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Li Z, Yang M, Zhou C, Shi P, Hu P, Liang B, Jiang Q, Zhang L, Liu X, Lai C, Zhang T, Song H. Deciphering the molecular toolkit: regulatory elements governing shell biomineralization in marine molluscs. Integr Zool 2024. [PMID: 39030865 DOI: 10.1111/1749-4877.12876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2024]
Abstract
The intricate process of shell biomineralization in marine molluscs is governed by a complex interplay of regulatory elements, encompassing secretomes, transporters, and noncoding RNA. This review delves into recent advancements in understanding these regulatory mechanisms, emphasizing their significance in elucidating the functions and evolutionary dynamics of the molluscan shell biomineralization process. Central to this intricate orchestration are secretomes with diverse functional domains, selectively exported to the extrapallial space, which directly regulate crystal growth and morphology. Transporters are crucial for substrate transportation in the calcification and maintenance of cellular homeostasis. Beyond proteins and transporters, noncoding RNA molecules are integral components influencing shell biomineralization. This review underscores the nonnegligible roles played by these genetic elements at the molecular level. To comprehend the complexity of biomineralization in mollusc, we explore the origin and evolutionary history of regulatory elements, primarily secretomes. While some elements have recently evolved, others are ancient genes that have been co-opted into the biomineralization toolkit. These elements undergo structural and functional evolution through rapidly evolving repetitive low-complexity domains and domain gain/loss/rearrangements, ultimately shaping a distinctive set of secretomes characterized by both conserved features and evolutionary innovations. This comprehensive review enhances our understanding of molluscan biomineralization at the molecular and genetic levels.
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Affiliation(s)
- Zhuoqing Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meijie Yang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cong Zhou
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pu Shi
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pengpeng Hu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bin Liang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingtian Jiang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Lili Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiaoyan Liu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Agricultural University, Qingdao, China
| | - Changping Lai
- Lianyungang Blue Carbon Marine Technology Co., Lianyungang, China
| | - Tao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Song
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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Jin C, Cheng K, Jiang R, Zhang Y, Luo W. A Novel Kunitz-Type Serine Protease Inhibitor (HcKuSPI) is Involved in Antibacterial Defense in Innate Immunity and Participates in Shell Formation of Hyriopsis cumingii. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:37-49. [PMID: 38117374 DOI: 10.1007/s10126-023-10275-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
Serine protease inhibitors (SPIs) are abundantly reported for its inhibition against specific proteases involved in the immune responses, but SPI data related to calcareous shells are scarce. Previously, our research group has reported the proteome analysis of non-nucleated pearl powder, and a candidate matrix protein containing two Kunitz domains in the acid soluble fraction caught our attention. In the present study, the full-length cDNA sequence of HcKuSPI was obtained from Hyriopsis cumingii. HcKuSPI was specifically expressed in the mantle, with hybridization signals mainly concentrated to dorsal epithelial cells at the mantle edge and weak signals at the mantle pallium, suggesting HcKuSPI was involved in shell formation. HcKuSPI expression in the mantle was upregulated after Aeromonas hydrophila and Staphylococcus aureus challenge to extrapallial fluids (EPFs). A glutathione S transferase (GST)-HcKuSPI recombinant protein showed strong inhibitory activity against the proteases, trypsin and chymotrypsin. Moreover, HcKuSPI expression in an experimental group was significantly higher when compared with a control group during pellicle growth and crystal deposition in shell regeneration processes, while the organic shell framework of newborn prisms and nacre tablets was completely destroyed after HcKuSPI RNA interference (RNAi). Therefore, HcKuSPI secreted by the mantle may effectively neutralize excess proteases and bacterial proteases in the EPF during bacterial infection and could prevent matrix protein extracellular degradation by suppressing protease proteolytic activity, thereby ensuring a smooth shell biomineralization. In addition, GST-HcKuSPI was also crucial for crystal morphology regulation. These results have important implications for our understanding of the potential roles of SPIs during shell biomineralization.
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Affiliation(s)
- Can Jin
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, People's Republic of China
| | - Kang Cheng
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, People's Republic of China
| | - Rui Jiang
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, People's Republic of China
| | - Yihang Zhang
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, People's Republic of China
| | - Wen Luo
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, People's Republic of China.
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Sleight VA. Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation. Brief Funct Genomics 2023; 22:509-516. [PMID: 37592885 PMCID: PMC10658180 DOI: 10.1093/bfgp/elad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/10/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
Biomineralisation is the process by which living organisms produce hard structures such as shells and bone. There are multiple independent origins of biomineralised skeletons across the tree of life. This review gives a glimpse into the diversity of spiralian biominerals and what they can teach us about the evolution of novelty. It discusses different levels of biological organisation that may be informative to understand the evolution of biomineralisation and considers the relationship between skeletal and non-skeletal biominerals. More specifically, this review explores if cell type and gene regulatory network approaches could enhance our understanding of the evolutionary origins of biomineralisation.
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Affiliation(s)
- Victoria A Sleight
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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4
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Bai Y, Liu S, Hu Y, Yu H, Kong L, Xu C, Li Q. Multi-omic insights into the formation and evolution of a novel shell microstructure in oysters. BMC Biol 2023; 21:204. [PMID: 37775818 PMCID: PMC10543319 DOI: 10.1186/s12915-023-01706-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Molluscan shell, composed of a diverse range of architectures and microstructures, is a classic model system to study the relationships between molecular evolution and biomineralized structure formation. The shells of oysters differ from those of other molluscs by possessing a novel microstructure, chalky calcite, which facilitates adaptation to the sessile lifestyle. However, the genetic basis and evolutionary origin of this adaptive innovation remain largely unexplored. RESULTS We report the first whole-genome assembly and shell proteomes of the Iwagaki oyster Crassostrea nippona. Multi-omic integrative analyses revealed that independently expanded and co-opted tyrosinase, peroxidase, TIMP genes may contribute to the chalky layer formation in oysters. Comparisons with other molluscan shell proteomes imply that von Willebrand factor type A and chitin-binding domains are basic members of molluscan biomineralization toolkit. Genome-wide identification and analyses of these two domains in 19 metazoans enabled us to propose that the well-known Pif may share a common origin in the last common ancestor of Bilateria. Furthermore, Pif and LamG3 genes acquire new genetic function for shell mineralization in bivalves and the chalky calcite formation in oysters likely through a combination of gene duplication and domain reorganization. CONCLUSIONS The spatial expression of SMP genes in the mantle and molecular evolution of Pif are potentially involved in regulation of the chalky calcite deposition, thereby shaping the high plasticity of the oyster shell to adapt to a sessile lifestyle. This study further highlights neo-functionalization as a crucial mechanism for the diversification of shell mineralization and microstructures in molluscs, which may be applied more widely for studies on the evolution of metazoan biomineralization.
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Affiliation(s)
- Yitian Bai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yiming Hu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, 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
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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Ujiié Y, Ishitani Y, Nagai Y, Takaki Y, Toyofuku T, Ishii S. Unique evolution of foraminiferal calcification to survive global changes. SCIENCE ADVANCES 2023; 9:eadd3584. [PMID: 37343099 DOI: 10.1126/sciadv.add3584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 05/15/2023] [Indexed: 06/23/2023]
Abstract
Foraminifera, the most ancient known calcium carbonate-producing eukaryotes, are crucial players in global biogeochemical cycles and well-used environmental indicators in biogeosciences. However, little is known about their calcification mechanisms. This impedes understanding the organismal responses to ocean acidification, which alters marine calcium carbonate production, potentially leading to biogeochemical cycle changes. We conducted comparative single-cell transcriptomics and fluorescent microscopy and identified calcium ion (Ca2+) transport/secretion genes and α-carbonic anhydrases that control calcification in a foraminifer. They actively take up Ca2+ to boost mitochondrial adenosine triphosphate synthesis during calcification but need to pump excess intracellular Ca2+ to the calcification site to prevent cell death. Unique α-carbonic anhydrase genes induce the generation of bicarbonate and proton from multiple CO2 sources. These control mechanisms have evolved independently since the Precambrian to enable the development of large cells and calcification despite decreasing Ca2+ concentrations and pH in seawater. The present findings provide previously unknown insights into the calcification mechanisms and their subsequent function in enduring ocean acidification.
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Affiliation(s)
- Yurika Ujiié
- Marine Core Research Institute, Kochi University, Kōchi, Japan
| | - Yoshiyuki Ishitani
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yukiko Nagai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- National Museum of Nature and Science, Tokyo, Japan
| | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takashi Toyofuku
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Tokyo University of Marine Science and Technology (TUMSAT), Tokyo, Japan
| | - Shun'ichi Ishii
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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6
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Li Z, Li Q, Xu C, Yu H. Histological, elemental, and ultrastructural analysis of melanin in mantle of Pacific oyster (Crassostrea gigas). Microsc Res Tech 2023; 86:283-293. [PMID: 36444959 DOI: 10.1002/jemt.24269] [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: 07/14/2022] [Revised: 10/20/2022] [Accepted: 11/19/2022] [Indexed: 11/30/2022]
Abstract
Colorful shell of bivalve is mainly because of the biological pigments, of which melanin plays an important role in shell color formation. More and more studies focus on the genes function involved in melanin synthesis, but relatively few studies address the biochemical character and ultrastructure of melanin in bivalve from microscopic perspective. Here, we investigated the histological structure of mantle of Crassostrea gigas with orange shell color. Distribution of melanin in mantle was verified with histochemical staining. In addition, immunofluorescence technique showed that strongly positive signal of CgTYR was specific to the mantle margin, which is consistence with the location of brown granules in H&E staining. The further result of elementary composition of melanin displayed that metal Ca, Fe, and Zn were detected using scanning transmission electron microscope and energy dispersive spectroscopy mapping methods. Next, based on TEM observations, it was speculated that the series of cellular events leading to the formation and release of melanin. Melanocyte in the primary stage showed many mitochondria and rough endoplasmic reticulum as well as an extensive Golgi complex with numerous vesicles intermingled with melanosome. Subsequently, melanosome was expended and their hue gradually intensified, and Golgi complex and mitochondria were still observed in the cytoplasm. Finally, after melanosome was discharged into intercellular spaces, the disintegration of membranes in some cells, and severe cellular vacuolization. These data enrich the understanding of ultrastructural characteristic and formation of melanin in mantle of bivalve and pave the way for further investigating shell coloration at the cellular level.
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Affiliation(s)
- Zhuanzhuan Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
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7
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Gold DA, Vermeij GJ. Deep resilience: An evolutionary perspective on calcification in an age of ocean acidification. Front Physiol 2023; 14:1092321. [PMID: 36818444 PMCID: PMC9935589 DOI: 10.3389/fphys.2023.1092321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
The success of today's calcifying organisms in tomorrow's oceans depends, in part, on the resilience of their skeletons to ocean acidification. To the extent this statement is true there is reason to have hope. Many marine calcifiers demonstrate resilience when exposed to environments that mimic near-term ocean acidification. The fossil record similarly suggests that resilience in skeletons has increased dramatically over geologic time. This "deep resilience" is seen in the long-term stability of skeletal chemistry, as well as a decreasing correlation between skeletal mineralogy and extinction risk over time. Such resilience over geologic timescales is often attributed to genetic canalization-the hardening of genetic pathways due to the evolution of increasingly complex regulatory systems. But paradoxically, our current knowledge on biomineralization genetics suggests an opposing trend, where genes are co-opted and shuffled at an evolutionarily rapid pace. In this paper we consider two possible mechanisms driving deep resilience in skeletons that fall outside of genetic canalization: microbial co-regulation and macroevolutionary trends in skeleton structure. The mechanisms driving deep resilience should be considered when creating risk assessments for marine organisms facing ocean acidification and provide a wealth of research avenues to explore.
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8
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Min Y, Li Q, Yu H. Characterization of larval shell formation and CgPOU2F1, CgSox5, and CgPax6 gene expression during shell morphogenesis in Crassostrea gigas. Comp Biochem Physiol B Biochem Mol Biol 2023; 263:110783. [PMID: 35926704 DOI: 10.1016/j.cbpb.2022.110783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022]
Abstract
Shell formation is a dynamic process involving organic matrix secretion and calcification. In this study, we characterized shell morphogenesis during larval development in Crassostrea gigas. Using scanning electron microscopy (SEM) and fluorescence staining, we demonstrated that shell field, the first morphologically distinguishable shell-forming tissue, became visible soon after enlargement of the blastopore at the anterior end of the trochophore. Shell organic matrix namely protein polysaccharides and calcified structure appeared as a slit at the dorsal side of the embryo. The early shell field began to extend along the dorsal side of the trochophore larvae, and became a saddle shaped shell field that gave rise to the prodissoconch I embryonic shell in the early D-shaped larvae. Subsequently, prodissoconch II shell was formed in the late D-shaped larvae with a characteristic appearance of growth lines. To identify gene expression markers for studying shell formation, we isolated three potential larval shell formation genes CgPOU2F1, CgSox5, and CgPax6 and analyzed their expression during shell morphogenesis. The three potential shell formation genes possessed a similar pattern of expression. Their expression was detected in the shell gland and shell field regions in early D-shaped larvae, hereafter, their expression was detected at the larval mantle edge in the calcified shell stages. Together, these studies provide knowledge of shell morphogenesis in pacific oyster and molecular markers for studying the molecular regulation of biomineralization and shell formation.
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Affiliation(s)
- Yue Min
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Hong Yu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
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Shimizu K, Negishi L, Ito T, Touma S, Matsumoto T, Awaji M, Kurumizaka H, Yoshitake K, Kinoshita S, Asakawa S, Suzuki M. Evolution of nacre- and prisms-related shell matrix proteins in the pen shell, Atrina pectinata. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 44:101025. [PMID: 36075178 DOI: 10.1016/j.cbd.2022.101025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 01/27/2023]
Abstract
The molluscan shell is a good model for understanding the mechanisms underlying biomineralization. It is composed of calcium carbonate crystals and many types of organic molecules, such as the matrix proteins, polysaccharides, and lipids. The pen shell Atrina pectinata (Pterioida, Pinnidae) has two shell microstructures: an outer prismatic layer and an inner nacreous layer. Similar microstructures are well known in pearl oysters (Pteriidae), such as Pinctada fucata, and many kinds of shell matrix proteins (SMPs) have been identified from their shells. However, the members of SMPs that consist of the nacreous and prismatic layers of Pinnidae bivalves remain unclear. In this study, we identified 114 SMPs in the nacreous and prismatic layers of A. pectinata, of which only seven were found in both microstructures. 54 of them were found to bind calcium carbonate. Comparative analysis of nine molluscan shell proteomes showed that 69 of 114 SMPs of A. pectinata were found to have sequential similarity with at least one or more SMPs of other molluscan species. For instance, nacrein, tyrosinase, Pif/BMSP-like, chitinase (CN), chitin-binding proteins, CD109, and Kunitz-type serine proteinase inhibitors are widely shared among bivalves and gastropods. Our results provide new insights for understanding the complex evolution of SMPs related to nacreous and prismatic layer formation in the pteriomorph bivalves.
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Affiliation(s)
- Keisuke Shimizu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Takumi Ito
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Shogo Touma
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Toshie Matsumoto
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhama, Minami-Ise, Watarai, Mie 516-0193, Japan
| | - Masahiko Awaji
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhama, Minami-Ise, Watarai, Mie 516-0193, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan.
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10
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Yoshida MA, Hirota K, Imoto J, Okuno M, Tanaka H, Kajitani R, Toyoda A, Itoh T, Ikeo K, Sasaki T, Setiamarga DHE. Gene Recruitments and Dismissals in the Argonaut Genome Provide Insights into Pelagic Lifestyle Adaptation and Shell-like Eggcase Reacquisition. Genome Biol Evol 2022; 14:evac140. [PMID: 36283693 PMCID: PMC9635652 DOI: 10.1093/gbe/evac140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2022] [Indexed: 10/01/2023] Open
Abstract
The paper nautilus or greater argonaut, Argonauta argo, is a species of octopods which is characterized by its pelagic lifestyle and by the presence of a protective spiral-shaped shell-like eggcase in females. To reveal the genomic background of how the species adapted to the pelagic lifestyle and acquired its shell-like eggcase, we sequenced the draft genome of the species. The genome size was 1.1 Gb, which is the smallest among the cephalopods known to date, with the top 215 scaffolds (average length 5,064,479 bp) covering 81% (1.09 Gb) of the total assembly. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified nearly intact HOX, Parahox, Wnt clusters, and some gene clusters that could probably be related to the pelagic lifestyle, such as reflectin, tyrosinase, and opsin. The gene models also revealed several homologous genes related to calcified shell formation in Conchiferan mollusks, such as Pif-like, SOD, and TRX. Interestingly, comparative genomics analysis revealed that the homologous genes for such genes were also found in the genome of the shell-less octopus, as well as Nautilus, which has a true outer shell. Therefore, the draft genome sequence of Arg. argo presented here has helped us to gain further insights into the genetic background of the dynamic recruitment and dismissal of genes to form an important, converging extended phenotypic structure such as the shell and the shell-like eggcase. Additionally, it allows us to explore the evolution of from benthic to pelagic lifestyles in cephalopods and octopods.
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Affiliation(s)
- Masa-aki Yoshida
- Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Science, Shimane University, Okinoshima, Shimane 685-0024, Japan
| | - Kazuki Hirota
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- Department of Applied Chemistry and Biochemistry, National Institute of Technology (KOSEN), Wakayama College, Gobo, Wakayama 644-0012, Japan
| | - Junichi Imoto
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
| | - Hiroyuki Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Kazuho Ikeo
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Takenori Sasaki
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- The University Museum, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Davin H E Setiamarga
- Department of Applied Chemistry and Biochemistry, National Institute of Technology (KOSEN), Wakayama College, Gobo, Wakayama 644-0012, Japan
- The University Museum, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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11
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Brachiopod and mollusc biomineralisation is a conserved process that was lost in the phoronid-bryozoan stem lineage. EvoDevo 2022; 13:17. [PMID: 36123753 PMCID: PMC9484238 DOI: 10.1186/s13227-022-00202-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brachiopods and molluscs are lophotrochozoans with hard external shells which are often believed to have evolved convergently. While palaeontological data indicate that both groups are descended from biomineralising Cambrian ancestors, the closest relatives of brachiopods, phoronids and bryozoans, are mineralised to a much lower extent and are comparatively poorly represented in the Palaeozoic fossil record. Although brachiopod and mollusc shells are structurally analogous, genomic and proteomic evidence indicates that their formation involves a complement of conserved, orthologous genes. Here, we study a set of genes comprised of 3 homeodomain transcription factors, one signalling molecule and 6 structural proteins which are implicated in mollusc and brachiopod shell formation, search for their orthologs in transcriptomes or genomes of brachiopods, phoronids and bryozoans, and present expression patterns of 8 of the genes in postmetamorphic juveniles of the rhynchonelliform brachiopod T. transversa. RESULTS Transcriptome and genome searches for the 10 target genes in the brachiopods Terebratalia transversa, Lingula anatina, Novocrania anomala, the bryozoans Bugula neritina and Membranipora membranacea, and the phoronids Phoronis australis and Phoronopsis harmeri resulted in the recovery of orthologs of the majority of the genes in all taxa. While the full complement of genes was present in all brachiopods with a single exception in L. anatina, a bloc of four genes could consistently not be retrieved from bryozoans and phoronids. The genes engrailed, distal-less, ferritin, perlucin, sp1 and sp2 were shown to be expressed in the biomineralising mantle margin of T. transversa juveniles. CONCLUSIONS The gene expression patterns we recovered indicate that while mineralised shells in brachiopods and molluscs are structurally analogous, their formation builds on a homologous process that involves a conserved complement of orthologous genes. Losses of some of the genes related to biomineralisation in bryozoans and phoronids indicate that loss of the capacity to form mineralised structures occurred already in the phoronid-bryozoan stem group and supports the idea that mineralised skeletons evolved secondarily in some of the bryozoan subclades.
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12
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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13
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Capasso L, Aranda M, Cui G, Pousse M, Tambutté S, Zoccola D. Investigating calcification-related candidates in a non-symbiotic scleractinian coral, Tubastraea spp. Sci Rep 2022; 12:13515. [PMID: 35933557 PMCID: PMC9357087 DOI: 10.1038/s41598-022-17022-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022] Open
Abstract
In hermatypic scleractinian corals, photosynthetic fixation of CO2 and the production of CaCO3 are intimately linked due to their symbiotic relationship with dinoflagellates of the Symbiodiniaceae family. This makes it difficult to study ion transport mechanisms involved in the different pathways. In contrast, most ahermatypic scleractinian corals do not share this symbiotic relationship and thus offer an advantage when studying the ion transport mechanisms involved in the calcification process. Despite this advantage, non-symbiotic scleractinian corals have been systematically neglected in calcification studies, resulting in a lack of data especially at the molecular level. Here, we combined a tissue micro-dissection technique and RNA-sequencing to identify calcification-related ion transporters, and other candidates, in the ahermatypic non-symbiotic scleractinian coral Tubastraea spp. Our results show that Tubastraea spp. possesses several calcification-related candidates previously identified in symbiotic scleractinian corals (such as SLC4-γ, AMT-1like, CARP, etc.). Furthermore, we identify and describe a role in scleractinian calcification for several ion transporter candidates (such as SLC13, -16, -23, etc.) identified for the first time in this study. Taken together, our results provide not only insights about the molecular mechanisms underlying non-symbiotic scleractinian calcification, but also valuable tools for the development of biotechnological solutions to better control the extreme invasiveness of corals belonging to this particular genus.
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Affiliation(s)
- Laura Capasso
- Marine Biology Department, Centre Scientifique de Monaco (CSM), 8 Quai Antoine 1er, Monte Carlo, 9800, Monaco
- Sorbonne Université, Collège Doctoral, 75005, Paris, France
| | - Manuel Aranda
- Marine Science Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Guoxin Cui
- Marine Science Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Melanie Pousse
- Université Côte d'Azur, CNRS, Inserm, Institut for Research On Cancer and Aging, Nice (IRCAN), Medical School of Nice, Nice, France
| | - Sylvie Tambutté
- Marine Biology Department, Centre Scientifique de Monaco (CSM), 8 Quai Antoine 1er, Monte Carlo, 9800, Monaco.
| | - Didier Zoccola
- Marine Biology Department, Centre Scientifique de Monaco (CSM), 8 Quai Antoine 1er, Monte Carlo, 9800, Monaco.
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14
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Algrain M, Hennebert E, Bertemes P, Wattiez R, Flammang P, Lengerer B. In the footsteps of sea stars: deciphering the catalogue of proteins involved in underwater temporary adhesion. Open Biol 2022; 12:220103. [PMID: 35975651 PMCID: PMC9382459 DOI: 10.1098/rsob.220103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Sea stars adhere strongly but temporarily to underwater substrata via the secretion of a blend of proteins, forming an adhesive footprint that they leave on the surface after detachment. Their tube feet enclose a duo-gland adhesive system comprising two types of adhesive cells, contributing different layers of the footprint and de-adhesive cells. In this study, we characterized the catalogue of sea star footprint proteins (Sfps) in the species Asterias rubens to gain insights in their potential function. We identified 16 Sfps and mapped their expression to type 1 and/or type 2 adhesive cells or to de-adhesive cells by double fluorescent in situ hybridization. Based on their cellular expression pattern and their conserved functional domains, we propose that the identified Sfps serve different functions during attachment, with two Sfps coupling to the surface, six providing cohesive strength and the rest forming a binding matrix. Immunolabelling of footprints with antibodies directed against one protein of each category confirmed these roles. A de-adhesive gland cell-specific astacin-like proteinase presumably weakens the bond between the adhesive material and the tube foot surface during detachment. Overall, we provide a model for temporary adhesion in sea stars, including a comprehensive list of the proteins involved.
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Affiliation(s)
- Morgane Algrain
- Laboratory of Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons 7000, Belgium
| | - Elise Hennebert
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons 7000, Belgium
| | - Philip Bertemes
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Technikerstr. 25, Innsbruck 6020, Austria
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons 7000, Belgium
| | - Patrick Flammang
- Laboratory of Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons 7000, Belgium
| | - Birgit Lengerer
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Technikerstr. 25, Innsbruck 6020, Austria
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15
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Salamanca-Díaz DA, Ritschard EA, Schmidbaur H, Wanninger A. Comparative Single-Cell Transcriptomics Reveals Novel Genes Involved in Bivalve Embryonic Shell Formation and Questions Ontogenetic Homology of Molluscan Shell Types. Front Cell Dev Biol 2022; 10:883755. [PMID: 35813198 PMCID: PMC9261976 DOI: 10.3389/fcell.2022.883755] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/19/2022] [Indexed: 12/29/2022] Open
Abstract
Mollusks are known for their highly diverse repertoire of body plans that often includes external armor in form of mineralized hardparts. Representatives of the Conchifera, one of the two major lineages that comprises taxa which originated from a uni-shelled ancestor (Monoplacophora, Gastropoda, Cephalopoda, Scaphopoda, Bivalvia), are particularly relevant regarding the evolution of mollusk shells. Previous studies have found that the shell matrix of the adult shell (teleoconch) is rapidly evolving and that the gene set involved in shell formation is highly taxon-specific. However, detailed annotation of genes expressed in tissues involved in the formation of the embryonic shell (protoconch I) or the larval shell (protoconch II) are currently lacking. Here, we analyzed the genetic toolbox involved in embryonic and larval shell formation in the quagga mussel Dreissena rostriformis using single cell RNA sequencing. We found significant differences in genes expressed during embryonic and larval shell secretion, calling into question ontogenetic homology of these transitory bivalve shell types. Further ortholog comparisons throughout Metazoa indicates that a common genetic biomineralization toolbox, that was secondarily co-opted into molluscan shell formation, was already present in the last common metazoan ancestor. Genes included are engrailed, carbonic anhydrase, and tyrosinase homologs. However, we found that 25% of the genes expressed in the embryonic shell field of D. rostriformis lack an ortholog match with any other metazoan. This indicates that not only adult but also embryonic mollusk shells may be fast-evolving structures. We raise the question as to what degree, and on which taxonomic level, the gene complement involved in conchiferan protoconch formation may be lineage-specific or conserved across taxa.
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Affiliation(s)
- David A. Salamanca-Díaz
- Unit for Integrative Zoology, Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Elena A. Ritschard
- Division of Molecular Evolution and Development, Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Hannah Schmidbaur
- Division of Molecular Evolution and Development, Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Andreas Wanninger
- Unit for Integrative Zoology, Department of Evolutionary Biology, University of Vienna, Vienna, Austria
- *Correspondence: Andreas Wanninger,
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16
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Badou A, Pont S, Auzoux-Bordenave S, Lebreton M, Bardeau JF. New insight on spatial localization and microstructures of calcite-aragonite interfaces in Haliotis tuberculata adults: investigations of wild and farmed abalones by FTIR and Raman mapping. J Struct Biol 2022; 214:107854. [DOI: 10.1016/j.jsb.2022.107854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/21/2022] [Accepted: 03/30/2022] [Indexed: 10/18/2022]
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17
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Gilbert PUPA, Bergmann KD, Boekelheide N, Tambutté S, Mass T, Marin F, Adkins JF, Erez J, Gilbert B, Knutson V, Cantine M, Hernández JO, Knoll AH. Biomineralization: Integrating mechanism and evolutionary history. SCIENCE ADVANCES 2022; 8:eabl9653. [PMID: 35263127 PMCID: PMC8906573 DOI: 10.1126/sciadv.abl9653] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Calcium carbonate (CaCO3) biomineralizing organisms have played major roles in the history of life and the global carbon cycle during the past 541 Ma. Both marine diversification and mass extinctions reflect physiological responses to environmental changes through time. An integrated understanding of carbonate biomineralization is necessary to illuminate this evolutionary record and to understand how modern organisms will respond to 21st century global change. Biomineralization evolved independently but convergently across phyla, suggesting a unity of mechanism that transcends biological differences. In this review, we combine CaCO3 skeleton formation mechanisms with constraints from evolutionary history, omics, and a meta-analysis of isotopic data to develop a plausible model for CaCO3 biomineralization applicable to all phyla. The model provides a framework for understanding the environmental sensitivity of marine calcifiers, past mass extinctions, and resilience in 21st century acidifying oceans. Thus, it frames questions about the past, present, and future of CaCO3 biomineralizing organisms.
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Affiliation(s)
- Pupa U. P. A. Gilbert
- Departments of Physics, Chemistry, Geoscience, and Materials Science, University of Wisconsin-Madison, Madison, WI 53706, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Corresponding author. (P.U.P.A.G.); (A.H.K.)
| | - Kristin D. Bergmann
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nicholas Boekelheide
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sylvie Tambutté
- Centre Scientifique de Monaco, Department of Marine Biology, 98000 Monaco, Principality of Monaco
| | - Tali Mass
- University of Haifa, Marine Biology Department, Mt. Carmel, Haifa 31905, Israel
| | - Frédéric Marin
- Université de Bourgogne–Franche-Comté (UBFC), Laboratoire Biogéosciences, UMR CNRS 6282, Bâtiment des Sciences Gabriel, 21000 Dijon, France
| | - Jess F. Adkins
- Geological and Planetary Sciences, California Institute of Technology, MS 100-23, Pasadena, CA 91125, USA
| | - Jonathan Erez
- The Hebrew University of Jerusalem, Institute of Earth Sciences, Jerusalem 91904, Israel
| | - Benjamin Gilbert
- Energy Geoscience Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Vanessa Knutson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Marjorie Cantine
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Goethe-Universität Frankfurt, 60438 Frankfurt am Main, Germany
| | - Javier Ortega Hernández
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Andrew H. Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Corresponding author. (P.U.P.A.G.); (A.H.K.)
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18
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McCartney MA, Auch B, Kono T, Mallez S, Zhang Y, Obille A, Becker A, Abrahante JE, Garbe J, Badalamenti JP, Herman A, Mangelson H, Liachko I, Sullivan S, Sone ED, Koren S, Silverstein KAT, Beckman KB, Gohl DM. The genome of the zebra mussel, Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol. G3 (BETHESDA, MD.) 2022; 12:6460334. [PMID: 34897429 PMCID: PMC9210306 DOI: 10.1093/g3journal/jkab423] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023]
Abstract
The zebra mussel, Dreissena polymorpha, continues to spread from its native range in Eurasia to Europe and North America, causing billions of dollars in damage and dramatically altering invaded aquatic ecosystems. Despite these impacts, there are few genomic resources for Dreissena or related bivalves. Although the D. polymorpha genome is highly repetitive, we have used a combination of long-read sequencing and Hi-C-based scaffolding to generate a high-quality chromosome-scale genome assembly. Through comparative analysis and transcriptomics experiments, we have gained insights into processes that likely control the invasive success of zebra mussels, including shell formation, synthesis of byssal threads, and thermal tolerance. We identified multiple intact steamer-like elements, a retrotransposon that has been linked to transmissible cancer in marine clams. We also found that D. polymorpha have an unusual 67 kb mitochondrial genome containing numerous tandem repeats, making it the largest observed in Eumetazoa. Together these findings create a rich resource for invasive species research and control efforts.
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Affiliation(s)
- Michael A McCartney
- Department of Fisheries, Wildlife and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, St. Paul, MN 55108, USA
| | - Benjamin Auch
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | - Thomas Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sophie Mallez
- Department of Fisheries, Wildlife and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, St. Paul, MN 55108, USA
| | - Ying Zhang
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Angelico Obille
- Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Aaron Becker
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, Minneapolis, MN 55455, USA
| | - John Garbe
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | | | - Adam Herman
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | | - Eli D Sone
- Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.,Department of Materials Science & Engineering, University of Toronto, Toronto, ON M5S 3E4 Canada.,Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Kevin A T Silverstein
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Daryl M Gohl
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA.,Department of Genetics, Cell Biology, and Developmental Biology, University of Minnesota, Minneapolis, MN 55455, USA
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19
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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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20
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Colgan DJ. The potential for using shell proteins in gastropod systematics, assessed in patellogastropod limpets. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
This investigation of the application of shell protein information to gastropod systematics initially utilized available Lottia gigantea sequences and a transcriptome of Patelloida mimula developed here. Levels of differentiation between predicted sequences of reciprocal best-hit potential homologues in P. mimula and L. gigantea suggested that they could be useful within families, and possibly in higher taxa using some shell-associated proteins, particularly the peroxidases. Subsequently, proteomic analyses of the acid-soluble fraction of extractions from 17 shells and five tissue samples were conducted by combined liquid chromatography/mass spectrometry with nano-electrospray ionization. All proteins with abundance more than 1.2% in the L. gigantea shell proteome were identified with 100% confidence in most extractions by SearchGui/PeptideShaker analyses. In total, 259 of 379 peptides predicted from in silico digestion of L. gigantea shell proteins were represented by validated peptide spectrum matches in one or more specimens. Systematics applications were investigated by analysing metrics such as protein coverage by peptides and phylogenetic analyses of peptide presence/absence. The investigation suggested that diagnostic profiles based on fixed presence/absence differences can be used to separate species pairs. However, further development of analytical techniques and accumulation of reference databases is required for realising fully the systematics potential of the shell proteome.
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Affiliation(s)
- Donald James Colgan
- Malacology, Australian Museum Research Institute, The Australian Museum, 1 William St, Sydney 2010, Australia
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21
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Peng M, Liu Z, Li Z, Qian S, Liu X, Li J. The temptin gene of the clade Lophotrochozoa is involved in formation of the prismatic layer during biomineralization in molluscs. Int J Biol Macromol 2021; 188:800-810. [PMID: 34339790 DOI: 10.1016/j.ijbiomac.2021.07.164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/25/2021] [Accepted: 07/26/2021] [Indexed: 11/18/2022]
Abstract
The biomineralization mechanism of mollusc shell has been studied for a long time, but there is a lack of understanding about the relationship between the shell formation in vitro and the signaling system in vivo. In this study, we cloned a novel shell matrix protein gene (hc-temptin), which only be characterized as a water-borne protein pheromone of molluscs in previous studies, from the freshwater mussel Hyriopsis cumingii. By bioinformatics analysis we found that temptin was a gene unique to the clade Lophotrochozoa, and it exists in all mollusc taxa except Cephalopoda. The current data supported the premise that temptin was generated in the early emergence of molluscs and that it maintained a high mutation rate to evolve relative independently. The specificity of hc-temptin expression in the mantle tissue suggests its potential to participate in biomineralization. Its sequence contained typical Ca2+ binding sites. Our experiments involving the pearl formation process, damaged shell repair process, and RNAi experiment showed that hc-temptin was a shell matrix protein that plays an important role in formation of the prismatic layer. The results of this study provided new insights about the origin of the temptin gene and its role in molluscs.
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Affiliation(s)
- Maoxiao Peng
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, China
| | - Zhenming Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, China
| | - Zhi Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, China
| | | | - Xiaojun Liu
- Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Zhejiang 314000, China.
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, China.
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22
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Zhang Y, Mao F, Mu H, Huang M, Bao Y, Wang L, Wong NK, Xiao S, Dai H, Xiang Z, Ma M, Xiong Y, Zhang Z, Zhang L, Song X, Wang F, Mu X, Li J, Ma H, Zhang Y, Zheng H, Simakov O, Yu Z. The genome of Nautilus pompilius illuminates eye evolution and biomineralization. Nat Ecol Evol 2021; 5:927-938. [PMID: 33972735 PMCID: PMC8257504 DOI: 10.1038/s41559-021-01448-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
Nautilus is the sole surviving externally shelled cephalopod from the Palaeozoic. It is unique within cephalopod genealogy and critical to understanding the evolutionary novelties of cephalopods. Here, we present a complete Nautilus pompilius genome as a fundamental genomic reference on cephalopod innovations, such as the pinhole eye and biomineralization. Nautilus shows a compact, minimalist genome with few encoding genes and slow evolutionary rates in both non-coding and coding regions among known cephalopods. Importantly, multiple genomic innovations including gene losses, independent contraction and expansion of specific gene families and their associated regulatory networks likely moulded the evolution of the nautilus pinhole eye. The conserved molluscan biomineralization toolkit and lineage-specific repetitive low-complexity domains are essential to the construction of the nautilus shell. The nautilus genome constitutes a valuable resource for reconstructing the evolutionary scenarios and genomic innovations that shape the extant cephalopods.
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Affiliation(s)
- Yang Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Fan Mao
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Huawei Mu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Minwei Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Yongbo Bao
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Lili Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Nai-Kei Wong
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Shu Xiao
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing, China
| | - Zhiming Xiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Mingli Ma
- Biomarker Technologies Corporation, Beijing, China
| | - Yuanyan Xiong
- State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ziwei Zhang
- State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lvping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Xiaoyuan Song
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Fan Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Xiyu Mu
- Biomarker Technologies Corporation, Beijing, China
| | - Jun Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Haitao Ma
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Yuehuan Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | | | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Ziniu Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
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23
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Yarra T, Ramesh K, Blaxter M, Hüning A, Melzner F, Clark MS. Transcriptomic analysis of shell repair and biomineralization in the blue mussel, Mytilus edulis. BMC Genomics 2021; 22:437. [PMID: 34112105 PMCID: PMC8194122 DOI: 10.1186/s12864-021-07751-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 05/27/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Biomineralization by molluscs involves regulated deposition of calcium carbonate crystals within a protein framework to produce complex biocomposite structures. Effective biomineralization is a key trait for aquaculture, and animal resilience under future climate change. While many enzymes and structural proteins have been identified from the shell and in mantle tissue, understanding biomieralization is impeded by a lack of fundamental knowledge of the genes and pathways involved. In adult bivalves, shells are secreted by the mantle tissue during growth, maintenance and repair, with the repair process, in particular, amenable to experimental dissection at the transcriptomic level in individual animals. RESULTS Gene expression dynamics were explored in the adult blue mussel, Mytilus edulis, during experimentally induced shell repair, using the two valves of each animal as a matched treatment-control pair. Gene expression was assessed using high-resolution RNA-Seq against a de novo assembled database of functionally annotated transcripts. A large number of differentially expressed transcripts were identified in the repair process. Analysis focused on genes encoding proteins and domains identified in shell biology, using a new database of proteins and domains previously implicated in biomineralization in mussels and other molluscs. The genes implicated in repair included many otherwise novel transcripts that encoded proteins with domains found in other shell matrix proteins, as well as genes previously associated with primary shell formation in larvae. Genes with roles in intracellular signalling and maintenance of membrane resting potential were among the loci implicated in the repair process. While haemocytes have been proposed to be actively involved in repair, no evidence was found for this in the M. edulis data. CONCLUSIONS The shell repair experimental model and a newly developed shell protein domain database efficiently identified transcripts involved in M. edulis shell production. In particular, the matched pair analysis allowed factoring out of much of the inherent high level of variability between individual mussels. This snapshot of the damage repair process identified a large number of genes putatively involved in biomineralization from initial signalling, through calcium mobilization to shell construction, providing many novel transcripts for future in-depth functional analyses.
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Affiliation(s)
- Tejaswi Yarra
- Ashworth Laboratories, University of Edinburgh, Institute of Evolutionary Biology, Charlotte Auerbach Road, EH9 3FL, Edinburgh, UK
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, CB3 0ET, Cambridge, UK
| | - Kirti Ramesh
- GEOMAR Helmholtz Centre for Ocean Research, 24105, Kiel, Germany
| | - Mark Blaxter
- Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, Saffron Walden, UK
| | - Anne Hüning
- GEOMAR Helmholtz Centre for Ocean Research, 24105, Kiel, Germany
| | - Frank Melzner
- GEOMAR Helmholtz Centre for Ocean Research, 24105, Kiel, Germany
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, CB3 0ET, Cambridge, UK.
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24
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Jackson HJ, Larsson J, Davison A. Quantitative measures and 3D shell models reveal interactions between bands and their position on growing snail shells. Ecol Evol 2021; 11:6634-6648. [PMID: 34141246 PMCID: PMC8207382 DOI: 10.1002/ece3.7517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/10/2021] [Accepted: 03/17/2021] [Indexed: 11/10/2022] Open
Abstract
The nature of shell growth in gastropods is useful because it preserves the ontogeny of shape, colour, and banding patterns, making them an ideal system for understanding how inherited variation develops, is established and maintained within a population. However, qualitative scoring of inherited shell characters means there is a lack of knowledge regarding the mechanisms that control fine variation. Here, we combine empirical measures of quantitative variation and 3D modeling of shells to understand how bands are placed and interact. By comparing five-banded Cepaea individuals to shells lacking individual bands, we show that individual band absence has minor but significant impacts upon the position of remaining bands, implying that the locus controlling band presence/absence mainly acts after position is established. Then, we show that the shell grows at a similar rate, except for the region below the lowermost band. This demonstrates that wider bands of Cepaea are not an artifact of greater shell growth on the lower shell; they begin wider and grow at the same rate as other bands. Finally, we show that 3D models of shell shape and banding pattern, inferred from 2D photos using ShellShaper software, are congruent with empirical measures. This work therefore establishes a method that may be used for comparative studies of quantitative banding variation in snail shells, extraction of growth parameters, and morphometrics. In the future, studies that link the banding phenotype to the network of shell matrix proteins involved in biomineralization and patterning may ultimately aid in understanding the diversity of shell forms found in molluscs.
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Affiliation(s)
| | - Jenny Larsson
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Angus Davison
- School of Life SciencesUniversity of NottinghamNottinghamUK
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25
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Abstract
Mollusc shells are a result of the deposition of crystalline and amorphous calcite catalysed by enzymes and shell matrix proteins. Developing a detailed understanding of bivalve mollusc biomineralization pathways is complicated not only by the multiplicity of shell forms and microstructures in this class, but also by the evolution of associated proteins by domain co-option and domain shuffling. In spite of this, a minimal biomineralization toolbox comprising proteins and protein domains critical for shell production across species has been identified. Using a matched pair design to reduce experimental noise from inter-individual variation, combined with damage-repair experiments and a database of biomineralization shell matrix proteins (SMP) derived from published works, proteins were identified that are likely to be involved in shell calcification. Eighteen new, shared proteins likely to be involved in the processes related to the calcification of shells were identified by analysis of genes expressed during repair in Crassostrea gigas, Mytilus edulis and Pecten maximus. Genes involved in ion transport were also identified as potentially involved in calcification either via the maintenance of cell acid-base balance or transport of critical ions to the extrapallial space, the site of shell assembly. These data expand the number of candidate biomineralization proteins in bivalve molluscs for future functional studies and define a minimal functional protein domain set required to produce solid microstructures from soluble calcium carbonate. This is important for understanding molluscan shell evolution, the likely impacts of environmental change on biomineralization processes, materials science, and biomimicry research.
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Affiliation(s)
- Tejaswi Yarra
- University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK.,British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Mark Blaxter
- Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
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26
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Czarkwiani A, Dylus DV, Carballo L, Oliveri P. FGF signalling plays similar roles in development and regeneration of the skeleton in the brittle star Amphiura filiformis. Development 2021; 148:dev180760. [PMID: 34042967 PMCID: PMC8180256 DOI: 10.1242/dev.180760] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 04/13/2021] [Indexed: 12/16/2022]
Abstract
Regeneration as an adult developmental process is in many aspects similar to embryonic development. Although many studies point out similarities and differences, no large-scale, direct and functional comparative analyses between development and regeneration of a specific cell type or structure in one animal exist. Here, we use the brittle star Amphiura filiformis to characterise the role of the FGF signalling pathway during skeletal development in embryos and arm regeneration. In both processes, we find ligands expressed in ectodermal cells that flank underlying skeletal mesenchymal cells, which express the receptors. Perturbation of FGF signalling showed inhibited skeleton formation in both embryogenesis and regeneration, without affecting other key developmental processes. Differential transcriptome analysis finds mostly differentiation genes rather than transcription factors to be downregulated in both contexts. Moreover, comparative gene analysis allowed us to discover brittle star-specific differentiation genes. In conclusion, our results show that the FGF pathway is crucial for skeletogenesis in the brittle star, as in other deuterostomes, and provide evidence for the re-deployment of a developmental gene regulatory module during regeneration.
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Affiliation(s)
- Anna Czarkwiani
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - David V. Dylus
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
- Centre for Mathematics, Physics and Engineering in the Life Sciences and Experimental Biology, University College London, London WC1E 6BT, UK
| | - Luisana Carballo
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Paola Oliveri
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
- Centre for Life's Origin and Evolution (CLOE), University College London, London WC1E 6BT, UK
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27
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Salman J, Stifler CA, Shahsafi A, Sun CY, Weibel SC, Frising M, Rubio-Perez BE, Xiao Y, Draves C, Wambold RA, Yu Z, Bradley DC, Kemeny G, Gilbert PUPA, Kats MA. Hyperspectral interference tomography of nacre. Proc Natl Acad Sci U S A 2021; 118:e2023623118. [PMID: 33833057 PMCID: PMC8053970 DOI: 10.1073/pnas.2023623118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Structural characterization of biologically formed materials is essential for understanding biological phenomena and their enviro-nment, and for generating new bio-inspired engineering concepts. For example, nacre-the inner lining of some mollusk shells-encodes local environmental conditions throughout its formation and has exceptional strength due to its nanoscale brick-and-mortar structure. This layered structure, comprising alternating transparent aragonite (CaCO3) tablets and thinner organic polymer layers, also results in stunning interference colors. Existing methods of structural characterization of nacre rely on some form of cross-sectional analysis, such as scanning or transmission electron microscopy or polarization-dependent imaging contrast (PIC) mapping. However, these techniques are destructive and too time- and resource-intensive to analyze large sample areas. Here, we present an all-optical, rapid, and nondestructive imaging technique-hyperspectral interference tomography (HIT)-to spatially map the structural parameters of nacre and other disordered layered materials. We combined hyperspectral imaging with optical-interference modeling to infer the mean tablet thickness and its disorder in nacre across entire mollusk shells from red and rainbow abalone (Haliotis rufescens and Haliotis iris) at various stages of development. We observed that in red abalone, unexpectedly, nacre tablet thickness decreases with age of the mollusk, despite roughly similar appearance of nacre at all ages and positions in the shell. Our rapid, inexpensive, and nondestructive method can be readily applied to in-field studies.
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Affiliation(s)
- Jad Salman
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Cayla A Stifler
- Department of Physics, University of Wisconsin-Madison, Madison, WI 53706
| | - Alireza Shahsafi
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Chang-Yu Sun
- Department of Physics, University of Wisconsin-Madison, Madison, WI 53706
| | | | - Michel Frising
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Bryan E Rubio-Perez
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Yuzhe Xiao
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | | | - Raymond A Wambold
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Zhaoning Yu
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI 53706
- Department of Physics, University of Wisconsin-Madison, Madison, WI 53706
| | - Daniel C Bradley
- Department of Physics, University of Wisconsin-Madison, Madison, WI 53706
| | | | - Pupa U P A Gilbert
- Department of Physics, University of Wisconsin-Madison, Madison, WI 53706;
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI 53706
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI 53706
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Mikhail A Kats
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI 53706;
- Department of Physics, University of Wisconsin-Madison, Madison, WI 53706
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI 53706
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28
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McCartney MA. Structure, function and parallel evolution of the bivalve byssus, with insights from proteomes and the zebra mussel genome. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200155. [PMID: 33813897 DOI: 10.1098/rstb.2020.0155] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The byssus is a structure unique to bivalves. Byssal threads composed of many proteins extend like tendons from muscle cells, ending in adhesive pads that attach underwater. Crucial to settlement and metamorphosis, larvae of virtually all species are byssate. By contrast, in adults, the byssus is scattered throughout bivalves, where it has had profound effects on morphological evolution and been key to adaptive radiations of epifaunal species. I compare byssus structure and proteins in blue mussels (Mytilus), by far the best characterized, to zebra mussels (Dreissena polymorpha), in which several byssal proteins have been isolated and sequenced. By mapping the adult byssus onto a recent phylogenomic tree, I confirm its independent evolution in these and other lineages, likely parallelisms with common origins in development. While the byssus is superficially similar in Dreissena and Mytilus, in finer detail it is not, and byssal proteins are dramatically different. I used the chromosome-scale D. polymorpha genome we recently assembled to search for byssal genes and found 37 byssal loci on 10 of the 16 chromosomes. Most byssal genes are in small families, with several amino acid substitutions between paralogs. Byssal proteins of zebra mussels and related quagga mussels (D. rostriformis) are divergent, suggesting rapid evolution typical of proteins with repetitive low complexity domains. Opportunities abound for proteomic and genomic work to further our understanding of this textbook example of a marine natural material. A priority should be invasive bivalves, given the role of byssal attachment in the spread of, and ecological and economic damage caused by zebra mussels, quagga mussels and others. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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29
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Le Roy N, Ganot P, Aranda M, Allemand D, Tambutté S. The skeletome of the red coral Corallium rubrum indicates an independent evolution of biomineralization process in octocorals. BMC Ecol Evol 2021; 21:1. [PMID: 33514311 PMCID: PMC7853314 DOI: 10.1186/s12862-020-01734-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 12/13/2020] [Indexed: 12/16/2022] Open
Abstract
Background The process of calcium carbonate biomineralization has arisen multiple times during metazoan evolution. In the phylum Cnidaria, biomineralization has mostly been studied in the subclass Hexacorallia (i.e. stony corals) in comparison to the subclass Octocorallia (i.e. red corals); the two diverged approximately 600 million years ago. The precious Mediterranean red coral, Corallium rubrum, is an octocorallian species, which produces two distinct high-magnesium calcite biominerals, the axial skeleton and the sclerites. In order to gain insight into the red coral biomineralization process and cnidarian biomineralization evolution, we studied the protein repertoire forming the organic matrix (OM) of its two biominerals. Results We combined High-Resolution Mass Spectrometry and transcriptome analysis to study the OM composition of the axial skeleton and the sclerites. We identified a total of 102 OM proteins, 52 are found in the two red coral biominerals with scleritin being the most abundant protein in each fraction. Contrary to reef building corals, the red coral organic matrix possesses a large number of collagen-like proteins. Agrin-like glycoproteins and proteins with sugar-binding domains are also predominant. Twenty-seven and 23 proteins were uniquely assigned to the axial skeleton and the sclerites, respectively. The inferred regulatory function of these OM proteins suggests that the difference between the two biominerals is due to the modeling of the matrix network, rather than the presence of specific structural components. At least one OM component could have been horizontally transferred from prokaryotes early during Octocorallia evolution. Conclusion Our results suggest that calcification of the red coral axial skeleton likely represents a secondary calcification of an ancestral gorgonian horny axis. In addition, the comparison with stony coral skeletomes highlighted the low proportion of similar proteins between the biomineral OMs of hexacorallian and octocorallian corals, suggesting an independent acquisition of calcification in anthozoans.
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Affiliation(s)
- Nathalie Le Roy
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC, 98000, Monaco. .,BOA UMR83, INRAe Centre Val de Loire, 37380, Nouzilly, France.
| | - Philippe Ganot
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC, 98000, Monaco
| | - Manuel Aranda
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC, 98000, Monaco
| | - Sylvie Tambutté
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC, 98000, Monaco
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30
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McDougall C, Aguilera F, Shokoohmand A, Moase P, Degnan BM. Pearl Sac Gene Expression Profiles Associated With Pearl Attributes in the Silver-Lip Pearl Oyster, Pinctada maxima. Front Genet 2021; 11:597459. [PMID: 33488672 PMCID: PMC7820862 DOI: 10.3389/fgene.2020.597459] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/07/2020] [Indexed: 11/21/2022] Open
Abstract
Pearls are highly prized biomineralized gemstones produced by molluscs. The appearance and mineralogy of cultured pearls can vary markedly, greatly affecting their commercial value. To begin to understand the role of pearl sacs—organs that form in host oysters from explanted mantle tissues that surround and synthesize pearls—we undertook transcriptomic analyses to identify genes that are differentially expressed in sacs producing pearls with different surface and structural characteristics. Our results indicate that gene expression profiles correlate with different pearl defects, suggesting that gene regulation in the pearl sac contributes to pearl appearance and quality. For instance, pearl sacs that produced pearls with surface non-lustrous calcification significantly down-regulate genes associated with cilia and microtubule function compared to pearl sacs giving rise to lustrous pearls. These results suggest that gene expression profiling can advance our understanding of processes that control biomineralization, which may be of direct value to the pearl industry, particularly in relation to defects that result in low value pearls.
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Affiliation(s)
- Carmel McDougall
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia.,Australian Rivers Institute, Griffith University, Nathan, QLD, Australia
| | - Felipe Aguilera
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Ali Shokoohmand
- Australian Rivers Institute, Griffith University, Nathan, QLD, Australia
| | - Patrick Moase
- Clipper Pearls and Autore Pearling, Broome, WA, Australia
| | - Bernard M Degnan
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
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31
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Shimizu K, Kintsu H, Awaji M, Matumoto T, Suzuki M. Evolution of Biomineralization Genes in the Prismatic Layer of the Pen Shell Atrina pectinata. J Mol Evol 2020; 88:742-758. [PMID: 33236260 DOI: 10.1007/s00239-020-09977-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/18/2020] [Indexed: 11/29/2022]
Abstract
Molluscan shells are composed of calcium carbonates, with small amounts of extracellular matrices secreted from mantle epithelial cells. Many types of shell matrix proteins (SMPs) have been identified from molluscan shells or mantle cells. The pen shell Atrina pectinata (Pinnidae) has two different shell microstructures, the nacreous and prismatic layers. Nacreous and prismatic layer-specific matrix proteins have been reported in Pteriidae bivalves, but remain unclear in Pinnidae. We performed transcriptome analysis using the mantle cells of A. pectinata to screen the candidate transcripts involved in its prismatic layer formation. We found Asprich and nine highly conserved prismatic layer-specific SMPs encoding transcript in P. fucata, P. margaritifera, and P. maxima (Tyrosinase, Chitinase, EGF-like proteins, Fibronectin, valine-rich proteins, and prismatic uncharacterized shell protein 2 [PUSP2]) using molecular phylogenetic analysis or multiple alignment. We confirmed these genes were expressed in the epithelial cells of the mantle edge (outer surface of the outer fold) and the mantle pallium. Phylogenetic character mapping of these SMPs was used to infer a possible evolutionary scenario of them in Pteriomorphia. EGF-like proteins, Fibronectin, and valine-rich proteins encoding genes each evolved in the linage leading to four Pteriomorphia (Mytilidae, Pinnidae, Ostreidae, and Pteriidae), PUSP2 evolved in the linage leading to three Pteriomorphia families (Pinnidae, Ostreidae, and Pteriidae), and chitinase was independently evolved as SMPs in Mytilidae and in other Pteriomorphia (Pinnidae, Ostreidae, and Pteriidae). Our results provide a new dataset for A. pectinata SMP annotation, and a basis for understanding the evolution of prismatic layer formation in bivalves.
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Affiliation(s)
- Keisuke Shimizu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Hiroyuki Kintsu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan.,Center for Health and Environmental Risk Research, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Masahiko Awaji
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhama, Minami-Ise, Watarai, Mie, 516-0193, Japan
| | - Toshie Matumoto
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhama, Minami-Ise, Watarai, Mie, 516-0193, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan.
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Arivalagan J, Marie B, Chiappetta G, Vinh J, Gallet X, Lebon M, M'Zoudi S, Dubois P, Berland S, Marie A. Deciphering shell proteome within different Baltic populations of mytilid mussels illustrates important local variability and potential consequences in the context of changing marine conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:140878. [PMID: 32721612 DOI: 10.1016/j.scitotenv.2020.140878] [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: 04/10/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Molluscs defend themselves against predation and environmental stressors through the possession of mineralized shells. Mussels are widely used to predict the effects of abiotic factors such as salinity and pH on marine calcifiers in the context of changing ocean conditions. Shell matrix proteins are part of the molecular control regulating the biomineralization processes underpinning shell production. Under changing environmental conditions, differential expression of these proteins leads to the phenotypic plasticity of shells seen in many mollusc species. Low salinity decreases the availability of calcium and inorganic carbon in seawater and consequently energetic constraints often lead to thin, small and fragile shells in Mytilid mussels inhabiting Baltic Sea. To understand how the modulation of shell matrix proteins alters biomineralization, we compared the shell proteomes of mussels living under full marine conditions in the North Sea to those living in the low saline Baltic Sea. Modulation of proteins comprising the Mytilus biomineralization tool kit is observed. These data showed a relative increase in chitin related proteins, decrease in SD-rich, GA-rich shell matrix proteins indicating that altered protein scaffolding and mineral nucleation lead to impaired shell microstructures influencing shell resistance in Baltic Mytilid mussels. Interestingly, proteins with immunity domains in the shell matrix are also found to be modulated. Shell traits such as periostracum thickness, organic content and fracture resistance qualitatively correlates with the modulation of SMPs in Mytilid mussels providing key insights into control of biomineralization at molecular level in the context of changing marine conditions.
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Affiliation(s)
- Jaison Arivalagan
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum national d'Histoire naturelle, 75005 Paris, France; UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum national d'Histoire naturelle, 75005 Paris, France
| | - Benjamin Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum national d'Histoire naturelle, 75005 Paris, France
| | | | - Joëlle Vinh
- USR3149, ESPCI ParisTech, 75005 Paris, France
| | - Xavier Gallet
- UMR 7194, Département de préhistoire, Musée de l'Homme, 75116 Paris, France
| | - Matthieu Lebon
- UMR 7194, Département de préhistoire, Musée de l'Homme, 75116 Paris, France
| | - Saloua M'Zoudi
- Laboratoire de Biologie marine CP160/15, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| | - Philippe Dubois
- Laboratoire de Biologie marine CP160/15, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| | - Sophie Berland
- UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum national d'Histoire naturelle, 75005 Paris, France
| | - Arul Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum national d'Histoire naturelle, 75005 Paris, France.
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Clark MS, Peck LS, Arivalagan J, Backeljau T, Berland S, Cardoso JCR, Caurcel C, Chapelle G, De Noia M, Dupont S, Gharbi K, Hoffman JI, Last KS, Marie A, Melzner F, Michalek K, Morris J, Power DM, Ramesh K, Sanders T, Sillanpää K, Sleight VA, Stewart-Sinclair PJ, Sundell K, Telesca L, Vendrami DLJ, Ventura A, Wilding TA, Yarra T, Harper EM. Deciphering mollusc shell production: the roles of genetic mechanisms through to ecology, aquaculture and biomimetics. Biol Rev Camb Philos Soc 2020; 95:1812-1837. [PMID: 32737956 DOI: 10.1111/brv.12640] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/17/2020] [Accepted: 07/17/2020] [Indexed: 12/20/2022]
Abstract
Most molluscs possess shells, constructed from a vast array of microstructures and architectures. The fully formed shell is composed of calcite or aragonite. These CaCO3 crystals form complex biocomposites with proteins, which although typically less than 5% of total shell mass, play significant roles in determining shell microstructure. Despite much research effort, large knowledge gaps remain in how molluscs construct and maintain their shells, and how they produce such a great diversity of forms. Here we synthesize results on how shell shape, microstructure, composition and organic content vary among, and within, species in response to numerous biotic and abiotic factors. At the local level, temperature, food supply and predation cues significantly affect shell morphology, whilst salinity has a much stronger influence across latitudes. Moreover, we emphasize how advances in genomic technologies [e.g. restriction site-associated DNA sequencing (RAD-Seq) and epigenetics] allow detailed examinations of whether morphological changes result from phenotypic plasticity or genetic adaptation, or a combination of these. RAD-Seq has already identified single nucleotide polymorphisms associated with temperature and aquaculture practices, whilst epigenetic processes have been shown significantly to modify shell construction to local conditions in, for example, Antarctica and New Zealand. We also synthesize results on the costs of shell construction and explore how these affect energetic trade-offs in animal metabolism. The cellular costs are still debated, with CaCO3 precipitation estimates ranging from 1-2 J/mg to 17-55 J/mg depending on experimental and environmental conditions. However, organic components are more expensive (~29 J/mg) and recent data indicate transmembrane calcium ion transporters can involve considerable costs. This review emphasizes the role that molecular analyses have played in demonstrating multiple evolutionary origins of biomineralization genes. Although these are characterized by lineage-specific proteins and unique combinations of co-opted genes, a small set of protein domains have been identified as a conserved biomineralization tool box. We further highlight the use of sequence data sets in providing candidate genes for in situ localization and protein function studies. The former has elucidated gene expression modularity in mantle tissue, improving understanding of the diversity of shell morphology synthesis. RNA interference (RNAi) and clustered regularly interspersed short palindromic repeats - CRISPR-associated protein 9 (CRISPR-Cas9) experiments have provided proof of concept for use in the functional investigation of mollusc gene sequences, showing for example that Pif (aragonite-binding) protein plays a significant role in structured nacre crystal growth and that the Lsdia1 gene sets shell chirality in Lymnaea stagnalis. Much research has focused on the impacts of ocean acidification on molluscs. Initial studies were predominantly pessimistic for future molluscan biodiversity. However, more sophisticated experiments incorporating selective breeding and multiple generations are identifying subtle effects and that variability within mollusc genomes has potential for adaption to future conditions. Furthermore, we highlight recent historical studies based on museum collections that demonstrate a greater resilience of molluscs to climate change compared with experimental data. The future of mollusc research lies not solely with ecological investigations into biodiversity, and this review synthesizes knowledge across disciplines to understand biomineralization. It spans research ranging from evolution and development, through predictions of biodiversity prospects and future-proofing of aquaculture to identifying new biomimetic opportunities and societal benefits from recycling shell products.
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Affiliation(s)
- Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, U.K
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, U.K
| | - Jaison Arivalagan
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France.,Proteomics Center of Excellence, Northwestern University, 710 N Fairbanks Ct, Chicago, IL, U.S.A
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, Brussels, B-1000, Belgium.,Evolutionary Ecology Group, University of Antwerp, Universiteitsplein 1, Antwerp, B-2610, Belgium
| | - Sophie Berland
- UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Joao C R Cardoso
- Centro de Ciencias do Mar, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Carlos Caurcel
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, U.K
| | - Gauthier Chapelle
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, Brussels, B-1000, Belgium
| | - Michele De Noia
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, Bielefeld, 33615, Germany.,Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, U.K
| | - Sam Dupont
- Department of Biological and Environmental Sciences, University of Göteburg, Box 463, Göteburg, SE405 30, Sweden
| | - Karim Gharbi
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, U.K
| | - Joseph I Hoffman
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, Bielefeld, 33615, Germany
| | - Kim S Last
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, PA37 1QA, U.K
| | - Arul Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Frank Melzner
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
| | - Kati Michalek
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, PA37 1QA, U.K
| | - James Morris
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, Brussels, B-1000, Belgium
| | - Deborah M Power
- Centro de Ciencias do Mar, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Kirti Ramesh
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
| | - Trystan Sanders
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
| | - Kirsikka Sillanpää
- Swemarc, Department of Biological and Environmental Science, University of Gothenburg, Box 463, Gothenburg, SE405 30, Sweden
| | - Victoria A Sleight
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, U.K
| | | | - Kristina Sundell
- Swemarc, Department of Biological and Environmental Science, University of Gothenburg, Box 463, Gothenburg, SE405 30, Sweden
| | - Luca Telesca
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, U.K
| | - David L J Vendrami
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, Bielefeld, 33615, Germany
| | - Alexander Ventura
- Department of Biological and Environmental Sciences, University of Göteburg, Box 463, Göteburg, SE405 30, Sweden
| | - Thomas A Wilding
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, PA37 1QA, U.K
| | - Tejaswi Yarra
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, U.K.,Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, U.K
| | - Elizabeth M Harper
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, U.K
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Sakalauskaite J, Marin F, Pergolizzi B, Demarchi B. Shell palaeoproteomics: First application of peptide mass fingerprinting for the rapid identification of mollusc shells in archaeology. J Proteomics 2020; 227:103920. [PMID: 32712371 DOI: 10.1016/j.jprot.2020.103920] [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: 04/02/2020] [Revised: 07/12/2020] [Accepted: 07/20/2020] [Indexed: 01/31/2023]
Abstract
Molluscs were one of the most widely-used natural resources in the past, and their shells are abundant among archaeological findings. However, our knowledge of the variety of shells that were circulating in prehistoric times (and thus their socio-economic and cultural value) is scarce due to the difficulty of achieving taxonomic determination of fragmented and/or worked remains. This study aims to obtain molecular barcodes based on peptide mass fingerprints (PMFs) of intracrystalline proteins, in order to obtain shell identification. Palaeoproteomic applications on shells are challenging, due to low concentration of molluscan proteins and an incomplete understanding of their sequences. We explore different approaches for protein extraction from small-size samples (<20 mg), followed by MALDI-TOF-MS analysis. The SP3 (single-pot, solid-phase) sample preparation method was found to be the most successful in retrieving the intracrystalline protein fraction from seven molluscan shell taxa, which belong to different phylogenetic groups, possess distinct microstructures and are relevant for archaeology. Furthermore, all the shells analysed, including a 7000-year-old specimen of the freshwater bivalve Pseudunio, yielded good-quality distinctive spectra, demonstrating that PMFs can be used for shell taxon determination. Our work suggests good potential for large-scale screening of archaeological molluscan remains. SIGNIFICANCE: We characterise for the first time the peptide mass fingerprints of the intracrystalline shell protein fraction isolated from different molluscan taxa. We demonstrate that these proteins yield distinctive PMFs, even for shells that are phylogenetically related and/or that display similar microstructures. Furthermore, we extend the range of sample preparation approaches for "shellomics" by testing the SP3 method, which proved to be well-suited to shell protein extraction from small-size and protein-poor samples. This work thus lays the foundations for future large-scale applications for the identification of mollusc shells and other invertebrate remains from the archaeological and palaeontological records.
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Affiliation(s)
- Jorune Sakalauskaite
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy; Biogéosciences, UMR CNRS 6282, University of Burgundy-Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France.
| | - Frédéric Marin
- Biogéosciences, UMR CNRS 6282, University of Burgundy-Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France
| | - Barbara Pergolizzi
- Department of Clinical and Biological Sciences, University of Turin, AOU S. Luigi, 10043 Orbassano, TO, Italy
| | - Beatrice Demarchi
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy.
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35
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Abstract
Much recent marine research has been directed towards understanding the effects of anthropogenic-induced environmental change on marine biodiversity, particularly for those animals with heavily calcified exoskeletons, such as corals, molluscs and urchins. This is because life in our oceans is becoming more challenging for these animals with changes in temperature, pH and salinity. In the future, it will be more energetically expensive to make marine skeletons and the increasingly corrosive conditions in seawater are expected to result in the dissolution of these external skeletons. However, initial predictions of wide-scale sensitivity are changing as we understand more about the mechanisms underpinning skeletal production (biomineralization). These studies demonstrate the complexity of calcification pathways and the cellular responses of animals to these altered conditions. Factors including parental conditioning, phenotypic plasticity and epigenetics can significantly impact the production of skeletons and thus future population success. This understanding is paralleled by an increase in our knowledge of the genes and proteins involved in biomineralization, particularly in some phyla, such as urchins, molluscs and corals. This Review will provide a broad overview of our current understanding of the factors affecting skeletal production in marine invertebrates. It will focus on the molecular mechanisms underpinning biomineralization and how knowledge of these processes affects experimental design and our ability to predict responses to climate change. Understanding marine biomineralization has many tangible benefits in our changing world, including improvements in conservation and aquaculture and exploitation of natural calcified structure design using biomimicry approaches that are aimed at producing novel biocomposites.
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Affiliation(s)
- Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
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36
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Murdock DJE. The ‘biomineralization toolkit’ and the origin of animal skeletons. Biol Rev Camb Philos Soc 2020; 95:1372-1392. [DOI: 10.1111/brv.12614] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 12/29/2022]
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37
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Klein AH, Ballard KR, Storey KB, Motti CA, Zhao M, Cummins SF. Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies. Brief Funct Genomics 2020; 18:377-394. [PMID: 31609407 DOI: 10.1093/bfgp/elz017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/06/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.
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Affiliation(s)
- Anne H Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kaylene R Ballard
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville Queensland 4810, Australia
| | - Min Zhao
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
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38
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Sakalauskaite J, Plasseraud L, Thomas J, Albéric M, Thoury M, Perrin J, Jamme F, Broussard C, Demarchi B, Marin F. The shell matrix of the european thorny oyster, Spondylus gaederopus: microstructural and molecular characterization. J Struct Biol 2020; 211:107497. [PMID: 32220629 DOI: 10.1016/j.jsb.2020.107497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/20/2020] [Accepted: 03/22/2020] [Indexed: 11/18/2022]
Abstract
Molluscs, the largest marine phylum, display extraordinary shell diversity and sophisticated biomineral architectures. However, mineral-associated biomolecules involved in biomineralization are still poorly characterised. We report the first comprehensive structural and biomolecular study of Spondylus gaederopus, a pectinoid bivalve with a peculiar shell texture. Used since prehistoric times, this is the best-known shell of Europe's cultural heritage. We find that Spondylus microstructure is very poor in mineral-bound organics, which are mostly intercrystalline and concentrated at the interface between structural layers. Using high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS) we characterized several shell protein fractions, isolated following different bleaching treatments. Several peptides were identified as well as six shell proteins, which display features and domains typically found in biomineralized tissues, including the prevalence of intrinsically disordered regions. It is very likely that these sequences only partially represent the full proteome of Spondylus, considering the lack of genomics data for this genus and the fact that most of the reconstructed peptides do not match with any known shell proteins, representing consequently lineage-specific sequences. This work sheds light onto the shell matrix involved in the biomineralization in spondylids. Our proteomics data suggest that Spondylus has evolved a shell-forming toolkit, distinct from that of other better studied pectinoids - fine-tuned to produce shell structures with high mechanical properties, while limited in organic content. This study therefore represents an important milestone for future studies on biomineralized skeletons and provides the first reference dataset for forthcoming molecular studies of Spondylus archaeological artifacts.
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Affiliation(s)
- Jorune Sakalauskaite
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy; Biogeosciences, UMR CNRS 6282, University of Burgundy-Franche-Comté (UBFC), 6 Boulevard Gabriel, 21000 Dijon, France.
| | - Laurent Plasseraud
- Institute of Molecular Chemistry, ICMUB UMR CNRS 6302, University of Burgundy-Franche-Comté (UBFC), 9 Avenue Alain Savary, 21000 Dijon, France
| | - Jérôme Thomas
- Biogeosciences, UMR CNRS 6282, University of Burgundy-Franche-Comté (UBFC), 6 Boulevard Gabriel, 21000 Dijon, France
| | - Marie Albéric
- Laboratoire Chimie de la Matière Condensée de Paris, UMR, CNRS 7574, Sorbonne Université, Place Jussieu 4, 75252 Paris, France
| | - Mathieu Thoury
- IPANEMA, CNRS, ministère de la Culture, UVSQ, USR3461, Université Paris-Saclay, F-91192 Gif-sur-Yvette, France
| | - Jonathan Perrin
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192 Gif sur Yvette Cedex, France
| | - Frédéric Jamme
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192 Gif sur Yvette Cedex, France
| | - Cédric Broussard
- 3P5 Proteomic Platform, University of Paris, Cochin Institute, INSERM, U1016, CNRS, UMR8104, F-75014 Paris, France
| | - Beatrice Demarchi
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy
| | - Frédéric Marin
- Biogeosciences, UMR CNRS 6282, University of Burgundy-Franche-Comté (UBFC), 6 Boulevard Gabriel, 21000 Dijon, France.
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Chandra Rajan K, Vengatesen T. Molecular adaptation of molluscan biomineralisation to high-CO 2 oceans - The known and the unknown. MARINE ENVIRONMENTAL RESEARCH 2020; 155:104883. [PMID: 32072987 DOI: 10.1016/j.marenvres.2020.104883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 01/11/2020] [Accepted: 01/19/2020] [Indexed: 06/10/2023]
Abstract
High-CO2 induced ocean acidification (OA) reduces the calcium carbonate (CaCO3) saturation level (Ω) and the pH of oceans. Consequently, OA is causing a serious threat to several ecologically and economically important biomineralising molluscs. Biomineralisation is a highly controlled biochemical process by which molluscs deposit their calcareous structures. In this process, shell matrix proteins aid the nucleation, growth and assemblage of the CaCO3 crystals in the shell. These molluscan shell proteins (MSPs) are, ultimately, responsible for determination of the diverse shell microstructures and mechanical strength. Recent studies have attempted to integrate gene and protein expression data of MSPs with shell structure and mechanical properties. These advances made in understanding the molecular mechanism of biomineralisation suggest that molluscs either succumb or adapt to OA stress. In this review, we discuss the fate of biomineralisation process in future high-CO2 oceans and its ultimate impact on the mineralised shell's structure and mechanical properties from the perspectives of limited substrate availability theory, proton flux limitation model and the omega myth theory. Furthermore, studying the interplay of energy availability and differential gene expression is an essential first step towards understanding adaptation of molluscan biomineralisation to OA, because if there is a need to change gene expression under stressors, any living system would require more energy than usual. To conclude, we have listed, four important future research directions for molecular adaptation of molluscan biomineralisation in high-CO2 oceans: 1) Including an energy budgeting factor while understanding differential gene expression of MSPs and ion transporters under OA. 2) Unraveling the genetic or epigenetic changes related to biomineralisation under stressors to help solving a bigger picture about future evolution of molluscs, and 3) Understanding Post Translational Modifications of MSPs with and without stressors. 4) Understanding carbon uptake mechanisms across taxa with and without OA to clarify the OA theories on Ω.
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Affiliation(s)
- Kanmani Chandra Rajan
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Marine Pollution, Hong Kong SAR, China.
| | - Thiyagarajan Vengatesen
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Marine Pollution, Hong Kong SAR, China.
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40
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Erwin DH. The origin of animal body plans: a view from fossil evidence and the regulatory genome. Development 2020; 147:147/4/dev182899. [DOI: 10.1242/dev.182899] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ABSTRACT
The origins and the early evolution of multicellular animals required the exploitation of holozoan genomic regulatory elements and the acquisition of new regulatory tools. Comparative studies of metazoans and their relatives now allow reconstruction of the evolution of the metazoan regulatory genome, but the deep conservation of many genes has led to varied hypotheses about the morphology of early animals and the extent of developmental co-option. In this Review, I assess the emerging view that the early diversification of animals involved small organisms with diverse cell types, but largely lacking complex developmental patterning, which evolved independently in different bilaterian clades during the Cambrian Explosion.
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Affiliation(s)
- Douglas H. Erwin
- Department of Paleobiology, MRC-121, National Museum of Natural History, PO Box 37012, Washington, DC 20013-7012, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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41
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Jiang K, Jiang L, Nie H, Huo Z, Yan X. Molecular cloning and expression analysis of tyrosinases ( tyr) in four shell-color strains of Manila clam Ruditapes philippinarum. PeerJ 2020; 8:e8641. [PMID: 32110498 PMCID: PMC7032058 DOI: 10.7717/peerj.8641] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/27/2020] [Indexed: 11/27/2022] Open
Abstract
The Manila clam (Ruditapes philippinarum) is an economically important molluscan bivalve with variation in pigmentation frequently observed in the shell. In nature, tyrosinase is widely distributed in invertebrates and vertebrates, and plays a crucial role in a variety of physiological activities. In this study, a tyrosinase gene (tyr 9) was cloned and the expression level of tyr genes (tyr 6, tyr 9, tyr 10, and tyr 11) were investigated in different shell colors. Quantitative real-time PCR showed that tyr genes were significantly expressed in the mantle, a shell formation and pigmentation-related tissue. Moreover, the expression pattern of the tyr genes in the mantle of different shell-color strains was different, suggesting that tyrosinases might be involved in different shell-color formation. In addition, the expression profile of tyr 6, tyr 9, tyr 10, and tyr 11 genes were detected at different early developmental stages and the expression level varied with embryonic and larval growth. RNA interference (RNAi) results showed that the expression level of tyr 9 in the RNAi group was significantly down-regulated compared to control and negative control groups, indicating that Rptyr 9 might participate in shell-color formation. Our results indicated that tyr genes were likely to play vital roles in the formation of shell and shell-color in R. philippinarum.
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Affiliation(s)
- Kunyin Jiang
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, School of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Liwen Jiang
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, School of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Hongtao Nie
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, School of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Zhongming Huo
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, School of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Xiwu Yan
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, School of Fisheries and Life Science, Dalian Ocean University, Dalian, China
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42
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Maltseva AL, Varfolomeeva MA, Lobov AA, Tikanova P, Panova M, Mikhailova NA, Granovitch AI. Proteomic similarity of the Littorinid snails in the evolutionary context. PeerJ 2020; 8:e8546. [PMID: 32095363 PMCID: PMC7024583 DOI: 10.7717/peerj.8546] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/10/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions. METHODS Here we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering-using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson-Foulds distance, the Fowlkes-Mallows index and cophenetic correlation. RESULTS Overall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two Littoraria species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related Littorina fabalis and L. obtusata, possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups ("saxatilis" and "obtusata" groups in the Littorina genus) and for genera (Littoraria and Echinolittorina species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five Littorina species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of species.
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Affiliation(s)
- Arina L. Maltseva
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
| | - Marina A. Varfolomeeva
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
| | - Arseniy A. Lobov
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Sciences, St. Petersburg, Russia
| | - Polina Tikanova
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
| | - Marina Panova
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
- Department of Marine Sciences, Tjärnö, University of Gothenburg, Sweden
| | - Natalia A. Mikhailova
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
- Centre of Cell Technologies, Institute of Cytology Russian Academy of Sciences, St. Petersburg, Russia
| | - Andrei I. Granovitch
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
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43
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Proteomic investigation of the blue mussel larval shell organic matrix. J Struct Biol 2019; 208:107385. [DOI: 10.1016/j.jsb.2019.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 11/22/2022]
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44
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Morales AE, Ruedi M, Field K, Carstens BC. Diversification rates have no effect on the convergent evolution of foraging strategies in the most speciose genus of bats,
Myotis
*. Evolution 2019; 73:2263-2280. [DOI: 10.1111/evo.13849] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Ariadna E. Morales
- Department of Evolution, Ecology and Organismal Biology Ohio State University Columbus Ohio 43210
- Department of Mammalogy and Herpetology, Division of Vertebrate Zoology American Museum of Natural History New York New York 10024
| | - Manuel Ruedi
- Department of Mammalogy and Ornithology Natural History Museum of Geneva Geneva 1208 Switzerland
| | - Kathryn Field
- Department of Evolution, Ecology and Organismal Biology Ohio State University Columbus Ohio 43210
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology Ohio State University Columbus Ohio 43210
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45
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Crystal growth kinetics as an architectural constraint on the evolution of molluscan shells. Proc Natl Acad Sci U S A 2019; 116:20388-20397. [PMID: 31551265 PMCID: PMC6789867 DOI: 10.1073/pnas.1907229116] [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] [Indexed: 02/06/2023] Open
Abstract
Using notions from classic materials science, we expand our understanding of the macroscopic morphospace of possible molluscan shell shapes to the level of possible ultrastructures that comprise them. This provides us with a unique opportunity to explore this morphospace using well-developed analytical, theoretical, and numerical tools and to test the effects of a discrete number of parameters on shell biomineralization. The physical model presented here sheds a new light on the evolutionary aspect of molluscan shell ultrastructural fabrication and suggests that the repeated “discovery” of some mineral morphologies partially reflects a series of architectural constraints provided by biomineral growth kinetics. Molluscan shells are a classic model system to study formation–structure–function relationships in biological materials and the process of biomineralized tissue morphogenesis. Typically, each shell consists of a number of highly mineralized ultrastructures, each characterized by a specific 3D mineral–organic architecture. Surprisingly, in some cases, despite the lack of a mutual biochemical toolkit for biomineralization or evidence of homology, shells from different independently evolved species contain similar ultrastructural motifs. In the present study, using a recently developed physical framework, which is based on an analogy to the process of directional solidification and simulated by phase-field modeling, we compare the process of ultrastructural morphogenesis of shells from 3 major molluscan classes: A bivalve Unio pictorum, a cephalopod Nautilus pompilius, and a gastropod Haliotis asinina. We demonstrate that the fabrication of these tissues is guided by the organisms by regulating the chemical and physical boundary conditions that control the growth kinetics of the mineral phase. This biomineralization concept is postulated to act as an architectural constraint on the evolution of molluscan shells by defining a morphospace of possible shell ultrastructures that is bounded by the thermodynamics and kinetics of crystal growth.
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46
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Evans JS. The Biomineralization Proteome: Protein Complexity for a Complex Bioceramic Assembly Process. Proteomics 2019; 19:e1900036. [DOI: 10.1002/pmic.201900036] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/04/2019] [Indexed: 12/20/2022]
Affiliation(s)
- John Spencer Evans
- Laboratory for Chemical PhysicsDepartment of Skeletal and Craniofacial BiologyNew York University College of Dentistry New York NY 10010 USA
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47
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Zhao R, Takeuchi T, Luo YJ, Ishikawa A, Kobayashi T, Koyanagi R, Villar-Briones A, Yamada L, Sawada H, Iwanaga S, Nagai K, Satoh N, Endo K. Dual Gene Repertoires for Larval and Adult Shells Reveal Molecules Essential for Molluscan Shell Formation. Mol Biol Evol 2019; 35:2751-2761. [PMID: 30169718 PMCID: PMC6231486 DOI: 10.1093/molbev/msy172] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Molluscan shells, mainly composed of calcium carbonate, also contain organic components such as proteins and polysaccharides. Shell organic matrices construct frameworks of shell structures and regulate crystallization processes during shell formation. To date, a number of shell matrix proteins (SMPs) have been identified, and their functions in shell formation have been studied. However, previous studies focused only on SMPs extracted from adult shells, secreted after metamorphosis. Using proteomic analyses combined with genomic and transcriptomic analyses, we have identified 31 SMPs from larval shells of the pearl oyster, Pinctada fucata, and 111 from the Pacific oyster, Crassostrea gigas. Larval SMPs are almost entirely different from those of adults in both species. RNA-seq data also confirm that gene expression profiles for larval and adult shell formation are nearly completely different. Therefore, bivalves have two repertoires of SMP genes to construct larval and adult shells. Despite considerable differences in larval and adult SMPs, some functional domains are shared by both SMP repertoires. Conserved domains include von Willebrand factor type A (VWA), chitin-binding (CB), carbonic anhydrase (CA), and acidic domains. These conserved domains are thought to play crucial roles in shell formation. Furthermore, a comprehensive survey of animal genomes revealed that the CA and VWA-CB domain-containing protein families expanded in molluscs after their separation from other Lophotrochozoan linages such as the Brachiopoda. After gene expansion, some family members were co-opted for molluscan SMPs that may have triggered to develop mineralized shells from ancestral, nonmineralized chitinous exoskeletons.
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Affiliation(s)
- Ran Zhao
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yi-Jyun Luo
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| | - Akito Ishikawa
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Tatsushi Kobayashi
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryo Koyanagi
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Alejandro Villar-Briones
- Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Lixy Yamada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, Japan
| | - Hitoshi Sawada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, Japan
| | | | - Kiyohito Nagai
- Pearl Research Institute, Mikimoto CO., LTD, Shima, Mie, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Kazuyoshi Endo
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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48
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Hilgers L, Hartmann S, Hofreiter M, von Rintelen T. Novel Genes, Ancient Genes, and Gene Co-Option Contributed to the Genetic Basis of the Radula, a Molluscan Innovation. Mol Biol Evol 2019; 35:1638-1652. [PMID: 29672732 PMCID: PMC5995198 DOI: 10.1093/molbev/msy052] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The radula is the central foraging organ and apomorphy of the Mollusca. However, in contrast to other innovations, including the mollusk shell, genetic underpinnings of radula formation remain virtually unknown. Here, we present the first radula formative tissue transcriptome using the viviparous freshwater snail Tylomelania sarasinorum and compare it to foot tissue and the shell-building mantle of the same species. We combine differential expression, functional enrichment, and phylostratigraphic analyses to identify both specific and shared genetic underpinnings of the three tissues as well as their dominant functions and evolutionary origins. Gene expression of radula formative tissue is very distinct, but nevertheless more similar to mantle than to foot. Generally, the genetic bases of both radula and shell formation were shaped by novel orchestration of preexisting genes and continuous evolution of novel genes. A significantly increased proportion of radula-specific genes originated since the origin of stem-mollusks, indicating that novel genes were especially important for radula evolution. Genes with radula-specific expression in our study are frequently also expressed during the formation of other lophotrochozoan hard structures, like chaetae (hes1, arx), spicules (gbx), and shells of mollusks (gbx, heph) and brachiopods (heph), suggesting gene co-option for hard structure formation. Finally, a Lophotrochozoa-specific chitin synthase with a myosin motor domain (CS-MD), which is expressed during mollusk and brachiopod shell formation, had radula-specific expression in our study. CS-MD potentially facilitated the construction of complex chitinous structures and points at the potential of molecular novelties to promote the evolution of different morphological innovations.
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Affiliation(s)
- Leon Hilgers
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- Adaptive Evolutionary Genomics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Corresponding author: E-mail:
| | - Stefanie Hartmann
- Adaptive Evolutionary Genomics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael Hofreiter
- Adaptive Evolutionary Genomics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Thomas von Rintelen
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
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49
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Jin C, Liu XJ, Li JL. A Kunitz proteinase inhibitor (HcKuPI) participated in antimicrobial process during pearl sac formation and induced the overgrowth of calcium carbonate in Hyriopsis cumingii. FISH & SHELLFISH IMMUNOLOGY 2019; 89:437-447. [PMID: 30980916 DOI: 10.1016/j.fsi.2019.04.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/06/2019] [Accepted: 04/07/2019] [Indexed: 06/09/2023]
Abstract
Proteinase inhibitors with the ability to inhibit specific proteinases are usually closely connected with the immune system. Interestingly, proteinase inhibitors are also a common ingredient in the organic matrix of mollusk shells. However, the molecular mechanism that underlies the role of proteinase inhibitors in immune system and shell mineralization is poorly known. In this study, a Kunitz serine proteinase inhibitor (HcKuPI) was isolated from the mussel Hyriopsis cumingii. HcKuPI was specifically expressed in dorsal epithelial cells of the mantle pallium and HcKuPI dsRNA injection caused an irregular surface and disordered deposition on the aragonite tablets of the nacreous layer. These results indicated that HcKuPI plays a vital role in shell nacreous layer biomineralization. Moreover, the expression pattern of HcKuPI during LPS challenge and pearl formation indicated its involvement in the antimicrobial process during pearl sac formation and nacre tablets accumulation during pearl formation. In the in vitro calcium carbonate crystallization assay, the addition of GST-HcKuPI increased the precipitation rate of calcium carbonate and induced the crystal overgrowth of calcium carbonate. Taken together, these results indicate that HcKuPI is involved in antimicrobial process during pearl formation, and participates in calcium carbonate deposition acceleration and morphological regulation of the crystals during nacreous layer formation. These findings extend our knowledge of the role of proteinase inhibitors in immune system and shell biomineralization.
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Affiliation(s)
- Can Jin
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai, 201306, China
| | - Xiao-Jun Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
| | - Jia-Le Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai, 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China.
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50
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Sakalauskaite J, Andersen SH, Biagi P, Borrello MA, Cocquerez T, Colonese AC, Dal Bello F, Girod A, Heumüller M, Koon H, Mandili G, Medana C, Penkman KE, Plasseraud L, Schlichtherle H, Taylor S, Tokarski C, Thomas J, Wilson J, Marin F, Demarchi B. 'Palaeoshellomics' reveals the use of freshwater mother-of-pearl in prehistory. eLife 2019; 8:45644. [PMID: 31060688 PMCID: PMC6542584 DOI: 10.7554/elife.45644] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/20/2019] [Indexed: 01/14/2023] Open
Abstract
The extensive use of mollusc shell as a versatile raw material is testament to its importance in prehistoric times. The consistent choice of certain species for different purposes, including the making of ornaments, is a direct representation of how humans viewed and exploited their environment. The necessary taxonomic information, however, is often impossible to obtain from objects that are small, heavily worked or degraded. Here we propose a novel biogeochemical approach to track the biological origin of prehistoric mollusc shell. We conducted an in-depth study of archaeological ornaments using microstructural, geochemical and biomolecular analyses, including ‘palaeoshellomics’, the first application of palaeoproteomics to mollusc shells (and indeed to any invertebrate calcified tissue). We reveal the consistent use of locally-sourced freshwater mother-of-pearl for the standardized manufacture of ‘double-buttons’. This craft is found throughout Europe between 4200–3800 BCE, highlighting the ornament-makers’ profound knowledge of the biogeosphere and the existence of cross-cultural traditions. Just like people do today, prehistoric humans liked to adorn themselves with beautiful objects. Shells, from creatures like clams and snails, were used to decorate clothing or worn as jewelry at least as far back as 100,000 years ago. Later people used shells as the raw materials to make beads or bracelets. Learning where the shells came from may help scientists understand why prehistoric people chose certain shells and not others. It may also offer clues about how they used natural resources and the cultural significance of these objects. But identifying the shells is difficult because they lose many of their original distinctive features when worked into ornaments. New tools that use DNA or proteins to identify the raw materials used to craft ancient artifacts have emerged that may help. So far, scientists have mostly used these genomic and proteomic tools to identify the source of materials made from animal hide, ivory or bone – where collagen is the most abundant protein molecule. Yet it is more challenging to extract and characterize proteins or genetic material from mollusc shells. This is partly because the amount of proteins in shells is at least 300 times lower than in bone, and also because the makeup of proteins in shells is not as well-known as in collagen. Sakalauskaite et al. have now overcome these issues by combining the analytical tools used to study the proteins and mineral content of modern shells with those of ancient protein research. They then used this approach, which they named palaeoshellomics, to extract proteins from seven “double-buttons” – pearl-like ornaments crafted by prehistoric people in Europe. The double-buttons were made between 4200 and 3800 BC and found at archeological sites in Denmark, Germany and Romania. Comparing the extracted proteins to those from various mollusc shells showed that the double-buttons were made from freshwater mussels belonging to a group known as the Unionoida. The discovery helps settle a decade-long debate in archeology about the origin of the shells used to make double-buttons in prehistoric Europe. Ancient people often crafted ornaments from marine shells, because they were exotic and considered more prestigious. But the results on the double-buttons suggest instead that mother-of-pearl from fresh water shells was valued and used by groups throughout Europe, even those living in coastal areas. The palaeoshellomics technique used by Sakalauskaite et al. may now help identify the origins of shells from archeological and palaeontological sites.
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Affiliation(s)
- Jorune Sakalauskaite
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.,UMR CNRS 6282 Biogéosciences, University of Burgundy-Franche-Comté, Dijon, France
| | | | - Paolo Biagi
- Department of Asian and North African Studies, University of Ca' Foscari, Venice, Italy
| | | | - Théophile Cocquerez
- UMR CNRS 6282 Biogéosciences, University of Burgundy-Franche-Comté, Dijon, France
| | | | - Federica Dal Bello
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | | | - Marion Heumüller
- Niedersächsisches Landesamt für Denkmalpflege, Hannover, Germany
| | - Hannah Koon
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, United Kingdom
| | - Giorgia Mandili
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.,Centre for Experimental and Clinical Studies, University of Turin, Turin, Italy
| | - Claudio Medana
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Kirsty Eh Penkman
- Department of Chemistry, University of York, Heslington, United Kingdom
| | - Laurent Plasseraud
- Institute of Molecular Chemistry, ICMUB UMR CNRS 6302, University of Burgundy-Franche-Comté, Dijon, France
| | - Helmut Schlichtherle
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Gaienhofen, Germany
| | - Sheila Taylor
- Department of Chemistry, University of York, Heslington, United Kingdom
| | - Caroline Tokarski
- Miniaturization for Synthesis, Analysis & Proteomics, USR CNRS 3290, University of Lille, Lille, France
| | - Jérôme Thomas
- UMR CNRS 6282 Biogéosciences, University of Burgundy-Franche-Comté, Dijon, France
| | - Julie Wilson
- Department of Mathematics, University of York, Heslington, United Kingdom
| | - Frédéric Marin
- UMR CNRS 6282 Biogéosciences, University of Burgundy-Franche-Comté, Dijon, France
| | - Beatrice Demarchi
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.,Department of Archaeology, University of York, Heslington, United Kingdom
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