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Perween N, Pekhale K, Haval G, Sirkar G, Bose GS, Mittal SPK, Ghaskadbi S, Ghaskadbi SS. Identification and characterization of multidomain monothiol glutaredoxin 3 from diploblastic Hydra. Comp Biochem Physiol B Biochem Mol Biol 2024; 273:110986. [PMID: 38703881 DOI: 10.1016/j.cbpb.2024.110986] [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: 12/30/2023] [Revised: 04/30/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Intracellular antioxidant glutaredoxin controls cell proliferation and survival. Based on the active site, structure, and conserved domain motifs, it is classified into two classes. Class I contains dithiol Grxs with two cysteines in the consensus active site sequence CXXC, while class II has monothiol Grxs with one cysteine residue in the active site. Monothiol Grxs can also have an additional N-terminal thioredoxin (Trx)-like domain. Previously, we reported the characterization of Grx1 from Hydra vulgaris (HvGrx1), which is a dithiol isoform. Here, we report the molecular cloning, expression, analysis, and characterization of another isoform of Grx, which is the multidomain monothiol glutaredoxin-3 from Hydra vulgaris (HvGrx3). It encodes a protein with 303 amino acids and is significantly larger and more divergent than HvGrx1. In-silico analysis revealed that Grx1 and Grx3 have 22.5% and 9.9% identical nucleotide and amino acid sequences, respectively. HvGrx3 has two glutaredoxin domains and a thioredoxin-like domain at its amino terminus, unlike HvGrx1, which has a single glutaredoxin domain. Like other monothiol glutaredoxins, HvGrx3 failed to reduce glutathione-hydroxyethyl disulfide. In the whole Hydra, HvGrx3 was found to be expressed all over the body column, and treatment with H2O2 led to a significant upregulation of HvGrx3. When transfected in HCT116 (human colon cancer cells) cells, HvGrx3 enhanced cell proliferation and migration, indicating that this isoform could be involved in these cellular functions. These transfected cells also tolerate oxidative stress better.
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Affiliation(s)
- Nusrat Perween
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India; Department of Zoology, M.C.E. Society's Abeda Inamdar Senior College, Pune 411001, India. https://twitter.com/nusratperween13
| | - Komal Pekhale
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
| | - Gauri Haval
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India; Department of Zoology, Abasaheb Garware College, Pune 411004, India
| | - Gargi Sirkar
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
| | - Ganesh S Bose
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Smriti P K Mittal
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Surendra Ghaskadbi
- Developmental Biology Group, MACS-Agharkar Research Institute, Pune 411004, India
| | - Saroj S Ghaskadbi
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India.
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Cheng M, Nie Y, Song M, Chen F, Yu Y. Forkhead box O proteins: steering the course of stem cell fate. CELL REGENERATION (LONDON, ENGLAND) 2024; 13:7. [PMID: 38466341 DOI: 10.1186/s13619-024-00190-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
Stem cells are pivotal players in the intricate dance of embryonic development, tissue maintenance, and regeneration. Their behavior is delicately balanced between maintaining their pluripotency and differentiating as needed. Disruptions in this balance can lead to a spectrum of diseases, underscoring the importance of unraveling the complex molecular mechanisms that govern stem cell fate. Forkhead box O (FOXO) proteins, a family of transcription factors, are at the heart of this intricate regulation, influencing a myriad of cellular processes such as survival, metabolism, and DNA repair. Their multifaceted role in steering the destiny of stem cells is evident, as they wield influence over self-renewal, quiescence, and lineage-specific differentiation in both embryonic and adult stem cells. This review delves into the structural and regulatory intricacies of FOXO transcription factors, shedding light on their pivotal roles in shaping the fate of stem cells. By providing insights into the specific functions of FOXO in determining stem cell fate, this review aims to pave the way for targeted interventions that could modulate stem cell behavior and potentially revolutionize the treatment and prevention of diseases.
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Affiliation(s)
- Mengdi Cheng
- Laboratory of Tissue Engineering, College of Life Sciences, Northwest University, Xi'an, China
| | - Yujie Nie
- Laboratory of Tissue Engineering, College of Life Sciences, Northwest University, Xi'an, China
| | - Min Song
- Laboratory of Tissue Engineering, College of Life Sciences, Northwest University, Xi'an, China
| | - Fulin Chen
- Laboratory of Tissue Engineering, College of Life Sciences, Northwest University, Xi'an, China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi'an, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China
| | - Yuan Yu
- Laboratory of Tissue Engineering, College of Life Sciences, Northwest University, Xi'an, China.
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi'an, China.
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China.
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Tan FH, Bronner ME. Regenerative loss in the animal kingdom as viewed from the mouse digit tip and heart. Dev Biol 2024; 507:44-63. [PMID: 38145727 PMCID: PMC10922877 DOI: 10.1016/j.ydbio.2023.12.008] [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: 08/06/2023] [Revised: 11/30/2023] [Accepted: 12/19/2023] [Indexed: 12/27/2023]
Abstract
The myriad regenerative abilities across the animal kingdom have fascinated us for centuries. Recent advances in developmental, molecular, and cellular biology have allowed us to unearth a surprising diversity of mechanisms through which these processes occur. Developing an all-encompassing theory of animal regeneration has thus proved a complex endeavor. In this chapter, we frame the evolution and loss of animal regeneration within the broad developmental constraints that may physiologically inhibit regenerative ability across animal phylogeny. We then examine the mouse as a model of regeneration loss, specifically the experimental systems of the digit tip and heart. We discuss the digit tip and heart as a positionally-limited system of regeneration and a temporally-limited system of regeneration, respectively. We delve into the physiological processes involved in both forms of regeneration, and how each phase of the healing and regenerative process may be affected by various molecular signals, systemic changes, or microenvironmental cues. Lastly, we also discuss the various approaches and interventions used to induce or improve the regenerative response in both contexts, and the implications they have for our understanding regenerative ability more broadly.
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Affiliation(s)
- Fayth Hui Tan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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Perween N, Pekhale K, Haval G, Bose GS, Mittal SPK, Ghaskadbi S, Ghaskadbi SS. Glutaredoxin 1 from Evolutionary Ancient Hydra: Characteristics of the Enzyme and Its Possible Functions in Cell. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:667-678. [PMID: 37331712 DOI: 10.1134/s0006297923050097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 06/20/2023]
Abstract
Glutaredoxin (Grx) is an antioxidant redox protein that uses glutathione (GSH) as an electron donor. Grx plays a crucial role in various cellular processes, such as antioxidant defense, control of cellular redox state, redox control of transcription, reversible S-glutathionylation of specific proteins, apoptosis, cell differentiation, etc. In the current study, we have isolated and characterized dithiol glutaredoxin from Hydra vulgaris Ind-Pune (HvGrx1). Sequence analysis showed that HvGrx1 belongs to the Grx family with the classical Grx motif (CPYC). Phylogenetic analysis and homology modeling revealed that HvGrx1 is closely related to Grx2 from zebrafish. HvGrx1 gene was cloned and expressed in Escherichia coli cells; the purified protein had a molecular weight of 11.82 kDa. HvGrx1 efficiently reduced β-hydroxyethyl disulfide (HED) with the temperature optimum of 25°C and pH optimum 8.0. HvGrx1 was ubiquitously expressed in all body parts of Hydra. Expression of HvGrx1 mRNA and enzymatic activity of HvGrx1 were significantly upregulated post H2O2 treatment. When expressed in human cells, HvGrx1 protected the cells from oxidative stress and enhanced cell proliferation and migration. Although Hydra is a simple invertebrate, HvGrx1 is evolutionary closer to its homologs from higher vertebrates (similar to many other Hydra proteins).
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Affiliation(s)
- Nusrat Perween
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India.
- Department of Zoology, M. C. E. Society's Abeda Inamdar Senior College, Pune, 411001, India
| | - Komal Pekhale
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India.
| | - Gauri Haval
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India.
- Department of Zoology, Abasaheb Garware College, Pune, 411004, India
| | - Ganesh S Bose
- Department of Biotechnology, Savitribai Phule Pune University, Pune, 411007, India.
| | - Smriti P K Mittal
- Department of Biotechnology, Savitribai Phule Pune University, Pune, 411007, India.
| | - Surendra Ghaskadbi
- Developmental Biology Group, Agharkar Research Institute, Pune, 411004, India.
| | - Saroj S Ghaskadbi
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India.
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Perween N, Pekhale K, Haval G, Khude G, Ghaskadbi S, Ghaskadbi SS. Glutathione synthetase from Hydra vulgaris: Molecular cloning, overexpression, purification and partial characterization. Protein Expr Purif 2023; 208-209:106292. [PMID: 37127055 DOI: 10.1016/j.pep.2023.106292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/03/2023]
Affiliation(s)
- Nusrat Perween
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India; Department of Zoology, M.C.E. Society's Abeda Inamdar Senior College, Pune, 411001, India
| | - Komal Pekhale
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India
| | - Gauri Haval
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India; Department of Zoology, Abasaheb Garware College, Pune, 411004, India
| | - Gaurav Khude
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India
| | - Surendra Ghaskadbi
- Developmental Biology Group, MACS-Agharkar Research Institute, Pune, 411004, India
| | - Saroj S Ghaskadbi
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India.
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Holstein TW. The Hydra stem cell system - Revisited. Cells Dev 2023; 174:203846. [PMID: 37121433 DOI: 10.1016/j.cdev.2023.203846] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/12/2023] [Accepted: 04/25/2023] [Indexed: 05/02/2023]
Abstract
Cnidarians are >600 million years old and are considered the sister group of Bilateria based on numerous molecular phylogenetic studies. Apart from Hydra, the genomes of all major clades of Cnidaria have been uncovered (e.g. Aurelia, Clytia, Nematostella and Acropora) and they reveal a remarkable completeness of the metazoan genomic toolbox. Of particular interest is Hydra, a model system of aging research, regenerative biology, and stem cell biology. With the knowledge gained from scRNA research, it is now possible to characterize the expression profiles of all cell types with great precision. In functional studies, our picture of the Hydra stem cell biology has changed, and we are in the process of obtaining a clear picture of the homeostasis and properties of the different stem cell populations. Even though Hydra is often compared to plant systems, the new data on germline and regeneration, but also on the dynamics and plasticity of the nervous system, show that Hydra with its simple body plan represents in a nutshell the prototype of an animal with stem cell lineages, whose properties correspond in many ways to Bilateria. This review provides an overview of the four stem cell lineages, the two epithelial lineages that constitute the ectoderm and the endoderm, as well as the multipotent somatic interstitial lineage (MPSC) and the germline stem cell lineage (GSC), also known as the interstitial cells of Hydra.
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Affiliation(s)
- Thomas W Holstein
- Heidelberg University, Centre for Organismal Studies (COS), Molecular Evolution and Genomics, Im Neuenheimer Feld 230, D-69120 Heidelberg, Germany.
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A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state. Genome Res 2023; 33:283-298. [PMID: 36639202 PMCID: PMC10069465 DOI: 10.1101/gr.277040.122] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
The epithelial and interstitial stem cells of the freshwater polyp Hydra are the best-characterized stem cell systems in any cnidarian, providing valuable insight into cell type evolution and the origin of stemness in animals. However, little is known about the transcriptional regulatory mechanisms that determine how these stem cells are maintained and how they give rise to their diverse differentiated progeny. To address such questions, a thorough understanding of transcriptional regulation in Hydra is needed. To this end, we generated extensive new resources for characterizing transcriptional regulation in Hydra, including new genome assemblies for Hydra oligactis and the AEP strain of Hydra vulgaris, an updated whole-animal single-cell RNA-seq atlas, and genome-wide maps of chromatin interactions, chromatin accessibility, sequence conservation, and histone modifications. These data revealed the existence of large kilobase-scale chromatin interaction domains in the Hydra genome that contain transcriptionally coregulated genes. We also uncovered the transcriptomic profiles of two previously molecularly uncharacterized cell types: isorhiza-type nematocytes and somatic gonad ectoderm. Finally, we identified novel candidate regulators of cell type-specific transcription, several of which have likely been conserved at least since the divergence of Hydra and the jellyfish Clytia hemisphaerica more than 400 million years ago.
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Tursch A, Holstein TW. From injury to patterning—MAPKs and Wnt signaling in Hydra. Curr Top Dev Biol 2023; 153:381-417. [PMID: 36967201 DOI: 10.1016/bs.ctdb.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Hydra has a regenerative capacity that is not limited to individual organs but encompasses the entire body. Various global and integrative genome, transcriptome and proteome approaches have shown that many of the signaling pathways and transcription factors present in vertebrates are already present in Cnidaria, the sister group of Bilateria, and are also activated in regeneration. It is now possible to investigate one of the central questions of regeneration biology, i.e., how does the patterning system become activated by the injury signals that initiate regeneration. This review will present the current data obtained in Hydra and draw parallels with regeneration in Bilateria. Important findings of this global analysis are that the Wnt signaling pathway has a dual function in the regeneration process. In the early phase Wnt is activated generically and in a second phase of pattern formation it is activated in a position specific manner. Thus, Wnt signaling is part of the generic injury response, in which mitogen-activated protein kinases (MAPKs) are initially activated via calcium and reactive oxygen species (ROS). The MAPKs, p38, c-Jun N-terminal kinases (JNKs) and extracellular signal-regulated kinases (ERK) are essential for Wnt activation in Hydra head and foot regenerates. Furthermore, the antagonism between the ERK signaling pathway and stress-induced MAPKs results in a balanced induction of apoptosis and mitosis. However, the early Wnt genes are activated by MAPK signaling rather than apoptosis. Early Wnt gene activity is differentially integrated with a stable, β-Catenin-based gradient along the primary body axis maintaining axial polarity and activating further Wnts in the regenerating head. Because MAPKs and Wnts are highly evolutionarily conserved, we hypothesize that this mechanism is also present in vertebrates but may be activated to different degrees at the level of early Wnt gene integration.
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Vogg MC, Ferenc J, Buzgariu WC, Perruchoud C, Sanchez PGL, Beccari L, Nuninger C, Le Cras Y, Delucinge-Vivier C, Papasaikas P, Vincent S, Galliot B, Tsiairis CD. The transcription factor Zic4 promotes tentacle formation and prevents epithelial transdifferentiation in Hydra. SCIENCE ADVANCES 2022; 8:eabo0694. [PMID: 36563144 PMCID: PMC9788771 DOI: 10.1126/sciadv.abo0694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The molecular mechanisms that maintain cellular identities and prevent dedifferentiation or transdifferentiation remain mysterious. However, both processes are transiently used during animal regeneration. Therefore, organisms that regenerate their organs, appendages, or even their whole body offer a fruitful paradigm to investigate the regulation of cell fate stability. Here, we used Hydra as a model system and show that Zic4, whose expression is controlled by Wnt3/β-catenin signaling and the Sp5 transcription factor, plays a key role in tentacle formation and tentacle maintenance. Reducing Zic4 expression suffices to induce transdifferentiation of tentacle epithelial cells into foot epithelial cells. This switch requires the reentry of tentacle battery cells into the cell cycle without cell division and is accompanied by degeneration of nematocytes embedded in these cells. These results indicate that maintenance of cell fate by a Wnt-controlled mechanism is a key process both during homeostasis and during regeneration.
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Affiliation(s)
- Matthias Christian Vogg
- Department of Genetics and Evolution, Institute of Genetics and Genomics (iGE3), Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, Geneva 4 1211, Switzerland
| | - Jaroslav Ferenc
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
- University of Basel, Petersplatz 1, Basel 4001, Switzerland
| | - Wanda Christa Buzgariu
- Department of Genetics and Evolution, Institute of Genetics and Genomics (iGE3), Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, Geneva 4 1211, Switzerland
| | - Chrystelle Perruchoud
- Department of Genetics and Evolution, Institute of Genetics and Genomics (iGE3), Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, Geneva 4 1211, Switzerland
| | - Paul Gerald Layague Sanchez
- Department of Genetics and Evolution, Institute of Genetics and Genomics (iGE3), Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, Geneva 4 1211, Switzerland
| | - Leonardo Beccari
- Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, University Claude Bernard Lyon 1, Lyon, France
| | - Clara Nuninger
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
- University of Basel, Petersplatz 1, Basel 4001, Switzerland
| | - Youn Le Cras
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
| | - Céline Delucinge-Vivier
- iGE3 Genomics Platform, University of Geneva, 1 Rue Michel-Servet, Geneva 4 1211, Switzerland
| | - Panagiotis Papasaikas
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel 4058, Switzerland
| | - Stéphane Vincent
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie, Lyon F-69364, France
| | - Brigitte Galliot
- Department of Genetics and Evolution, Institute of Genetics and Genomics (iGE3), Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, Geneva 4 1211, Switzerland
- Corresponding author. (B.G.); (C.D.T.)
| | - Charisios D. Tsiairis
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
- Corresponding author. (B.G.); (C.D.T.)
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Puntin G, Sweet M, Fraune S, Medina M, Sharp K, Weis VM, Ziegler M. Harnessing the Power of Model Organisms To Unravel Microbial Functions in the Coral Holobiont. Microbiol Mol Biol Rev 2022; 86:e0005322. [PMID: 36287022 PMCID: PMC9769930 DOI: 10.1128/mmbr.00053-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Stony corals build the framework of coral reefs, ecosystems of immense ecological and economic importance. The existence of these ecosystems is threatened by climate change and other anthropogenic stressors that manifest in microbial dysbiosis such as coral bleaching and disease, often leading to coral mortality. Despite a significant amount of research, the mechanisms ultimately underlying these destructive phenomena, and what could prevent or mitigate them, remain to be resolved. This is mostly due to practical challenges in experimentation on corals and the highly complex nature of the coral holobiont that also includes bacteria, archaea, protists, and viruses. While the overall importance of these partners is well recognized, their specific contributions to holobiont functioning and their interspecific dynamics remain largely unexplored. Here, we review the potential of adopting model organisms as more tractable systems to address these knowledge gaps. We draw on parallels from the broader biological and biomedical fields to guide the establishment, implementation, and integration of new and emerging model organisms with the aim of addressing the specific needs of coral research. We evaluate the cnidarian models Hydra, Aiptasia, Cassiopea, and Astrangia poculata; review the fast-evolving field of coral tissue and cell cultures; and propose a framework for the establishment of "true" tropical reef-building coral models. Based on this assessment, we also suggest future research to address key aspects limiting our ability to understand and hence improve the response of reef-building corals to future ocean conditions.
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Affiliation(s)
- Giulia Puntin
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Sebastian Fraune
- Institute for Zoology and Organismic Interactions, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Koty Sharp
- Department of Biology, Marine Biology, and Environmental Science, Roger Williams University, Bristol, Rhode Island, USA
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
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Bosch TCG. Beyond Lynn Margulis’ green hydra. Symbiosis 2022. [DOI: 10.1007/s13199-022-00849-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AbstractLynn Margulis has made it clear that in nature partnerships are the predominant form of life; that life processes can only be understood in terms of the interactions of such partnerships; and that their inherent complexity can only be understood by taking a holistic approach. Here I attempt to relate Lynn Margulis´ observations on the freshwater polyp hydra to the perceptions and problems of today’s Hydra research. To accomplish this, I will synthesize our current understanding of how symbionts influence the phenotype and fitness of hydra. Based on this new findings, a fundamental paradigm shift and a new era is emerging in the way that we consider organisms such as hydra as multi-organismic metaorganisms, just as Lynn Margulis may have thought about it.
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Comparisons of cell proliferation and cell death from tornaria larva to juvenile worm in the hemichordate Schizocardium californicum. EvoDevo 2022; 13:13. [PMID: 35668535 PMCID: PMC9169294 DOI: 10.1186/s13227-022-00198-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/13/2022] [Indexed: 12/06/2022] Open
Abstract
Background There are a wide range of developmental strategies in animal phyla, but most insights into adult body plan formation come from direct-developing species. For indirect-developing species, there are distinct larval and adult body plans that are linked together by metamorphosis. Some outstanding questions in the development of indirect-developing organisms include the extent to which larval tissue undergoes cell death during the process of metamorphosis and when and where the tissue that will give rise to the adult originates. How do the processes of cell division and cell death redesign the body plans of indirect developers? In this study, we present patterns of cell proliferation and cell death during larval body plan development, metamorphosis, and adult body plan formation, in the hemichordate Schizocardium californium (Cameron and Perez in Zootaxa 3569:79–88, 2012) to answer these questions. Results We identified distinct patterns of cell proliferation between larval and adult body plan formation of S. californicum. We found that some adult tissues proliferate during the late larval phase prior to the start of overt metamorphosis. In addition, using an irradiation and transcriptomic approach, we describe a genetic signature of proliferative cells that is shared across the life history states, as well as markers that are unique to larval or juvenile states. Finally, we observed that cell death is minimal in larval stages but begins with the onset of metamorphosis. Conclusions Cell proliferation during the development of S. californicum has distinct patterns in the formation of larval and adult body plans. However, cell death is very limited in larvae and begins during the onset of metamorphosis and into early juvenile development in specific domains. The populations of cells that proliferated and gave rise to the larvae and juveniles have a genetic signature that suggested a heterogeneous pool of proliferative progenitors, rather than a set-aside population of pluripotent cells. Taken together, we propose that the gradual morphological transformation of S. californicum is mirrored at the cellular level and may be more representative of the development strategies that characterize metamorphosis in many metazoan animals. Supplementary Information The online version contains supplementary material available at 10.1186/s13227-022-00198-1.
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A novel regulatory gene promotes novel cell fate by suppressing ancestral fate in the sea anemone Nematostella vectensis. Proc Natl Acad Sci U S A 2022; 119:e2113701119. [PMID: 35500123 PMCID: PMC9172639 DOI: 10.1073/pnas.2113701119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In this study, we demonstrate how a new cell type can arise through duplication of an ancestral cell type followed by functional divergence of the new daughter cell. Specifically, we show that stinging cells in a cnidarian (namely, a sea anemone) emerged by duplication of an ancestral neuron followed by inhibition of the RFamide neuropeptide it once secreted. This finding is evidence that stinging cells evolved from a specific subtype of neurons and suggests other neuronal subtypes may have been coopted for other novel secretory functions. Cnidocytes (i.e., stinging cells) are an unequivocally novel cell type used by cnidarians (i.e., corals, jellyfish, and their kin) to immobilize prey. Although they are known to share a common evolutionary origin with neurons, the developmental program that promoted the emergence of cnidocyte fate is not known. Using functional genomics in the sea anemone, Nematostella vectensis, we show that cnidocytes develop by suppression of neural fate in a subset of neurons expressing RFamide. We further show that a single regulatory gene, a C2H2-type zinc finger transcription factor (ZNF845), coordinates both the gain of novel (cnidocyte-specific) traits and the inhibition of ancestral (neural) traits during cnidocyte development and that this gene arose by domain shuffling in the stem cnidarian. Thus, we report a mechanism by which a truly novel regulatory gene (ZNF845) promotes the development of a truly novel cell type (cnidocyte) through duplication of an ancestral cell lineage (neuron) and inhibition of its ancestral identity (RFamide).
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14
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Ying H, Hayward DC, Klimovich A, Bosch TCG, Baldassarre L, Neeman T, Forêt S, Huttley G, Reitzel AM, Fraune S, Ball EE, Miller DJ. The role of DNA methylation in genome defense in Cnidaria and other invertebrates. Mol Biol Evol 2022; 39:6516040. [PMID: 35084499 PMCID: PMC8857917 DOI: 10.1093/molbev/msac018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Considerable attention has recently been focused on the potential involvement of DNA methylation in regulating gene expression in cnidarians. Much of this work has been centered on corals, in the context of changes in methylation perhaps facilitating adaptation to higher seawater temperatures and other stressful conditions. Although first proposed more than 30 years ago, the possibility that DNA methylation systems function in protecting animal genomes against the harmful effects of transposon activity has largely been ignored since that time. Here, we show that transposons are specifically targeted by the DNA methylation system in cnidarians, and that the youngest transposons (i.e., those most likely to be active) are most highly methylated. Transposons in longer and highly active genes were preferentially methylated and, as transposons aged, methylation levels declined, reducing the potentially harmful side effects of CpG methylation. In Cnidaria and a range of other invertebrates, correlation between the overall extent of methylation and transposon content was strongly supported. Present transposon burden is the dominant factor in determining overall level of genomic methylation in a range of animals that diverged in or before the early Cambrian, suggesting that genome defense represents the ancestral role of CpG methylation.
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Affiliation(s)
- Hua Ying
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - David C Hayward
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Thomas C G Bosch
- Zoological Institute, Christian Albrechts University, Kiel, Germany.,Collaborative Research Center for the Origin and Function of Metaorganisms, Christian Albrechts University, Kiel, Germany
| | - Laura Baldassarre
- Department of Zoology and Organismal Interactions, Heinrich-Heine-University Düsseldorf, Germany
| | - Teresa Neeman
- Biological Data Institute, Australian National University, Canberra, ACT, Australia
| | - Sylvain Forêt
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, Australia
| | - Gavin Huttley
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina, Charlotte, USA
| | - Sebastian Fraune
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Eldon E Ball
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.,Marine Climate Change Unit, Okinawa Institute of Science and Technology, Japan
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15
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Salamanca-Díaz DA, Schulreich SM, Cole AG, Wanninger A. Single-Cell RNA Sequencing Atlas From a Bivalve Larva Enhances Classical Cell Lineage Studies. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.783984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Ciliated trochophore-type larvae are widespread among protostome animals with spiral cleavage. The respective phyla are often united into the superclade Spiralia or Lophotrochozoa that includes, for example, mollusks, annelids, and platyhelminths. Mollusks (bivalves, gastropods, cephalopods, polyplacophorans, and their kin) in particular are known for their morphological innovations and lineage-specific plasticity of homologous characters (e.g., radula, shell, foot, neuromuscular systems), raising questions concerning the cell types and the molecular toolkit that underlie this variation. Here, we report on the gene expression profile of individual cells of the trochophore larva of the invasive freshwater bivalve Dreissena rostriformis as inferred from single cell RNA sequencing. We generated transcriptomes of 632 individual cells and identified seven transcriptionally distinct cell populations. Developmental trajectory analyses identify cell populations that, for example, share an ectodermal origin such as the nervous system, the shell field, and the prototroch. To annotate these cell populations, we examined ontology terms from the gene sets that characterize each individual cluster. These were compared to gene expression data previously reported from other lophotrochozoans. Genes expected to be specific to certain tissues, such as Hox1 (in the shell field), Caveolin (in prototrochal cells), or FoxJ (in other cillia-bearing cells) provide evidence that the recovered cell populations contribute to various distinct tissues and organs known from morphological studies. This dataset provides the first molecular atlas of gene expression underlying bivalve organogenesis and generates an important framework for future comparative studies into cell and tissue type development in Mollusca and Metazoa as a whole.
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16
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Buzgariu W, Aubry-Lachainaye JP, Galliot B. Studying Stem Cell Biology in Intact and Whole-Body Regenerating Hydra by Flow Cytometry. Methods Mol Biol 2022; 2450:373-398. [PMID: 35359319 PMCID: PMC9761490 DOI: 10.1007/978-1-0716-2172-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The freshwater Hydra polyp is a versatile model to study whole-body regeneration from a developmental as well as a cellular point of view. The outstanding regenerative capacities of Hydra are based on its three populations of adult stem cells located in the central body column of the animal. There, these three populations, gastrodermal epithelial, epidermal epithelial, and interstitial, continuously cycle in homeostatic conditions, and their activity is locally regulated after mid-gastric bisection. Moreover, they present an unusual cycling behavior with a short G1 phase and a pausing in G2. This particular cell cycle has been studied for a long time with classical microscopic methods. We describe here two flow cytometry methods that provide accurate and reproducible quantitative data to monitor cell cycle regulation in homeostatic and regenerative contexts. We also present a cell sorting procedure based on flow cytometry, whereby stem cells expressing a fluorescent reporter protein in transgenic lines can be enriched for use in applications such as transcriptomic, proteomic, or cell cycle analysis.
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Affiliation(s)
- Wanda Buzgariu
- Department of Genetics and Evolution, iGE3, Faculty of Sciences, University of Geneva, Geneva, Switzerland.
| | | | - Brigitte Galliot
- Department of Genetics and Evolution, iGE3, Faculty of Sciences, University of Geneva, Geneva, Switzerland
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17
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Vogg MC, Buzgariu W, Suknovic NS, Galliot B. Cellular, Metabolic, and Developmental Dimensions of Whole-Body Regeneration in Hydra. Cold Spring Harb Perspect Biol 2021; 13:a040725. [PMID: 34230037 PMCID: PMC8635000 DOI: 10.1101/cshperspect.a040725] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Here we discuss the developmental and homeostatic conditions necessary for Hydra regeneration. Hydra is characterized by populations of adult stem cells paused in the G2 phase of the cell cycle, ready to respond to injury signals. The body column can be compared to a blastema-like structure, populated with multifunctional epithelial stem cells that show low sensitivity to proapoptotic signals, and high inducibility of autophagy that promotes resistance to stress and starvation. Intact Hydra polyps also exhibit a dynamic patterning along the oral-aboral axis under the control of homeostatic organizers whose activity results from regulatory loops between activators and inhibitors. As in bilaterians, injury triggers the immediate production of reactive oxygen species (ROS) signals that promote wound healing and contribute to the reactivation of developmental programs via cell death and the de novo formation of new organizing centers from somatic tissues. In aging Hydra, regeneration is rapidly lost as homeostatic conditions are no longer pro-regenerative.
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Affiliation(s)
- Matthias Christian Vogg
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Sciences, University of Geneva, Geneva 4, Switzerland
| | - Wanda Buzgariu
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Sciences, University of Geneva, Geneva 4, Switzerland
| | - Nenad Slavko Suknovic
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Sciences, University of Geneva, Geneva 4, Switzerland
| | - Brigitte Galliot
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Sciences, University of Geneva, Geneva 4, Switzerland
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18
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Chari T, Weissbourd B, Gehring J, Ferraioli A, Leclère L, Herl M, Gao F, Chevalier S, Copley RR, Houliston E, Anderson DJ, Pachter L. Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across Clytia medusa cell types. SCIENCE ADVANCES 2021; 7:eabh1683. [PMID: 34826233 PMCID: PMC8626072 DOI: 10.1126/sciadv.abh1683] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 10/06/2021] [Indexed: 05/12/2023]
Abstract
We present an organism-wide, transcriptomic cell atlas of the hydrozoan medusa Clytia hemisphaerica and describe how its component cell types respond to perturbation. Using multiplexed single-cell RNA sequencing, in which individual animals were indexed and pooled from control and perturbation conditions into a single sequencing run, we avoid artifacts from batch effects and are able to discern shifts in cell state in response to organismal perturbations. This work serves as a foundation for future studies of development, function, and regeneration in a genetically tractable jellyfish species. Moreover, we introduce a powerful workflow for high-resolution, whole-animal, multiplexed single-cell genomics that is readily adaptable to other traditional or nontraditional model organisms.
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Affiliation(s)
- Tara Chari
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Brandon Weissbourd
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Tianqiao and Chrissy Chen Institute for Neuroscience, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jase Gehring
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Anna Ferraioli
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230, France
| | - Lucas Leclère
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230, France
| | - Makenna Herl
- University of New Hampshire School of Law, Concord, NH 03301, USA
| | - Fan Gao
- Caltech Bioinformatics Resource Center, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sandra Chevalier
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230, France
| | - Richard R. Copley
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230, France
| | - Evelyn Houliston
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230, France
| | - David J. Anderson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Tianqiao and Chrissy Chen Institute for Neuroscience, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA
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19
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Transgenesis in the acoel worm Hofstenia miamia. Dev Cell 2021; 56:3160-3170.e4. [PMID: 34752780 DOI: 10.1016/j.devcel.2021.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 07/20/2021] [Accepted: 10/12/2021] [Indexed: 12/27/2022]
Abstract
The acoel worm Hofstenia miamia, which can replace tissue lost to injury via differentiation of a population of stem cells, has emerged as a new research organism for studying regeneration. To enhance the depth of mechanistic studies in this system, we devised a protocol for microinjection into embryonic cells that resulted in stable transgene integration into the genome and generated animals with tissue-specific fluorescent transgene expression in epidermis, gut, and muscle. We demonstrate that transgenic Hofstenia are amenable to the isolation of specific cell types, investigations of regeneration, tracking of photoconverted molecules, and live imaging. Further, our stable transgenic lines revealed insights into the biology of Hofstenia, including a high-resolution three-dimensional view of cell morphology and the organization of muscle as a cellular scaffold for other tissues. Our work positions Hofstenia as a powerful system with multiple toolkits for mechanistic investigations of development, whole-body regeneration, and stem cell biology.
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20
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Nematostella vectensis, an Emerging Model for Deciphering the Molecular and Cellular Mechanisms Underlying Whole-Body Regeneration. Cells 2021; 10:cells10102692. [PMID: 34685672 PMCID: PMC8534814 DOI: 10.3390/cells10102692] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/18/2022] Open
Abstract
The capacity to regenerate lost or injured body parts is a widespread feature within metazoans and has intrigued scientists for centuries. One of the most extreme types of regeneration is the so-called whole body regenerative capacity, which enables regeneration of fully functional organisms from isolated body parts. While not exclusive to this habitat, whole body regeneration is widespread in aquatic/marine invertebrates. Over the past decade, new whole-body research models have emerged that complement the historical models Hydra and planarians. Among these, the sea anemone Nematostella vectensis has attracted increasing interest in regard to deciphering the cellular and molecular mechanisms underlying the whole-body regeneration process. This manuscript will present an overview of the biological features of this anthozoan cnidarian as well as the available tools and resources that have been developed by the scientific community studying Nematostella. I will further review our current understanding of the cellular and molecular mechanisms underlying whole-body regeneration in this marine organism, with emphasis on how comparing embryonic development and regeneration in the same organism provides insight into regeneration specific elements.
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21
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Rinkevich B, Ballarin L, Martinez P, Somorjai I, Ben-Hamo O, Borisenko I, Berezikov E, Ereskovsky A, Gazave E, Khnykin D, Manni L, Petukhova O, Rosner A, Röttinger E, Spagnuolo A, Sugni M, Tiozzo S, Hobmayer B. A pan-metazoan concept for adult stem cells: the wobbling Penrose landscape. Biol Rev Camb Philos Soc 2021; 97:299-325. [PMID: 34617397 PMCID: PMC9292022 DOI: 10.1111/brv.12801] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022]
Abstract
Adult stem cells (ASCs) in vertebrates and model invertebrates (e.g. Drosophila melanogaster) are typically long‐lived, lineage‐restricted, clonogenic and quiescent cells with somatic descendants and tissue/organ‐restricted activities. Such ASCs are mostly rare, morphologically undifferentiated, and undergo asymmetric cell division. Characterized by ‘stemness’ gene expression, they can regulate tissue/organ homeostasis, repair and regeneration. By contrast, analysis of other animal phyla shows that ASCs emerge at different life stages, present both differentiated and undifferentiated phenotypes, and may possess amoeboid movement. Usually pluri/totipotent, they may express germ‐cell markers, but often lack germ‐line sequestering, and typically do not reside in discrete niches. ASCs may constitute up to 40% of animal cells, and participate in a range of biological phenomena, from whole‐body regeneration, dormancy, and agametic asexual reproduction, to indeterminate growth. They are considered legitimate units of selection. Conceptualizing this divergence, we present an alternative stemness metaphor to the Waddington landscape: the ‘wobbling Penrose’ landscape. Here, totipotent ASCs adopt ascending/descending courses of an ‘Escherian stairwell’, in a lifelong totipotency pathway. ASCs may also travel along lower stemness echelons to reach fully differentiated states. However, from any starting state, cells can change their stemness status, underscoring their dynamic cellular potencies. Thus, vertebrate ASCs may reflect just one metazoan ASC archetype.
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Affiliation(s)
- Baruch Rinkevich
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Loriano Ballarin
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35121, Italy
| | - Pedro Martinez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain.,Institut Català de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, 08010, Spain
| | - Ildiko Somorjai
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Oshrat Ben-Hamo
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Ilya Borisenko
- Department of Embryology, Faculty of Biology, Saint-Petersburg State University, University Embankment, 7/9, Saint-Petersburg, 199034, Russia
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Alexander Ereskovsky
- Department of Embryology, Faculty of Biology, Saint-Petersburg State University, University Embankment, 7/9, Saint-Petersburg, 199034, Russia.,Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), Aix Marseille University, CNRS, IRD, Avignon University, Jardin du Pharo, 58 Boulevard Charles Livon, Marseille, 13007, France.,Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Ulitsa Vavilova, 26, Moscow, 119334, Russia
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques Monod, Paris, F-75006, France
| | - Denis Khnykin
- Department of Pathology, Oslo University Hospital, Bygg 19, Gaustad Sykehus, Sognsvannsveien 21, Oslo, 0188, Norway
| | - Lucia Manni
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35121, Italy
| | - Olga Petukhova
- Collection of Vertebrate Cell Cultures, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - Amalia Rosner
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, 06107, France.,Université Côte d'Azur, Federative Research Institute - Marine Resources (IFR MARRES), 28 Avenue de Valrose, Nice, 06103, France
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy (ESP), Università degli Studi di Milano, Via Celoria 26, Milan, 20133, Italy
| | - Stefano Tiozzo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06234 Villefranche-sur-Mer, Villefranche sur Mer, Cedex, France
| | - Bert Hobmayer
- Institute of Zoology and Center for Molecular Biosciences, University of Innsbruck, Technikerstr, Innsbruck, 256020, Austria
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22
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Presnell JS, Browne WE. Krüppel-like factor gene function in the ctenophore Mnemiopsis leidyi assessed by CRISPR/Cas9-mediated genome editing. Development 2021; 148:272041. [PMID: 34373891 DOI: 10.1242/dev.199771] [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: 05/01/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022]
Abstract
The Krüppel-like factor (Klf) gene family encodes transcription factors that play an important role in the regulation of stem cell proliferation, cell differentiation and development in bilaterians. Although Klf genes have been shown to specify functionally various cell types in non-bilaterian animals, their role in early-diverging animal lineages has not been assessed. Thus, the ancestral activity of these transcription factors in animal development is not well understood. The ctenophore Mnemiopsis leidyi has emerged as an important non-bilaterian model system for understanding early animal evolution. Here, we characterize the expression and functional role of Klf genes during M. leidyi embryogenesis. Zygotic Klf gene function was assessed with both CRISPR/Cas9-mediated genome editing and splice-blocking morpholino oligonucleotide knockdown approaches. Abrogation of zygotic Klf expression during M. leidyi embryogenesis resulted in abnormal development of several organs, including the pharynx, tentacle bulbs and apical organ. Our data suggest an ancient role for Klf genes in regulating endodermal patterning, possibly through regulation of cell proliferation.
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Affiliation(s)
- Jason S Presnell
- Department of Biology, University of Miami, Cox Science Center, 1301 Memorial Drive, Miami, FL 33146, USA
| | - William E Browne
- Department of Biology, University of Miami, Cox Science Center, 1301 Memorial Drive, Miami, FL 33146, USA
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23
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Abstract
The evolutionary theory of aging has set the foundations for a comprehensive understanding of aging. The biology of aging has listed and described the "hallmarks of aging," i.e., cellular and molecular mechanisms involved in human aging. The present paper is the first to infer the order of appearance of the hallmarks of bilaterian and thereby human aging throughout evolution from their presence in progressively narrower clades. Its first result is that all organisms, even non-senescent, have to deal with at least one mechanism of aging - the progressive accumulation of misfolded or unstable proteins. Due to their cumulation, these mechanisms are called "layers of aging." A difference should be made between the first four layers of unicellular aging, present in some unicellular organisms and in all multicellular opisthokonts, that stem and strike "from the inside" of individual cells and span from increasingly abnormal protein folding to deregulated nutrient sensing, and the last four layers of metacellular aging, progressively appearing in metazoans, that strike the cells of a multicellular organism "from the outside," i.e., because of other cells, and span from transcriptional alterations to the disruption of intercellular communication. The evolution of metazoans and eumetazoans probably solved the problem of aging along with the problem of unicellular aging. However, metacellular aging originates in the mechanisms by which the effects of unicellular aging are kept under control - e.g., the exhaustion of stem cells that contribute to replace damaged somatic cells. In bilaterians, additional functions have taken a toll on generally useless potentially limited lifespan to increase the fitness of organisms at the price of a progressively less efficient containment of the damage of unicellular aging. In the end, this picture suggests that geroscience should be more efficient in targeting conditions of metacellular aging rather than unicellular aging itself.
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Affiliation(s)
- Maël Lemoine
- CNRS, ImmunoConcEpT, UMR 5164, Univ. Bordeaux, Bordeaux, France
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24
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Srivastava M. Beyond Casual Resemblances: Rigorous Frameworks for Comparing Regeneration Across Species. Annu Rev Cell Dev Biol 2021; 37:415-440. [PMID: 34288710 DOI: 10.1146/annurev-cellbio-120319-114716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The majority of animal phyla have species that can regenerate. Comparing regeneration across animals can reconstruct the molecular and cellular evolutionary history of this process. Recent studies have revealed some similarity in regeneration mechanisms, but rigorous comparative methods are needed to assess whether these resemblances are ancestral pathways (homology) or are the result of convergent evolution (homoplasy). This review aims to provide a framework for comparing regeneration across animals, focusing on gene regulatory networks (GRNs), which are substrates for assessing process homology. The homology of the wound-induced activation of Wnt signaling and of adult stem cells are discussed as examples of ongoing studies of regeneration that enable comparisons in a GRN framework. Expanding the study of regeneration GRNs in currently studied species and broadening taxonomic sampling for these approaches will identify processes that are unifying principles of regeneration biology across animals. These insights are important both for evolutionary studies of regeneration and for human regenerative medicine. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Mansi Srivastava
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;
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25
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Pillai A, Gungi A, Reddy PC, Galande S. Epigenetic Regulation in Hydra: Conserved and Divergent Roles. Front Cell Dev Biol 2021; 9:663208. [PMID: 34041242 PMCID: PMC8141815 DOI: 10.3389/fcell.2021.663208] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Transitions in gene regulatory processes responsible for the emergence of specialized cell types and spatiotemporal regulation of developmental signaling prior to the divergence of Cnidaria and Bilateria are poorly understood. As a sister group of Bilateria, the phylum Cnidaria can provide significant insights into these processes. Among the cnidarians, hydrae have been studied for >250 years to comprehend the mechanisms underlying their unique immortality and robust regenerative capacity. Studies on Hydra spp. and other pre-bilaterians alike have advanced our understanding of the evolutionary underpinnings governing eumetazoan tissue development, homeostasis, and regeneration. In addition to its regenerative potential, Hydra exhibits continuously active axial patterning due to its peculiar tissue dynamics. These distinctive physiological processes necessitate large scale gene expression changes that are governed by the multitude of epigenetic mechanisms operating in cells. This review highlights the contemporary knowledge of epigenetic regulation in Hydra with contemporary studies from other members of Cnidaria, as well as the interplay between regulatory mechanisms wherever demonstrated. The studies covered in the scope of this review reveal both ancestral and divergent roles played by conserved epigenetic mechanisms with emphasis on transcriptional regulation. Additionally, single-cell transcriptomics data was mined to predict the physiological relevance of putative gene regulatory components, which is in agreement with published findings and yielded insights into the possible functions of the gene regulatory mechanisms that are yet to be deciphered in Hydra, such as DNA methylation. Finally, we delineate potentially rewarding epigenetics research avenues that can further leverage the unique biology of Hydra.
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Affiliation(s)
| | | | - Puli Chandramouli Reddy
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Sanjeev Galande
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, India
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26
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Cazet JF, Cho A, Juliano CE. Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra. eLife 2021; 10:60562. [PMID: 33779545 PMCID: PMC8049744 DOI: 10.7554/elife.60562] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 03/28/2021] [Indexed: 12/13/2022] Open
Abstract
During whole-body regeneration, a bisection injury can trigger two different types of regeneration. To understand the transcriptional regulation underlying this adaptive response, we characterized transcript abundance and chromatin accessibility during oral and aboral regeneration in the cnidarian Hydra vulgaris. We found that the initial response to amputation at both wound sites is identical and includes widespread apoptosis and the activation of the oral-specifying Wnt signaling pathway. By 8 hr post amputation, Wnt signaling became restricted to oral regeneration. Wnt pathway genes were also upregulated in puncture wounds, and these wounds induced the formation of ectopic oral structures if pre-existing organizers were simultaneously amputated. Our work suggests that oral patterning is activated as part of a generic injury response in Hydra, and that alternative injury outcomes are dependent on signals from the surrounding tissue. Furthermore, Wnt signaling is likely part of a conserved wound response predating the split of cnidarians and bilaterians.
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Affiliation(s)
- Jack F Cazet
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Adrienne Cho
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Celina E Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
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27
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Reyes-Bermudez A, Hidaka M, Mikheyev A. Transcription Profiling of Cultured Acropora digitifera Adult Cells Reveals the Existence of Ancestral Genome Regulatory Modules Underlying Pluripotency and Cell Differentiation in Cnidaria. Genome Biol Evol 2021; 13:6121108. [PMID: 33501945 PMCID: PMC7936024 DOI: 10.1093/gbe/evab008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2021] [Indexed: 12/24/2022] Open
Abstract
Due to their pluripotent nature and unlimited cell renewal, stem cells have been proposed as an ideal material for establishing long-term cnidarian cell cultures. However, the lack of unifying principles associated with "stemness" across the phylum complicates stem cells' identification and isolation. Here, we for the first time report gene expression profiles for cultured coral cells, focusing on regulatory gene networks underlying pluripotency and differentiation. Cultures were initiated from Acropora digitifera tip fragments, the fastest growing tissue in Acropora. Overall, in vitro transcription resembled early larvae, overexpressing orthologs of premetazoan and Hydra stem cell markers, and transcripts with roles in cell division, migration, and differentiation. Our results suggest the presence of pluripotent cell types in cultures and indicate the existence of ancestral genome regulatory modules underlying pluripotency and cell differentiation in cnidaria. Cultured cells appear to be synthesizing protein, differentiating, and proliferating.
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Affiliation(s)
| | - Michio Hidaka
- Department of Chemistry, Biology, and Marine Science, University of the Ryukyus, Okinawa, Japan
| | - Alexander Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Okinawa, Japan.,Research School of Biology, Division of Ecology and Evolution, Australian National University, Canberra, ACT, Australia
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28
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Skokan TD, Vale RD, McKinley KL. Cell Sorting in Hydra vulgaris Arises from Differing Capacities for Epithelialization between Cell Types. Curr Biol 2020; 30:3713-3723.e3. [PMID: 32795440 PMCID: PMC7541579 DOI: 10.1016/j.cub.2020.07.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/05/2020] [Accepted: 07/09/2020] [Indexed: 12/22/2022]
Abstract
Hydra vulgaris exhibits a remarkable capacity to reassemble its body plan from a disordered aggregate of cells. Reassembly begins by sorting two epithelial cell types, endoderm and ectoderm, into inner and outer layers, respectively. The cellular features and behaviors that distinguish ectodermal and endodermal lineages to drive sorting have not been fully elucidated. To dissect this process, we use micromanipulation to position single cells of diverse lineages on the surface of defined multicellular aggregates and monitor sorting outcomes by live imaging. Although sorting has previously been attributed to intrinsic differences between the epithelial lineages, we find that single cells of all lineages sort to the interior of ectodermal aggregates, including single ectodermal cells. This reveals that cells of the same lineage can adopt opposing positions when sorting as individuals or a collective. Ectodermal cell collectives adopt their position at the aggregate exterior by rapidly reforming an epithelium that engulfs cells adhered to its surface through a collective spreading behavior. In contrast, aggregated endodermal cells persistently lose epithelial features. These non-epithelialized aggregates, like isolated cells of all lineages, are adherent passengers for engulfment by the ectodermal epithelium. We find that collective spreading of the ectoderm and persistent de-epithelialization in the endoderm also arise during local wounding in Hydra, suggesting that Hydra's wound-healing and self-organization capabilities may employ similar mechanisms. Together, our data suggest that differing propensities for epithelialization can sort cell types into distinct compartments to build and restore complex tissue architecture.
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Affiliation(s)
- Taylor D Skokan
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ronald D Vale
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA.
| | - Kara L McKinley
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
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29
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Schenkelaars Q, Perez-Cortes D, Perruchoud C, Galliot B. The polymorphism of Hydra microsatellite sequences provides strain-specific signatures. PLoS One 2020; 15:e0230547. [PMID: 32986740 PMCID: PMC7521734 DOI: 10.1371/journal.pone.0230547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 09/04/2020] [Indexed: 11/18/2022] Open
Abstract
Hydra are freshwater polyps widely studied for their amazing regenerative capacity, adult stem cell populations, low senescence and value as ecotoxicological marker. Many wild-type strains of H. vulgaris have been collected worldwide and maintained effectively under laboratory conditions by asexual reproduction, while stable transgenic lines have been continuously produced since 2006. Efforts are now needed to ensure the genetic characterization of all these strains, which despite similar morphologies, show significant variability in their response to gene expression silencing procedures, pharmacological treatments or environmental conditions. Here, we established a rapid and reliable procedure at the single polyp level to produce via PCR amplification of three distinct microsatellite sequences molecular signatures that distinguish between Hydra strains and species. The TG-rich region of an uncharacterized gene (ms-c25145) helps to distinguish between Eurasian H. vulgaris-Pallas strains (Hm-105, Basel1, Basel2 and reg-16), between Eurasian and North American H. vulgaris strains (H. carnea, AEP), and between the H. vulgaris and H. oligactis species. The AT-rich microsatellite sequences located in the AIP gene (Aryl Hydrocarbon Receptor Interaction Protein, ms-AIP) also differ between Eurasian and North American H. vulgaris strains. Finally, the AT-rich microsatellite located in the Myb-Like cyclin D-binding transcription factor1 gene (ms-DMTF1) gene helps to distinguish certain transgenic AEP lines. This study shows that the analysis of microsatellite sequences, which is capable of tracing genomic variations between closely related lineages of Hydra, provides a sensitive and robust tool for characterizing the Hydra strains.
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Affiliation(s)
- Quentin Schenkelaars
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Diego Perez-Cortes
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Chrystelle Perruchoud
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Brigitte Galliot
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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30
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Klimovich A, Giacomello S, Björklund Å, Faure L, Kaucka M, Giez C, Murillo-Rincon AP, Matt AS, Willoweit-Ohl D, Crupi G, de Anda J, Wong GCL, D'Amato M, Adameyko I, Bosch TCG. Prototypical pacemaker neurons interact with the resident microbiota. Proc Natl Acad Sci U S A 2020; 117:17854-17863. [PMID: 32647059 PMCID: PMC7395494 DOI: 10.1073/pnas.1920469117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Pacemaker neurons exert control over neuronal circuit function by their intrinsic ability to generate rhythmic bursts of action potential. Recent work has identified rhythmic gut contractions in human, mice, and hydra to be dependent on both neurons and the resident microbiota. However, little is known about the evolutionary origin of these neurons and their interaction with microbes. In this study, we identified and functionally characterized prototypical ANO/SCN/TRPM ion channel-expressing pacemaker cells in the basal metazoan Hydra by using a combination of single-cell transcriptomics, immunochemistry, and functional experiments. Unexpectedly, these prototypical pacemaker neurons express a rich set of immune-related genes mediating their interaction with the microbial environment. Furthermore, functional experiments gave a strong support to a model of the evolutionary emergence of pacemaker cells as neurons using components of innate immunity to interact with the microbial environment and ion channels to generate rhythmic contractions.
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Affiliation(s)
- Alexander Klimovich
- Department of Cell and Developmental Biology, Zoological Institute, University of Kiel, D-24118 Kiel, Germany;
| | - Stefania Giacomello
- Department of Biochemistry and Biophysics, National Infrastructure of Sweden, Science for Life Laboratory, Stockholm University, 17121 Solna, Sweden
- Department of Gene Technology, Science for Life Laboratory, Kungligia Tekniska Högskolan Royal Institute of Technology, 17121 Solna, Sweden
| | - Åsa Björklund
- Department of Cell and Molecular Biology, National Infrastructure of Sweden, Science for Life Laboratory, Uppsala University, 75237 Uppsala, Sweden
| | - Louis Faure
- Department of Molecular Neurosciences, Center for Brain Research, Medical University Vienna, 1090 Vienna, Austria
| | - Marketa Kaucka
- Department of Molecular Neurosciences, Center for Brain Research, Medical University Vienna, 1090 Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, SH 24306 Plön, Germany
| | - Christoph Giez
- Department of Cell and Developmental Biology, Zoological Institute, University of Kiel, D-24118 Kiel, Germany
| | - Andrea P Murillo-Rincon
- Department of Cell and Developmental Biology, Zoological Institute, University of Kiel, D-24118 Kiel, Germany
| | - Ann-Sophie Matt
- Department of Cell and Developmental Biology, Zoological Institute, University of Kiel, D-24118 Kiel, Germany
| | - Doris Willoweit-Ohl
- Department of Cell and Developmental Biology, Zoological Institute, University of Kiel, D-24118 Kiel, Germany
| | - Gabriele Crupi
- Department of Cell and Developmental Biology, Zoological Institute, University of Kiel, D-24118 Kiel, Germany
| | - Jaime de Anda
- Department of Bioengineering, California NanoSystems Institute, University of California, Los Angeles, CA 90095-1600
- Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095-1600
| | - Gerard C L Wong
- Department of Bioengineering, California NanoSystems Institute, University of California, Los Angeles, CA 90095-1600
- Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095-1600
| | - Mauro D'Amato
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Igor Adameyko
- Department of Molecular Neurosciences, Center for Brain Research, Medical University Vienna, 1090 Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Thomas C G Bosch
- Department of Cell and Developmental Biology, Zoological Institute, University of Kiel, D-24118 Kiel, Germany;
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31
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Sun S, White RR, Fischer KE, Zhang Z, Austad SN, Vijg J. Inducible aging in Hydra oligactis implicates sexual reproduction, loss of stem cells, and genome maintenance as major pathways. GeroScience 2020; 42:1119-1132. [PMID: 32578072 DOI: 10.1007/s11357-020-00214-z] [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: 05/20/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023] Open
Abstract
Freshwater polyps of the genus Hydra do not age. However, temperature stress induces aging and a shift from reproduction by asexual budding to sexual gamete production in a cold-sensitive (CS) strain of H. oligactis. We sequenced the transcriptome of a male CS strain before and after this life history shift and compared changes in gene expression relative to those seen in a cold-resistant (CR) strain that does not undergo a life history shift in response to altered temperature. We found that the switch from non-aging asexual reproduction to aging and sexual reproduction involves upregulation of genes not only involved in gametogenesis but also genes involved in cellular senescence, apoptosis, and DNA repair accompanied by a downregulation of genes involved in stem cell maintenance. These results suggest that aging is a byproduct of sexual reproduction-associated cellular reprogramming and underscore the power of these H. oligactis strains to identify intrinsic mechanisms of aging.
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Affiliation(s)
- Shixiang Sun
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ryan R White
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.,Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Kathleen E Fischer
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Zhengdong Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Steven N Austad
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA. .,Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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32
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Teefy BB, Siebert S, Cazet JF, Lin H, Juliano CE. PIWI-piRNA pathway-mediated transposable element repression in Hydra somatic stem cells. RNA (NEW YORK, N.Y.) 2020; 26:550-563. [PMID: 32075940 PMCID: PMC7161359 DOI: 10.1261/rna.072835.119] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/17/2020] [Indexed: 05/09/2023]
Abstract
Transposable elements (TEs) can damage genomes, thus organisms use a variety of mechanisms to repress TE expression. The PIWI-piRNA pathway is a small RNA pathway that represses TE expression in the germline of animals. Here we explore the function of the pathway in the somatic stem cells of Hydra, a long-lived freshwater cnidarian. Hydra have three stem cell populations, all of which express PIWI proteins; endodermal and ectodermal epithelial stem cells (ESCs) are somatic, whereas the interstitial stem cells have germline competence. To study somatic function of the pathway, we isolated piRNAs from Hydra that lack the interstitial lineage and found that these somatic piRNAs map predominantly to TE transcripts and display the conserved sequence signatures typical of germline piRNAs. Three lines of evidence suggest that the PIWI-piRNA pathway represses TEs in Hydra ESCs. First, epithelial knockdown of the Hydra piwi gene hywi resulted in up-regulation of TE expression. Second, degradome sequencing revealed evidence of PIWI-mediated cleavage of TE RNAs in epithelial cells using the ping-pong mechanism. Finally, we demonstrated a direct association between Hywi protein and TE transcripts in epithelial cells using RNA immunoprecipitation. Altogether, our data reveal that the PIWI-piRNA pathway represses TE expression in the somatic cell lineages of Hydra, which we propose contributes to the extreme longevity of the organism. Furthermore, our results, in combination with others, suggest that somatic TE repression is an ancestral function of the PIWI-piRNA pathway.
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Affiliation(s)
- Bryan B Teefy
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
| | - Stefan Siebert
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
| | - Jack F Cazet
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
| | - Haifan Lin
- Department of Cell Biology, Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Celina E Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
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33
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Frank U, Nicotra ML, Schnitzler CE. The colonial cnidarian Hydractinia. EvoDevo 2020; 11:7. [PMID: 32226598 PMCID: PMC7098123 DOI: 10.1186/s13227-020-00151-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/12/2020] [Indexed: 11/27/2022] Open
Abstract
Hydractinia, a genus of colonial marine cnidarians, has been used as a model organism for developmental biology and comparative immunology for over a century. It was this animal where stem cells and germ cells were first studied. However, protocols for efficient genetic engineering have only recently been established by a small but interactive community of researchers. The animal grows well in the lab, spawns daily, and its relatively short life cycle allows genetic studies. The availability of genomic tools and resources opens further opportunities for research using this animal. Its accessibility to experimental manipulation, growth- and cellular-plasticity, regenerative ability, and resistance to aging and cancer place Hydractinia as an emerging model for research in many biological and environmental disciplines.
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Affiliation(s)
- Uri Frank
- 1Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Matthew L Nicotra
- 2Departments of Surgery and Immunology, Center for Evolutionary Biology and Medicine, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Christine E Schnitzler
- 3Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 320803 USA.,4Department of Biology, University of Florida, Gainesville, FL 32611 USA
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34
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Rathje K, Mortzfeld B, Hoeppner MP, Taubenheim J, Bosch TCG, Klimovich A. Dynamic interactions within the host-associated microbiota cause tumor formation in the basal metazoan Hydra. PLoS Pathog 2020; 16:e1008375. [PMID: 32191776 PMCID: PMC7081986 DOI: 10.1371/journal.ppat.1008375] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 02/01/2020] [Indexed: 02/07/2023] Open
Abstract
The extent to which disturbances in the resident microbiota can compromise an animal’s health is poorly understood. Hydra is one of the evolutionary oldest animals with naturally occurring tumors. Here, we found a causal relationship between an environmental spirochete (Turneriella spec.) and tumorigenesis in Hydra. Unexpectedly, virulence of this pathogen requires the presence of Pseudomonas spec., a member of Hydra´s beneficial microbiome indicating that dynamic interactions between a resident bacterium and a pathogen cause tumor formation. The observation points to the crucial role of commensal bacteria in maintaining tissue homeostasis and adds support to the view that microbial community interactions are essential for disease. These findings in an organism that shares deep evolutionary connections with all animals have implications for our understanding of cancer. Here we follow up on our initial observation of tumor formation in the basal metazoan Hydra and demonstrate that tumor development in one of the evolutionary oldest animals is caused by a dynamic interplay between an environmental spirochete, the host-associated resident microbiota, and the tissue homeostasis within the animal. Unexpectedly, the pathogenicity of the environmental bacterium Turneriella is context-dependent: the virulence of this pathogen requires the presence of a member of Hydra’s beneficial microbiome—the Pseudomonas bacterium. Dynamic interactions between two microbiota members have profound effects onto the host tissue homeostasis and fitness. Our data provide direct evidence for the important role of the resident microbiome in maintaining tissue homeostasis and pathogen defense, a fundamental process that is likely to take place in every tissue of every animal species. In summary, our study uncovers an evolutionary conserved role of the resident microbiome in guarding host’s tissue homeostasis.
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Affiliation(s)
- Kai Rathje
- Zoological Institute, Kiel University, Kiel, Germany
| | - Benedikt Mortzfeld
- Zoological Institute, Kiel University, Kiel, Germany
- Department of Biology, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, United States of America
| | - Marc P. Hoeppner
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Jan Taubenheim
- Zoological Institute, Kiel University, Kiel, Germany
- Institute for Zoology and Organismic Interactions, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Thomas C. G. Bosch
- Zoological Institute, Kiel University, Kiel, Germany
- * E-mail: (TCGB); (AK)
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35
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Abstract
Regeneration is a remarkable phenomenon that has been the subject of awe and bafflement for hundreds of years. Although regeneration competence is found in highly divergent organisms throughout the animal kingdom, recent advances in tools used for molecular and genomic characterization have uncovered common genes, molecular mechanisms, and genomic features in regenerating animals. In this review we focus on what is known about how genome regulation modulates cellular potency during regeneration. We discuss this regulation in the context of complex tissue regeneration in animals, from Hydra to humans, with reference to ex vivo-cultured cell models of pluripotency when appropriate. We emphasize the importance of a detailed molecular understanding of both the mechanisms that regulate genomic output and the functional assays that assess the biological relevance of such molecular characterizations.
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Affiliation(s)
- Elizabeth M Duncan
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA
| | - Alejandro Sánchez Alvarado
- Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA;
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36
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Boundary maintenance in the ancestral metazoan Hydra depends on histone acetylation. Dev Biol 2019; 458:200-214. [PMID: 31738910 DOI: 10.1016/j.ydbio.2019.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 11/04/2019] [Accepted: 11/12/2019] [Indexed: 12/24/2022]
Abstract
Much of boundary formation during development remains to be understood, despite being a defining feature of many animal taxa. Axial patterning of Hydra, a member of the ancient phylum Cnidaria which diverged prior to the bilaterian radiation, involves a steady-state of production and loss of tissue, and is dependent on an organizer located in the upper part of the head. We show that the sharp boundary separating tissue in the body column from head and foot tissue depends on histone acetylation. Histone deacetylation disrupts the boundary by affecting numerous developmental genes including Wnt components and prevents stem cells from entering the position dependent differentiation program. Overall, our results suggest that reversible histone acetylation is an ancient regulatory mechanism for partitioning the body axis into domains with specific identity, which was present in the common ancestor of cnidarians and bilaterians, at least 600 million years ago.
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37
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Abstract
The freshwater polyp Hydra provides a potent model system for investigating the conditions that promote wound healing, reactivation of a developmental process and, ultimately, regeneration of an amputated body part. Hydra polyps can also be dissociated to the single cell level and can regenerate a complete body axis from aggregates, behaving as natural organoids. In recent years, the ability to exploit Hydra has been expanded with the advent of new live-imaging approaches, genetic manipulations that include stable transgenesis, gene silencing and genome editing, and the accumulation of high-throughput omics data. In this Primer, we provide an overview of Hydra as a model system for studying regeneration, highlighting recent results that question the classical self-enhancement and long-range inhibition model supposed to drive Hydra regeneration. We underscore the need for integrative explanations incorporating biochemical as well as mechanical signalling.
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Affiliation(s)
- Matthias C Vogg
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Brigitte Galliot
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Charisios D Tsiairis
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
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38
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Condamine T, Jager M, Leclère L, Blugeon C, Lemoine S, Copley RR, Manuel M. Molecular characterisation of a cellular conveyor belt in Clytia medusae. Dev Biol 2019; 456:212-225. [PMID: 31509769 DOI: 10.1016/j.ydbio.2019.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/29/2019] [Accepted: 09/07/2019] [Indexed: 11/25/2022]
Abstract
The tentacular system of Clytia hemisphaerica medusa (Cnidaria, Hydrozoa) has recently emerged as a promising experimental model to tackle the developmental mechanisms that regulate cell lineage progression in an early-diverging animal phylum. From a population of proximal stem cells, the successive steps of tentacle stinging cell (nematocyte) elaboration, are spatially ordered along a "cellular conveyor belt". Furthermore, the C. hemisphaerica tentacular system exhibits bilateral organisation, with two perpendicular polarity axes (proximo-distal and oral-aboral). We aimed to improve our knowledge of this cellular system by combining RNAseq-based differential gene expression analyses and expression studies of Wnt signalling genes. RNAseq comparisons of gene expression levels were performed (i) between the tentacular system and a control medusa deprived of all tentacles, nematogenic sites and gonads, and (ii) between three samples staggered along the cellular conveyor belt. The behaviour in these differential expression analyses of two reference gene sets (stem cell genes; nematocyte genes), as well as the relative representations of selected gene ontology categories, support the validity of the cellular conveyor belt model. Expression patterns obtained by in situ hybridisation for selected highly differentially expressed genes and for Wnt signalling genes are largely consistent with the results from RNAseq. Wnt signalling genes exhibit complex spatial deployment along both polarity axes of the tentacular system, with the Wnt/β-catenin pathway probably acting along the oral-aboral axis rather than the proximo-distal axis. These findings reinforce the idea that, despite overall radial symmetry, cnidarians have a full potential for elaboration of bilateral structures based on finely orchestrated deployment of an ancient developmental gene toolkit.
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Affiliation(s)
- Thomas Condamine
- Sorbonne Université, MNHN, CNRS, EPHE, Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Paris, France
| | - Muriel Jager
- Sorbonne Université, MNHN, CNRS, EPHE, Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Paris, France
| | - Lucas Leclère
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV) UMR7009, 181 chemin du Lazaret, 06230, Villefranche-sur-mer, France
| | - Corinne Blugeon
- Genomic Paris Centre, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Sophie Lemoine
- Genomic Paris Centre, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Richard R Copley
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV) UMR7009, 181 chemin du Lazaret, 06230, Villefranche-sur-mer, France
| | - Michaël Manuel
- Sorbonne Université, MNHN, CNRS, EPHE, Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Paris, France.
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Fujita S, Kuranaga E, Nakajima YI. Cell proliferation controls body size growth, tentacle morphogenesis, and regeneration in hydrozoan jellyfish Cladonema pacificum. PeerJ 2019; 7:e7579. [PMID: 31523518 PMCID: PMC6714968 DOI: 10.7717/peerj.7579] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/29/2019] [Indexed: 12/25/2022] Open
Abstract
Jellyfish have existed on the earth for around 600 million years and have evolved in response to environmental changes. Hydrozoan jellyfish, members of phylum Cnidaria, exist in multiple life stages, including planula larvae, vegetatively-propagating polyps, and sexually-reproducing medusae. Although free-swimming medusae display complex morphology and exhibit increase in body size and regenerative ability, their underlying cellular mechanisms are poorly understood. Here, we investigate the roles of cell proliferation in body-size growth, appendage morphogenesis, and regeneration using Cladonema pacificum as a hydrozoan jellyfish model. By examining the distribution of S phase cells and mitotic cells, we revealed spatially distinct proliferating cell populations in medusae, uniform cell proliferation in the umbrella, and clustered cell proliferation in tentacles. Blocking cell proliferation by hydroxyurea caused inhibition of body size growth and defects in tentacle branching, nematocyte differentiation, and regeneration. Local cell proliferation in tentacle bulbs is observed in medusae of two other hydrozoan species, Cytaeis uchidae and Rathkea octopunctata, indicating that it may be a conserved feature among hydrozoan jellyfish. Altogether, our results suggest that hydrozoan medusae possess actively proliferating cells and provide experimental evidence regarding the role of cell proliferation in body-size control, tentacle morphogenesis, and regeneration.
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Affiliation(s)
- Sosuke Fujita
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Erina Kuranaga
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yu-Ichiro Nakajima
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan.,Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
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Siebert S, Farrell JA, Cazet JF, Abeykoon Y, Primack AS, Schnitzler CE, Juliano CE. Stem cell differentiation trajectories in Hydra resolved at single-cell resolution. Science 2019; 365:eaav9314. [PMID: 31346039 PMCID: PMC7104783 DOI: 10.1126/science.aav9314] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/11/2019] [Indexed: 12/31/2022]
Abstract
The adult Hydra polyp continually renews all of its cells using three separate stem cell populations, but the genetic pathways enabling this homeostatic tissue maintenance are not well understood. We sequenced 24,985 Hydra single-cell transcriptomes and identified the molecular signatures of a broad spectrum of cell states, from stem cells to terminally differentiated cells. We constructed differentiation trajectories for each cell lineage and identified gene modules and putative regulators expressed along these trajectories, thus creating a comprehensive molecular map of all developmental lineages in the adult animal. In addition, we built a gene expression map of the Hydra nervous system. Our work constitutes a resource for addressing questions regarding the evolution of metazoan developmental processes and nervous system function.
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Affiliation(s)
- Stefan Siebert
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA.
| | - Jeffrey A Farrell
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Jack F Cazet
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Yashodara Abeykoon
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Abby S Primack
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Christine E Schnitzler
- Whitney Laboratory for Marine Bioscience and Department of Biology, University of Florida, St. Augustine, FL, USA
| | - Celina E Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA.
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41
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Transgenesis in Hydra to characterize gene function and visualize cell behavior. Nat Protoc 2019; 14:2069-2090. [DOI: 10.1038/s41596-019-0173-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/04/2019] [Indexed: 12/13/2022]
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42
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Moyers BA, Zhang J. Toward Reducing Phylostratigraphic Errors and Biases. Genome Biol Evol 2018; 10:2037-2048. [PMID: 30060201 PMCID: PMC6105108 DOI: 10.1093/gbe/evy161] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 01/03/2023] Open
Abstract
Phylostratigraphy is a method for estimating gene age, usually applied to large numbers of genes in order to detect nonrandom age-distributions of gene properties that could shed light on mechanisms of gene origination and evolution. However, phylostratigraphy underestimates gene age with a nonnegligible probability. The underestimation is severer for genes with certain properties, creating spurious age distributions of these properties and those correlated with these properties. Here we explore three strategies to reduce phylostratigraphic error/bias. First, we test several alternative homology detection methods (PSIBLAST, HMMER, PHMMER, OMA, and GLAM2Scan) in phylostratigraphy, but fail to find any that noticeably outperforms the commonly used BLASTP. Second, using machine learning, we look for predictors of error-prone genes to exclude from phylostratigraphy, but cannot identify reliable predictors. Finally, we remove from phylostratigraphic analysis genes exhibiting errors in simulation, which by definition minimizes error/bias if the simulation is sufficiently realistic. Using this last approach, we show that some previously reported phylostratigraphic trends (e.g., younger proteins tend to evolve more rapidly and be shorter) disappear or even reverse, reconfirming the necessity of controlling phylostratigraphic error/bias. Taken together, our analyses demonstrate that phylostratigraphic errors/biases are refractory to several potential solutions but can be controlled at least partially by the exclusion of error-prone genes identified via realistic simulations. These results are expected to stimulate the judicious use of error-aware phylostratigraphy and reevaluation of previous phylostratigraphic findings.
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Affiliation(s)
- Bryan A Moyers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
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43
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Tohmonda T, Kamiya A, Ishiguro A, Iwaki T, Fujimi TJ, Hatayama M, Aruga J. Identification and Characterization of Novel Conserved Domains in Metazoan Zic Proteins. Mol Biol Evol 2018; 35:2205-2229. [DOI: 10.1093/molbev/msy122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Takahide Tohmonda
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Akiko Kamiya
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Akira Ishiguro
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Takashi Iwaki
- Meguro Parasitological Museum, Meguro-Ku, Tokyo, Japan
| | - Takahiko J Fujimi
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Minoru Hatayama
- Department of Medical Pharmacology, Nagasaki University Institute of Biomedical Sciences, Nagasaki, Japan
| | - Jun Aruga
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
- Department of Medical Pharmacology, Nagasaki University Institute of Biomedical Sciences, Nagasaki, Japan
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44
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Mortzfeld BM, Taubenheim J, Fraune S, Klimovich AV, Bosch TCG. Stem Cell Transcription Factor FoxO Controls Microbiome Resilience in Hydra. Front Microbiol 2018; 9:629. [PMID: 29666616 PMCID: PMC5891625 DOI: 10.3389/fmicb.2018.00629] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/19/2018] [Indexed: 01/18/2023] Open
Abstract
The aging process is considered to be the result of accumulating cellular deterioration in an individual organism over time. It can be affected by the combined influence of genetic, epigenetic, and environmental factors including life-style-associated events. In the non-senescent freshwater polyp Hydra, one of the classical model systems for evolutionary developmental biology and regeneration, transcription factor FoxO modulates both stem cell proliferation and innate immunity. This provides strong support for the role of FoxO as a critical rate-of-aging regulator. However, how environmental factors interact with FoxO remains unknown. Here, we find that deficiency in FoxO signaling in Hydra leads to dysregulation of antimicrobial peptide expression and that FoxO loss-of-function polyps are impaired in selection for bacteria resembling the native microbiome and more susceptible to colonization of foreign bacteria. These findings reveal a key role of FoxO signaling in the communication between host and microbiota and embed the evolutionary conserved longevity factor FoxO into the holobiont concept.
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Affiliation(s)
| | - Jan Taubenheim
- Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Sebastian Fraune
- Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | | | - Thomas C G Bosch
- Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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Cell-Type Transcriptomes of the Multicellular Green Alga Volvox carteri Yield Insights into the Evolutionary Origins of Germ and Somatic Differentiation Programs. G3-GENES GENOMES GENETICS 2018; 8:531-550. [PMID: 29208647 PMCID: PMC5919742 DOI: 10.1534/g3.117.300253] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Germ-soma differentiation is a hallmark of complex multicellular organisms, yet its origins are not well understood. Volvox carteri is a simple multicellular green alga that has recently evolved a simple germ-soma dichotomy with only two cell-types: large germ cells called gonidia and small terminally differentiated somatic cells. Here, we provide a comprehensive characterization of the gonidial and somatic transcriptomes of V. carteri to uncover fundamental differences between the molecular and metabolic programming of these cell-types. We found extensive transcriptome differentiation between cell-types, with somatic cells expressing a more specialized program overrepresented in younger, lineage-specific genes, and gonidial cells expressing a more generalist program overrepresented in more ancient genes that shared striking overlap with stem cell-specific genes from animals and land plants. Directed analyses of different pathways revealed a strong dichotomy between cell-types with gonidial cells expressing growth-related genes and somatic cells expressing an altruistic metabolic program geared toward the assembly of flagella, which support organismal motility, and the conversion of storage carbon to sugars, which act as donors for production of extracellular matrix (ECM) glycoproteins whose secretion enables massive organismal expansion. V. carteri orthologs of diurnally controlled genes from C. reinhardtii, a single-celled relative, were analyzed for cell-type distribution and found to be strongly partitioned, with expression of dark-phase genes overrepresented in somatic cells and light-phase genes overrepresented in gonidial cells- a result that is consistent with cell-type programs in V. carteri arising by cooption of temporal regulons in a unicellular ancestor. Together, our findings reveal fundamental molecular, metabolic, and evolutionary mechanisms that underlie the origins of germ-soma differentiation in V. carteri and provide a template for understanding the acquisition of germ-soma differentiation in other multicellular lineages.
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46
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Lai AG, Aboobaker AA. EvoRegen in animals: Time to uncover deep conservation or convergence of adult stem cell evolution and regenerative processes. Dev Biol 2018; 433:118-131. [PMID: 29198565 DOI: 10.1016/j.ydbio.2017.10.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 01/08/2023]
Abstract
How do animals regenerate specialised tissues or their entire body after a traumatic injury, how has this ability evolved and what are the genetic and cellular components underpinning this remarkable feat? While some progress has been made in understanding mechanisms, relatively little is known about the evolution of regenerative ability. Which elements of regeneration are due to lineage specific evolutionary novelties or have deeply conserved roots within the Metazoa remains an open question. The renaissance in regeneration research, fuelled by the development of modern functional and comparative genomics, now enable us to gain a detailed understanding of both the mechanisms and evolutionary forces underpinning regeneration in diverse animal phyla. Here we review existing and emerging model systems, with the focus on invertebrates, for studying regeneration. We summarize findings across these taxa that tell us something about the evolution of adult stem cell types that fuel regeneration and the growing evidence that many highly regenerative animals harbor adult stem cells with a gene expression profile that overlaps with germline stem cells. We propose a framework in which regenerative ability broadly evolves through changes in the extent to which stem cells generated through embryogenesis are maintained into the adult life history.
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Affiliation(s)
- Alvina G Lai
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
| | - A Aziz Aboobaker
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
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Abstract
Zic family genes encode five C2H2-type zinc finger domain-containing proteins that have many roles in animal development and maintenance. Recent phylogenetic analyses showed that Zic family genes are distributed in metazoans (multicellular animals), except Porifera (sponges) and Ctenophora (comb jellies). The sequence comparisons revealed that the zinc finger domains were absolutely conserved among the Zic family genes. Zic zinc finger domains are similar to, but distinct from those of the Gli, Glis, and Nkl gene family, and these zinc finger protein families are proposed to have been derived from a common ancestor gene. The Gli-Glis-Nkl-Zic superfamily and some other eukaryotic zinc finger proteins share a tandem CWCH2 (tCWCH2) motif, a hallmark for inter-zinc finger interaction between two adjacent C2H2 zinc fingers. In Zic family proteins, there exist additional evolutionally conserved domains known as ZOC and ZFNC, both of which may have appeared before cnidarian-bilaterian divergence. Comparison of the exon-intron boundaries in the Zic zinc finger domains revealed an intron (A-intron) that was absolutely conserved in bilaterians (metazoans with bilateral symmetry) and a placozoan (a simple nonparasitic metazoan). In vertebrates, there are five to seven Zic paralogs among which Zic1, Zic2, and Zic3 are generated through a tandem gene duplication and carboxy-terminal truncation in a vertebrate common ancestor, sharing a conserved carboxy-terminal sequence. Several hypotheses have been proposed to explain the Zic family phylogeny, including their origin, unique features in the first and second zinc finger motif, evolution of the nuclear localization signal, significance of the animal taxa-selective degeneration, gene multiplication in the vertebrate lineage, and involvement in the evolutionary alteration of the animal body plan.
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48
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Roles of Germline Stem Cells and Somatic Multipotent Stem Cells in Hydra Sexual Reproduction. DIVERSITY AND COMMONALITY IN ANIMALS 2018. [DOI: 10.1007/978-4-431-56609-0_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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49
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Impact of cycling cells and cell cycle regulation on Hydra regeneration. Dev Biol 2018; 433:240-253. [DOI: 10.1016/j.ydbio.2017.11.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 10/31/2017] [Accepted: 11/08/2017] [Indexed: 01/12/2023]
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50
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Abstract
The recent flood of single-cell data not only boosts our knowledge of cells and cell types, but also provides new insight into development and evolution from a cellular perspective. For example, assaying the genomes of multiple cells during development reveals developmental lineage trees-the kinship lineage-whereas cellular transcriptomes inform us about the regulatory state of cells and their gradual restriction in potency-the Waddington lineage. Beyond that, the comparison of single-cell data across species allows evolutionary changes to be tracked at all stages of development from the zygote, via different kinds of stem cells, to the differentiating cells. We discuss recent insights into the evolution of stem cells and initial attempts to reconstruct the evolutionary cell type tree of the mammalian forebrain, for example, by the comparative analysis of neuron types in the mesencephalic floor. These studies illustrate the immense potential of single-cell genomics to open up a new era in developmental and evolutionary research.
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Affiliation(s)
- John C Marioni
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom;
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Detlev Arendt
- Developmental Biology Unit, EMBL, 69117 Heidelberg, Germany;
- Centre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany
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