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Karakostis K, Costa C, Zito F, Brümmer F, Matranga V. Characterization of an Alpha Type Carbonic Anhydrase from Paracentrotus lividus Sea Urchin Embryos. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:384-395. [PMID: 27230618 DOI: 10.1007/s10126-016-9701-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/10/2016] [Indexed: 06/05/2023]
Abstract
Carbonic anhydrases (CA) are zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide to bicarbonate. In the sea urchin, CA has a role in the formation of the calcitic skeleton during embryo development. Here, we report a newly identified mRNA sequence from embryos of the sea urchin Paracentrotus lividus, referred to as Pl-can. The complete coding sequence was identified with the aid of both EST databases and experimental procedures. Pl-CAN is a 447 aa-long protein, with an estimated molecular mass of 48.5 kDa and an isoelectric point of 6.83. The in silico study of functional domains showed, in addition to the alpha type CA-specific domain, the presence of an unexpected glycine-rich region at the N-terminal of the molecule. This is not found in any other species described so far, but probably it is restricted to the sea urchins. The phylogenetic analysis indicated that Pl-CAN is evolutionarily closer to human among chordates than to other species. The putative role(s) of the identified domains is discussed. The Pl-can temporal and spatial expression profiles, analyzed throughout embryo development by comparative qPCR and whole-mount in situ hybridization (WMISH), showed that Pl-can mRNA is specifically expressed in the primary mesenchyme cells (PMC) of the embryo and levels increase along with the growth of the embryonic skeleton, reaching a peak at the pluteus stage. A recombinant fusion protein was produced in E. coli and used to raise specific antibodies in mice recognized the endogenous Pl-CAN by Western blot in embryo extracts from gastrula and pluteus.
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Affiliation(s)
- Konstantinos Karakostis
- Institute of Biomedicine and Molecular Immunology "A. Monroy", National Research Council, Via Ugo La Malfa, 153-90146, Palermo, Italy
- Institute for Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
- INSERM - UMR 1162, Institute de Génétique Moléculaire, Hôpital St. Louis, 27 rue Juliette Dodu, 75010, Paris, France
| | - Caterina Costa
- Institute of Biomedicine and Molecular Immunology "A. Monroy", National Research Council, Via Ugo La Malfa, 153-90146, Palermo, Italy.
| | - Francesca Zito
- Institute of Biomedicine and Molecular Immunology "A. Monroy", National Research Council, Via Ugo La Malfa, 153-90146, Palermo, Italy
| | - Franz Brümmer
- Institute for Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Valeria Matranga
- Institute of Biomedicine and Molecular Immunology "A. Monroy", National Research Council, Via Ugo La Malfa, 153-90146, Palermo, Italy
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Sharmankina VV, Kiselev KV. Expression of SM30(A–F) genes encoding spicule matrix proteins in intact and damaged sea urchin Strongylocentrotus intermedius at the six-armed pluteus. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416020125] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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53
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Piacentino ML, Chung O, Ramachandran J, Zuch DT, Yu J, Conaway EA, Reyna AE, Bradham CA. Zygotic LvBMP5-8 is required for skeletal patterning and for left–right but not dorsal–ventral specification in the sea urchin embryo. Dev Biol 2016; 412:44-56. [DOI: 10.1016/j.ydbio.2016.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 01/31/2016] [Accepted: 02/18/2016] [Indexed: 01/25/2023]
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Israel JW, Martik ML, Byrne M, Raff EC, Raff RA, McClay DR, Wray GA. Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris. PLoS Biol 2016; 14:e1002391. [PMID: 26943850 PMCID: PMC4778923 DOI: 10.1371/journal.pbio.1002391] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/26/2016] [Indexed: 01/08/2023] Open
Abstract
The ecologically significant shift in developmental strategy from planktotrophic (feeding) to lecithotrophic (nonfeeding) development in the sea urchin genus Heliocidaris is one of the most comprehensively studied life history transitions in any animal. Although the evolution of lecithotrophy involved substantial changes to larval development and morphology, it is not known to what extent changes in gene expression underlie the developmental differences between species, nor do we understand how these changes evolved within the context of the well-defined gene regulatory network (GRN) underlying sea urchin development. To address these questions, we used RNA-seq to measure expression dynamics across development in three species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph H. tuberculata, and an outgroup planktotroph Lytechinus variegatus. Using well-established statistical methods, we developed a novel framework for identifying, quantifying, and polarizing evolutionary changes in gene expression profiles across the transcriptome and within the GRN. We found that major changes in gene expression profiles were more numerous during the evolution of lecithotrophy than during the persistence of planktotrophy, and that genes with derived expression profiles in the lecithotroph displayed specific characteristics as a group that are consistent with the dramatically altered developmental program in this species. Compared to the transcriptome, changes in gene expression profiles within the GRN were even more pronounced in the lecithotroph. We found evidence for conservation and likely divergence of particular GRN regulatory interactions in the lecithotroph, as well as significant changes in the expression of genes with known roles in larval skeletogenesis. We further use coexpression analysis to identify genes of unknown function that may contribute to both conserved and derived developmental traits between species. Collectively, our results indicate that distinct evolutionary processes operate on gene expression during periods of life history conservation and periods of life history divergence, and that this contrast is even more pronounced within the GRN than across the transcriptome as a whole.
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Affiliation(s)
- Jennifer W. Israel
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Megan L. Martik
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Maria Byrne
- Schools of Medical and Biological Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Elizabeth C. Raff
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Rudolf A. Raff
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - David R. McClay
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Gregory A. Wray
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
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Karakostis K, Zanella-Cléon I, Immel F, Guichard N, Dru P, Lepage T, Plasseraud L, Matranga V, Marin F. A minimal molecular toolkit for mineral deposition? Biochemistry and proteomics of the test matrix of adult specimens of the sea urchin Paracentrotus lividus. J Proteomics 2016; 136:133-44. [DOI: 10.1016/j.jprot.2016.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/22/2015] [Accepted: 01/04/2016] [Indexed: 12/16/2022]
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Koga H, Fujitani H, Morino Y, Miyamoto N, Tsuchimoto J, Shibata TF, Nozawa M, Shigenobu S, Ogura A, Tachibana K, Kiyomoto M, Amemiya S, Wada H. Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton. PLoS One 2016; 11:e0149067. [PMID: 26866800 PMCID: PMC4750990 DOI: 10.1371/journal.pone.0149067] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/27/2016] [Indexed: 11/19/2022] Open
Abstract
Over the course of evolution, the acquisition of novel structures has ultimately led to wide variation in morphology among extant multicellular organisms. Thus, the origins of genetic systems for new morphological structures are a subject of great interest in evolutionary biology. The larval skeleton is a novel structure acquired in some echinoderm lineages via the activation of the adult skeletogenic machinery. Previously, VEGF signaling was suggested to have played an important role in the acquisition of the larval skeleton. In the present study, we compared expression patterns of Alx genes among echinoderm classes to further explore the factors involved in the acquisition of a larval skeleton. We found that the alx1 gene, originally described as crucial for sea urchin skeletogenesis, may have also played an essential role in the evolution of the larval skeleton. Unlike those echinoderms that have a larval skeleton, we found that alx1 of starfish was barely expressed in early larvae that have no skeleton. When alx1 overexpression was induced via injection of alx1 mRNA into starfish eggs, the expression patterns of certain genes, including those possibly involved in skeletogenesis, were altered. This suggested that a portion of the skeletogenic program was induced solely by alx1. However, we observed no obvious external phenotype or skeleton. We concluded that alx1 was necessary but not sufficient for the acquisition of the larval skeleton, which, in fact, requires several genetic events. Based on these results, we discuss how the larval expression of alx1 contributed to the acquisition of the larval skeleton in the putative ancestral lineage of echinoderms.
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Affiliation(s)
- Hiroyuki Koga
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Haruka Fujitani
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yoshiaki Morino
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Norio Miyamoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Jun Tsuchimoto
- Division of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
- Institute for Molecular Science of Medicine, Aichi Medical University, Nagakute, Japan
| | | | - Masafumi Nozawa
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
- Department of Genetics, The Graduate University for Advanced Studies, Mishima, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki, Japan
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
| | - Atsushi Ogura
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Kazunori Tachibana
- Graduate School of Bioscience, Tokyo Institute of Technology, Yokohama, Japan
| | - Masato Kiyomoto
- Marine and Coastal Research Center, Ochanomizu University, Tateyama, Japan
| | - Shonan Amemiya
- Marine and Coastal Research Center, Ochanomizu University, Tateyama, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Research and Education Center of Natural Sciences, Keio University, Yokohama, Japan
| | - Hiroshi Wada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Dylus DV, Czarkwiani A, Stångberg J, Ortega-Martinez O, Dupont S, Oliveri P. Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks. EvoDevo 2016; 7:2. [PMID: 26759711 PMCID: PMC4709884 DOI: 10.1186/s13227-015-0039-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 12/21/2015] [Indexed: 11/20/2022] Open
Abstract
Background The evolutionary mechanisms involved in shaping complex gene regulatory networks (GRN) that encode for morphologically similar structures in distantly related animals remain elusive. In this context, echinoderm larval skeletons found in brittle stars and sea urchins provide an ideal system. Here, we characterize for the first time the development of the larval skeleton in the ophiuroid Amphiura filiformis and compare it systematically with its counterpart in sea urchin. Results We show that ophiuroids and euechinoids, that split at least 480 Million years ago (Mya), have remarkable similarities in tempo and mode of skeletal development. Despite morphological and ontological similarities, our high-resolution study of the dynamics of genetic regulatory states in A. filiformis highlights numerous differences in the architecture of their underlying GRNs. Importantly, the A.filiformispplx, the closest gene to the sea urchin double negative gate (DNG) repressor pmar1, fails to drive the skeletogenic program in sea urchin, showing important evolutionary differences in protein function. hesC, the second repressor of the DNG, is co-expressed with most of the genes that are repressed in sea urchin, indicating the absence of direct repression of tbr, ets1/2, and delta in A. filiformis. Furthermore, the absence of expression in later stages of brittle star skeleton development of key regulatory genes, such as foxb and dri, shows significantly different regulatory states. Conclusion Our data fill up an important gap in the picture of larval mesoderm in echinoderms and allows us to explore the evolutionary implications relative to the recently established phylogeny of echinoderm classes. In light of recent studies on other echinoderms, our data highlight a high evolutionary plasticity of the same nodes throughout evolution of echinoderm skeletogenesis. Finally, gene duplication, protein function diversification, and cis-regulatory element evolution all contributed to shape the regulatory program for larval skeletogenesis in different branches of echinoderms. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0039-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David Viktor Dylus
- Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK ; CoMPLEX/SysBio, UCL, Gower Street, London, WC1E 6BT UK ; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Anna Czarkwiani
- Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK
| | - Josefine Stångberg
- Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK ; Research Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Olga Ortega-Martinez
- Department of Biological and Environmental Sciences, Sven Lovén Centre for Marine Sciences, University of Gothenburg, Kristineberg 566, 451 78 Fiskebäckskil, Sweden
| | - Sam Dupont
- Department of Biological and Environmental Sciences, Sven Lovén Centre for Marine Sciences, University of Gothenburg, Kristineberg 566, 451 78 Fiskebäckskil, Sweden
| | - Paola Oliveri
- Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK
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58
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Abstract
In the sea urchin morphogenesis follows extensive molecular specification. The specification controls the many morphogenetic events and these, in turn, precede patterning steps that establish the larval body plan. To understand how the embryo is built it was necessary to understand those series of molecular steps. Here an example of the historical sequence of those discoveries is presented as it unfolded over the last 50 years, the years during which major progress in understanding development of many animals and plants was documented by CTDB. In sea urchin development a rich series of experimental studies first established many of the phenomenological components of skeletal morphogenesis and patterning without knowledge of the molecular components. The many discoveries of transcription factors, signals, and structural proteins that contribute to the shape of the endoskeleton of the sea urchin larva then followed as molecular tools became available. A number of transcription factors and signals were discovered that were necessary for specification, morphogenesis, and patterning. Perturbation of the transcription factors and signals provided the means for assembling models of the gene regulatory networks used for specification and controlled the subsequent morphogenetic events. The earlier experimental information informed perturbation experiments that asked how patterning worked. As a consequence it was learned that ectoderm provides a series of patterning signals to the skeletogenic cells and as a consequence the skeletogenic cells secrete a highly patterned skeleton based on their ability to genotypically decode the localized reception of several signals. We still do not understand the complexity of the signals received by the skeletogenic cells, nor do we understand in detail how the genotypic information shapes the secreted skeletal biomineral, but the current knowledge at least outlines the sequence of events and provides a useful template for future discoveries.
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Affiliation(s)
- David R McClay
- Department of Biology, Duke University, Durham, North Carolina, USA.
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59
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Barsi JC, Tu Q, Calestani C, Davidson EH. Genome-wide assessment of differential effector gene use in embryogenesis. Development 2015; 142:3892-901. [PMID: 26417044 DOI: 10.1242/dev.127746] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 09/16/2015] [Indexed: 01/12/2023]
Abstract
Six different populations of cells were isolated by fluorescence-activated cell sorting from disaggregated late blastula- and gastrula-stage sea urchin embryos according to the regulatory states expressed in these cells, as reported by recombineered bacterial artificial chromosomes producing fluorochromes. Transcriptomes recovered from these embryonic cell populations revealed striking, early differential expression of large cohorts of effector genes. The six cell populations were presumptive pigment cells, presumptive neurogenic cells, presumptive skeletogenic cells, cells from the stomodeal region of the oral ectoderm, ciliated band cells and cells from the endoderm/ectoderm boundary that will give rise both to hindgut and to border ectoderm. Transcriptome analysis revealed that each of these domains specifically expressed several hundred effector genes at significant levels. Annotation indicated the qualitative individuality of the functional nature of each cell population, even though they were isolated from embryos only 1-2 days old. In no case was more than a tiny fraction of the transcripts enriched in one population also enriched in any other of the six populations studied. As was particularly clear in the cases of the presumptive pigment, neurogenic and skeletogenic cells, all three of which represent precociously differentiating cell types of this embryo, most specifically expressed genes of given cell types are not significantly expressed at all in the other cell types. Thus, at the effector gene level, a dramatic, cell type-specific pattern of differential gene regulation is established well before any significant embryonic morphogenesis has occurred.
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Affiliation(s)
- Julius C Barsi
- Division of Biology and Bioengineering, Caltech, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Qiang Tu
- Division of Biology and Bioengineering, Caltech, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Cristina Calestani
- Department of Biology, Valdosta State University, Valdosta, GA 31698, USA
| | - Eric H Davidson
- Division of Biology and Bioengineering, Caltech, 1200 East California Boulevard, Pasadena, CA 91125, USA
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60
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Stepicheva NA, Song JL. microRNA-31 modulates skeletal patterning in the sea urchin embryo. Development 2015; 142:3769-80. [PMID: 26400092 DOI: 10.1242/dev.127969] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/03/2015] [Indexed: 01/25/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that repress the translation and reduce the stability of target mRNAs in animal cells. microRNA-31 (miR-31) is known to play a role in cancer, bone formation and lymphatic development. However, studies to understand the function of miR-31 in embryogenesis have been limited. We examined the regulatory role of miR-31 in early development using the sea urchin as a model. miR-31 is expressed at all stages of development and its knockdown (KD) disrupts the patterning and function of primary mesenchyme cells (PMCs), which form the embryonic skeleton spicules. We identified that miR-31 directly represses Pmar1, Alx1, Snail and VegfR7 within the PMC gene regulatory network using reporter constructs. Further, blocking the miR-31-mediated repression of Alx1 and/or VegfR7 in the developing embryo resulted in defects in PMC patterning and skeletogenesis. The majority of the mislocalized PMCs in miR-31 KD embryos did not express VegfR10, indicating that miR-31 regulates VegfR gene expression within PMCs. In addition, miR-31 indirectly suppresses Vegf3 expression in the ectoderm. These results indicate that miR-31 coordinately suppresses genes within the PMCs and in the ectoderm to impact PMC patterning and skeletogenesis. This study identifies the novel function and molecular mechanism of miR-31-mediated regulation in the developing embryo.
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Affiliation(s)
- Nadezda A Stepicheva
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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61
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Schatzberg D, Lawton M, Hadyniak SE, Ross EJ, Carney T, Beane WS, Levin M, Bradham CA. H(+)/K(+) ATPase activity is required for biomineralization in sea urchin embryos. Dev Biol 2015; 406:259-70. [PMID: 26282894 DOI: 10.1016/j.ydbio.2015.08.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/26/2015] [Accepted: 08/13/2015] [Indexed: 12/31/2022]
Abstract
The bioelectrical signatures associated with regeneration, wound healing, development, and cancer are changes in the polarization state of the cell that persist over long durations, and are mediated by ion channel activity. To identify physiologically relevant bioelectrical changes that occur during normal development of the sea urchin Lytechinus variegatus, we tested a range of ion channel inhibitors, and thereby identified SCH28080, a chemical inhibitor of the H(+)/K(+) ATPase (HKA), as an inhibitor of skeletogenesis. In sea urchin embryos, the primary mesodermal lineage, the PMCs, produce biomineral in response to signals from the ectoderm. However, in SCH28080-treated embryos, aside from randomization of the left-right axis, the ectoderm is normally specified and differentiated, indicating that the block to skeletogenesis observed in SCH28080-treated embryos is PMC-specific. HKA inhibition did not interfere with PMC specification, and was sufficient to block continuing biomineralization when embryos were treated with SCH28080 after the initiation of skeletogenesis, indicating that HKA activity is continuously required during biomineralization. Ion concentrations and voltage potential were abnormal in the PMCs in SCH28080-treated embryos, suggesting that these bioelectrical abnormalities prevent biomineralization. Our results indicate that this effect is due to the inhibition of amorphous calcium carbonate precipitation within PMC vesicles.
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Affiliation(s)
| | - Matthew Lawton
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Erik J Ross
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Tamara Carney
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Wendy S Beane
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, USA
| | - Michael Levin
- Department of Biology, Tufts University, Medford, MA 02155, USA
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Evolutionary rewiring of gene regulatory network linkages at divergence of the echinoid subclasses. Proc Natl Acad Sci U S A 2015; 112:E4075-84. [PMID: 26170318 DOI: 10.1073/pnas.1509845112] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Evolution of animal body plans occurs with changes in the encoded genomic programs that direct development, by alterations in the structure of encoded developmental gene-regulatory networks (GRNs). However, study of this most fundamental of evolutionary processes requires experimentally tractable, phylogenetically divergent organisms that differ morphologically while belonging to the same monophyletic clade, plus knowledge of the relevant GRNs operating in at least one of the species. These conditions are met in the divergent embryogenesis of the two extant, morphologically distinct, echinoid (sea urchin) subclasses, Euechinoidea and Cidaroidea, which diverged from a common late Paleozoic ancestor. Here we focus on striking differences in the mode of embryonic skeletogenesis in a euechinoid, the well-known model Strongylocentrotus purpuratus (Sp), vs. the cidaroid Eucidaris tribuloides (Et). At the level of descriptive embryology, skeletogenesis in Sp and Et has long been known to occur by distinct means. The complete GRN controlling this process is known for Sp. We carried out targeted functional analyses on Et skeletogenesis to identify the presence, or demonstrate the absence, of specific regulatory linkages and subcircuits key to the operation of the Sp skeletogenic GRN. Remarkably, most of the canonical design features of the Sp skeletogenic GRN that we examined are either missing or operate differently in Et. This work directly implies a dramatic reorganization of genomic regulatory circuitry concomitant with the divergence of the euechinoids, which began before the end-Permian extinction.
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63
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Rebeiz M, Patel NH, Hinman VF. Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development. Annu Rev Genomics Hum Genet 2015; 16:103-31. [PMID: 26079281 DOI: 10.1146/annurev-genom-091212-153423] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The molecular and genetic basis for the evolution of anatomical diversity is a major question that has inspired evolutionary and developmental biologists for decades. Because morphology takes form during development, a true comprehension of how anatomical structures evolve requires an understanding of the evolutionary events that alter developmental genetic programs. Vast gene regulatory networks (GRNs) that connect transcription factors to their target regulatory sequences control gene expression in time and space and therefore determine the tissue-specific genetic programs that shape morphological structures. In recent years, many new examples have greatly advanced our understanding of the genetic alterations that modify GRNs to generate newly evolved morphologies. Here, we review several aspects of GRN evolution, including their deep preservation, their mechanisms of alteration, and how they originate to generate novel developmental programs.
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Affiliation(s)
- Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260;
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64
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Suzuki N, Ogiso S, Yachiguchi K, Kawabe K, Makino F, Toriba A, Kiyomoto M, Sekiguchi T, Tabuchi Y, Kondo T, Kitamura KI, Hong CS, Srivastav AK, Oshima Y, Hattori A, Hayakawa K. Monohydroxylated polycyclic aromatic hydrocarbons influence spicule formation in the early development of sea urchins (Hemicentrotus pulcherrimus). Comp Biochem Physiol C Toxicol Pharmacol 2015; 171:55-60. [PMID: 25737366 DOI: 10.1016/j.cbpc.2015.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 02/14/2015] [Accepted: 02/24/2015] [Indexed: 11/26/2022]
Abstract
We previously demonstrated that monohydroxylated polycyclic aromatic hydrocarbons (OHPAHs), which are metabolites of polycyclic aromatic hydrocarbons (PAHs), act on calcified tissue and suppress osteoblastic and osteoclastic activity in the scales of teleost fish. The compounds may possibly influence other calcified tissues. Thus, the present study noted the calcified spicules in sea urchins and examined the effect of both PAHs and OHPAHs on spicule formation during the embryogenesis of sea urchins. After fertilization, benz[a]anthracene (BaA) and 4-hydroxybenz[a]anthracene (4-OHBaA) were added to seawater at concentrations of 10(-8) and 10(-7) M and kept at 18 °C. The influence of the compound was given at the time of the pluteus larva. At this stage, the length of the spicule was significantly suppressed by 4-OHBaA (10(-8) and 10(-7) M). BaA (10(-7) M) decreased the length of the spicule significantly, while the length did not change with BaA (10(-8) M). The expression of mRNAs (spicule matrix protein and transcription factors) in the 4-OHBaA (10(-7) M)-treated embryos was more strongly inhibited than were those in the BaA (10(-7) M)-treated embryos. This is the first study to demonstrate that OHPAHs suppress spicule formation in sea urchins.
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Affiliation(s)
- Nobuo Suzuki
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Housu-gun, Ishikawa 927-0553, Japan.
| | - Shouzo Ogiso
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Housu-gun, Ishikawa 927-0553, Japan
| | - Koji Yachiguchi
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Housu-gun, Ishikawa 927-0553, Japan
| | - Kimi Kawabe
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma, Ishikawa 920-1192, Japan
| | - Fumiya Makino
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma, Ishikawa 920-1192, Japan
| | - Akira Toriba
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma, Ishikawa 920-1192, Japan
| | - Masato Kiyomoto
- Marine and Coastal Research Center, Ochanomizu University, Tateyama, Chiba 294-0301, Japan
| | - Toshio Sekiguchi
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Housu-gun, Ishikawa 927-0553, Japan
| | - Yoshiaki Tabuchi
- Division of Molecular Genetics Research, Life Science Research Center, University of Toyama, Toyama 930-0194, Japan
| | - Takashi Kondo
- Department of Radiological Sciences, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Kei-ichiro Kitamura
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa 920-0942, Japan
| | - Chun-Sang Hong
- Research and Business Foundation, Hankuk University of Foreign Studies, 81, Oedae-ro, Mohyeon-myeon, Cheoin-gu, Yongin-si, Gyeonggi-do 449-791, Republic of Korea
| | - Ajai K Srivastav
- Department of Zoology, D.D.U. Gorakhpur University, Gorakhpur 273-009, India
| | - Yuji Oshima
- Faculty of Agriculture, Kyushu University, Hakozaki, Fukuoka 812-8581, Japan
| | - Atsuhiko Hattori
- Department of Biology, College of Liberal Arts and Sciences, Tokyo Medical Dental University, Ichikawa, Chiba 272-0827, Japan
| | - Kazuichi Hayakawa
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma, Ishikawa 920-1192, Japan
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Gao F, Thompson JR, Petsios E, Erkenbrack E, Moats RA, Bottjer DJ, Davidson EH. Juvenile skeletogenesis in anciently diverged sea urchin clades. Dev Biol 2015; 400:148-58. [PMID: 25641694 DOI: 10.1016/j.ydbio.2015.01.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/19/2014] [Accepted: 01/20/2015] [Indexed: 10/24/2022]
Abstract
Mechanistic understanding of evolutionary divergence in animal body plans devolves from analysis of those developmental processes that, in forms descendant from a common ancestor, are responsible for their morphological differences. The last common ancestor of the two extant subclasses of sea urchins, i.e., euechinoids and cidaroids, existed well before the Permian/Triassic extinction (252 mya). Subsequent evolutionary divergence of these clades offers in principle a rare opportunity to solve the developmental regulatory events underlying a defined evolutionary divergence process. Thus (i) there is an excellent and fairly dense (if yet incompletely analyzed) fossil record; (ii) cladistically confined features of the skeletal structures of modern euechinoid and cidaroid sea urchins are preserved in fossils of ancestral forms; (iii) euechinoids and cidaroids are among current laboratory model systems in molecular developmental biology (here Strongylocentrotus purpuratus [Sp] and Eucidaris tribuloides [Et]); (iv) skeletogenic specification in sea urchins is uncommonly well understood at the causal level of interactions of regulatory genes with one another, and with known skeletogenic effector genes, providing a ready arsenal of available molecular tools. Here we focus on differences in test and perignathic girdle skeletal morphology that distinguish all modern euechinoid from all modern cidaroid sea urchins. We demonstrate distinct canonical test and girdle morphologies in juveniles of both species by use of SEM and X-ray microtomography. Among the sharply distinct morphological features of these clades are the internal skeletal structures of the perignathic girdle to which attach homologous muscles utilized for retraction and protraction of Aristotles׳ lantern and its teeth. We demonstrate that these structures develop de novo between one and four weeks after metamorphosis. In order to study the underlying developmental processes, a method of section whole mount in situ hybridization was adapted. This method displays current gene expression in the developing test and perignathic girdle skeletal elements of both Sp and Et juveniles. Active, specific expression of the sm37 biomineralization gene in these muscle attachment structures accompanies morphogenetic development of these clade-specific features in juveniles of both species. Skeletogenesis at these clade-specific muscle attachment structures displays molecular earmarks of the well understood embryonic skeletogenic GRN: thus the upstream regulatory gene alx1 and the gene encoding the vegfR signaling receptor are both expressed at the sites where they are formed. This work opens the way to analysis of the alternative spatial specification processes that were installed at the evolutionary divergence of the two extant subclasses of sea urchins.
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Affiliation(s)
- Feng Gao
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, United States
| | - Jeffrey R Thompson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, United States
| | - Elizabeth Petsios
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, United States
| | - Eric Erkenbrack
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, United States
| | - Rex A Moats
- Translational Biomedical Imaging Laboratory, Department of Radiology, The Saban Research Institute, Children׳s Hospital Los Angeles, Keck School of Medicine USC, Los Angeles, CA 90027, United States
| | - David J Bottjer
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, United States
| | - Eric H Davidson
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, United States.
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66
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Hojo M, Omi A, Hamanaka G, Shindo K, Shimada A, Kondo M, Narita T, Kiyomoto M, Katsuyama Y, Ohnishi Y, Irie N, Takeda H. Unexpected link between polyketide synthase and calcium carbonate biomineralization. ZOOLOGICAL LETTERS 2015; 1:3. [PMID: 26605048 PMCID: PMC4604110 DOI: 10.1186/s40851-014-0001-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 10/15/2014] [Indexed: 06/05/2023]
Abstract
INTRODUCTION Calcium carbonate biominerals participate in diverse physiological functions. Despite intensive studies, little is known about how mineralization is initiated in organisms. RESULTS We analyzed the medaka spontaneous mutant, ha, defective in otolith (calcareous ear stone) formation. ha lacks a trigger for otolith mineralization, and the causative gene was found to encode polyketide synthase (pks), a multifunctional enzyme mainly found in bacteria, fungi, and plant. Subsequent experiments demonstrate that the products of medaka PKS, most likely polyketides or their derivatives, act as nucleation facilitators in otolith mineralization. The generality of this novel PKS function is supported by the essential role of echinoderm PKS in calcareous skeleton formation together with the presence of PKSs in a much wider range of animals from coral to vertebrates. CONCLUSION The present study first links PKS to biomineralization and provides a genetic cue for biogeochemistry of carbon and calcium cycles.
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Affiliation(s)
- Motoki Hojo
- />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 Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24–1, Hyakunincho, Shinju-ku, Tokyo 169-0073 Japan
| | - Ai Omi
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
- />Present address: Division of Molecular Pathology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022 Japan
| | - Gen Hamanaka
- />Tateyama Marine Laboratory, Marine and Coastal Research Center, Ochanomizu University, Kou-yatsu 11, Tateyama, Chiba 294-0301 Japan
| | - Kazutoshi Shindo
- />Department of Food and Nutrition, Japan Women’s University, 2-8-1, Mejirodai, Bunkyo-ku, Tokyo 112-8681 Japan
| | - Atsuko Shimada
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Mariko Kondo
- />Misaki Marine Biological Station, Graduate School of Science, University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa 238-0225 Japan
| | - Takanori Narita
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
- />Present address: Laboratory of Veterinary Biochemistry, Nihon University College of Bioresource Sciences, 1866 Kameino, Fujisawa, Kanagawa 252-0880 Japan
| | - Masato Kiyomoto
- />Tateyama Marine Laboratory, Marine and Coastal Research Center, Ochanomizu University, Kou-yatsu 11, Tateyama, Chiba 294-0301 Japan
| | - Yohei Katsuyama
- />Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Yasuo Ohnishi
- />Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Naoki Irie
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Hiroyuki Takeda
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
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67
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Heyland A, Hodin J, Bishop C. Manipulation of developing juvenile structures in purple sea urchins (Strongylocentrotus purpuratus) by morpholino injection into late stage larvae. PLoS One 2014; 9:e113866. [PMID: 25436992 PMCID: PMC4250057 DOI: 10.1371/journal.pone.0113866] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/30/2014] [Indexed: 11/19/2022] Open
Abstract
Sea urchins have been used as experimental organisms for developmental biology for over a century. Yet, as is the case for many other marine invertebrates, understanding the development of the juveniles and adults has lagged far behind that of their embryos and larvae. The reasons for this are, in large part, due to the difficulty of experimentally manipulating juvenile development. Here we develop and validate a technique for injecting compounds into juvenile rudiments of the purple sea urchin, Strongylocentrotus purpuratus. We first document the distribution of rhodaminated dextran injected into different compartments of the juvenile rudiment of sea urchin larvae. Then, to test the potential of this technique to manipulate development, we injected Vivo-Morpholinos (vMOs) designed to knock down p58b and p16, two proteins involved in the elongation of S. purpuratus larval skeleton. Rudiments injected with these vMOs showed a delay in the growth of some juvenile skeletal elements relative to controls. These data provide the first evidence that vMOs, which are designed to cross cell membranes, can be used to transiently manipulate gene function in later developmental stages in sea urchins. We therefore propose that injection of vMOs into juvenile rudiments, as shown here, is a viable approach to testing hypotheses about gene function during development, including metamorphosis.
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Affiliation(s)
- Andreas Heyland
- Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Jason Hodin
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States of America
| | - Cory Bishop
- Department of Biology, St. Francis Xavier University, Antigonish, NS, Canada
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68
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Signal-dependent regulation of the sea urchin skeletogenic gene regulatory network. Gene Expr Patterns 2014; 16:93-103. [PMID: 25460514 DOI: 10.1016/j.gep.2014.10.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/07/2014] [Accepted: 10/08/2014] [Indexed: 11/23/2022]
Abstract
The endoskeleton of the sea urchin embryo is produced by primary mesenchyme cells (PMCs). Maternal inputs activate a complex gene regulatory network (GRN) in the PMC lineage in a cell-autonomous fashion during early development, initially creating a uniform population of prospective skeleton-forming cells. Previous studies showed that at post-blastula stages of development, several effector genes in the network exhibit non-uniform patterns of expression, suggesting that their regulation becomes subject to local, extrinsic cues. Other studies have identified the VEGF and MAPK pathways as regulators of PMC migration, gene expression, and biomineralization. In this study, we used whole mount in situ hybridization (WMISH) to examine the spatial expression patterns of 39 PMC-specific/enriched mRNAs in Strongylocentrotus purpuratus embryos at the late gastrula, early prism and pluteus stages. We found that all 39 mRNAs (including several regulatory genes) showed non-uniform patterns of expression within the PMC syncytium, revealing a global shift in the regulation of the skeletogenic GRN from a cell-autonomous to a signal-dependent mode. In general, localized regions of elevated gene expression corresponded to sites of rapid biomineral deposition. We used a VEGFR inhibitor (axitinib) and a MEK inhibitor (U0126) to show that VEGF signaling and the MAPK pathway are essential for maintaining high levels of gene expression in PMCs at the tips of rods that extend from the ventral region of the embryo. These inhibitors affected gene expression in the PMCs in similar ways, suggesting that VEGF acts via the MAPK pathway. In contrast, axitinib and U0126 did not affect the localized expression of genes in PMCs at the tips of the body rods, which form on the dorsal side of the embryo. Our results therefore indicate that multiple signaling pathways regulate the skeletogenic GRN during late stages of embryogenesis-VEGF/MAPK signaling on the ventral side and a separate, unidentified pathway on the dorsal side. These two signaling pathways appear to be activated sequentially (ventral followed by dorsal) and many effector genes are subject to regulation by both pathways.
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69
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Cheatle Jarvela AM, Brubaker L, Vedenko A, Gupta A, Armitage BA, Bulyk ML, Hinman VF. Modular evolution of DNA-binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks. Mol Biol Evol 2014; 31:2672-88. [PMID: 25016582 PMCID: PMC4166925 DOI: 10.1093/molbev/msu213] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Gene regulatory networks (GRNs) describe the progression of transcriptional states that take a single-celled zygote to a multicellular organism. It is well documented that GRNs can evolve extensively through mutations to cis-regulatory modules (CRMs). Transcription factor proteins that bind these CRMs may also evolve to produce novelty. Coding changes are considered to be rarer, however, because transcription factors are multifunctional and hence are more constrained to evolve in ways that will not produce widespread detrimental effects. Recent technological advances have unearthed a surprising variation in DNA-binding abilities, such that individual transcription factors may recognize both a preferred primary motif and an additional secondary motif. This provides a source of modularity in function. Here, we demonstrate that orthologous transcription factors can also evolve a changed preference for a secondary binding motif, thereby offering an unexplored mechanism for GRN evolution. Using protein-binding microarray, surface plasmon resonance, and in vivo reporter assays, we demonstrate an important difference in DNA-binding preference between Tbrain protein orthologs in two species of echinoderms, the sea star, Patiria miniata, and the sea urchin, Strongylocentrotus purpuratus. Although both orthologs recognize the same primary motif, only the sea star Tbr also has a secondary binding motif. Our in vivo assays demonstrate that this difference may allow for greater evolutionary change in timing of regulatory control. This uncovers a layer of transcription factor binding divergence that could exist for many pairs of orthologs. We hypothesize that this divergence provides modularity that allows orthologous transcription factors to evolve novel roles in GRNs through modification of binding to secondary sites.
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Affiliation(s)
| | - Lisa Brubaker
- Department of Biological Sciences, Carnegie Mellon University
| | - Anastasia Vedenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Anisha Gupta
- Department of Chemistry, Carnegie Mellon University
| | | | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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70
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Wessel GM, Brayboy L, Fresques T, Gustafson EA, Oulhen N, Ramos I, Reich A, Swartz SZ, Yajima M, Zazueta V. The biology of the germ line in echinoderms. Mol Reprod Dev 2014; 81:679-711. [PMID: 23900765 PMCID: PMC4102677 DOI: 10.1002/mrd.22223] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 07/23/2013] [Indexed: 12/16/2022]
Abstract
The formation of the germ line in an embryo marks a fresh round of reproductive potential. The developmental stage and location within the embryo where the primordial germ cells (PGCs) form, however, differs markedly among species. In many animals, the germ line is formed by an inherited mechanism, in which molecules made and selectively partitioned within the oocyte drive the early development of cells that acquire this material to a germ-line fate. In contrast, the germ line of other animals is fated by an inductive mechanism that involves signaling between cells that directs this specialized fate. In this review, we explore the mechanisms of germ-line determination in echinoderms, an early-branching sister group to the chordates. One member of the phylum, sea urchins, appears to use an inherited mechanism of germ-line formation, whereas their relatives, the sea stars, appear to use an inductive mechanism. We first integrate the experimental results currently available for germ-line determination in the sea urchin, for which considerable new information is available, and then broaden the investigation to the lesser-known mechanisms in sea stars and other echinoderms. Even with this limited insight, it appears that sea stars, and perhaps the majority of the echinoderm taxon, rely on inductive mechanisms for germ-line fate determination. This enables a strongly contrasted picture for germ-line determination in this phylum, but one for which transitions between different modes of germ-line determination might now be experimentally addressed.
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Affiliation(s)
- Gary M. Wessel
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Lynae Brayboy
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Tara Fresques
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Eric A. Gustafson
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Nathalie Oulhen
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Isabela Ramos
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Adrian Reich
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - S. Zachary Swartz
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Mamiko Yajima
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Vanessa Zazueta
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
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71
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Russo R, Pinsino A, Costa C, Bonaventura R, Matranga V, Zito F. The newly characterizedPl-jun is specifically expressed in skeletogenic cells of theParacentrotus lividussea urchin embryo. FEBS J 2014; 281:3828-43. [DOI: 10.1111/febs.12911] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 06/24/2014] [Accepted: 07/03/2014] [Indexed: 01/17/2023]
Affiliation(s)
- Roberta Russo
- Institute of Biomedicine and Molecular Immunology ‘A. Monroy’; National Research Council; Palermo Italy
| | - Annalisa Pinsino
- Institute of Biomedicine and Molecular Immunology ‘A. Monroy’; National Research Council; Palermo Italy
| | - Caterina Costa
- Institute of Biomedicine and Molecular Immunology ‘A. Monroy’; National Research Council; Palermo Italy
| | - Rosa Bonaventura
- Institute of Biomedicine and Molecular Immunology ‘A. Monroy’; National Research Council; Palermo Italy
| | - Valeria Matranga
- Institute of Biomedicine and Molecular Immunology ‘A. Monroy’; National Research Council; Palermo Italy
| | - Francesca Zito
- Institute of Biomedicine and Molecular Immunology ‘A. Monroy’; National Research Council; Palermo Italy
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72
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Lyons DC, Martik ML, Saunders LR, McClay DR. Specification to biomineralization: following a single cell type as it constructs a skeleton. Integr Comp Biol 2014; 54:723-33. [PMID: 25009306 DOI: 10.1093/icb/icu087] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The sea urchin larva is shaped by a calcite endoskeleton. That skeleton is built by 64 primary mesenchyme cells (PMCs) in Lytechinus variegatus. The PMCs originate as micromeres due to an unequal fourth cleavage in the embryo. Micromeres are specified in a well-described molecular sequence and enter the blastocoel at a precise time using a classic epithelial-mesenchymal transition. To make the skeleton, the PMCs receive signaling inputs from the overlying ectoderm, which provides positional information as well as control of the growth of initial skeletal tri-radiates. The patterning of the skeleton is the result both of autonomous inputs from PMCs, including production of proteins that are included in the skeletal matrix, and of non-autonomous dynamic information from the ectoderm. Here, we summarize the wealth of information known about how a PMC contributes to the skeletal structure. The larval skeleton is a model for understanding how information encoded in DNA is translated into a three-dimensional crystalline structure.
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Affiliation(s)
- Deirdre C Lyons
- Department of Biology, Duke University, 124 Science Drive, Box 90338, Durham, NC 27708, USA
| | - Megan L Martik
- Department of Biology, Duke University, 124 Science Drive, Box 90338, Durham, NC 27708, USA
| | - Lindsay R Saunders
- Department of Biology, Duke University, 124 Science Drive, Box 90338, Durham, NC 27708, USA
| | - David R McClay
- Department of Biology, Duke University, 124 Science Drive, Box 90338, Durham, NC 27708, USA
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73
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Chen SH, Li KL, Lu IH, Wang YB, Tung CH, Ting HC, Lin CY, Lin CY, Su YH, Yu JK. Sequencing and analysis of the transcriptome of the acorn worm Ptychodera flava, an indirect developing hemichordate. Mar Genomics 2014; 15:35-43. [PMID: 24823299 DOI: 10.1016/j.margen.2014.04.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/28/2014] [Accepted: 04/28/2014] [Indexed: 12/13/2022]
Abstract
Hemichordates are the sister group of echinoderms, and together they are closely related to chordates within the deuterostome lineage. Therefore, hemichordates represent an important animal group for the understanding of both the evolution of developmental mechanisms in deuterostome animals and the origin of chordates. Recently, the majority of studies investigating hemichordates have focused on the direct-developing enteropneust hemichordate Saccoglossus kowalevskii; few have focused on the indirect-developing hemichordates, partly because of the lack of extensive genomic resources in these animals. In this study, we report the sequencing and analysis of a transcriptome from an indirect-developing enteropneust hemichordate Ptychodera flava. We sequenced a mixed cDNA library from six developmental stages using the Roche GS FLX Titanium System to generate more than 879,000 reads. These reads were assembled into 17,990 contigs with an average length of 1316bp. We found that 60% of the assembled contigs, along with 28% of the unassembled singleton reads, had significant hits to sequences in the NCBI database by a BLASTx search, and we also annotated these sequences and obtained Gene Ontology (GO) terms for 6744 contigs and 5802 singletons. We further identified candidate P. flava transcripts corresponding to genes involved in major developmental signaling pathways, including the Wnt, Notch and TGF-β signaling pathways. Using available genome/transcriptome datasets from the direct-developing hemichordate S. kowalevskii, the echinoderm Strongylocentrotus purpuratus and the chordate Branchiostoma floridae, we found that 90%, 80% and 73% of the annotated protein sequences in these respective species matched our P. flava transcriptome in a homology search. We also constructed a database for the P. flava transcriptome, and researchers can easily access this dataset online. Our dataset significantly increases the amount of available P. flava sequence data and can serve as a reference transcriptome for future studies using this species.
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Affiliation(s)
- Shu-Hwa Chen
- Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Kun-Lin Li
- Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan
| | - I-Hsuan Lu
- Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Yu-Bin Wang
- Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Che-Huang Tung
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Hsiu-Chi Ting
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Ching-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Chung-Yen Lin
- Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan; Institute of Population Health Sciences, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan.
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan.
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
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74
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Ettensohn CA. Horizontal transfer of themsp130gene supported the evolution of metazoan biomineralization. Evol Dev 2014; 16:139-48. [DOI: 10.1111/ede.12074] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Charles A. Ettensohn
- Department of Biological Sciences; Carnegie Mellon University; 4400 Fifth Avenue Pittsburgh PA 15213 USA
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75
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Rafiq K, Shashikant T, McManus CJ, Ettensohn CA. Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins. Development 2014; 141:950-61. [PMID: 24496631 DOI: 10.1242/dev.105585] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A central challenge of developmental and evolutionary biology is to understand the transformation of genetic information into morphology. Elucidating the connections between genes and anatomy will require model morphogenetic processes that are amenable to detailed analysis of cell/tissue behaviors and to systems-level approaches to gene regulation. The formation of the calcified endoskeleton of the sea urchin embryo is a valuable experimental system for developing such an integrated view of the genomic regulatory control of morphogenesis. A transcriptional gene regulatory network (GRN) that underlies the specification of skeletogenic cells (primary mesenchyme cells, or PMCs) has recently been elucidated. In this study, we carried out a genome-wide analysis of mRNAs encoded by effector genes in the network and uncovered transcriptional inputs into many of these genes. We used RNA-seq to identify >400 transcripts differentially expressed by PMCs during gastrulation, when these cells undergo a striking sequence of behaviors that drives skeletal morphogenesis. Our analysis expanded by almost an order of magnitude the number of known (and candidate) downstream effectors that directly mediate skeletal morphogenesis. We carried out genome-wide analysis of (1) functional targets of Ets1 and Alx1, two pivotal, early transcription factors in the PMC GRN, and (2) functional targets of MAPK signaling, a pathway that plays an essential role in PMC specification. These studies identified transcriptional inputs into >200 PMC effector genes. Our work establishes a framework for understanding the genomic regulatory control of a major morphogenetic process and has important implications for reconstructing the evolution of biomineralization in metazoans.
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Affiliation(s)
- Kiran Rafiq
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
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76
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Ebert TA, Hernández JC, Clemente S. Annual reversible plasticity of feeding structures: cyclical changes of jaw allometry in a sea urchin. Proc Biol Sci 2014; 281:20132284. [PMID: 24500161 DOI: 10.1098/rspb.2013.2284] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A wide variety of organisms show morphologically plastic responses to environmental stressors but in general these changes are not reversible. Though less common, reversible morphological structures are shown by a range of species in response to changes in predators, competitors or food. Theoretical analysis indicates that reversible plasticity increases fitness if organisms are long-lived relative to the frequency of changes in the stressor and morphological changes are rapid. Many sea urchin species show differences in the sizes of jaws (demi-pyramids) of the feeding apparatus, Aristotle's lantern, relative to overall body size, and these differences have been correlated with available food. The question addressed here is whether reversible changes of relative jaw size occur in the field as available food changes with season. Monthly samples of the North American Pacific coast sea urchin Strongylocentrotus purpuratus were collected from Gregory Point on the Oregon (USA) coast and showed an annual cycle of relative jaw size together with a linear trend from 2007 to 2009. Strongylocentrotus purpuratus is a long-lived species and under field conditions individuals experience multiple episodes of changes in food resources both seasonally and from year to year. Their rapid and reversible jaw plasticity fits well with theoretical expectations.
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Affiliation(s)
- Thomas A Ebert
- Department of Zoology, Oregon State University, , Corvallis, OR 97331, USA, Department of Biology, Villanova University, , Villanova, PA 19085, USA
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Barsi JC, Tu Q, Davidson EH. General approach for in vivo recovery of cell type-specific effector gene sets. Genome Res 2014; 24:860-8. [PMID: 24604781 PMCID: PMC4009615 DOI: 10.1101/gr.167668.113] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Differentially expressed, cell type-specific effector gene sets hold the key to multiple important problems in biology, from theoretical aspects of developmental gene regulatory networks (GRNs) to various practical applications. Although individual cell types of interest have been recovered by various methods and analyzed, systematic recovery of multiple cell type-specific gene sets from whole developing organisms has remained problematic. Here we describe a general methodology using the sea urchin embryo, a material of choice because of the large-scale GRNs already solved for this model system. This method utilizes the regulatory states expressed by given cells of the embryo to define cell type and includes a fluorescence activated cell sorting (FACS) procedure that results in no perturbation of transcript representation. We have extensively validated the method by spatial and qualitative analyses of the transcriptome expressed in isolated embryonic skeletogenic cells and as a consequence, generated a prototypical cell type-specific transcriptome database.
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Affiliation(s)
- Julius C Barsi
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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78
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Adomako-Ankomah A, Ettensohn CA. Growth factors and early mesoderm morphogenesis: insights from the sea urchin embryo. Genesis 2014; 52:158-72. [PMID: 24515750 DOI: 10.1002/dvg.22746] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 01/24/2014] [Accepted: 02/05/2014] [Indexed: 12/16/2022]
Abstract
The early morphogenesis of the mesoderm is critically important in establishing the body plan of the embryo. Recent research has led to a better understanding of the mechanisms that underlie this process, and growth factor signaling pathways have emerged as key regulators of the directional movements of mesoderm cells during gastrulation. In this review, we undertake a comparative analysis of the various essential functions of growth factor signaling pathways in regulating early mesoderm morphogenesis, with an emphasis on recent advances in the sea urchin embryo. We focus on the roles of the vascular endothelial growth factor (VEGF) and fibroblast growth factor (FGF) pathways in the migration of primary mesenchyme cells and the formation of the embryonic endoskeleton. We compare the functions of VEGF and FGF in sea urchins with the roles that these and other growth factors play in regulating mesoderm migration during gastrulation in Drosophila and vertebrates.
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79
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Saunders LR, McClay DR. Sub-circuits of a gene regulatory network control a developmental epithelial-mesenchymal transition. Development 2014; 141:1503-13. [PMID: 24598159 DOI: 10.1242/dev.101436] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Epithelial-mesenchymal transition (EMT) is a fundamental cell state change that transforms epithelial to mesenchymal cells during embryonic development, adult tissue repair and cancer metastasis. EMT includes a complex series of intermediate cell state changes including remodeling of the basement membrane, apical constriction, epithelial de-adhesion, directed motility, loss of apical-basal polarity, and acquisition of mesenchymal adhesion and polarity. Transcriptional regulatory state changes must ultimately coordinate the timing and execution of these cell biological processes. A well-characterized gene regulatory network (GRN) in the sea urchin embryo was used to identify the transcription factors that control five distinct cell changes during EMT. Single transcription factors were perturbed and the consequences followed with in vivo time-lapse imaging or immunostaining assays. The data show that five different sub-circuits of the GRN control five distinct cell biological activities, each part of the complex EMT process. Thirteen transcription factors (TFs) expressed specifically in pre-EMT cells were required for EMT. Three TFs highest in the GRN specified and activated EMT (alx1, ets1, tbr) and the 10 TFs downstream of those (tel, erg, hex, tgif, snail, twist, foxn2/3, dri, foxb, foxo) were also required for EMT. No single TF functioned in all five sub-circuits, indicating that there is no EMT master regulator. Instead, the resulting sub-circuit topologies suggest EMT requires multiple simultaneous regulatory mechanisms: forward cascades, parallel inputs and positive-feedback lock downs. The interconnected and overlapping nature of the sub-circuits provides one explanation for the seamless orchestration by the embryo of cell state changes leading to successful EMT.
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McIntyre DC, Lyons DC, Martik M, McClay DR. Branching out: origins of the sea urchin larval skeleton in development and evolution. Genesis 2014; 52:173-85. [PMID: 24549853 PMCID: PMC3990003 DOI: 10.1002/dvg.22756] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/14/2014] [Accepted: 02/14/2014] [Indexed: 11/08/2022]
Abstract
It is a challenge to understand how the information encoded in DNA is used to build a three-dimensional structure. To explore how this works the assembly of a relatively simple skeleton has been examined at multiple control levels. The skeleton of the sea urchin embryo consists of a number of calcite rods produced by 64 skeletogenic cells. The ectoderm supplies spatial cues for patterning, essentially telling the skeletogenic cells where to position themselves and providing the factors for skeletal growth. Here, we describe the information known about how this works. First the ectoderm must be patterned so that the signaling cues are released from precise positions. The skeletogenic cells respond by initiating skeletogenesis immediately beneath two regions (one on the right and the other on the left side). Growth of the skeletal rods requires additional signaling from defined ectodermal locations, and the skeletogenic cells respond to produce a membrane-bound template in which the calcite crystal grows. Important in this process are three signals, fibroblast growth factor, vascular endothelial growth factor, and Wnt5. Each is necessary for explicit tasks in skeleton production.
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Affiliation(s)
| | | | - Megan Martik
- Department of Biology, Duke University, Durham, NC
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81
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McIntyre DC, Seay NW, Croce JC, McClay DR. Short-range Wnt5 signaling initiates specification of sea urchin posterior ectoderm. Development 2013; 140:4881-9. [PMID: 24227654 DOI: 10.1242/dev.095844] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The border between the posterior ectoderm and the endoderm is a location where two germ layers meet and establish an enduring relationship that also later serves, in deuterostomes, as the anatomical site of the anus. In the sea urchin, a prototypic deuterostome, the ectoderm-endoderm boundary is established before gastrulation, and ectodermal cells at the boundary are thought to provide patterning inputs to the underlying mesenchyme. Here we show that a short-range Wnt5 signal from the endoderm actively patterns the adjacent boundary ectoderm. This signal activates a unique subcircuit of the ectoderm gene regulatory network, including the transcription factors IrxA, Nk1, Pax2/5/8 and Lim1, which are ultimately restricted to subregions of the border ectoderm (BE). Surprisingly, Nodal and BMP2/4, previously shown to be activators of ectodermal specification and the secondary embryonic axis, instead restrict the expression of these genes to subregions of the BE. A detailed examination showed that endodermal Wnt5 functions as a short-range signal that activates only a narrow band of ectodermal cells, even though all ectoderm is competent to receive the signal. Thus, cells in the BE integrate positive and negative signals from both the primary and secondary embryonic axes to correctly locate and specify the border ectoderm.
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Czarkwiani A, Dylus DV, Oliveri P. Expression of skeletogenic genes during arm regeneration in the brittle star Amphiura filiformis. Gene Expr Patterns 2013; 13:464-72. [PMID: 24051028 PMCID: PMC3838619 DOI: 10.1016/j.gep.2013.09.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 09/05/2013] [Accepted: 09/07/2013] [Indexed: 11/19/2022]
Abstract
Analysis of brittle star regenerating arms using differentiation markers. Identification of the early segregation of skeletal and muscle progenitor cells. Expression of skeletal and non-skeletal genes at different stages of regeneration. Combinatorial role of TF genes in early specification of skeletal cells. Same TF genes identify different skeletal structures later in regeneration.
The brittle star Amphiura filiformis, which regenerates its arms post autotomy, is emerging as a useful model for studying the molecular underpinnings of regeneration, aided by the recent availability of some molecular resources. During regeneration a blastema initially is formed distally to the amputation site, and then a rapid rebuild is obtained by adding metameric units, which will eventually differentiate and become fully functional. In this work we first characterize the developmental process of the regenerating arms using two differentiation markers for muscle and skeletal structures – Afi-trop-1 and Afi-αcoll. Both genes are not expressed in the blastema and newly added undifferentiated metameric units. Their expression at different regenerating stages shows an early segregation of muscle and skeletal cells during the regenerating process, long before the metameric units become functional. We then studied the expression of a set of genes orthologous of the sea urchin transcription factors involved in the development of skeletal and non-skeletal mesoderm: Afi-ets1/2, Afi-alx1, Afi-tbr, Afi-foxB and Afi-gataC. We found that Afi-ets1/2, Afi-alx1, Afi-foxB and Afi-gataC are all expressed at the blastemal stage. As regeneration progresses those genes are expressed in a similar small undifferentiated domain beneath the distal growth cap, while in more advanced metameric units they become restricted to different skeletal domains. Afi-foxB becomes expressed in non-skeletal structures. This suggests that they might play a combinatorial role only in the early cell specification process and that subsequently they function independently in the differentiation of different structures. Afi-tbr is not present in the adult arm tissue at any stage of regeneration. In situ hybridization results have been confirmed with a new strategy for quantitative PCR (QPCR), using a subdivision of the three stages of regeneration into proximal (differentiated) and distal (undifferentiated) arm segments.
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Affiliation(s)
- Anna Czarkwiani
- Research Department of Genetics, Evolution and Environment, UCL, Gower Street, London WC1E 6BT, UK
| | - David V. Dylus
- Research Department of Genetics, Evolution and Environment, UCL, Gower Street, London WC1E 6BT, UK
- CoMPLEX/SysBio, UCL, Gower Street, London WC1E 6BT, UK
| | - Paola Oliveri
- Research Department of Genetics, Evolution and Environment, UCL, Gower Street, London WC1E 6BT, UK
- Corresponding author. Address: Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London WC1E 6BT, UK. Tel.: +44 020 767 93719; fax: +44 020 7679 7193.
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83
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Adomako-Ankomah A, Ettensohn CA. Growth factor-mediated mesodermal cell guidance and skeletogenesis during sea urchin gastrulation. Development 2013; 140:4214-25. [PMID: 24026121 DOI: 10.1242/dev.100479] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Growth factor signaling pathways provide essential cues to mesoderm cells during gastrulation in many metazoans. Recent studies have implicated the VEGF and FGF pathways in providing guidance and differentiation cues to primary mesenchyme cells (PMCs) during sea urchin gastrulation, although the relative contributions of these pathways and the cell behaviors they regulate are not fully understood. Here, we show that FGF and VEGF ligands are expressed in distinct domains in the embryonic ectoderm of Lytechinus variegatus. We find that PMC guidance is specifically disrupted in Lv-vegf3 morphants and these embryos fail to form skeletal elements. By contrast, PMC migration is unaffected in Lv-fgfa morphants, and well-patterned but shortened skeletal elements form. We use a VEGFR inhibitor, axitinib, to show that VEGF signaling is essential not only for the initial phase of PMC migration (subequatorial ring formation), but also for the second phase (migration towards the animal pole). VEGF signaling is not required, however, for PMC fusion. Inhibition of VEGF signaling after the completion of PMC migration causes significant defects in skeletogenesis, selectively blocking the elongation of skeletal rods that support the larval arms, but not rods that form in the dorsal region of the embryo. Nanostring nCounter analysis of ∼100 genes in the PMC gene regulatory network shows a decrease in the expression of many genes with proven or predicted roles in biomineralization in vegf3 morphants. Our studies lead to a better understanding of the roles played by growth factors in sea urchin gastrulation and skeletogenesis.
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84
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Wilt F, Killian CE, Croker L, Hamilton P. SM30 protein function during sea urchin larval spicule formation. J Struct Biol 2013; 183:199-204. [PMID: 23583702 DOI: 10.1016/j.jsb.2013.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/20/2013] [Accepted: 04/01/2013] [Indexed: 10/26/2022]
Abstract
A central issue in better understanding the process of biomineralization is to elucidate the function of occluded matrix proteins present in mineralized tissues. A potent approach to addressing this issue utilizes specific inhibitors of expression of known genes. Application of antisense oligonucleotides that specifically suppress translation of a given mRNA are capable of causing aberrant biomineralization, thereby revealing, at least in part, a likely function of the protein and gene under investigation. We have applied this approach to study the possible function(s) of the SM30 family of proteins, which are found in spicules, teeth, spines, and tests of Strongylocentrotus purpuratus as well as other euechinoid sea urchins. It is possible using the anti-SM30 morpholino-oligonucleotides (MO's) to reduce the level of these proteins to very low levels, yet the development of skeletal spicules in the embryo shows little or no aberration. This surprising result requires re-thinking about the role of these, and possibly other occluded matrix proteins.
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Affiliation(s)
- Fred Wilt
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3200, United States.
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85
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Ettensohn CA. Encoding anatomy: Developmental gene regulatory networks and morphogenesis. Genesis 2013; 51:383-409. [PMID: 23436627 DOI: 10.1002/dvg.22380] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/06/2013] [Accepted: 02/07/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Charles A. Ettensohn
- Department of Biological Sciences; Carnegie Mellon University; Pittsburgh; Pennsylvania
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