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Cole AG, Steger J, Hagauer J, Denner A, Ferrer Murguia P, Knabl P, Narayanaswamy S, Wick B, Montenegro JD, Technau U. Updated single cell reference atlas for the starlet anemone Nematostella vectensis. Front Zool 2024; 21:8. [PMID: 38500146 PMCID: PMC10946136 DOI: 10.1186/s12983-024-00529-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/08/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND The recent combination of genomics and single cell transcriptomics has allowed to assess a variety of non-conventional model organisms in much more depth. Single cell transcriptomes can uncover hidden cellular complexity and cell lineage relationships within organisms. The recent developmental cell atlases of the sea anemone Nematostella vectensis, a representative of the basally branching Cnidaria, has provided new insights into the development of all cell types (Steger et al Cell Rep 40(12):111370, 2022; Sebé-Pedrós et al. Cell 173(6):1520-1534.e20). However, the mapping of the single cell reads still suffers from relatively poor gene annotations and a draft genome consisting of many scaffolds. RESULTS Here we present a new wildtype resource of the developmental single cell atlas, by re-mapping of sequence data first published in Steger et al. (2022) and Cole et al. (Nat Commun 14(1):1747, 2023), to the new chromosome-level genome assembly and corresponding gene models in Zimmermann et al. (Nat Commun 14, 8270 (2023). https://doi.org/10.1038/s41467-023-44080-7 ). We expand the pre-existing dataset through the incorporation of additional sequence data derived from the capture and sequencing of cell suspensions from four additional samples: 24 h gastrula, 2d planula, an inter-parietal region of the bodywall from a young unsexed animal, and another adult mesentery from a mature male animal. CONCLUSION Our analyses of the full cell-state inventory provide transcriptomic signatures for 127 distinct cell states, of which 47 correspond to neuroglandular subtypes. We also identify two distinct putatively immune-related transcriptomic profiles that segregate between the inner and outer cell layers. Furthermore, the new gene annotation Nv2 has markedly improved the mapping on the single cell transcriptome data and will therefore be of great value for the community and anyone using the dataset.
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Affiliation(s)
- Alison G Cole
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Research Platform Single Cell Regulation of Stem Cells, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Julia Steger
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Julia Hagauer
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Andreas Denner
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Patricio Ferrer Murguia
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Paul Knabl
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Sanjay Narayanaswamy
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Brittney Wick
- UCSC Cellbrowser, University of California, Santa Cruz, USA
| | - Juan D Montenegro
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Ulrich Technau
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Research Platform Single Cell Regulation of Stem Cells, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Max Perutz Labs, University of Vienna, Dr. Bohrgasse 9, 1090, Vienna, Austria.
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2
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Carrión PJA, Desai N, Brennan JJ, Fifer JE, Siggers T, Davies SW, Gilmore TD. Starvation decreases immunity and immune regulatory factor NF-κB in the starlet sea anemone Nematostella vectensis. Commun Biol 2023; 6:698. [PMID: 37420095 PMCID: PMC10329013 DOI: 10.1038/s42003-023-05084-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 06/28/2023] [Indexed: 07/09/2023] Open
Abstract
Lack of proper nutrition has important consequences for the physiology of all organisms, and nutritional status can affect immunity, based on many studies in terrestrial animals. Here we show a positive correlation between nutrition and immunity in the sea anemone Nematostella vectensis. Gene expression profiling of adult anemones shows downregulation of genes involved in nutrient metabolism, cellular respiration, and immunity in starved animals. Starved adult anemones also have reduced protein levels and activity of immunity transcription factor NF-κB. Starved juvenile anemones have increased sensitivity to bacterial infection and also have lower NF-κB protein levels, as compared to fed controls. Weighted Gene Correlation Network Analysis (WGCNA) is used to identify significantly correlated gene networks that were downregulated with starvation. These experiments demonstrate a correlation between nutrition and immunity in an early diverged marine metazoan, and the results have implications for the survival of marine organisms as they encounter changing environments.
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Affiliation(s)
| | - Niharika Desai
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Joseph J Brennan
- Department of Biology, Boston University, Boston, MA, 02215, USA
- Pfizer, Inc., 1 Portland St, Cambridge, MA, 02139, USA
| | - James E Fifer
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Trevor Siggers
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Thomas D Gilmore
- Department of Biology, Boston University, Boston, MA, 02215, USA.
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3
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Medeiros IPM, Souza MM. Cell volume maintenance capacity of the sea anemone Bunodosoma cangicum: the effect of copper. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:50057-50066. [PMID: 36787068 DOI: 10.1007/s11356-023-25834-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/06/2023] [Indexed: 02/15/2023]
Abstract
Cell volume regulation is an essential strategy for the maintenance of life under unfavorable osmotic conditions. Mechanisms aimed at minimizing the physiological challenges caused by environmental changes are crucial in anisosmotic environments. However, aquatic ecosystems experience multiple stressors, including variations in salinity and heavy metal pollution. The accumulation of heavy metals in aquatic ecosystems has a significant effect on the biota, leading to impaired function. The aim of this study was to investigate the capacity of volume regulation in isolated cells of the sea anemone Bunodosoma cangicum exposed to nominal copper (Cu) concentrations of 5 and 50 µg L-1, associated or not with hypoosmotic (15‰) or hyperosmotic (45‰) shock for 15 min. In the absence of the metal, our results showed volume maintenance in all osmotic conditions. Our results showed that cell volume was maintained under all osmotic conditions in the absence of Cu. Similarly, no significant differences were observed in cell volumes under isosmotic and hyperosmotic conditions in the presence of both Cu concentrations. A similar homeostatic response was observed under the hypoosmotic condition with 5 µg L-1 Cu. Our results showed an increase in cell volume with exposure of the cells to the hypoosmotic condition and 50 µg L-1 Cu. The response could be associated with the increased bioavailability of Cu, reduced ability to resist multixenobiotics and their efflux pathways, and the impairment of water efflux in specialized transmembrane proteins. Therefore, B. cangicum pedal disk cells can tolerate osmotic variations in aquatic ecosystems. However, the capacity to regulate cell volume under hypoosmotic conditions can be affected by the presence of a metal contaminant (50 µg L-1 Cu), which could be due to the inhibition of water channels.
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Affiliation(s)
- Isadora Porto Martins Medeiros
- Programa de Pós-Graduação Em Ciências Fisiológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, Rio Grande Do Sul, Brazil.
| | - Marta Marques Souza
- Programa de Pós-Graduação Em Ciências Fisiológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, Rio Grande Do Sul, Brazil.,Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, Rio Grande Do Sul, Brazil
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4
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Bove CB, Ingersoll MV, Davies SW. Help Me, Symbionts, You're My Only Hope: Approaches to Accelerate our Understanding of Coral Holobiont Interactions. Integr Comp Biol 2022; 62:1756-1769. [PMID: 36099871 DOI: 10.1093/icb/icac141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/24/2022] [Accepted: 09/05/2022] [Indexed: 01/05/2023] Open
Abstract
Tropical corals construct the three-dimensional framework for one of the most diverse ecosystems on the planet, providing habitat to a plethora of species across taxa. However, these ecosystem engineers are facing unprecedented challenges, such as increasing disease prevalence and marine heatwaves associated with anthropogenic global change. As a result, major declines in coral cover and health are being observed across the world's oceans, often due to the breakdown of coral-associated symbioses. Here, we review the interactions between the major symbiotic partners of the coral holobiont-the cnidarian host, algae in the family Symbiodiniaceae, and the microbiome-that influence trait variation, including the molecular mechanisms that underlie symbiosis and the resulting physiological benefits of different microbial partnerships. In doing so, we highlight the current framework for the formation and maintenance of cnidarian-Symbiodiniaceae symbiosis, and the role that immunity pathways play in this relationship. We emphasize that understanding these complex interactions is challenging when you consider the vast genetic variation of the cnidarian host and algal symbiont, as well as their highly diverse microbiome, which is also an important player in coral holobiont health. Given the complex interactions between and among symbiotic partners, we propose several research directions and approaches focused on symbiosis model systems and emerging technologies that will broaden our understanding of how these partner interactions may facilitate the prediction of coral holobiont phenotype, especially under rapid environmental change.
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Affiliation(s)
- Colleen B Bove
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA 02215, USA
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5
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Williams LM, Gilmore TD. An innate ability: How do basal invertebrates manage their chronic exposure to microbes? PLoS Pathog 2022; 18:e1010897. [PMID: 36315570 PMCID: PMC9621439 DOI: 10.1371/journal.ppat.1010897] [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] [Indexed: 11/06/2022] Open
Abstract
Homologs of mammalian innate immune sensing and downstream pathway proteins have been discovered in a variety of basal invertebrates, including cnidarians and sponges, as well as some single-celled protists. Although the structures of these proteins vary among the basal organisms, many of the activities found in their mammalian counterparts are conserved. This is especially true for the Toll-like receptor (TLR) and cGAS-STING pathways that lead to downstream activation of transcription factor NF-κB. In this short perspective, we describe the evidence that TLR and cGAS-STING signaling to NF-κB is also involved in immunity in basal animals, as well as in the maintenance of microbial symbionts. Different from terrestrial animals, immunity in many marine invertebrates might have a constitutively active state (to protect against continual exposure to resident or waterborne microbes), as well as a hyperactive state that can be induced by pathogens at both transcriptional and posttranscriptional levels. Research on basal immunity may be important for (1) understanding different approaches that organisms take to sensing and protecting against microbes, as well as in maintaining microbial symbionts; (2) the identification of novel antimicrobial effector genes and processes; and (3) the molecular pathways that are being altered in basal marine invertebrates in the face of the effects of a changing environment.
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Affiliation(s)
- Leah M. Williams
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Thomas D. Gilmore
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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6
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Ozment E, Tamvacakis AN, Zhou J, Rosiles-Loeza PY, Escobar-Hernandez EE, Fernandez-Valverde SL, Nakanishi N. Cnidarian hair cell development illuminates an ancient role for the class IV POU transcription factor in defining mechanoreceptor identity. eLife 2021; 10:74336. [PMID: 34939935 PMCID: PMC8846589 DOI: 10.7554/elife.74336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/22/2021] [Indexed: 12/04/2022] Open
Abstract
Although specialized mechanosensory cells are found across animal phylogeny, early evolutionary histories of mechanoreceptor development remain enigmatic. Cnidaria (e.g. sea anemones and jellyfishes) is the sister group to well-studied Bilateria (e.g. flies and vertebrates), and has two mechanosensory cell types – a lineage-specific sensory effector known as the cnidocyte, and a classical mechanosensory neuron referred to as the hair cell. While developmental genetics of cnidocytes is increasingly understood, genes essential for cnidarian hair cell development are unknown. Here, we show that the class IV POU homeodomain transcription factor (POU-IV) – an indispensable regulator of mechanosensory cell differentiation in Bilateria and cnidocyte differentiation in Cnidaria – controls hair cell development in the sea anemone cnidarian Nematostella vectensis. N. vectensis POU-IV is postmitotically expressed in tentacular hair cells, and is necessary for development of the apical mechanosensory apparatus, but not of neurites, in hair cells. Moreover, it binds to deeply conserved DNA recognition elements, and turns on a unique set of effector genes – including the transmembrane receptor-encoding gene polycystin 1 – specifically in hair cells. Our results suggest that POU-IV directs differentiation of cnidarian hair cells and cnidocytes via distinct gene regulatory mechanisms, and support an evolutionarily ancient role for POU-IV in defining the mature state of mechanosensory neurons.
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Affiliation(s)
- Ethan Ozment
- Department of Biological Sciences, University of Arkansas, Fayetteville, United States
| | - Arianna N Tamvacakis
- Department of Biological Sciences, University of Arkansas, Fayetteville, United States
| | - Jianhong Zhou
- Department of Biological Sciences, University of Arkansas, Fayetteville, United States
| | - Pablo Yamild Rosiles-Loeza
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | | | - Selene L Fernandez-Valverde
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Nagayasu Nakanishi
- Department of Biological Sciences, University of Arkansas, Fayetteville, United States
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7
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Klein S, Frazier V, Readdean T, Lucas E, Diaz-Jimenez EP, Sogin M, Ruff ES, Echeverri K. Common Environmental Pollutants Negatively Affect Development and Regeneration in the Sea Anemone Nematostella vectensis Holobiont. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.786037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The anthozoan sea anemone Nematostella vectensis belongs to the phylum of cnidarians which also includes jellyfish and corals. Nematostella are native to United States East Coast marsh lands, where they constantly adapt to changes in salinity, temperature, oxygen concentration and pH. Its natural ability to continually acclimate to changing environments coupled with its genetic tractability render Nematostella a powerful model organism in which to study the effects of common pollutants on the natural development of these animals. Potassium nitrate, commonly used in fertilizers, and Phthalates, a component of plastics are frequent environmental stressors found in coastal and marsh waters. Here we present data showing how early exposure to these pollutants lead to dramatic defects in development of the embryos and eventual mortality possibly due to defects in feeding ability. Additionally, we examined the microbiome of the animals and identified shifts in the microbial community that correlated with the type of water that was used to grow the animals, and with their exposure to pollutants.
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8
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The cyclic dinucleotide 2'3'-cGAMP induces a broad antibacterial and antiviral response in the sea anemone Nematostella vectensis. Proc Natl Acad Sci U S A 2021; 118:2109022118. [PMID: 34903650 PMCID: PMC8713801 DOI: 10.1073/pnas.2109022118] [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: 11/05/2021] [Indexed: 11/18/2022] Open
Abstract
In mammals, cyclic dinucleotides (CDNs) bind and activate STING to initiate an antiviral type I interferon response. CDNs and STING originated in bacteria and are present in most animals. By contrast, interferons are believed to have emerged in vertebrates; thus, the function of CDN signaling in invertebrates is unclear. Here, we use a CDN, 2'3' cyclic guanosine monophosphate-adenosine monophosphate (2'3'-cGAMP), to activate immune responses in a model cnidarian invertebrate, the starlet sea anemone Nematostella vectensis Using RNA sequencing, we found that 2'3'-cGAMP induces robust transcription of both antiviral and antibacterial genes in N. vectensis Many of the antiviral genes induced by 2'3'-cGAMP are homologs of vertebrate interferon-stimulated genes, implying that the interferon response predates the evolution of interferons. Knockdown experiments identified a role for NF-κB in specifically inducing antibacterial genes downstream of 2'3'-cGAMP. Some of these putative antibacterial genes were also found to be induced during Pseudomonas aeruginosa infection. We characterized the protein product of one of the putative antibacterial genes, the N. vectensis homolog of Dae4, and found that it has conserved antibacterial activity. This work suggests that a broad antibacterial and antiviral transcriptional response is an evolutionarily ancestral output of 2'3'-cGAMP signaling in animals.
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9
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Comparison of NF-κB from the protists Capsaspora owczarzaki and Acanthoeca spectabilis reveals extensive evolutionary diversification of this transcription factor. Commun Biol 2021; 4:1404. [PMID: 34916615 PMCID: PMC8677719 DOI: 10.1038/s42003-021-02924-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 11/24/2021] [Indexed: 12/14/2022] Open
Abstract
We provide a functional characterization of transcription factor NF-κB in protists and provide information about the evolution and diversification of this biologically important protein. We characterized NF-κB in two protists using phylogenetic, cellular, and biochemical techniques. NF-κB of the holozoan Capsaspora owczarzaki (Co) has an N-terminal DNA-binding domain and a C-terminal Ankyrin repeat (ANK) domain, and its DNA-binding specificity is more similar to metazoan NF-κB proteins than to Rel proteins. Removal of the ANK domain allows Co-NF-κB to enter the nucleus, bind DNA, and activate transcription. However, C-terminal processing of Co-NF-κB is not induced by IκB kinases in human cells. Overexpressed Co-NF-κB localizes to the cytoplasm in Co cells. Co-NF-κB mRNA and DNA-binding levels differ across three Capsaspora life stages. RNA-sequencing and GO analyses identify possible gene targets of Co-NF-κB. Three NF-κB-like proteins from the choanoflagellate Acanthoeca spectabilis (As) contain conserved Rel Homology domain sequences, but lack C-terminal ANK repeats. All three As-NF-κB proteins constitutively enter the nucleus of cells, but differ in their DNA-binding abilities, transcriptional activation activities, and dimerization properties. These results provide a basis for understanding the evolutionary origins of this key transcription factor and could have implications for the origins of regulated immunity in higher taxa. Transcription factor NF-ĸB is a key regulator of immunity in mammals, but its function in protists like Capsaspora and choanoflagellates is not known. Here, Leah Williams et al. characterize and compare the structure, activity, and regulation of NF-ĸB from Capsaspora and one choanoflagellate, providing further insight into the origins of NF-ĸB.
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10
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The Tentacular Spectacular: Evolution of Regeneration in Sea Anemones. Genes (Basel) 2021; 12:genes12071072. [PMID: 34356088 PMCID: PMC8306839 DOI: 10.3390/genes12071072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/03/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
Sea anemones vary immensely in life history strategies, environmental niches and their ability to regenerate. While the sea anemone Nematostella vectensis is the starlet of many key regeneration studies, recent work is emerging on the diverse regeneration strategies employed by other sea anemones. This manuscript will explore current molecular mechanisms of regeneration employed by non-model sea anemones Exaiptasia diaphana (an emerging model species for coral symbiosis studies) and Calliactis polypus (a less well-studied species) and examine how these species compare to the model sea anemone N. vectensis. We summarize the field of regeneration within sea anemones, within the greater context of phylum Cnidaria and in other invertebrate models of regeneration. We also address the current knowledge on two key systems that may be implemented in regeneration: the innate immune system and developmental pathways, including future aspects of work and current limitations.
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11
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Aguirre Carrión PJ, Williams LM, Gilmore TD. Molecular and Biochemical Approaches to Study the Evolution of NF-κB Signaling in Basal Metazoans. Methods Mol Biol 2021; 2366:67-91. [PMID: 34236633 DOI: 10.1007/978-1-0716-1669-7_5] [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] [Indexed: 12/05/2022]
Abstract
Extensive genomic and transcriptomic sequencing over the past decade has revealed NF-κB signaling pathway homologs in organisms basal to insects, for example, in members of the phyla Cnidaria (e.g., sea anemones, corals, hydra, jellyfish) and Porifera (sponges), and in several single-celled protists (e.g., Capsaspora owczarzaki, some choanoflagellates). Therefore, methods are required to study the function of NF-κB and its pathway members in early branching organisms, many of which do not have histories as model organisms. Here, we describe a combination of cellular, molecular, and biochemical techniques that have been used for studying NF-κB, and related pathway proteins, in some of these basal organisms. These methods are useful for studying the evolution of NF-κB signaling, and may be adaptable to the study of NF-κB in other non-model organisms.
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12
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Abstract
The diversified NF-κB transcription factor family has been extensively characterized in organisms ranging from flies to humans. However, homologs of NF-κB and many upstream signaling components have recently been characterized in basal phyla, including Cnidaria (sea anemones, corals, hydras, and jellyfish), Porifera (sponges), and single-celled protists, including Capsaspora owczarzaki and some choanoflagellates. Herein, we review what is known about basal NF-κBs and how that knowledge informs on the evolution and conservation of key sequences and domains in NF-κB, as well as the regulation of NF-κB activity. The structures and DNA-binding activities of basal NF-κB proteins resemble those of mammalian NF-κB p100 proteins, and their posttranslational activation appears to have aspects of both canonical and noncanonical pathways in mammals. Several studies suggest that the single NF-κB proteins found in some basal organisms have dual roles in development and immunity. Further research on NF-κB in invertebrates will reveal information about the evolutionary roots of this major signaling pathway, will shed light on the origins of regulated innate immunity, and may have relevance to our understanding of the responses of ecologically important organisms to changing environmental conditions and emerging pathogen-based diseases.
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Affiliation(s)
- Leah M Williams
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Thomas D Gilmore
- Department of Biology, Boston University, Boston, Massachusetts, USA
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13
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Williams LM, Inge MM, Mansfield KM, Rasmussen A, Afghani J, Agrba M, Albert C, Andersson C, Babaei M, Babaei M, Bagdasaryants A, Bonilla A, Browne A, Carpenter S, Chen T, Christie B, Cyr A, Dam K, Dulock N, Erdene G, Esau L, Esonwune S, Hanchate A, Huang X, Jennings T, Kasabwala A, Kehoe L, Kobayashi R, Lee M, LeVan A, Liu Y, Murphy E, Nambiar A, Olive M, Patel D, Pavesi F, Petty CA, Samofalova Y, Sanchez S, Stejskal C, Tang Y, Yapo A, Cleary JP, Yunes SA, Siggers T, Gilmore TD. Transcription factor NF-κB in a basal metazoan, the sponge, has conserved and unique sequences, activities, and regulation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 104:103559. [PMID: 31751628 DOI: 10.1016/j.dci.2019.103559] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/15/2019] [Accepted: 11/17/2019] [Indexed: 06/10/2023]
Abstract
Herein, we characterize transcription factor NF-κB from the demosponge Amphimedon queenslandica (Aq). Aq-NF-κB is most similar to NF-κB p100/p105 among vertebrate proteins, with an N-terminal DNA-binding domain, a C-terminal Ankyrin (ANK) repeat domain, and a DNA binding-site profile akin to human NF-κB proteins. Like mammalian NF-κB p100, C-terminal truncation allows nuclear translocation of Aq-NF-κB and increases its transcriptional activation activity. Expression of IκB kinases (IKKs) induces proteasome-dependent C-terminal processing of Aq-NF-κB in human cells, and processing requires C-terminal serines in Aq-NF-κB. Unlike NF-κB p100, C-terminal sequences of Aq-NF-κB do not inhibit its DNA-binding activity. Tissue of a black encrusting demosponge contains NF-κB site DNA-binding activity, as well as nuclear and processed NF-κB. Treatment of sponge tissue with LPS increases both DNA-binding activity and processing of NF-κB. A. queenslandica transcriptomes contain homologs to upstream NF-κB pathway components. This is first functional characterization of NF-κB in sponge, the most basal multicellular animal.
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Affiliation(s)
- Leah M Williams
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Melissa M Inge
- Department of Biology, Boston University, Boston, MA, 02215, USA; Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | | | - Anna Rasmussen
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Jamie Afghani
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Mikhail Agrba
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Colleen Albert
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Cecilia Andersson
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Milad Babaei
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Mohammad Babaei
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Abigail Bagdasaryants
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Arianna Bonilla
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Amanda Browne
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Sheldon Carpenter
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Tiffany Chen
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Blake Christie
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Andrew Cyr
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Katie Dam
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Nicholas Dulock
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Galbadrakh Erdene
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Lindsie Esau
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Stephanie Esonwune
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Anvita Hanchate
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Xinli Huang
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Timothy Jennings
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Aarti Kasabwala
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Leanne Kehoe
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Ryan Kobayashi
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Migi Lee
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Andre LeVan
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Yuekun Liu
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Emily Murphy
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Avanti Nambiar
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Meagan Olive
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Devansh Patel
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Flaminio Pavesi
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Christopher A Petty
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Yelena Samofalova
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Selma Sanchez
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Camilla Stejskal
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Yinian Tang
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Alia Yapo
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - John P Cleary
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Sarah A Yunes
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Trevor Siggers
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Thomas D Gilmore
- Department of Biology, Boston University, Boston, MA, 02215, USA.
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14
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Brennan JJ, Gilmore TD. Evolutionary Origins of Toll-like Receptor Signaling. Mol Biol Evol 2019; 35:1576-1587. [PMID: 29590394 DOI: 10.1093/molbev/msy050] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Toll-like receptors (TLRs) are transmembrane pattern recognition receptors that are best known for their roles in innate immunity for the detection of and defense against microbial pathogens. However, TLRs also have roles in many nonimmune processes, most notably development. TLRs direct both immune and developmental programs by activation of downstream signaling pathways, often by activation of the NF-κB pathway. There are two primary TLR subtypes: 1) TLRs with multiple cysteine clusters in their ectodomain (mccTLRs) and 2) TLRs with a single cysteine cluster in their ectodomain (sccTLRs). For some time, it has been known that TLRs and the biological processes that they control are conserved in organisms from insects to mammals. However, genome and transcriptome sequencing has revealed that many basal metazoans also have TLRs and downstream NF-κB signaling components. In this review, we discuss what is known about the structure, biological function, and downstream signaling pathways of TLRs found in phyla from Porifera through Annelida. From these analyses, we hypothesize that mccTLRs emerged in the phylum Cnidaria, that sccTLRs evolved in the phylum Mollusca, and that TLRs have dual immune and developmental biological functions in organisms as ancient as cnidarians.
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15
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Nie L, Cai SY, Shao JZ, Chen J. Toll-Like Receptors, Associated Biological Roles, and Signaling Networks in Non-Mammals. Front Immunol 2018; 9:1523. [PMID: 30034391 PMCID: PMC6043800 DOI: 10.3389/fimmu.2018.01523] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/19/2018] [Indexed: 01/18/2023] Open
Abstract
The innate immune system is the first line of defense against pathogens, which is initiated by the recognition of pathogen-associated molecular patterns (PAMPs) and endogenous damage-associated molecular patterns (DAMPs) by pattern recognition receptors (PRRs). Among all the PRRs identified, the toll-like receptors (TLRs) are the most ancient class, with the most extensive spectrum of pathogen recognition. Since the first discovery of Toll in Drosophila melanogaster, numerous TLRs have been identified across a wide range of invertebrate and vertebrate species. It seems that TLRs, the signaling pathways that they initiate, or related adaptor proteins are essentially conserved in a wide variety of organisms, from Porifera to mammals. Molecular structure analysis indicates that most TLR homologs share similar domain patterns and that some vital participants of TLR signaling co-evolved with TLRs themselves. However, functional specification and emergence of new signaling pathways, as well as adaptors, did occur during evolution. In addition, ambiguities and gaps in knowledge still exist regarding the TLR network, especially in lower organisms. Hence, a systematic review from the comparative angle regarding this tremendous signaling system and the scenario of evolutionary pattern across Animalia is needed. In the current review, we present overview and possible evolutionary patterns of TLRs in non-mammals, hoping that this will provide clues for further investigations in this field.
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Affiliation(s)
- Li Nie
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Shi-Yu Cai
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Jian-Zhong Shao
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jiong Chen
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
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16
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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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17
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Mansfield KM, Carter NM, Nguyen L, Cleves PA, Alshanbayeva A, Williams LM, Crowder C, Penvose AR, Finnerty JR, Weis VM, Siggers TW, Gilmore TD. Transcription factor NF-κB is modulated by symbiotic status in a sea anemone model of cnidarian bleaching. Sci Rep 2017; 7:16025. [PMID: 29167511 PMCID: PMC5700166 DOI: 10.1038/s41598-017-16168-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/08/2017] [Indexed: 02/06/2023] Open
Abstract
Transcription factor NF-κB plays a central role in immunity from fruit flies to humans, and NF-κB activity is altered in many human diseases. To investigate a role for NF-κB in immunity and disease on a broader evolutionary scale we have characterized NF-κB in a sea anemone (Exaiptasia pallida; called Aiptasia herein) model for cnidarian symbiosis and dysbiosis (i.e., “bleaching”). We show that the DNA-binding site specificity of Aiptasia NF-κB is similar to NF-κB proteins from a broad expanse of organisms. Analyses of NF-κB and IκB kinase proteins from Aiptasia suggest that non-canonical NF-κB processing is an evolutionarily ancient pathway, which can be reconstituted in human cells. In Aiptasia, NF-κB protein levels, DNA-binding activity, and tissue expression increase when loss of the algal symbiont Symbiodinium is induced by heat or chemical treatment. Kinetic analysis of NF-κB levels following loss of symbiosis show that NF-κB levels increase only after Symbiodinium is cleared. Moreover, introduction of Symbiodinium into naïve Aiptasia larvae results in a decrease in NF-κB expression. Our results suggest that Symbiodinium suppresses NF-κB in order to enable establishment of symbiosis in Aiptasia. These results are the first to demonstrate a link between changes in the conserved immune regulatory protein NF-κB and cnidarian symbiotic status.
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Affiliation(s)
| | - Nicole M Carter
- Department of Biology, Boston University, Boston, Massachusetts, 02215, USA
| | - Linda Nguyen
- Department of Biology, Boston University, Boston, Massachusetts, 02215, USA
| | - Phillip A Cleves
- Department of Genetics, Stanford University, School of Medicine, Stanford, California, 94305, USA
| | - Anar Alshanbayeva
- Department of Biology, Boston University, Boston, Massachusetts, 02215, USA
| | - Leah M Williams
- Department of Biology, Boston University, Boston, Massachusetts, 02215, USA
| | - Camerron Crowder
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Ashley R Penvose
- Department of Biology, Boston University, Boston, Massachusetts, 02215, USA
| | - John R Finnerty
- Department of Biology, Boston University, Boston, Massachusetts, 02215, USA
| | - Virginia M Weis
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Trevor W Siggers
- Department of Biology, Boston University, Boston, Massachusetts, 02215, USA
| | - Thomas D Gilmore
- Department of Biology, Boston University, Boston, Massachusetts, 02215, USA.
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18
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Brennan JJ, Messerschmidt JL, Williams LM, Matthews BJ, Reynoso M, Gilmore TD. Sea anemone model has a single Toll-like receptor that can function in pathogen detection, NF-κB signal transduction, and development. Proc Natl Acad Sci U S A 2017; 114:E10122-E10131. [PMID: 29109290 PMCID: PMC5703304 DOI: 10.1073/pnas.1711530114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In organisms from insects to vertebrates, Toll-like receptors (TLRs) are primary pathogen detectors that activate downstream pathways, specifically those that direct expression of innate immune effector genes. TLRs also have roles in development in many species. The sea anemone Nematostella vectensis is a useful cnidarian model to study the origins of TLR signaling because its genome encodes a single TLR and homologs of many downstream signaling components, including the NF-κB pathway. We have characterized the single N. vectensis TLR (Nv-TLR) and demonstrated that it can activate canonical NF-κB signaling in human cells. Furthermore, we show that the intracellular Toll/IL-1 receptor (TIR) domain of Nv-TLR can interact with the human TLR adapter proteins MAL and MYD88. We demonstrate that the coral pathogen Vibrio coralliilyticus causes a rapidly lethal disease in N. vectensis and that heat-inactivated V. coralliilyticus and bacterial flagellin can activate a reconstituted Nv-TLR-to-NF-κB pathway in human cells. By immunostaining of anemones, we show that Nv-TLR is expressed in a subset of cnidocytes and that many of these Nv-TLR-expressing cells also express Nv-NF-κB. Additionally, the nematosome, which is a Nematostella-specific multicellular structure, expresses Nv-TLR and many innate immune pathway homologs and can engulf V. coralliilyticus Morpholino knockdown indicates that Nv-TLR also has an essential role during early embryonic development. Our characterization of this primitive TLR and identification of a bacterial pathogen for N. vectensis reveal ancient TLR functions and provide a model for studying the molecular basis of cnidarian disease and immunity.
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19
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Traylor-Knowles N, Rose NH, Palumbi SR. The cell specificity of gene expression in the response to heat stress in corals. ACTA ACUST UNITED AC 2017; 220:1837-1845. [PMID: 28254881 DOI: 10.1242/jeb.155275] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/23/2017] [Indexed: 12/21/2022]
Abstract
Previous transcriptional studies in heat-stressed corals have shown that many genes are responsive to generalized heat stress whereas the expression patterns of specific gene networks after heat stress show strong correlations with variation in bleaching outcomes. However, where these specific genes are expressed is unknown. In this study, we employed in situ hybridization to identify patterns of spatial gene expression of genes previously predicted to be involved in general stress response and bleaching. We found that tumor necrosis factor receptors (TNFRs), known to be strong responders to heat stress, were not expressed in gastrodermal symbiont-containing cells but were widely expressed in specific cells of the epidermal layer. The transcription factors AP-1 and FosB, implicated as early signals of heat stress, were widely expressed throughout the oral gastrodermis and epidermis. By contrast, a G protein-coupled receptor gene (GPCR) and a fructose bisphosphate aldolase C gene (aldolase), previously implicated in bleaching, were expressed in symbiont-containing gastrodermal cells and in the epidermal tissue. Finally, chordin-like/kielin (chordin-like), a gene highly correlated to bleaching, was expressed solely in the oral gastrodermis. From this study, we confirm that heat-responsive genes occur widely in coral tissues outside of symbiont-containing cells. Joint information about expression patterns in response to heat and cell specificity will allow greater dissection of the regulatory pathways and specific cell reactions that lead to coral bleaching.
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Affiliation(s)
- Nikki Traylor-Knowles
- Hopkins Marine Station, Stanford University, 120 Oceanview Blvd, Pacific Grove, CA 93950, USA
| | - Noah H Rose
- Hopkins Marine Station, Stanford University, 120 Oceanview Blvd, Pacific Grove, CA 93950, USA
| | - Stephen R Palumbi
- Hopkins Marine Station, Stanford University, 120 Oceanview Blvd, Pacific Grove, CA 93950, USA
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20
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Rentzsch F, Layden M, Manuel M. The cellular and molecular basis of cnidarian neurogenesis. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2016; 6. [PMID: 27882698 PMCID: PMC6680159 DOI: 10.1002/wdev.257] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 08/30/2016] [Accepted: 09/21/2016] [Indexed: 12/22/2022]
Abstract
Neurogenesis initiates during early development and it continues through later developmental stages and in adult animals to enable expansion, remodeling, and homeostasis of the nervous system. The generation of nerve cells has been analyzed in detail in few bilaterian model organisms, leaving open many questions about the evolution of this process. As the sister group to bilaterians, cnidarians occupy an informative phylogenetic position to address the early evolution of cellular and molecular aspects of neurogenesis and to understand common principles of neural development. Here we review studies in several cnidarian model systems that have revealed significant similarities and interesting differences compared to neurogenesis in bilaterian species, and between different cnidarian taxa. Cnidarian neurogenesis is currently best understood in the sea anemone Nematostella vectensis, where it includes epithelial neural progenitor cells that express transcription factors of the soxB and atonal families. Notch signaling regulates the number of these neural progenitor cells, achaete‐scute and dmrt genes are required for their further development and Wnt and BMP signaling appear to be involved in the patterning of the nervous system. In contrast to many vertebrates and Drosophila, cnidarians have a high capacity to generate neurons throughout their lifetime and during regeneration. Utilizing this feature of cnidarian biology will likely allow gaining new insights into the similarities and differences of embryonic and regenerative neurogenesis. The use of different cnidarian model systems and their expanding experimental toolkits will thus continue to provide a better understanding of evolutionary and developmental aspects of nervous system formation. WIREs Dev Biol 2017, 6:e257. doi: 10.1002/wdev.257 This article is categorized under:
Gene Expression and Transcriptional Hierarchies > Cellular Differentiation Signaling Pathways > Cell Fate Signaling Comparative Development and Evolution > Organ System Comparisons Between Species
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Affiliation(s)
- Fabian Rentzsch
- Sars Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | | | - Michaël Manuel
- Sorbonne Universités, UMPC Univ Paris 06, CNRS, Evolution Paris-Seine, Institut de Biologie Paris-Seine (IBPS), Paris, France
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21
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Tarrant AM, Gilmore TD, Reitzel AM, Levy O, Technau U, Martindale MQ. Current directions and future perspectives from the third Nematostella research conference. ZOOLOGY 2014; 118:135-40. [PMID: 25450665 DOI: 10.1016/j.zool.2014.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 06/16/2014] [Accepted: 06/17/2014] [Indexed: 12/16/2022]
Abstract
The third Nematostella vectensis Research Conference took place in December 2013 in Eilat, Israel, as a satellite to the 8th International Conference on Coelenterate Biology. The starlet sea anemone, N. vectensis, has emerged as a powerful cnidarian model, in large part due to the extensive genomic and transcriptomic resources and molecular approaches that are becoming available for Nematostella, which were the focus of several presentations. In addition, research was presented highlighting the broader utility of this species for studies of development, circadian rhythms, signal transduction, and gene-environment interactions.
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Affiliation(s)
- Ann M Tarrant
- Biology Department, Woods Hole Oceanographic Institution, 45 Water Street, Woods Hole, MA 02543, USA.
| | - Thomas D Gilmore
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | - Adam M Reitzel
- Department of Biological Sciences, The University of North Carolina at Charlotte, Woodward Hall 245, Charlotte, NC 28223, USA
| | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel
| | - Ulrich Technau
- Department of Molecular Evolution and Development, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St. Augustine, FL 32136, USA
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22
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Elran R, Raam M, Kraus R, Brekhman V, Sher N, Plaschkes I, Chalifa-Caspi V, Lotan T. Early and late response of Nematostella vectensis transcriptome to heavy metals. Mol Ecol 2014; 23:4722-36. [PMID: 25145541 DOI: 10.1111/mec.12891] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/22/2014] [Accepted: 08/13/2014] [Indexed: 12/28/2022]
Abstract
Environmental contamination from heavy metals poses a global concern for the marine environment, as heavy metals are passed up the food chain and persist in the environment long after the pollution source is contained. Cnidarians play an important role in shaping marine ecosystems, but environmental pollution profoundly affects their vitality. Among the cnidarians, the sea anemone Nematostella vectensis is an advantageous model for addressing questions in molecular ecology and toxicology as it tolerates extreme environments and its genome has been published. Here, we employed a transcriptome-wide RNA-Seq approach to analyse N. vectensis molecular defence mechanisms against four heavy metals: Hg, Cu, Cd and Zn. Altogether, more than 4800 transcripts showed significant changes in gene expression. Hg had the greatest impact on up-regulating transcripts, followed by Cu, Zn and Cd. We identified, for the first time in Cnidaria, co-up-regulation of immediate-early transcription factors such as Egr1, AP1 and NF-κB. Time-course analysis of these genes revealed their early expression as rapidly as one hour after exposure to heavy metals, suggesting that they may complement or substitute for the roles of the metal-mediating Mtf1 transcription factor. We further characterized the regulation of a large array of stress-response gene families, including Hsp, ABC, CYP members and phytochelatin synthase, that may regulate synthesis of the metal-binding phytochelatins instead of the metallothioneins that are absent from Cnidaria genome. This study provides mechanistic insight into heavy metal toxicity in N. vectensis and sheds light on ancestral stress adaptations.
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Affiliation(s)
- Ron Elran
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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23
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Babonis LS, Martindale MQ. Old cell, new trick? Cnidocytes as a model for the evolution of novelty. Integr Comp Biol 2014; 54:714-22. [PMID: 24771087 DOI: 10.1093/icb/icu027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding how new cell types arise is critical for understanding the evolution of organismal complexity. Questions of this nature, however, can be difficult to answer due to the challenge associated with defining the identity of a truly novel cell. Cnidarians (anemones, jellies, and their allies) provide a unique opportunity to investigate the molecular regulation and development of cell-novelty because they possess a cell that is unique to the cnidarian lineage and that also has a very well-characterized phenotype: the cnidocyte (stinging cell). Because cnidocytes are thought to differentiate from the cell lineage that also gives rise to neurons, cnidocytes can be expected to express many of the same genes expressed in their neural "sister" cells. Conversely, only cnidocytes posses a cnidocyst (the explosive organelle that gives cnidocytes their sting); therefore, those genes or gene-regulatory relationships required for the development of the cnidocyst can be expected to be expressed uniquely (or in unique combination) in cnidocytes. This system provides an important opportunity to: (1) construct the gene-regulatory network (GRN) underlying the differentiation of cnidocytes, (2) assess the relative contributions of both conserved and derived genes in the cnidocyte GRN, and (3) test hypotheses about the role of novel regulatory relationships in the generation of novel cell types. In this review, we summarize common challenges to studying the evolution of novelty, introduce the utility of cnidocyte differentiation in the model cnidarian, Nematostella vectensis, as a means of overcoming these challenges, and describe an experimental approach that leverages comparative tissue-specific transcriptomics to generate hypotheses about the GRNs underlying the acquisition of the cnidocyte identity.
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Affiliation(s)
- Leslie S Babonis
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 N Oceanshore Blvd, St. Augustine, FL 32080, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 N Oceanshore Blvd, St. Augustine, FL 32080, USA
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24
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Cell damage induced by copper: An explant model to study anemone cells. Toxicol In Vitro 2014; 28:365-72. [DOI: 10.1016/j.tiv.2013.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 10/08/2013] [Accepted: 11/29/2013] [Indexed: 11/23/2022]
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25
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Stefanik DJ, Lubinski TJ, Granger BR, Byrd AL, Reitzel AM, DeFilippo L, Lorenc A, Finnerty JR. Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian. BMC Genomics 2014; 15:71. [PMID: 24467778 PMCID: PMC3909931 DOI: 10.1186/1471-2164-15-71] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/11/2013] [Indexed: 12/20/2022] Open
Abstract
Background The lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading from a larva to either a free-living polyp or a vermiform parasite that inhabits the mesoglea of a ctenophore host. Additionally, E. lineata is confamilial with the model cnidarian Nematostella vectensis, providing an opportunity for comparative genomic, molecular and organismal studies. Description We generated a reference transcriptome for E. lineata via high-throughput sequencing of RNA isolated from five developmental stages (parasite; parasite-to-larva transition; larva; larva-to-adult transition; adult). The transcriptome comprises 90,440 contigs assembled from >15 billion nucleotides of DNA sequence. Using a molecular clock approach, we estimated the divergence between E. lineata and N. vectensis at 215–364 million years ago. Based on gene ontology and metabolic pathway analyses and gene family surveys (bHLH-PAS, deiodinases, Fox genes, LIM homeodomains, minicollagens, nuclear receptors, Sox genes, and Wnts), the transcriptome of E. lineata is comparable in depth and completeness to N. vectensis. Analyses of protein motifs and revealed extensive conservation between the proteins of these two edwardsiid anemones, although we show the NF-κB protein of E. lineata reflects the ancestral structure, while the NF-κB protein of N. vectensis has undergone a split that separates the DNA-binding domain from the inhibitory domain. All contigs have been deposited in a public database (EdwardsiellaBase), where they may be searched according to contig ID, gene ontology, protein family motif (Pfam), enzyme commission number, and BLAST. The alignment of the raw reads to the contigs can also be visualized via JBrowse. Conclusions The transcriptomic data and database described here provide a platform for studying the evolutionary developmental genomics of a derived parasitic life cycle. In addition, these data from E. lineata will aid in the interpretation of evolutionary novelties in gene sequence or structure that have been reported for the model cnidarian N. vectensis (e.g., the split NF-κB locus). Finally, we include custom computational tools to facilitate the annotation of a transcriptome based on high-throughput sequencing data obtained from a “non-model system.”
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Affiliation(s)
| | | | | | | | | | | | | | - John R Finnerty
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA.
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26
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Layden MJ, Röttinger E, Wolenski FS, Gilmore TD, Martindale MQ. Microinjection of mRNA or morpholinos for reverse genetic analysis in the starlet sea anemone, Nematostella vectensis. Nat Protoc 2013; 8:924-34. [PMID: 23579781 DOI: 10.1038/nprot.2013.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe a protocol for microinjection of embryos for an emerging model system, the cnidarian sea anemone, Nematostella vectensis. In addition, we provide protocols for carrying out overexpression and knockdown of gene function through microinjection of in vitro-translated mRNAs or gene-specific oligonucleotide morpholinos (MOs), respectively. Our approach is simple, and it takes advantage of the natural adherence properties of the early embryo to position them in a single layer on a polystyrene dish. Embryos are visualized on a dissecting microscope equipped with epifluorescence and injected with microinjection needles using a picospritzer forced-air injection system. A micromanipulator is used to guide the needle to impale individual embryos. Injection takes ∼1.5 h, and an experienced researcher can inject ∼2,000 embryos in a single session. With the availability of the published Nematostella genome, the entire protocol, including cloning and transcription of mRNAs, can be carried out in ∼1 week.
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Affiliation(s)
- Michael J Layden
- The Whitney Marine Laboratory for Marine Science, University of Florida, St. Augustine, Florida, USA
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Wolenski FS, Layden MJ, Martindale MQ, Gilmore TD, Finnerty JR. Characterizing the spatiotemporal expression of RNAs and proteins in the starlet sea anemone, Nematostella vectensis. Nat Protoc 2013; 8:900-15. [PMID: 23579779 DOI: 10.1038/nprot.2013.014] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In an effort to reconstruct the early evolution of animal genes and proteins, there is an increasing focus on basal animal lineages such as sponges, cnidarians, ctenophores and placozoans. Among the basal animals, the starlet sea anemone Nematostella vectensis (phylum Cnidaria) has emerged as a leading laboratory model organism partly because it is well suited to experimental techniques for monitoring and manipulating gene expression. Here we describe protocols adapted for use in Nematostella to characterize the expression of RNAs by in situ hybridization using either chromogenic or fluorescence immunohistochemistry (∼1 week), as well as to characterize protein expression by whole-mount immunofluorescence (∼3 d). We also provide a protocol for labeling cnidocytes (∼3 h), the phylum-specific sensory-effector cell type that performs a variety of functions in cnidarians, including the delivery of their venomous sting.
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A report from the second Nematostella vectensis research conference. Dev Genes Evol 2013; 223:207-11. [PMID: 23314922 DOI: 10.1007/s00427-012-0434-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 11/29/2012] [Indexed: 02/02/2023]
Abstract
This report summarizes information discussed at the second Nematostella vectensis research conference, which took place on August 27, 2012 in Boston, MA, USA. The startlet sea anemone Nematostella is emerging as one of leading model organisms among cnidarians, in part because of the extensive genome and transcriptome resources that are becoming available for Nematostella, which were the focus of several presentations. In addition, research was presented on the use of Nematostella in developmental, regeneration, signal transduction, host-symbiont, and gene-environment interaction studies.
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