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Sheloukhova L, Watanabe H. Evolution of glial cells: a non-bilaterian perspective. Neural Dev 2024; 19:10. [PMID: 38907299 PMCID: PMC11193209 DOI: 10.1186/s13064-024-00184-4] [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: 09/19/2023] [Accepted: 06/06/2024] [Indexed: 06/23/2024] Open
Abstract
Nervous systems of bilaterian animals generally consist of two cell types: neurons and glial cells. Despite accumulating data about the many important functions glial cells serve in bilaterian nervous systems, the evolutionary origin of this abundant cell type remains unclear. Current hypotheses regarding glial evolution are mostly based on data from model bilaterians. Non-bilaterian animals have been largely overlooked in glial studies and have been subjected only to morphological analysis. Here, we provide a comprehensive overview of conservation of the bilateral gliogenic genetic repertoire of non-bilaterian phyla (Cnidaria, Placozoa, Ctenophora, and Porifera). We overview molecular and functional features of bilaterian glial cell types and discuss their possible evolutionary history. We then examine which glial features are present in non-bilaterians. Of these, cnidarians show the highest degree of gliogenic program conservation and may therefore be crucial to answer questions about glial evolution.
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Affiliation(s)
- Larisa Sheloukhova
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan
| | - Hiroshi Watanabe
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan.
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2
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Mörsdorf D, Knabl P, Genikhovich G. Highly conserved and extremely evolvable: BMP signalling in secondary axis patterning of Cnidaria and Bilateria. Dev Genes Evol 2024; 234:1-19. [PMID: 38472535 PMCID: PMC11226491 DOI: 10.1007/s00427-024-00714-4] [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: 12/07/2023] [Accepted: 03/06/2024] [Indexed: 03/14/2024]
Abstract
Bilateria encompass the vast majority of the animal phyla. As the name states, they are bilaterally symmetric, that is with a morphologically clear main body axis connecting their anterior and posterior ends, a second axis running between their dorsal and ventral surfaces, and with a left side being roughly a mirror image of their right side. Bone morphogenetic protein (BMP) signalling has widely conserved functions in the formation and patterning of the second, dorso-ventral (DV) body axis, albeit to different extents in different bilaterian species. Whilst initial findings in the fruit fly Drosophila and the frog Xenopus highlighted similarities amongst these evolutionarily very distant species, more recent analyses featuring other models revealed considerable diversity in the mechanisms underlying dorsoventral patterning. In fact, as phylogenetic sampling becomes broader, we find that this axis patterning system is so evolvable that even its core components can be deployed differently or lost in different model organisms. In this review, we will try to highlight the diversity of ways by which BMP signalling controls bilaterality in different animals, some of which do not belong to Bilateria. Future research combining functional analyses and modelling is bound to give us some understanding as to where the limits to the extent of the evolvability of BMP-dependent axial patterning may lie.
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Affiliation(s)
- David Mörsdorf
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria
| | - Paul Knabl
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of Vienna, Vienna, Austria
| | - Grigory Genikhovich
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria.
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3
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Zhao Y, Song M, Yu Z, Pang L, Zhang L, Karakassis I, Dimitriou PD, Yuan X. Transcriptomic Responses of a Lightly Calcified Echinoderm to Experimental Seawater Acidification and Warming during Early Development. BIOLOGY 2023; 12:1520. [PMID: 38132346 PMCID: PMC10740944 DOI: 10.3390/biology12121520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
Ocean acidification (OA) and ocean warming (OW) are potential obstacles to the survival and growth of marine organisms, particularly those that rely on calcification. This study investigated the single and joint effects of OA and OW on sea cucumber Apostichopus japonicus larvae raised under combinations of two temperatures (19 °C or 22 °C) and two pCO2 levels (400 or 1000 μatm) that reflect the current and end-of-21st-century projected ocean scenarios. The investigation focused on assessing larval development and identifying differences in gene expression patterns at four crucial embryo-larval stages (blastula, gastrula, auricularia, and doliolaria) of sea cucumbers, using RNA-seq. Results showed the detrimental effect of OA on the early development and body growth of A. japonicus larvae and a reduction in the expression of genes associated with biomineralization, skeletogenesis, and ion homeostasis. This effect was particularly pronounced during the doliolaria stage, indicating the presence of bottlenecks in larval development at this transition phase between the larval and megalopa stages in response to OA. OW accelerated the larval development across four stages of A. japonicus, especially at the blastula and doliolaria stages, but resulted in a widespread upregulation of genes related to heat shock proteins, antioxidant defense, and immune response. Significantly, the negative effects of elevated pCO2 on the developmental process of larvae appeared to be mitigated when accompanied by increased temperatures at the expense of reduced immune resilience and increased system fragility. These findings suggest that alterations in gene expression within the larvae of A. japonicus provide a mechanism to adapt to stressors arising from a rapidly changing oceanic environment.
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Affiliation(s)
- Ye Zhao
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Ocean School, Yantai University, Yantai 264005, China
| | - Mingshan Song
- Ministry of Ecology and Environment, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Zhenglin Yu
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Lei Pang
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ioannis Karakassis
- Marine Ecology Laboratory, Department of Biology, University of Crete, GR 70013 Heraklion, Greece
| | - Panagiotis D. Dimitriou
- Marine Ecology Laboratory, Department of Biology, University of Crete, GR 70013 Heraklion, Greece
| | - Xiutang Yuan
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Ministry of Ecology and Environment, National Marine Environmental Monitoring Center, Dalian 116023, China
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4
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Warner JF, Besemer R, Schickle A, Borbee E, Changsut IV, Sharp K, Babonis LS. Microinjection, gene knockdown, and CRISPR-mediated gene knock-in in the hard coral, Astrangia poculata. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567385. [PMID: 38948709 PMCID: PMC11213136 DOI: 10.1101/2023.11.16.567385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Cnidarians have become valuable models for understanding many aspects of developmental biology including the evolution of body plan diversity, novel cell type specification, and regeneration. Most of our understanding of gene function during early development in cnidarians comes from a small number of experimental systems including the sea anemone, Nematostella vectensis. Few molecular tools have been developed for use in hard corals, limiting our understanding of this diverse and ecologically important clade. Here, we report the development of a suite of tools for manipulating and analyzing gene expression during early development in the northern star coral, Astrangia poculata. We present methods for gene knockdown using short hairpin RNAs, gene overexpression using exogenous mRNAs, and endogenous gene tagging using CRISPR-mediated gene knock-in. Combined with our ability to control spawning in the laboratory, these tools make A. poculata a tractable experimental system for investigative studies of coral development. Further application of these tools will enable functional analyses of embryonic patterning and morphogenesis across Anthozoa and open new frontiers in coral biology research.
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Affiliation(s)
- Jacob F. Warner
- Department of Biology and Marine Biology, UNC Wilmington, Wilmington, NC, 28409
| | - Ryan Besemer
- Department of Biology and Marine Biology, UNC Wilmington, Wilmington, NC, 28409
| | - Alicia Schickle
- Feinstein School of Social and Natural Sciences, Roger Williams University, Bristol, RI 02871
| | - Erin Borbee
- Department of Biology, Texas State University, San Marcos, TX, 78666
| | | | - Koty Sharp
- Feinstein School of Social and Natural Sciences, Roger Williams University, Bristol, RI 02871
| | - Leslie S. Babonis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853
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5
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Colgren J, Burkhardt P. Evolution: Was the nuclear-to-cytoplasmic ratio a key factor in the origin of animal multicellularity? Curr Biol 2023; 33:R298-R300. [PMID: 37098330 DOI: 10.1016/j.cub.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The ichthyosporean Sphaeroforma arctica, a protist closely related to animals, displays coenocytic development followed by cellularization and cell release. A new study reveals that the nuclear-to-cytoplasmic ratio drives cellularization in these fascinating organisms.
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Affiliation(s)
- Jeffrey Colgren
- Michael Sars Centre, University of Bergen, 5008 Bergen, Norway.
| | - Pawel Burkhardt
- Michael Sars Centre, University of Bergen, 5008 Bergen, Norway.
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6
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Nguyen NM, Merle T, Broders-Bondon F, Brunet AC, Battistella A, Land EBL, Sarron F, Jha A, Gennisson JL, Röttinger E, Fernández-Sánchez ME, Farge E. Mechano-biochemical marine stimulation of inversion, gastrulation, and endomesoderm specification in multicellular Eukaryota. Front Cell Dev Biol 2022; 10:992371. [PMID: 36531949 PMCID: PMC9754125 DOI: 10.3389/fcell.2022.992371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/01/2022] [Indexed: 07/29/2023] Open
Abstract
The evolutionary emergence of the primitive gut in Metazoa is one of the decisive events that conditioned the major evolutionary transition, leading to the origin of animal development. It is thought to have been induced by the specification of the endomesoderm (EM) into the multicellular tissue and its invagination (i.e., gastrulation). However, the biochemical signals underlying the evolutionary emergence of EM specification and gastrulation remain unknown. Herein, we find that hydrodynamic mechanical strains, reminiscent of soft marine flow, trigger active tissue invagination/gastrulation or curvature reversal via a Myo-II-dependent mechanotransductive process in both the metazoan Nematostella vectensis (cnidaria) and the multicellular choanoflagellate Choanoeca flexa. In the latter, our data suggest that the curvature reversal is associated with a sensory-behavioral feeding response. Additionally, like in bilaterian animals, gastrulation in the cnidarian Nematostella vectensis is shown to participate in the biochemical specification of the EM through mechanical activation of the β-catenin pathway via the phosphorylation of Y654-βcatenin. Choanoflagellates are considered the closest living relative to metazoans, and the common ancestor of choanoflagellates and metazoans dates back at least 700 million years. Therefore, the present findings using these evolutionarily distant species suggest that the primitive emergence of the gut in Metazoa may have been initiated in response to marine mechanical stress already in multicellular pre-Metazoa. Then, the evolutionary transition may have been achieved by specifying the EM via a mechanosensitive Y654-βcatenin dependent mechanism, which appeared during early Metazoa evolution and is specifically conserved in all animals.
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Affiliation(s)
- Ngoc Minh Nguyen
- Mechanics and Genetics of Embryonic Development Group, Institut Curie, Centre OCAV PSL Research University, CNRS, UMR168, Inserm, Sorbonne University, Paris, France
| | - Tatiana Merle
- Mechanics and Genetics of Embryonic Development Group, Institut Curie, Centre OCAV PSL Research University, CNRS, UMR168, Inserm, Sorbonne University, Paris, France
| | - Florence Broders-Bondon
- Mechanics and Genetics of Embryonic Development Group, Institut Curie, Centre OCAV PSL Research University, CNRS, UMR168, Inserm, Sorbonne University, Paris, France
| | - Anne-Christine Brunet
- Mechanics and Genetics of Embryonic Development Group, Institut Curie, Centre OCAV PSL Research University, CNRS, UMR168, Inserm, Sorbonne University, Paris, France
| | - Aude Battistella
- Biochemistry, Molecular Biology, and Cells Platform, Institut Curie, CNRS, UMR 168, Inserm, Sorbonne University, Paris, France
| | - Emelie Britt Linnea Land
- Mechanics and Genetics of Embryonic Development Group, Institut Curie, Centre OCAV PSL Research University, CNRS, UMR168, Inserm, Sorbonne University, Paris, France
| | - Florian Sarron
- Sorbonne Université, CNRS, UMR 7095, Institut d'Astrophysique de Paris, Paris, France
| | - Aditya Jha
- Laboratoire Physique et Mécanique des Milieux Hétérogènes (PMMH), CNRS, ESPCI ParisTech, Université Pierre et Marie Curie, Université Paris Diderot, Paris, France
| | - Jean-Luc Gennisson
- Université Paris-Saclay, CEA, CNRS, Inserm, BioMaps, Service Hospitalier Frédéric Joliot, Orsay, France
| | - Eric Röttinger
- Université Côte d’Azur, CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Nice, France
- Université Côte d’Azur, Institut Fédératif de Recherche Ressources Marines (IFR MARRES), Nice, France
| | - María Elena Fernández-Sánchez
- Mechanics and Genetics of Embryonic Development Group, Institut Curie, Centre OCAV PSL Research University, CNRS, UMR168, Inserm, Sorbonne University, Paris, France
| | - Emmanuel Farge
- Mechanics and Genetics of Embryonic Development Group, Institut Curie, Centre OCAV PSL Research University, CNRS, UMR168, Inserm, Sorbonne University, Paris, France
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7
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Schwaiger M, Andrikou C, Dnyansagar R, Murguia PF, Paganos P, Voronov D, Zimmermann B, Lebedeva T, Schmidt HA, Genikhovich G, Benvenuto G, Arnone MI, Technau U. An ancestral Wnt-Brachyury feedback loop in axial patterning and recruitment of mesoderm-determining target genes. Nat Ecol Evol 2022; 6:1921-1939. [PMID: 36396969 DOI: 10.1038/s41559-022-01905-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/12/2022] [Indexed: 11/18/2022]
Abstract
Transcription factors are crucial drivers of cellular differentiation during animal development and often share ancient evolutionary origins. The T-box transcription factor Brachyury plays a pivotal role as an early mesoderm determinant and neural repressor in vertebrates; yet, the ancestral function and key evolutionary transitions of the role of this transcription factor remain obscure. Here, we present a genome-wide target-gene screen using chromatin immunoprecipitation sequencing in the sea anemone Nematostella vectensis, an early branching non-bilaterian, and the sea urchin Strongylocentrotus purpuratus, a representative of the sister lineage of chordates. Our analysis reveals an ancestral gene regulatory feedback loop connecting Brachyury, FoxA and canonical Wnt signalling involved in axial patterning that predates the cnidarian-bilaterian split about 700 million years ago. Surprisingly, we also found that part of the gene regulatory network controlling the fate of neuromesodermal progenitors in vertebrates was already present in the common ancestor of cnidarians and bilaterians. However, while several endodermal and neuronal Brachyury target genes are ancestrally shared, hardly any of the key mesodermal downstream targets in vertebrates are found in the sea anemone or the sea urchin. Our study suggests that a limited number of target genes involved in mesoderm formation were newly acquired in the vertebrate lineage, leading to a dramatic shift in the function of this ancestral developmental regulator.
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Affiliation(s)
- Michaela Schwaiger
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
- Friedrich Miescher Institute for Biomedical Research, Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Carmen Andrikou
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Rohit Dnyansagar
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | - Patricio Ferrer Murguia
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | | | - Danila Voronov
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | - Tatiana Lebedeva
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | - Heiko A Schmidt
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Grigory Genikhovich
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | | | | | - Ulrich Technau
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria.
- Max Perutz Labs, University of Vienna, Vienna, Austria.
- Research Platform 'Single Cell Regulation of Stem Cells', University of Vienna, Vienna, Austria.
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8
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Ozernyuk ND, Isaeva VV. Early Stages of Animal Mesoderm Evolution. Russ J Dev Biol 2022. [DOI: 10.1134/s1062360422020096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Keenan SE, Avdeeva M, Yang L, Alber DS, Wieschaus EF, Shvartsman SY. Dynamics of Drosophila endoderm specification. Proc Natl Acad Sci U S A 2022; 119:e2112892119. [PMID: 35412853 PMCID: PMC9169638 DOI: 10.1073/pnas.2112892119] [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: 07/15/2021] [Accepted: 02/06/2022] [Indexed: 11/18/2022] Open
Abstract
During early Drosophila embryogenesis, a network of gene regulatory interactions orchestrates terminal patterning, playing a critical role in the subsequent formation of the gut. We utilized CRISPR gene editing at endogenous loci to create live reporters of transcription and light-sheet microscopy to monitor the individual components of the posterior gut patterning network across 90 min prior to gastrulation. We developed a computational approach for fusing imaging datasets of the individual components into a common multivariable trajectory. Data fusion revealed low intrinsic dimensionality of posterior patterning and cell fate specification in wild-type embryos. The simple structure that we uncovered allowed us to construct a model of interactions within the posterior patterning regulatory network and make testable predictions about its dynamics at the protein level. The presented data fusion strategy is a step toward establishing a unified framework that would explore how stochastic spatiotemporal signals give rise to highly reproducible morphogenetic outcomes.
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Affiliation(s)
- Shannon E. Keenan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
| | - Maria Avdeeva
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010
| | - Liu Yang
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
| | - Daniel S. Alber
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
| | - Eric F. Wieschaus
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540
| | - Stanislav Y. Shvartsman
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540
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10
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Erofeeva TV, Grigorenko AP, Gusev FE, Kosevich IA, Rogaev EI. Studying of Molecular Regulation of Developmental Processes of Lower Metazoans Exemplified by Cnidaria Using High-Throughput Sequencing. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:269-293. [PMID: 35526848 DOI: 10.1134/s0006297922030075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/13/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
A unique set of features and characteristics of species of the Cnidaria phylum is the one reason that makes them a model for a various studies. The plasticity of a life cycle and the processes of cell differentiation and development of an integral multicellular organism associated with it are of a specific scientific interest. A new stage of development of molecular genetic methods, including methods for high-throughput genome, transcriptome, and epigenome sequencing, both at the level of the whole organism and at the level of individual cells, makes it possible to obtain a detailed picture of the development of these animals. This review examines some modern approaches and advances in the reconstruction of the processes of ontogenesis of cnidarians by studying the regulatory signal transduction pathways and their interactions.
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Affiliation(s)
- Taisia V Erofeeva
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anastasia P Grigorenko
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Fedor E Gusev
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Igor A Kosevich
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Evgeny I Rogaev
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
- Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA
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11
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Croce O, Röttinger E. Creating a User-Friendly and Open-Access Gene Expression Database for Comparing Embryonic Development and Regeneration in Nematostella vectensis. Methods Mol Biol 2022; 2450:649-662. [PMID: 35359334 PMCID: PMC9761911 DOI: 10.1007/978-1-0716-2172-1_35] [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] [Indexed: 06/14/2023]
Abstract
The sea anemone Nematostella vectensis has emerged as a powerful research model to understand at the gene regulatory network level, to what extend regeneration recapitulates embryonic development. Such comparison involves massive transcriptomic analysis, a routine approach for identifying differential gene expression. Here we present a workflow to build a user-friendly, mineable, and open-access database providing access to the scientific community to various RNAseq datasets.
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Affiliation(s)
- Olivier Croce
- Institute for Research on Cancer and Aging in Nice (IRCAN), Université Côte d'Azur, CNRS, INSERM, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Eric Röttinger
- Institute for Research on Cancer and Aging in Nice (IRCAN), Université Côte d'Azur, CNRS, INSERM, Nice, France.
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France.
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12
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Klein S, Frazier V, Readdean T, Lucas E, Diaz-Jimenez EP, Sogin M, Ruff ES, Echeverri K. Common Environmental Pollutants Negatively Affect Development and Regeneration in the Sea Anemone Nematostella vectensis Holobiont. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.786037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The anthozoan sea anemone Nematostella vectensis belongs to the phylum of cnidarians which also includes jellyfish and corals. Nematostella are native to United States East Coast marsh lands, where they constantly adapt to changes in salinity, temperature, oxygen concentration and pH. Its natural ability to continually acclimate to changing environments coupled with its genetic tractability render Nematostella a powerful model organism in which to study the effects of common pollutants on the natural development of these animals. Potassium nitrate, commonly used in fertilizers, and Phthalates, a component of plastics are frequent environmental stressors found in coastal and marsh waters. Here we present data showing how early exposure to these pollutants lead to dramatic defects in development of the embryos and eventual mortality possibly due to defects in feeding ability. Additionally, we examined the microbiome of the animals and identified shifts in the microbial community that correlated with the type of water that was used to grow the animals, and with their exposure to pollutants.
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13
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Vetrova AA, Lebedeva TS, Saidova AA, Kupaeva DM, Kraus YA, Kremnyov SV. From apolar gastrula to polarized larva: Embryonic development of a marine hydroid, Dynamena pumila. Dev Dyn 2021; 251:795-825. [PMID: 34787911 DOI: 10.1002/dvdy.439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In almost all metazoans examined to this respect, the axial patterning system based on canonical Wnt (cWnt) signaling operates throughout the course of development. In most metazoans, gastrulation is polar, and embryos develop morphological landmarks of axial polarity, such as blastopore under control/regulation from cWnt signaling. However, in many cnidarian species, gastrulation is morphologically apolar. The question remains whether сWnt signaling providing the establishment of a body axis controls morphogenetic processes involved in apolar gastrulation. RESULTS In this study, we focused on the embryonic development of Dynamena pumila, a cnidarian species with apolar gastrulation. We thoroughly described cell behavior, proliferation, and ultrastructure and examined axial patterning in the embryos of this species. We revealed that the first signs of morphological polarity appear only after the end of gastrulation, while molecular prepatterning of the embryo does exist during gastrulation. We have shown experimentally that in D. pumila, the direction of the oral-aboral axis is highly robust against perturbations in cWnt activity. CONCLUSIONS Our results suggest that morphogenetic processes are uncoupled from molecular axial patterning during gastrulation in D. pumila. Investigation of D. pumila might significantly expand our understanding of the ways in which morphological polarization and axial molecular patterning are linked in Metazoa.
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Affiliation(s)
- Alexandra A Vetrova
- Laboratory of Morphogenesis Evolution, Koltzov Institute of Developmental Biology RAS, Moscow, Russia
| | - Tatiana S Lebedeva
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Aleena A Saidova
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Daria M Kupaeva
- Laboratory of Morphogenesis Evolution, Koltzov Institute of Developmental Biology RAS, Moscow, Russia
| | - Yulia A Kraus
- Laboratory of Morphogenesis Evolution, Koltzov Institute of Developmental Biology RAS, Moscow, Russia.,Department of Evolutionary Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Stanislav V Kremnyov
- Laboratory of Morphogenesis Evolution, Koltzov Institute of Developmental Biology RAS, Moscow, Russia.,Department of Embryology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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14
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Wijesena N, Sun H, Kumburegama S, Wikramanayake AH. Distinct Frizzled receptors independently mediate endomesoderm specification and primary archenteron invagination during gastrulation in Nematostella. Dev Biol 2021; 481:215-225. [PMID: 34767794 DOI: 10.1016/j.ydbio.2021.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 11/03/2022]
Abstract
Endomesodermal cell fate specification and archenteron formation during gastrulation are tightly linked developmental processes in most metazoans. However, studies have shown that in the anthozoan cnidarian Nematostella vectensis, Wnt/β-catenin (cWnt) signalling-mediated endomesodermal cell fate specification can be experimentally uncoupled from Wnt/Planar Cell Polarity (PCP) signalling-mediated primary archenteron invagination. The upstream signalling mechanisms regulating cWnt signalling-dependent endomesoderm cell fate specification and Wnt/PCP signalling-mediated primary archenteron invagination in Nematostella embryos are not well understood. By screening for potential upstream mediators of cWnt and Wnt/PCP signalling, we identified two Nematostella Frizzled homologs that are expressed early in development. NvFzd1 is expressed maternally and in a broad pattern during early development while NvFzd10 is zygotically expressed at the animal pole in blastula stage embryos and is restricted to the invaginating cells of the presumptive endomesoderm. Molecular and morphological characterization of NvFzd1 and NvFzd10 knock-down phenotypes provide evidence for distinct regulatory roles for the two receptors in endomesoderm cell fate specification and primary archenteron invagination. These results provide further experimental evidence for the independent regulation of endomesodermal cell fate specification and primary archenteron invagination during gastrulation in Nematostella. Moreover, these results provide additional support for the previously proposed two-step model for the independent evolution of cWnt-mediated cell fate specification and Wnt/PCP-mediated primary archenteron invagination.
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Affiliation(s)
- Naveen Wijesena
- Department of Biology, University of Miami, Coral Gables, FL33146, USA; Department of Biology, University of Bergen, Bergen, Norway
| | - Hongyan Sun
- Department of Biology, University of Miami, Coral Gables, FL33146, USA
| | - Shalika Kumburegama
- Department of Biology, University of Miami, Coral Gables, FL33146, USA; Department of Zoology, University of Peradeniya, Peradeniya, Sri Lanka
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15
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Nematostella vectensis, an Emerging Model for Deciphering the Molecular and Cellular Mechanisms Underlying Whole-Body Regeneration. Cells 2021; 10:cells10102692. [PMID: 34685672 PMCID: PMC8534814 DOI: 10.3390/cells10102692] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/18/2022] Open
Abstract
The capacity to regenerate lost or injured body parts is a widespread feature within metazoans and has intrigued scientists for centuries. One of the most extreme types of regeneration is the so-called whole body regenerative capacity, which enables regeneration of fully functional organisms from isolated body parts. While not exclusive to this habitat, whole body regeneration is widespread in aquatic/marine invertebrates. Over the past decade, new whole-body research models have emerged that complement the historical models Hydra and planarians. Among these, the sea anemone Nematostella vectensis has attracted increasing interest in regard to deciphering the cellular and molecular mechanisms underlying the whole-body regeneration process. This manuscript will present an overview of the biological features of this anthozoan cnidarian as well as the available tools and resources that have been developed by the scientific community studying Nematostella. I will further review our current understanding of the cellular and molecular mechanisms underlying whole-body regeneration in this marine organism, with emphasis on how comparing embryonic development and regeneration in the same organism provides insight into regeneration specific elements.
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16
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Amiel AR, Michel V, Carvalho JE, Shkreli M, Petit C, Röttinger E. [The sea anemone Nematostella vectensis, an emerging model for biomedical research: Mechano-sensitivity, extreme regeneration and longevity]. Med Sci (Paris) 2021; 37:167-177. [PMID: 33591260 DOI: 10.1051/medsci/2020282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Nematostella has fascinating features such as whole-body regeneration, the absence of signs of aging and importantly, the absence of age-related diseases. Easy to culture and spawn, this little sea anemone in spite of its "simple" aspect, displays interesting morphological characteristics similar to vertebrates and an unexpected similarity in gene content/genome organization. Importantly, the scientific community working on Nematostella is developing a variety of functional genomics tools that enable scientists to use this anemone in the field of regenerative medicine, longevity and mecano-sensory diseases. As a complementary research model to vertebrates, this marine invertebrate is emerging and promising to dig deeper into those fields of research in an integrative manner (entire organism) and provides new opportunities for scientists to lift specific barriers that can be encountered with other commonly used animal models.
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Affiliation(s)
- Aldine R Amiel
- Université Côte d'Azur, CNRS, Inserm - Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), 06107 Nice, France - Université Côte d'Azur - Institut fédératif de recherche - ressources marines, 06107 Nice, France
| | - Vincent Michel
- Institut de l'audition, Institut Pasteur, Inserm UMRS 1120, 75012 Paris, France
| | - João E Carvalho
- Université Côte d'Azur, CNRS, Inserm - Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), 06107 Nice, France - Université Côte d'Azur - Institut fédératif de recherche - ressources marines, 06107 Nice, France
| | - Marina Shkreli
- Université Côte d'Azur, CNRS, Inserm - Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), 06107 Nice, France
| | - Christine Petit
- Institut de l'audition, Institut Pasteur, Inserm UMRS 1120, 75012 Paris, France - Collège de France, 75005 Paris, France
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, Inserm - Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), 06107 Nice, France - Université Côte d'Azur - Institut fédératif de recherche - ressources marines, 06107 Nice, France
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17
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Zullo L, Bozzo M, Daya A, Di Clemente A, Mancini FP, Megighian A, Nesher N, Röttinger E, Shomrat T, Tiozzo S, Zullo A, Candiani S. The Diversity of Muscles and Their Regenerative Potential across Animals. Cells 2020; 9:cells9091925. [PMID: 32825163 PMCID: PMC7563492 DOI: 10.3390/cells9091925] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023] Open
Abstract
Cells with contractile functions are present in almost all metazoans, and so are the related processes of muscle homeostasis and regeneration. Regeneration itself is a complex process unevenly spread across metazoans that ranges from full-body regeneration to partial reconstruction of damaged organs or body tissues, including muscles. The cellular and molecular mechanisms involved in regenerative processes can be homologous, co-opted, and/or evolved independently. By comparing the mechanisms of muscle homeostasis and regeneration throughout the diversity of animal body-plans and life cycles, it is possible to identify conserved and divergent cellular and molecular mechanisms underlying muscle plasticity. In this review we aim at providing an overview of muscle regeneration studies in metazoans, highlighting the major regenerative strategies and molecular pathways involved. By gathering these findings, we wish to advocate a comparative and evolutionary approach to prompt a wider use of “non-canonical” animal models for molecular and even pharmacological studies in the field of muscle regeneration.
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Affiliation(s)
- Letizia Zullo
- Istituto Italiano di Tecnologia, Center for Micro-BioRobotics & Center for Synaptic Neuroscience and Technology (NSYN), 16132 Genova, Italy;
- IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy
- Correspondence: (L.Z.); (A.Z.)
| | - Matteo Bozzo
- Laboratory of Developmental Neurobiology, Department of Earth, Environment and Life Sciences, University of Genova, Viale Benedetto XV 5, 16132 Genova, Italy; (M.B.); (S.C.)
| | - Alon Daya
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel; (A.D.); (N.N.); (T.S.)
| | - Alessio Di Clemente
- Istituto Italiano di Tecnologia, Center for Micro-BioRobotics & Center for Synaptic Neuroscience and Technology (NSYN), 16132 Genova, Italy;
- Department of Experimental Medicine, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | | | - Aram Megighian
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy;
- Padova Neuroscience Center, University of Padova, 35131 Padova, Italy
| | - Nir Nesher
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel; (A.D.); (N.N.); (T.S.)
| | - Eric Röttinger
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, CNRS, INSERM, 06107 Nice, France;
| | - Tal Shomrat
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel; (A.D.); (N.N.); (T.S.)
| | - Stefano Tiozzo
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Paris, France;
| | - Alberto Zullo
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy;
- Correspondence: (L.Z.); (A.Z.)
| | - Simona Candiani
- Laboratory of Developmental Neurobiology, Department of Earth, Environment and Life Sciences, University of Genova, Viale Benedetto XV 5, 16132 Genova, Italy; (M.B.); (S.C.)
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18
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Technau U. Gastrulation and germ layer formation in the sea anemone Nematostella vectensis and other cnidarians. Mech Dev 2020; 163:103628. [PMID: 32603823 DOI: 10.1016/j.mod.2020.103628] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/23/2020] [Accepted: 06/19/2020] [Indexed: 01/03/2023]
Abstract
Among the basally branching metazoans, cnidarians display well-defined gastrulation processes leading to a diploblastic body plan, consisting of an endodermal and an ectodermal cell layer. As the outgroup to all Bilateria, cnidarians are an interesting group to investigate ancestral developmental mechanisms. Interestingly, all known gastrulation mechanisms known in Bilateria are already found in different species of Cnidaria. Here I review the morphogenetic processes found in different Cnidaria and focus on the investigation of the cellular and molecular mechanisms in the sea anemone Nematostella vectensis, which has been a major model organism among cnidarians for evolutionary developmental biology. Many of the genes involved in germ layer specification and morphogenetic processes in Bilateria are also found active during gastrulation of Nematostella and other cnidarians, suggesting an ancestral role of this process. The molecular analyses indicate a tight link between gastrulation and axis patterning processes by Wnt and FGF signaling. Interestingly, the endodermal layer displays many features of the mesodermal layer in Bilateria, while the pharyngeal ectoderm has an endodermal expression profile. Comparative analyses as well as experimental studies using embryonic aggregates suggest that minor differences in the gene regulatory networks allow the embryo to transition relatively easily from one mode of gastrulation to another.
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Affiliation(s)
- Ulrich Technau
- University of Vienna, Dept. of Neurosciences and Developmental Biology, Althanstrasse 14, 1090 Wien, Austria.
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19
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DuBuc TQ, Ryan JF, Martindale MQ. "Dorsal-Ventral" Genes Are Part of an Ancient Axial Patterning System: Evidence from Trichoplax adhaerens (Placozoa). Mol Biol Evol 2019; 36:966-973. [PMID: 30726986 PMCID: PMC6501881 DOI: 10.1093/molbev/msz025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Placozoa are a morphologically simplistic group of marine animals found globally in tropical and subtropical environments. They consist of two named species, Trichoplax adhaerens and more recently Hoilungia hongkongensis, both with roughly six morphologically distinct cell types. With a sequenced genome, a limited number of cell types, and a simple flattened morphology, Trichoplax is an ideal model organism from which to explore the biology of an animal with a cellular complexity analagous to that of the earliest animals. Using a new approach for identification of gene expression patterns, this research looks at the relationship of Chordin/TgfΒ signaling and the axial patterning system of Placozoa. Our results suggest that placozoans have an oral-aboral axis similar to cnidarians and that the parahoxozoan ancestor (common ancestor of Placozoa and Cnidaria) was likely radially symmetric.
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Affiliation(s)
- Timothy Q DuBuc
- Whitney Lab for Marine Bioscience and the Department of Biology, University of Florida, St. Augustine, FL
- Kewalo Marine Laboratory and the Department of Biology, University of Hawaii, Manoa, Honolulu, HI
- Centre for Chromosome Biology, Bioscience Building, National University of Ireland Galway, Galway, Ireland
| | - Joseph F Ryan
- Whitney Lab for Marine Bioscience and the Department of Biology, University of Florida, St. Augustine, FL
| | - Mark Q Martindale
- Whitney Lab for Marine Bioscience and the Department of Biology, University of Florida, St. Augustine, FL
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20
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Nathaniel Clarke D, Lowe CJ, James Nelson W. The cadherin-catenin complex is necessary for cell adhesion and embryogenesis in Nematostella vectensis. Dev Biol 2019; 447:170-181. [PMID: 30629955 PMCID: PMC6433513 DOI: 10.1016/j.ydbio.2019.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/20/2018] [Accepted: 01/04/2019] [Indexed: 01/22/2023]
Abstract
The cadherin-catenin complex is a conserved, calcium-dependent cell-cell adhesion module that is necessary for normal development and the maintenance of tissue integrity in bilaterian animals. Despite longstanding evidence of a deep ancestry of calcium-dependent cell adhesion in animals, the requirement of the cadherin-catenin complex to coordinate cell-cell adhesion has not been tested directly in a non-bilaterian organism. Here, we provide the first analysis of classical cadherins and catenins in the Starlet Sea Anemone, Nematostella vectensis. Gene expression, protein localization, siRNA-mediated knockdown of α-catenin, and calcium-dependent cell aggregation assays provide evidence that a bonafide cadherin-catenin complex is present in the early embryo, and that α-catenin is required for normal embryonic development and the formation of cell-cell adhesions between cells dissociated from whole embryos. Together these results support the hypothesis that the cadherin-catenin complex was likely a complete and functional cell-cell adhesion module in the last common cnidarian-bilaterian ancestor. SUMMARY STATEMENT: Embryonic manipulations and ex vivo adhesion assays in the sea anemone, Nematostella vectensis, indicate that the necessity of the cadherin-catenin complex for mediating cell-cell adhesion is deeply conserved in animal evolution.
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Affiliation(s)
- D Nathaniel Clarke
- Department of Biology, Stanford University, Stanford CA 94305, United States.
| | - Christopher J Lowe
- Department of Biology, Stanford University, Stanford CA 94305, United States.
| | - W James Nelson
- Department of Biology, Stanford University, Stanford CA 94305, United States; Department of Molecular and Cellular Physiology, Stanford University, Stanford CA 94305, United States.
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21
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Leclère L, Horin C, Chevalier S, Lapébie P, Dru P, Peron S, Jager M, Condamine T, Pottin K, Romano S, Steger J, Sinigaglia C, Barreau C, Quiroga Artigas G, Ruggiero A, Fourrage C, Kraus JEM, Poulain J, Aury JM, Wincker P, Quéinnec E, Technau U, Manuel M, Momose T, Houliston E, Copley RR. The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle. Nat Ecol Evol 2019; 3:801-810. [PMID: 30858591 DOI: 10.1038/s41559-019-0833-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/30/2019] [Indexed: 12/14/2022]
Abstract
Jellyfish (medusae) are a distinctive life-cycle stage of medusozoan cnidarians. They are major marine predators, with integrated neurosensory, muscular and organ systems. The genetic foundations of this complex form are largely unknown. We report the draft genome of the hydrozoan jellyfish Clytia hemisphaerica and use multiple transcriptomes to determine gene use across life-cycle stages. Medusa, planula larva and polyp are each characterized by distinct transcriptome signatures reflecting abrupt life-cycle transitions and all deploy a mixture of phylogenetically old and new genes. Medusa-specific transcription factors, including many with bilaterian orthologues, associate with diverse neurosensory structures. Compared to Clytia, the polyp-only hydrozoan Hydra has lost many of the medusa-expressed transcription factors, despite similar overall rates of gene content evolution and sequence evolution. Absence of expression and gene loss among Clytia orthologues of genes patterning the anthozoan aboral pole, secondary axis and endomesoderm support simplification of planulae and polyps in Hydrozoa, including loss of bilateral symmetry. Consequently, although the polyp and planula are generally considered the ancestral cnidarian forms, in Clytia the medusa maximally deploys the ancestral cnidarian-bilaterian transcription factor gene complement.
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Affiliation(s)
- Lucas Leclère
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Coralie Horin
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Sandra Chevalier
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Pascal Lapébie
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France
| | - Philippe Dru
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Sophie Peron
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Muriel Jager
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France
| | - Thomas Condamine
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France
| | - Karen Pottin
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France.,Laboratoire de Biologie du Développement (IBPS-LBD, UMR7622), Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Paris, France
| | - Séverine Romano
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Julia Steger
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Laboratoire de Biologie du Développement (IBPS-LBD, UMR7622), Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Paris, France
| | - Chiara Sinigaglia
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS UMR 5242-INRA USC 1370, Lyon cedex 07, France
| | - Carine Barreau
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Gonzalo Quiroga Artigas
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Antonella Ruggiero
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Centre de Recherche de Biologie cellulaire de Montpellier, CNRS UMR 5237, Université de Montpellier, Montpellier Cedex 5, France
| | - Cécile Fourrage
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Service de Génétique UMR 781, Hôpital Necker-APHP, Paris, France
| | - Johanna E M Kraus
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Vienna, Austria.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique, Université Paris-Saclay, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Eric Quéinnec
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France
| | - Ulrich Technau
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Vienna, Austria
| | - Michaël Manuel
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France
| | - Tsuyoshi Momose
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Evelyn Houliston
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Richard R Copley
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.
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22
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Rothenberg EV. Encounters across networks: Windows into principles of genomic regulation. Mar Genomics 2019; 44:3-12. [PMID: 30661741 DOI: 10.1016/j.margen.2019.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/06/2019] [Accepted: 01/06/2019] [Indexed: 12/13/2022]
Abstract
Gene regulatory networks account for the ability of the genome to program development in complex multi-cellular organisms. Such networks are based on principles of gene regulation by combinations of transcription factors that bind to specific cis-regulatory DNA sites to activate transcription. These cis-regulatory regions mediate logic processing at each network node, enabling progressive increases in organismal complexity with development. Gene regulatory network explanations of development have been shown to account for patterning and cell type diversification in fly and sea urchin embryonic systems, where networks are characterized by fast coupling between transcriptional inputs and changes in target gene transcription rates, and crucial cis-regulatory elements are concentrated relatively close to the protein coding sequences of the target genes, thus facilitating their identification. Stem cell-based development in post-embryonic mammalian systems also depends on gene networks, but differs from the fly and sea urchin systems. First, the number of regulatory elements per gene and the distances between regulatory elements and the genes they control are considerably larger, forcing searches via genome-wide transcription factor binding surveys rather than functional assays. Second, the intrinsic timing of network state transitions can be slowed considerably by the need to undo stem-cell chromatin configurations, which presumably add stability to stem-cell states but retard responses to transcription factor changes during differentiation. The dispersed, partially redundant cis-regulatory systems controlling gene expression and the slow state transition kinetics in these systems already reveal new insights and opportunities to extend understanding of the repertoire of gene networks and regulatory system logic.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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23
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Love AC, Yoshida Y. Reflections on Model Organisms in Evolutionary Developmental Biology. Results Probl Cell Differ 2019; 68:3-20. [PMID: 31598850 DOI: 10.1007/978-3-030-23459-1_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This chapter reflects on and makes explicit the distinctiveness of reasoning practices associated with model organisms in the context of evolutionary developmental research. Model organisms in evo-devo instantiate a unique synthesis of model systems strategies from developmental biology and comparative strategies from evolutionary biology that negotiate a tension between developmental conservation and evolutionary change to address scientific questions about the evolution of development and the developmental basis of evolutionary change. We review different categories of model systems that have been advanced to understand practices found in the life sciences in order to comprehend how evo-devo model organisms instantiate this synthesis in the context of three examples: the starlet sea anemone and the evolution of bilateral symmetry, leeches and the origins of segmentation in bilaterians, and the corn snake to understand major evolutionary change in axial and appendicular morphology.
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Affiliation(s)
- Alan C Love
- Department of Philosophy and Minnesota Center for Philosophy of Science, University of Minnesota - Twin Cities, Minneapolis, MN, USA.
| | - Yoshinari Yoshida
- Department of Philosophy and Minnesota Center for Philosophy of Science, University of Minnesota - Twin Cities, Minneapolis, MN, USA
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24
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Yasuoka Y, Tando Y, Kubokawa K, Taira M. Evolution of cis-regulatory modules for the head organizer gene goosecoid in chordates: comparisons between Branchiostoma and Xenopus. ZOOLOGICAL LETTERS 2019; 5:27. [PMID: 31388442 PMCID: PMC6679436 DOI: 10.1186/s40851-019-0143-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 07/12/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND In cephalochordates (amphioxus), the notochord runs along the dorsal to the anterior tip of the body. In contrast, the vertebrate head is formed anterior to the notochord, as a result of head organizer formation in anterior mesoderm during early development. A key gene for the vertebrate head organizer, goosecoid (gsc), is broadly expressed in the dorsal mesoderm of amphioxus gastrula. Amphioxus gsc expression subsequently becomes restricted to the posterior notochord from the early neurula. This has prompted the hypothesis that a change in expression patterns of gsc led to development of the vertebrate head during chordate evolution. However, molecular mechanisms of head organizer evolution involving gsc have never been elucidated. RESULTS To address this question, we compared cis-regulatory modules of vertebrate organizer genes between amphioxus, Branchiostoma japonicum, and frogs, Xenopus laevis and Xenopus tropicalis. Here we show conservation and diversification of gene regulatory mechanisms through cis-regulatory modules for gsc, lim1/lhx1, and chordin in Branchiostoma and Xenopus. Reporter analysis using Xenopus embryos demonstrates that activation of gsc by Nodal/FoxH1 signal through the 5' upstream region, that of lim1 by Nodal/FoxH1 signal through the first intron, and that of chordin by Lim1 through the second intron, are conserved between amphioxus and Xenopus. However, activation of gsc by Lim1 and Otx through the 5' upstream region in Xenopus are not conserved in amphioxus. Furthermore, the 5' region of amphioxus gsc recapitulated the amphioxus-like posterior mesoderm expression of the reporter gene in transgenic Xenopus embryos. CONCLUSIONS On the basis of this study, we propose a model, in which the gsc gene acquired the cis-regulatory module bound with Lim1 and Otx at its 5' upstream region to be activated persistently in anterior mesoderm, in the vertebrate lineage. Because Gsc globally represses trunk (notochord) genes in the vertebrate head organizer, this cooption of gsc in vertebrates appears to have resulted in inhibition of trunk genes and acquisition of the head organizer and its derivative prechordal plate.
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Affiliation(s)
- Yuuri Yasuoka
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495 Japan
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Yukiko Tando
- Center for Advance Marine Research, Ocean Research Institute, The University of Tokyo, 1-15-1, Minamidai, Nakano-ku, Tokyo, 164-8639 Japan
- Present address: Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Kaoru Kubokawa
- Center for Advance Marine Research, Ocean Research Institute, The University of Tokyo, 1-15-1, Minamidai, Nakano-ku, Tokyo, 164-8639 Japan
- Present address: SIRC, Teikyo University, 2-11-1, Itabashi-ku, Tokyo, 173-8605 Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Present address: Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551 Japan
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25
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Onai T. Canonical Wnt/β-catenin and Notch signaling regulate animal/vegetal axial patterning in the cephalochordate amphioxus. Evol Dev 2018; 21:31-43. [PMID: 30288919 DOI: 10.1111/ede.12273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In bilaterians, animal/vegetal axial (A/V) patterning is a fundamental early developmental event for establishment of animal/vegetal polarity and following specification of the germ layers (ectoderm, mesoderm, endoderm), of which the evolutionary origin is enigmatic. Understanding A/V axial patterning in a basal animal from each phylum would help to reconstruct the ancestral state of germ layer specification in bilaterians and thus, the evolution of mesoderm, the third intermediate cell layer. Herein, data show that the canonical Wnt/β-catenin (cWnt) and Notch signaling pathways control mesoderm specification from the early endomesoderm in the basal chordate amphioxus. Amphioxus belongs to the deuterostome, one of the main superphyla in Bilateria. In the present study, genes (tcf, dsh, axin, gsk3β) encoding cWnt components were expressed in the endomesoderm during the gastrula stages. Excess cWnt signaling by BIO, a GSK3 inhibitor, expanded the expression domains of outer endomesodermal genes that include future mesodermal ones and suppressed inner endomesodermal and ectodermal genes. Interfering Notch signaling by DAPT, a γ-secretase inhibitor, resulted in decreased expression of ectodermal and endomesodermal markers. These results suggest that cWnt and Notch have important roles in mesoderm specification in amphioxus embryos. The evolution of the mesoderm is also discussed.
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Affiliation(s)
- Takayuki Onai
- Department of Anatomy, University of Fukui, School of Medical Sciences, Fukui, Japan.,Life Science Innovation Center, University of Fukui, Fukui, Japan
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26
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Osborne CC, Perry KJ, Shankland M, Henry JQ. Ectomesoderm and epithelial-mesenchymal transition-related genes in spiralian development. Dev Dyn 2018; 247:1097-1120. [PMID: 30133032 DOI: 10.1002/dvdy.24667] [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: 06/18/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Spiralians (e.g., annelids, molluscs, and flatworms) possess two sources of mesoderm. One is from endodermal precursors (endomesoderm), which is considered to be the ancestral source in metazoans. The second is from ectoderm (ectomesoderm) and may represent a novel cell type in the Spiralia. In the mollusc Crepidula fornicata, ectomesoderm is derived from micromere daughters within the A and B cell quadrants. Their progeny lie along the anterolateral edges of the blastopore. There they undergo epithelial-mesenchymal transition (EMT), become rounded and undergo delamination/ingression. Subsequently, they assume the mesenchymal phenotype, and migrate beneath the surface ectoderm to differentiate various cell types, including muscles and pigment cells. RESULTS We examined expression of several genes whose homologs are known to regulate Type 1 EMT in other metazoans. Most of these genes were expressed within spiralian ectomesoderm during EMT. CONCLUSIONS We propose that spiralian ectomesoderm, which exhibits analogous cellular behaviors to other populations of mesenchymal cells, may be controlled by the same genes that drive EMT in other metazoans. Perhaps these genes comprise a conserved metazoan EMT gene regulatory network (GRN). This study represents the first step in elucidating the GRN controlling the development of a novel spiralian cell type (ectomesoderm). Developmental Dynamics 247:1097-1120, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- C Cornelia Osborne
- University of Illinois, Department of Cell and Developmental Biology, Urbana, Illinois
| | - Kimberly J Perry
- University of Illinois, Department of Cell and Developmental Biology, Urbana, Illinois
| | - Marty Shankland
- University of Illinois, Department of Cell and Developmental Biology, Urbana, Illinois
| | - Jonathan Q Henry
- University of Illinois, Department of Cell and Developmental Biology, Urbana, Illinois
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27
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Salinas-Saavedra M, Rock AQ, Martindale MQ. Germ layer-specific regulation of cell polarity and adhesion gives insight into the evolution of mesoderm. eLife 2018; 7:e36740. [PMID: 30063005 PMCID: PMC6067901 DOI: 10.7554/elife.36740] [Citation(s) in RCA: 26] [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: 03/19/2018] [Accepted: 06/29/2018] [Indexed: 12/20/2022] Open
Abstract
In triploblastic animals, Par-proteins regulate cell-polarity and adherens junctions of both ectodermal and endodermal epithelia. But, in embryos of the diploblastic cnidarian Nematostella vectensis, Par-proteins are degraded in all cells in the bifunctional gastrodermal epithelium. Using immunohistochemistry, CRISPR/Cas9 mutagenesis, and mRNA overexpression, we describe the functional association between Par-proteins, ß-catenin, and snail transcription factor genes in N. vectensis embryos. We demonstrate that the aPKC/Par complex regulates the localization of ß-catenin in the ectoderm by stabilizing its role in cell-adhesion, and that endomesodermal epithelial cells are organized by a different cell-adhesion system than overlying ectoderm. We also show that ectopic expression of snail genes, which are expressed in mesodermal derivatives in bilaterians, is sufficient to downregulate Par-proteins and translocate ß-catenin from the junctions to the cytoplasm in ectodermal cells. These data provide molecular insight into the evolution of epithelial structure and distinct cell behaviors in metazoan embryos.
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Affiliation(s)
- Miguel Salinas-Saavedra
- The Whitney
Laboratory for Marine BioscienceUniversity of
FloridaFloridaUnited
States
- Department of
BiologyUniversity of
FloridaFloridaUnited
States
| | - Amber Q Rock
- The Whitney
Laboratory for Marine BioscienceUniversity of
FloridaFloridaUnited
States
| | - Mark Q Martindale
- The Whitney
Laboratory for Marine BioscienceUniversity of
FloridaFloridaUnited
States
- Department of
BiologyUniversity of
FloridaFloridaUnited
States
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28
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Žídek R, Machoň O, Kozmik Z. Wnt/β-catenin signalling is necessary for gut differentiation in a marine annelid, Platynereis dumerilii. EvoDevo 2018; 9:14. [PMID: 29942461 PMCID: PMC5996498 DOI: 10.1186/s13227-018-0100-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/20/2018] [Indexed: 11/10/2022] Open
Abstract
Background Wnt/β-catenin (or canonical) signalling pathway activity is necessary and used independently several times for specification of vegetal fate and endoderm, gut differentiation, maintenance of epithelium in adult intestine and the development of gut-derived organs in various vertebrate and non-vertebrate organisms. However, its conservation in later stages of digestive tract development still remains questionable due to the lack of detailed data, mainly from Spiralia. Results Here we characterize the Pdu-Tcf gene, a Tcf/LEF orthologue and a component of Wnt/β-catenin pathway from Platynereis dumerilii, a spiralian, marine annelid worm. Pdu-Tcf undergoes extensive alternative splicing in the C-terminal region of the gene generating as many as eight mRNA isoforms some of which differ in the presence or absence of a C-clamp domain which suggests a distinct DNA binding activity of individual protein variants. Pdu-Tcf is broadly expressed throughout development which is indicative of many functions. One of the most prominent domains that exhibits rather strong Pdu-Tcf expression is in the putative precursors of endodermal gut cells which are detected after 72 h post-fertilization (hpf). At day 5 post-fertilization (dpf), Pdu-Tcf is expressed in the hindgut and pharynx (foregut), whereas at 7 dpf stage, it is strongly transcribed in the now-cellularized midgut for the first time. In order to gain insight into the role of Wnt/β-catenin signalling, we disrupted its activity using pharmacological inhibitors between day 5 and 7 of development. The inhibition of Wnt/β-catenin signalling led to the loss of midgut marker genes Subtilisin-1, Subtilisin-2, α-Amylase and Otx along with a drop in β-catenin protein levels, Axin expression in the gut and nearly the complete loss of proliferative activity throughout the body of larva. At the same time, a hindgut marker gene Legumain was expanded to the midgut compartment under the same conditions. Conclusions Our findings suggest that high Wnt/β-catenin signalling in the midgut might be necessary for proper differentiation of the endoderm to an epithelium capable of secreting digestive enzymes. Together, our data provide evidence for the role of Wnt/β-catenin signalling in gut differentiation in Platynereis.
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Affiliation(s)
- Radim Žídek
- 1Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Ondřej Machoň
- 1Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic.,2Present Address: Institute of Experimental Medicine, Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Zbyněk Kozmik
- 1Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
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29
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Abstract
Distantly related animals have spectacularly different shapes and body plans, which can render it difficult to understand which of their body parts may have a shared evolutionary origin. Studying the molecular regulation of the development of these body parts during embryogenesis can help identifying commonalities that are not visible by eye.
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30
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Hox and Wnt pattern the primary body axis of an anthozoan cnidarian before gastrulation. Nat Commun 2018; 9:2007. [PMID: 29789526 PMCID: PMC5964151 DOI: 10.1038/s41467-018-04184-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 04/06/2018] [Indexed: 11/17/2022] Open
Abstract
Hox gene transcription factors are important regulators of positional identity along the anterior–posterior axis in bilaterian animals. Cnidarians (e.g., sea anemones, corals, and hydroids) are the sister group to the Bilateria and possess genes related to both anterior and central/posterior class Hox genes. Here we report a previously unrecognized domain of Hox expression in the starlet sea anemone, Nematostella vectensis, beginning at early blastula stages. We explore the relationship of two opposing Hox genes (NvAx6/NvAx1) expressed on each side of the blastula during early development. Functional perturbation reveals that NvAx6 and NvAx1 not only regulate their respective expression domains, but also interact with Wnt genes to pattern the entire oral–aboral axis. These findings suggest an ancient link between Hox/Wnt patterning during axis formation and indicate that oral–aboral domains are likely established during blastula formation in anthozoan cnidarians. Hox genes regulate anterior–posterior axis formation but their role in cnidarians is unclear. Here, the authors disrupt Hox genes NvAx1 and NvAx6 in the starlet sea anemone, Nematostella vectensis, showing antagonist function in patterning the oral–aboral axis and a link to Wnt signaling.
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31
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β-Catenin-dependent mechanotransduction dates back to the common ancestor of Cnidaria and Bilateria. Proc Natl Acad Sci U S A 2018; 115:6231-6236. [PMID: 29784822 PMCID: PMC6004442 DOI: 10.1073/pnas.1713682115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Besides genetic regulation, mechanical forces have been identified as important cues in numerous developmental processes. Mechanical forces can activate biochemical cascades in a process called mechanotransduction. Recent studies in vertebrates and flies elucidated the role of mechanical forces for mesodermal gene expression. However, it remains unclear whether mechanotransduction is a universal regulatory mechanism throughout Metazoa. Here, we show in the sea anemone Nematostella vectensis that mechanical pressure can ectopically activate or restore brachyury expression. This mechanotransduction is dependent on β-catenin, similar to vertebrates. We propose that a regulatory feedback loop between genetic and mechanical gene activation exists during gastrulation and the β-catenin–dependent mechanotransduction is an ancient regulatory mechanism, which was present in the common ancestor of cnidarians and bilaterians. Although the genetic regulation of cellular differentiation processes is well established, recent studies have revealed the role of mechanotransduction on a variety of biological processes, including regulation of gene expression. However, it remains unclear how universal and widespread mechanotransduction is in embryonic development of animals. Here, we investigate mechanosensitive gene expression during gastrulation of the starlet sea anemone Nematostella vectensis, a cnidarian model organism. We show that the blastoporal marker gene brachyury is down-regulated by blocking myosin II-dependent gastrulation movements. Brachyury expression can be restored by applying external mechanical force. Using CRISPR/Cas9 and morpholino antisense technology, we also show that mechanotransduction leading to brachyury expression is β-catenin dependent, similar to recent findings in fish and Drosophila [Brunet T, et al. (2013) Nat Commun 4:1–15]. Finally, we demonstrate that prolonged application of mechanical stress on the embryo leads to ectopic brachyury expression. Thus, our data indicate that β-catenin–dependent mechanotransduction is an ancient gene regulatory mechanism, which was present in the common ancestor of cnidarians and bilaterians, at least 600 million years ago.
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32
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Warner JF, Guerlais V, Amiel AR, Johnston H, Nedoncelle K, Röttinger E. NvERTx: a gene expression database to compare embryogenesis and regeneration in the sea anemone Nematostella vectensis. Development 2018; 145:dev.162867. [PMID: 29739837 DOI: 10.1242/dev.162867] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 04/25/2018] [Indexed: 01/28/2023]
Abstract
For over a century, researchers have been comparing embryogenesis and regeneration hoping that lessons learned from embryonic development will unlock hidden regenerative potential. This problem has historically been a difficult one to investigate because the best regenerative model systems are poor embryonic models and vice versa. Recently, however, there has been renewed interest in this question, as emerging models have allowed researchers to investigate these processes in the same organism. This interest has been further fueled by the advent of high-throughput transcriptomic analyses that provide virtual mountains of data. Here, we present Nematostella vectensis Embryogenesis and Regeneration Transcriptomics (NvERTx), a platform for comparing gene expression during embryogenesis and regeneration. NvERTx consists of close to 50 transcriptomic data sets spanning embryogenesis and regeneration in Nematostella These data were used to perform a robust de novo transcriptome assembly, with which users can search, conduct BLAST analyses, and plot the expression of multiple genes during these two developmental processes. The site is also home to the results of gene clustering analyses, to further mine the data and identify groups of co-expressed genes. The site can be accessed at http://nvertx.kahikai.org.
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Affiliation(s)
- Jacob F Warner
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), 06107 Nice, France
| | - Vincent Guerlais
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), 06107 Nice, France
| | - Aldine R Amiel
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), 06107 Nice, France
| | - Hereroa Johnston
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), 06107 Nice, France
| | - Karine Nedoncelle
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), 06107 Nice, France
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), 06107 Nice, France
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33
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Wijesena N, Martindale MQ. Reengineering the primary body axis by ectopic cWnt signaling. Curr Biol 2018; 28:R206-R207. [PMID: 29510105 DOI: 10.1016/j.cub.2018.01.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The evolution of gastrulation, the embryonic formation of distinct tissue layers, was a pivotal event in the metazoan radiation, as it paved the way for diversification of animal body plans from a hollow, ciliated, radially symmetrical ancestor [1]. The position of the site of gastrulation (that segregates internal endomesodermal precursors from outer ectodermal tissue) has played a role in our understanding of patterns of body plan evolution and is tightly regulated during development. In bilaterians (a large clade of bilaterally symmetrical animals that represent over 99% of all extant species), the site of gastrulation is determined by a localized molecular asymmetry resulting from a differential distribution of maternal determinants [2] along the so-called animal-vegetal axis (A-V axis) where the animal pole is marked by the site of polar body release during meiosis [1,3]. In most bilaterians, the site of gastrulation occurs at the vegetal pole (the side opposite the animal pole); however, in cnidarians (corals, sea anemones, and jellyfish) [3], the sister group to all bilaterians and ctenophores (comb jellies), likely to be the earliest branching group of extant metazoans [3], gastrulation occurs at the animal pole [3,4]. Here we show that components of the canonical Wnt-β-catenin (cWnt) signaling pathway mediate endomesoderm formation and patterns the adult primary body axis.
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Affiliation(s)
- Naveen Wijesena
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, Florida, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, Florida, USA.
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34
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Duffy DJ, Krstic A, Schwarzl T, Halasz M, Iljin K, Fey D, Haley B, Whilde J, Haapa-Paananen S, Fey V, Fischer M, Westermann F, Henrich KO, Bannert S, Higgins DG, Kolch W. Wnt signalling is a bi-directional vulnerability of cancer cells. Oncotarget 2018; 7:60310-60331. [PMID: 27531891 PMCID: PMC5312386 DOI: 10.18632/oncotarget.11203] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 07/26/2016] [Indexed: 12/30/2022] Open
Abstract
Wnt signalling is involved in the formation, metastasis and relapse of a wide array of cancers. However, there is ongoing debate as to whether activation or inhibition of the pathway holds the most promise as a therapeutic treatment for cancer, with conflicting evidence from a variety of tumour types. We show that Wnt/β-catenin signalling is a bi-directional vulnerability of neuroblastoma, malignant melanoma and colorectal cancer, with hyper-activation or repression of the pathway both representing a promising therapeutic strategy, even within the same cancer type. Hyper-activation directs cancer cells to undergo apoptosis, even in cells oncogenically driven by β-catenin. Wnt inhibition blocks proliferation of cancer cells and promotes neuroblastoma differentiation. Wnt and retinoic acid co-treatments synergise, representing a promising combination treatment for MYCN-amplified neuroblastoma. Additionally, we report novel cross-talks between MYCN and β-catenin signalling, which repress normal β-catenin mediated transcriptional regulation. A β-catenin target gene signature could predict patient outcome, as could the expression level of its DNA binding partners, the TCF/LEFs. This β-catenin signature provides a tool to identify neuroblastoma patients likely to benefit from Wnt-directed therapy. Taken together, we show that Wnt/β-catenin signalling is a bi-directional vulnerability of a number of cancer entities, and potentially a more broadly conserved feature of malignant cells.
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Affiliation(s)
- David J Duffy
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Current address: The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, USA
| | - Aleksandar Krstic
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Thomas Schwarzl
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Current address: European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Melinda Halasz
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | | | - Dirk Fey
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Bridget Haley
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Jenny Whilde
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | | | - Vidal Fey
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Matthias Fischer
- Department of Paediatric Haematology and Oncology and Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Frank Westermann
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kai-Oliver Henrich
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Bannert
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Desmond G Higgins
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.,School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.,School of Medicine, University College Dublin, Belfield, Dublin, Ireland
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35
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Abstract
Bilaterality – the possession of two orthogonal body axes – is the name-giving trait of all bilaterian animals. These body axes are established during early embryogenesis and serve as a three-dimensional coordinate system that provides crucial spatial cues for developing cells, tissues, organs and appendages. The emergence of bilaterality was a major evolutionary transition, as it allowed animals to evolve more complex body plans. Therefore, how bilaterality evolved and whether it evolved once or several times independently is a fundamental issue in evolutionary developmental biology. Recent findings from non-bilaterian animals, in particular from Cnidaria, the sister group to Bilateria, have shed new light into the evolutionary origin of bilaterality. Here, we compare the molecular control of body axes in radially and bilaterally symmetric cnidarians and bilaterians, identify the minimal set of traits common for Bilateria, and evaluate whether bilaterality arose once or more than once during evolution.
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Affiliation(s)
- Grigory Genikhovich
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
| | - Ulrich Technau
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
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36
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Steinmetz PRH, Aman A, Kraus JEM, Technau U. Gut-like ectodermal tissue in a sea anemone challenges germ layer homology. Nat Ecol Evol 2017; 1:1535-1542. [PMID: 29185520 DOI: 10.1038/s41559-017-0285-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 07/19/2017] [Indexed: 12/11/2022]
Abstract
Cnidarians (for example, sea anemones and jellyfish) develop from an outer ectodermal and inner endodermal germ layer, whereas bilaterians (for example, vertebrates and flies) additionally have a mesodermal layer as intermediate germ layer. Currently, cnidarian endoderm (that is, 'mesendoderm') is considered homologous to both bilaterian endoderm and mesoderm. Here we test this hypothesis by studying the fate of germ layers, the localization of gut cell types, and the expression of numerous 'endodermal' and 'mesodermal' transcription factor orthologues in the anthozoan sea anemone Nematostella vectensis. Surprisingly, we find that the developing pharyngeal ectoderm and its derivatives display a transcription-factor expression profile (foxA, hhex, islet, soxB1, hlxB9, tbx2/3, nkx6 and nkx2.2) and cell-type combination (exocrine and insulinergic) reminiscent of the developing bilaterian midgut, and, in particular, vertebrate pancreatic tissue. Endodermal derivatives, instead, display cell functions and transcription-factor profiles similar to bilaterian mesoderm derivatives (for example, somatic gonad and heart). Thus, our data supports an alternative model of germ layer homologies, where cnidarian pharyngeal ectoderm corresponds to bilaterian endoderm, and the cnidarian endoderm is homologous to bilaterian mesoderm.
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Affiliation(s)
- Patrick R H Steinmetz
- Department for Molecular Evolution and Development, Centre for Organismal Systems Biology, University of Vienna, Althanstraße 14, A-1090, Vienna, Austria. .,Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5006, Bergen, Norway.
| | - Andy Aman
- Department for Molecular Evolution and Development, Centre for Organismal Systems Biology, University of Vienna, Althanstraße 14, A-1090, Vienna, Austria.,Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | - Johanna E M Kraus
- Department for Molecular Evolution and Development, Centre for Organismal Systems Biology, University of Vienna, Althanstraße 14, A-1090, Vienna, Austria.,Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5006, Bergen, Norway
| | - Ulrich Technau
- Department for Molecular Evolution and Development, Centre for Organismal Systems Biology, University of Vienna, Althanstraße 14, A-1090, Vienna, Austria.
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Babonis LS, Martindale MQ. PaxA, but not PaxC, is required for cnidocyte development in the sea anemone Nematostella vectensis. EvoDevo 2017; 8:14. [PMID: 28878874 PMCID: PMC5584322 DOI: 10.1186/s13227-017-0077-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/16/2017] [Indexed: 12/25/2022] Open
Abstract
Background Pax genes are a family of conserved transcription factors that regulate many aspects of developmental morphogenesis, notably the development of ectodermal sensory structures including eyes. Nematostella vectensis, the starlet sea anemone, has numerous Pax orthologs, many of which are expressed early during embryogenesis. The function of Pax genes in this eyeless cnidarian is unknown. Results Here, we show that PaxA, but not PaxC, plays a critical role in the development of cnidocytes in N. vectensis. Knockdown of PaxA results in a loss of developing cnidocytes and downregulation of numerous cnidocyte-specific genes, including a variant of the transcription factor Mef2. We also demonstrate that the co-expression of Mef2 in a subset of the PaxA-expressing cells is associated with the development with a second lineage of cnidocytes and show that knockdown of the neural progenitor gene SoxB2 results in downregulation of expression of PaxA, Mef2, and several cnidocyte-specific genes. Because PaxA is not co-expressed with SoxB2 at any time during cnidocyte development, we propose a simple model for cnidogenesis whereby a SoxB2-expressing progenitor cell population undergoes division to give rise to PaxA-expressing cnidocytes, some of which also express Mef2. Discussion The role of PaxA in cnidocyte development among hydrozoans has not been studied, but the conserved role of SoxB2 in regulating the fate of a progenitor cell that gives rise to neurons and cnidocytes in Nematostella and Hydractinia echinata suggests that this SoxB2/PaxA pathway may well be conserved across cnidarians.
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Affiliation(s)
- Leslie S Babonis
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL 32080 USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL 32080 USA.,Department of Biology, University of Florida, Gainesville, FL 32611 USA
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Servetnick MD, Steinworth B, Babonis LS, Simmons D, Salinas-Saavedra M, Martindale MQ. Cas9-mediated excision of Nematostella brachyury disrupts endoderm development, pharynx formation and oral-aboral patterning. Development 2017; 144:2951-2960. [PMID: 28705897 PMCID: PMC5592810 DOI: 10.1242/dev.145839] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 07/05/2017] [Indexed: 12/26/2022]
Abstract
The mesoderm is a key novelty in animal evolution, although we understand little of how the mesoderm arose. brachyury, the founding member of the T-box gene family, is a key gene in chordate mesoderm development. However, the brachyury gene was present in the common ancestor of fungi and animals long before mesoderm appeared. To explore ancestral roles of brachyury prior to the evolution of definitive mesoderm, we excised the gene using CRISPR/Cas9 in the diploblastic cnidarian Nematostella vectensis Nvbrachyury is normally expressed in precursors of the pharynx, which separates endoderm from ectoderm. In knockout embryos, the pharynx does not form, embryos fail to elongate, and endoderm organization, ectodermal cell polarity and patterning along the oral-aboral axis are disrupted. Expression of many genes both inside and outside the Nvbrachyury expression domain is affected, including downregulation of Wnt genes at the oral pole. Our results point to an ancient role for brachyury in morphogenesis, cell polarity and the patterning of both ectodermal and endodermal derivatives along the primary body axis.
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Affiliation(s)
- Marc D Servetnick
- Division of Biological Sciences, University of Washington Bothell, Bothell, WA 98011, USA
| | - Bailey Steinworth
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL 32080, USA
| | - Leslie S Babonis
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL 32080, USA
| | - David Simmons
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL 32080, USA
| | - Miguel Salinas-Saavedra
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL 32080, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL 32080, USA
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A bipolar role of the transcription factor ERG for cnidarian germ layer formation and apical domain patterning. Dev Biol 2017; 430:346-361. [PMID: 28818668 DOI: 10.1016/j.ydbio.2017.08.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/29/2017] [Accepted: 08/09/2017] [Indexed: 02/06/2023]
Abstract
Germ layer formation and axial patterning are biological processes that are tightly linked during embryonic development of most metazoans. In addition to canonical WNT, it has been proposed that ERK-MAPK signaling is involved in specifying oral as well as aboral territories in cnidarians. However, the effector and the molecular mechanism underlying latter phenomenon is unknown. By screening for potential effectors of ERK-MAPK signaling in both domains, we identified a member of the ETS family of transcription factors, Nverg that is bi-polarily expressed prior to gastrulation. We further describe the crucial role of NvERG for gastrulation, endomesoderm as well as apical domain formation. The molecular characterization of the obtained NvERG knock-down phenotype using previously described as well as novel potential downstream targets, provides evidence that a single transcription factor, NvERG, simultaneously controls expression of two different sets of downstream targets, leading to two different embryonic gene regulatory networks (GRNs) in opposite poles of the developing embryo. We also highlight the molecular interaction of cWNT and MEK/ERK/ERG signaling that provides novel insight into the embryonic axial organization of Nematostella, and show a cWNT repressive role of MEK/ERK/ERG signaling in segregating the endomesoderm in two sub-domains, while a common input of both pathways is required for proper apical domain formation. Taking together, we build the first blueprint for a global cnidarian embryonic GRN that is the foundation for additional gene specific studies addressing the evolution of embryonic and larval development.
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Ruocco N, Maria Fedele A, Costantini S, Romano G, Ianora A, Costantini M. New inter-correlated genes targeted by diatom-derived polyunsaturated aldehydes in the sea urchin Paracentrotus lividus. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 142:355-362. [PMID: 28437727 DOI: 10.1016/j.ecoenv.2017.04.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 06/07/2023]
Abstract
The marine environment is continually subjected to the action of stressors (including natural toxins), which represent a constant danger for benthic communities. In the present work using network analysis we identified ten genes on the basis of associated functions (FOXA, FoxG, GFI-1, nodal, JNK, OneCut/Hnf6, TAK1, tcf4, TCF7, VEGF) in the sea urchin Paracentrotus lividus, having key roles in different processes, such as embryonic development and asymmetry, cell fate specification, cell differentiation and morphogenesis, and skeletogenesis. These genes are correlated with three HUB genes, Foxo, Jun and HIF1A. Real Time qPCR revealed that during sea urchin embryonic development the expression levels of these genes were modulated by three diatom-derived polyunsaturated aldehydes (PUAs), decadienal, heptadienal and octadienal. Our findings show how changes in gene expression levels may be used as an early indicator of stressful conditions in the marine environment. The identification of key genes and the molecular pathways in which they are involved represents a fundamental tool in understanding how marine organisms try to afford protection against toxicants, to avoid deleterious consequences and irreversible damages. The genes identified in this work as targets for PUAs can be considered as possible biomarkers to detect exposure to different environmental pollutants.
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Affiliation(s)
- Nadia Ruocco
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy; Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, Pozzuoli, Naples 80078, Italy
| | - Anna Maria Fedele
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Susan Costantini
- Unità di Farmacologia Sperimentale, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, 80131 Napoli, Italy
| | - Giovanna Romano
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Adrianna Ianora
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Maria Costantini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
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Antagonistic BMP-cWNT signaling in the cnidarian Nematostella vectensis reveals insight into the evolution of mesoderm. Proc Natl Acad Sci U S A 2017; 114:E5608-E5615. [PMID: 28652368 DOI: 10.1073/pnas.1701607114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Gastrulation was arguably the key evolutionary innovation that enabled metazoan diversification, leading to the formation of distinct germ layers and specialized tissues. Differential gene expression specifying cell fate is governed by the inputs of intracellular and/or extracellular signals. Beta-catenin/Tcf and the TGF-beta bone morphogenetic protein (BMP) provide critical molecular signaling inputs during germ layer specification in bilaterian metazoans, but there has been no direct experimental evidence for a specific role for BMP signaling during endomesoderm specification in the early branching metazoan Nematostella vectensis (an anthozoan cnidarian). Using forward transcriptomics, we show that beta-catenin/Tcf signaling and BMP2/4 signaling provide differential inputs into the cnidarian endomesodermal gene regulatory network (GRN) at the onset of gastrulation (24 h postfertilization) in N. vectensis Surprisingly, beta-catenin/Tcf signaling and BMP2/4 signaling regulate a subset of common downstream target genes in the GRN in opposite ways, leading to the spatial and temporal differentiation of fields of cells in the developing embryo. Thus, we show that regulatory interactions between beta-catenin/Tcf signaling and BMP2/4 signaling are required for the specification and determination of different embryonic regions and the patterning of the oral-aboral axis in Nematostella We also show functionally that the conserved "kernel" of the bilaterian heart mesoderm GRN is operational in N. vectensis, which reinforces the hypothesis that the endoderm and mesoderm in triploblastic bilaterians evolved from the bifunctional endomesoderm (gastrodermis) of a diploblastic ancestor, and that slow rhythmic contractions might have been one of the earliest functions of mesodermal tissue.
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Abdol AM, Röttinger E, Jansson F, Kaandorp JA. A novel technique to combine and analyse spatial and temporal expression datasets: A case study with the sea anemone Nematostella vectensis to identify potential gene interactions. Dev Biol 2017; 428:204-214. [PMID: 28602952 DOI: 10.1016/j.ydbio.2017.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/28/2017] [Accepted: 06/02/2017] [Indexed: 11/30/2022]
Abstract
Understanding genetic interactions during early development of a given organism, is the first step toward unveiling gene regulatory networks (GRNs) that govern a biological process of interest. Predicting such interactions from large expression datasets by performing targeted knock-down/knock-out approaches is a challenging task. We use the currently available expression datasets (in situ hybridization images & qPCR time series) for a basal anthozoan the sea anemone N. vectensis to construct continuous spatiotemporal gene expression patterns during its early development. Moreover, by combining cluster results from each dataset we develop a method that provides testable hypotheses about potential genetic interactions. We show that the analysis of spatial gene expression patterns reveals functional regions of the embryo during the gastrulation. The clustering results from qPCR time series unveils significant temporal events and highlights genes potentially involved in N. vectensis gastrulation. Furthermore, we introduce a method for merging the clustering results from spatial and temporal datasets by which we can group genes that are expressed in the same region and at the time. We demonstrate that the merged clusters can be used to identify GRN interactions involved in various processes and to predict possible activators or repressors of any gene in the dataset. Finally, we validate our methods and results by predicting the repressor effect of NvErg on NvBra in the central domain during the gastrulation that has recently been confirmed by functional analysis.
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Affiliation(s)
- Amir M Abdol
- Computational Science Lab, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Nice, France.
| | - Fredrik Jansson
- Computational Science Lab, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Jaap A Kaandorp
- Computational Science Lab, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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Abstract
The leap from simple unicellularity to complex multicellularity remains one of life's major enigmas. The origins of metazoan developmental gene regulatory mechanisms are sought by analyzing gene regulation in extant eumetazoans, sponges, and unicellular organisms. The main hypothesis of this manuscript is that, developmental enhancers evolved from unicellular inducible promoters that diversified the expression of regulatory genes during metazoan evolution. Promoters and enhancers are functionally similar; both can regulate the transcription of distal promoters and both direct local transcription. Additionally, enhancers have experimentally characterized structural features that reveal their origin from inducible promoters. The distal co-operative regulation among promoters identified in unicellular opisthokonts possibly represents the precursor of distal regulation of promoters by enhancers. During metazoan evolution, constitutive-type promoters of regulatory genes would have acquired novel receptivity to distal regulatory inputs from promoters of inducible genes that eventually specialized as enhancers. The novel regulatory interactions would have caused constitutively expressed genes controlling differential gene expression in unicellular organisms to become themselves differentially expressed. The consequence of the novel regulatory interactions was that regulatory pathways of unicellular organisms became interlaced and ultimately evolved into the intricate developmental gene regulatory networks (GRNs) of extant metazoans.
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Affiliation(s)
- César Arenas-Mena
- Department of Biology, College of Staten Island and Graduate Center, The City University of New York (CUNY), Staten Island, NY 10314, USA
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Leclère L, Röttinger E. Diversity of Cnidarian Muscles: Function, Anatomy, Development and Regeneration. Front Cell Dev Biol 2017; 4:157. [PMID: 28168188 PMCID: PMC5253434 DOI: 10.3389/fcell.2016.00157] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/30/2016] [Indexed: 12/12/2022] Open
Abstract
The ability to perform muscle contractions is one of the most important and distinctive features of eumetazoans. As the sister group to bilaterians, cnidarians (sea anemones, corals, jellyfish, and hydroids) hold an informative phylogenetic position for understanding muscle evolution. Here, we review current knowledge on muscle function, diversity, development, regeneration and evolution in cnidarians. Cnidarian muscles are involved in various activities, such as feeding, escape, locomotion and defense, in close association with the nervous system. This variety is reflected in the large diversity of muscle organizations found in Cnidaria. Smooth epithelial muscle is thought to be the most common type, and is inferred to be the ancestral muscle type for Cnidaria, while striated muscle fibers and non-epithelial myocytes would have been convergently acquired within Cnidaria. Current knowledge of cnidarian muscle development and its regeneration is limited. While orthologs of myogenic regulatory factors such as MyoD have yet to be found in cnidarian genomes, striated muscle formation potentially involves well-conserved myogenic genes, such as twist and mef2. Although satellite cells have yet to be identified in cnidarians, muscle plasticity (e.g., de- and re-differentiation, fiber repolarization) in a regenerative context and its potential role during regeneration has started to be addressed in a few cnidarian systems. The development of novel tools to study those organisms has created new opportunities to investigate in depth the development and regeneration of cnidarian muscle cells and how they contribute to the regenerative process.
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Affiliation(s)
- Lucas Leclère
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV) Villefranche-sur-mer, France
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN) Nice, France
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Roux M, Dosseto A. From direct to indirect lithium targets: a comprehensive review of omics data. Metallomics 2017; 9:1326-1351. [DOI: 10.1039/c7mt00203c] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metal ions are critical to a wide range of biological processes.
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Affiliation(s)
| | - Anthony Dosseto
- Wollongong Isotope Geochronology Laboratory
- School of Earth & Environmental Sciences
- University of Wollongong
- Wollongong
- Australia
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Rentzsch F, Layden M, Manuel M. The cellular and molecular basis of cnidarian neurogenesis. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2016; 6. [PMID: 27882698 PMCID: PMC6680159 DOI: 10.1002/wdev.257] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 08/30/2016] [Accepted: 09/21/2016] [Indexed: 12/22/2022]
Abstract
Neurogenesis initiates during early development and it continues through later developmental stages and in adult animals to enable expansion, remodeling, and homeostasis of the nervous system. The generation of nerve cells has been analyzed in detail in few bilaterian model organisms, leaving open many questions about the evolution of this process. As the sister group to bilaterians, cnidarians occupy an informative phylogenetic position to address the early evolution of cellular and molecular aspects of neurogenesis and to understand common principles of neural development. Here we review studies in several cnidarian model systems that have revealed significant similarities and interesting differences compared to neurogenesis in bilaterian species, and between different cnidarian taxa. Cnidarian neurogenesis is currently best understood in the sea anemone Nematostella vectensis, where it includes epithelial neural progenitor cells that express transcription factors of the soxB and atonal families. Notch signaling regulates the number of these neural progenitor cells, achaete‐scute and dmrt genes are required for their further development and Wnt and BMP signaling appear to be involved in the patterning of the nervous system. In contrast to many vertebrates and Drosophila, cnidarians have a high capacity to generate neurons throughout their lifetime and during regeneration. Utilizing this feature of cnidarian biology will likely allow gaining new insights into the similarities and differences of embryonic and regenerative neurogenesis. The use of different cnidarian model systems and their expanding experimental toolkits will thus continue to provide a better understanding of evolutionary and developmental aspects of nervous system formation. WIREs Dev Biol 2017, 6:e257. doi: 10.1002/wdev.257 This article is categorized under:
Gene Expression and Transcriptional Hierarchies > Cellular Differentiation Signaling Pathways > Cell Fate Signaling Comparative Development and Evolution > Organ System Comparisons Between Species
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Affiliation(s)
- Fabian Rentzsch
- Sars Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | | | - Michaël Manuel
- Sorbonne Universités, UMPC Univ Paris 06, CNRS, Evolution Paris-Seine, Institut de Biologie Paris-Seine (IBPS), Paris, France
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Yasuoka Y, Shinzato C, Satoh N. The Mesoderm-Forming Gene brachyury Regulates Ectoderm-Endoderm Demarcation in the Coral Acropora digitifera. Curr Biol 2016; 26:2885-2892. [PMID: 27693135 DOI: 10.1016/j.cub.2016.08.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 07/25/2016] [Accepted: 08/04/2016] [Indexed: 12/27/2022]
Abstract
Blastoporal expression of the T-box transcription factor gene brachyury is conserved in most metazoans [1, 2]. Its role in mesoderm formation has been intensively studied in vertebrates [3-6]. However, its fundamental function near the blastopore is poorly understood in other phyla. Cnidarians are basal metazoans that are important for understanding evolution of metazoan body plans [7, 8]. Because they lack mesoderm, they have been used to investigate the evolutionary origins of mesoderm [1, 9-11]. Here, we focus on corals, a primitive clade of cnidarians that diverged from sea anemones ∼500 mya [12]. We developed a microinjection method for coral eggs to examine Brachyury functions during embryogenesis of the scleractinian coral, Acropora digitifera. Because Acropora embryos undergo pharynx formation after the blastopore closes completely [13-15], they are useful to understand Brachyury functions in gastrulation movement and pharynx formation. We show that blastoporal expression of brachyury is directly activated by Wnt/β-catenin signaling in the ectoderm of coral embryos, indicating that the regulatory axis from Wnt/β-catenin signaling to brachyury is highly conserved among eumetazoans. Loss-of-function analysis demonstrated that Brachyury is required for pharynx formation but not for gastrulation movement. Genome-wide transcriptome analysis demonstrated that genes positively regulated by Brachyury are expressed in the ectoderm of Acropora gastrulae, while negatively regulated genes are in endoderm. Therefore, germ layer demarcation around the blastopore appears to be the evolutionarily conserved role of Brachyury during gastrulation. Compared with Brachyury functions in vertebrate mesoderm-ectoderm and mesoderm-endoderm demarcation [4-6], our results suggest that the vertebrate-type mesoderm may have originated from brachyury-expressing ectoderm adjacent to endoderm.
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Affiliation(s)
- Yuuri Yasuoka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan.
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
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Henry JQ, Lyons DC. Molluscan models: Crepidula fornicata. Curr Opin Genet Dev 2016; 39:138-148. [PMID: 27526387 DOI: 10.1016/j.gde.2016.05.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 05/16/2016] [Accepted: 05/30/2016] [Indexed: 12/11/2022]
Abstract
Gastropod snails in the genus Crepidula have emerged as model systems for studying a metazoan super clade, the Spiralia. Recent work on one species in particular, Crepidula fornicata, has produced high-resolution cell lineage fate maps, details of morphogenetic events during gastrulation, key insights into the molecular underpinnings of early development, and the first demonstration of CRISPR/Cas9 genome editing in the Spiralia. Furthermore, invasive species of Crepidula are a significant ecological threat, while one of these, C. fornicata, is also being harvested for food. This review highlights progress towards developing these animals as models for evolutionary, developmental, and ecological studies. Such studies have contributed greatly to our understanding of biology in a major clade of bilaterians. This information may also help us to control and cultivate these snails.
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Affiliation(s)
- Jonathan Q Henry
- University of Illinois, Department of Cell & Developmental Biology, 601 South Goodwin Avenue, Urbana, IL 61801, United States.
| | - Deirdre C Lyons
- University of California, San Diego, Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, United States.
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Layden MJ, Johnston H, Amiel AR, Havrilak J, Steinworth B, Chock T, Röttinger E, Martindale MQ. MAPK signaling is necessary for neurogenesis in Nematostella vectensis. BMC Biol 2016; 14:61. [PMID: 27480076 PMCID: PMC4968017 DOI: 10.1186/s12915-016-0282-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 07/04/2016] [Indexed: 11/16/2022] Open
Abstract
Background The nerve net of Nematostella is generated using a conserved cascade of neurogenic transcription factors. For example, NvashA, a homolog of the achaete-scute family of basic helix-loop-helix transcription factors, is necessary and sufficient to specify a subset of embryonic neurons. However, positive regulators required for the expression of neurogenic transcription factors remain poorly understood. Results We show that treatment with the MEK/MAPK inhibitor U0126 severely reduces the expression of known neurogenic genes, Nvath-like, NvsoxB(2), and NvashA, and known markers of differentiated neurons, suggesting that MAPK signaling is necessary for neural development. Interestingly, ectopic NvashA fails to rescue the expression of neural markers in U0126-treated animals. Double fluorescence in situ hybridization and transgenic analysis confirmed that NvashA targets represent both unique and overlapping populations of neurons. Finally, we used a genome-wide microarray to identify additional patterning genes downstream of MAPK that might contribute to neurogenesis. We identified 18 likely neural transcription factors, and surprisingly identified ~40 signaling genes and transcription factors that are expressed in either the aboral domain or animal pole that gives rise to the endomesoderm at late blastula stages. Conclusions Together, our data suggest that MAPK is a key early regulator of neurogenesis, and that it is likely required at multiple steps. Initially, MAPK promotes neurogenesis by positively regulating expression of NvsoxB(2), Nvath-like, and NvashA. However, we also found that MAPK is necessary for the activity of the neurogenic transcription factor NvashA. Our forward molecular approach provided insight about the mechanisms of embryonic neurogenesis. For instance, NvashA suppression of Nvath-like suggests that inhibition of progenitor identity is an active process in newly born neurons, and we show that downstream targets of NvashA reflect multiple neural subtypes rather than a uniform neural fate. Lastly, analysis of the MAPK targets in the early embryo suggests that MAPK signaling is critical not only to neurogenesis, but also endomesoderm formation and aboral patterning. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0282-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael J Layden
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
| | - Hereroa Johnston
- Université Nice Sophia Antipolis UMR 7284, CNRS UMR 7284, INSERM U1081, Institute for Research on Cancer and Aging, Nice, France
| | - Aldine R Amiel
- Université Nice Sophia Antipolis UMR 7284, CNRS UMR 7284, INSERM U1081, Institute for Research on Cancer and Aging, Nice, France
| | - Jamie Havrilak
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Bailey Steinworth
- The Whitney Marine Laboratory for Marine Science, University of Florida, St. Augustine, Florida, USA
| | - Taylor Chock
- The Whitney Marine Laboratory for Marine Science, University of Florida, St. Augustine, Florida, USA
| | - Eric Röttinger
- Université Nice Sophia Antipolis UMR 7284, CNRS UMR 7284, INSERM U1081, Institute for Research on Cancer and Aging, Nice, France
| | - Mark Q Martindale
- The Whitney Marine Laboratory for Marine Science, University of Florida, St. Augustine, Florida, USA.
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Perry KJ, Lyons DC, Truchado-Garcia M, Fischer AHL, Helfrich LW, Johansson KB, Diamond JC, Grande C, Henry JQ. Deployment of regulatory genes during gastrulation and germ layer specification in a model spiralian mollusc Crepidula. Dev Dyn 2016. [PMID: 26197970 DOI: 10.1002/dvdy.24308] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND During gastrulation, endoderm and mesoderm are specified from a bipotential precursor (endomesoderm) that is argued to be homologous across bilaterians. Spiralians also generate mesoderm from ectodermal precursors (ectomesoderm), which arises near the blastopore. While a conserved gene regulatory network controls specification of endomesoderm in deuterostomes and ecdysozoans, little is known about genes controlling specification or behavior of either source of spiralian mesoderm or the digestive tract. RESULTS Using the mollusc Crepidula, we examined conserved regulatory factors and compared their expression to fate maps to score expression in the germ layers, blastopore lip, and digestive tract. Many genes were expressed in both ecto- and endomesoderm, but only five were expressed in ectomesoderm exclusively. The latter may contribute to epithelial-to-mesenchymal transition seen in ectomesoderm. CONCLUSIONS We present the first comparison of genes expressed during spiralian gastrulation in the context of high-resolution fate maps. We found variation of genes expressed in the blastopore lip, mouth, and cells that will form the anus. Shared expression of many genes in both mesodermal sources suggests that components of the conserved endomesoderm program were either co-opted for ectomesoderm formation or that ecto- and endomesoderm are derived from a common mesodermal precursor that became subdivided into distinct domains during evolution.
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Affiliation(s)
- Kimberly J Perry
- University of Illinois, Department of Cell and Developmental Biology, Urbana, Illinois
| | | | - Marta Truchado-Garcia
- Departamento de Biología Molecular and Centro de Biología Molecular, "Severo Ochoa" (CSIC, Universidad Autónoma de Madrid), Madrid, Spain
| | - Antje H L Fischer
- Department of Metabolic Biochemistry, Ludwig-Maximilians-University, Munich, Germany.,Marine Biological Laboratory, Woods Hole, Massachusetts
| | | | - Kimberly B Johansson
- Marine Biological Laboratory, Woods Hole, Massachusetts.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts
| | | | - Cristina Grande
- Departamento de Biología Molecular and Centro de Biología Molecular, "Severo Ochoa" (CSIC, Universidad Autónoma de Madrid), Madrid, Spain
| | - Jonathan Q Henry
- University of Illinois, Department of Cell and Developmental Biology, Urbana, Illinois
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