for future functional investigations.
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Affiliation(s)
- Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA.
| | | | - Arnaud Tanguy
- Station Biologique de Roscoff, UPMC-CNRS, Roscoff, France
| | - Fanny Jeffroy
- Institut Universitaire Européen de la Mer, Plouzané, France
| | - Cedric Le Bris
- Institut Universitaire Européen de la Mer, Plouzané, France
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Aguilera F, McDougall C, Degnan BM. Evolution of the tyrosinase gene family in bivalve molluscs: independent expansion of the mantle gene repertoire. Acta Biomater 2014; 10:3855-65. [PMID: 24704693 DOI: 10.1016/j.actbio.2014.03.031] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/08/2014] [Accepted: 03/26/2014] [Indexed: 12/27/2022]
Abstract
Tyrosinase is a copper-containing enzyme that mediates the hydroxylation of monophenols and oxidation of o-diphenols to o-quinones. This enzyme is involved in a variety of biological processes, including pigment production, innate immunity, wound healing, and exoskeleton fabrication and hardening (e.g. arthropod skeleton and mollusc shell). Here we show that the tyrosinase gene family has undergone large expansions in pearl oysters (Pinctada spp.) and the Pacific oyster (Crassostrea gigas). Phylogenetic analysis reveals that pearl oysters possess at least four tyrosinase genes that are not present in the Pacific oyster. Likewise, C. gigas has multiple tyrosinase genes that are not orthologous to the Pinctada genes, indicating that this gene family has expanded independently in these bivalve lineages. Many of the tyrosinase genes in these bivalves are expressed at relatively high levels in the mantle, the organ responsible for shell fabrication. Detailed comparisons of tyrosinase gene expression in different regions of the mantle in two closely related pearl oysters, P. maxima and P. margaritifera, reveals that recently evolved orthologous tyrosinase genes can have markedly different expression profiles. The expansion of tyrosinase genes in these oysters and their co-option into the mantle's gene regulatory network is consistent with mollusc shell formation being underpinned by a rapidly evolving transcriptome.
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Affiliation(s)
- Felipe Aguilera
- Centre for Marine Sciences, School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia
| | - Carmel McDougall
- Centre for Marine Sciences, School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia
| | - Bernard M Degnan
- Centre for Marine Sciences, School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia.
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Splice variants of perlucin from Haliotis laevigata modulate the crystallisation of CaCO3. PLoS One 2014; 9:e97126. [PMID: 24824517 PMCID: PMC4019660 DOI: 10.1371/journal.pone.0097126] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/15/2014] [Indexed: 12/13/2022] Open
Abstract
Perlucin is one of the proteins of the organic matrix of nacre (mother of pearl) playing an important role in biomineralisation. This nacreous layer can be predominately found in the mollusc lineages and is most intensively studied as a compound of the shell of the marine Australian abalone Haliotis laevigata. A more detailed analysis of Perlucin will elucidate some of the still unknown processes in the complex interplay of the organic/inorganic compounds involved in the formation of nacre as a very interesting composite material not only from a life science-based point of view. Within this study we discovered three unknown Perlucin splice variants of the Australian abalone H. laevigata. The amplified cDNAs vary from 562 to 815 base pairs and the resulting translation products differ predominantly in the absence or presence of a varying number of a 10 mer peptide C-terminal repeat. The splice variants could further be confirmed by matrix-assisted laser desorption ionisation time of flight mass spectrometry (MALDI-ToF MS) analysis as endogenous Perlucin, purified from decalcified abalone shell. Interestingly, we observed that the different variants expressed as maltose-binding protein (MBP) fusion proteins in E. coli showed strong differences in their influence on precipitating CaCO3 and that these differences might be due to a splice variant-specific formation of large protein aggregates influenced by the number of the 10 mer peptide repeats. Our results are evidence for a more complex situation with respect to Perlucin functional regulation by demonstrating that Perlucin splice variants modulate the crystallisation of calcium carbonate. The identification of differentially behaving Perlucin variants may open a completely new perspective for the field of nacre biomineralisation.
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Pohl A, Weiss IM. Real-time monitoring of calcium carbonate and cationic peptide deposition on carboxylate-SAM using a microfluidic SAW biosensor. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2014; 5:1823-35. [PMID: 25383294 PMCID: PMC4222353 DOI: 10.3762/bjnano.5.193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 09/28/2014] [Indexed: 05/10/2023]
Abstract
A microfluidic biosensor with surface acoustic wave technology was used in this study to monitor the interaction of calcium carbonate with standard carboxylate self-assembled monolayer sensor chips. Different fluids, with and without biomolecular components, were investigated. The pH-dependent surface interactions of two bio-inspired cationic peptides, AS8 and ES9, which are similar to an extracellular domain of the chitin synthase involved in mollusc shell formation, were also investigated in a biological buffer system. A range of experimental conditions are described that are suitable to study non-covalent molecular interactions in the presence of ionic substances, such as, mineral precursors below the solubility equilibrium. The peptide ES9, equal to the mollusc chitin synthase epitope, is less sensitive to changes in pH than its counterpart AS8 with a penta-lysine core, which lacks the flanking acidic residues. This study demonstrates the extraordinary potential of microfluidic surface acoustic wave biosensors to significantly expand our experimental capabilities for studying the principles underlying biomineralization in vitro.
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Affiliation(s)
- Anna Pohl
- INM – Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
- Saarland University, Campus D2 2, 66123 Saarbrücken, Germany
| | - Ingrid M Weiss
- INM – Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
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Chaturvedi R, Singha PK, Dey S. Water soluble bioactives of nacre mediate antioxidant activity and osteoblast differentiation. PLoS One 2013; 8:e84584. [PMID: 24367677 PMCID: PMC3868599 DOI: 10.1371/journal.pone.0084584] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/20/2013] [Indexed: 11/18/2022] Open
Abstract
The water soluble matrix of nacre is a proven osteoinductive material. In spite of the differences in the biomolecular compositions of nacre obtained from multiple species of oysters, the common biochemical properties of those principles substantiate their biological activity. However, the mechanism by which nacre stimulates bone differentiation remains largely unknown. Since the positive impact of antioxidants on bone metabolism is well acknowledged, in this study we investigated the antioxidant potential of a water soluble matrix (WSM) obtained from the nacre of the marine oyster Pinctada fucata, which could regulate its osteoblast differentiation activity. Enhanced levels of ALP activity observed in pre-osteoblast cells upon treatment with WSM, suggested the induction of bone differentiation events. Furthermore, bone nodule formation and up-regulation of bone differentiation marker transcripts, i.e. collagen type-1 and osteocalcin by WSM confirmed its ability to induce differentiation of the pre-osteoblasts into mature osteoblasts. Remarkably, same WSM fraction upon pre-treatment lowered the H2O2 and UV-B induced oxidative damages in keratinocytes, thus indicating the antioxidant potential of WSM. This was further confirmed from the in vitro scavenging of ABTS and DPPH free radicals and inhibition of lipid peroxidation by WSM. Together, these results indicate that WSM poses both antioxidant potential and osteoblast differentiation property. Thus, bioactivities associated with nacre holds potential in the development of therapeutics for bone regeneration and against oxidative stress induced damages in cells.
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Affiliation(s)
- Ratna Chaturvedi
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
- * E-mail:
| | - Prajjal Kanti Singha
- Department of Pathology, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Satyahari Dey
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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