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Bates L, Wiseman E, Whetzel A, Carroll DJ. A Novel Method to Profile Transcripts Encoding SH2 Domains in the Patiria miniata Mature Egg Transcriptome. Cells 2024; 13:1898. [PMID: 39594646 PMCID: PMC11593052 DOI: 10.3390/cells13221898] [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: 09/24/2024] [Revised: 10/29/2024] [Accepted: 11/13/2024] [Indexed: 11/28/2024] Open
Abstract
The critical mechanism to restart zygote metabolism and prevent polyspermy during fertilization is the intracellular Ca2+ increase. All of the signaling molecules leading to the Ca2+ rise are not fully known in any species. In the sea star Patiria miniata, SFK1, SFK3, and PLCγ participate in this fertilization Ca2+ increase. These proteins share common regulatory features, including signaling via tyrosine phosphorylation and their SH2 domains. In this study, we explore two different bioinformatic strategies to identify transcripts in the Patiria miniata mature egg transcriptome (Accession PRJNA398668) that code for proteins possessing an SH2 domain. The first identified the longest open reading frame for each transcript and then utilized similarity searching tools to provide identities for each transcript. The second, novel, method involved a six-frame translation of the entire transcriptome to identify SH2 domain-containing proteins. The identified transcripts were aligned against the NCBI non-redundant database and the SwissProt database. Eighty-two transcripts that encoded SH2 domains were identified. Of these, 33 were only found using the novel method. This work furthers research into egg activation by providing possible target proteins for future experiments and a novel method for identifying specific proteins of interest within a de novo transcriptome.
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Affiliation(s)
- Lauren Bates
- Biology Professional and Transfer Programs, Southern West Virginia Community and Technical College, Logan, WV 25601, USA;
- Department of Biomedical Engineering and Science, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Emily Wiseman
- BioSkryb Genomics, Durham, NC 27713, USA;
- Department of Biomedical Engineering and Science, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Alexis Whetzel
- Department of Biochemistry and Molecular Genetics, Midwestern University, Glendale, AZ 85308, USA;
| | - David J. Carroll
- Department of Biochemistry and Molecular Genetics, Midwestern University, Glendale, AZ 85308, USA;
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2
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Oulhen N, Morita S, Pieplow C, Onorato TM, Foster S, Wessel G. Conservation and contrast in cell states of echinoderm ovaries. Mol Reprod Dev 2024; 91:e23721. [PMID: 38054259 PMCID: PMC11153327 DOI: 10.1002/mrd.23721] [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: 10/25/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023]
Abstract
Echinoderms produce functional gametes throughout their lifespan, in some cases exceeding 200 years. The histology and ultrastructure of echinoderm ovaries has been described but how these ovaries function and maintain the production of high-quality gametes remains a mystery. Here, we present the first single cell RNA sequencing data sets of mature ovaries from two sea urchin species (Strongylocentrotus purpuratus [Sp] and Lytechinus variegatus [Lv]), and one sea star species (Patiria miniata [Pm]). We find 14 cell states in the Sp ovary, 16 cell states in the Lv ovary and 13 cell states in the ovary of the sea star. This resource is essential to understand the structure and functional biology of the ovary in echinoderms, and better informs decisions in the utilization of in situ RNA hybridization probes selective for various cell types. We link key genes with cell clusters in validation of this approach. This resource also aids in the identification of the stem cells for prolonged and continuous gamete production, is a foundation for testing changes in the annual reproductive cycle, and is essential for understanding the evolution of reproduction of this important phylum.
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Affiliation(s)
- Nathalie Oulhen
- Department of Molecular and Cellular Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Shumpei Morita
- Department of Molecular and Cellular Biology & Biochemistry, Brown University, Providence, RI 02912, USA
- Asamushi Research Center for Marine Biology, Tohoku University, Aomori, 039-3501, Japan
| | - Cosmo Pieplow
- Department of Molecular and Cellular Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Thomas M. Onorato
- Department of Molecular and Cellular Biology & Biochemistry, Brown University, Providence, RI 02912, USA
- Department of Natural Sciences, LaGuardia Community College, Long Island City, NY 11101, USA
| | - Stephany Foster
- Department of Molecular and Cellular Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Gary Wessel
- Department of Molecular and Cellular Biology & Biochemistry, Brown University, Providence, RI 02912, USA
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3
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Spurrell M, Oulhen N, Foster S, Perillo M, Wessel G. Gene regulatory divergence amongst echinoderms underlies appearance of pigment cells in sea urchin development. Dev Biol 2023; 494:13-25. [PMID: 36519720 PMCID: PMC9870932 DOI: 10.1016/j.ydbio.2022.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/14/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
Larvae of the sea urchin, Strongylocentrotus purpuratus, have pigmented migratory cells implicated in immune defense and gut patterning. The transcription factor SpGcm activates the expression of many pigment cell-specific genes, including those involved in pigment biosynthesis (SpPks1 and SpFmo3) and immune related genes (e.g. SpMif5). Despite the importance of this cell type in sea urchins, pigmented cells are absent in larvae of the sea star, Patiria miniata. In this study, we tested the premises that sea stars lack genes to synthesize echinochrome pigment, that the genes are present but are not expressed in the larvae, or rather that the homologous gene expression does not contribute to echinochrome synthesis. Our results show that orthologs of sea urchin pigment cell-specific genes (PmPks1, PmFmo3-1 and PmMifL1-2) are present in the sea star genome and expressed in the larvae. Although no cell lineage homologous to migratory sea urchin pigment cells is present, dynamic gene activation accomplishes a similar spatial and temporal expression profile. The mechanisms regulating the expression of these genes, though, is highly divergent. In sea stars, PmGcm lacks the central role in pigment gene expression since it is not expressed in PmPks1 and PmFmo3-1-positive cells, and knockdown of Gcm does not abrogate pigment gene expression. Pigment genes are instead expressed in the coelomic mesoderm early in development before later being expressed in the ectoderm. These findings were supported by in situ RNA hybridization and comparative scRNA-seq analyses. We conclude that simply the coexpression of Pks1 and Fmo3 orthologs in cells of the sea star is not sufficient to underlie the emergence of the larval pigment cell in the sea urchin.
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Affiliation(s)
- Maxwell Spurrell
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA
| | - Nathalie Oulhen
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA
| | - Stephany Foster
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA
| | - Margherita Perillo
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA
| | - Gary Wessel
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA.
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4
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Krishnan N, Tanaka T, Fiorito G, Genta FA, Imperadore P. Editorial: Methods and applications in invertebrate physiology. Front Physiol 2023; 14:1158972. [PMID: 36875030 PMCID: PMC9982125 DOI: 10.3389/fphys.2023.1158972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023] Open
Affiliation(s)
- Natraj Krishnan
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, United States
| | - Tetsuya Tanaka
- Laboratory of Infectious Diseases, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Fernando Ariel Genta
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Pamela Imperadore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
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Carroll DJ. Integrating experience with databases, bioinformatics, and wet lab exercises for students in an introductory genetics course. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 50:457-459. [PMID: 35904089 PMCID: PMC10661174 DOI: 10.1002/bmb.21649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/25/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Students often have no exposure to the incredible amount of genomic and proteomic data that is freely and easily accessible online. Becoming familiar with these resources, and seeing how they could be applied to a specific research question, is a prerequisite for students to apply them to their own scientific development. Many students have to "see it" and "do it" before they "get it." This paper describes a teaching laboratory for undergraduate Genetics students that combines exploration of several publicly available databases with some simple bioinformatic exercises and "'real" live experience in a wet lab exercise. The goal is to teach skills in applying genomic data to a real scientific question. In this exercise, students identify a target protein after exploring several protein and signal transduction databases, such as the Kyoto Encyclopedia of Genes and Genomes database. They then search for the encoding RNA in a newly available sea star mature egg transcriptome database and for the DNA in an existing sea star genome database. The students design primers against specific regions or domains in their target RNA and amplify these by reverse transcription PCR against RNA purified from fresh sea star eggs. The PCR reactions are analyzed by agarose gel electrophoresis. It is hoped that the combination of the computational biology exercises with the real lab work will excite the students and stimulate them to explore this exciting new biology further.
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Affiliation(s)
- David J Carroll
- Department of Biochemistry and Molecular Genetics, Midwestern University, Glendale, Arizona, USA
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Pal D, Visconti F, Sepúlveda-Ramírez SP, Swartz SZ, Shuster CB. Use of Echinoderm Gametes and Early Embryos for Studying Meiosis and Mitosis. Methods Mol Biol 2022; 2415:1-17. [PMID: 34972942 DOI: 10.1007/978-1-0716-1904-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The early embryos of sea urchins and other echinoderms have served as experimental models for the study of cell division since the nineteenth century. Their rapid development, optical clarity, and ease of manipulation continue to offer advantages for studying spindle assembly and cytokinesis. In the absence of transgenic lines, alternative strategies must be employed to visualize microtubules and actin. Here, we describe methods to visualize actin and microtubule using either purified, recombinant proteins, or probes in in vitro-transcribed mRNAs.
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Affiliation(s)
- Debadrita Pal
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | | | | | | | - Charles B Shuster
- Department of Biology, New Mexico State University, Las Cruces, NM, USA.
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Identification of SH2 Domain-Mediated Protein Interactions that Operate at Fertilization in the Sea Star Patiria miniata. Methods Mol Biol 2021. [PMID: 33074537 DOI: 10.1007/978-1-0716-0974-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The signaling mechanisms controlling internal calcium release at fertilization in animals are still largely unknown. Echinoderms, such as the sea star Patiria miniata, produce abundant and easily accessible sperm and eggs. In addition, eggs are naturally synchronized at the same cell cycle stage, collectively making these animals an attractive model to study the signaling proteins controlling fertilization. However, the lack of antibodies to identify proteins in this model system has slowed progress in identifying key signaling molecules. With the advances in mass spectrometry, we present a method for identifying tyrosine phosphorylated proteins binding to GST-tagged SH2 domains in sea star cell lysates for downstream mass spectrometry analysis.
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A Highly Prevalent and Pervasive Densovirus Discovered among Sea Stars from the North American Atlantic Coast. Appl Environ Microbiol 2020; 86:AEM.02723-19. [PMID: 31924612 PMCID: PMC7054102 DOI: 10.1128/aem.02723-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 12/27/2019] [Indexed: 12/04/2022] Open
Abstract
Sea star wasting syndrome is a disease primarily observed on the Pacific and Atlantic Coasts of North America that has significantly impacted sea star populations. The etiology of this disease is unknown, although it is hypothesized to be caused by a densovirus, SSaDV. However, previous studies have not found a correlation between SSaDV and sea star wasting syndrome on the North American Atlantic Coast. This study suggests that this observation may be explained by the presence of a genetically similar densovirus, AfaDV, that may have confounded previous studies. SSaDV was not present in sea stars screened in this study, and instead, AfaDV was commonly found in sea star populations across the New England region, with no apparent signs of disease. These results suggest that sea star densoviruses may be common constituents of the animals’ microbiome, and the diversity and extent of these viruses among wild populations may be greater than previously recognized. The etiology of sea star wasting syndrome is hypothesized to be caused by a densovirus, sea star-associated densovirus (SSaDV), that has previously been reported on the Pacific and Atlantic Coasts of the United States. In this study, we reevaluated the presence of SSaDV among sea stars from the North American Atlantic Coast and in doing so discovered a novel densovirus that we have named Asterias forbesi-associated densovirus (AfaDV), which shares 78% nucleotide pairwise identity with SSaDV. In contrast to previous studies, SSaDV was not detected in sea stars from the North American Atlantic Coast. Using a variety of PCR-based techniques, we investigated the tissue tropism, host specificity, and prevalence of AfaDV among populations of sea stars at five locations along the Atlantic Coast. AfaDV was detected in three sea star species (Asterias forbesi, Asterias rubens, and Henricia sp.) found in this region and was highly prevalent (>80% of individuals tested; n = 134), among sampled populations. AfaDV was detected in the body wall, gonads, and pyloric caeca (digestive gland) of specimens but was not detected in their coelomic fluid. A significant difference in viral load (copies mg−1) was found between tissue types, with the pyloric caeca having the highest viral loads. Further investigation of Asterias forbesi gonad tissue found germ line cells (oocytes) to be virus positive, suggesting a potential route of vertical transmission. Taken together, these observations show that the presence of AfaDV is not an indicator of sea star wasting syndrome because AfaDV is a common constituent of these animals’ microbiome, regardless of health. IMPORTANCE Sea star wasting syndrome is a disease primarily observed on the Pacific and Atlantic Coasts of North America that has significantly impacted sea star populations. The etiology of this disease is unknown, although it is hypothesized to be caused by a densovirus, SSaDV. However, previous studies have not found a correlation between SSaDV and sea star wasting syndrome on the North American Atlantic Coast. This study suggests that this observation may be explained by the presence of a genetically similar densovirus, AfaDV, that may have confounded previous studies. SSaDV was not present in sea stars screened in this study, and instead, AfaDV was commonly found in sea star populations across the New England region, with no apparent signs of disease. These results suggest that sea star densoviruses may be common constituents of the animals’ microbiome, and the diversity and extent of these viruses among wild populations may be greater than previously recognized.
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9
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Swartz SZ, McKay LS, Su KC, Bury L, Padeganeh A, Maddox PS, Knouse KA, Cheeseman IM. Quiescent Cells Actively Replenish CENP-A Nucleosomes to Maintain Centromere Identity and Proliferative Potential. Dev Cell 2019; 51:35-48.e7. [PMID: 31422918 PMCID: PMC6783363 DOI: 10.1016/j.devcel.2019.07.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 05/28/2019] [Accepted: 07/15/2019] [Indexed: 12/20/2022]
Abstract
Centromeres provide a robust model for epigenetic inheritance as they are specified by sequence-independent mechanisms involving the histone H3-variant centromere protein A (CENP-A). Prevailing models indicate that the high intrinsic stability of CENP-A nucleosomes maintains centromere identity indefinitely. Here, we demonstrate that CENP-A is not stable at centromeres but is instead gradually and continuously incorporated in quiescent cells including G0-arrested tissue culture cells and prophase I-arrested oocytes. Quiescent CENP-A incorporation involves the canonical CENP-A deposition machinery but displays distinct requirements from cell cycle-dependent deposition. We demonstrate that Plk1 is required specifically for G1 CENP-A deposition, whereas transcription promotes CENP-A incorporation in quiescent oocytes. Preventing CENP-A deposition during quiescence results in significantly reduced CENP-A levels and perturbs chromosome segregation following the resumption of cell division. In contrast to quiescent cells, terminally differentiated cells fail to maintain CENP-A levels. Our work reveals that quiescent cells actively maintain centromere identity providing an indicator of proliferative potential.
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Affiliation(s)
- S Zachary Swartz
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Liliana S McKay
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Kuan-Chung Su
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Leah Bury
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Abbas Padeganeh
- Biology Department, UNC Chapel Hill, 120 South Road, Chapel Hill, NC 27599-3280, USA
| | - Paul S Maddox
- Biology Department, UNC Chapel Hill, 120 South Road, Chapel Hill, NC 27599-3280, USA
| | - Kristin A Knouse
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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10
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Abstract
Echinoderms and especially echinoids have a rich history as model systems for the study of oogenesis, fertilization, and early embryogenesis. The ease of collecting and maintaining adults, as well as in obtaining gametes and culturing large quantities of synchronous embryos, is complemented by the ability to do biochemistry, reverse genetics, embryo manipulations and study gene regulatory networks. The diversity of species and developmental modes as well as unparalleled transparency in early developmental stages also makes echinoderms an excellent system in which to study evolutionary aspects of developmental biology. This chapter provides a practical guide to experimental methods for procuring adults and gametes, achieving synchronous in vitro fertilization, and culturing embryos through early larval stages for several echinoderm species representing four classes (Echinoidea, Asteroidea, Ophiuroidea, and Holothuroidea). We provide specific examples of protocols for obtaining adults and gametes and for culturing embryos of a selected number of species for experimental analysis of their development. The species were chosen to provide breadth across the phylum Echinodermata, as well as to provide practical guidelines for handling some of the more commonly studied species. For each species, we highlight specific advantages, and special note is made of key issues to consider when handling adults, collecting gametes, or setting and maintaining embryo cultures. Finally, information regarding interspecific crosses is provided.
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11
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Microinjection to deliver protein, mRNA, and DNA into zygotes of the cnidarian endosymbiosis model Aiptasia sp. Sci Rep 2018; 8:16437. [PMID: 30401930 PMCID: PMC6219564 DOI: 10.1038/s41598-018-34773-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/26/2018] [Indexed: 01/19/2023] Open
Abstract
Reef-building corals depend on an intracellular symbiosis with photosynthetic dinoflagellates for their survival in nutrient-poor oceans. Symbionts are phagocytosed by coral larvae from the environment and transfer essential nutrients to their hosts. Aiptasia, a small tropical marine sea anemone, is emerging as a tractable model system for coral symbiosis; however, to date functional tools and genetic transformation are lacking. Here we have established an efficient workflow to collect Aiptasia eggs for in vitro fertilization and microinjection as the basis for experimental manipulations in the developing embryo and larvae. We demonstrate that protein, mRNA, and DNA can successfully be injected into live Aiptasia zygotes to label actin with recombinant Lifeact-eGFP protein; to label nuclei and cell membranes with NLS-eGFP and farnesylated mCherry translated from injected mRNA; and to transiently drive transgene expression from an Aiptasia-specific promoter, respectively, in embryos and larvae. These proof-of-concept approaches pave the way for future functional studies of development and symbiosis establishment in Aiptasia, a powerful model to unravel the molecular mechanisms underlying intracellular coral-algal symbiosis.
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12
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Wiseman E, Bates L, Dubé A, Carroll DJ. Starfish as a Model System for Analyzing Signal Transduction During Fertilization. Results Probl Cell Differ 2018; 65:49-67. [PMID: 30083915 DOI: 10.1007/978-3-319-92486-1_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
The starfish oocyte and egg offer advantages for use as a model system for signal transduction research. Some of these have been recognized for over a century, including the ease of procuring gametes, in vitro fertilization, and culturing the embryos. New advances, particularly in genomics, have also opened up opportunities for the use of these animals. In this chapter, we give a few examples of the historical use of the starfish for research in cell biology and then describe some new areas in which we believe the starfish can contribute to our understanding of signal transduction-particularly in fertilization.
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Affiliation(s)
- Emily Wiseman
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, USA
| | - Lauren Bates
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, USA
| | - Altair Dubé
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, USA
| | - David J Carroll
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, USA.
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13
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Oulhen N, Heyland A, Carrier TJ, Zazueta-Novoa V, Fresques T, Laird J, Onorato TM, Janies D, Wessel G. Regeneration in bipinnaria larvae of the bat star Patiria miniata induces rapid and broad new gene expression. Mech Dev 2016; 142:10-21. [PMID: 27555501 PMCID: PMC5154901 DOI: 10.1016/j.mod.2016.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/12/2016] [Accepted: 08/16/2016] [Indexed: 11/23/2022]
Abstract
BACKGROUND Some metazoa have the capacity to regenerate lost body parts. This phenomenon in adults has been classically described in echinoderms, especially in sea stars (Asteroidea). Sea star bipinnaria larvae can also rapidly and effectively regenerate a complete larva after surgical bisection. Understanding the capacity to reverse cell fates in the larva is important from both a developmental and biomedical perspective; yet, the mechanisms underlying regeneration in echinoderms are poorly understood. RESULTS Here, we describe the process of bipinnaria regeneration after bisection in the bat star Patiria miniata. We tested transcriptional, translational, and cell proliferation activity after bisection in anterior and posterior bipinnaria halves as well as expression of SRAP, reported as a sea star regeneration associated protease (Vickery et al., 2001b). Moreover, we found several genes whose transcripts increased in abundance following bisection, including: Vasa, dysferlin, vitellogenin 1 and vitellogenin 2. CONCLUSION These results show a transformation following bisection, especially in the anterior halves, of cell fate reassignment in all three germ layers, with clear and predictable changes. These results define molecular events that accompany the cell fate changes coincident to the regenerative response in echinoderm larvae.
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Affiliation(s)
- Nathalie Oulhen
- Brown University, Molecular Biology, Cell Biology, and Biochemistry, USA
| | - Andreas Heyland
- Brown University, Molecular Biology, Cell Biology, and Biochemistry, USA; University of Guelph, Integrative Biology, Canada.
| | - Tyler J Carrier
- Brown University, Molecular Biology, Cell Biology, and Biochemistry, USA; University of North Carolina at Charlotte, Department of Biological Sciences, USA
| | | | - Tara Fresques
- Brown University, Molecular Biology, Cell Biology, and Biochemistry, USA
| | - Jessica Laird
- Brown University, Molecular Biology, Cell Biology, and Biochemistry, USA
| | | | - Daniel Janies
- University of North Carolina at Charlotte, Department of Bioinformatics and Genomics, USA
| | - Gary Wessel
- Brown University, Molecular Biology, Cell Biology, and Biochemistry, USA.
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14
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Oulhen N, Wessel GM. Differential Nanos 2 protein stability results in selective germ cell accumulation in the sea urchin. Dev Biol 2016; 418:146-156. [PMID: 27424271 DOI: 10.1016/j.ydbio.2016.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 06/21/2016] [Accepted: 07/12/2016] [Indexed: 01/18/2023]
Abstract
Nanos is a translational regulator required for the survival and maintenance of primordial germ cells. In the sea urchin, Strongylocentrotus purpuratus (Sp), Nanos 2 mRNA is broadly transcribed but accumulates specifically in the small micromere (sMic) lineage, in part because of the 3'UTR element GNARLE leads to turnover in somatic cells but retention in the sMics. Here we found that the Nanos 2 protein is also selectively stabilized; it is initially translated throughout the embryo but turned over in the future somatic cells and retained only in the sMics, the future germ line in this animal. This differential stability of Nanos protein is dependent on the open reading frame (ORF), and is independent of the sumoylation and ubiquitylation pathways. Manipulation of the ORF indicates that 68 amino acids in the N terminus of the Nanos protein are essential for its stability in the sMics whereas a 45 amino acid element adjacent to the zinc fingers targets its degradation. Further, this regulation of Nanos protein is cell autonomous, following formation of the germ line. These results are paradigmatic for the unique presence of Nanos in the germ line by a combination of selective RNA retention, distinctive translational control mechanisms (Oulhen et al., 2013), and now also by defined Nanos protein stability.
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Affiliation(s)
- Nathalie Oulhen
- Department of Molecular and Cell Biology and Biochemistry, Brown University, 185 Meeting St., Providence, RI 02912, USA
| | - Gary M Wessel
- Department of Molecular and Cell Biology and Biochemistry, Brown University, 185 Meeting St., Providence, RI 02912, USA.
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15
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Fresques T, Swartz SZ, Juliano C, Morino Y, Kikuchi M, Akasaka K, Wada H, Yajima M, Wessel GM. The diversity of nanos expression in echinoderm embryos supports different mechanisms in germ cell specification. Evol Dev 2016; 18:267-78. [PMID: 27402572 PMCID: PMC4943673 DOI: 10.1111/ede.12197] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Specification of the germ cell lineage is required for sexual reproduction in all animals. However, the timing and mechanisms of germ cell specification is remarkably diverse in animal development. Echinoderms, such as sea urchins and sea stars, are excellent model systems to study the molecular and cellular mechanisms that contribute to germ cell specification. In several echinoderm embryos tested, the germ cell factor Vasa accumulates broadly during early development and is restricted after gastrulation to cells that contribute to the germ cell lineage. In the sea urchin, however, the germ cell factor Vasa is restricted to a specific lineage by the 32-cell stage. We therefore hypothesized that the germ cell specification program in the sea urchin/Euechinoid lineage has evolved to an earlier developmental time point. To test this hypothesis we determined the expression pattern of a second germ cell factor, Nanos, in four out of five extant echinoderm clades. Here we find that Nanos mRNA does not accumulate until the blastula stage or later during the development of all other echinoderm embryos except those that belong to the Echinoid lineage. Instead, Nanos is expressed in a restricted domain at the 32-128 cell stage in Echinoid embryos. Our results support the model that the germ cell specification program underwent a heterochronic shift in the Echinoid lineage. A comparison of Echinoid and non-Echinoid germ cell specification mechanisms will contribute to our understanding of how these mechanisms have changed during animal evolution.
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Affiliation(s)
- Tara Fresques
- Department of Molecular Biology, Cell Biology and Biochemistry, 185 Meeting Street, Brown University, Providence RI 02912
| | - S. Zachary Swartz
- Department of Molecular Biology, Cell Biology and Biochemistry, 185 Meeting Street, Brown University, Providence RI 02912
| | - Celina Juliano
- Department of Molecular Biology, Cell Biology and Biochemistry, 185 Meeting Street, Brown University, Providence RI 02912
- Department of Molecular and Cellular Biology, College of Biological Sciences, One Shields Avenue, University of California, Davis, Davis CA 95616
| | - Yoshiaki Morino
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Mani Kikuchi
- Misaki Marine Biological Station, Graduate School of Science, University of Tokyo, Koajiro 1024, Misaki, Miura 238-0225, Japan
| | - Koji Akasaka
- Misaki Marine Biological Station, Graduate School of Science, University of Tokyo, Koajiro 1024, Misaki, Miura 238-0225, Japan
| | - Hiroshi Wada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Mamiko Yajima
- Department of Molecular Biology, Cell Biology and Biochemistry, 185 Meeting Street, Brown University, Providence RI 02912
| | - Gary M. Wessel
- Department of Molecular Biology, Cell Biology and Biochemistry, 185 Meeting Street, Brown University, Providence RI 02912
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16
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Reich A, Dunn C, Akasaka K, Wessel G. Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa. PLoS One 2015; 10:e0119627. [PMID: 25794146 PMCID: PMC4368666 DOI: 10.1371/journal.pone.0119627] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/12/2015] [Indexed: 12/01/2022] Open
Abstract
Echinoderms (sea urchins, sea stars, brittle stars, sea lilies and sea cucumbers) are a group of diverse organisms, second in number within deuterostome species to only the chordates. Echinoderms serve as excellent model systems for developmental biology due to their diverse developmental mechanisms, tractable laboratory use, and close phylogenetic distance to chordates. In addition, echinoderms are very well represented in the fossil record, including some larval features, making echinoderms a valuable system for studying evolutionary development. The internal relationships of Echinodermata have not been consistently supported across phylogenetic analyses, however, and this has hindered the study of other aspects of their biology. In order to test echinoderm phylogenetic relationships, we sequenced 23 de novo transcriptomes from all five clades of echinoderms. Using multiple phylogenetic methods at a variety of sampling depths we have constructed a well-supported phylogenetic tree of Echinodermata, including support for the sister groups of Asterozoa (sea stars and brittle stars) and Echinozoa (sea urchins and sea cucumbers). These results will help inform developmental and evolutionary studies specifically in echinoderms and deuterostomes in general.
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Affiliation(s)
- Adrian Reich
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Casey Dunn
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Koji Akasaka
- Misaki Marine Biological Station, University of Tokyo, Miura, Japan
| | - Gary Wessel
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
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Angione SL, Oulhen N, Brayboy LM, Tripathi A, Wessel GM. Simple perfusion apparatus for manipulation, tracking, and study of oocytes and embryos. Fertil Steril 2014; 103:281-90.e5. [PMID: 25450296 DOI: 10.1016/j.fertnstert.2014.09.039] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/25/2014] [Accepted: 09/26/2014] [Indexed: 01/04/2023]
Abstract
OBJECTIVE To develop and implement a device and protocol for oocyte analysis at a single cell level. The device must be capable of high resolution imaging, temperature control, perfusion of media, drugs, sperm, and immunolabeling reagents all at defined flow rates. Each oocyte and resultant embryo must remain spatially separated and defined. DESIGN Experimental laboratory study. SETTING University and academic center for reproductive medicine. PATIENT(S)/ANIMAL(S) Women with eggs retrieved for intracytoplasmic sperm injection (ICSI) cycles, adult female FVBN and B6C3F1 mouse strains, sea stars. INTERVENTION(S) Real-time, longitudinal imaging of oocytes after fluorescent labeling, insemination, and viability tests. MAIN OUTCOME MEASURE(S) Cell and embryo viability, immunolabeling efficiency, live cell endocytosis quantification, precise metrics of fertilization, and embryonic development. RESULT(S) Single oocytes were longitudinally imaged after significant changes in media, markers, endocytosis quantification, and development, all with supreme control by microfluidics. Cells remained viable, enclosed, and separate for precision measurements, repeatability, and imaging. CONCLUSION(S) We engineered a simple device to load, visualize, experiment, and effectively record individual oocytes and embryos without loss of cells. Prolonged incubation capabilities provide longitudinal studies without need for transfer and potential loss of cells. This simple perfusion apparatus provides for careful, precise, and flexible handling of precious samples facilitating clinical IVF approaches.
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Affiliation(s)
- Stephanie L Angione
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island
| | - Nathalie Oulhen
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Lynae M Brayboy
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Women & Infants Hospital, Providence, Rhode Island; The Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island
| | - Gary M Wessel
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island.
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Ramos I, Reich A, Wessel GM. Two-pore channels function in calcium regulation in sea star oocytes and embryos. Development 2014; 141:4598-609. [PMID: 25377554 DOI: 10.1242/dev.113563] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Egg activation at fertilization is an excellent process for studying calcium regulation. Nicotinic acid adenine dinucleotide-phosphate (NAADP), a potent calcium messenger, is able to trigger calcium release, likely through two-pore channels (TPCs). Concomitantly, a family of ectocellular enzymes, the ADP-ribosyl cyclases (ARCs), has emerged as being able to change their enzymatic mode from one of nucleotide cyclization in formation of cADPR to a base-exchange reaction in the generation of NAADP. Using sea star oocytes we gain insights into the functions of endogenously expressed TPCs and ARCs in the context of the global calcium signals at fertilization. Three TPCs and one ARC were found in the sea star (Patiria miniata) that were localized in the cortex of the oocytes and eggs. PmTPCs were localized in specialized secretory organelles called cortical granules, and PmARCs accumulated in a different, unknown, set of vesicles, closely apposed to the cortical granules in the egg cortex. Using morpholino knockdown of PmTPCs and PmARC in the oocytes, we found that both calcium regulators are essential for early embryo development, and that knockdown of PmTPCs leads to aberrant construction of the fertilization envelope at fertilization and changes in cortical granule pH. The calcium signals at fertilization are not significantly altered when individual PmTPCs are silenced, but the timing and shape of the cortical flash and calcium wave are slightly changed when the expression of all three PmTPCs is perturbed concomitantly, suggesting a cooperative activity among TPC isoforms in eliciting calcium signals that may influence localized physiological activities.
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Affiliation(s)
- Isabela Ramos
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI 02912, USA Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Adrian Reich
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Gary M Wessel
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
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Oulhen N, Xu D, Wessel GM. Conservation of sequence and function in fertilization of the cortical granule serine protease in echinoderms. Biochem Biophys Res Commun 2014; 450:1135-41. [PMID: 24878526 DOI: 10.1016/j.bbrc.2014.05.098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 05/21/2014] [Indexed: 11/17/2022]
Abstract
Conservation of the cortical granule serine protease during fertilization in echinoderms was tested both functionally in sea stars, and computationally throughout the echinoderm phylum. We find that the inhibitor of serine protease (soybean trypsin inhibitor) effectively blocks proper transition of the sea star fertilization envelope into a protective sperm repellent, whereas inhibitors of the other main types of proteases had no effect. Scanning the transcriptomes of 15 different echinoderm ovaries revealed sequences of high conservation to the originally identified sea urchin cortical serine protease, CGSP1. These conserved sequences contained the catalytic triad necessary for enzymatic activity, and the tandemly repeated LDLr-like repeats. We conclude that the protease involved in the slow block to polyspermy is an essential and conserved element of fertilization in echinoderms, and may provide an important reagent for identification and testing of the cell surface proteins in eggs necessary for sperm binding.
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Affiliation(s)
- Nathalie Oulhen
- Department of Molecular and Cell Biology and Biochemistry, Brown University, 185 Meeting St., Providence, RI 02912, USA
| | - Dongdong Xu
- Department of Molecular and Cell Biology and Biochemistry, Brown University, 185 Meeting St., Providence, RI 02912, USA; Marine Fishery Institute of Zhejiang Province, Key Lab of Mariculture and Enhancement of Zhejiang Province, 316100 Zhoushan, Zhejiang Province, PR China
| | - Gary M Wessel
- Department of Molecular and Cell Biology and Biochemistry, Brown University, 185 Meeting St., Providence, RI 02912, USA.
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Wessel GM, Fresques T, Kiyomoto M, Yajima M, Zazueta V. Origin and development of the germ line in sea stars. Genesis 2014; 52:367-77. [PMID: 24648114 PMCID: PMC4116737 DOI: 10.1002/dvg.22772] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 03/14/2014] [Indexed: 12/17/2022]
Abstract
This review summarizes and integrates our current understanding of how sea stars make gametes. Although little is known of the mechanism of germ line formation in these animals, recent results point to specific cells and to cohorts of molecules in the embryos and larvae that may lay the ground work for future research efforts. A coelomic outpocketing forms in the posterior of the gut in larvae, referred to as the posterior enterocoel (PE), that when removed, significantly reduces the number of germ cell later in larval growth. This same PE structure also selectively accumulates several germ-line associated factors-vasa, nanos, piwi-and excludes factors involved in somatic cell fate. Since its formation is relatively late in development, these germ cells may form by inductive mechanisms. When integrated into the morphological observations of germ cells and gonad development in larvae, juveniles, and adults, the field of germ line determination appears to have a good model system to study inductive germ line determination to complement the recent work on the molecular mechanisms in mice. We hope this review will also guide investigators interested in germ line determination and regulation of the germ line into how these animals can help in this research field. The review is not intended to be comprehensive-sea star reproduction has been studied for over 100 years and many reviews are comprehensive in their coverage of, for example, seasonal growth of the gonads in response to light, nutrient, and temperature. Rather the intent of this review is to help the reader focus on new experimental results attached to the historical underpinnings of how the germ cell functions in sea stars with particular emphasis to clarify the important areas of priority for future research.
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Affiliation(s)
- Gary M. Wessel
- Department of Molecular and Cellular Biology, Brown University, Providence RI USA
| | - Tara Fresques
- Department of Molecular and Cellular Biology, Brown University, Providence RI USA
| | | | - Mamiko Yajima
- Department of Molecular and Cellular Biology, Brown University, Providence RI USA
| | - Vanesa Zazueta
- Department of Molecular and Cellular Biology, Brown University, Providence RI USA
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21
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Oulhen N, Onorato TM, Ramos I, Wessel GM. Dysferlin is essential for endocytosis in the sea star oocyte. Dev Biol 2013; 388:94-102. [PMID: 24368072 DOI: 10.1016/j.ydbio.2013.12.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/05/2013] [Accepted: 12/11/2013] [Indexed: 11/25/2022]
Abstract
Dysferlin is a calcium-binding transmembrane protein involved in membrane fusion and membrane repair. In humans, mutations in the dysferlin gene are associated with muscular dystrophy. In this study, we isolated plasma membrane-enriched fractions from full-grown immature oocytes of the sea star, and identified dysferlin by mass spectrometry analysis. The full-length dysferlin sequence is highly conserved between human and the sea star. We learned that in the sea star Patiria miniata, dysferlin RNA and protein are expressed from oogenesis to gastrulation. Interestingly, the protein is highly enriched in the plasma membrane of oocytes. Injection of a morpholino against dysferlin leads to a decrease of endocytosis in oocytes, and to a developmental arrest during gastrulation. These results suggest that dysferlin is critical for normal endocytosis during oogenesis and for embryogenesis in the sea star and that this animal may be a useful model for studying the relationship of dysferlin structure as it relates to its function.
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Affiliation(s)
- Nathalie Oulhen
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence RI 02912, USA
| | - Thomas M Onorato
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence RI 02912, USA
| | - Isabela Ramos
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence RI 02912, USA
| | - Gary M Wessel
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence RI 02912, USA.
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22
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Abstract
Cell surface changes in an egg at fertilization are essential to begin development and for protecting the zygote. Most fertilized eggs construct a barrier around themselves by modifying their original extracellular matrix. This construction usually results from calcium-induced exocytosis of cortical granules, the contents of which in sea urchins function to form the fertilization envelope (FE), an extracellular matrix of cortical granule contents built upon a vitelline layer scaffold. Here, we examined the molecular mechanism of this process in sea stars, a close relative of the sea urchins, and analyze the evolutionary changes that likely occurred in the functionality of this structure between these two organisms. We find that the FE of sea stars is more permeable than in sea urchins, allowing diffusion of molecules in excess of 2 megadaltons. Through a proteomic and transcriptomic approach, we find that most, but not all, of the proteins present in the sea urchin envelope are present in sea stars, including SFE9, proteoliaisin, and rendezvin. The mRNAs encoding these FE proteins accumulated most densely in early oocytes, and then beginning with vitellogenesis, these mRNAs decreased in abundance to levels nearly undetectable in eggs. Antibodies to the SFE9 protein of sea stars showed that the cortical granules in sea star also accumulated most significantly in early oocytes, but different from sea urchins, they translocated to the cortex of the oocytes well before meiotic initiation. These results suggest that the preparation for cell surface changes in sea urchins has been shifted to later in oogenesis, and perhaps reflects the meiotic differences among the species-sea star oocytes are stored in prophase of meiosis and fertilized during the meiotic divisions, as in most animals, whereas sea urchins are one of the few taxons in which eggs have completed meiosis prior to fertilization.
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Affiliation(s)
- Nathalie Oulhen
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Adrian Reich
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Julian L. Wong
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Gary M. Wessel
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
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