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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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DiRusso CJ, DeMaria AM, Wong J, Wang W, Jordanides JJ, Whitty A, Allen KN, Gilmore TD. A conserved core region of the scaffold NEMO is essential for signal-induced conformational change and liquid-liquid phase separation. J Biol Chem 2023; 299:105396. [PMID: 37890781 PMCID: PMC10694592 DOI: 10.1016/j.jbc.2023.105396] [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: 05/23/2023] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Scaffold proteins help mediate interactions between protein partners, often to optimize intracellular signaling. Herein, we use comparative, biochemical, biophysical, molecular, and cellular approaches to investigate how the scaffold protein NEMO contributes to signaling in the NF-κB pathway. Comparison of NEMO and the related protein optineurin from a variety of evolutionarily distant organisms revealed that a central region of NEMO, called the Intervening Domain (IVD), is conserved between NEMO and optineurin. Previous studies have shown that this central core region of the IVD is required for cytokine-induced activation of IκB kinase (IKK). We show that the analogous region of optineurin can functionally replace the core region of the NEMO IVD. We also show that an intact IVD is required for the formation of disulfide-bonded dimers of NEMO. Moreover, inactivating mutations in this core region abrogate the ability of NEMO to form ubiquitin-induced liquid-liquid phase separation droplets in vitro and signal-induced puncta in vivo. Thermal and chemical denaturation studies of truncated NEMO variants indicate that the IVD, while not intrinsically destabilizing, can reduce the stability of surrounding regions of NEMO due to the conflicting structural demands imparted on this region by flanking upstream and downstream domains. This conformational strain in the IVD mediates allosteric communication between the N- and C-terminal regions of NEMO. Overall, these results support a model in which the IVD of NEMO participates in signal-induced activation of the IKK/NF-κB pathway by acting as a mediator of conformational changes in NEMO.
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Affiliation(s)
| | - Anthony M DeMaria
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Judy Wong
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Wei Wang
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Jack J Jordanides
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, Massachusetts, USA.
| | - Thomas D Gilmore
- Department of Biology, Boston University, Boston, Massachusetts, USA.
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3
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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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4
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DiRusso CJ, DeMaria AM, Wong J, Jordanides JJ, Whitty A, Allen KN, Gilmore TD. A Conserved Core Region of the Scaffold NEMO is Essential for Signal-induced Conformational Change and Liquid-liquid Phase Separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542299. [PMID: 37292615 PMCID: PMC10245932 DOI: 10.1101/2023.05.25.542299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Scaffold proteins help mediate interactions between protein partners, often to optimize intracellular signaling. Herein, we use comparative, biochemical, biophysical, molecular, and cellular approaches to investigate how the scaffold protein NEMO contributes to signaling in the NF-κB pathway. Comparison of NEMO and the related protein optineurin from a variety of evolutionarily distant organisms revealed that a central region of NEMO, called the Intervening Domain (IVD), is conserved between NEMO and optineurin. Previous studies have shown that this central core region of the IVD is required for cytokine-induced activation of IκB kinase (IKK). We show that the analogous region of optineurin can functionally replace the core region of the NEMO IVD. We also show that an intact IVD is required for the formation of disulfide-bonded dimers of NEMO. Moreover, inactivating mutations in this core region abrogate the ability of NEMO to form ubiquitin-induced liquid-liquid phase separation droplets in vitro and signal-induced puncta in vivo. Thermal and chemical denaturation studies of truncated NEMO variants indicate that the IVD, while not intrinsically destabilizing, can reduce the stability of surrounding regions of NEMO, due to the conflicting structural demands imparted on this region by flanking upstream and downstream domains. This conformational strain in the IVD mediates allosteric communication between N- and C-terminal regions of NEMO. Overall, these results support a model in which the IVD of NEMO participates in signal-induced activation of the IKK/NF-κB pathway by acting as a mediator of conformational changes in NEMO.
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Affiliation(s)
| | | | - Judy Wong
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Karen N. Allen
- Department of Chemistry, Boston University, Boston, MA 02215, USA
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5
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Vila IK, Guha S, Kalucka J, Olagnier D, Laguette N. Alternative pathways driven by STING: From innate immunity to lipid metabolism. Cytokine Growth Factor Rev 2022; 68:54-68. [PMID: 36085258 DOI: 10.1016/j.cytogfr.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 08/29/2022] [Indexed: 01/30/2023]
Abstract
The Stimulator of Interferon Genes (STING) is a major adaptor protein that is central to the initiation of type I interferon responses and proinflammatory signalling. STING-dependent signalling is triggered by the presence of cytosolic nucleic acids that are generated following pathogen infection or cellular stress. Beyond this central role in controlling immune responses through the production of cytokines and chemokines, recent reports have uncovered inflammation-independent STING functions. Amongst these, a rapidly growing body of evidence demonstrates a key role of STING in controlling metabolic pathways at several levels. Since immunity and metabolic homeostasis are tightly interconnected, these findings deepen our understanding of the involvement of STING in human pathologies. Here, we discuss these findings and reflect on their impact on our current understanding of how nucleic acid immunity controls homeostasis and promotes pathological outcomes.
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Affiliation(s)
- Isabelle K Vila
- Institut de Génétique Humaine, Univ Montpellier, CNRS, Montpellier, France.
| | - Soumyabrata Guha
- Institut de Génétique Humaine, Univ Montpellier, CNRS, Montpellier, France
| | - Joanna Kalucka
- Aarhus University, Department of Biomedicine, Aarhus, Denmark
| | - David Olagnier
- Aarhus University, Department of Biomedicine, Aarhus, Denmark
| | - Nadine Laguette
- Institut de Génétique Humaine, Univ Montpellier, CNRS, Montpellier, France.
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6
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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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7
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Microbiota mediated plasticity promotes thermal adaptation in the sea anemone Nematostella vectensis. Nat Commun 2022; 13:3804. [PMID: 35778405 PMCID: PMC9249911 DOI: 10.1038/s41467-022-31350-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/31/2022] [Indexed: 12/13/2022] Open
Abstract
At the current rate of climate change, it is unlikely that multicellular organisms will be able to adapt to changing environmental conditions through genetic recombination and natural selection alone. Thus, it is critical to understand alternative mechanisms that allow organisms to cope with rapid environmental changes. Here, we use the sea anemone Nematostella vectensis, which has evolved the capability of surviving in a wide range of temperatures and salinities, as a model to investigate the microbiota as a source of rapid adaptation. We long-term acclimate polyps of Nematostella to low, medium, and high temperatures, to test the impact of microbiota-mediated plasticity on animal acclimation. Using the same animal clonal line, propagated from a single polyp, allows us to eliminate the effects of the host genotype. The higher thermal tolerance of animals acclimated to high temperature can be transferred to non-acclimated animals through microbiota transplantation. The offspring fitness is highest from F0 females acclimated to high temperature and specific members of the acclimated microbiota are transmitted to the next generation. These results indicate that microbiota plasticity can contribute to animal thermal acclimation and its transmission to the next generation may represent a rapid mechanism for thermal adaptation. This study shows that sea anemones acclimated to high temperatures exhibit increased resistance to thermal stress and that this improved fitness can be transferred by microbiome transplantation. These results indicate that plasticity mediated by the microbiota might be an important factor facilitating thermal adaptations in animals.
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8
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Zhu M, Su F, Leng J, Jian S, Yi P, Wen C, Hu B. Two NF-κB subunits are associated with antimicrobial immunity in Hyriopsis cumingii. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 129:104336. [PMID: 34921862 DOI: 10.1016/j.dci.2021.104336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 12/09/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
The NF-κB pathway activated by bacteria and viruses produces a series of antimicrobial peptides that participate in the innate immune response. In this study, two NF-κB subunits were cloned and identified from Hyriopsis cumingii (named Hcp65 and Hcp105) using RT-PCR and RACE. The predicted Hcp65 protein possessed a N-terminal Rel homology domain (RHD) and an Ig-like/plexins/transcription factors domain (IPT); the Hcp105 contained an RHD, an IPT domain, 6 ankyrin (ANK) domain and a death domain. Quantitative reverse transcription PCR (qRT-PCR) showed that Hcp65 and Hcp105 were constitutively expressed in the detected tissues, and were significantly up-regulated in hemocytes, hepatopancreas and gill of mussels challenged with lipopolysaccharide (LPS), peptidoglycan (PGN) and polyinosinic-polycytidylic acid (poly I: C). The dsRNA-mediated silencing of Hcp65 and Hcp105 caused significant reduction of immune genes such as lysozyme (HcLyso), theromacin (Hcther), whey acid protein (HcWAP), LPS-binding protein/bactericidal permeability protein (HcLBP/BPI) 1 and 2. In addition, subcellular localization experiments showed that Hcp65 and Hcp105 proteins were expressed in both the nucleus and cytoplasm of HEK-293T cells, and Hcp50 proteins (mature peptide of Hcp105) were mainly localized in the nucleus. The recombinant Hcp65 and Hcp50 protein could form homodimer and heterodimer and bind κB site in vitro. These results provide useful information for understanding the role of NF-κB in mollusks.
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Affiliation(s)
- Mingxing Zhu
- Department of Aquatic Science, College of Life Science, Nanchang University, Xuefu Avenue, Nanchang, Jiangxi Province, 330031, China
| | - Feixiang Su
- Department of Aquatic Science, College of Life Science, Nanchang University, Xuefu Avenue, Nanchang, Jiangxi Province, 330031, China
| | - Jianghe Leng
- Department of Aquatic Science, College of Life Science, Nanchang University, Xuefu Avenue, Nanchang, Jiangxi Province, 330031, China
| | - Shaoqing Jian
- Department of Aquatic Science, College of Life Science, Nanchang University, Xuefu Avenue, Nanchang, Jiangxi Province, 330031, China
| | - Peipei Yi
- Zhejiang Normal University, 688 Yingbin Road, Jinhua, Zhejiang Province, 321001, China
| | - Chungen Wen
- Department of Aquatic Science, College of Life Science, Nanchang University, Xuefu Avenue, Nanchang, Jiangxi Province, 330031, China
| | - Baoqing Hu
- Department of Aquatic Science, College of Life Science, Nanchang University, Xuefu Avenue, Nanchang, Jiangxi Province, 330031, China.
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9
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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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10
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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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11
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Emery MA, Dimos BA, Mydlarz LD. Cnidarian Pattern Recognition Receptor Repertoires Reflect Both Phylogeny and Life History Traits. Front Immunol 2021; 12:689463. [PMID: 34248980 PMCID: PMC8260672 DOI: 10.3389/fimmu.2021.689463] [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: 03/31/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
Pattern recognition receptors (PRRs) are evolutionarily ancient and crucial components of innate immunity, recognizing danger-associated molecular patterns (DAMPs) and activating host defenses. Basal non-bilaterian animals such as cnidarians must rely solely on innate immunity to defend themselves from pathogens. By investigating cnidarian PRR repertoires we can gain insight into the evolution of innate immunity in these basal animals. Here we utilize the increasing amount of available genomic resources within Cnidaria to survey the PRR repertoires and downstream immune pathway completeness within 15 cnidarian species spanning two major cnidarian clades, Anthozoa and Medusozoa. Overall, we find that anthozoans possess prototypical PRRs, while medusozoans appear to lack these immune proteins. Additionally, anthozoans consistently had higher numbers of PRRs across all four classes relative to medusozoans, a trend largely driven by expansions in NOD-like receptors and C-type lectins. Symbiotic, sessile, and colonial cnidarians also have expanded PRR repertoires relative to their non-symbiotic, mobile, and solitary counterparts. Interestingly, cnidarians seem to lack key components of mammalian innate immune pathways, though similar to PRR numbers, anthozoans possess more complete immune pathways than medusozoans. Together, our data indicate that anthozoans have greater immune specificity than medusozoans, which we hypothesize to be due to life history traits common within Anthozoa. Overall, this investigation reveals important insights into the evolution of innate immune proteins within these basal animals.
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Affiliation(s)
- Madison A Emery
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| | - Bradford A Dimos
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| | - Laura D Mydlarz
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
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12
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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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13
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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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14
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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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15
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Dimos BA, Butler CC, Ricci CA, MacKnight NJ, Mydlarz LD. Responding to Threats Both Foreign and Domestic: NOD-Like Receptors in Corals. Integr Comp Biol 2020; 59:819-829. [PMID: 31236558 DOI: 10.1093/icb/icz111] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Historically mechanisms with which basal animals such as reef-building corals use to respond to changing and increasingly stressful environments have remained elusive. However, the increasing availability of genomic and transcriptomic data from these organisms has provided fundamental insights into the biology of these critically important ecosystem engineers. Notably, insights into cnidarians gained in the post-genomics age have revealed a surprisingly complex immune system which bears a surprising level of similarity with the vertebrate innate immune system. This system has been critically linked to how corals respond to the two most prominent threats on a global scale, emerging coral diseases and increasing water temperature, which are recognized cellularly as either foreign or domestic threats, respectively. These threats can arise from pathogenic microbes or internal cellular dysfunction, underscoring the need to further understand mechanisms corals use to sense and respond to threats to their cellular integrity. In this investigation and meta-analysis, we utilize resources only recently available in the post-genomic era to identify and characterize members of an underexplored class of molecules known as NOD-like receptors in the endangered Caribbean coral Orbicella faveolata. We then leverage these data to identify pathways possibly mediated by NLRs in both O. faveolata and the ecologically important branching coral Acropora digitifera. Overall, we find support that this class of proteins may provide a mechanistic link to how reef-building corals respond to threats both foreign and domestic.
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Affiliation(s)
- Bradford A Dimos
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Caleb C Butler
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Contessa A Ricci
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Nicholas J MacKnight
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Laura D Mydlarz
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
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16
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Traylor-Knowles N, Vandepas LE, Browne WE. Still Enigmatic: Innate Immunity in the Ctenophore Mnemiopsis leidyi. Integr Comp Biol 2020; 59:811-818. [PMID: 31251332 DOI: 10.1093/icb/icz116] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Innate immunity is an ancient physiological response critical for protecting metazoans from invading pathogens. It is the primary pathogen defense mechanism among invertebrates. While innate immunity has been studied extensively in diverse invertebrate taxa, including mollusks, crustaceans, and cnidarians, this system has not been well characterized in ctenophores. The ctenophores comprise an exclusively marine, non-bilaterian lineage that diverged early during metazoan diversification. The phylogenetic position of ctenophore lineage suggests that characterization of the ctenophore innate immune system will reveal important features associated with the early evolution of the metazoan innate immune system. Here, we review current understanding of the ctenophore immune repertoire and identify innate immunity genes recovered from three ctenophore species. We also isolate and characterize Mnemiopsis leidyi cells that display macrophage-like behavior when challenged with bacteria. Our results indicate that ctenophores possess cells capable of phagocytosing microbes and that two distantly related ctenophores, M. leidyi and Hormiphora californiensis, possess many candidate innate immunity proteins.
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Affiliation(s)
- Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, FL 33149, USA
| | - Lauren E Vandepas
- Benaroya Research Institute, 1201 9th Avenue, Seattle, WA 98101, USA.,Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - William E Browne
- Department of Biology, University of Miami, Cox Science Building, 1301 Memorial Drive, Miami, FL 33146, USA
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17
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Leach WB, Carrier TJ, Reitzel AM. Diel patterning in the bacterial community associated with the sea anemone Nematostella vectensis. Ecol Evol 2019; 9:9935-9947. [PMID: 31534705 PMCID: PMC6745676 DOI: 10.1002/ece3.5534] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/11/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
Microbes can play an important role in the physiology of animals by providing essential nutrients, inducing immune pathways, and influencing the specific species that compose the microbiome through competitive or facilitatory interactions. The community of microbes associated with animals can be dynamic depending on the local environment, and factors that influence the composition of the microbiome are essential to our understanding of how microbes may influence the biology of their animal hosts. Regularly repeated changes in the environment, such as diel lighting, can result in two different organismal responses: a direct response to the presence and absence of exogenous light and endogenous rhythms resulting from a molecular circadian clock, both of which can influence the associated microbiota. Here, we report how diel lighting and a potential circadian clock impacts the diversity and relative abundance of bacteria in the model cnidarian Nematostella vectensis using an amplicon-based sequencing approach. Comparisons of bacterial communities associated with anemones cultured in constant darkness and in light:dark conditions revealed that individuals entrained in the dark had a more diverse microbiota. Overall community composition showed little variation over a 24-hr period in either treatment; however, abundances of individual bacterial OTUs showed significant cycling in each treatment. A comparative analysis of genes involved in the innate immune system of cnidarians showed differential expression between lighting conditions in N. vectensis, with significant up-regulation during long-term darkness for a subset of genes. Together, our studies support a hypothesis that the bacterial community associated with this species is relatively stable under diel light conditions when compared with static conditions and that particular bacterial members may have time-dependent abundance that coincides with the diel photoperiod in an otherwise stable community.
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Affiliation(s)
- Whitney B. Leach
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Tyler J. Carrier
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Adam M. Reitzel
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
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18
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Kabacaoglu D, Ruess DA, Ai J, Algül H. NF-κB/Rel Transcription Factors in Pancreatic Cancer: Focusing on RelA, c-Rel, and RelB. Cancers (Basel) 2019; 11:E937. [PMID: 31277415 PMCID: PMC6679104 DOI: 10.3390/cancers11070937] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 06/26/2019] [Accepted: 07/02/2019] [Indexed: 02/07/2023] Open
Abstract
Regulation of Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB)/Rel transcription factors (TFs) is extremely cell-type-specific owing to their ability to act disparately in the context of cellular homeostasis driven by cellular fate and the microenvironment. This is also valid for tumor cells in which every single component shows heterogenic effects. Whereas many studies highlighted a per se oncogenic function for NF-κB/Rel TFs across cancers, recent advances in the field revealed their additional tumor-suppressive nature. Specifically, pancreatic ductal adenocarcinoma (PDAC), as one of the deadliest malignant diseases, shows aberrant canonical-noncanonical NF-κB signaling activity. Although decades of work suggest a prominent oncogenic activity of NF-κB signaling in PDAC, emerging evidence points to the opposite including anti-tumor effects. Considering the dual nature of NF-κB signaling and how it is closely linked to many other cancer related signaling pathways, it is essential to dissect the roles of individual Rel TFs in pancreatic carcinogenesis and tumor persistency and progression. Here, we discuss recent knowledge highlighting the role of Rel TFs RelA, RelB, and c-Rel in PDAC development and maintenance. Next to providing rationales for therapeutically harnessing Rel TF function in PDAC, we compile strategies currently in (pre-)clinical evaluation.
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Affiliation(s)
- Derya Kabacaoglu
- Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Dietrich A Ruess
- Department of Surgery, Faculty of Medicine, Medical Center, University of Freiburg, 79106 Freiburg, Germany
| | - Jiaoyu Ai
- Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Hana Algül
- Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany.
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19
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Chiaramonte M, Arizza V, Russo R. Evolutionary conserved pathway of the innate immune response after a viral insult in
Paracentrotus lividus
sea urchin. Int J Immunogenet 2019; 46:192-202. [DOI: 10.1111/iji.12424] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Marco Chiaramonte
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche Università degli Studi di Palermo Palermo Italy
- Consiglio Nazionale delle Ricerche Istituto di Biomedicina e Immunologia Molecolare “Alberto Monroy” Palermo Italy
| | - Vincenzo Arizza
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche Università degli Studi di Palermo Palermo Italy
| | - Roberta Russo
- Consiglio Nazionale delle Ricerche Istituto di Biomedicina e Immunologia Molecolare “Alberto Monroy” Palermo Italy
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20
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Williams LM, Fuess LE, Brennan JJ, Mansfield KM, Salas-Rodriguez E, Welsh J, Awtry J, Banic S, Chacko C, Chezian A, Dowers D, Estrada F, Hsieh YH, Kang J, Li W, Malchiodi Z, Malinowski J, Matuszak S, McTigue T, Mueller D, Nguyen B, Nguyen M, Nguyen P, Nguyen S, Njoku N, Patel K, Pellegrini W, Pliakas T, Qadir D, Ryan E, Schiffer A, Thiel A, Yunes SA, Spilios KE, Pinzón C JH, Mydlarz LD, Gilmore TD. A conserved Toll-like receptor-to-NF-κB signaling pathway in the endangered coral Orbicella faveolata. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 79:128-136. [PMID: 29080785 DOI: 10.1016/j.dci.2017.10.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 06/07/2023]
Abstract
Herein, we characterize the Toll-like receptor (TLR)-to-NF-κB innate immune pathway of Orbicella faveolata (Of), which is an ecologically important, disease-susceptible, reef-building coral. As compared to human TLRs, the intracellular TIR domain of Of-TLR is most similar to TLR4, and it can interact in vitro with the human TLR4 adapter MYD88. Treatment of O. faveolata tissue with lipopolysaccharide, a ligand for mammalian TLR4, resulted in gene expression changes consistent with NF-κB pathway mobilization. Biochemical and cell-based assays revealed that Of-NF-κB resembles the mammalian non-canonical NF-κB protein p100 in that C-terminal truncation results in translocation of Of-NF-κB to the nucleus and increases its DNA-binding and transcriptional activation activities. Moreover, human IκB kinase (IKK) and Of-IKK can both phosphorylate conserved residues in Of-NF-κB in vitro and induce C-terminal processing of Of-NF-κB in vivo. These results are the first characterization of TLR-to-NF-κB signaling proteins in an endangered coral, and suggest that these corals have conserved innate immune pathways.
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Affiliation(s)
- Leah M Williams
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Lauren E Fuess
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | | | | | | | - Julianne Welsh
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Jake Awtry
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Sarah Banic
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Cecilia Chacko
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Aarthia Chezian
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Donovan Dowers
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Felicia Estrada
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Yu-Hsuan Hsieh
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Jiawen Kang
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Wanwen Li
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Zoe Malchiodi
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - John Malinowski
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Sean Matuszak
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Thomas McTigue
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - David Mueller
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Brian Nguyen
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Michelle Nguyen
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Phuong Nguyen
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Sinead Nguyen
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Ndidi Njoku
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Khusbu Patel
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - William Pellegrini
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Tessa Pliakas
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Deena Qadir
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Emma Ryan
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Alex Schiffer
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Amber Thiel
- 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
| | - Kathryn E Spilios
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Jorge H Pinzón C
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Laura D Mydlarz
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Thomas D Gilmore
- Department of Biology, Boston University, Boston, MA 02215, USA.
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21
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Yu M, Chen J, Bao Y, Li J. Genomic analysis of NF-κB signaling pathway reveals its complexity in Crassostrea gigas. FISH & SHELLFISH IMMUNOLOGY 2018; 72:510-518. [PMID: 29162540 DOI: 10.1016/j.fsi.2017.11.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/09/2017] [Accepted: 11/17/2017] [Indexed: 06/07/2023]
Abstract
NF-κB signaling pathway is an evolutionarily conserved pathway that plays highly important roles in several developmental, cellular and immune response processes. With the recent release of the draft Pacific oyster (Crassostra gigas) genome sequence, we have sought to identify the various components of the NF-κB signaling pathway in these mollusks and investigate their gene structure. We further constructed phylogenetic trees to establish the evolutionary relationship of the oyster proteins with their homologues in vertebrates and invertebrates using BLASTX and neighbor-joining method. We report the presence of two classic NF-κB/Rel homologues in the pacific oyster namely Cgp100 and CgRel, which possess characteristic RHD domain and a consensus nuclear localization signal, similar to mammalian homologues and an additional CgRel-like protein, unique to C. gigas. Further, in addition to two classical IκB homologues, CgIκB1 and CgIκB2, we have identified three atypical IκB family members namely CgIκB3, CgIκB4 and CgBCL3 which lack the IκB degradation motif and consist of only one exon that might have arisen by retrotransposition from CgIκB1. Finally, we report the presence of three IKKs and one NEMO genes in oyster genome, named CgIKK1, CgIKK2, CgIKK3 and CgNEMO, respectively. While CgIKK1 and CgIKK3 domain structure is similar to their mammalian homologues, CgIKK2 was found to lack the HLH and NBD domains. Overall, the high conservation of the NF-κB/Rel, IκB and IKK family components in the pacific oyster and their structural similarity to the vertebrate and invertebrate homologues underline the functional importance of this pathway in regulation of critical cellular processes across species.
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Affiliation(s)
- Mingjia Yu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
| | - Jianming Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
| | - Yongbo Bao
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, China.
| | - Jun Li
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
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22
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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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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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Margolis SR, Wilson SC, Vance RE. Evolutionary Origins of cGAS-STING Signaling. Trends Immunol 2017; 38:733-743. [DOI: 10.1016/j.it.2017.03.004] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/19/2017] [Accepted: 03/20/2017] [Indexed: 12/25/2022]
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Kato K, Omura H, Ishitani R, Nureki O. Cyclic GMP-AMP as an Endogenous Second Messenger in Innate Immune Signaling by Cytosolic DNA. Annu Rev Biochem 2017; 86:541-566. [PMID: 28399655 DOI: 10.1146/annurev-biochem-061516-044813] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The innate immune system functions as the first line of defense against invading bacteria and viruses. In this context, the cGAS/STING [cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase/STING] signaling axis perceives the nonself DNA associated with bacterial and viral infections, as well as the leakage of self DNA by cellular dysfunction and stresses, to elicit the host's immune responses. In this pathway, the noncanonical cyclic dinucleotide 2',3'-cyclic GMP-AMP (2',3'-cGAMP) functions as a second messenger for signal transduction: 2',3'-cGAMP is produced by the enzyme cGAS upon its recognition of double-stranded DNA, and then the 2',3'-cGAMP is recognized by the receptor STING to induce the phosphorylation of downstream factors, including TBK1 (TANK binding kinase 1) and IRF3 (interferon regulatory factor 3). Numerous crystal structures of the components of this cGAS/STING signaling axis have been reported and these clarify the structural basis for their signal transduction mechanisms. In this review, we summarize recent progress made in the structural dissection of this signaling pathway and indicate possible directions of forthcoming research.
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Affiliation(s)
- Kazuki Kato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan; ,
| | - Hiroki Omura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan; ,
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan; ,
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan; ,
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Fuess LE, Pinzόn C JH, Weil E, Mydlarz LD. Associations between transcriptional changes and protein phenotypes provide insights into immune regulation in corals. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 62:17-28. [PMID: 27109903 DOI: 10.1016/j.dci.2016.04.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 06/05/2023]
Abstract
Disease outbreaks in marine ecosystems have driven worldwide declines of numerous taxa, including corals. Some corals, such as Orbicella faveolata, are particularly susceptible to disease. To explore the mechanisms contributing to susceptibility, colonies of O. faveolata were exposed to immune challenge with lipopolysaccharides. RNA sequencing and protein activity assays were used to characterize the response of corals to immune challenge. Differential expression analyses identified 17 immune-related transcripts that varied in expression post-immune challenge. Network analyses revealed several groups of transcripts correlated to immune protein activity. Several transcripts, which were annotated as positive regulators of immunity were included in these groups, and some were downregulated following immune challenge. Correlations between expression of these transcripts and protein activity results further supported the role of these transcripts in positive regulation of immunity. The observed pattern of gene expression and protein activity may elucidate the processes contributing to the disease susceptibility of species like O. faveolata.
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Affiliation(s)
- Lauren E Fuess
- Department of Biology, University of Texas Arlington, Arlington, TX, USA
| | - Jorge H Pinzόn C
- Department of Biology, University of Texas Arlington, Arlington, TX, USA
| | - Ernesto Weil
- Department of Marine Sciences, University of Puerto Rico, Mayagüez, PR, USA
| | - Laura D Mydlarz
- Department of Biology, University of Texas Arlington, Arlington, TX, USA.
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Humphries J, Harter B. Identification of nuclear factor kappaB (NF-κB) binding motifs in Biomphalaria glabrata. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 53:366-70. [PMID: 26277107 DOI: 10.1016/j.dci.2015.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 05/16/2023]
Abstract
Biomphalaria glabrata acts as the intermediate host to the parasite, Schistosoma mansoni, and for this reason, the immune system of B. glabrata has been researched extensively. Several studies have demonstrated that the transcriptome profile of B. glabrata changes following exposure to a variety of pathogens, yet very little is known regarding the regulation of gene expression in this species. Nuclear factor kappaB (NF-κB) homologues have recently been identified in B. glabrata but few functional studies have been carried out on this family of transcription factors. The aims of this study therefore were to identify NF-κB binding sites (κB motifs) in B. glabrata and examine them via functional assays. Two different κB motifs were predicted. Furthermore, the Rel homology domain (RHD) of a B. glabrata NF-κB was able to bind these κB motifs in EMSAs, as well as a vertebrate κB motif.
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28
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Morgan M, Goodner K, Ross J, Poole AZ, Stepp E, Stuart CH, Wilbanks C, Weil E. Development and application of molecular biomarkers for characterizing Caribbean Yellow Band Disease in Orbicella faveolata. PeerJ 2015; 3:e1371. [PMID: 26557440 PMCID: PMC4636412 DOI: 10.7717/peerj.1371] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/13/2015] [Indexed: 12/28/2022] Open
Abstract
Molecular stress responses associated with coral diseases represent an under-studied area of cnidarian transcriptome investigations. Caribbean Yellow Band Disease (CYBD) is considered a disease of Symbiodinium within the tissues of the coral host Orbicella faveolata. There is a paucity of diagnostic tools to assist in the early detection and characterization of coral diseases. The validity of a diagnostic test is determined by its ability to distinguish host organisms that have the disease from those that do not. The ability to detect and identify disease-affected tissue before visible signs of the disease are evident would then be a useful diagnostic tool for monitoring and managing disease outbreaks. Representational Difference Analysis (RDA) was utilized to isolate differentially expressed genes in O. faveolata exhibiting CYBD. Preliminary screening of RDA products identified a small number of genes of interest (GOI) which included an early growth response factor and ubiquitin ligase from the coral host as well as cytochrome oxidase from the algal symbiont. To further characterize the specificity of response, quantitative real-time PCR (qPCR) was utilized to compare the expression profiles of these GOIs within diseased tissues (visible lesions), tissues that precede visible lesions by 2–4 cm (transition area), and tissues from healthy-looking colonies with no signs of disease. Results show there are distinctive differences in the expression profiles of these three GOIs within each tissue examined. Collectively, this small suite of GOIs can provide a molecular “finger print” which is capable of differentiating between infected and uninfected colonies on reefs where CYBD is known to occur.
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Affiliation(s)
- Michael Morgan
- Department of Biology, Berry College , Mount Berry, GA , United States
| | - Kylia Goodner
- Department of Genetics, Yale University , New Haven, CT , United States
| | - James Ross
- Department of Biology, Berry College , Mount Berry, GA , United States
| | - Angela Z Poole
- Department of Biology, Western Oregon University , Monmouth, OR , United States
| | - Elizabeth Stepp
- The Medical College of Georgia, Georgia Regents University , Augusta, GA , United States
| | - Christopher H Stuart
- Department of Molecular Medicine, Wake Forest School of Medicine , Winston-Salem, NC , United States
| | - Cydney Wilbanks
- Department of Biology, Berry College , Mount Berry, GA , United States
| | - Ernesto Weil
- Department of Marine Sciences, University of Puerto Rico , Lajas, Puerto Rico , United States
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SINKOVICS JOSEPHG. The cnidarian origin of the proto-oncogenes NF-κB/STAT and WNT-like oncogenic pathway drives the ctenophores (Review). Int J Oncol 2015; 47:1211-29. [PMID: 26239915 PMCID: PMC4583530 DOI: 10.3892/ijo.2015.3102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 06/26/2015] [Indexed: 01/09/2023] Open
Abstract
The cell survival pathways of the diploblastic early multicellular eukaryotic hosts contain and operate the molecular machinery resembling those of malignantly transformed individual cells of highly advanced multicellular hosts (including Homo). In the present review, the STAT/NF-κB pathway of the cnidarian Nematostella vectensis is compared with that of human tumors (malignant lymphomas, including Reed-Sternberg cells) pointing out similarities, including possible viral initiation in both cases. In the ctenophore genome and proteome, β-catenin gains intranuclear advantages due to a physiologically weak destructive complex in the cytoplasm, and lack of natural inhibitors (the dickkopfs). Thus, a scenario similar to what tumor cells initiate and achieve is presented through several constitutive loss-of-function type mutations in the destructive complex and in the elimination of inhibitors. Vice versa, malignantly transformed individual cells of advanced multicellular hosts assume pheno-genotypic resemblance to cells of unicellular or early multicellular hosts, and presumably to their ancient predecessors, by returning to the semblance of immortality and to the resumption of the state of high degree of resistance to physicochemical insults. Human leukemogenic and oncogenic pathways are presented for comparisons. The supreme bioengineers RNA/DNA complex encoded both the malignantly transformed immortal cell and the human cerebral cortex. The former generates molecules for the immortality of cellular life in the Universe. The latter invents the inhibitors of the process in order to gain control over it.
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Affiliation(s)
- JOSEPH G. SINKOVICS
- St. Joseph Hospital's Cancer Institute Affiliated with the H.L. Moffitt Comprehensive Cancer Center; Department of Molecular Medicine, The University of South Florida Morsani College of Medicine, Tampa, FL, USA
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Kranzusch PJ, Wilson SC, Lee ASY, Berger JM, Doudna JA, Vance RE. Ancient Origin of cGAS-STING Reveals Mechanism of Universal 2',3' cGAMP Signaling. Mol Cell 2015; 59:891-903. [PMID: 26300263 PMCID: PMC4575873 DOI: 10.1016/j.molcel.2015.07.022] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/08/2015] [Accepted: 07/17/2015] [Indexed: 11/17/2022]
Abstract
In humans, the cGAS-STING immunity pathway signals in response to cytosolic DNA via 2',3' cGAMP, a cyclic dinucleotide (CDN) second messenger containing mixed 2'-5' and 3'-5' phosphodiester bonds. Prokaryotes also produce CDNs, but these are exclusively 3' linked, and thus the evolutionary origins of human 2',3' cGAMP signaling are unknown. Here we illuminate the ancient origins of human cGAMP signaling by discovery of a functional cGAS-STING pathway in Nematostella vectensis, an anemone species >500 million years diverged from humans. Anemone cGAS appears to produce a 3',3' CDN that anemone STING recognizes through nucleobase-specific contacts not observed in human STING. Nevertheless, anemone STING binds mixed-linkage 2',3' cGAMP indistinguishably from human STING, trapping a unique structural conformation not induced by 3',3' CDNs. These results reveal that human mixed-linkage cGAMP achieves universal signaling by exploiting a deeply conserved STING conformational intermediate, providing critical insight for therapeutic targeting of the STING pathway.
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Affiliation(s)
- Philip J Kranzusch
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA; Howard Hughes Medical Institute (HHMI), University of California, Berkeley, CA 94720, USA
| | - Stephen C Wilson
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Amy S Y Lee
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA; Center for RNA Systems Biology, University of California, Berkeley, CA 94720, USA
| | - James M Berger
- Department of Biophysics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jennifer A Doudna
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, CA 94720, USA; Center for RNA Systems Biology, University of California, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Innovative Genomics Initiative, University of California, Berkeley, CA 94720, USA; Howard Hughes Medical Institute (HHMI), University of California, Berkeley, CA 94720, USA.
| | - Russell E Vance
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA; Cancer Research Laboratory, University of California, Berkeley, CA 94720, USA; Howard Hughes Medical Institute (HHMI), University of California, Berkeley, CA 94720, USA.
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31
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Finnerty JR, Gilmore TD. Methods for analyzing the evolutionary relationship of NF-κB proteins using free, web-driven bioinformatics and phylogenetic tools. Methods Mol Biol 2015; 1280:631-46. [PMID: 25736776 DOI: 10.1007/978-1-4939-2422-6_37] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Phylogenetic analysis enables one to reconstruct the functional evolution of proteins. Current understanding of NF-κB signaling derives primarily from studies of a relatively small number of laboratory models-mainly vertebrates and insects-that represent a tiny fraction of animal evolution. As such, NF-κB has been the subject of limited phylogenetic analysis. The recent discovery of NF-κB proteins in "basal" marine animals (e.g., sponges, sea anemones, corals) and NF-κB-like proteins in non-metazoan lineages extends the origin of NF-κB signaling by several hundred million years and provides the opportunity to investigate the early evolution of this pathway using phylogenetic approaches. Here, we describe a combination of bioinformatic and phylogenetic analyses based on menu-driven, open-source computer programs that are readily accessible to molecular biologists without formal training in phylogenetic methods. These phylogenetically based comparisons of NF-κB proteins are powerful in that they reveal deep conservation and repeated instances of parallel evolution in the sequence and structure of NF-κB in distant animal groups, which suggest that important functional constraints limit the evolution of this protein.
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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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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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Reitzel AM, Passamaneck YJ, Karchner SI, Franks DG, Martindale MQ, Tarrant AM, Hahn ME. Aryl hydrocarbon receptor (AHR) in the cnidarian Nematostella vectensis: comparative expression, protein interactions, and ligand binding. Dev Genes Evol 2013; 224:13-24. [PMID: 24292160 DOI: 10.1007/s00427-013-0458-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 10/16/2013] [Indexed: 10/26/2022]
Abstract
The aryl hydrocarbon receptor (AHR) is a member of the basic helix-loop-helix/Per-ARNT-Sim (bHLH-PAS) family of transcription factors and has diverse roles in development, physiology, and environmental sensing in bilaterian animals. Studying the expression of conserved genes and function of proteins in outgroups to protostomes and deuterostomes assists in understanding the antiquity of gene function and deciphering lineage-specific differences in these bilaterian clades. We describe the developmental expression of AHR from the sea anemone Nematostella vectensis and compare its expression with three other members of the bHLH-PAS family (AHR nuclear translocator (ARNT), Cycle, and a proto-Single-Minded/Trachealess). NvAHR expression was highest early in the larval stage with spatial expression in the basal portion of the ectoderm that became increasingly restricted to the oral pole with concentrated expression in tentacles of the juvenile polyp. The other bHLH-PAS genes showed a divergent expression pattern in later larval stages and polyps, in which gene expression was concentrated in the aboral end, with broader expression in the endoderm later in development. In co-immunoprecipitation assays, we found no evidence for heterodimerization of AHR with ARNT, contrary to the conservation of this specific interaction in all bilaterians studied to date. Similar to results with other invertebrate AHRs but in contrast to vertebrate AHRs, NvAHR failed to bind two prototypical xenobiotic AHR ligands (2,3,7,8-tetrachlorodibenzo-p-dioxin, β-naphthoflavone). Together, our data suggest that AHR's original function in Eumetazoa likely involved developmental patterning, potentially of neural tissue. The role of heterodimerization in the function of AHR may have arisen after the cnidarian-bilaterian ancestor. The absence of xenobiotic binding to NvAHR further supports a hypothesis for a derived role of this protein in chemical sensing within the chordates.
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Affiliation(s)
- Adam M Reitzel
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA,
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Dunlap WC, Starcevic A, Baranasic D, Diminic J, Zucko J, Gacesa R, van Oppen MJH, Hranueli D, Cullum J, Long PF. KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome. BMC Genomics 2013; 14:509. [PMID: 23889801 PMCID: PMC3750612 DOI: 10.1186/1471-2164-14-509] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/15/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics. DESCRIPTION Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics. CONCLUSIONS We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives.
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Affiliation(s)
- Walter C Dunlap
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Antonio Starcevic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Damir Baranasic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Janko Diminic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Jurica Zucko
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ranko Gacesa
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Madeleine JH van Oppen
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
| | - Daslav Hranueli
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - John Cullum
- Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany
| | - Paul F Long
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
- Department of Chemistry King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
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35
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Welker AF, Moreira DC, Campos ÉG, Hermes-Lima M. Role of redox metabolism for adaptation of aquatic animals to drastic changes in oxygen availability. Comp Biochem Physiol A Mol Integr Physiol 2013; 165:384-404. [PMID: 23587877 DOI: 10.1016/j.cbpa.2013.04.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 03/26/2013] [Accepted: 04/04/2013] [Indexed: 12/14/2022]
Abstract
Large changes in oxygen availability in aquatic environments, ranging from anoxia through to hyperoxia, can lead to corresponding wide variation in the production of reactive oxygen species (ROS) by animals with aquatic respiration. Therefore, animals living in marine, estuarine and freshwater environments have developed efficient antioxidant defenses to minimize oxidative stress and to regulate the cellular actions of ROS. Changes in oxygen levels may lead to bursts of ROS generation that can be particularly harmful. This situation is commonly experienced by aquatic animals during abrupt transitions from periods of hypoxia/anoxia back to oxygenated conditions (e.g. intertidal cycles). The strategies developed differ significantly among aquatic species and are (i) improvement of their endogenous antioxidant system under hyperoxia (that leads to increased ROS formation) or other similar ROS-related stresses, (ii) increase in antioxidant levels when displaying higher metabolic rates, (iii) presence of constitutively high levels of antioxidants, that attenuates oxidative stress derived from fluctuations in oxygen availability, or (iv) increase in the activity of antioxidant enzymes (and/or the levels of their mRNAs) during hypometabolic states associated with anoxia/hypoxia. This enhancement of the antioxidant system - coined over a decade ago as "preparation for oxidative stress" - controls the possible harmful effects of increased ROS formation during hypoxia/reoxygenation. The present article proposes a novel explanation for the biochemical and molecular mechanisms involved in this phenomenon that could be triggered by hypoxia-induced ROS formation. We also discuss the connections among oxygen sensing, oxidative damage and regulation of the endogenous antioxidant defense apparatus in animals adapted to many natural or man-made challenges of the aquatic environment.
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Affiliation(s)
- Alexis F Welker
- Laboratório de Radicais Livres, Departamento de Biologia Celular, Universidade de Brasília, Brasília, 70910-900 DF, Brazil
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Stefanik DJ, Wolenski FS, Friedman LE, Gilmore TD, Finnerty JR. Isolation of DNA, RNA and protein from the starlet sea anemone Nematostella vectensis. Nat Protoc 2013; 8:892-9. [PMID: 23579778 DOI: 10.1038/nprot.2012.151] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Among marine invertebrates, the starlet sea anemone Nematostella vectensis has emerged as an important laboratory model system. One advantage of working with this species relative to many other marine invertebrates is the ease of isolating relatively pure DNA, RNA and protein. Nematostella can be raised at high densities, under clean culture conditions, and it lacks integumentary or skeletal structures that can impede the recovery of DNA, RNA or protein. Here we describe methods used in our lab to isolate DNA, RNA and protein from Nematostella embryos, larvae and adults. The methods described here are less expensive than commercial kits and are more easily scalable to larger tissue amounts. Preparation of DNA can be completed in ∼7 h, RNA preparation in ∼1.5 h and protein preparation in ∼1 h.
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Affiliation(s)
- Derek J Stefanik
- Department of Biology, Boston University, Boston, Massachusetts, 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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Ryzhakov G, Teixeira A, Saliba D, Blazek K, Muta T, Ragoussis J, Udalova IA. Cross-species analysis reveals evolving and conserved features of the nuclear factor κB (NF-κB) proteins. J Biol Chem 2013; 288:11546-54. [PMID: 23508954 PMCID: PMC3630861 DOI: 10.1074/jbc.m113.451153] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
NF-κB is a key regulator of immune gene expression in metazoans. It is currently unclear what changes occurred in NF-κB during animal evolution and what features remained conserved. To address this question, we compared the biochemical and functional properties of NF-κB proteins derived from human and the starlet sea anemone (Nematostella vectensis) in 1) a high-throughput assay of in vitro preferences for DNA sequences, 2) ChIP analysis of in vivo recruitment to the promoters of target genes, 3) a LUMIER-assisted examination of interactions with cofactors, and 4) a transactivation assay. We observed a remarkable evolutionary conservation of the DNA binding preferences of the animal NF-κB orthologs. We also show that NF-κB dimerization properties, nuclear localization signals, and binding to cytosolic IκBs are conserved. Surprisingly, the Bcl3-type nuclear IκB proteins functionally pair up only with NF-κB derived from their own species. The basis of the differential NF-κB recognition by IκB subfamilies is discussed.
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Affiliation(s)
- Grigory Ryzhakov
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, London W6 8LH, United Kingdom.
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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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Wolenski FS, Bradham CA, Finnerty JR, Gilmore TD. NF-κB is required for cnidocyte development in the sea anemone Nematostella vectensis. Dev Biol 2012; 373:205-15. [PMID: 23063796 DOI: 10.1016/j.ydbio.2012.10.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 09/12/2012] [Accepted: 10/04/2012] [Indexed: 01/29/2023]
Abstract
The sea anemone Nematostella vectensis (Nv) is a leading model organism for the phylum Cnidaria, which includes anemones, corals, jellyfishes and hydras. A defining trait across this phylum is the cnidocyte, an ectodermal cell type with a variety of functions including defense, prey capture and environmental sensing. Herein, we show that the Nv-NF-κB transcription factor and its inhibitor Nv-IκB are expressed in a subset of cnidocytes in the body column of juvenile and adult anemones. The size and distribution of the Nv-NF-κB-positive cnidocytes suggest that they are in a subtype known as basitrichous haplonema cnidocytes. Nv-NF-κB is primarily cytoplasmic in cnidocytes in juvenile and adult animals, but is nuclear when first detected in the 30-h post-fertilization embryo. Morpholino-mediated knockdown of Nv-NF-κB expression results in greatly reduced cnidocyte formation in the 5 day-old animal. Taken together, these results indicate that NF-κB plays a key role in the development of the phylum-specific cnidocyte cell type in Nematostella, likely by nuclear Nv-NF-κB-dependent activation of genes required for cnidocyte development.
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Affiliation(s)
- Francis S Wolenski
- Boston University, Department of Biology, 5 Cummington Mall, Boston, MA 02215, USA
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Hinz M, Arslan SÇ, Scheidereit C. It takes two to tango: IκBs, the multifunctional partners of NF-κB. Immunol Rev 2012; 246:59-76. [PMID: 22435547 DOI: 10.1111/j.1600-065x.2012.01102.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The inhibitory IκB proteins have been discovered as fundamental regulators of the inducible transcription factor nuclear factor-κB (NF-κB). As a generally excepted model, stimulus-dependent destruction of inhibitory IκBs and processing of precursor molecules, both promoted by components of the signal integrating IκB kinase complex, are the key events for the release of various NF-κB/Rel dimers and subsequent transcriptional activation. Intense research of more than 20 years provides evidence that the extending family of IκBs act not simply as reversible inhibitors of NF-κB activation but rather as a complex regulatory module, which assures feedback regulation of the NF-κB system and either can inhibit or promote transcriptional activity in a stimulus-dependent manner. Thus, IκB and NF-κB/Rel family proteins establish a complex interrelationship that allows modulated NF-κB-dependent transcription, tailored to the physiological environment.
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Affiliation(s)
- Michael Hinz
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
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Abstract
The vast majority of research on nuclear factor κB (NF-κB) signaling in the past 25 years has focused on its roles in normal and disease-related processes in vertebrates, especially mice and humans. Recent genome and transcriptome sequencing efforts have shown that homologs of NF-κB transcription factors, inhibitor of NF-κB (IκB) proteins, and IκB kinases are present in a variety of invertebrates, including several in phyla simpler than Arthropoda, the phylum containing insects such Drosophila. Moreover, many invertebrates also contain genes encoding homologs of upstream signaling proteins in the Toll-like receptor signaling pathway, which is well-known for its downstream activation of NF-κB for innate immunity. This review describes what we now know or can infer and speculate about the evolution of the core elements of NF-κB signaling as well as the biological processes controlled by NF-κB in invertebrates. Further research on NF-κB in invertebrates is likely to uncover information about the evolutionary origins of this key human signaling pathway and may have relevance to our management of the responses of ecologically and economically important organisms to environmental and adaptive pressures.
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Affiliation(s)
- Thomas D Gilmore
- Department of Biology, Boston University, Boston, MA 02215, USA.
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Weston AJ, Dunlap WC, Shick JM, Klueter A, Iglic K, Vukelic A, Starcevic A, Ward M, Wells ML, Trick CG, Long PF. A profile of an endosymbiont-enriched fraction of the coral Stylophora pistillata reveals proteins relevant to microbial-host interactions. Mol Cell Proteomics 2012; 11:M111.015487. [PMID: 22351649 DOI: 10.1074/mcp.m111.015487] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
This study examines the response of Symbiodinium sp. endosymbionts from the coral Stylophora pistillata to moderate levels of thermal "bleaching" stress, with and without trace metal limitation. Using quantitative high throughput proteomics, we identified 8098 MS/MS events relating to individual peptides from the endosymbiont-enriched fraction, including 109 peptides meeting stringent criteria for quantification, of which only 26 showed significant change in our experimental treatments; 12 of 26 increased expression in response to thermal stress with little difference affected by iron limitation. Surprisingly, there were no significant increases in antioxidant or heat stress proteins; those induced to higher expression were generally involved in protein biosynthesis. An outstanding exception was a massive 114-fold increase of a viral replication protein indicating that thermal stress may substantially increase viral load and thereby contribute to the etiology of coral bleaching and disease. In the absence of a sequenced genome for Symbiodinium or other photosymbiotic dinoflagellate, this proteome reveals a plethora of proteins potentially involved in microbial-host interactions. This includes photosystem proteins, DNA repair enzymes, antioxidant enzymes, metabolic redox enzymes, heat shock proteins, globin hemoproteins, proteins of nitrogen metabolism, and a wide range of viral proteins associated with these endosymbiont-enriched samples. Also present were 21 unusual peptide/protein toxins thought to originate from either microbial consorts or from contamination by coral nematocysts. Of particular interest are the proteins of apoptosis, vesicular transport, and endo/exocytosis, which are discussed in context of the cellular processes of coral bleaching. Notably, the protein complement provides evidence that, rather than being expelled by the host, stressed endosymbionts may mediate their own departure.
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Affiliation(s)
- Andrew J Weston
- King's College London Proteomics Facility, Institute of Psychiatry, London SE5 8AF, United Kingdom
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Wolenski FS, Chandani S, Stefanik DJ, Jiang N, Chu E, Finnerty JR, Gilmore TD. Two polymorphic residues account for the differences in DNA binding and transcriptional activation by NF-κB proteins encoded by naturally occurring alleles in Nematostella vectensis. J Mol Evol 2011; 73:325-36. [PMID: 22198650 DOI: 10.1007/s00239-011-9479-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 12/08/2011] [Indexed: 12/17/2022]
Abstract
The NF-κB family of transcription factors is activated in response to many environmental and biological stresses, and plays a key role in innate immunity across a broad evolutionary expanse of animals. A simple NF-κB pathway is present in the sea anemone Nematostella vectensis, an important model organism in the phylum Cnidaria. Nematostella has previously been shown to have two naturally occurring NF-κB alleles (Nv-NF-κB-C and Nv-NF-κB-S) that encode proteins with different DNA-binding and transactivation abilities. We show here that polymorphic residues 67 (Cys vs. Ser) and 269 (Ala vs. Glu) play complementary roles in determining the DNA-binding activity of the NF-κB proteins encoded by these two alleles and that residue 67 is primarily responsible for the difference in their transactivation ability. Phylogenetic analysis indicates that Nv-NF-κB-S is the derived allele, consistent with its restricted geographic distribution. These results define polymorphic residues that are important for the DNA-binding and transactivating activities of two naturally occurring variants of Nv-NF-κB. The implications for the appearance of the two Nv-NF-κB alleles in natural populations of sea anemones are discussed.
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Reitzel AM, Ryan JF, Tarrant AM. Establishing a model organism: A report from the first annual Nematostella meeting. Bioessays 2011; 34:158-61. [DOI: 10.1002/bies.201100145] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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