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Batachari LE, Dai AY, Troemel ER. Caenorhabditis elegans RIG-I-like receptor DRH-1 signals via CARDs to activate antiviral immunity in intestinal cells. Proc Natl Acad Sci U S A 2024; 121:e2402126121. [PMID: 38980902 DOI: 10.1073/pnas.2402126121] [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: 02/06/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Upon sensing viral RNA, mammalian RIG-I-like receptors (RLRs) activate downstream signals using caspase activation and recruitment domains (CARDs), which ultimately promote transcriptional immune responses that have been well studied. In contrast, the downstream signaling mechanisms for invertebrate RLRs are much less clear. For example, the Caenorhabditis elegans RLR DRH-1 lacks annotated CARDs and up-regulates the distinct output of RNA interference. Here, we found that similar to mammal RLRs, DRH-1 signals through two tandem CARDs (2CARD) to induce a transcriptional immune response. Expression of DRH-1(2CARD) alone in the intestine was sufficient to induce immune gene expression, increase viral resistance, and promote thermotolerance, a phenotype previously associated with immune activation in C. elegans. We also found that DRH-1 is required in the intestine to induce immune gene expression, and we demonstrate subcellular colocalization of DRH-1 puncta with double-stranded RNA inside the cytoplasm of intestinal cells upon viral infection. Altogether, our results reveal mechanistic and spatial insights into antiviral signaling in C. elegans, highlighting unexpected parallels in RLR signaling between C. elegans and mammals.
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Affiliation(s)
- Lakshmi E Batachari
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - Alyssa Y Dai
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - Emily R Troemel
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
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Batachari LE, Sarmiento MB, Wernet N, Troemel ER. Orsay Virus Infection in Caenorhabditis elegans. Curr Protoc 2024; 4:e1098. [PMID: 38967546 DOI: 10.1002/cpz1.1098] [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] [Indexed: 07/06/2024]
Abstract
Orsay virus infection in the nematode Caenorhabditis elegans presents an opportunity to study host-virus interactions in an easily culturable, whole-animal host. Previously, a major limitation of C. elegans as a model for studying antiviral immunity was the lack of viruses known to naturally infect the worm. With the 2011 discovery of the Orsay virus, a naturally occurring viral pathogen, C. elegans has emerged as a compelling model for research on antiviral defense. From the perspective of the host, the genetic tractability of C. elegans enables mechanistic studies of antiviral immunity while the transparency of this animal allows for the observation of subcellular processes in vivo. Preparing infective virus filtrate and performing infections can be achieved with relative ease in a laboratory setting. Moreover, several tools are available to measure the outcome of infection. Here, we describe workflows for generating infective virus filtrate, achieving reproducible infection of C. elegans, and assessing the outcome of viral infection using molecular biology approaches and immunofluorescence. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of Orsay virus filtrate Support Protocol: Synchronize C. elegans development by bleaching Basic Protocol 2: Orsay virus infection Basic Protocol 3: Quantification of Orsay virus RNA1/RNA2 transcript levels by qRT-PCR Basic Protocol 4: Quantification of infection rate and fluorescence in situ hybridization (FISH) fluorescence intensity Basic Protocol 5: Immunofluorescent labeling of dsRNA in virus-infected intestinal tissue.
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Affiliation(s)
- Lakshmi E Batachari
- School of Biological Sciences, University of California San Diego, La Jolla, California
| | | | - Nicole Wernet
- School of Biological Sciences, University of California San Diego, La Jolla, California
| | - Emily R Troemel
- School of Biological Sciences, University of California San Diego, La Jolla, California
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3
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Bardan Sarmiento M, Gang SS, van Oosten-Hawle P, Troemel ER. CUL-6/cullin ubiquitin ligase-mediated degradation of HSP-90 by intestinal lysosomes promotes thermotolerance. Cell Rep 2024; 43:114279. [PMID: 38795346 PMCID: PMC11238739 DOI: 10.1016/j.celrep.2024.114279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/10/2024] [Accepted: 05/10/2024] [Indexed: 05/27/2024] Open
Abstract
Heat shock can be a lethal stressor. Previously, we described a CUL-6/cullin-ring ubiquitin ligase complex in the nematode Caenorhabditis elegans that is induced by intracellular intestinal infection and proteotoxic stress and that promotes improved survival upon heat shock (thermotolerance). Here, we show that CUL-6 promotes thermotolerance by targeting the heat shock protein HSP-90 for degradation. We show that CUL-6-mediated lowering of HSP-90 protein levels, specifically in the intestine, improves thermotolerance. Furthermore, we show that lysosomal function is required for CUL-6-mediated promotion of thermotolerance and that CUL-6 directs HSP-90 to lysosome-related organelles upon heat shock. Altogether, these results indicate that a CUL-6 ubiquitin ligase promotes organismal survival upon heat shock by promoting HSP-90 degradation in intestinal lysosomes. Thus, HSP-90, a protein commonly associated with protection against heat shock and promoting degradation of other proteins, is itself degraded to protect against heat shock.
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Affiliation(s)
| | - Spencer S Gang
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Emily R Troemel
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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Alkan C, Brésard G, Frézal L, Richaud A, Ruaud A, Zhang G, Félix MA. Natural variation in infection specificity of Caenorhabditis briggsae isolates by two RNA viruses. PLoS Pathog 2024; 20:e1012259. [PMID: 38861582 PMCID: PMC11195985 DOI: 10.1371/journal.ppat.1012259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/24/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024] Open
Abstract
Antagonistic relationships such as host-virus interactions potentially lead to rapid evolution and specificity in interactions. The Orsay virus is so far the only horizontal virus naturally infecting the nematode C. elegans. In contrast, several related RNA viruses infect its congener C. briggsae, including Santeuil (SANTV) and Le Blanc (LEBV) viruses. Here we focus on the host's intraspecific variation in sensitivity to these two intestinal viruses. Many temperate-origin C. briggsae strains, including JU1264 and JU1498, are sensitive to both, while many tropical strains, such as AF16, are resistant to both. Interestingly, some C. briggsae strains exhibit a specific resistance, such as the HK104 strain, specifically resistant to LEBV. The viral sensitivity pattern matches the strains' geographic and genomic relationships. The heavily infected strains mount a seemingly normal small RNA response that is insufficient to suppress viral infection, while the resistant strains show no small RNA response, suggesting an early block in viral entry or replication. We use a genetic approach from the host side to map genomic regions participating in viral resistance polymorphisms. Using Advanced Intercrossed Recombinant Inbred Lines (RILs) between virus-resistant AF16 and SANTV-sensitive HK104, we detect Quantitative Trait Loci (QTLs) on chromosomes IV and III. Building RILs between virus-sensitive JU1498 and LEBV-resistant HK104 followed by bulk segregant analysis, we identify a chromosome II QTL. In both cases, further introgressions of the regions confirmed the QTLs. This diversity provides an avenue for studying virus entry, replication, and exit mechanisms, as well as host-virus specificity and the host response to a specific virus infection.
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Affiliation(s)
- Cigdem Alkan
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Gautier Brésard
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Lise Frézal
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques Paris, Paris, France
| | - Aurélien Richaud
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Albane Ruaud
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Gaotian Zhang
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Marie-Anne Félix
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
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Gang SS, Lažetić V. Microsporidia: Pervasive natural pathogens of Caenorhabditis elegans and related nematodes. J Eukaryot Microbiol 2024:e13027. [PMID: 38702921 DOI: 10.1111/jeu.13027] [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: 01/15/2024] [Accepted: 02/02/2024] [Indexed: 05/06/2024]
Abstract
The nematode Caenorhabditis elegans is an invaluable host model for studying infections caused by various pathogens, including microsporidia. Microsporidia represent the first natural pathogens identified in C. elegans, revealing the previously unknown Nematocida genus of microsporidia. Following this discovery, the utilization of nematodes as a model host has rapidly expanded our understanding of microsporidia biology and has provided key insights into the cell and molecular mechanisms of antimicrosporidia defenses. Here, we first review the isolation history, morphological characteristics, life cycles, tissue tropism, genetics, and host immune responses for the four most well-characterized Nematocida species that infect C. elegans. We then highlight additional examples of microsporidia that infect related terrestrial and aquatic nematodes, including parasitic nematodes. To conclude, we assess exciting potential applications of the nematode-microsporidia system while addressing the technical advances necessary to facilitate future growth in this field.
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Affiliation(s)
- Spencer S Gang
- Molecular Biology Department, Colorado College, Colorado Springs, Colorado, USA
| | - Vladimir Lažetić
- Department of Biological Sciences, Columbian College of Arts & Sciences, The George Washington University, Washington, District of Columbia, USA
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González R, Félix MA. Caenorhabditis elegans immune responses to microsporidia and viruses. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 154:105148. [PMID: 38325500 DOI: 10.1016/j.dci.2024.105148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
The model organism Caenorhabditis elegans is susceptible to infection by obligate intracellular pathogens, specifically microsporidia and viruses. These intracellular pathogens infect intestinal cells, or, for some microsporidia, epidermal cells. Strikingly, intestinal cell infections by viruses or microsporidia trigger a common transcriptional response, activated in part by the ZIP-1 transcription factor. Among the strongest activated genes in this response are ubiquitin-pathway members and members of the pals family, an intriguing gene family with cross-regulations of different members of genomic clusters. Some of the induced genes participate in host defense against the pathogens, for example through ubiquitin-mediated inhibition. Other mechanisms defend the host specifically against viral infections, including antiviral RNA interference and uridylation. These various immune responses are altered by environmental factors and by intraspecific genetic variation of the host. These pathogens were first isolated 15 years ago and much remains to be discovered using C. elegans genetics; also, other intracellular pathogens of C. elegans may yet to be discovered.
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Affiliation(s)
- Rubén González
- Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, 75005, Paris, France.
| | - Marie-Anne Félix
- Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, 75005, Paris, France
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Grover M, Gang SS, Troemel ER, Barkoulas M. Proteasome inhibition triggers tissue-specific immune responses against different pathogens in C. elegans. PLoS Biol 2024; 22:e3002543. [PMID: 38466732 PMCID: PMC10957088 DOI: 10.1371/journal.pbio.3002543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 03/21/2024] [Accepted: 02/09/2024] [Indexed: 03/13/2024] Open
Abstract
Protein quality control pathways play important roles in resistance against pathogen infection. For example, the conserved transcription factor SKN-1/NRF up-regulates proteostasis capacity after blockade of the proteasome and also promotes resistance against bacterial infection in the nematode Caenorhabditis elegans. SKN-1/NRF has 3 isoforms, and the SKN-1A/NRF1 isoform, in particular, regulates proteasomal gene expression upon proteasome dysfunction as part of a conserved bounce-back response. We report here that, in contrast to the previously reported role of SKN-1 in promoting resistance against bacterial infection, loss-of-function mutants in skn-1a and its activating enzymes ddi-1 and png-1 show constitutive expression of immune response programs against natural eukaryotic pathogens of C. elegans. These programs are the oomycete recognition response (ORR), which promotes resistance against oomycetes that infect through the epidermis, and the intracellular pathogen response (IPR), which promotes resistance against intestine-infecting microsporidia. Consequently, skn-1a mutants show increased resistance to both oomycete and microsporidia infections. We also report that almost all ORR/IPR genes induced in common between these programs are regulated by the proteasome and interestingly, specific ORR/IPR genes can be induced in distinct tissues depending on the exact trigger. Furthermore, we show that increasing proteasome function significantly reduces oomycete-mediated induction of multiple ORR markers. Altogether, our findings demonstrate that proteasome regulation keeps innate immune responses in check in a tissue-specific manner against natural eukaryotic pathogens of the C. elegans epidermis and intestine.
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Affiliation(s)
- Manish Grover
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Spencer S. Gang
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Emily R. Troemel
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
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Hédelin L, Thiébaut A, Huang J, Li X, Lemoine A, Haas G, Meignin C, Cai H, Waterhouse RM, Martins N, Imler JL. Investigating the Evolution of Drosophila STING-Dependent Antiviral Innate Immunity by Multispecies Comparison of 2'3'-cGAMP Responses. Mol Biol Evol 2024; 41:msae032. [PMID: 38377349 PMCID: PMC10917227 DOI: 10.1093/molbev/msae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 02/22/2024] Open
Abstract
Viruses represent a major threat to all animals, which defend themselves through induction of a large set of virus-stimulated genes that collectively control the infection. In vertebrates, these genes include interferons that play a critical role in the amplification of the response to infection. Virus- and interferon-stimulated genes include restriction factors targeting the different steps of the viral replication cycle, in addition to molecules associated with inflammation and adaptive immunity. Predictably, antiviral genes evolve dynamically in response to viral pressure. As a result, each animal has a unique arsenal of antiviral genes. Here, we exploit the capacity to experimentally activate the evolutionarily conserved stimulator of IFN genes (STING) signaling pathway by injection of the cyclic dinucleotide 2'3'-cyclic guanosine monophosphate-adenosine monophosphate into flies to define the repertoire of STING-regulated genes in 10 Drosophila species, spanning 40 million years of evolution. Our data reveal a set of conserved STING-regulated factors, including STING itself, a cGAS-like-receptor, the restriction factor pastel, and the antiviral protein Vago, but also 2 key components of the antiviral RNA interference pathway, Dicer-2, and Argonaute2. In addition, we identify unknown species- or lineage-specific genes that have not been previously associated with resistance to viruses. Our data provide insight into the core antiviral response in Drosophila flies and pave the way for the characterization of previously unknown antiviral effectors.
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Affiliation(s)
- Léna Hédelin
- CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Antonin Thiébaut
- Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Jingxian Huang
- School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Xiaoyan Li
- School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Aurélie Lemoine
- CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Gabrielle Haas
- CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Carine Meignin
- CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Hua Cai
- School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Robert M Waterhouse
- Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Nelson Martins
- CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Jean-Luc Imler
- CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
- School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
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Batachari LE, Dai AY, Troemel ER. C. elegans RIG-I-like receptor DRH-1 signals via CARDs to activate anti-viral immunity in intestinal cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.578694. [PMID: 38370651 PMCID: PMC10871272 DOI: 10.1101/2024.02.05.578694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Upon sensing viral RNA, mammalian RIG-I-like receptors activate downstream signals using caspase activation and recruitment domains (CARDs), which ultimately promote transcriptional immune responses that have been well-studied. In contrast, the downstream signaling mechanisms for invertebrate RIG-I-like receptors are much less clear. For example, the Caenorhabditis elegans RIG-I-like receptor DRH-1 lacks annotated CARDs and upregulates the distinct output of RNA interference (RNAi). Here we found that, similar to mammal RIG-I-like receptors, DRH-1 signals through two tandem caspase activation and recruitment domains (2CARD) to induce a transcriptional immune response. Expression of DRH-1(2CARD) alone in the intestine was sufficient to induce immune gene expression, increase viral resistance, and promote thermotolerance, a phenotype previously associated with immune activation. We also found that DRH-1 is required in the intestine to induce immune gene expression, and we demonstrate subcellular colocalization of DRH-1 puncta with double-stranded RNA inside the cytoplasm of intestinal cells upon viral infection. Altogether, our results reveal mechanistic and spatial insights into anti-viral signaling in C. elegans, highlighting unexpected parallels in RIG-I-like receptor signaling between C. elegans and mammals.
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Affiliation(s)
- Lakshmi E Batachari
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States
| | - Alyssa Y Dai
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States
| | - Emily R Troemel
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States
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