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Gold DA, Vermeij GJ. Deep resilience: An evolutionary perspective on calcification in an age of ocean acidification. Front Physiol 2023; 14:1092321. [PMID: 36818444 PMCID: PMC9935589 DOI: 10.3389/fphys.2023.1092321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
The success of today's calcifying organisms in tomorrow's oceans depends, in part, on the resilience of their skeletons to ocean acidification. To the extent this statement is true there is reason to have hope. Many marine calcifiers demonstrate resilience when exposed to environments that mimic near-term ocean acidification. The fossil record similarly suggests that resilience in skeletons has increased dramatically over geologic time. This "deep resilience" is seen in the long-term stability of skeletal chemistry, as well as a decreasing correlation between skeletal mineralogy and extinction risk over time. Such resilience over geologic timescales is often attributed to genetic canalization-the hardening of genetic pathways due to the evolution of increasingly complex regulatory systems. But paradoxically, our current knowledge on biomineralization genetics suggests an opposing trend, where genes are co-opted and shuffled at an evolutionarily rapid pace. In this paper we consider two possible mechanisms driving deep resilience in skeletons that fall outside of genetic canalization: microbial co-regulation and macroevolutionary trends in skeleton structure. The mechanisms driving deep resilience should be considered when creating risk assessments for marine organisms facing ocean acidification and provide a wealth of research avenues to explore.
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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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The Evolution of Biomineralization through the Co-Option of Organic Scaffold Forming Networks. Cells 2022; 11:cells11040595. [PMID: 35203246 PMCID: PMC8870065 DOI: 10.3390/cells11040595] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/05/2022] Open
Abstract
Biomineralization is the process in which organisms use minerals to generate hard structures like teeth, skeletons and shells. Biomineralization is proposed to have evolved independently in different phyla through the co-option of pre-existing developmental programs. Comparing the gene regulatory networks (GRNs) that drive biomineralization in different species could illuminate the molecular evolution of biomineralization. Skeletogenesis in the sea urchin embryo was extensively studied and the underlying GRN shows high conservation within echinoderms, larval and adult skeletogenesis. The organic scaffold in which the calcite skeletal elements form in echinoderms is a tubular compartment generated by the syncytial skeletogenic cells. This is strictly different than the organic cartilaginous scaffold that vertebrates mineralize with hydroxyapatite to make their bones. Here I compare the GRNs that drive biomineralization and tubulogenesis in echinoderms and in vertebrates. The GRN that drives skeletogenesis in the sea urchin embryo shows little similarity to the GRN that drives bone formation and high resemblance to the GRN that drives vertebrates’ vascular tubulogenesis. On the other hand, vertebrates’ bone-GRNs show high similarity to the GRNs that operate in the cells that generate the cartilage-like tissues of basal chordate and invertebrates that do not produce mineralized tissue. These comparisons suggest that biomineralization in deuterostomes evolved through the phylum specific co-option of GRNs that control distinct organic scaffolds to mineralization.
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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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5
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Liu C, Zhang R. Biomineral proteomics: A tool for multiple disciplinary studies. J Proteomics 2021; 238:104171. [PMID: 33652138 DOI: 10.1016/j.jprot.2021.104171] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/06/2021] [Accepted: 02/21/2021] [Indexed: 12/11/2022]
Abstract
The hard tissues of animals, such as skeletons and teeth, are constructed by a biologically controlled process called biomineralization. In invertebrate animals, biominerals are considered important for their evolutionary success. These biominerals are hieratical biocomposites with excellent mechanical properties, and their formation has intrigued researchers for decades. Although proteins account for ~5 wt% of biominerals, they are critical players in biomineralization. With the development of high-throughput analysis methods, such as proteomics, biomineral protein data are rapidly accumulating, thus necessitating a refined model for biomineralization. This review focuses on biomineral proteomics in invertebrate animals to highlight the diversity of biomineral proteins (generally 40-80 proteins), and the results indicate that biomineralization includes thermodynamic crystal growth as well as intense extracellular matrix activity and/or vesicle transport. Biominerals have multiple functions linked to biological immunity and antipathogen activity. A comparison of proteomes across species and biomineral types showed that von Willebrand factor type A and epidermal growth factor, which frequently couple with other extracellular domains, are the most common domains. Combined with species-specific repetitive low complexity domains, shell matrix proteins can be employed to predict biomineral types. Furthermore, this review discusses the applications of biomineral proteomics in diverse fields, such as tissue regeneration, developmental biology, archeology, environmental science, and material science.
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Affiliation(s)
- Chuang Liu
- College of Oceanography, Hohai University, Xikang Road, Nanjing, Jiangsu 210098, China.
| | - Rongqing Zhang
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, 705 Yatai Road, Jiaxing 314006, PR China; College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China.
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6
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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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7
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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: 15] [Impact Index Per Article: 3.8] [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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8
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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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9
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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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10
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Flores RL, Livingston BT. The skeletal proteome of the sea star Patiria miniata and evolution of biomineralization in echinoderms. BMC Evol Biol 2017; 17:125. [PMID: 28583083 PMCID: PMC5460417 DOI: 10.1186/s12862-017-0978-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 05/23/2017] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Proteomic studies of skeletal proteins have revealed large, complex mixtures of proteins occluded within the mineral. Many skeletal proteomes contain rapidly evolving proteins with repetitive domains, further complicating our understanding. In echinoderms, proteomic analysis of the skeletal proteomes of mineralized tissues of the sea urchin Strongylocentrotus purpuratus prominently featured spicule matrix proteins with repetitive sequences linked to a C-type lectin domain. A comparative study of the brittle star Ophiocoma wendtii skeletal proteome revealed an order of magnitude fewer proteins containing C-type lectin domains. A number of other proteins conserved in the skeletons of the two groups were identified. Here we report the complete skeletal proteome of the sea star Patiria miniata and compare it to that of the other echinoderm groups. RESULTS We have identified eighty-five proteins in the P. miniata skeletal proteome. Forty-two percent of the proteins were determined to be homologous to proteins found in the S. purpuratus skeletal proteomes. An additional 34 % were from similar functional classes as proteins in the urchin proteomes. Thirteen percent of the P. miniata proteins had homologues in the O. wendtii skeletal proteome with an additional 29% showing similarity to brittle star skeletal proteins. The P. miniata skeletal proteome did not contain any proteins with C-lectin domains or with acidic repetitive regions similar to the sea urchin or brittle star spicule matrix proteins. MSP130 proteins were also not found. We did identify a number of proteins homologous between the three groups. Some of the highly conserved proteins found in echinoderm skeletons have also been identified in vertebrate skeletons. CONCLUSIONS The presence of proteins conserved in the skeleton in three different echinoderm groups indicates these proteins are important in skeleton formation. That a number of these proteins are involved in skeleton formation in vertebrates suggests a common origin for some of the fundamental processes co-opted for skeleton formation in deuterostomes. The proteins we identify suggest transport of proteins and calcium via endosomes was co-opted to this function in a convergent fashion. Our data also indicate that modifications to the process of skeleton formation can occur through independent co-option of proteins following species divergence as well as through domain shuffling.
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Affiliation(s)
- Rachel L. Flores
- Department of Biological Sciences, California State University, 1250 Bellflower Blvd, Long Beach, CA 90840 USA
| | - Brian T. Livingston
- Department of Biological Sciences, California State University, 1250 Bellflower Blvd, Long Beach, CA 90840 USA
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11
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Organic matrices in metazoan calcium carbonate skeletons: Composition, functions, evolution. J Struct Biol 2016; 196:98-106. [DOI: 10.1016/j.jsb.2016.04.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/04/2016] [Accepted: 04/12/2016] [Indexed: 11/23/2022]
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12
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Kocot KM, Aguilera F, McDougall C, Jackson DJ, Degnan BM. Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization. Front Zool 2016; 13:23. [PMID: 27279892 PMCID: PMC4897951 DOI: 10.1186/s12983-016-0155-z] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/27/2016] [Indexed: 12/21/2022] Open
Abstract
An external skeleton is an essential part of the body plan of many animals and is thought to be one of the key factors that enabled the great expansion in animal diversity and disparity during the Cambrian explosion. Molluscs are considered ideal to study the evolution of biomineralization because of their diversity of highly complex, robust and patterned shells. The molluscan shell forms externally at the interface of animal and environment, and involves controlled deposition of calcium carbonate within a framework of macromolecules that are secreted from the dorsal mantle epithelium. Despite its deep conservation within Mollusca, the mantle is capable of producing an incredible diversity of shell patterns, and macro- and micro-architectures. Here we review recent developments within the field of molluscan biomineralization, focusing on the genes expressed in the mantle that encode secreted proteins. The so-called mantle secretome appears to regulate shell deposition and patterning and in some cases becomes part of the shell matrix. Recent transcriptomic and proteomic studies have revealed marked differences in the mantle secretomes of even closely-related molluscs; these typically exceed expected differences based on characteristics of the external shell. All mantle secretomes surveyed to date include novel genes encoding lineage-restricted proteins and unique combinations of co-opted ancient genes. A surprisingly large proportion of both ancient and novel secreted proteins containing simple repetitive motifs or domains that are often modular in construction. These repetitive low complexity domains (RLCDs) appear to further promote the evolvability of the mantle secretome, resulting in domain shuffling, expansion and loss. RLCD families further evolve via slippage and other mechanisms associated with repetitive sequences. As analogous types of secreted proteins are expressed in biomineralizing tissues in other animals, insights into the evolution of the genes underlying molluscan shell formation may be applied more broadly to understanding the evolution of metazoan biomineralization.
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Affiliation(s)
- Kevin M Kocot
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072 Australia.,Current address: Department of Biological Sciences and Alabama Museum of Natural History, The University of Alabama, Tuscaloosa, Alabama 35487 USA
| | - Felipe Aguilera
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072 Australia.,Current address: Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, Bergen, 5008 Norway
| | - Carmel McDougall
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072 Australia
| | - Daniel J Jackson
- Department of Geobiology, Goldschmidtstr.3, Georg-August University of Göttingen, 37077 Göttingen, Germany
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072 Australia
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Czarkwiani A, Ferrario C, Dylus DV, Sugni M, Oliveri P. Skeletal regeneration in the brittle star Amphiura filiformis. Front Zool 2016; 13:18. [PMID: 27110269 PMCID: PMC4841056 DOI: 10.1186/s12983-016-0149-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 04/12/2016] [Indexed: 12/17/2022] Open
Abstract
Background Brittle stars regenerate their whole arms post-amputation. Amphiura filiformis can now be used for molecular characterization of arm regeneration due to the availability of transcriptomic data. Previous work showed that specific developmental transcription factors known to take part in echinoderm skeletogenesis are expressed during adult arm regeneration in A. filiformis; however, the process of skeleton formation remained poorly understood. Here, we present the results of an in-depth microscopic analysis of skeletal morphogenesis during regeneration, using calcein staining, EdU labeling and in situ hybridization. Results To better compare different samples, we propose a staging system for the early A. filiformis arm regeneration stages based on morphological landmarks identifiable in living animals and supported by histological analysis. We show that the calcified spicules forming the endoskeleton first appear very early during regeneration in the dermal layer of regenerates. These spicules then mature into complex skeletal elements of the differentiated arm during late regeneration. The mesenchymal cells in the dermal area express the skeletal marker genes Afi-c-lectin, Afi-p58b and Afi-p19; however, EdU labeling shows that these dermal cells do not proliferate. Conclusions A. filiformis arms regenerate through a consistent set of developmental stages using a distalization-intercalation mode, despite variability in regeneration rate. Skeletal elements form in a mesenchymal cell layer that does not proliferate and thus must be supplied from a different source. Our work provides the basis for future cellular and molecular studies of skeleton regeneration in brittle stars. Electronic supplementary material The online version of this article (doi:10.1186/s12983-016-0149-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Czarkwiani
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Cinzia Ferrario
- Department of Biosciences, University of Milan, Milan, Italy
| | - David Viktor Dylus
- Department of Genetics, Evolution and Environment, University College London, London, UK ; Centre for Mathematics, Physics and Engineering in the Life Sciences and Experimental Biology, University College London, London, UK ; Present address: Department of Ecology and Evolution & Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Michela Sugni
- Department of Biosciences, University of Milan, Milan, Italy
| | - Paola Oliveri
- Department of Genetics, Evolution and Environment, University College London, London, UK ; Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK
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Janies DA, Witter Z, Linchangco GV, Foltz DW, Miller AK, Kerr AM, Jay J, Reid RW, Wray GA. EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. BMC Bioinformatics 2016; 17:48. [PMID: 26800861 PMCID: PMC4724074 DOI: 10.1186/s12859-016-0883-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 01/07/2016] [Indexed: 02/06/2023] Open
Abstract
Background One of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-generation transcriptome data. The current dataset is the largest assembled for echinoderm phylogeny and transcriptomics. We used RNA-Seq to profile adult tissues from 42 echinoderm specimens from 24 orders and 37 families. In order to achieve sampling members of clades that span key evolutionary divergence, many of our exemplars were collected from deep and polar seas. Description A small fraction of the transcriptome data we produced is being used for phylogenetic reconstruction. Thus to make a larger dataset available to researchers with a wide variety of interests, we made a web-based application, EchinoDB (http://echinodb.uncc.edu). EchinoDB is a repository of orthologous transcripts from echinoderms that is searchable via keywords and sequence similarity. Conclusions From transcripts we identified 749,397 clusters of orthologous loci. We have developed the information technology to manage and search the loci their annotations with respect to the Sea Urchin (Strongylocentrotus purpuratus) genome. Several users have already taken advantage of these data for spin-off projects in developmental biology, gene family studies, and neuroscience. We hope others will search EchinoDB to discover datasets relevant to a variety of additional questions in comparative biology. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0883-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel A Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223-0001, USA.
| | - Zach Witter
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223-0001, USA
| | - Gregorio V Linchangco
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223-0001, USA
| | - David W Foltz
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Allison K Miller
- Marine Laboratory, University of Guam, University Dr, Mangilao, 96923, Guam
| | - Alexander M Kerr
- Marine Laboratory, University of Guam, University Dr, Mangilao, 96923, Guam
| | - Jeremy Jay
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223-0001, USA
| | - Robert W Reid
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223-0001, USA
| | - Gregory A Wray
- Department of Biology, Duke University, Durham, NC, 27708, USA
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L. Flores R, Gonzales K, W. Seaver R, T. Livingston B. The skeletal proteome of the brittle star <em>Ophiothrix spiculata</em> identifies C-type lectins and other proteins conserved in echinoderm skeleton formation. AIMS MOLECULAR SCIENCE 2016. [DOI: 10.3934/molsci.2016.3.357] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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