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Tate HM, Barone V, Schrankel CS, Hamdoun A, Lyons DC. Localization and origins of juvenile skeletogenic cells in the sea urchin Lytechinuspictus. Dev Biol 2024; 514:12-27. [PMID: 38862087 DOI: 10.1016/j.ydbio.2024.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 06/13/2024]
Abstract
The development of the sea urchin larval body plan is well understood from extensive studies of embryonic patterning. However, fewer studies have investigated the late larval stages during which the unique pentaradial adult body plan develops. Previous work on late larval development highlights major tissue changes leading up to metamorphosis, but the location of specific cell types during juvenile development is less understood. Here, we improve on technical limitations by applying highly sensitive hybridization chain reaction fluorescent in situ hybridization (HCR-FISH) to the fast-developing and transparent sea urchin Lytechinus pictus, with a focus on skeletogenic cells. First, we show that HCR-FISH can be used in L. pictus to precisely localize skeletogenic cells in the rudiment. In doing so, we provide a detailed staging scheme for the appearance of skeletogenic cells around the rudiment prior to and during biomineralization and show that many skeletogenic cells unassociated with larval rods localize outside of the rudiment prior to localizing inside. Second, we show that downstream biomineralization genes have similar expression patterns during larval and juvenile skeletogenesis, suggesting some conservation of skeletogenic mechanisms during development between stages. Third, we find co-expression of blastocoelar and skeletogenic cell markers around juvenile skeleton located outside of the rudiment, which is consistent with data showing that cells from the non-skeletogenic mesoderm embryonic lineage contribute to the juvenile skeletogenic cell lineage. This work sets the foundation for subsequent studies of other cell types in the late larva of L. pictus to better understand juvenile body plan development, patterning, and evolution.
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Affiliation(s)
- Heidi M Tate
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
| | - Vanessa Barone
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
| | - Catherine S Schrankel
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA; San Diego State University, San Diego, CA, USA
| | - Amro Hamdoun
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
| | - Deirdre C Lyons
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA.
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2
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Taylor E, Corsini M, Heyland A. Shared regulatory function of non-genomic thyroid hormone signaling in echinoderm skeletogenesis. EvoDevo 2024; 15:10. [PMID: 39113104 PMCID: PMC11304627 DOI: 10.1186/s13227-024-00226-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/22/2024] [Indexed: 08/10/2024] Open
Abstract
Thyroid hormones are crucial regulators of metamorphosis and development in bilaterians, particularly in chordate deuterostomes. Recent evidence suggests a role for thyroid hormone signaling, principally via 3,5,3',5'-Tetraiodo-L-thyronine (T4), in the regulation of metamorphosis, programmed cell death and skeletogenesis in echinoids (sea urchins and sand dollars) and sea stars. Here, we test whether TH signaling in skeletogenesis is a shared trait of Echinozoa (Echinoida and Holothouroida) and Asterozoa (Ophiourida and Asteroida). We demonstrate dramatic acceleration of skeletogenesis after TH treatment in three classes of echinoderms: sea urchins, sea stars, and brittle stars (echinoids, asteroids, and ophiuroids). Fluorescently labeled thyroid hormone analogues reveal thyroid hormone binding to cells proximal to regions of skeletogenesis in the gut and juvenile rudiment. We also identify, for the first time, a potential source of thyroxine during gastrulation in sea urchin embryos. Thyroxine-positive cells are present in tip of the archenteron. In addition, we detect thyroid hormone binding to the cell membrane and nucleus during metamorphic development in echinoderms. Immunohistochemistry of phosphorylated MAPK in the presence and absence of TH-binding inhibitors suggests that THs may act via phosphorylation of MAPK (ERK1/2) to accelerate initiation of skeletogenesis in the three echinoderm groups. Together, these results indicate that TH regulation of mesenchyme cell activity via integrin-mediated MAPK signaling may be a conserved mechanism for the regulation of skeletogenesis in echinoderm development. In addition, TH action via a nuclear thyroid hormone receptor may regulate metamorphic development. Our findings shed light on potentially ancient pathways of thyroid hormone activity in echinoids, ophiuroids, and asteroids, or on a signaling system that has been repeatedly co-opted to coordinate metamorphic development in bilaterians.
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Affiliation(s)
- Elias Taylor
- College of Biological Sciences, University of Guelph, Integrative Biology, Guelph, ON, N1G-2W1, Canada.
| | - Megan Corsini
- College of Biological Sciences, University of Guelph, Integrative Biology, Guelph, ON, N1G-2W1, Canada
| | - Andreas Heyland
- College of Biological Sciences, University of Guelph, Integrative Biology, Guelph, ON, N1G-2W1, Canada
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3
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Parey E, Ortega-Martinez O, Delroisse J, Piovani L, Czarkwiani A, Dylus D, Arya S, Dupont S, Thorndyke M, Larsson T, Johannesson K, Buckley KM, Martinez P, Oliveri P, Marlétaz F. The brittle star genome illuminates the genetic basis of animal appendage regeneration. Nat Ecol Evol 2024; 8:1505-1521. [PMID: 39030276 PMCID: PMC11310086 DOI: 10.1038/s41559-024-02456-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/29/2024] [Indexed: 07/21/2024]
Abstract
Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars are a species-rich class of echinoderms with outstanding regenerative abilities, but investigations into the genetic bases of regeneration in this group have been hindered by the limited genomic resources. Here we report a chromosome-scale genome assembly for the brittle star Amphiura filiformis. We show that the brittle star genome is the most rearranged among echinoderms sequenced so far, featuring a reorganized Hox cluster reminiscent of the rearrangements observed in sea urchins. In addition, we performed an extensive profiling of gene expression during brittle star adult arm regeneration and identified sequential waves of gene expression governing wound healing, proliferation and differentiation. We conducted comparative transcriptomic analyses with other invertebrate and vertebrate models for appendage regeneration and uncovered hundreds of genes with conserved expression dynamics, particularly during the proliferative phase of regeneration. Our findings emphasize the crucial importance of echinoderms to detect long-range expression conservation between vertebrates and classical invertebrate regeneration model systems.
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Affiliation(s)
- Elise Parey
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Olga Ortega-Martinez
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Jérôme Delroisse
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Laura Piovani
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Anna Czarkwiani
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Technische Universität Dresden, Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany
| | - David Dylus
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Roche Pharmaceutical Research and Early Development (pRED), Cardiovascular and Metabolism, Immunology, Infectious Disease, and Ophthalmology (CMI2O), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Srishti Arya
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK
| | - Samuel Dupont
- Department of Biology and Environmental Science, University of Gothenburg, Kristineberg Marine Research Station, Fiskebäckskil, Sweden
- IAEA Marine Environment Laboratories, Radioecology Laboratory, Quai Antoine 1er, Monaco
| | - Michael Thorndyke
- Department of Biology and Environmental Science, University of Gothenburg, Kristineberg Marine Research Station, Fiskebäckskil, Sweden
| | - Tomas Larsson
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kerstin Johannesson
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | | | - Pedro Martinez
- Departament de Genètica, Microbiologia, i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Paola Oliveri
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Ferdinand Marlétaz
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
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4
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Sampilo NF, Song JL. microRNA-1 regulates sea urchin skeletogenesis by directly targeting skeletogenic genes and modulating components of signaling pathways. Dev Biol 2024; 508:123-137. [PMID: 38290645 PMCID: PMC10985635 DOI: 10.1016/j.ydbio.2024.01.010] [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: 05/08/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/01/2024]
Abstract
microRNAs are evolutionarily conserved non-coding RNAs that direct post-transcriptional regulation of target transcripts. In vertebrates, microRNA-1 (miR-1) is expressed in muscle and has been found to play critical regulatory roles in vertebrate angiogenesis, a process that has been proposed to be analogous to sea urchin skeletogenesis. Results indicate that both miR-1 inhibitor and miR-1 mimic-injected larvae have significantly less F-actin enriched circumpharyngeal muscle fibers and fewer gut contractions. In addition, miR-1 regulates the positioning of skeletogenic primary mesenchyme cells (PMCs) and skeletogenesis of the sea urchin embryo. Interestingly, the gain-of-function of miR-1 leads to more severe PMC patterning and skeletal branching defects than its loss-of-function. The results suggest that miR-1 directly suppresses Ets1/2, Tbr, and VegfR7 of the skeletogenic gene regulatory network, and Nodal, and Wnt1 signaling components. This study identifies potential targets of miR-1 that impacts skeletogenesis and muscle formation and contributes to a deeper understanding of miR-1's function during development.
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Affiliation(s)
- Nina Faye Sampilo
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
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5
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Khor JM, Guerrero-Santoro J, Ettensohn CA. Molecular compartmentalization in a syncytium: restricted mobility of proteins within the sea urchin skeletogenic mesenchyme. Development 2023; 150:dev201804. [PMID: 37902109 DOI: 10.1242/dev.201804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/23/2023] [Indexed: 10/31/2023]
Abstract
Multinucleated cells, or syncytia, are found in diverse taxa. Their biological function is often associated with the compartmentalization of biochemical or cellular activities within the syncytium. How such compartments are generated and maintained is poorly understood. The sea urchin embryonic skeleton is secreted by a syncytium, and local patterns of skeletal growth are associated with distinct sub-domains of gene expression within the syncytium. For such molecular compartments to be maintained and to control local patterns of skeletal growth: (1) the mobility of TFs must be restricted to produce stable differences in the transcriptional states of nuclei within the syncytium; and (2) the mobility of biomineralization proteins must also be restricted to produce regional differences in skeletal growth. To test these predictions, we expressed fluorescently tagged forms of transcription factors and biomineralization proteins in sub-domains of the skeletogenic syncytium. We found that both classes of proteins have restricted mobility within the syncytium and identified motifs that limit their mobility. Our findings have general implications for understanding the functional and molecular compartmentalization of syncytia.
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Affiliation(s)
- Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15218, USA
| | - Jennifer Guerrero-Santoro
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15218, USA
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15218, USA
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Lee Y, Tjeerdema E, Kling S, Chang N, Hamdoun A. Solute carrier (SLC) expression reveals skeletogenic cell diversity. Dev Biol 2023; 503:68-82. [PMID: 37611888 DOI: 10.1016/j.ydbio.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
Within the developing embryo is a microcosm of cell type diversity. Single cell RNA-sequencing (scRNA-seq) is used to reveal cell types, typically by grouping cells according to their gene regulatory states. However, both across and within these regulatory states are additional layers of cellular diversity represented by the differential expression of genes that govern cell function. Here, we analyzed scRNA-seq data representing the late gastrula stage of Strongylocentrotus purpuratus (purple sea urchin) to understand the patterning of transporters belonging to the ABC and SLC families. These transporters handle diverse substrates from amino acids to signaling molecules, nutrients and xenobiotics. Using transporter-based clustering, we identified unique transporter patterns that are both shared across cell lineages, as well as those that were unique to known cell types. We further explored three patterns of transporter expression in mesodermal cells including secondary mesenchyme cells (pigment cells and blastocoelar cells) and skeletogenic cells (primary mesenchyme cells). The results revealed the enrichment of SMTs potentially involved in nutrient absorption (SLC5A9, SLC7A11, SLC35F3, and SLC52A3) and skeletogenesis (SLC9A3, SLC13A2/3/5, and SLC39A13) in pigment cells and blastocoelar cells respectively. The results indicated that the strategy of clustering by cellular activity can be useful for discovering cellular populations that would otherwise remain obscured.
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Affiliation(s)
- Yoon Lee
- Center for Marine Biology and Biomedicine Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Evan Tjeerdema
- Center for Marine Biology and Biomedicine Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Svenja Kling
- Center for Marine Biology and Biomedicine Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Nathan Chang
- Center for Marine Biology and Biomedicine Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Amro Hamdoun
- Center for Marine Biology and Biomedicine Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92037, USA.
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7
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Yamakawa S, Yamazaki A, Morino Y, Wada H. Early expression onset of tissue-specific effector genes during the specification process in sea urchin embryos. EvoDevo 2023; 14:7. [PMID: 37101206 PMCID: PMC10131483 DOI: 10.1186/s13227-023-00210-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/01/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND In the course of animal developmental processes, various tissues are differentiated through complex interactions within the gene regulatory network. As a general concept, differentiation has been considered to be the endpoint of specification processes. Previous works followed this view and provided a genetic control scheme of differentiation in sea urchin embryos: early specification genes generate distinct regulatory territories in an embryo to express a small set of differentiation driver genes; these genes eventually stimulate the expression of tissue-specific effector genes, which provide biological identity to differentiated cells, in each region. However, some tissue-specific effector genes begin to be expressed in parallel with the expression onset of early specification genes, raising questions about the simplistic regulatory scheme of tissue-specific effector gene expression and the current concept of differentiation itself. RESULTS Here, we examined the dynamics of effector gene expression patterns during sea urchin embryogenesis. Our transcriptome-based analysis indicated that many tissue-specific effector genes begin to be expressed and accumulated along with the advancing specification GRN in the distinct cell lineages of embryos. Moreover, we found that the expression of some of the tissue-specific effector genes commences before cell lineage segregation occurs. CONCLUSIONS Based on this finding, we propose that the expression onset of tissue-specific effector genes is controlled more dynamically than suggested in the previously proposed simplistic regulation scheme. Thus, we suggest that differentiation should be conceptualized as a seamless process of accumulation of effector expression along with the advancing specification GRN. This pattern of effector gene expression may have interesting implications for the evolution of novel cell types.
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Affiliation(s)
- Shumpei Yamakawa
- Institute of Zoology and Evolutionary Research, Friedrich-Shiller University Jena, Erbertstraße 1, 07747, Jena, Germany.
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Atsuko Yamazaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hiroshi Wada
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
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8
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Lopez-Anido RN, Batzel GO, Ramirez G, Goodheart JA, Wang Y, Neal S, Lyons DC. Spatial-temporal expression analysis of lineage-restricted shell matrix proteins reveals shell field regionalization and distinct cell populations in the slipper snail Crepidula atrasolea. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.18.532128. [PMID: 36993573 PMCID: PMC10055211 DOI: 10.1101/2023.03.18.532128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Molluscs are one of the most morphologically diverse clades of metazoans, exhibiting an immense diversification of calcium carbonate structures, such as the shell. Biomineralization of the calcified shell is dependent on shell matrix proteins (SMPs). While SMP diversity is hypothesized to drive molluscan shell diversity, we are just starting to unravel SMP evolutionary history and biology. Here we leveraged two complementary model mollusc systems, Crepidula fornicata and Crepidula atrasolea , to determine the lineage-specificity of 185 Crepidula SMPs. We found that 95% of the adult C. fornicata shell proteome belongs to conserved metazoan and molluscan orthogroups, with molluscan-restricted orthogroups containing half of all SMPs in the shell proteome. The low number of C. fornicata -restricted SMPs contradicts the generally-held notion that an animal’s biomineralization toolkit is dominated by mostly novel genes. Next, we selected a subset of lineage-restricted SMPs for spatial-temporal analysis using in situ hybridization chain reaction (HCR) during larval stages in C. atrasolea . We found that 12 out of 18 SMPs analyzed are expressed in the shell field. Notably, these genes are present in 5 expression patterns, which define at least three distinct cell populations within the shell field. These results represent the most comprehensive analysis of gastropod SMP evolutionary age and shell field expression patterns to date. Collectively, these data lay the foundation for future work to interrogate the molecular mechanisms and cell fate decisions underlying molluscan mantle specification and diversification.
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9
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Nanglu K, Cole SR, Wright DF, Souto C. Worms and gills, plates and spines: the evolutionary origins and incredible disparity of deuterostomes revealed by fossils, genes, and development. Biol Rev Camb Philos Soc 2023; 98:316-351. [PMID: 36257784 DOI: 10.1111/brv.12908] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 01/12/2023]
Abstract
Deuterostomes are the major division of animal life which includes sea stars, acorn worms, and humans, among a wide variety of ecologically and morphologically disparate taxa. However, their early evolution is poorly understood, due in part to their disparity, which makes identifying commonalities difficult, as well as their relatively poor early fossil record. Here, we review the available morphological, palaeontological, developmental, and molecular data to establish a framework for exploring the origins of this important and enigmatic group. Recent fossil discoveries strongly support a vermiform ancestor to the group Hemichordata, and a fusiform active swimmer as ancestor to Chordata. The diverse and anatomically bewildering variety of forms among the early echinoderms show evidence of both bilateral and radial symmetry. We consider four characteristics most critical for understanding the form and function of the last common ancestor to Deuterostomia: Hox gene expression patterns, larval morphology, the capacity for biomineralization, and the morphology of the pharyngeal region. We posit a deuterostome last common ancestor with a similar antero-posterior gene regulatory system to that found in modern acorn worms and cephalochordates, a simple planktonic larval form, which was later elaborated in the ambulacrarian lineage, the ability to secrete calcium minerals in a limited fashion, and a pharyngeal respiratory region composed of simple pores. This animal was likely to be motile in adult form, as opposed to the sessile origins that have been historically suggested. Recent debates regarding deuterostome monophyly as well as the wide array of deuterostome-affiliated problematica further suggest the possibility that those features were not only present in the last common ancestor of Deuterostomia, but potentially in the ur-bilaterian. The morphology and development of the early deuterostomes, therefore, underpin some of the most significant questions in the study of metazoan evolution.
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Affiliation(s)
- Karma Nanglu
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Selina R Cole
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK, 73072, USA.,School of Geosciences, University of Oklahoma, 100 E Boyd Street, Norman, OK, 73019, USA
| | - David F Wright
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK, 73072, USA.,School of Geosciences, University of Oklahoma, 100 E Boyd Street, Norman, OK, 73019, USA
| | - Camilla Souto
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,School of Natural Sciences & Mathematics, Stockton University, 101 Vera King Farris Dr, Galloway, NJ, 08205, USA
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10
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Mittal V, Reid RW, Machado DJ, Mashanov V, Janies DA. EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms. BMC Genom Data 2022; 23:75. [PMID: 36274129 PMCID: PMC9590158 DOI: 10.1186/s12863-022-01090-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Here we release a new version of EchinoDB, EchinoDB v2.0 ( https://echinodb.uncc.edu ). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity. RESULTS The updated version of EchinoDB includes two new major datasets: the RNA-Seq data of the brittle star Ophioderma brevispinum and the high-quality genomic assembly data of the green sea urchin Lytechinus variegatus. In addition, we enabled keyword searches for annotated data and installed an updated version of Sequenceserver to allow Basic Local Alignment Search Tool (BLAST) searches. The data are downloadable in FASTA format. The first version of EchinoDB appeared in 2016 and was implemented in GO on a local server. The new version has been updated using R Shiny to include new features and improvements in the application. Furthermore, EchinoDB now runs entirely in the cloud for increased reliability and scaling. CONCLUSION EchinoDB serves a user base drawn from the fields of phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration. As use cases, we illustrate the function of EchinoDB in retrieving components of signaling pathways involved in the tissue regeneration process of different echinoderms, including the emerging model species Ophioderma brevispinum. Moreover, we use EchinoDB to shed light on the conservation of the molecular components involved in two echinoderm-specific phenomena: spicule matrix proteins involved in the formation of stereom endoskeleton and the tensilin protein that contributes to the capacity of the connective tissues to quickly change its mechanical properties. The genes involved in the former had been previously studied in echinoids, while gene sequences involved in the latter had been previously described in holothuroids. Specifically, we ask (a) if the biomineralization-related proteins previously reported only in sea urchins are also present in other, non-echinoid, echinoderms and (b) if tensilin, the protein responsible for the control of stiffness of the mutable collagenous tissue, previously described in sea cucumbers, is conserved across the phylum.
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Affiliation(s)
- Varnika Mittal
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA.
| | - Robert W Reid
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
| | - Vladimir Mashanov
- Wake Forest Institute for Regenerative Medicine, 91 Technology Way NE, Winston-Salem, NC, 27101, USA
| | - Daniel A Janies
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
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11
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Extracellular carbonic anhydrase activity promotes a carbon concentration mechanism in metazoan calcifying cells. Proc Natl Acad Sci U S A 2022; 119:e2203904119. [PMID: 36161891 DOI: 10.1073/pnas.2203904119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many calcifying organisms utilize metabolic CO2 to generate CaCO3 minerals to harden their shells and skeletons. Carbonic anhydrases are evolutionary ancient enzymes that have been proposed to play a key role in the calcification process, with the underlying mechanisms being little understood. Here, we used the calcifying primary mesenchyme cells (PMCs) of sea urchin larva to study the role of cytosolic (iCAs) and extracellular carbonic anhydrases (eCAs) in the cellular carbon concentration mechanism (CCM). Molecular analyses identified iCAs and eCAs in PMCs and highlight the prominent expression of a glycosylphosphatidylinositol-anchored membrane-bound CA (Cara7). Intracellular pH recordings in combination with CO2 pulse experiments demonstrated iCA activity in PMCs. iCA activity measurements, together with pharmacological approaches, revealed an opposing contribution of iCAs and eCAs on the CCM. H+-selective electrodes were used to demonstrate eCA-catalyzed CO2 hydration rates at the cell surface. Knockdown of Cara7 reduced extracellular CO2 hydration rates accompanied by impaired formation of specific skeletal segments. Finally, reduced pHi regulatory capacities during inhibition and knockdown of Cara7 underscore a role of this eCA in cellular HCO3- uptake. This work reveals the function of CAs in the cellular CCM of a marine calcifying animal. Extracellular hydration of metabolic CO2 by Cara7 coupled to HCO3- uptake mechanisms mitigates the loss of carbon and reduces the cellular proton load during the mineralization process. The findings of this work provide insights into the cellular mechanisms of an ancient biological process that is capable of utilizing CO2 to generate a versatile construction material.
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12
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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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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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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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15
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Chiarelli R, Scudiero R, Memoli V, Roccheri MC, Martino C. Toxicity of Vanadium during Development of Sea Urchin Embryos: Bioaccumulation, Calcium Depletion, ERK Modulation and Cell-Selective Apoptosis. Int J Mol Sci 2022; 23:ijms23116239. [PMID: 35682917 PMCID: PMC9181554 DOI: 10.3390/ijms23116239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 11/22/2022] Open
Abstract
Vanadium toxicology is a topic of considerable importance as this metal is widely used in industrial and biomedical fields. However, it represents a potential emerging environmental pollutant because wastewater treatment plants do not adequately remove metal compounds that are subsequently released into the environment. Vanadium applications are limited due to its toxicity, so it is urgent to define this aspect. This metal is associated with sea urchin embryo toxicity as it perturbs embryogenesis and skeletogenesis, triggering several stress responses. Here we investigated its bioaccumulation and the correlation with cellular and molecular developmental pathways. We used cytotoxic concentrations of 1 mM and 500 μM to perform quantitative analyses, showing that vanadium accumulation interferes with calcium uptake during sea urchin development and provokes a disruption in the biomineralization process. At the end of the whole treatment, the accumulation of vanadium was about 14 and 8 μg for embryos treated respectively with 1 mM and 500 μM, showing a dose-dependent response. Then, we monitored the cell signaling perturbation, analyzing key molecular markers of cell survival/cell death mechanisms and the DNA fragmentation associated with apoptosis. This paper clarifies vanadium’s trend to accumulate directly into embryonic cells, interfering with calcium uptake. In addition, our results indicate that vanadium can modulate the ERK pathway and activate a cell-selective apoptosis. These results endorse the sea urchin embryo as an adequate experimental model to study metal-related cellular/molecular responses.
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Affiliation(s)
- Roberto Chiarelli
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Building 16, 90128 Palermo, Italy; (M.C.R.); (C.M.)
- Correspondence:
| | - Rosaria Scudiero
- Department of Biology, University Federico II, 80126 Napoli, Italy; (R.S.); (V.M.)
| | - Valeria Memoli
- Department of Biology, University Federico II, 80126 Napoli, Italy; (R.S.); (V.M.)
| | - Maria Carmela Roccheri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Building 16, 90128 Palermo, Italy; (M.C.R.); (C.M.)
| | - Chiara Martino
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Building 16, 90128 Palermo, Italy; (M.C.R.); (C.M.)
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16
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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: 60] [Impact Index Per Article: 30.0] [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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17
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Ettensohn CA, Guerrero-Santoro J, Khor JM. Lessons from a transcription factor: Alx1 provides insights into gene regulatory networks, cellular reprogramming, and cell type evolution. Curr Top Dev Biol 2022; 146:113-148. [PMID: 35152981 DOI: 10.1016/bs.ctdb.2021.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The skeleton-forming cells of sea urchins and other echinoderms have been studied by developmental biologists as models of cell specification and morphogenesis for many decades. The gene regulatory network (GRN) deployed in the embryonic skeletogenic cells of euechinoid sea urchins is one of the best understood in any developing animal. Recent comparative studies have leveraged the information contained in this GRN, bringing renewed attention to the diverse patterns of skeletogenesis within the phylum and the evolutionary basis for this diversity. The homeodomain-containing transcription factor, Alx1, was originally shown to be a core component of the skeletogenic GRN of the sea urchin embryo. Alx1 has since been found to be key regulator of skeletal cell identity throughout the phylum. As such, Alx1 is currently serving as a lens through which multiple developmental processes are being investigated. These include not only GRN organization and evolution, but also cell reprogramming, cell type evolution, and the gene regulatory control of morphogenesis. This review summarizes our current state of knowledge concerning Alx1 and highlights the insights it is yielding into these important developmental and evolutionary processes.
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Affiliation(s)
- Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States.
| | | | - Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
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18
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Chang WL, Su YH. Zygotic hypoxia-inducible factor alpha regulates spicule elongation in the sea urchin embryo. Dev Biol 2022; 484:63-74. [DOI: 10.1016/j.ydbio.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 01/28/2022] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
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19
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Kahil K, Weiner S, Addadi L, Gal A. Ion Pathways in Biomineralization: Perspectives on Uptake, Transport, and Deposition of Calcium, Carbonate, and Phosphate. J Am Chem Soc 2021; 143:21100-21112. [PMID: 34881565 PMCID: PMC8704196 DOI: 10.1021/jacs.1c09174] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Indexed: 12/19/2022]
Abstract
Minerals are formed by organisms in all of the kingdoms of life. Mineral formation pathways all involve uptake of ions from the environment, transport of ions by cells, sometimes temporary storage, and ultimately deposition in or outside of the cells. Even though the details of how all this is achieved vary enormously, all pathways need to respect both the chemical limitations of ion manipulation, as well as the many "housekeeping" roles of ions in cell functioning. Here we provide a chemical perspective on the biological pathways of biomineralization. Our approach is to compare and contrast the ion pathways involving calcium, phosphate, and carbonate in three very different organisms: the enormously abundant unicellular marine coccolithophores, the well investigated sea urchin larval model for single crystal formation, and the complex pathways used by vertebrates to form their bones. The comparison highlights both common and unique processes. Significantly, phosphate is involved in regulating calcium carbonate deposition and carbonate is involved in regulating calcium phosphate deposition. One often overlooked commonality is that, from uptake to deposition, the solutions involved are usually supersaturated. This therefore requires not only avoiding mineral deposition where it is not needed but also exploiting this saturated state to produce unstable mineral precursors that can be conveniently stored, redissolved, and manipulated into diverse shapes and upon deposition transformed into more ordered and hence often functional final deposits.
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Affiliation(s)
- Keren Kahil
- Department
of Chemical and Structural Biology and Department of Plant and Environmental
Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Steve Weiner
- Department
of Chemical and Structural Biology and Department of Plant and Environmental
Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Lia Addadi
- Department
of Chemical and Structural Biology and Department of Plant and Environmental
Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Assaf Gal
- Department
of Chemical and Structural Biology and Department of Plant and Environmental
Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
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20
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Enzymatic Approach in Calcium Phosphate Biomineralization: A Contribution to Reconcile the Physicochemical with the Physiological View. Int J Mol Sci 2021; 22:ijms222312957. [PMID: 34884758 PMCID: PMC8657759 DOI: 10.3390/ijms222312957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 01/22/2023] Open
Abstract
Biomineralization is the process by which organisms produce hard inorganic matter from soft tissues with outstanding control of mineral deposition in time and space. For this purpose, organisms deploy a sophisticated "toolkit" that has resulted in significant evolutionary innovations, for which calcium phosphate (CaP) is the biomineral selected for the skeleton of vertebrates. While CaP mineral formation in aqueous media can be investigated by studying thermodynamics and kinetics of phase transitions in supersaturated solutions, biogenic mineralization requires coping with the inherent complexity of biological systems. This mainly includes compartmentalization and homeostatic processes used by organisms to regulate key physiological factors, including temperature, pH and ion concentration. A detailed analysis of the literature shows the emergence of two main views describing the mechanism of CaP biomineralization. The first one, more dedicated to the study of in vivo systems and supported by researchers in physiology, often involves matrix vesicles (MVs). The second one, more investigated by the physicochemistry community, involves collagen intrafibrillar mineralization particularly through in vitro acellular models. Herein, we show that there is an obvious need in the biological systems to control both where and when the mineral forms through an in-depth survey of the mechanism of CaP mineralization. This necessity could gather both communities of physiologists and physicochemists under a common interest for an enzymatic approach to better describe CaP biomineralization. Both homogeneous and heterogeneous enzymatic catalyses are conceivable for these systems, and a few preliminary promising results on CaP mineralization for both types of enzymatic catalysis are reported in this work. Through them, we aim to describe the relevance of our point of view and the likely findings that could be obtained when adding an enzymatic approach to the already rich and creative research field dealing with CaP mineralization. This complementary approach could lead to a better understanding of the biomineralization mechanism and inspire the biomimetic design of new materials.
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21
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Ehrlich H, Bailey E, Wysokowski M, Jesionowski T. Forced Biomineralization: A Review. Biomimetics (Basel) 2021; 6:46. [PMID: 34287234 PMCID: PMC8293141 DOI: 10.3390/biomimetics6030046] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 12/31/2022] Open
Abstract
Biologically induced and controlled mineralization of metals promotes the development of protective structures to shield cells from thermal, chemical, and ultraviolet stresses. Metal biomineralization is widely considered to have been relevant for the survival of life in the environmental conditions of ancient terrestrial oceans. Similar behavior is seen among extremophilic biomineralizers today, which have evolved to inhabit a variety of industrial aqueous environments with elevated metal concentrations. As an example of extreme biomineralization, we introduce the category of "forced biomineralization", which we use to refer to the biologically mediated sequestration of dissolved metals and metalloids into minerals. We discuss forced mineralization as it is known to be carried out by a variety of organisms, including polyextremophiles in a range of psychrophilic, thermophilic, anaerobic, alkaliphilic, acidophilic, and halophilic conditions, as well as in environments with very high or toxic metal ion concentrations. While much additional work lies ahead to characterize the various pathways by which these biominerals form, forced biomineralization has been shown to provide insights for the progression of extreme biomimetics, allowing for promising new forays into creating the next generation of composites using organic-templating approaches under biologically extreme laboratory conditions relevant to a wide range of industrial conditions.
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Affiliation(s)
- Hermann Ehrlich
- Institute of Electronic and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany
- Center for Advanced Technology, Adam Mickiewicz University, 61614 Poznan, Poland
- Centre for Climate Change Research, Toronto, ON M4P 1J4, Canada
- ICUBE-University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Elizabeth Bailey
- Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064, USA;
| | - Marcin Wysokowski
- Faculty of Chemical Technology, Institute of Chemical Technology and Engineering, Poznan University of Technology, 60-965 Poznan, Poland
| | - Teofil Jesionowski
- Faculty of Chemical Technology, Institute of Chemical Technology and Engineering, Poznan University of Technology, 60-965 Poznan, Poland
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22
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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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23
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Yong LW, Lu TM, Tung CH, Chiou RJ, Li KL, Yu JK. Somite Compartments in Amphioxus and Its Implications on the Evolution of the Vertebrate Skeletal Tissues. Front Cell Dev Biol 2021; 9:607057. [PMID: 34041233 PMCID: PMC8141804 DOI: 10.3389/fcell.2021.607057] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Mineralized skeletal tissues of vertebrates are an evolutionary novelty within the chordate lineage. While the progenitor cells that contribute to vertebrate skeletal tissues are known to have two embryonic origins, the mesoderm and neural crest, the evolutionary origin of their developmental process remains unclear. Using cephalochordate amphioxus as our model, we found that cells at the lateral wall of the amphioxus somite express SPARC (a crucial gene for tissue mineralization) and various collagen genes. During development, some of these cells expand medially to surround the axial structures, including the neural tube, notochord and gut, while others expand laterally and ventrally to underlie the epidermis. Eventually these cell populations are found closely associated with the collagenous matrix around the neural tube, notochord, and dorsal aorta, and also with the dense collagen sheets underneath the epidermis. Using known genetic markers for distinct vertebrate somite compartments, we showed that the lateral wall of amphioxus somite likely corresponds to the vertebrate dermomyotome and lateral plate mesoderm. Furthermore, we demonstrated a conserved role for BMP signaling pathway in somite patterning of both amphioxus and vertebrates. These results suggest that compartmentalized somites and their contribution to primitive skeletal tissues are ancient traits that date back to the chordate common ancestor. The finding of SPARC-expressing skeletal scaffold in amphioxus further supports previous hypothesis regarding SPARC gene family expansion in the elaboration of the vertebrate mineralized skeleton.
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Affiliation(s)
- Luok Wen Yong
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Tsai-Ming Lu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Che-Huang Tung
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Department of Aquatic Biology, Chia-Yi University, Chia-Yi, Taiwan
| | - Ruei-Jen Chiou
- Department of Anatomy and Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Kun-Lung Li
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
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24
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Sampilo NF, Stepicheva NA, Song JL. microRNA-31 regulates skeletogenesis by direct suppression of Eve and Wnt1. Dev Biol 2021; 472:98-114. [PMID: 33484703 PMCID: PMC7956219 DOI: 10.1016/j.ydbio.2021.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/23/2020] [Accepted: 01/11/2021] [Indexed: 11/22/2022]
Abstract
microRNAs (miRNAs) play a critical role in a variety of biological processes, including embryogenesis and the physiological functions of cells. Evolutionarily conserved microRNA-31 (miR-31) has been found to be involved in cancer, bone formation, and lymphatic development. We previously discovered that, in the sea urchin, miR-31 knockdown (KD) embryos have shortened dorsoventral connecting rods, mispatterned skeletogenic primary mesenchyme cells (PMCs) and shifted and expanded Vegf3 expression domain. Vegf3 itself does not contain miR-31 binding sites; however, we identified its upstream regulators Eve and Wnt1 to be directly suppressed by miR-31. Removal of miR-31's suppression of Eve and Wnt1 resulted in skeletal and PMC patterning defects, similar to miR-31 KD phenotypes. Additionally, removal of miR-31's suppression of Eve and Wnt1 results in an expansion and anterior shift in expression of Veg1 ectodermal genes, including Vegf3 in the blastulae. This indicates that miR-31 indirectly regulates Vegf3 expression through directly suppressing Eve and Wnt1. Furthermore, removing miR-31 suppression of Eve is sufficient to cause skeletogenic defects, revealing a novel regulatory role of Eve in skeletogenesis and PMC patterning. Overall, this study provides a proposed molecular mechanism of miR-31's regulation of skeletogenesis and PMC patterning through its cross-regulation of a Wnt signaling ligand and a transcription factor of the endodermal and ectodermal gene regulatory network.
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Affiliation(s)
- Nina Faye Sampilo
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Nadezda A Stepicheva
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
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25
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Zaquin T, Malik A, Drake JL, Putnam HM, Mass T. Evolution of Protein-Mediated Biomineralization in Scleractinian Corals. Front Genet 2021; 12:618517. [PMID: 33633782 PMCID: PMC7902050 DOI: 10.3389/fgene.2021.618517] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/08/2021] [Indexed: 12/19/2022] Open
Abstract
While recent strides have been made in understanding the biological process by which stony corals calcify, much remains to be revealed, including the ubiquity across taxa of specific biomolecules involved. Several proteins associated with this process have been identified through proteomic profiling of the skeletal organic matrix (SOM) extracted from three scleractinian species. However, the evolutionary history of this putative “biomineralization toolkit,” including the appearance of these proteins’ throughout metazoan evolution, remains to be resolved. Here we used a phylogenetic approach to examine the evolution of the known scleractinians’ SOM proteins across the Metazoa. Our analysis reveals an evolutionary process dominated by the co-option of genes that originated before the cnidarian diversification. Each one of the three species appears to express a unique set of the more ancient genes, representing the independent co-option of SOM proteins, as well as a substantial proportion of proteins that evolved independently. In addition, in some instances, the different species expressed multiple orthologous proteins sharing the same evolutionary history. Furthermore, the non-random clustering of multiple SOM proteins within scleractinian-specific branches suggests the conservation of protein function between distinct species for what we posit is part of the scleractinian “core biomineralization toolkit.” This “core set” contains proteins that are likely fundamental to the scleractinian biomineralization mechanism. From this analysis, we infer that the scleractinians’ ability to calcify was achieved primarily through multiple lineage-specific protein expansions, which resulted in a new functional role that was not present in the parent gene.
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Affiliation(s)
- Tal Zaquin
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Assaf Malik
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Jeana L Drake
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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26
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Piovani L, Czarkwiani A, Ferrario C, Sugni M, Oliveri P. Ultrastructural and molecular analysis of the origin and differentiation of cells mediating brittle star skeletal regeneration. BMC Biol 2021; 19:9. [PMID: 33461552 PMCID: PMC7814545 DOI: 10.1186/s12915-020-00937-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 12/02/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Regeneration is the ability to re-grow body parts or tissues after trauma, and it is widespread across metazoans. Cells involved in regeneration can arise from a pool of undifferentiated proliferative cells or be recruited from pre-existing differentiated tissues. Both mechanisms have been described in different phyla; however, the cellular and molecular mechanisms employed by different animals to restore lost tissues as well as the source of cells involved in regeneration remain largely unknown. Echinoderms are a clade of deuterostome invertebrates that show striking larval and adult regenerative abilities in all extant classes. Here, we use the brittle star Amphiura filiformis to investigate the origin and differentiation of cells involved in skeletal regeneration using a combination of microscopy techniques and molecular markers. RESULTS Our ultrastructural analyses at different regenerative stages identify a population of morphologically undifferentiated cells which appear in close contact with the proliferating epithelium of the regenerating aboral coelomic cavity. These cells express skeletogenic marker genes, such as the transcription factor alx1 and the differentiation genes c-lectin and msp130L, and display a gradient of morphological differentiation from the aboral coelomic cavity towards the epidermis. Cells closer to the epidermis, which are in contact with developing spicules, have the morphology of mature skeletal cells (sclerocytes), and express several skeletogenic transcription factors and differentiation genes. Moreover, as regeneration progresses, sclerocytes show a different combinatorial expression of genes in various skeletal elements. CONCLUSIONS We hypothesize that sclerocyte precursors originate from the epithelium of the proliferating aboral coelomic cavity. As these cells migrate towards the epidermis, they differentiate and start secreting spicules. Moreover, our study shows that molecular and cellular processes involved in skeletal regeneration resemble those used during skeletal development, hinting at a possible conservation of developmental programmes during adult regeneration. Finally, we highlight that many genes involved in echinoderm skeletogenesis also play a role in vertebrate skeleton formation, suggesting a possible common origin of the deuterostome endoskeleton pathway.
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Affiliation(s)
- Laura Piovani
- Department of Environmental Science and Policy, University of Milan, Via Celoria, 2, 20133, Milan, Italy
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Center for Life Origins and Evolution, University College London, London, UK
| | - Anna Czarkwiani
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Present Address: DFG-Center for Regenerative Therapies Technische Universität Dresden (CRTD), Dresden, Germany
| | - Cinzia Ferrario
- Department of Environmental Science and Policy, University of Milan, Via Celoria, 2, 20133, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Via Celoria, 16, 20133, Milan, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria, 2, 20133, Milan, Italy.
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Via Celoria, 16, 20133, Milan, Italy.
- GAIA 2050 Center, Department of Environmental Science and Policy, University of Milan, Via Celoria, 2, 20133, Milan, Italy.
| | - Paola Oliveri
- Department of Genetics, Evolution and Environment, University College London, London, UK.
- Center for Life Origins and Evolution, University College London, London, UK.
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27
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Lang A, Mijowska S, Polishchuk I, Fermani S, Falini G, Katsman A, Marin F, Pokroy B. Acidic Monosaccharides become Incorporated into Calcite Single Crystals*. Chemistry 2020; 26:16860-16868. [PMID: 33405235 DOI: 10.1002/chem.202003344] [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: 07/15/2020] [Revised: 08/13/2020] [Indexed: 02/06/2023]
Abstract
Carbohydrates, along with proteins and peptides, are known to represent a major class of biomacromolecules involved in calcium carbonate biomineralization. However, in spite of multiple physical and biochemical characterizations, the explicit role of saccharide macromolecules (long chains of carbohydrate molecules) in mineral deposition is not yet understood. In this study, we investigated the influence of two common acidic monosaccharides (MSs), the two simplest forms of acidic carbohydrates, namely glucuronic and galacturonic acids, on the formation of calcite crystals in vitro. We show here that the size, morphology, and microstructure of calcite crystals are altered when they are grown in the presence of these MSs. More importantly, these MSs were found to become incorporated into the calcite crystalline lattice and induce anisotropic lattice distortions, a phenomenon widely studied for other biomolecules related to CaCO3 biomineralization, but never before reported in the case of single MSs. Changes in the calcite lattice induced by MSs incorporation were precisely determined by high-resolution synchrotron powder X-ray diffraction. We believe that the results of this research may deepen our understanding of the interaction of saccharide polymers with an inorganic host and shed light on the implications of carbohydrates for biomineralization processes.
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Affiliation(s)
- Arad Lang
- Department of Materials Science and Engineering, and the, Russell Berrie Nanotechnology Institute, Technion-Israel Institute of, Technology, Technion City, 320003, Haifa, Israel
| | - Sylwia Mijowska
- Department of Materials Science and Engineering, and the, Russell Berrie Nanotechnology Institute, Technion-Israel Institute of, Technology, Technion City, 320003, Haifa, Israel
| | - Iryna Polishchuk
- Department of Materials Science and Engineering, and the, Russell Berrie Nanotechnology Institute, Technion-Israel Institute of, Technology, Technion City, 320003, Haifa, Israel
| | - Simona Fermani
- Faculty of Chemistry, University of Bologna, 2 Via Selmi, 40126, Bologna BO, Italy
| | - Giuseppe Falini
- Faculty of Chemistry, University of Bologna, 2 Via Selmi, 40126, Bologna BO, Italy
| | - Alexander Katsman
- Department of Materials Science and Engineering, and the, Russell Berrie Nanotechnology Institute, Technion-Israel Institute of, Technology, Technion City, 320003, Haifa, Israel
| | - Frédéric Marin
- UMR CNRS 6282 Biogeosciences, University of Burgundy-Franche-Comté, 6 Boulevard Gabriel, Dijon, 21000, France
| | - Boaz Pokroy
- Department of Materials Science and Engineering, and the, Russell Berrie Nanotechnology Institute, Technion-Israel Institute of, Technology, Technion City, 320003, Haifa, Israel
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28
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Khor JM, Ettensohn CA. Transcription Factors of the Alx Family: Evolutionarily Conserved Regulators of Deuterostome Skeletogenesis. Front Genet 2020; 11:569314. [PMID: 33329706 PMCID: PMC7719703 DOI: 10.3389/fgene.2020.569314] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
Members of the alx gene family encode transcription factors that contain a highly conserved Paired-class, DNA-binding homeodomain, and a C-terminal OAR/Aristaless domain. Phylogenetic and comparative genomic studies have revealed complex patterns of alx gene duplications during deuterostome evolution. Remarkably, alx genes have been implicated in skeletogenesis in both echinoderms and vertebrates. In this review, we provide an overview of current knowledge concerning alx genes in deuterostomes. We highlight their evolutionarily conserved role in skeletogenesis and draw parallels and distinctions between the skeletogenic gene regulatory circuitries of diverse groups within the superphylum.
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Affiliation(s)
- Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
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29
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Huang S, Jiang H, Zhang L, Gu Q, Wang W, Wen Y, Luo F, Jin W, Cao X. Integrated proteomic and transcriptomic analysis reveals that polymorphic shell colors vary with melanin synthesis in Bellamya purificata snail. J Proteomics 2020; 230:103950. [PMID: 32871245 DOI: 10.1016/j.jprot.2020.103950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
The snail Bellamya purificata is an ecologically and economically important freshwater gastropod species. However, limited genomic resources are available for this snail. In this study, the transcriptome of mantle tissues and proteome of shells of B. purificata with two shell colors (namely light-cyan line (LC) and light-purple line (LP)) were deeply sequenced and characterized. A total of 5.72 million contigs were assembled into 157,015 unigenes, 21,455 (13.66%) of these unigenes were significantly matched to NR, Swiss-Prot, KOG, GO and KEGG database. 1807 differentially expressed genes (DEGs) were identified between the two different shell color lines. These DEGs were significantly enriched in five KEGG pathways including tyrosine metabolism, tryptophan metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, and histidine metabolism, which suggested that the shell color polymorphism in B. purificata was a result of melanin synthesis variation. A total of 1521 proteins were identified in B. purificata here as well. The differentially expressed protein analysis showed that the tyrosinase content in LP was significantly decreased in comparison to LC, which agreed with the transcriptome analysis results. This study provides valuable genomic resources of B. purificata and improves our understanding of molecular mechanisms of biomineralization and shell color polymorphism in snail.
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Affiliation(s)
- Songqian Huang
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, the University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Hanjun Jiang
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Zhang
- College of Marxism, Shanghai University of Finance and Economics, Shanghai 200433, China
| | - Qianhong Gu
- The State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
| | - Weimin Wang
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanhong Wen
- Liuzhou Aquaculture Technology Extending Station, Liuzhou, China
| | - Fuguang Luo
- Liuzhou Aquaculture Technology Extending Station, Liuzhou, China
| | - Wu Jin
- Sino-US Cooperative Laboratory for Germplasm Conservation and Utilization of Freshwater Mollusks, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, Jiangsu, China.
| | - Xiaojuan Cao
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
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30
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Li Y, Omori A, Flores RL, Satterfield S, Nguyen C, Ota T, Tsurugaya T, Ikuta T, Ikeo K, Kikuchi M, Leong JCK, Reich A, Hao M, Wan W, Dong Y, Ren Y, Zhang S, Zeng T, Uesaka M, Uchida Y, Li X, Shibata TF, Bino T, Ogawa K, Shigenobu S, Kondo M, Wang F, Chen L, Wessel G, Saiga H, Cameron RA, Livingston B, Bradham C, Wang W, Irie N. Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms. Commun Biol 2020; 3:371. [PMID: 32651448 PMCID: PMC7351957 DOI: 10.1038/s42003-020-1091-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 06/19/2020] [Indexed: 12/13/2022] Open
Abstract
Echinoderms are an exceptional group of bilaterians that develop pentameral adult symmetry from a bilaterally symmetric larva. However, the genetic basis in evolution and development of this unique transformation remains to be clarified. Here we report newly sequenced genomes, developmental transcriptomes, and proteomes of diverse echinoderms including the green sea urchin (L. variegatus), a sea cucumber (A. japonicus), and with particular emphasis on a sister group of the earliest-diverged echinoderms, the feather star (A. japonica). We learned that the last common ancestor of echinoderms retained a well-organized Hox cluster reminiscent of the hemichordate, and had gene sets involved in endoskeleton development. Further, unlike in other animal groups, the most conserved developmental stages were not at the body plan establishing phase, and genes normally involved in bilaterality appear to function in pentameric axis development. These results enhance our understanding of the divergence of protostomes and deuterostomes almost 500 Mya. Li et al. investigate the evolution and genetic basis of the adult pentameral body plan in echinoderms using genomic, transcriptomic, and proteomic data. They determine that the last common ancestor of echinoderms contained an organized Hox cluster and endoskeleton genes, and suggest that cooption of bilateral development genes was involved in evolution of the pentameric body plan.
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Affiliation(s)
- Yongxin Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Akihito Omori
- Sado Island Center for Ecological Sustainability, Niigata University, Niigata, Japan
| | - Rachel L Flores
- Dept. of Biological Sciences, California State Univesity, Long Beach, CA, USA
| | - Sheri Satterfield
- Dept. of Biological Sciences, California State Univesity, Long Beach, CA, USA
| | - Christine Nguyen
- Dept. of Biological Sciences, California State Univesity, Long Beach, CA, USA
| | | | | | - Tetsuro Ikuta
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, Japan.,Tokyo Metropolitan University, Yokosuka, Tokyo, Japan
| | | | | | - Jason C K Leong
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Adrian Reich
- Providence Institute of Molecular Oogenesis, Brown University, Providence, RI, USA
| | - Meng Hao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wenting Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yang Dong
- Yunnan Agricultural University, Kunming, China
| | - Yaondong Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Si Zhang
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Tao Zeng
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Masahiro Uesaka
- RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo, Japan
| | - Yui Uchida
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, University of Tokyo, Tokyo, Japan
| | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Tomoko F Shibata
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takahiro Bino
- NIBB Core Research Facilities, National Institute of Basic Biology, Okazaki, Aichi, Japan
| | - Kota Ogawa
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute of Basic Biology, Okazaki, Aichi, Japan
| | - Mariko Kondo
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Fayou Wang
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Luonan Chen
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
| | - Gary Wessel
- Providence Institute of Molecular Oogenesis, Brown University, Providence, RI, USA
| | - Hidetoshi Saiga
- Tokyo Metropolitan University, Yokosuka, Tokyo, Japan.,Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Chuo University, Tokyo, Japan
| | - R Andrew Cameron
- Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Brian Livingston
- Dept. of Biological Sciences, California State Univesity, Long Beach, CA, USA
| | | | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
| | - Naoki Irie
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. .,Universal Biology Institute, University of Tokyo, Tokyo, Japan.
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31
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Di Giglio S, Spatafora D, Milazzo M, M'Zoudi S, Zito F, Dubois P, Costa C. Are control of extracellular acid-base balance and regulation of skeleton genes linked to resistance to ocean acidification in adult sea urchins? THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137443. [PMID: 32325563 DOI: 10.1016/j.scitotenv.2020.137443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Sarah Di Giglio
- Laboratoire de Biologie Marine, Université Libre de Bruxelles, 1050 Bruxelles, Belgium.
| | - Davide Spatafora
- Department of Earth and Marine Science (DiSTeM), Università degli studi di Palermo, 90146 Palermo, Italy
| | - Marco Milazzo
- Department of Earth and Marine Science (DiSTeM), Università degli studi di Palermo, 90146 Palermo, Italy
| | - Saloua M'Zoudi
- Laboratoire de Biologie Marine, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Francesca Zito
- Consiglio Nazionale Delle Ricerche, Istituto per la Ricerca e per l'Innovazione Biomedica (IRIB), Via Ugo La Malfa 153, 90146 Palermo, Italy
| | - Philippe Dubois
- Laboratoire de Biologie Marine, Université Libre de Bruxelles, 1050 Bruxelles, Belgium.
| | - Caterina Costa
- Consiglio Nazionale Delle Ricerche, Istituto per la Ricerca e per l'Innovazione Biomedica (IRIB), Via Ugo La Malfa 153, 90146 Palermo, Italy.
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32
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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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33
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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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Skeletal development in the sea urchin relies upon protein families that contain intrinsic disorder, aggregation-prone, and conserved globular interactive domains. PLoS One 2019; 14:e0222068. [PMID: 31574084 PMCID: PMC6771980 DOI: 10.1371/journal.pone.0222068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/21/2019] [Indexed: 12/02/2022] Open
Abstract
The formation of the sea urchin spicule skeleton requires the participation of hydrogel-forming protein families that regulate mineral nucleation and nanoparticle assembly processes that give rise to the spicule. However, the structure and molecular behavior of these proteins is not well established, and thus our ability to understand this process is hampered. We embarked on a study of sea urchin spicule proteins using a combination of biophysical and bioinformatics techniques. Our biophysical findings indicate that recombinant variants of the two most studied spicule matrix proteins, SpSM50 and SpSM30B/C (S. purpuratus) have a conformational landscape that include a C-terminal random coil/intrinsically disordered MAPQG sequence coupled to a conserved, folded N-terminal C-type lectin-like (CTLL) domain, with SpSM50 > SpSM30B/C with regard to intrinsic disorder. Both proteins possess solvent-accessible unfolded MAQPG sequence regions where Asn, Gln, and Arg residues may be accessible for protein hydrogel interactions with water molecules. Our bioinformatics study included seven other spicule matrix proteins where we note similarities between these proteins and rare, unusual proteins that possess folded and unfolded traits. Moreover, spicule matrix proteins possess three types of sequences: intrinsically disordered, amyloid-like, and folded protein-protein interactive. Collectively these reactive domains would be capable of driving protein assembly and hydrogel formation. Interestingly, three types of global conformations are predicted for the nine member protein set, wherein we note variations in the arrangement of intrinsically disordered and interactive globular domains. These variations may reflect species-specific requirements for spiculogenesis. We conclude that the molecular landscape of spicule matrix protein families enables them to function as hydrogelators, nucleators, and assemblers of mineral nanoparticles.
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35
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Glycan Binding Profiling of Jacalin-Related Lectins from the Pteria Penguin Pearl Shell. Int J Mol Sci 2019; 20:ijms20184629. [PMID: 31540487 PMCID: PMC6769917 DOI: 10.3390/ijms20184629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/14/2019] [Accepted: 09/15/2019] [Indexed: 11/25/2022] Open
Abstract
We determined the primary structures of jacalin-related lectins termed PPL3s (PPL3A, 3B, and 3C, which are dimers consisting of sequence variants α + α, α + β, β + β, respectively) and PPL4, which is heterodimer consisting of α + β subunits, isolated from mantle secretory fluid of Pteria penguin (Mabe) pearl shell. Their carbohydrate-binding properties were analyzed, in addition to that of PPL2A, which was previously reported as a matrix protein. PPL3s and PPL4 shared only 35–50% homology to PPL2A, respectively; they exhibited significantly different carbohydrate-binding specificities based on the multiple glycan binding profiling data sets from frontal affinity chromatography analysis. The carbohydrate-binding specificity of PPL3s was similar to that of PPL2A, except only for Man3Fuc1Xyl1GlcNAc2 oligosaccharide, while PPL4 showed different carbohydrate-binding specificity compared with PPL2A and PPL3s. PPL2A and PPL3s mainly recognize agalactosylated- and galactosylated-type glycans. On the other hand, PPL4 binds to high-mannose-and hybrid-type N-linked glycans but not agalactosylated- and galactosylated-type glycans.
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PI3K inhibition highlights new molecular interactions involved in the skeletogenesis of Paracentrotus lividus embryos. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1867:118558. [PMID: 31525406 DOI: 10.1016/j.bbamcr.2019.118558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 09/05/2019] [Accepted: 09/10/2019] [Indexed: 02/02/2023]
Abstract
The sea urchin embryo develops a well-defined biomineralized endoskeleton, synthesized exclusively by the skeletogenic cells, supported by ectodermal cues for the correct skeleton patterning. The biomineralization process is tightly regulated via a hierarchical order of gene expression, including transcription and growth factors, biomineralization proteins. Recently, the role of kinases and intracellular signaling pathways in sea urchin skeletogenesis has been addressed, although the downstream components still remain unknown. In this study, we investigated the role of phosphatidylinositide 3-kinase (PI3K)-mediated signaling pathway in Paracentrotus lividus, to identify its genes/proteins targets. The effects of LY294002 (LY), a PI3K-specific inhibitor, were evaluated at morphological and molecular levels. Treatment with 40 μM LY from the blastula stage completely blocked skeleton deposition, which was reversed by wash out experiments. Besides, LY caused a slight delay in the tripartite gut development. Despite the skeleton absence, a few skeleton-specific proteins/mRNAs were regularly expressed and localized in LY-treated embryos, as shown for MSP130 and SM50 by immunofluorescence and in situ hybridization experiments. QPCR analyses showed that LY differently affected the expression of genes coding for other biomineralization proteins, transcription and growth factors. SM30 and carbonic anhydrase expression was severely downregulated, while almost all the transcription factors analyzed were upregulated. Based on the present results and in silico analyses, we propose an "interactomic" model simulating PI3K connections in P. lividus embryos. Our findings define a novel regulatory step in the embryonic skeletogenesis, and provide valuable molecular data for further studies on the role of PI3K signaling in invertebrate biomineralization.
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Chai Y, Okuda M, Otsuka Y, Ohnuma K, Tagaya M. Comparison of two fabrication processes for biomimetic collagen/hydroxyapatite hybrids. ADV POWDER TECHNOL 2019. [DOI: 10.1016/j.apt.2019.04.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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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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Martino C, Chiarelli R, Roccheri MC, Matranga V, Byrne M. Effects of magnesium deprivation on development and biomineralization in the sea urchin Arbacia lixula. INVERTEBR REPROD DEV 2019. [DOI: 10.1080/07924259.2019.1611670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Chiara Martino
- Dipartimento Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università di Palermo, Palermo, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare “Alberto Monroy”, Palermo, Italy
| | - Roberto Chiarelli
- Dipartimento Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università di Palermo, Palermo, Italy
| | - Maria Carmela Roccheri
- Dipartimento Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università di Palermo, Palermo, Italy
| | - Valeria Matranga
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare “Alberto Monroy”, Palermo, Italy
| | - Maria Byrne
- Department of Anatomy and Histology, F13, University of Sydney, Sydney, NSW, Australia
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Le Luyer J, Auffret P, Quillien V, Leclerc N, Reisser C, Vidal-Dupiol J, Ky CL. Whole transcriptome sequencing and biomineralization gene architecture associated with cultured pearl quality traits in the pearl oyster, Pinctada margaritifera. BMC Genomics 2019; 20:111. [PMID: 30727965 PMCID: PMC6366105 DOI: 10.1186/s12864-019-5443-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/09/2019] [Indexed: 01/31/2023] Open
Abstract
Background Cultured pearls are unique gems produced by living organisms, mainly molluscs of the Pinctada genus, through the biomineralization properties of pearl sac tissue. Improvement of P. margaritifera pearl quality is one of the biggest challenges that Polynesian research has faced to date. To achieve this goal, a better understanding of the complex mechanisms related to nacre and pearl formation is essential and can now be approached through the use of massive parallel sequencing technologies. The aim of this study was to use RNA-seq to compare whole transcriptome expression of pearl sacs that had producing pearls with high and low quality. For this purpose, a comprehensive reference transcriptome of P. margaritifera was built based on multi-tissue sampling (mantle, gonad, whole animal), including different living stages (juvenile, adults) and phenotypes (colour morphotypes, sex). Results Strikingly, few genes were found to be up-regulated for high quality pearls (n = 16) compared to the up-regulated genes in low quality pearls (n = 246). Biomineralization genes up-regulated in low quality pearls were specific to prismatic and prism-nacre layers. Alternative splicing was further identified in several key biomineralization genes based on a recent P. margaritifera draft genome. Conclusion This study lifts the veil on the multi-level regulation of biomineralization genes associated with pearl quality determination. Electronic supplementary material The online version of this article (10.1186/s12864-019-5443-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Le Luyer
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia
| | - P Auffret
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia
| | - V Quillien
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia
| | - N Leclerc
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia
| | - C Reisser
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia
| | - J Vidal-Dupiol
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia.,Ifremer, UMR 5244 Interactions Hôtes-Pathogènes-Environnements, Université de Montpellier, Place Eugène Bataillon CC 80, 34095, Montpellier, France
| | - C-L Ky
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia.
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Shimizu K, Kimura K, Isowa Y, Oshima K, Ishikawa M, Kagi H, Kito K, Hattori M, Chiba S, Endo K. Insights into the Evolution of Shells and Love Darts of Land Snails Revealed from Their Matrix Proteins. Genome Biol Evol 2019; 11:380-397. [PMID: 30388206 PMCID: PMC6368272 DOI: 10.1093/gbe/evy242] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2018] [Indexed: 12/14/2022] Open
Abstract
Over the past decade, many skeletal matrix proteins that are possibly related to calcification have been reported in various calcifying animals. Molluscs are among the most diverse calcifying animals and some gastropods have adapted to terrestrial ecological niches. Although many shell matrix proteins (SMPs) have already been reported in molluscs, most reports have focused on marine molluscs, and the SMPs of terrestrial snails remain unclear. In addition, some terrestrial stylommatophoran snails have evolved an additional unique calcified character, called a "love dart," used for mating behavior. We identified 54 SMPs in the terrestrial snail Euhadra quaesita, and found that they contain specific domains that are widely conserved in molluscan SMPs. However, our results also suggest that some of them possibly have evolved independently by domain shuffling, domain recruitment, or gene co-option. We then identified four dart matrix proteins, and found that two of them are the same proteins as those identified as SMPs. Our results suggest that some dart matrix proteins possibly have evolved by independent gene co-option from SMPs during dart evolution events. These results provide a new perspective on the evolution of SMPs and "love darts" in land snails.
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Affiliation(s)
- Keisuke Shimizu
- Department of Earth and Planetary Science, The University of Tokyo, Hongo, Japan
- College of Life and Environmental Sciences, University of Exeter, United Kingdom
| | - Kazuki Kimura
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
- Research Institute for Ulleungdo and Dokdo Islands, Kyungpook National University, Bukgu, Daegu, Korea
| | - Yukinobu Isowa
- Organization for the Strategic Coordination of Research and Intellectual Properties, Meiji University, Kawasaki, Kanagawa, Japan
| | - Kenshiro Oshima
- Center for Omics and Bioinformatics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Makiko Ishikawa
- Department of Earth and Planetary Science, The University of Tokyo, Hongo, Japan
- Faculty of Animal Health Technology, Yamazaki University of Animal Health Technology, Hachioji, Tokyo, Japan
| | - Hiroyuki Kagi
- Geochemical Research Center, Graduate School of Science, The University of Tokyo, Hongo, Japan
| | - Keiji Kito
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Masahira Hattori
- Center for Omics and Bioinformatics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
- Cooperative Major of Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Japan
| | - Satoshi Chiba
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Kazuyoshi Endo
- Department of Earth and Planetary Science, The University of Tokyo, Hongo, Japan
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Wang L, Koppitch K, Cutting A, Dong P, Kudtarkar P, Zeng J, Cameron RA, Davidson EH. Developmental effector gene regulation: Multiplexed strategies for functional analysis. Dev Biol 2019; 445:68-79. [PMID: 30392838 DOI: 10.1016/j.ydbio.2018.10.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 01/18/2023]
Abstract
The staggering complexity of the genome controls for developmental processes is revealed through massively parallel cis-regulatory analysis using new methods of perturbation and readout. The choice of combinations of these new methods is tailored to the system, question and resources at hand. Our focus is on issues that include the necessity or sufficiency of given cis-regulatory modules, cis-regulatory function in the normal spatial genomic context, and easily accessible high throughput and multiplexed analysis methods. In the sea urchin embryonic model, recombineered BACs offer new opportunities for consecutive modes of cis-regulatory analyses that answer these requirements, as we here demonstrate on a diverse suite of previously unstudied sea urchin effector genes expressed in skeletogenic cells. Positively active cis-regulatory modules were located in single Nanostring experiments per BAC containing the gene of interest, by application of our previously reported "barcode" tag vectors of which> 100 can be analyzed at one time. Computational analysis of DNA sequences that drive expression, based on the known skeletogenic regulatory state, then permitted effective identification of functional target site clusters. Deletion of these sub-regions from the parent BACs revealed module necessity, as simultaneous tests of the same regions in short constructs revealed sufficiency. Predicted functional inputs were then confirmed by site mutations, all generated and tested in multiplex formats. There emerged the simple conclusion that each effector gene utilizes a small subset of inputs from the skeletogenic GRN. These inputs may function to only adjust expression levels or in some cases necessary for expression. Since we know the GRN architecture upstream of the effector genes, we could then conceptually isolate and compare the wiring of the effector gene driver sub-circuits and identify the inputs whose removal abolish expression.
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Affiliation(s)
- Lijun Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Kari Koppitch
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Ann Cutting
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Ping Dong
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Parul Kudtarkar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Jenny Zeng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - R Andrew Cameron
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States.
| | - Eric H Davidson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
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Shashikant T, Khor JM, Ettensohn CA. From genome to anatomy: The architecture and evolution of the skeletogenic gene regulatory network of sea urchins and other echinoderms. Genesis 2018; 56:e23253. [PMID: 30264451 PMCID: PMC6294693 DOI: 10.1002/dvg.23253] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/14/2018] [Accepted: 09/23/2018] [Indexed: 01/19/2023]
Abstract
The skeletogenic gene regulatory network (GRN) of sea urchins and other echinoderms is one of the most intensively studied transcriptional networks in any developing organism. As such, it serves as a preeminent model of GRN architecture and evolution. This review summarizes our current understanding of this developmental network. We describe in detail the most comprehensive model of the skeletogenic GRN, one developed for the euechinoid sea urchin Strongylocentrotus purpuratus, including its initial deployment by maternal inputs, its elaboration and stabilization through regulatory gene interactions, and its control of downstream effector genes that directly drive skeletal morphogenesis. We highlight recent comparative studies that have leveraged the euechinoid GRN model to examine the evolution of skeletogenic programs in diverse echinoderms, studies that have revealed both conserved and divergent features of skeletogenesis within the phylum. Last, we summarize the major insights that have emerged from analysis of the structure and evolution of the echinoderm skeletogenic GRN and identify key, unresolved questions as a guide for future work.
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Affiliation(s)
- Tanvi Shashikant
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
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Pendola M, Jain G, Huang YC, Gebauer D, Evans JS. Secrets of the Sea Urchin Spicule Revealed: Protein Cooperativity Is Responsible for ACC Transformation, Intracrystalline Incorporation, and Guided Mineral Particle Assembly in Biocomposite Material Formation. ACS OMEGA 2018; 3:11823-11830. [PMID: 30320276 PMCID: PMC6173553 DOI: 10.1021/acsomega.8b01697] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/11/2018] [Indexed: 05/12/2023]
Abstract
The formation of the sea urchin spicule involves the stabilization and transformation of amorphous calcium carbonate (ACC) and assembly of ACC nanoparticle precursors into a mesoscale single crystal of fracture-resistant calcite. This process of particle assembly or attachment is under the control of a family of proteins known as the spicule matrix [Strongylocentrotus purpuratus (SpSM)] proteome. Recently, two members of this proteome, SpSM50 and the glycoprotein SpSM30B/C-G (in recombinant forms), were found to interact together via SpSM30B/C-G oligosaccharide-SpSM50 protein interactions to form hybrid protein hydrogels with unique physical properties. In this study, we investigate the mineralization properties of this hybrid hydrogel alongside the hydrogels formed by SpSM50 and SpSM30B/C-G individually. We find that the SpSM50 + SpSM30B/C-G hybrid hydrogel is synergistic with regard to surface modifications and intracrystalline inclusions of existing calcite crystals, the inhibition of ACC formation, and the kinetic destabilization of ACC to form a crystalline phase. Most importantly, the hybrid hydrogel phase assembles and organizes mineral particles into discrete clusters or domains within in vitro mineralization environments. Thus, the interactions of SpSM50 and SpSM30B/C-G, mediated by carbohydrate-protein binding, reflect the need for protein cooperativity for the ACC-to-crystalline transformation, intracrystalline void formation, and guided mineral particle assembly processes that are instrumental in spicule formation.
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Affiliation(s)
- Martin Pendola
- Laboratory
for Chemical Physics, Center for Skeletal and Craniofacial Biology, New York University, 345 E. 24th Street, New
York, New York 10010, United States
| | - Gaurav Jain
- Laboratory
for Chemical Physics, Center for Skeletal and Craniofacial Biology, New York University, 345 E. 24th Street, New
York, New York 10010, United States
| | - Yu-Chieh Huang
- Department
of Chemistry, Physical Chemistry, Universität
Konstanz, Universitätstrasse 10, Konstanz D-78457, Germany
| | - Denis Gebauer
- Department
of Chemistry, Physical Chemistry, Universität
Konstanz, Universitätstrasse 10, Konstanz D-78457, Germany
| | - John Spencer Evans
- Laboratory
for Chemical Physics, Center for Skeletal and Craniofacial Biology, New York University, 345 E. 24th Street, New
York, New York 10010, United States
- E-mail: (J.S.E.)
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Exploring the drivers of early biomineralization. Emerg Top Life Sci 2018; 2:201-212. [PMID: 32412623 DOI: 10.1042/etls20170164] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/12/2018] [Accepted: 05/15/2018] [Indexed: 11/17/2022]
Abstract
The first biomineralized hard parts are known from ∼810 Million years ago (Ma), consisting of phosphatic plates of probable protists formed under active biological control. Large skeletons in diverse taxa, probably including total-group poriferans and total-group cnidarians, first appear in the terminal Ediacaran, ∼550 Ma. This is followed by a substantial increase in abundance, diversity and mineralogy during the early Cambrian. The biological relationship of Ediacaran to early Cambrian skeletal biota is unclear, but tubular skeletal fossils such as Cloudina and Anabarites straddle the transition. Many Ediacaran skeletal biota are found exclusively in carbonate settings, and present skeletons whose form infers an organic scaffold which provided the framework for interactions between extracellular matrix and mineral ions. Several taxa have close soft-bodied counterparts hosted in contemporary clastic rocks. This supports the assertion that the calcification was an independent and derived feature that appeared in diverse groups, which was initially acquired with minimal biological control in the highly saturated, high-alkalinity carbonate settings of the Ediacaran, where the carbonate polymorph was further controlled by seawater chemistry. The trigger for Ediacaran-Cambrian biomineralization is far from clear, but may have been either changing seawater Mg/Ca ratios that facilitated widespread aragonite and high-Mg calcite precipitation, and/or increasing or stabilizing oxygen levels. By the Early Cambrian, the diversity of biomineralization styles may have been an escalating defensive response to increasing predation pressure, with skeletal hard parts first appearing in abundance in clastic settings by the Fortunian. This marks full independence from ambient seawater chemistry and significant biological control of biomineralization.
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Jain G, Pendola M, Koutsoumpeli E, Johnson S, Evans JS. Glycosylation Fosters Interactions between Model Sea Urchin Spicule Matrix Proteins. Implications for Embryonic Spiculogenesis and Biomineralization. Biochemistry 2018; 57:3032-3035. [PMID: 29757633 DOI: 10.1021/acs.biochem.8b00207] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of embryonic mineralized skeletal elements (spicules) in the sea urchin requires the participation of proteins, many of which may interact with one another and assist in the creation of an extracellular matrix wherein mineral formation takes place. To probe this, we created a sea urchin spicule recombinant model protein pair system wherein we tested the interactions between two major spicule proteins, SpSM50 and the glycoprotein, SpSM30B/C. Both proteins are strong hydrogelators that manipulate early and later events in mineral formation. We discovered that the anionic glycan moieties of SpSM30B/C are required for interaction with the SpSM50 protein and that these interactions are Ca(II)-independent. In addition, when these proteins form a complex, they create hybrid hydrogel particles that are physically distinct from their individual counterparts. Thus, glycan-mediated interactions play an important role in in vitro spicule protein assembly and most likely within the spicule itself.
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Affiliation(s)
- Gaurav Jain
- Laboratory for Chemical Physics, Center for Skeletal and Craniofacial Biology , New York University , 345 East 24th Street , New York , New York 10010 , United States
| | - Martin Pendola
- Laboratory for Chemical Physics, Center for Skeletal and Craniofacial Biology , New York University , 345 East 24th Street , New York , New York 10010 , United States
| | - Eleni Koutsoumpeli
- Department of Electronic Engineering , University of York , Heslington, York YO105DD , United Kingdom
| | - Steven Johnson
- Department of Electronic Engineering , University of York , Heslington, York YO105DD , United Kingdom
| | - John Spencer Evans
- Laboratory for Chemical Physics, Center for Skeletal and Craniofacial Biology , New York University , 345 East 24th Street , New York , New York 10010 , United States
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Shashikant T, Khor JM, Ettensohn CA. Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling. BMC Genomics 2018; 19:206. [PMID: 29558892 PMCID: PMC5859501 DOI: 10.1186/s12864-018-4542-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/13/2018] [Indexed: 12/11/2022] Open
Abstract
Background The developmental gene regulatory network (GRN) that underlies skeletogenesis in sea urchins and other echinoderms is a paradigm of GRN structure, function, and evolution. This transcriptional network is deployed selectively in skeleton-forming primary mesenchyme cells (PMCs) of the early embryo. To advance our understanding of this model developmental GRN, we used genome-wide chromatin accessibility profiling to identify and characterize PMC cis-regulatory modules (CRMs). Results ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) analysis of purified PMCs provided a global picture of chromatin accessibility in these cells. We used both ATAC-seq and DNase-seq (DNase I hypersensitive site sequencing) to identify > 3000 sites that exhibited increased accessibility in PMCs relative to other embryonic cell lineages, and provide both computational and experimental evidence that a large fraction of these sites represent bona fide skeletogenic CRMs. Putative PMC CRMs were preferentially located near genes differentially expressed by PMCs and consensus binding sites for two key transcription factors in the PMC GRN, Alx1 and Ets1, were enriched in these CRMs. Moreover, a high proportion of candidate CRMs drove reporter gene expression specifically in PMCs in transgenic embryos. Surprisingly, we found that PMC CRMs were partially open in other embryonic lineages and exhibited hyperaccessibility as early as the 128-cell stage. Conclusions Our work provides a comprehensive picture of chromatin accessibility in an early embryonic cell lineage. By identifying thousands of candidate PMC CRMs, we significantly enhance the utility of the sea urchin skeletogenic network as a general model of GRN architecture and evolution. Our work also shows that differential chromatin accessibility, which has been used for the high-throughput identification of enhancers in differentiated cell types, is a powerful approach for the identification of CRMs in early embryonic cells. Lastly, we conclude that in the sea urchin embryo, CRMs that control the cell type-specific expression of effector genes are hyperaccessible several hours in advance of gene activation. Electronic supplementary material The online version of this article (10.1186/s12864-018-4542-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tanvi Shashikant
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
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48
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Dylus DV, Czarkwiani A, Blowes LM, Elphick MR, Oliveri P. Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution. Genome Biol 2018; 19:26. [PMID: 29490679 PMCID: PMC5831733 DOI: 10.1186/s13059-018-1402-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/01/2018] [Indexed: 12/13/2022] Open
Abstract
Background Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/. Results We have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation. Conclusions Our findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in echinoderms. Electronic supplementary material The online version of this article (10.1186/s13059-018-1402-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David V Dylus
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.,CoMPLEX/SysBio, UCL, Gower Street, London, WC1E 6BT, UK.,Present address: Department of Computational Biology, UNIL, Genopode, 1005, Lausanne, Switzerland
| | - Anna Czarkwiani
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Liisa M Blowes
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.,Present address: Centre for Cell Biology & Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Maurice R Elphick
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Paola Oliveri
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK. .,Centre for Life's Origins and Evolution (CLOE), UCL, Gower Street, London, WC1E 6BT, UK.
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49
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McDougall C, Degnan BM. The evolution of mollusc shells. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 7:e313. [DOI: 10.1002/wdev.313] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 11/09/2017] [Accepted: 12/09/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Carmel McDougall
- Centre for Marine Sciences, School of Biological SciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | - Bernard M. Degnan
- Centre for Marine Sciences, School of Biological SciencesThe University of QueenslandBrisbaneQueenslandAustralia
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50
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Wood R, Ivantsov AY, Zhuravlev AY. First macrobiota biomineralization was environmentally triggered. Proc Biol Sci 2018; 284:rspb.2017.0059. [PMID: 28356454 DOI: 10.1098/rspb.2017.0059] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/02/2017] [Indexed: 01/12/2023] Open
Abstract
Why large and diverse skeletons first appeared ca 550 Ma is not well understood. Many Ediacaran skeletal biota show evidence of flexibility, and bear notably thin skeletal walls with simple, non-hierarchical microstructures of either aragonite or high-Mg calcite. We present evidence that the earliest skeletal macrobiota, found only in carbonate rocks, had close soft-bodied counterparts hosted in contemporary clastic rocks. This includes the calcareous discoidal fossil Suvorovella, similar to holdfasts of Ediacaran biota taxa previously known only as casts and moulds, as well as tubular and vase-shaped fossils. In sum, these probably represent taxa of diverse affinity including unicellular eukaryotes, total group cnidarians and problematica. Our findings support the assertion that the calcification was an independent and derived feature that appeared in diverse groups where an organic scaffold was the primitive character, which provided the framework for interactions between the extracellular matrix and mineral ions. We conclude that such skeletons may have been acquired with relative ease in the highly saturated, high alkalinity carbonate settings of the Ediacaran, where carbonate polymorph was further controlled by seawater chemistry. The trigger for Ediacaran biomineralization may have been either changing seawater Mg/Ca and/or increasing oxygen levels. By the Early Cambrian, however, biomineralization styles and the range of biominerals had significantly diversified, perhaps as an escalating defensive response to increasing predation pressure. Indeed skeletal hardparts had appeared in clastic settings by Cambrian Stage 1, suggesting independence from ambient seawater chemistry where genetic and molecular mechanisms controlled biomineralization and mineralogy had become evolutionarily constrained.
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Affiliation(s)
- Rachel Wood
- School of GeoSciences, University of Edinburgh, James Hutton Road, Edinburgh EH9 3FE, UK
| | - Andrey Yu Ivantsov
- Borissiak Paleontological Institute, Russian Academy of Sciences, ul. Profsoyuznaya 123, Moscow 117997, Russia
| | - Andrey Yu Zhuravlev
- Department of Biological Evolution, Faculty of Biology, Lomonosov Moscow State University, Leninskie gory 1(12), Moscow 119234, Russia.,Geological Institute, Russian Academy of Sciences, Pyzhevskiy per. 7, Moscow 119017, Russia
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