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Othonicar MF, Garcia GS, Oliveira MT. The alternative enzymes-bearing tunicates lack multiple widely distributed genes coding for peripheral OXPHOS subunits. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149046. [PMID: 38642871 DOI: 10.1016/j.bbabio.2024.149046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 04/01/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
The respiratory chain alternative enzymes (AEs) NDX and AOX from the tunicate Ciona intestinalis (Ascidiacea) have been xenotopically expressed and characterized in human cells in culture and in the model organisms Drosophila melanogaster and mouse, with the purpose of developing bypass therapies to combat mitochondrial diseases in human patients with defective complexes I and III/IV, respectively. The fact that the genes coding for NDX and AOX have been lost from genomes of evolutionarily successful animal groups, such as vertebrates and insects, led us to investigate if the composition of the respiratory chain of Ciona and other tunicates differs significantly from that of humans and Drosophila, to accommodate the natural presence of AEs. We have failed to identify in tunicate genomes fifteen orthologous genes that code for subunits of the respiratory chain complexes; all of these putatively missing subunits are peripheral to complexes I, III and IV in mammals, and many are important for complex-complex interaction in supercomplexes (SCs), such as NDUFA11, UQCR11 and COX7A. Modeling of all respiratory chain subunit polypeptides of Ciona indicates significant structural divergence that is consistent with the lack of these fifteen clear orthologous subunits. We also provide evidence using Ciona AOX expressed in Drosophila that this AE cannot access the coenzyme Q pool reduced by complex I, but it is readily available to oxidize coenzyme Q molecules reduced by glycerophosphate oxidase, a mitochondrial inner membrane-bound dehydrogenase that is not involved in SCs. Altogether, our results suggest that Ciona AEs might have evolved in a mitochondrial inner membrane environment much different from that of mammals and insects, possibly without SCs; this correlates with the preferential functional interaction between these AEs and non-SC dehydrogenases in heterologous mammalian and insect systems. We discuss the implications of these findings for the applicability of Ciona AEs in human bypass therapies and for our understanding of the evolution of animal respiratory chain.
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Affiliation(s)
- Murilo F Othonicar
- Departamento de Biotecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - Geovana S Garcia
- Departamento de Biotecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - Marcos T Oliveira
- Departamento de Biotecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil.
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2
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Copley RR, Buttin J, Arguel MJ, Williaume G, Lebrigand K, Barbry P, Hudson C, Yasuo H. Early transcriptional similarities between two distinct neural lineages during ascidian embryogenesis. Dev Biol 2024; 514:1-11. [PMID: 38878991 DOI: 10.1016/j.ydbio.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/31/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024]
Abstract
In chordates, the central nervous system arises from precursors that have distinct developmental and transcriptional trajectories. Anterior nervous systems are ontogenically associated with ectodermal lineages while posterior nervous systems are associated with mesoderm. Taking advantage of the well-documented cell lineage of ascidian embryos, we asked to what extent the transcriptional states of the different neural lineages become similar during the course of progressive lineage restriction. We performed single-cell RNA sequencing (scRNA-seq) analyses on hand-dissected neural precursor cells of the two distinct lineages, together with those of their sister cell lineages, with a high temporal resolution covering five successive cell cycles from the 16-cell to neural plate stages. A transcription factor binding site enrichment analysis of neural specific genes at the neural plate stage revealed limited evidence for shared transcriptional control between the two neural lineages, consistent with their different ontogenies. Nevertheless, PCA analysis and hierarchical clustering showed that, by neural plate stages, the two neural lineages cluster together. Consistent with this, we identified a set of genes enriched in both neural lineages at the neural plate stage, including miR-124, Celf3.a, Zic.r-b, and Ets1/2. Altogether, the current study has revealed genome-wide transcriptional dynamics of neural progenitor cells of two distinct developmental origins. Our scRNA-seq dataset is unique and provides a valuable resource for future analyses, enabling a precise temporal resolution of cell types not previously described from dissociated embryos.
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Affiliation(s)
- Richard R Copley
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS UMR7009, 06230, Villefranche-sur-mer, France.
| | - Julia Buttin
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS UMR7009, 06230, Villefranche-sur-mer, France
| | - Marie-Jeanne Arguel
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, CNRS UMR 7275, 06560, Sophia Antipolis, France
| | - Géraldine Williaume
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS UMR7009, 06230, Villefranche-sur-mer, France
| | - Kevin Lebrigand
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, CNRS UMR 7275, 06560, Sophia Antipolis, France
| | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, CNRS UMR 7275, 06560, Sophia Antipolis, France
| | - Clare Hudson
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS UMR7009, 06230, Villefranche-sur-mer, France
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS UMR7009, 06230, Villefranche-sur-mer, France.
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3
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Ohta N, Christiaen L. Cellular remodeling and JAK inhibition promote zygotic gene expression in the Ciona germline. EMBO Rep 2024; 25:2188-2201. [PMID: 38649664 PMCID: PMC11094015 DOI: 10.1038/s44319-024-00139-0] [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: 01/30/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/25/2024] Open
Abstract
Transcription control is a major determinant of cell fate decisions in somatic tissues. By contrast, early germline fate specification in numerous vertebrate and invertebrate species relies extensively on RNA-level regulation, exerted on asymmetrically inherited maternal supplies, with little-to-no zygotic transcription. However delayed, a maternal-to-zygotic transition is nevertheless poised to complete the deployment of pre-gametic programs in the germline. Here, we focus on early germline specification in the tunicate Ciona to study zygotic genome activation. We first demonstrate that a peculiar cellular remodeling event excludes localized postplasmic Pem-1 mRNA, which encodes the general inhibitor of transcription. Subsequently, zygotic transcription begins in Pem-1-negative primordial germ cells (PGCs), as revealed by histochemical detection of elongating RNA Polymerase II, and nascent Mef2 transcripts. In addition, we uncover a provisional antagonism between JAK and MEK/BMPRI/GSK3 signaling, which controls the onset of zygotic gene expression, following cellular remodeling of PGCs. We propose a 2-step model for the onset of zygotic transcription in the Ciona germline and discuss the significance of germ plasm dislocation and remodeling in the context of developmental fate specification.
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Affiliation(s)
- Naoyuki Ohta
- Michael Sars Centre, University of Bergen, Bergen, Norway.
| | - Lionel Christiaen
- Michael Sars Centre, University of Bergen, Bergen, Norway.
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA.
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4
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Frese AN, Mariossi A, Levine MS, Wühr M. Quantitative proteome dynamics across embryogenesis in a model chordate. iScience 2024; 27:109355. [PMID: 38510129 PMCID: PMC10951915 DOI: 10.1016/j.isci.2024.109355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/11/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
The evolution of gene expression programs underlying the development of vertebrates remains poorly characterized. Here, we present a comprehensive proteome atlas of the model chordate Ciona, covering eight developmental stages and ∼7,000 translated genes, accompanied by a multi-omics analysis of co-evolution with the vertebrate Xenopus. Quantitative proteome comparisons argue against the widely held hourglass model, based solely on transcriptomic profiles, whereby peak conservation is observed during mid-developmental stages. Our analysis reveals maximal divergence at these stages, particularly gastrulation and neurulation. Together, our work provides a valuable resource for evaluating conservation and divergence of multi-omics profiles underlying the diversification of vertebrates.
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Affiliation(s)
- Alexander N. Frese
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Andrea Mariossi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael S. Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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5
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Negrón-Piñeiro LJ, Wu Y, Popsuj S, José-Edwards DS, Stolfi A, Di Gregorio A. Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona. Nat Commun 2024; 15:3025. [PMID: 38589372 PMCID: PMC11001920 DOI: 10.1038/s41467-024-46850-3] [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: 11/03/2022] [Accepted: 03/12/2024] [Indexed: 04/10/2024] Open
Abstract
Tissue-specific gene expression is fundamental in development and evolution, and is mediated by transcription factors and by the cis-regulatory regions (enhancers) that they control. Transcription factors and their respective tissue-specific enhancers are essential components of gene regulatory networks responsible for the development of tissues and organs. Although numerous transcription factors have been characterized from different organisms, the knowledge of the enhancers responsible for their tissue-specific expression remains fragmentary. Here we use Ciona to study the enhancers associated with ten transcription factors expressed in the notochord, an evolutionary hallmark of the chordate phylum. Our results illustrate how two evolutionarily conserved transcription factors, Brachyury and Foxa2, coordinate the deployment of other notochord transcription factors. The results of these detailed cis-regulatory analyses delineate a high-resolution view of the essential notochord gene regulatory network of Ciona, and provide a reference for studies of transcription factors, enhancers, and their roles in development, disease, and evolution.
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Affiliation(s)
- Lenny J Negrón-Piñeiro
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Yushi Wu
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Sydney Popsuj
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Diana S José-Edwards
- Post-Baccalaureate Premedical Program, Washington University, St. Louis, MO, 63130, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anna Di Gregorio
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA.
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6
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de Abreu Mello A, Motta Portal T, Allodi S, Nunes da Fonseca R, Monteiro de Barros C. Adrenoreceptor phylogeny and novel functions of nitric oxide in ascidian immune cells. J Invertebr Pathol 2024; 203:108057. [PMID: 38176675 DOI: 10.1016/j.jip.2023.108057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/27/2023] [Accepted: 12/31/2023] [Indexed: 01/06/2024]
Abstract
Nitric oxide (NO) is a simple molecule involved in many biological processes and functions in the cardiovascular, neural, and immune systems. In recent years, NO has also been recognized as a crucial messenger in communication between the nervous and immune systems. Together with NO, catecholamines are the main group of neurotransmitters involved in cross-talk between the nervous and immune systems. Catecholamines such as noradrenaline, can act on immune cells through adrenoreceptors (ARs) present on the cell surface, and NO can cross the cell membrane and interact with secondary messengers, modulating catecholamine production. Here, we analyzed the mutual modulation by noradrenaline and NO in Phallusia nigra immune cells for specific subtypes of ARs. We also investigated the involvement of protein kinases A and C as secondary messengers to these specific subtypes of ARs in the adrenergic signaling pathway that culminates in NO modulation, and the phylogenetic distribution of ARs in deuterostome genomes. This analysis provided evidence for single-copy orthologs of α1, α2 and β-AR in ascidian genomes, suggesting that NO and NA act on a less diverse set of ARs in urochordates. Pharmacological assays showed that high levels of NO can induce ascidian immune cells to produce catecholamines. We also observed that protein kinases A and C are the secondary messengers involved in downstream modulation of NO production through an ancestral β-AR. Taken together, these results provide new information on NO as a modulator of immune cells, and reveal the molecules involved in the signaling pathway of ARs. The results also indicate that ARs may participate in NO modulation. Finally, our results suggest that the common ancestor of urochordates possessed a less complex system of ARs required for immune action and diverse pharmacological responses, since the α-ARs are phylogenetically more related to D1-receptors than are the β-ARs.
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Affiliation(s)
- Andressa de Abreu Mello
- Laboratório Integrado de Biociências Translacionais, Instituto de Biodiversidade e Sustentabilidade, NUPEM, Universidade Federal do Rio de Janeiro, UFRJ, Macaé, RJ, Brazil; Laboratório de Neurobiologia Comparativa e do Desenvolvimento, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, RJ, Brazil
| | - Taynan Motta Portal
- Laboratório Integrado de Biociências Translacionais, Instituto de Biodiversidade e Sustentabilidade, NUPEM, Universidade Federal do Rio de Janeiro, UFRJ, Macaé, RJ, Brazil
| | - Silvana Allodi
- Laboratório de Neurobiologia Comparativa e do Desenvolvimento, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, RJ, Brazil
| | - Rodrigo Nunes da Fonseca
- Laboratório Integrado de Ciências Morfofuncionais, Instituto de Biodiversidade e Sustentabilidade- NUPEM, Universidade Federal do Rio de Janeiro, Campus UFRJ-Macaé, RJ, Brazil
| | - Cintia Monteiro de Barros
- Laboratório Integrado de Biociências Translacionais, Instituto de Biodiversidade e Sustentabilidade, NUPEM, Universidade Federal do Rio de Janeiro, UFRJ, Macaé, RJ, Brazil.
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7
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Matsubara S, Iguchi R, Ogasawara M, Nakamura H, Kataoka TR, Shiraishi A, Osugi T, Kawada T, Satake H. A Novel Hemocyte-Derived Peptide and Its Possible Roles in Immune Response of Ciona intestinalis Type A. Int J Mol Sci 2024; 25:1979. [PMID: 38396656 PMCID: PMC10888236 DOI: 10.3390/ijms25041979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/24/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
A wide variety of bioactive peptides have been identified in the central nervous system and several peripheral tissues in the ascidian Ciona intestinalis type A (Ciona robusta). However, hemocyte endocrine peptides have yet to be explored. Here, we report a novel 14-amino-acid peptide, CiEMa, that is predominant in the granular hemocytes and unilocular refractile granulocytes of Ciona. RNA-seq and qRT-PCR revealed the high CiEma expression in the adult pharynx and stomach. Immunohistochemistry further revealed the highly concentrated CiEMa in the hemolymph of the pharynx and epithelial cells of the stomach, suggesting biological roles in the immune response. Notably, bacterial lipopolysaccharide stimulation of isolated hemocytes for 1-4 h resulted in 1.9- to 2.4-fold increased CiEMa secretion. Furthermore, CiEMa-stimulated pharynx exhibited mRNA upregulation of the growth factor (Fgf3/7/10/22), vanadium binding proteins (CiVanabin1 and CiVanabin3), and forkhead and homeobox transcription factors (Foxl2, Hox3, and Dbx) but not antimicrobial peptides (CrPap-a and CrMam-a) or immune-related genes (Tgfbtun3, Tnfa, and Il17-2). Collectively, these results suggest that CiEMa plays roles in signal transduction involving tissue development or repair in the immune response, rather than in the direct regulation of immune response genes. The present study identified a novel Ciona hemocyte peptide, CiEMa, which paves the way for research on the biological roles of hemocyte peptides in chordates.
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Affiliation(s)
- Shin Matsubara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun 619-0284, Kyoto, Japan (H.S.)
| | - Rin Iguchi
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku 263-8522, Chiba, Japan
| | - Michio Ogasawara
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku 263-8522, Chiba, Japan
| | - Hiroya Nakamura
- Department of Pathology, Iwate Medical University, 2-1-1 Idaidori, Yahaba-cho, Shiwa-gun 028-3695, Iwate, Japan (T.R.K.)
| | - Tatsuki R. Kataoka
- Department of Pathology, Iwate Medical University, 2-1-1 Idaidori, Yahaba-cho, Shiwa-gun 028-3695, Iwate, Japan (T.R.K.)
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun 619-0284, Kyoto, Japan (H.S.)
| | - Tomohiro Osugi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun 619-0284, Kyoto, Japan (H.S.)
| | - Tsuyoshi Kawada
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun 619-0284, Kyoto, Japan (H.S.)
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun 619-0284, Kyoto, Japan (H.S.)
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8
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Pickett CJ, Gruner HN, Davidson B. Lhx3/4 initiates a cardiopharyngeal-specific transcriptional program in response to widespread FGF signaling. PLoS Biol 2024; 22:e3002169. [PMID: 38271304 PMCID: PMC10810493 DOI: 10.1371/journal.pbio.3002169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
Individual signaling pathways, such as fibroblast growth factors (FGFs), can regulate a plethora of inductive events. According to current paradigms, signal-dependent transcription factors (TFs), such as FGF/MapK-activated Ets family factors, partner with lineage-determining factors to achieve regulatory specificity. However, many aspects of this model have not been rigorously investigated. One key question relates to whether lineage-determining factors dictate lineage-specific responses to inductive signals or facilitate these responses in collaboration with other inputs. We utilize the chordate model Ciona robusta to investigate mechanisms generating lineage-specific induction. Previous studies in C. robusta have shown that cardiopharyngeal progenitor cells are specified through the combined activity of FGF-activated Ets1/2.b and an inferred ATTA-binding transcriptional cofactor. Here, we show that the homeobox TF Lhx3/4 serves as the lineage-determining TF that dictates cardiopharyngeal-specific transcription in response to pleiotropic FGF signaling. Targeted knockdown of Lhx3/4 leads to loss of cardiopharyngeal gene expression. Strikingly, ectopic expression of Lhx3/4 in a neuroectodermal lineage subject to FGF-dependent specification leads to ectopic cardiopharyngeal gene expression in this lineage. Furthermore, ectopic Lhx3/4 expression disrupts neural plate morphogenesis, generating aberrant cell behaviors associated with execution of incompatible morphogenetic programs. Based on these findings, we propose that combinatorial regulation by signal-dependent and lineage-determinant factors represents a generalizable, previously uncategorized regulatory subcircuit we term "cofactor-dependent induction." Integration of this subcircuit into theoretical models will facilitate accurate predictions regarding the impact of gene regulatory network rewiring on evolutionary diversification and disease ontogeny.
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Affiliation(s)
- C. J. Pickett
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Hannah N. Gruner
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Bradley Davidson
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America
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9
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Cano-Fernández H, Tissot T, Brun-Usan M, Salazar-Ciudad I. On the origins of developmental robustness: modeling buffering mechanisms against cell-level noise. Development 2023; 150:dev201911. [PMID: 38032004 DOI: 10.1242/dev.201911] [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: 04/25/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023]
Abstract
During development, cells are subject to stochastic fluctuations in their positions (i.e. cell-level noise) that can potentially lead to morphological noise (i.e. stochastic differences between morphologies that are expected to be equal, e.g. the right and left sides of bilateral organisms). In this study, we explore new and existing hypotheses on buffering mechanisms against cell-level noise. Many of these hypotheses focus on how the boundaries between territories of gene expression remain regular and well defined, despite cell-level noise and division. We study these hypotheses and how irregular territory boundaries lead to morphological noise. To determine the consistency of the different hypotheses, we use a general computational model of development: EmbryoMaker. EmbryoMaker can implement arbitrary gene networks regulating basic cell behaviors (contraction, adhesion, etc.), signaling and tissue biomechanics. We found that buffering mechanisms based on the orientation of cell divisions cannot lead to regular boundaries but that other buffering mechanisms can (homotypic adhesion, planar contraction, non-dividing boundaries, constant signaling and majority rule hypotheses). We also explore the effects of the shape and size of the territories on morphological noise.
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Affiliation(s)
- Hugo Cano-Fernández
- Genomics, Bioinformatics and Evolution group, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
| | - Tazzio Tissot
- Electronics and Computer Science Department, University of Southampton, Southampton SO17 1BJ, UK
| | - Miguel Brun-Usan
- Departamento de Biologia, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Isaac Salazar-Ciudad
- Genomics, Bioinformatics and Evolution group, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
- Centre de Recerca Matemàtica (CRM), Cerdanyola del Vallès 08193, Spain
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10
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Papadogiannis V, Hockman D, Mercurio S, Ramsay C, Hintze M, Patthey C, Streit A, Shimeld SM. Evolution of the expression and regulation of the nuclear hormone receptor ERR gene family in the chordate lineage. Dev Biol 2023; 504:12-24. [PMID: 37696353 DOI: 10.1016/j.ydbio.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/01/2023] [Accepted: 09/09/2023] [Indexed: 09/13/2023]
Abstract
The Estrogen Related Receptor (ERR) nuclear hormone receptor genes have a wide diversity of roles in vertebrate development. In embryos, ERR genes are expressed in several tissues, including the central and peripheral nervous systems. Here we seek to establish the evolutionary history of chordate ERR genes, their expression and their regulation. We examine ERR expression in mollusc, amphioxus and sea squirt embryos, finding the single ERR orthologue is expressed in the nervous system in all three, with muscle expression also found in the two chordates. We show that most jawed vertebrates and lampreys have four ERR paralogues, and that vertebrate ERR genes were ancestrally linked to Estrogen Receptor genes. One of the lamprey paralogues shares conserved expression domains with jawed vertebrate ERRγ in the embryonic vestibuloacoustic ganglion, eye, brain and spinal cord. Hypothesising that conserved expression derives from conserved regulation, we identify a suite of pan-vertebrate conserved non-coding sequences in ERR introns. We use transgenesis in lamprey and chicken embryos to show that these sequences are regulatory and drive reporter gene expression in the nervous system. Our data suggest an ancient association between ERR and the nervous system, including expression in cells associated with photosensation and mechanosensation. This includes the origin in the vertebrate common ancestor of a suite of regulatory elements in the 3' introns that drove nervous system expression and have been conserved from this point onwards.
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Affiliation(s)
| | - Dorit Hockman
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Silvia Mercurio
- Department of Environmental Science and Policy, Università Degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Claire Ramsay
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Mark Hintze
- Centre for Craniofacial & Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Cedric Patthey
- Department of Radiosciences, Umeå University, 901 85, Umeå, Sweden
| | - Andrea Streit
- Centre for Craniofacial & Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Sebastian M Shimeld
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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11
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Sumner JT, Andrasz CL, Johnson CA, Wax S, Anderson P, Keeling EL, Davidson JM. De novo genome assembly and comparative genomics for the colonial ascidian Botrylloides violaceus. G3 (BETHESDA, MD.) 2023; 13:jkad181. [PMID: 37555394 PMCID: PMC10542563 DOI: 10.1093/g3journal/jkad181] [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: 01/25/2023] [Revised: 01/25/2023] [Accepted: 07/12/2023] [Indexed: 08/10/2023]
Abstract
Ascidians have the potential to reveal fundamental biological insights related to coloniality, regeneration, immune function, and the evolution of these traits. This study implements a hybrid assembly technique to produce a genome assembly and annotation for the botryllid ascidian, Botrylloides violaceus. A hybrid genome assembly was produced using Illumina, Inc. short and Oxford Nanopore Technologies long-read sequencing technologies. The resulting assembly is comprised of 831 contigs, has a total length of 121 Mbp, N50 of 1 Mbp, and a BUSCO score of 96.1%. Genome annotation identified 13 K protein-coding genes. Comparative genomic analysis with other tunicates reveals patterns of conservation and divergence within orthologous gene families even among closely related species. Characterization of the Wnt gene family, encoding signaling ligands involved in development and regeneration, reveals conserved patterns of subfamily presence and gene copy number among botryllids. This supports the use of genomic data from nonmodel organisms in the investigation of biological phenomena.
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Affiliation(s)
- Jack T Sumner
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Cassidy L Andrasz
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Christine A Johnson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Sarah Wax
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Paul Anderson
- Department of Computer Science and Software Engineering, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Elena L Keeling
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Jean M Davidson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
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12
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Makabe KW, Jensen HI, Fodor ACA, Jeffery WR, Satoh N, Swalla BJ. Cymric, a Maternal and Zygotic HTK-16-Like SHARK Family Tyrosine Kinase Gene, Is Disrupted in Molgula occulta, a Tailless Ascidian. THE BIOLOGICAL BULLETIN 2023; 245:1-8. [PMID: 38820291 PMCID: PMC11147163 DOI: 10.1086/730536] [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] [Indexed: 06/02/2024]
Abstract
AbstractWe describe the cloning and expression of a nonreceptor tyrosine kinase, cymric (Uro-1), a HTK-16-like (HydraTyrosineKinase-16) gene, identified in a subtractive screen for maternal ascidian cDNAs in Molgula oculata, an ascidian species with a tadpole larva. The cymric gene encodes a 4-kb mRNA expressed in gonads, eggs, and embryos in the tailed M. oculata but is not detected in eggs or embryos of the closely related tailless species Molgula occulta. There is a large insertion in cymric in the M. occulta genome, as shown by transcriptome and genome analyses, resulting in it becoming a pseudogene. The cymric amino acid sequence encodes a nonreceptor tyrosine kinase with an N-terminal region containing two SH2 domains and five ankyrin repeats, similar to the HTK-16-like gene found in other ascidians. Thus, the ascidian cymric genes are members of the SHARK (Src-homology ankyrin-repeat containing tyrosine kinase) family of nonreceptor tyrosine kinases, which are found throughout invertebrates and missing from vertebrates. We show that cymric is lacking the tyrosine kinase domain in the tailless M. occulta, although the truncated mRNA is still expressed in transcriptome data. This maternal and zygotic HTK-16-like tyrosine kinase is another described pseudogene from M. occulta and appears not to be necessary for adult development.
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Affiliation(s)
- Kazuhiro W. Makabe
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima 770-8506, Japan
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Hannah I. Jensen
- Biology Department and Friday Harbor Laboratories, University of Washington, Seattle, WA 98195
| | - Alexander C. A. Fodor
- Biology Department and Friday Harbor Laboratories, University of Washington, Seattle, WA 98195
| | - William R. Jeffery
- Station Biologique, Roscoff, France
- Biology Department, University of Maryland, College Park, MD, 20742
| | - Noriyuki Satoh
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Billie J. Swalla
- Biology Department and Friday Harbor Laboratories, University of Washington, Seattle, WA 98195
- Station Biologique, Roscoff, France
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13
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Schuster HC, Hirth F. Phylogenetic tracing of midbrain-specific regulatory sequences suggests single origin of eubilaterian brains. SCIENCE ADVANCES 2023; 9:eade8259. [PMID: 37224241 PMCID: PMC10208574 DOI: 10.1126/sciadv.ade8259] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 04/18/2023] [Indexed: 05/26/2023]
Abstract
Conserved cis-regulatory elements (CREs) control Engrailed-, Pax2-, and dachshund-related gene expression networks directing the formation and function of corresponding midbrain circuits in arthropods and vertebrates. Polarized outgroup analyses of 31 sequenced metazoan genomes representing all animal clades reveal the emergence of Pax2- and dachshund-related CRE-like sequences in anthozoan Cnidaria. The full complement, including Engrailed-related CRE-like sequences, is only detectable in spiralians, ecdysozoans, and chordates that have a brain; they exhibit comparable genomic locations and extensive nucleotide identities that reveal the presence of a conserved core domain, all of which are absent in non-neural genes and, together, distinguish them from randomly assembled sequences. Their presence concurs with a genetic boundary separating the rostral from caudal nervous systems, demonstrated for the metameric brains of annelids, arthropods, and chordates and the asegmental cycloneuralian and urochordate brain. These findings suggest that gene regulatory networks for midbrain circuit formation evolved within the lineage that led to the common ancestor of protostomes and deuterostomes.
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Affiliation(s)
- Helen C. Schuster
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, and Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
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14
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Fouché G, Argelaguet F, Faure E, Kervrann C. Immersive and interactive visualization of 3D spatio-temporal data using a space time hypercube: Application to cell division and morphogenesis analysis. FRONTIERS IN BIOINFORMATICS 2023; 3:998991. [PMID: 36969798 PMCID: PMC10031126 DOI: 10.3389/fbinf.2023.998991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 02/21/2023] [Indexed: 03/11/2023] Open
Abstract
The analysis of multidimensional time-varying datasets faces challenges, notably regarding the representation of the data and the visualization of temporal variations. We propose an extension of the well-known Space-Time Cube (STC) visualization technique in order to visualize time-varying 3D spatial data, taking advantage of the interaction capabilities of Virtual Reality (VR). First, we propose the Space-Time Hypercube (STH) as an abstraction for 3D temporal data, extended from the STC concept. Second, through the example of embryo development imaging dataset, we detail the construction and visualization of a STC based on a user-driven projection of the spatial and temporal information. This projection yields a 3D STC visualization, which can also encode additional numerical and categorical data. Additionally, we propose a set of tools allowing the user to filter and manipulate the 3D STC which benefits the visualization, exploration and interaction possibilities offered by VR. Finally, we evaluated the proposed visualization method in the context of 3D temporal cell imaging data analysis, through a user study (n = 5) reporting the feedback from five biologists. These domain experts also accompanied the application design as consultants, providing insights on how the STC visualization could be used for the exploration of complex 3D temporal morphogenesis data.
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Affiliation(s)
- Gwendal Fouché
- Inria de l’Université de Rennes, IRISA, CNRS, Rennes, France
| | - Ferran Argelaguet
- Inria de l’Université de Rennes, IRISA, CNRS, Rennes, France
- *Correspondence: Ferran Argelaguet, ; Charles Kervrann,
| | - Emmanuel Faure
- LIRMM, Université Montpellier, CNRS, Montpellier, France
| | - Charles Kervrann
- Inria de l’Université de Rennes, Rennes, France
- UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universités, Paris, France
- *Correspondence: Ferran Argelaguet, ; Charles Kervrann,
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15
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Improved Genome Editing in the Ascidian Ciona with CRISPR/Cas9 and TALEN. Methods Mol Biol 2023; 2637:375-388. [PMID: 36773161 DOI: 10.1007/978-1-0716-3016-7_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The ascidian Ciona intestinalis type A (or Ciona robusta) is an important organism for elucidating the mechanisms that make the chordate body plan. CRISPR/Cas9 and TAL effector nuclease (TALEN) are widely used to quickly address genetic functions in Ciona. Our previously reported method of CRISPR/Cas9-mediated mutagenesis in this animal has inferior mutation rates compared to those of TALENs. We here describe an updated way to effectively mutate genes with CRISPR/Cas9 in Ciona. Although the construction of TALENs is much more laborious than that of CRISPR/Cas9, this technique is useful for tissue-specific knockouts that are not easy even by the optimized CRISPR/Cas9 method.
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16
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Bettoni R, Hudson C, Williaume G, Sirour C, Yasuo H, de Buyl S, Dupont G. Model of neural induction in the ascidian embryo. PLoS Comput Biol 2023; 19:e1010335. [PMID: 36735746 PMCID: PMC9931142 DOI: 10.1371/journal.pcbi.1010335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 02/15/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
How cell specification can be controlled in a reproducible manner is a fundamental question in developmental biology. In ascidians, a group of invertebrate chordates, geometry plays a key role in achieving this control. Here, we use mathematical modeling to demonstrate that geometry dictates the neural-epidermal cell fate choice in the 32-cell stage ascidian embryo by a two-step process involving first the modulation of ERK signaling and second, the expression of the neural marker gene, Otx. The model describes signal transduction by the ERK pathway that is stimulated by FGF and attenuated by ephrin, and ERK-mediated control of Otx gene expression, which involves both an activator and a repressor of ETS-family transcription factors. Considering the measured area of cell surface contacts with FGF- or ephrin-expressing cells as inputs, the solutions of the model reproduce the experimental observations about ERK activation and Otx expression in the different cells under normal and perturbed conditions. Sensitivity analyses and computations of Hill coefficients allow us to quantify the robustness of the specification mechanism controlled by cell surface area and to identify the respective role played by each signaling input. Simulations also predict in which conditions the dual control of gene expression by an activator and a repressor that are both under the control of ERK can induce a robust ON/OFF control of neural fate induction.
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Affiliation(s)
- Rossana Bettoni
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
- Applied Physics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Brussels, Belgium
| | - Clare Hudson
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
- * E-mail: (CH); (GD)
| | - Géraldine Williaume
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Cathy Sirour
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Sophie de Buyl
- Applied Physics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Brussels, Belgium
| | - Geneviève Dupont
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Brussels, Belgium
- * E-mail: (CH); (GD)
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17
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Roca M, Besnardeau L, Christians E, McDougall A, Chenevert J, Castagnetti S. Acquisition of the spindle assembly checkpoint and its modulation by cell fate and cell size in a chordate embryo. Development 2023; 150:285941. [PMID: 36515557 DOI: 10.1242/dev.201145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
Abstract
The spindle assembly checkpoint (SAC) is a surveillance system that preserves genome integrity by delaying anaphase onset until all chromosomes are correctly attached to spindle microtubules. Recruitment of SAC proteins to unattached kinetochores generates an inhibitory signal that prolongs mitotic duration. Chordate embryos are atypical in that spindle defects do not delay mitotic progression during early development, implying that either the SAC is inactive or the cell-cycle target machinery is unresponsive. Here, we show that in embryos of the chordate Phallusia mammillata, the SAC delays mitotic progression from the 8th cleavage divisions. Unattached kinetochores are not recognized by the SAC machinery until the 7th cell cycle, when the SAC is acquired. After acquisition, SAC strength, which manifests as the degree of mitotic lengthening induced by spindle perturbations, is specific to different cell types and is modulated by cell size, showing similarity to SAC control in early Caenorhabditis elegans embryos. We conclude that SAC acquisition is a process that is likely specific to chordate embryos, while modulation of SAC efficiency in SAC proficient stages depends on cell fate and cell size, which is similar to non-chordate embryos.
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Affiliation(s)
- Marianne Roca
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), 06230 Villefranche-sur-Mer, France
| | - Lydia Besnardeau
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), 06230 Villefranche-sur-Mer, France
| | - Elisabeth Christians
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), 06230 Villefranche-sur-Mer, France
| | - Alex McDougall
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), 06230 Villefranche-sur-Mer, France
| | - Janet Chenevert
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), 06230 Villefranche-sur-Mer, France
| | - Stefania Castagnetti
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), 06230 Villefranche-sur-Mer, France
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18
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Ikenaga J, Aratake S, Yoshida K, Yoshida M. A novel role for ATP2B in ascidians: Ascidian-specific mutations in ATP2B contribute to sperm chemotaxis. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:430-437. [PMID: 35468255 DOI: 10.1002/jez.b.23133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 03/06/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Sperm chemotaxis, in which sperms are attracted to conspecific eggs via species-specific attractants, plays an important role in fertilization. This phenomenon has been observed in various animals and species-specific sperm attractants have been reported in some species. However, the mechanisms involved in the reception and recognition of the species-specific attractant by the sperms is poorly studied. Previously, we found that the plasma membrane-type Ca2+ /ATPase (PMCA) is the receptor for the sperm-activating and -attracting factor (SAAF) in the ascidian Ciona intestinalis. To determine the role of PMCA in species-specific sperm chemotaxis, we identified the amino acid sequences of PMCAs derived from six Phlebobranchia species. The testis-specific splice variant of PMCA was found to be present in all the species investigated and the ascidian-specific sequence was detected near the 3'-terminus. Moreover, dN/dS analysis revealed that the extracellular loops 1, 2, and 4 in ascidian PMCA underwent a positive selection. These findings suggest that PMCA recognizes the species-specific structure of SAAF at the extracellular loops 1, 2, and 4, and its testis-specific C-terminal region is involved in the activation and chemotaxis of ascidian sperms.
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Affiliation(s)
- Jumpei Ikenaga
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Kanagawa, Japan
| | - Satoe Aratake
- Department of Urology, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Kaoru Yoshida
- Faculty of Biomedical Engineering, Toin University of Yokohama, 225-8503, Yokohama, Kanagawa, Japan
| | - Manabu Yoshida
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Kanagawa, Japan
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19
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Daugavet MA, Dobrynina MI, Shaposhnikova TG, Solovyeva AI, Mittenberg AG, Shabelnikov SV, Babkina IY, Grinchenko AV, Ilyaskina DV, Podgornaya OI. New putative phenol oxidase in ascidian blood cells. Sci Rep 2022; 12:14326. [PMID: 35995990 PMCID: PMC9395347 DOI: 10.1038/s41598-022-18283-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
The phenol oxidase system is ancient and ubiquitously distributed in all living organisms. In various groups it serves for the biosynthesis of pigments and neurotransmitters (dopamine), defence reactions and tissue hardening. Ascidians belong to subphylum Tunicata, which is considered the closest living relative to Vertebrates. Two phenol oxidases previously described for ascidians are vertebrate-like and arthropod-like phenol oxidases. In our present study, we described a new ascidian protein, Tuphoxin, with putative phenol oxidase function, which bears no sequence similarity with two enzymes described previously. The closest related proteins to Tuphoxin are mollusc haemocyanins. Unlike haemocyanins, which are oxygen transporting plasma proteins, Tuphoxin is synthesised in ascidian blood cells and secreted in the extracellular matrix of the tunic—ascidian outer coverings. Single mature transcript coding for this phenol oxidase can give several protein products of different sizes. Thus limited proteolysis of the initial protein is suggested. A unique feature of Tuphoxins and their homologues among Tunicata is the presence of thrombospondin first type repeats (TSP1) domain in their sequence which is supposed to provide interaction with extracellular matrix. The finding of TSP1 in the structure of phenol oxidases is new and we consider this to be an innovation of Tunicata evolutionary lineage.
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Affiliation(s)
- M A Daugavet
- Institute of Cytology of Russian Academy of Sciences, St. Petersburg, Russia.
| | - M I Dobrynina
- Institute of Cytology of Russian Academy of Sciences, St. Petersburg, Russia
| | | | - A I Solovyeva
- Institute of Cytology of Russian Academy of Sciences, St. Petersburg, Russia.,Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
| | - A G Mittenberg
- Institute of Cytology of Russian Academy of Sciences, St. Petersburg, Russia
| | - S V Shabelnikov
- Institute of Cytology of Russian Academy of Sciences, St. Petersburg, Russia
| | - I Yu Babkina
- Saint-Petersburg State University, St. Petersburg, Russia
| | - A V Grinchenko
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Vladivostok, Russia
| | - D V Ilyaskina
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Vladivostok, Russia.,Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - O I Podgornaya
- Institute of Cytology of Russian Academy of Sciences, St. Petersburg, Russia.,Saint-Petersburg State University, St. Petersburg, Russia
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20
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Chowdhury R, Roure A, le Pétillon Y, Mayeur H, Daric V, Darras S. Highly distinct genetic programs for peripheral nervous system formation in chordates. BMC Biol 2022; 20:152. [PMID: 35761237 PMCID: PMC9238270 DOI: 10.1186/s12915-022-01355-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/20/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Vertebrates develop their peripheral nervous system (PNS) from transient unique embryonic structures, the neural crest, and the ectodermal placodes that are located at the border of the forming central nervous system. By contrast, in the invertebrate chordates, amphioxus and ascidians, a large part of the PNS originates at the opposite of the embryo, in the ventral ectoderm. In both groups, a biphasic mechanism regulates ventral PNS formation: high BMP levels specify a neurogenic territory within which glutamatergic epidermal sensory neuron formation is controlled by the Notch pathway. Given these similarities and the phylogenetic relationships within chordates, it is likely that ventral PNS is an ancestral feature in chordates and that it has been lost in vertebrates.
Results
In order to get insights into the molecular control of ventral PNS formation and to test the hypothesis of their homology and potential contribution to the emergence of vertebrate PNS, we undertook a close comparison of ventral PNS formation in the ascidian Phallusia mammillata and the amphioxus Branchiostoma lanceolatum. Using timed RNA-seq series, we identified novel markers of the ventral PNS during different phases of its development in both species. By extensively determining the expression of paralogous and orthologous genes, we observed that only a minority of genes have a shared expression in the ventral PNS. However, a large fraction of ventral PNS orthologous genes are expressed in the dorsally forming PNS of vertebrates.
Conclusions
Our work has significantly increased the molecular characterization of ventral PNS formation in invertebrate chordates. The low observed conservation of gene expression in the ventral PNS suggests that the amphioxus and ascidian ventral PNS are either not homologous, or alternatively extensive drift has occurred in their regulatory mechanisms following a long period (600 My) of separate evolution and accelerated evolution in the ascidian lineage. The homology to genes expressed in the dorsally forming PNS of vertebrates suggests that ancestral sensory neurons gene networks have been redeployed in vertebrates.
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21
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Papadogiannis V, Pennati A, Parker HJ, Rothbächer U, Patthey C, Bronner ME, Shimeld SM. Hmx gene conservation identifies the origin of vertebrate cranial ganglia. Nature 2022; 605:701-705. [PMID: 35585239 DOI: 10.1038/s41586-022-04742-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/07/2022] [Indexed: 12/30/2022]
Abstract
The evolutionary origin of vertebrates included innovations in sensory processing associated with the acquisition of a predatory lifestyle1. Vertebrates perceive external stimuli through sensory systems serviced by cranial sensory ganglia, whose neurons arise predominantly from cranial placodes; however, the understanding of the evolutionary origin of placodes and cranial sensory ganglia is hampered by the anatomical differences between living lineages and the difficulty in assigning homology between cell types and structures. Here we show that the homeobox transcription factor Hmx is a constitutive component of vertebrate sensory ganglion development and that in the tunicate Ciona intestinalis, Hmx is necessary and sufficient to drive the differentiation programme of bipolar tail neurons, cells previously thought to be homologues of neural crest2,3. Using Ciona and lamprey transgenesis, we demonstrate that a unique, tandemly duplicated enhancer pair regulated Hmx expression in the stem-vertebrate lineage. We also show notably robust vertebrate Hmx enhancer function in Ciona, demonstrating that deep conservation of the upstream regulatory network spans the evolutionary origin of vertebrates. These experiments demonstrate regulatory and functional conservation between Ciona and vertebrate Hmx, and point to bipolar tail neurons as homologues of cranial sensory ganglia.
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Affiliation(s)
- Vasileios Papadogiannis
- Department of Zoology, University of Oxford, Oxford, UK.,Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes, Crete, Greece
| | - Alessandro Pennati
- Department of Zoology, University of Oxford, Oxford, UK.,Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Ute Rothbächer
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Cedric Patthey
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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22
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Vanni V, Salonna M, Gasparini F, Martini M, Anselmi C, Gissi C, Manni L. Yamanaka Factors in the Budding Tunicate Botryllus schlosseri Show a Shared Spatio-Temporal Expression Pattern in Chordates. Front Cell Dev Biol 2022; 10:782722. [PMID: 35342743 PMCID: PMC8948423 DOI: 10.3389/fcell.2022.782722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/09/2022] [Indexed: 01/22/2023] Open
Abstract
In vertebrates, the four transcription factors Sox2, c-Myc, Pou5f1 and Klf4 are involved in the differentiation of several tissues during vertebrate embryogenesis; moreover, they are normally co-expressed in embryonic stem cells and play roles in pluripotency, self-renewal, and maintenance of the undifferentiated state in adult cells. The in vitro forced co-expression of these factors, named Yamanaka factors (YFs), induces pluripotency in human or mouse fibroblasts. Botryllus schlosseri is a colonial tunicate undergoing continuous stem cell-mediated asexual development, providing a valuable model system for the study of pluripotency in the closest living relatives of vertebrates. In this study, we identified B. schlosseri orthologs of human Sox2 and c-Myc genes, as well as the closest homologs of the vertebrate-specific Pou5f1 gene, through an in-depth evolutionary analysis of the YF gene families in tunicates and other deuterostomes. Then, we studied the expression of these genes during the asexual cycle of B. schlosseri using in situ hybridization in order to investigate their possible involvement in tissue differentiation and in pluripotency maintenance. Our results show a shared spatio-temporal expression pattern consistent with the reported functions of these genes in invertebrate and vertebrate embryogenesis. Moreover, Myc, SoxB1 and Pou3 were expressed in candidate stem cells residing in their niches, while Pou2 was found expressed exclusively in the immature previtellogenic oocytes, both in gonads and circulating in the colonial vascular system. Our data suggest that Myc, SoxB1 and Pou3 may be individually involved in the differentiation of the same territories seen in other chordates, and that, together, they may play a role in stemness even in this colonial ascidian.
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Affiliation(s)
- Virginia Vanni
- Department of Biology, University of Padova, Padova, Italy
| | - Marika Salonna
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | | | | | - Chiara Anselmi
- Stanford University, Hopkins Marine Station, Pacific Grove, CA, United States.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Carmela Gissi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy.,IBIOM, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale Delle Ricerche, Bari, Italy.,CoNISMa, Consorzio Nazionale Interuniversitario per le Scienze Del Mare, Roma, Italy
| | - Lucia Manni
- Department of Biology, University of Padova, Padova, Italy
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23
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Tokuoka M, Kobayashi K, Lemaire P, Satou Y. Protein kinases and protein phosphatases encoded in the Ciona robusta genome. Genesis 2022; 60:e23471. [PMID: 35261143 DOI: 10.1002/dvg.23471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/24/2022] [Accepted: 02/27/2022] [Indexed: 11/06/2022]
Abstract
Protein kinases (PKs) and protein phosphatases (PPs) regulate the phosphorylation of proteins that are involved in a variety of biological processes. To study such biological processes systematically, it is important to know the whole repertoire of PKs and PPs encoded in a genome. In the present study, we surveyed the genome of an ascidian (Ciona robusta or Ciona intestinalis type A) to comprehensively identify the genes that encoded PKs and PPs. Because ascidians belong to the sister group of vertebrates, a comparison of the whole repertoire of PKs and PPs of ascidians with those of vertebrates may help to delineate the complements of these proteins that were present in the last common ancestor of these two groups of animals. Our results show that the repertory of PPs was much more expanded in vertebrates than the repertory of PKs. We also showed that approximately 75% of PKs and PPs were expressed during development from eggs to larvae. Thus, the present study provides catalogs for PKs and PPs encoded in the ascidian genome. These catalogs will be useful for systematic studies of biological processes that involve phosphorylation and for evolutionary studies of the origin of vertebrates.
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Affiliation(s)
- Miki Tokuoka
- Institut de Biologie du Développement de Marseille (IBDM), CNRS, Aix-Marseille Université, Marseille, France.,Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Kenji Kobayashi
- Institut de Biologie du Développement de Marseille (IBDM), CNRS, Aix-Marseille Université, Marseille, France.,Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Patrick Lemaire
- Institut de Biologie du Développement de Marseille (IBDM), CNRS, Aix-Marseille Université, Marseille, France.,Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), CNRS, Université de Montpellier, Montpellier, France
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
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24
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Satou Y, Tokuoka M, Oda-Ishii I, Tokuhiro S, Ishida T, Liu B, Iwamura Y. A Manually Curated Gene Model Set for an Ascidian, Ciona robusta (Ciona intestinalis Type A). Zoolog Sci 2022; 39:253-260. [DOI: 10.2108/zs210102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/15/2022] [Indexed: 11/17/2022]
Affiliation(s)
- Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Miki Tokuoka
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Izumi Oda-Ishii
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Sinichi Tokuhiro
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Tasuku Ishida
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Boqi Liu
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yuri Iwamura
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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25
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Aase-Remedios ME, Coll-Lladó C, Ferrier DEK. Amphioxus muscle transcriptomes reveal vertebrate-like myoblast fusion genes and a highly conserved role of insulin signalling in the metabolism of muscle. BMC Genomics 2022; 23:93. [PMID: 35105312 PMCID: PMC8805411 DOI: 10.1186/s12864-021-08222-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/25/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The formation and functioning of muscles are fundamental aspects of animal biology, and the evolution of 'muscle genes' is central to our understanding of this tissue. Feeding-fasting-refeeding experiments have been widely used to assess muscle cellular and metabolic responses to nutrition. Though these studies have focused on vertebrate models and only a few invertebrate systems, they have found similar processes are involved in muscle degradation and maintenance. Motivation for these studies stems from interest in diseases whose pathologies involve muscle atrophy, a symptom also triggered by fasting, as well as commercial interest in the muscle mass of animals kept for consumption. Experimentally modelling atrophy by manipulating nutritional state causes muscle mass to be depleted during starvation and replenished with refeeding so that the genetic mechanisms controlling muscle growth and degradation can be understood. RESULTS Using amphioxus, the earliest branching chordate lineage, we address the gap in previous work stemming from comparisons between distantly related vertebrate and invertebrate models. Our amphioxus feeding-fasting-refeeding muscle transcriptomes reveal a highly conserved myogenic program and that the pro-orthologues of many vertebrate myoblast fusion genes were present in the ancestral chordate, despite these invertebrate chordates having unfused mononucleate myocytes. We found that genes differentially expressed between fed and fasted amphioxus were orthologous to the genes that respond to nutritional state in vertebrates. This response is driven in a large part by the highly conserved IGF/Akt/FOXO pathway, where depleted nutrient levels result in activation of FOXO, a transcription factor with many autophagy-related gene targets. CONCLUSION Reconstruction of these gene networks and pathways in amphioxus muscle provides a key point of comparison between the distantly related groups assessed thus far, significantly refining the reconstruction of the ancestral state for chordate myoblast fusion genes and identifying the extensive role of duplicated genes in the IGF/Akt/FOXO pathway across animals. Our study elucidates the evolutionary trajectory of muscle genes as they relate to the increased complexity of vertebrate muscles and muscle development.
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Affiliation(s)
- Madeleine E Aase-Remedios
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK
| | - Clara Coll-Lladó
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK
| | - David E K Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK.
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26
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Wu Y, Devotta A, José-Edwards DS, Kugler JE, Negrón-Piñeiro LJ, Braslavskaya K, Addy J, Saint-Jeannet JP, Di Gregorio A. Xbp1 and Brachyury establish an evolutionarily conserved subcircuit of the notochord gene regulatory network. eLife 2022; 11:e73992. [PMID: 35049502 PMCID: PMC8803312 DOI: 10.7554/elife.73992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Gene regulatory networks coordinate the formation of organs and structures that compose the evolving body plans of different organisms. We are using a simple chordate model, the Ciona embryo, to investigate the essential gene regulatory network that orchestrates morphogenesis of the notochord, a structure necessary for the proper development of all chordate embryos. Although numerous transcription factors expressed in the notochord have been identified in different chordates, several of them remain to be positioned within a regulatory framework. Here, we focus on Xbp1, a transcription factor expressed during notochord formation in Ciona and other chordates. Through the identification of Xbp1-downstream notochord genes in Ciona, we found evidence of the early co-option of genes involved in the unfolded protein response to the notochord developmental program. We report the regulatory interplay between Xbp1 and Brachyury, and by extending these results to Xenopus, we show that Brachyury and Xbp1 form a cross-regulatory subcircuit of the notochord gene regulatory network that has been consolidated during chordate evolution.
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Affiliation(s)
- Yushi Wu
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| | - Arun Devotta
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| | - Diana S José-Edwards
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| | - Jamie E Kugler
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| | - Lenny J Negrón-Piñeiro
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| | - Karina Braslavskaya
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| | - Jermyn Addy
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| | | | - Anna Di Gregorio
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
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27
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Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva Pérez N, Fornes O, Leung T, Aguirre A, Hammal F, Schmelter D, Baranasic D, Ballester B, Sandelin A, Lenhard B, Vandepoele K, Wasserman WW, Parcy F, Mathelier A. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res 2022; 50:D165-D173. [PMID: 34850907 PMCID: PMC8728201 DOI: 10.1093/nar/gkab1113] [Citation(s) in RCA: 795] [Impact Index Per Article: 397.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022] Open
Abstract
JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.
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Affiliation(s)
- Jaime A Castro-Mondragon
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Rafael Riudavets-Puig
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Ieva Rauluseviciute
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Roza Berhanu Lemma
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Laura Turchi
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
| | - Romain Blanc-Mathieu
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
| | - Jeremy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
| | - Paul Boddie
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Aziz Khan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305, USA
| | - Nicolás Manosalva Pérez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Oriol Fornes
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Tiffany Y Leung
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Alejandro Aguirre
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | | | - Daniel Schmelter
- UCSC Genome Browser, University of California Santa Cruz, Santa Cruz, CA95060, USA
| | - Damir Baranasic
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | | | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK2200 Copenhagen N, Denmark
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
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28
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Santana-Garcia W, Castro-Mondragon JA, Padilla-Gálvez M, Nguyen NT, Elizondo-Salas A, Ksouri N, Gerbes F, Thieffry D, Vincens P, Contreras-Moreira B, van Helden J, Thomas-Chollier M, Medina-Rivera A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:W670-W676. [PMID: 35544234 PMCID: PMC9252783 DOI: 10.1093/nar/gkac312] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/12/2022] [Accepted: 04/20/2022] [Indexed: 11/12/2022] Open
Abstract
RSAT (Regulatory Sequence Analysis Tools) enables the detection and the analysis of cis-regulatory elements in genomic sequences. This software suite performs (i) de novo motif discovery (including from genome-wide datasets like ChIP-seq/ATAC-seq) (ii) genomic sequences scanning with known motifs, (iii) motif analysis (quality assessment, comparisons and clustering), (iv) analysis of regulatory variations and (v) comparative genomics. RSAT comprises 50 tools. Six public Web servers (including a teaching server) are offered to meet the needs of different biological communities. RSAT philosophy and originality are: (i) a multi-modal access depending on the user needs, through web forms, command-line for local installation and programmatic web services, (ii) a support for virtually any genome (animals, bacteria, plants, totalizing over 10 000 genomes directly accessible). Since the 2018 NAR Web Software Issue, we have developed a large REST API, extended the support for additional genomes and external motif collections, enhanced some tools and Web forms, and developed a novel tool that builds or refine gene regulatory networks using motif scanning (network-interactions). The RSAT website provides extensive documentation, tutorials and published protocols. RSAT code is under open-source license and now hosted in GitHub. RSAT is available at http://www.rsat.eu/.
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Affiliation(s)
| | | | - Mónica Padilla-Gálvez
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Blvd Juriquilla 3001, 76230 Santiago de Querétaro, México
| | - Nga Thi Thuy Nguyen
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Ana Elizondo-Salas
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Blvd Juriquilla 3001, 76230 Santiago de Querétaro, México
| | - Najla Ksouri
- Estación Experimental de Aula Dei-CSIC, 50059 Zaragoza, Spain
| | - François Gerbes
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
| | - Denis Thieffry
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Pierre Vincens
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
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29
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Yu D, Iwamura Y, Satou Y, Oda-Ishii I. Tbx15/18/22 shares a binding site with Tbx6-r.b to maintain expression of a muscle structural gene in ascidian late embryos. Dev Biol 2021; 483:1-12. [PMID: 34963554 DOI: 10.1016/j.ydbio.2021.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 12/25/2022]
Abstract
The ascidian larval tail contains muscle cells for swimming. Most of these muscle cells differentiate autonomously. The genetic program behind this autonomy has been studied extensively and the genetic cascade from maternal factors to initiation of expression of a muscle structural gene, Myl.c, has been uncovered; Myl.c expression is directed initially by transcription factor Tbx6-r.b at the 64-cell stage and then by the combined actions of Tbx6-r.b and Mrf from the gastrula to early tailbud stages. In the present study, we showed that transcription of Myl.c continued in late tailbud embryos and larvae, although a fusion protein of Tbx6-r.b and GFP was hardly detectable in late tailbud embryos. A knockdown experiment, reporter assay, and in vitro binding assay indicated that an essential cis-regulatory element of Myl.c that bound Tbx6-r.b in early embryos bound Tbx15/18/22 in late embryos to maintain expression of Myl.c. We also found that Tbx15/18/22 was controlled by Mrf, which constitutes a regulatory loop with Tbx6-r.b. Therefore, our data indicated that Tbx15/18/22 was activated initially under control of this regulatory loop as in the case of Myl.c, and then Tbx15/18/22 maintained the expression of Myl.c after Tbx6-r.b had disappeared. RNA-sequencing of Tbx15/18/22 morphant embryos revealed that many muscle structural genes were regulated similarly by Tbx15/18/22. Thus, the present study revealed the mechanisms of maintenance of transcription of muscle structural genes in late embryos in which Tbx15/18/22 takes the place of Tbx6-r.b.
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Affiliation(s)
- Deli Yu
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Yuri Iwamura
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan.
| | - Izumi Oda-Ishii
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
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30
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Funakoshi HM, Shito TT, Oka K, Hotta K. Developmental Table and Three-Dimensional Embryological Image Resource of the Ascidian Ascidiella aspersa. Front Cell Dev Biol 2021; 9:789046. [PMID: 34977032 PMCID: PMC8718802 DOI: 10.3389/fcell.2021.789046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Ascidiella aspersa is an ascidian in the class of chordates—the closest relatives of vertebrates. A. aspersa is a potential model organism for bio-imaging studies due to its extremely transparent embryos as well as is a globally distributed cosmopolitan species. However, there is no standard developmental table for this organism. Here, as a first step to establish A. aspersa as a model organism, we report a standard developmental table as a web-based digital image resource. This resource used confocal laser scanning microscopy to scan more than 3,000 cross-sectional images and 3D-reconstructed images of A. aspersa embryos during embryogenesis. With reference to the standardized developmental table of Ciona intestinalis type A, 26 different developmental stages (Stages 1–26) from fertilized eggs to hatched larvae were redefined for A. aspersa. Cell lineages up to the cleavage period were annotated: The cleavage patterns, the embryonic morphology, and the developmental time were then compared with Ciona. We found that the cleavage patterns and developmental time up to the neurula period in A. aspersa were extremely conserved versus. Ciona. The ratio of the trunk and tail length in the tailbud period were smaller than Ciona indicating a relatively short tail. In addition, the timing of the bending of the tail is earlier than Ciona. This A. aspersa standard 3D digital resource is essential for connecting different omics data to different spatiotemporal hierarchies and is useful for a system-level understanding of chordate development and evolution.
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Affiliation(s)
- Haruka M. Funakoshi
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Takumi T. Shito
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Kotaro Oka
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, Shinjuku, Japan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Kohji Hotta
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
- *Correspondence: Kohji Hotta,
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31
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Parra-Rincón E, Velandia-Huerto CA, Gittenberger A, Fallmann J, Gatter T, Brown FD, Stadler PF, Bermúdez-Santana CI. The Genome of the "Sea Vomit" Didemnum vexillum. Life (Basel) 2021; 11:life11121377. [PMID: 34947908 PMCID: PMC8704543 DOI: 10.3390/life11121377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 11/25/2022] Open
Abstract
Tunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes have not been studied extensively in the past, and comparative studies of tunicate genomes have remained scarce. The carpet sea squirt Didemnum vexillum, commonly known as “sea vomit”, is a colonial tunicate considered an invasive species with substantial ecological and economical risk. We report the assembly of the D. vexillum genome using a hybrid approach that combines 28.5 Gb Illumina and 12.35 Gb of PacBio data. The new hybrid scaffolded assembly has a total size of 517.55 Mb that increases contig length about eightfold compared to previous, Illumina-only assembly. As a consequence of an unusually high genetic diversity of the colonies and the moderate length of the PacBio reads, presumably caused by the unusually acidic milieu of the tunic, the assembly is highly fragmented (L50 = 25,284, N50 = 6539). It is sufficient, however, for comprehensive annotations of both protein-coding genes and non-coding RNAs. Despite its shortcomings, the draft assembly of the “sea vomit” genome provides a valuable resource for comparative tunicate genomics and for the study of the specific properties of colonial ascidians.
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Affiliation(s)
- Ernesto Parra-Rincón
- Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C 111321, Colombia; (E.P.-R.); (P.F.S.)
| | - Cristian A. Velandia-Huerto
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany; (J.F.); (T.G.)
- Correspondence: (C.A.V.-H.); (C.I.B.-S.)
| | - Adriaan Gittenberger
- GiMaRIS, Rijksstraatweg 75, 2171 AK Sassenheim, The Netherlands;
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany; (J.F.); (T.G.)
| | - Thomas Gatter
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany; (J.F.); (T.G.)
| | - Federico D. Brown
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, Rua do Matão, Tr. 14 no. 101, São Paulo 05508-090, Brazil;
- Centro de Biologia Marinha, Universidade de São Paulo, Rod. Manuel Hypólito do Rego km. 131.5, São Sebastião 11612-109, Brazil
| | - Peter F. Stadler
- Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C 111321, Colombia; (E.P.-R.); (P.F.S.)
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany; (J.F.); (T.G.)
- Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria
- Santa Fe Institute, Santa Fe, NM 87506, USA
| | - Clara I. Bermúdez-Santana
- Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C 111321, Colombia; (E.P.-R.); (P.F.S.)
- Correspondence: (C.A.V.-H.); (C.I.B.-S.)
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32
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Williaume G, de Buyl S, Sirour C, Haupaix N, Bettoni R, Imai KS, Satou Y, Dupont G, Hudson C, Yasuo H. Cell geometry, signal dampening, and a bimodal transcriptional response underlie the spatial precision of an ERK-mediated embryonic induction. Dev Cell 2021; 56:2966-2979.e10. [PMID: 34672970 DOI: 10.1016/j.devcel.2021.09.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 07/16/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Precise control of lineage segregation is critical for the development of multicellular organisms, but our quantitative understanding of how variable signaling inputs are integrated to activate lineage-specific gene programs remains limited. Here, we show how precisely two out of eight ectoderm cells adopt neural fates in response to ephrin and FGF signals during ascidian neural induction. In each ectoderm cell, FGF signals activate ERK to a level that mirrors its cell contact surface with FGF-expressing mesendoderm cells. This gradual interpretation of FGF inputs is followed by a bimodal transcriptional response of the immediate early gene, Otx, resulting in its activation specifically in the neural precursors. At low levels of ERK, Otx is repressed by an ETS family transcriptional repressor, ERF2. Ephrin signals are critical for dampening ERK activation levels across ectoderm cells so that only neural precursors exhibit above-threshold levels, evade ERF repression, and "switch on" Otx transcription.
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Affiliation(s)
- Géraldine Williaume
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Sophie de Buyl
- Applied Physics Research Group, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, 1050 Brussels, Belgium
| | - Cathy Sirour
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Nicolas Haupaix
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Rossana Bettoni
- Applied Physics Research Group, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, 1050 Brussels, Belgium; Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Kaoru S Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Geneviève Dupont
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium.
| | - Clare Hudson
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France.
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France.
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33
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Ferrández-Roldán A, Fabregà-Torrus M, Sánchez-Serna G, Duran-Bello E, Joaquín-Lluís M, Bujosa P, Plana-Carmona M, Garcia-Fernàndez J, Albalat R, Cañestro C. Cardiopharyngeal deconstruction and ancestral tunicate sessility. Nature 2021; 599:431-435. [PMID: 34789899 DOI: 10.1038/s41586-021-04041-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/17/2021] [Indexed: 12/26/2022]
Abstract
A central question in chordate evolution is the origin of sessility in adult ascidians, and whether the appendicularian complete free-living style represents a primitive or derived condition among tunicates1. According to the 'a new heart for a new head' hypothesis, the evolution of the cardiopharyngeal gene regulatory network appears as a pivotal aspect to understand the evolution of the lifestyles of chordates2-4. Here we show that appendicularians experienced massive ancestral losses of cardiopharyngeal genes and subfunctions, leading to the 'deconstruction' of two ancestral modules of the tunicate cardiopharyngeal gene regulatory network. In ascidians, these modules are related to early and late multipotency, which is involved in lineage cell-fate determination towards the first and second heart fields and siphon muscles. Our work shows that the deconstruction of the cardiopharyngeal gene regulatory network involved the regressive loss of the siphon muscle, supporting an evolutionary scenario in which ancestral tunicates had a sessile ascidian-like adult lifestyle. In agreement with this scenario, our findings also suggest that this deconstruction contributed to the acceleration of cardiogenesis and the redesign of the heart into an open-wide laminar structure in appendicularians as evolutionary adaptations during their transition to a complete pelagic free-living style upon the innovation of the food-filtering house5.
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Affiliation(s)
- Alfonso Ferrández-Roldán
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Marc Fabregà-Torrus
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Gaspar Sánchez-Serna
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Enya Duran-Bello
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Martí Joaquín-Lluís
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Paula Bujosa
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Marcos Plana-Carmona
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Jordi Garcia-Fernàndez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain. .,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
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34
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Winkley KM, Reeves WM, Veeman MT. Single-cell analysis of cell fate bifurcation in the chordate Ciona. BMC Biol 2021; 19:180. [PMID: 34465302 PMCID: PMC8408944 DOI: 10.1186/s12915-021-01122-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/12/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Inductive signaling interactions between different cell types are a major mechanism for the further diversification of embryonic cell fates. Most blastomeres in the model chordate Ciona robusta become restricted to a single predominant fate between the 64-cell and mid-gastrula stages. The deeply stereotyped and well-characterized Ciona embryonic cell lineages allow the transcriptomic analysis of newly established cell types very early in their divergence from sibling cell states without the pseudotime inference needed in the analysis of less synchronized cell populations. This is the first ascidian study to use droplet scRNAseq with large numbers of analyzed cells as early as the 64-cell stage when major lineages such as primary notochord first become fate restricted. RESULTS AND CONCLUSIONS We identify 59 distinct cell states, including new subregions of the b-line neural lineage and the early induction of the tail tip epidermis. We find that 34 of these cell states are directly or indirectly dependent on MAPK-mediated signaling critical to early Ciona patterning. Most of the MAPK-dependent bifurcations are canalized with the signal-induced cell fate lost upon MAPK inhibition, but the posterior endoderm is unique in being transformed into a novel state expressing some but not all markers of both endoderm and muscle. Divergent gene expression between newly bifurcated sibling cell types is dominated by upregulation in the induced cell type. The Ets family transcription factor Elk1/3/4 is uniquely upregulated in nearly all the putatively direct inductions. Elk1/3/4 upregulation together with Ets transcription factor binding site enrichment analysis enables inferences about which bifurcations are directly versus indirectly controlled by MAPK signaling. We examine notochord induction in detail and find that the transition between a Zic/Ets-mediated regulatory state and a Brachyury/FoxA-mediated regulatory state is unexpectedly late. This supports a "broad-hourglass" model of cell fate specification in which many early tissue-specific genes are induced in parallel to key tissue-specific transcriptional regulators via the same set of transcriptional inputs.
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Affiliation(s)
- Konner M Winkley
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Wendy M Reeves
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Michael T Veeman
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
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35
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Marotta P, Salatiello F, Ambrosino L, Berruto F, Chiusano ML, Locascio A. The Ascidia Ciona robusta Provides Novel Insights on the Evolution of the AP-1 Transcriptional Complex. Front Cell Dev Biol 2021; 9:709696. [PMID: 34414189 PMCID: PMC8369891 DOI: 10.3389/fcell.2021.709696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
The Activator Protein-1 transcription factor family (AP-1) transcriptional complex is historically defined as an early response group of transcription factors formed by dimeric complexes of the Jun, Fos, Atf, and Maf bZIP proteins that control cell proliferation and differentiation by regulating gene expression. It has been greatly investigated in many model organisms across metazoan evolution. Nevertheless, its complexity and variability of action made its multiple functions difficult to be defined. Here, we place the foundations for understanding the complexity of AP-1 transcriptional members in tunicates. We investigated the gene members of this family in the ascidian Ciona robusta and identified single copies of Jun, Fos, Atf3, Atf2/7, and Maf bZIP-related factors that could have a role in the formation of the AP-1 complex. We highlight that mesenchyme is a common cellular population where all these factors are expressed during embryonic development, and that, moreover, Fos shows a wider pattern of expression including also notochord and neural cells. By ectopic expression in transgenic embryos of Jun and Fos genes alone or in combination, we investigated the phenotypic alterations induced by these factors and highlighted a degree of functional conservation of the AP-1 complex between Ciona and vertebrates. The lack of gene redundancy and the first pieces of evidence of conserved functions in the control of cell movements and structural organization exerted by these factors open the way for using Ciona as a helpful model system to uncover the multiple potentialities of this highly complex family of bZIP transcription factors.
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Affiliation(s)
- Pina Marotta
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Naples, Italy.,Stazione Zoologica Anton Dohrn, Department of Research Infrastructures for Marine Biological Resources, Naples, Italy
| | - Federica Salatiello
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
| | - Luca Ambrosino
- Stazione Zoologica Anton Dohrn, Department of Research Infrastructures for Marine Biological Resources, Naples, Italy
| | - Federica Berruto
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
| | - Maria Luisa Chiusano
- Stazione Zoologica Anton Dohrn, Department of Research Infrastructures for Marine Biological Resources, Naples, Italy.,Department of Agriculture, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Annamaria Locascio
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
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36
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Fiuza UM, Lemaire P. Mechanical and genetic control of ascidian endoderm invagination during gastrulation. Semin Cell Dev Biol 2021; 120:108-118. [PMID: 34393069 DOI: 10.1016/j.semcdb.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/26/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Gastrulation is a near universal developmental process of animal embryogenesis, during which dramatic morphogenetic events take place: the mesodermal and endodermal tissues are internalized, the ectoderm spreads to cover the embryo surface, and the animal body plan and germ layers are established. Morphogenesis during gastrulation has long been considered the result of spatio-temporally localised forces driven by the transcriptional programme of the embryo. Recent work has shown that tissue rheological properties, which define the mechanical response of tissues to internally-generated or external forces, are also important dynamic regulators of gastrulation. Here, we first introduce how embryonic mechanics can be represented, before outlining current knowledge of the mechanical and genetic control of gastrulation in ascidians, invertebrate marine chordates which develop with invariant cell lineages and a solid-like rheological behaviour until the neurula stages. We discuss the potential of these organisms for the experimental and computational whole-embryo characterisation of the mechanisms shaping gastrulation, and how they may inform the more complex tissue internalization strategies used by other model organisms.
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Affiliation(s)
- Ulla-Maj Fiuza
- Systems Bioengineering, DCEXS, Universidad Pompeu Fabra, Doctor Aiguader, 88, 08003 Barcelona, Spain.
| | - Patrick Lemaire
- Centre de Recherches de Biologie cellulaire de Montpellier, CRBM, Université de Montpellier, CNRS, 1919 route de Mende, Montpellier, France.
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37
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Aase-Remedios ME, Ferrier DEK. Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.703163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Comparative approaches to understanding chordate genomes have uncovered a significant role for gene duplications, including whole genome duplications (WGDs), giving rise to and expanding gene families. In developmental biology, gene families created and expanded by both tandem and WGDs are paramount. These genes, often involved in transcription and signalling, are candidates for underpinning major evolutionary transitions because they are particularly prone to retention and subfunctionalisation, neofunctionalisation, or specialisation following duplication. Under the subfunctionalisation model, duplication lays the foundation for the diversification of paralogues, especially in the context of gene regulation. Tandemly duplicated paralogues reside in the same regulatory environment, which may constrain them and result in a gene cluster with closely linked but subtly different expression patterns and functions. Ohnologues (WGD paralogues) often diversify by partitioning their expression domains between retained paralogues, amidst the many changes in the genome during rediploidisation, including chromosomal rearrangements and extensive gene losses. The patterns of these retentions and losses are still not fully understood, nor is the full extent of the impact of gene duplication on chordate evolution. The growing number of sequencing projects, genomic resources, transcriptomics, and improvements to genome assemblies for diverse chordates from non-model and under-sampled lineages like the coelacanth, as well as key lineages, such as amphioxus and lamprey, has allowed more informative comparisons within developmental gene families as well as revealing the extent of conserved synteny across whole genomes. This influx of data provides the tools necessary for phylogenetically informed comparative genomics, which will bring us closer to understanding the evolution of chordate body plan diversity and the changes underpinning the origin and diversification of vertebrates.
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38
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Hudson C, Yasuo H. Neuromesodermal Lineage Contribution to CNS Development in Invertebrate and Vertebrate Chordates. Genes (Basel) 2021; 12:genes12040592. [PMID: 33920662 PMCID: PMC8073528 DOI: 10.3390/genes12040592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Ascidians are invertebrate chordates and the closest living relative to vertebrates. In ascidian embryos a large part of the central nervous system arises from cells associated with mesoderm rather than ectoderm lineages. This seems at odds with the traditional view of vertebrate nervous system development which was thought to be induced from ectoderm cells, initially with anterior character and later transformed by posteriorizing signals, to generate the entire anterior-posterior axis of the central nervous system. Recent advances in vertebrate developmental biology, however, show that much of the posterior central nervous system, or spinal cord, in fact arises from cells that share a common origin with mesoderm. This indicates a conserved role for bi-potential neuromesoderm precursors in chordate CNS formation. However, the boundary between neural tissue arising from these distinct neural lineages does not appear to be fixed, which leads to the notion that anterior-posterior patterning and neural fate formation can evolve independently.
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39
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Aase-Remedios ME, Coll-Lladó C, Ferrier DEK. More Than One-to-Four via 2R: Evidence of an Independent Amphioxus Expansion and Two-Gene Ancestral Vertebrate State for MyoD-Related Myogenic Regulatory Factors (MRFs). Mol Biol Evol 2021; 37:2966-2982. [PMID: 32520990 PMCID: PMC7530620 DOI: 10.1093/molbev/msaa147] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The evolutionary transition from invertebrates to vertebrates involved extensive gene duplication, but understanding precisely how such duplications contributed to this transition requires more detailed knowledge of specific cases of genes and gene families. Myogenic differentiation (MyoD) has long been recognized as a master developmental control gene and member of the MyoD family of bHLH transcription factors (myogenic regulatory factors [MRFs]) that drive myogenesis across the bilaterians. Phylogenetic reconstructions within this gene family are complicated by multiple instances of gene duplication and loss in several lineages. Following two rounds of whole-genome duplication (2R WGD) at the origin of the vertebrates, the ancestral function of MRFs is thought to have become partitioned among the daughter genes, so that MyoD and Myf5 act early in myogenic determination, whereas Myog and Myf6 are expressed later, in differentiating myoblasts. Comparing chordate MRFs, we find an independent expansion of MRFs in the invertebrate chordate amphioxus, with evidence for a parallel instance of subfunctionalization relative to that of vertebrates. Conserved synteny between chordate MRF loci supports the 2R WGD events as a major force in shaping the evolution of vertebrate MRFs. We also resolve vertebrate MRF complements and organization, finding a new type of vertebrate MRF gene in the process, which allowed us to infer an ancestral two-gene state in the vertebrates corresponding to the early- and late-acting types of MRFs. This necessitates a revision of previous conclusions about the simple one-to-four origin of vertebrate MRFs.
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Affiliation(s)
- Madeleine E Aase-Remedios
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Clara Coll-Lladó
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
| | - David E K Ferrier
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
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40
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Leclère L, Nir TS, Bazarsky M, Braitbard M, Schneidman-Duhovny D, Gat U. Dynamic Evolution of the Cthrc1 Genes, a Newly Defined Collagen-Like Family. Genome Biol Evol 2020; 12:3957-3970. [PMID: 32022859 PMCID: PMC7058181 DOI: 10.1093/gbe/evaa020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2020] [Indexed: 12/11/2022] Open
Abstract
Collagen triple helix repeat containing protein 1 (Cthrc1) is a secreted glycoprotein reported to regulate collagen deposition and to be linked to the Transforming growth factor β/Bone morphogenetic protein and the Wnt/planar cell polarity pathways. It was first identified as being induced upon injury to rat arteries and was found to be highly expressed in multiple human cancer types. Here, we explore the phylogenetic and evolutionary trends of this metazoan gene family, previously studied only in vertebrates. We identify Cthrc1 orthologs in two distant cnidarian species, the sea anemone Nematostella vectensis and the hydrozoan Clytia hemisphaerica, both of which harbor multiple copies of this gene. We find that Cthrc1 clade-specific diversification occurred multiple times in cnidarians as well as in most metazoan clades where we detected this gene. Many other groups, such as arthropods and nematodes, have entirely lost this gene family. Most vertebrates display a single highly conserved gene, and we show that the sequence evolutionary rate of Cthrc1 drastically decreased within the gnathostome lineage. Interestingly, this reduction coincided with the origin of its conserved upstream neighboring gene, Frizzled 6 (FZD6), which in mice has been shown to functionally interact with Cthrc1. Structural modeling methods further reveal that the yet uncharacterized C-terminal domain of Cthrc1 is similar in structure to the globular C1q superfamily domain, also found in the C-termini of collagens VIII and X. Thus, our studies show that the Cthrc1 genes are a collagen-like family with a variable short collagen triple helix domain and a highly conserved C-terminal domain structure resembling the C1q family.
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Affiliation(s)
- Lucas Leclère
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Tal S Nir
- Department of Cell and Developmental Biology, Silberman Life Sciences Institute, The Hebrew University of Jerusalem, Israel
| | - Michael Bazarsky
- Department of Cell and Developmental Biology, Silberman Life Sciences Institute, The Hebrew University of Jerusalem, Israel
| | - Merav Braitbard
- Department of Biochemistry, Silberman Life Sciences Institute, The Hebrew University of Jerusalem, Israel
| | - Dina Schneidman-Duhovny
- Department of Biochemistry, Silberman Life Sciences Institute, The Hebrew University of Jerusalem, Israel.,School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Uri Gat
- Department of Cell and Developmental Biology, Silberman Life Sciences Institute, The Hebrew University of Jerusalem, Israel
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41
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Phylogenetic comparison of egg transparency in ascidians by hyperspectral imaging. Sci Rep 2020; 10:20829. [PMID: 33257720 PMCID: PMC7709464 DOI: 10.1038/s41598-020-77585-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/12/2020] [Indexed: 12/01/2022] Open
Abstract
The transparency of animals is an important biological feature. Ascidian eggs have various degrees of transparency, but this characteristic has not yet been measured quantitatively and comprehensively. In this study, we established a method for evaluating the transparency of eggs to first characterize the transparency of ascidian eggs across different species and to infer a phylogenetic relationship among multiple taxa in the class Ascidiacea. We measured the transmittance of 199 eggs from 21 individuals using a hyperspectral camera. The spectrum of the visual range of wavelengths (400–760 nm) varied among individuals and we calculated each average transmittance of the visual range as bio-transparency. When combined with phylogenetic analysis based on the nuclear 18S rRNA and the mitochondrial cytochrome c oxidase subunit I gene sequences, the bio-transparencies of 13 species were derived from four different families: Ascidiidae, Cionidae, Pyuridae, and Styelidae. The bio-transparency varied 10–90% and likely evolved independently in each family. Ascidiella aspersa showed extremely high (88.0 ± 1.6%) bio-transparency in eggs that was maintained in the “invisible” larva. In addition, it was indicated that species of the Ascidiidae family may have a phylogenetic constraint of egg transparency.
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42
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Coulcher JF, Roure A, Chowdhury R, Robert M, Lescat L, Bouin A, Carvajal Cadavid J, Nishida H, Darras S. Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos. eLife 2020; 9:e59157. [PMID: 33191918 PMCID: PMC7710358 DOI: 10.7554/elife.59157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/13/2020] [Indexed: 01/23/2023] Open
Abstract
Ascidians with very similar embryos but highly divergent genomes are thought to have undergone extensive developmental system drift. We compared, in four species (Ciona and Phallusia for Phlebobranchia, Molgula and Halocynthia for Stolidobranchia), gene expression and gene regulation for a network of six transcription factors regulating peripheral nervous system (PNS) formation in Ciona. All genes, but one in Molgula, were expressed in the PNS with some differences correlating with phylogenetic distance. Cross-species transgenesis indicated strong levels of conservation, except in Molgula, in gene regulation despite lack of sequence conservation of the enhancers. Developmental system drift in ascidians is thus higher for gene regulation than for gene expression and is impacted not only by phylogenetic distance, but also in a clade-specific manner and unevenly within a network. Finally, considering that Molgula is divergent in our analyses, this suggests deep conservation of developmental mechanisms in ascidians after 390 My of separate evolution.
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Affiliation(s)
- Joshua F Coulcher
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
| | - Agnès Roure
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
| | - Rafath Chowdhury
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
| | - Méryl Robert
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
| | - Laury Lescat
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
| | - Aurélie Bouin
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
| | - Juliana Carvajal Cadavid
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka UniversityToyonakaJapan
| | - Sébastien Darras
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM)Banyuls-sur-MerFrance
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43
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Tessler M, Gaffney JP, Oliveira AG, Guarnaccia A, Dobi KC, Gujarati NA, Galbraith M, Mirza JD, Sparks JS, Pieribone VA, Wood RJ, Gruber DF. A putative chordate luciferase from a cosmopolitan tunicate indicates convergent bioluminescence evolution across phyla. Sci Rep 2020; 10:17724. [PMID: 33082360 PMCID: PMC7576829 DOI: 10.1038/s41598-020-73446-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/10/2020] [Indexed: 01/17/2023] Open
Abstract
Pyrosomes are tunicates in the phylum Chordata, which also contains vertebrates. Their gigantic blooms play important ecological and biogeochemical roles in oceans. Pyrosoma, meaning "fire-body", derives from their brilliant bioluminescence. The biochemistry of this light production is unknown, but has been hypothesized to be bacterial in origin. We found that mixing coelenterazine-a eukaryote-specific luciferin-with Pyrosoma atlanticum homogenate produced light. To identify the bioluminescent machinery, we sequenced P. atlanticum transcriptomes and found a sequence match to a cnidarian luciferase (RLuc). We expressed this novel luciferase (PyroLuc) and, combined with coelenterazine, it produced light. A similar gene was recently predicted from a bioluminescent brittle star, indicating that RLuc-like luciferases may have evolved convergently from homologous dehalogenases across phyla (Cnidaria, Echinodermata, and Chordata). This report indicates that a widespread gene may be able to functionally converge, resulting in bioluminescence across animal phyla, and describes and characterizes the first putative chordate luciferase.
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Affiliation(s)
- Michael Tessler
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA. .,Department of Biology, St. Francis College, Brooklyn, NY, USA.
| | - Jean P Gaffney
- Department of Natural Sciences, Baruch College, City University of New York, New York, NY, 10010, USA. .,The Graduate Center, PhD Program in Biology, City University of New York, New York, USA.
| | - Anderson G Oliveira
- Departamento de Oceanografia Física, Química e, Geológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, 05508-120, Brazil
| | - Andrew Guarnaccia
- Department of Natural Sciences, Baruch College, City University of New York, New York, NY, 10010, USA.,The Graduate Center, PhD Program in Biology, City University of New York, New York, USA
| | - Krista C Dobi
- Department of Natural Sciences, Baruch College, City University of New York, New York, NY, 10010, USA.,The Graduate Center, PhD Program in Biology, City University of New York, New York, USA
| | - Nehaben A Gujarati
- Department of Natural Sciences, Baruch College, City University of New York, New York, NY, 10010, USA
| | - Moira Galbraith
- Institute of Ocean Sciences, 9860 West Saanich Road, P.O. Box 6000, Sidney, BC, V8L 4B2, Canada
| | - Jeremy D Mirza
- Departamento de Oceanografia Física, Química e, Geológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, 05508-120, Brazil.,Departamento de Química, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - John S Sparks
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.,Division of Vertebrate Zoology, Department of Ichthyology, American Museum of Natural History, New York, NY, 10024, USA
| | | | - Robert J Wood
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - David F Gruber
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA. .,Department of Natural Sciences, Baruch College, City University of New York, New York, NY, 10010, USA. .,The Graduate Center, PhD Program in Biology, City University of New York, New York, USA.
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44
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Coppola U, Kamal AK, Stolfi A, Ristoratore F. The Cis-Regulatory Code for Kelch-like 21/30 Specific Expression in Ciona robusta Sensory Organs. Front Cell Dev Biol 2020; 8:569601. [PMID: 33043001 PMCID: PMC7517041 DOI: 10.3389/fcell.2020.569601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/17/2020] [Indexed: 12/18/2022] Open
Abstract
The tunicate Ciona robusta is an emerging model system to study the evolution of the nervous system. Due to their small embryos and compact genomes, tunicates, like Ciona robusta, have great potential to comprehend genetic circuitry underlying cell specific gene repertoire, among different neuronal cells. Their simple larvae possess a sensory vesicle comprising two pigmented sensory organs, the ocellus and the otolith. We focused here on Klhl21/30, a gene belonging to Kelch family, that, in Ciona robusta, starts to be expressed in pigmented cell precursors, becoming specifically maintained in the otolith precursor during embryogenesis. Evolutionary analyses demonstrated the conservation of Klhl21/30 in all the chordates. Cis-regulatory analyses and CRISPR/Cas9 mutagenesis of potential upstream factors, revealed that Klhl21/30 expression is controlled by the combined action of three transcription factors, Mitf, Dmrt, and Msx, which are downstream of FGF signaling. The central role of Mitf is consistent with its function as a fundamental regulator of vertebrate pigment cell development. Moreover, our results unraveled a new function for Dmrt and Msx as transcriptional co-activators in the context of the Ciona otolith.
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Affiliation(s)
- Ugo Coppola
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Ashwani Kumar Kamal
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Filomena Ristoratore
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
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45
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Coppola U, Olivo P, D’Aniello E, Johnson CJ, Stolfi A, Ristoratore F. Rimbp, a New Marker for the Nervous System of the Tunicate Ciona robusta. Genes (Basel) 2020; 11:genes11091006. [PMID: 32867148 PMCID: PMC7565545 DOI: 10.3390/genes11091006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/16/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Establishment of presynaptic mechanisms by proteins that regulate neurotransmitter release in the presynaptic active zone is considered a fundamental step in animal evolution. Rab3 interacting molecule-binding proteins (Rimbps) are crucial components of the presynaptic active zone and key players in calcium homeostasis. Although Rimbp involvement in these dynamics has been described in distantly related models such as fly and human, the role of this family in most invertebrates remains obscure. To fill this gap, we defined the evolutionary history of Rimbp family in animals, from sponges to mammals. We report, for the first time, the expression of the two isoforms of the unique Rimbp family member in Ciona robusta in distinct domains of the larval nervous system. We identify intronic enhancers that are able to drive expression in different nervous system territories partially corresponding to Rimbp endogenous expression. The analysis of gene expression patterns and the identification of regulatory elements of Rimbp will positively impact our understanding of this family of genes in the context of Ciona embryogenesis.
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Affiliation(s)
- Ugo Coppola
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy; (U.C.); (P.O.); (E.D.)
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Paola Olivo
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy; (U.C.); (P.O.); (E.D.)
| | - Enrico D’Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy; (U.C.); (P.O.); (E.D.)
| | | | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- Correspondence: (A.S.); (F.R.)
| | - Filomena Ristoratore
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy; (U.C.); (P.O.); (E.D.)
- Correspondence: (A.S.); (F.R.)
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46
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Wang K, Tomura R, Chen W, Kiyooka M, Ishizaki H, Aizu T, Minakuchi Y, Seki M, Suzuki Y, Omotezako T, Suyama R, Masunaga A, Plessy C, Luscombe NM, Dantec C, Lemaire P, Itoh T, Toyoda A, Nishida H, Onuma TA. A genome database for a Japanese population of the larvacean Oikopleura dioica. Dev Growth Differ 2020; 62:450-461. [PMID: 32677034 DOI: 10.1111/dgd.12689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 06/10/2020] [Accepted: 06/10/2020] [Indexed: 01/01/2023]
Abstract
The larvacean Oikopleura dioica is a planktonic chordate and is a tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of 5 days make it a promising model organism for the study of developmental biology. The genome browser OikoBase was established in 2013 using Norwegian O. dioica. However, genome information for other populations is not available, even though many researchers have studied local populations. In the present study, we sequenced using Illumina and PacBio RSII technologies the genome of O. dioica from a southwestern Japanese population that was cultured in our laboratory for 3 years. The genome of Japanese O. dioica was assembled into 576 scaffold sequences with a total length and N50 length of 56.6 and 1.5 Mb, respectively. A total of 18,743 gene models (transcript models) were predicted in the genome assembly, named OSKA2016. In addition, 19,277 non-redundant transcripts were assembled using RNA-seq data. The OSKA2016 has global sequence similarity of only 86.5% when compared with the OikoBase, highlighting the sequence difference between the two far distant O. dioica populations on the globe. The genome assembly, transcript assembly, and transcript models were incorporated into ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and BLAST searches. Mapping of reads obtained from male- or female-specific genome libraries yielded male-specific scaffolds in the OSKA2016 and revealed that over 2.6 Mb of sequence were included in the male-specific Y-region. The genome and transcriptome resources from two distinct populations will be useful datasets for developmental biology, evolutionary biology, and molecular ecology using this model organism.
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Affiliation(s)
- Kai Wang
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Ryo Tomura
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Wei Chen
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Miho Kiyooka
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hinako Ishizaki
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tomoyuki Aizu
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yohei Minakuchi
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masahide Seki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Tatsuya Omotezako
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Ritsuko Suyama
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Aki Masunaga
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Charles Plessy
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Nicholas M Luscombe
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Christelle Dantec
- Centre de Recherches de Biochimie Macromoleculaire (CRBM), UMR5237, CNRS-Universite de Montpellier, Montpellier, France
| | - Patrick Lemaire
- Centre de Recherches de Biochimie Macromoleculaire (CRBM), UMR5237, CNRS-Universite de Montpellier, Montpellier, France
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
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47
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Guignard L, Fiúza UM, Leggio B, Laussu J, Faure E, Michelin G, Biasuz K, Hufnagel L, Malandain G, Godin C, Lemaire P. Contact area-dependent cell communication and the morphological invariance of ascidian embryogenesis. Science 2020; 369:369/6500/eaar5663. [PMID: 32646972 DOI: 10.1126/science.aar5663] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/29/2020] [Indexed: 12/18/2022]
Abstract
Marine invertebrate ascidians display embryonic reproducibility: Their early embryonic cell lineages are considered invariant and are conserved between distantly related species, despite rapid genomic divergence. Here, we address the drivers of this reproducibility. We used light-sheet imaging and automated cell segmentation and tracking procedures to systematically quantify the behavior of individual cells every 2 minutes during Phallusia mammillata embryogenesis. Interindividual reproducibility was observed down to the area of individual cell contacts. We found tight links between the reproducibility of embryonic geometries and asymmetric cell divisions, controlled by differential sister cell inductions. We combined modeling and experimental manipulations to show that the area of contact between signaling and responding cells is a key determinant of cell communication. Our work establishes the geometric control of embryonic inductions as an alternative to classical morphogen gradients and suggests that the range of cell signaling sets the scale at which embryonic reproducibility is observed.
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Affiliation(s)
- Léo Guignard
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France.,Virtual Plants, Université de Montpellier, CIRAD, INRA, Inria, 34095 Montpellier, France.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ulla-Maj Fiúza
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Bruno Leggio
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France.,Virtual Plants, Université de Montpellier, CIRAD, INRA, Inria, 34095 Montpellier, France.,Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Inria, 69342 Lyon, France
| | - Julien Laussu
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France
| | - Emmanuel Faure
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France.,Virtual Plants, Université de Montpellier, CIRAD, INRA, Inria, 34095 Montpellier, France.,Institut de Recherche en Informatique de Toulouse (IRIT), Universités Toulouse I et III, CNRS, INPT, ENSEEIHT, 31071 Toulouse, France
| | - Gaël Michelin
- Morpheme, Université Côte d'Azur, Inria, CNRS, I3S, France
| | - Kilian Biasuz
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France
| | - Lars Hufnagel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | | | - Christophe Godin
- Virtual Plants, Université de Montpellier, CIRAD, INRA, Inria, 34095 Montpellier, France. .,Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Inria, 69342 Lyon, France
| | - Patrick Lemaire
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France.
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48
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Shotgun Proteomics of Ascidians Tunic Gives New Insights on Host-Microbe Interactions by Revealing Diverse Antimicrobial Peptides. Mar Drugs 2020; 18:md18070362. [PMID: 32668814 PMCID: PMC7401272 DOI: 10.3390/md18070362] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 12/26/2022] Open
Abstract
Ascidians are marine invertebrates associated with diverse microbial communities, embedded in their tunic, conferring special ecological and biotechnological relevance to these model organisms used in evolutionary and developmental studies. Next-generation sequencing tools have increased the knowledge of ascidians’ associated organisms and their products, but proteomic studies are still scarce. Hence, we explored the tunic of three ascidian species using a shotgun proteomics approach. Proteins extracted from the tunic of Ciona sp., Molgula sp., and Microcosmus sp. were processed using a nano LC-MS/MS system (Ultimate 3000 liquid chromatography system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap mass spectrometer). Raw data was searched against UniProtKB – the Universal Protein Resource Knowledgebase (Bacteria and Metazoa section) using Proteome Discoverer software. The resulting proteins were merged with a non-redundant Antimicrobial Peptides (AMPs) database and analysed with MaxQuant freeware. Overall, 337 metazoan and 106 bacterial proteins were identified being mainly involved in basal metabolism, cytoskeletal and catalytic functions. 37 AMPs were identified, most of them attributed to eukaryotic origin apart from bacteriocins. These results and the presence of “Biosynthesis of antibiotics” as one of the most highlighted pathways revealed the tunic as a very active tissue in terms of bioactive compounds production, giving insights on the interactions between host and associated organisms. Although the present work constitutes an exploratory study, the approach employed revealed high potential for high-throughput characterization and biodiscovery of the ascidians’ tunic and its microbiome.
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49
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Kim K, Gibboney S, Razy-Krajka F, Lowe EK, Wang W, Stolfi A. Regulation of Neurogenesis by FGF Signaling and Neurogenin in the Invertebrate Chordate Ciona. Front Cell Dev Biol 2020; 8:477. [PMID: 32656209 PMCID: PMC7324659 DOI: 10.3389/fcell.2020.00477] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/21/2020] [Indexed: 12/22/2022] Open
Abstract
Neurogenesis is a complex sequence of cellular processes and behaviors driven by the coordinated expression of conserved effectors. The bipolar tail neurons (BTNs) of Ciona develop according to a highly dynamic, yet highly stereotyped developmental program and thus could serve as an accessible model system for neurogenesis, including underlying cell behaviors like neuronal delamination, migration, and polarized axon outgrowth. Here we investigate both the upstream events that shape BTN neurogenesis through spatiotemporal regulation of the conserved proneural factor Neurog, spatiotemporal, and the gene expression profile of differentiating BTNs downstream of Neurog activity. We show that, although early FGF signaling is required for Neurog expression and BTN specification, Fgf8/17/18 is expressed in tail tip cells at later stages and suppresses sustained Neurog expression in the anterior BTN (aBTN) lineage, such that only one cell (the one furthest from the source of Fgf8/17/18) maintains Neurog expression and becomes a neuron. Curiously, Fgf8/17/18 might not affect neurogenesis of the posterior BTNs (pBTNs), which are in direct contact with the Fgf8/17/18-expressing cells. Finally, to profile gene expression associated with BTN neurogenesis we performed RNAseq of isolated BTN lineage cells in which BTN neurogenesis was enhanced or suppressed by perturbing Neurog function. This allowed us to identify several candidate genes that might play conserved roles in neurogenesis and neuronal migration in other animals, including mammals.
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Affiliation(s)
- Kwantae Kim
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Susanne Gibboney
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Florian Razy-Krajka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Elijah K. Lowe
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Wei Wang
- Department of Biology, New York University, New York, NY, United States
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
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50
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Li D, Hsu S, Purushotham D, Sears RL, Wang T. WashU Epigenome Browser update 2019. Nucleic Acids Res 2020; 47:W158-W165. [PMID: 31165883 PMCID: PMC6602459 DOI: 10.1093/nar/gkz348] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/23/2019] [Accepted: 05/31/2019] [Indexed: 12/20/2022] Open
Abstract
The WashU Epigenome Browser (https://epigenomegateway.wustl.edu/) provides visualization, integration and analysis tools for epigenomic datasets. Since 2010, it has provided the scientific community with data from large consortia including the Roadmap Epigenomics and the ENCODE projects. Recently, we refactored the codebase, redesigned the user interface, and developed various novel features. New features include: (i) visualization using virtual reality (VR), which has implications in biology education and the study of 3D chromatin structure; (ii) expanded public data hubs, including data from the 4DN, ENCODE, Roadmap Epigenomics, TaRGET, IHEC and TCGA consortia; (iii) a more responsive user interface; (iv) a history of interactions, which enables undo and redo; (v) a feature we call Live Browsing, which allows multiple users to collaborate remotely on the same session; (vi) the ability to visualize local tracks and data hubs. Amazon Web Services also hosts the redesign at https://epigenomegateway.org/.
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Affiliation(s)
- Daofeng Li
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Silas Hsu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Deepak Purushotham
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Renee L Sears
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
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