1
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Nair T, Weathers BA, Stuhr NL, Nhan JD, Curran SP. Serotonin deficiency from constitutive SKN-1 activation drives pathogen apathy. Nat Commun 2024; 15:8129. [PMID: 39285192 PMCID: PMC11405893 DOI: 10.1038/s41467-024-52233-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 08/29/2024] [Indexed: 09/20/2024] Open
Abstract
When an organism encounters a pathogen, the host innate immune system activates to defend against pathogen colonization and toxic xenobiotics produced. C. elegans employ multiple defense systems to ensure survival when exposed to Pseudomonas aeruginosa including activation of the cytoprotective transcription factor SKN-1/NRF2. Although wildtype C. elegans quickly learn to avoid pathogens, here we describe a peculiar apathy-like behavior towards PA14 in animals with constitutive activation of SKN-1, whereby animals choose not to leave and continue to feed on the pathogen even when a non-pathogenic and healthspan-promoting food option is available. Although lacking the urgency to escape the infectious environment, animals with constitutive SKN-1 activity are not oblivious to the presence of the pathogen and display the typical pathogen-induced intestinal distension and eventual demise. SKN-1 activation, specifically in neurons and intestinal tissues, orchestrates a unique transcriptional program which leads to defects in serotonin signaling that is required from both neurons and non-neuronal tissues. Serotonin depletion from SKN-1 activation limits pathogen defenses capacity, drives the pathogen-associated apathy behaviors and induces a synthetic sensitivity to selective serotonin reuptake inhibitors. Taken together, our work reveals interesting insights into how animals perceive environmental pathogens and subsequently alter behavior and cellular programs to promote survival.
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Affiliation(s)
- Tripti Nair
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Brandy A Weathers
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Nicole L Stuhr
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - James D Nhan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Sean P Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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2
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Balsam PD, Simpson EH, Taylor K, Kalmbach A, Gallistel CR. Learning depends on the information conveyed by temporal relationships between events and is reflected in the dopamine response to cues. SCIENCE ADVANCES 2024; 10:eadi7137. [PMID: 39241065 PMCID: PMC11378905 DOI: 10.1126/sciadv.adi7137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/30/2024] [Indexed: 09/08/2024]
Abstract
Contemporary theories guiding the search for neural mechanisms of learning and memory assume that associative learning results from the temporal pairing of cues and reinforcers resulting in coincident activation of associated neurons, strengthening their synaptic connection. While enduring, this framework has limitations: Temporal pairing-based models of learning do not fit with many experimental observations and cannot be used to make quantitative predictions about behavior. Here, we present behavioral data that support an alternative, information-theoretic conception: The amount of information that cues provide about the timing of reward delivery predicts behavior. Furthermore, this approach accounts for the rate and depth of both inhibitory and excitatory learning across paradigms and species. We also show that dopamine release in the ventral striatum reflects cue-predicted changes in reinforcement rates consistent with subjects understanding temporal relationships between task events. Our results reshape the conceptual and biological framework for understanding associative learning.
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Affiliation(s)
- Peter D Balsam
- Department of Psychology, Barnard College, New York City, NY, USA
- Columbia University and New York State Psychiatric Institute, New York City, NY, USA
| | - Eleanor H Simpson
- Columbia University and New York State Psychiatric Institute, New York City, NY, USA
| | - Kathleen Taylor
- Department of Psychology, Barnard College, New York City, NY, USA
| | - Abigail Kalmbach
- Columbia University and New York State Psychiatric Institute, New York City, NY, USA
| | - Charles R Gallistel
- Department of Psychology and the Rutgers Center for Cognitive Science, Rutgers University, New Brunswick, NJ, USA
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3
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Zhang Y, Iino Y, Schafer WR. Behavioral plasticity. Genetics 2024; 228:iyae105. [PMID: 39158469 DOI: 10.1093/genetics/iyae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 06/10/2024] [Indexed: 08/20/2024] Open
Abstract
Behavioral plasticity allows animals to modulate their behavior based on experience and environmental conditions. Caenorhabditis elegans exhibits experience-dependent changes in its behavioral responses to various modalities of sensory cues, including odorants, salts, temperature, and mechanical stimulations. Most of these forms of behavioral plasticity, such as adaptation, habituation, associative learning, and imprinting, are shared with other animals. The C. elegans nervous system is considerably tractable for experimental studies-its function can be characterized and manipulated with molecular genetic methods, its activity can be visualized and analyzed with imaging approaches, and the connectivity of its relatively small number of neurons are well described. Therefore, C. elegans provides an opportunity to study molecular, neuronal, and circuit mechanisms underlying behavioral plasticity that are either conserved in other animals or unique to this species. These findings reveal insights into how the nervous system interacts with the environmental cues to generate behavioral changes with adaptive values.
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Affiliation(s)
- Yun Zhang
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Yuichi Iino
- Department of Biological Sciences, University of Tokyo, Tokyo 113-0032, Japan
| | - William R Schafer
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH, UK
- Department of Biology, KU Leuven, 3000 Leuven, Belgium
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4
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Huang X, Ye Q, Dai W, Zheng J, Li Y, Wang C, Luo Z, Yang J, Zhuo W, Wan QL. Cadmium exposure induces multigenerational inheritance of germ cell apoptosis and fertility suppression in Caenorhabditis elegans. ENVIRONMENT INTERNATIONAL 2024; 191:108952. [PMID: 39159515 DOI: 10.1016/j.envint.2024.108952] [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: 12/18/2023] [Revised: 08/01/2024] [Accepted: 08/13/2024] [Indexed: 08/21/2024]
Abstract
Cadmium is a significant environmental pollutant that poses a substantial health hazard to humans due to its propensity to accumulate in the body and resist excretion. We have a comprehensive understanding of the damage caused by Cd exposure and the mechanisms of tolerance, however, the intricate mechanisms underlying multigenerational effects resulting from Cd exposure remain poorly understood. In this study, Caenorhabditis elegans were used as a model organism to investigate Cd-induced multigenerational effects and its association with epigenetic modifications. The results showed that Cd exposure leads to an increase in germ cell apoptosis and a decrease in fertility, which can be passed down to subsequent generations. Further analysis revealed that transcription factors DAF-16/FOXO and SKN-1/Nrf2 play essential roles in responding to Cd exposure and in the transgenerational induction of germ cell apoptosis. Additionally, histone H3K4 trimethylation (H3K4me3) marks stress-responsive genes and enhances their transcription, ultimately triggering multigenerational germ cell apoptosis. This study provides compelling evidence that the detrimental effects of Cd on the reproductive system can be inherited across generations. These findings enhance our understanding of the multigenerational effects of environmental pollutants and may inform strategies for the prevention and control of such pollutants.
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Affiliation(s)
- Xiaobing Huang
- Department of Pathogen Biology, School of Medicine, Jinan University, Guangzhou 510632, Guangdong, China; Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai 519000, Guangdong, China; The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, Guangdong, China
| | - Qunshan Ye
- Department of Pathogen Biology, School of Medicine, Jinan University, Guangzhou 510632, Guangdong, China; The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, Guangdong, China
| | - Wenyu Dai
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, Guangdong, China; Department of Biochemistry and Molecular Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, Guangdong, China
| | - Jingming Zheng
- Department of Pathogen Biology, School of Medicine, Jinan University, Guangzhou 510632, Guangdong, China; The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, Guangdong, China
| | - Yimin Li
- Department of Pathogen Biology, School of Medicine, Jinan University, Guangzhou 510632, Guangdong, China; The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, Guangdong, China
| | - Cheng Wang
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, Guangdong, China
| | - Zhenhuan Luo
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, Guangdong, China
| | - Jing Yang
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, Guangdong, China; Department of Biochemistry and Molecular Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, Guangdong, China
| | - Wenyan Zhuo
- Department of Neurology, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai 519000, Guangdong, China
| | - Qin-Li Wan
- Department of Pathogen Biology, School of Medicine, Jinan University, Guangzhou 510632, Guangdong, China.
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5
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Wang J, Barr MM, Wehman AM. Extracellular vesicles. Genetics 2024; 227:iyae088. [PMID: 38884207 PMCID: PMC11304975 DOI: 10.1093/genetics/iyae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
Extracellular vesicles (EVs) encompass a diverse array of membrane-bound organelles released outside cells in response to developmental and physiological cell needs. EVs play important roles in remodeling the shape and content of differentiating cells and can rescue damaged cells from toxic or dysfunctional content. EVs can send signals and transfer metabolites between tissues and organisms to regulate development, respond to stress or tissue damage, or alter mating behaviors. While many EV functions have been uncovered by characterizing ex vivo EVs isolated from body fluids and cultured cells, research using the nematode Caenorhabditis elegans has provided insights into the in vivo functions, biogenesis, and uptake pathways. The C. elegans EV field has also developed methods to analyze endogenous EVs within the organismal context of development and adult physiology in free-living, behaving animals. In this review, we summarize major themes that have emerged for C. elegans EVs and their relevance to human health and disease. We also highlight the diversity of biogenesis mechanisms, locations, and functions of worm EVs and discuss open questions and unexplored topics tenable in C. elegans, given the nematode model is ideal for light and electron microscopy, genetic screens, genome engineering, and high-throughput omics.
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Affiliation(s)
- Juan Wang
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Maureen M Barr
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Ann M Wehman
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
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6
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Boraschi D, Toepfer E, Italiani P. Innate and germline immune memory: specificity and heritability of the ancient immune mechanisms for adaptation and survival. Front Immunol 2024; 15:1386578. [PMID: 38903500 PMCID: PMC11186993 DOI: 10.3389/fimmu.2024.1386578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
The immune memory is one of the defensive strategies developed by both unicellular and multicellular organisms for ensuring their integrity and functionality. While the immune memory of the vertebrate adaptive immune system (based on somatic recombination) is antigen-specific, encompassing the generation of memory T and B cells that only recognize/react to a specific antigen epitope, the capacity of vertebrate innate cells to remember past events is a mostly non-specific mechanism of adaptation. This "innate memory" can be considered as germline-encoded because its effector tools (such as innate receptors) do not need somatic recombination for being active. Also, in several organisms the memory-related information is integrated in the genome of germline cells and can be transmitted to the progeny for several generations, but it can also be erased depending on the environmental conditions. Overall, depending on the organism, its environment and its living habits, innate immune memory appears to be a mechanism for achieving better protection and survival against repeated exposure to microbes/stressful agents present in the same environment or occurring in the same anatomical district, able to adapt to changes in the environmental cues. The anatomical and functional complexity of the organism and its lifespan drive the generation of different immune memory mechanisms, for optimal adaptation to changes in the living/environmental conditions. The concept of innate immunity being non-specific needs to be revisited, as a wealth of evidence suggests a significant degree of specificity both in the primary immune reaction and in the ensuing memory-like responses. This is clearly evident in invertebrate metazoans, in which distinct scenarios can be observed, with both non-specific (immune enhancement) or specific (immune priming) memory-like responses. In the case of mammals, there is evidence that some degree of specificity can be attained in different situations, for instance as organ-specific protection rather than microorganism-specific reaction. Thus, depending on the challenges and conditions, innate memory can be non-specific or specific, can be integrated in the germline and transmitted to the progeny or be short-lived, thereby representing an exceptionally plastic mechanism of defensive adaptation for ensuring individual and species survival.
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Affiliation(s)
- Diana Boraschi
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen University of Advanced Technology, Shenzhen, China
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, Italy
- Stazione Zoologica Anton Dorhn, Napoli, Italy
- China-Italy Joint Laboratory of Pharmacobiotechnology for Medical Application, Shenzhen, China
| | | | - Paola Italiani
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, Italy
- Stazione Zoologica Anton Dorhn, Napoli, Italy
- China-Italy Joint Laboratory of Pharmacobiotechnology for Medical Application, Shenzhen, China
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7
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Seto R, Brown R, Kaletsky R, Parsons LR, Moore RS, Murphy CT. Pseudomonas fluorescens 15 small RNA Pfs1 mediates transgenerational epigenetic inheritance of pathogen avoidance in C. elegans through the Ephrin receptor VAB-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595334. [PMID: 38826453 PMCID: PMC11142145 DOI: 10.1101/2024.05.23.595334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
C. elegans are exposed to a variety of pathogenic and non-pathogenic bacteria species in their natural environment. Correspondingly, C. elegans has evolved an ability to discern between nutritive and infectious bacterial food sources. Here we show that C. elegans can learn to avoid the pathogenic bacteria Pseudomonas fluorescens 15 (PF15), and that this learned avoidance behavior is passed on to progeny for four generations, as we previously demonstrated for Pseudomonas aeruginosa (PA14) and Pseudomonas vranovensis, using similar mechanisms, including the involvement of both the TGF-β ligand DAF-7 and Cer1 retrotransposon-encoded virus-like particles. PF15 small RNAs are both necessary and sufficient to induce this transgenerational avoidance behavior. Unlike PA14 or P. vranovensis, PF15 does not use P11, Pv1, or a small RNA with maco-1 homology for this avoidance; instead, an unrelated PF15 small RNA, Pfs1, that targets the C. elegans vab-1 Ephrin receptor gene is necessary and sufficient for learned avoidance, suggesting the evolution of yet another bacterial sRNA/C. elegans gene target pair involved in transgenerational inheritance of pathogen avoidance. As VAB-2 Ephrin receptor ligand and MACO-1 knockdown also induce PF15 avoidance, we have begun to understand the genetic pathway involved in small RNA targeted pathogenic avoidance. Moreover, these data show that axon guidance pathway genes (VAB-1 and VAB-2) have previously unknown adult roles in regulating neuronal function. C. elegans may have evolved multiple bacterial specificity-encoded small RNA-dependent mechanisms to avoid different pathogenic bacteria species, thereby providing progeny with a survival advantage in a dynamic environment.
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Affiliation(s)
- Renee Seto
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton NJ 08544
| | - Rachel Brown
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton NJ 08544
| | - Rachel Kaletsky
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton NJ 08544
| | - Lance R. Parsons
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton NJ 08544
| | - Rebecca S. Moore
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton NJ 08544
| | - Coleen T. Murphy
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton NJ 08544
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8
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Lei M, Tan Y, Tu H, Tan W. Neuronal basis and diverse mechanisms of pathogen avoidance in Caenorhabditis elegans. Front Immunol 2024; 15:1353747. [PMID: 38751431 PMCID: PMC11094273 DOI: 10.3389/fimmu.2024.1353747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Pathogen avoidance behaviour has been observed across animal taxa as a vital host-microbe interaction mechanism. The nematode Caenorhabditis elegans has evolved multiple diverse mechanisms for pathogen avoidance under natural selection pressure. We summarise the current knowledge of the stimuli that trigger pathogen avoidance, including alterations in aerotaxis, intestinal bloating, and metabolites. We then survey the neural circuits involved in pathogen avoidance, transgenerational epigenetic inheritance of pathogen avoidance, signalling crosstalk between pathogen avoidance and innate immunity, and C. elegans avoidance of non-Pseudomonas bacteria. In this review, we highlight the latest advances in understanding host-microbe interactions and the gut-brain axis.
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Affiliation(s)
- Ming Lei
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Yanheng Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan, China
| | - Haijun Tu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan, China
| | - Weihong Tan
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
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9
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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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10
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Harris JC, Trigg NA, Goshu B, Yokoyama Y, Dohnalová L, White EK, Harman A, Murga-Garrido SM, Ting-Chun Pan J, Bhanap P, Thaiss CA, Grice EA, Conine CC, Kambayashi T. The microbiota and T cells non-genetically modulate inherited phenotypes transgenerationally. Cell Rep 2024; 43:114029. [PMID: 38573852 PMCID: PMC11102039 DOI: 10.1016/j.celrep.2024.114029] [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: 07/12/2023] [Revised: 01/21/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
The host-microbiota relationship has evolved to shape mammalian physiology, including immunity, metabolism, and development. Germ-free models are widely used to study microbial effects on host processes such as immunity. Here, we find that both germ-free and T cell-deficient mice exhibit a robust sebum secretion defect persisting across multiple generations despite microbial colonization and T cell repletion. These phenotypes are inherited by progeny conceived during in vitro fertilization using germ-free sperm and eggs, demonstrating that non-genetic information in the gametes is required for microbial-dependent phenotypic transmission. Accordingly, gene expression in early embryos derived from gametes from germ-free or T cell-deficient mice is strikingly and similarly altered. Our findings demonstrate that microbial- and immune-dependent regulation of non-genetic information in the gametes can transmit inherited phenotypes transgenerationally in mice. This mechanism could rapidly generate phenotypic diversity to enhance host adaptation to environmental perturbations.
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Affiliation(s)
- Jordan C Harris
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Natalie A Trigg
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Bruktawit Goshu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuichi Yokoyama
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lenka Dohnalová
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ellen K White
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adele Harman
- Transgenic Core, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sofía M Murga-Garrido
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamie Ting-Chun Pan
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Preeti Bhanap
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christoph A Thaiss
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elizabeth A Grice
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Colin C Conine
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Taku Kambayashi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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11
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Chang NC, Wells JN, Wang AY, Schofield P, Huang YC, Truong VH, Simoes-Costa M, Feschotte C. Gag proteins encoded by endogenous retroviruses are required for zebrafish development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586437. [PMID: 38585793 PMCID: PMC10996621 DOI: 10.1101/2024.03.25.586437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. The process by which TEs become coopted remains obscure because most cases involve ancient, transpositionally inactive elements. Reports of active TEs serving beneficial functions are scarce and often contentious due to difficulties in manipulating repetitive sequences. Here we show that recently active TEs in zebrafish encode products critical for embryonic development. Knockdown and rescue experiments demonstrate that the endogenous retrovirus family BHIKHARI-1 (Bik-1) encodes a Gag protein essential for mesoderm development. Mechanistically, Bik-1 Gag associates with the cell membrane and its ectopic expression in chicken embryos alters cell migration. Similarly, depletion of BHIKHARI-2 Gag, a relative of Bik-1, causes defects in neural crest development in zebrafish. We propose an "addiction" model to explain how active TEs can be integrated into conserved developmental processes.
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Affiliation(s)
- Ni-Chen Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Jonathan N Wells
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Andrew Y Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Phillip Schofield
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Yi-Chia Huang
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Vinh H Truong
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Marcos Simoes-Costa
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
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12
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Sengupta T, St. Ange J, Kaletsky R, Moore RS, Seto RJ, Marogi J, Myhrvold C, Gitai Z, Murphy CT. A natural bacterial pathogen of C. elegans uses a small RNA to induce transgenerational inheritance of learned avoidance. PLoS Genet 2024; 20:e1011178. [PMID: 38547071 PMCID: PMC10977744 DOI: 10.1371/journal.pgen.1011178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/09/2024] [Indexed: 04/02/2024] Open
Abstract
C. elegans can learn to avoid pathogenic bacteria through several mechanisms, including bacterial small RNA-induced learned avoidance behavior, which can be inherited transgenerationally. Previously, we discovered that a small RNA from a clinical isolate of Pseudomonas aeruginosa, PA14, induces learned avoidance and transgenerational inheritance of that avoidance in C. elegans. Pseudomonas aeruginosa is an important human pathogen, and there are other Pseudomonads in C. elegans' natural habitat, but it is unclear whether C. elegans ever encounters PA14-like bacteria in the wild. Thus, it is not known if small RNAs from bacteria found in C. elegans' natural habitat can also regulate host behavior and produce heritable behavioral effects. Here we screened a set of wild habitat bacteria, and found that a pathogenic Pseudomonas vranovensis strain isolated from the C. elegans microbiota, GRb0427, regulates worm behavior: worms learn to avoid this pathogenic bacterium following exposure, and this learned avoidance is inherited for four generations. The learned response is entirely mediated by bacterially-produced small RNAs, which induce avoidance and transgenerational inheritance, providing further support that such mechanisms of learning and inheritance exist in the wild. We identified Pv1, a small RNA expressed in P. vranovensis, that has a 16-nucleotide match to an exon of the C. elegans gene maco-1. Pv1 is both necessary and sufficient to induce learned avoidance of Grb0427. However, Pv1 also results in avoidance of a beneficial microbiome strain, P. mendocina. Our findings suggest that bacterial small RNA-mediated regulation of host behavior and its transgenerational inheritance may be functional in C. elegans' natural environment, and that this potentially maladaptive response may favor reversal of the transgenerational memory after a few generations. Our data also suggest that different bacterial small RNA-mediated regulation systems evolved independently, but define shared molecular features of bacterial small RNAs that produce transgenerationally-inherited effects.
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Affiliation(s)
- Titas Sengupta
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jonathan St. Ange
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Rachel Kaletsky
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Rebecca S. Moore
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Renee J. Seto
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jacob Marogi
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Coleen T. Murphy
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
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13
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Camara H, Inan MD, Vergani-Junior CA, Pinto S, Knittel TL, Salgueiro WG, Tonon-da-Silva G, Ramirez J, de Moraes D, Braga DL, De-Souza EA, Mori MA. Tissue-specific overexpression of systemic RNA interference components limits lifespan in C. elegans. Gene 2024; 895:148014. [PMID: 37984536 DOI: 10.1016/j.gene.2023.148014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
Intertissue RNA transport recently emerged as a novel signaling mechanism. In mammals, mounting evidence suggests that small RNA transfer between cells is widespread and used in various physiological contexts. In the nematode C. elegans, a similar mechanism is conferred by the systemic RNAi pathway. Members of the Systemic RNA Interference Defective (SID) family act at different steps of cellular RNA uptake and export. The limiting step in systemic RNA interference (RNAi) is the import of extracellular RNAs via the conserved double-stranded (dsRNA)-gated dsRNA channel SID-1. To better understand the role of RNAs as intertissue signaling molecules, we modified the function of SID-1 in specific tissues of C. elegans. We observed that sid-1 loss-of-function mutants are as healthy as wild-type worms. Conversely, overexpression of sid-1 in C. elegans intestine, muscle, or neurons rendered worms short-lived. The effects of intestinal sid-1 overexpression were attenuated by silencing the components of systemic RNAi sid-1, sid-2 and sid-5, implicating systemic RNA signaling in the lifespan reduction. Accordingly, tissue-specific overexpression of sid-2 and sid-5 also reduced worm lifespan. Additionally, an RNAi screen for components of several non-coding RNA pathways revealed that silencing the miRNA biogenesis proteins PASH-1 and DCR-1 rendered the lifespan of worms with intestinal sid-1 overexpression similar to controls. Collectively, our data support the notion that systemic RNA signaling must be tightly regulated, and unbalancing that process provokes a reduction in lifespan. We termed this phenomenon Intercellular/Extracellular Systemic RNA imbalance (InExS).
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Affiliation(s)
- Henrique Camara
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil; Program in Molecular Biology, Universidade Federal de São Paulo, Brazil
| | - Mehmet Dinçer Inan
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Carlos A Vergani-Junior
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Silas Pinto
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil; Program in Molecular Biology, Universidade Federal de São Paulo, Brazil
| | - Thiago L Knittel
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Willian G Salgueiro
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Guilherme Tonon-da-Silva
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Juliana Ramirez
- Program in Molecular Biology, Universidade Federal de São Paulo, Brazil
| | - Diogo de Moraes
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Deisi L Braga
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Evandro A De-Souza
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Molecular Biology, Universidade Federal de São Paulo, Brazil; Program in Molecular Biology and Biotechnology, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Marcelo A Mori
- Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil; Program in Molecular Biology, Universidade Federal de São Paulo, Brazil; Obesity and Comorbidities Research Center (OCRC), Universidade Estadual de Campinas, Campinas, SP, Brazil; Experimental Medicine Research Cluster (EMRC), Universidade Estadual de Campinas, Campinas, SP, Brazil.
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14
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Nair T, Weathers BA, Stuhr NL, Nhan JD, Curran SP. Serotonin deficiency from constitutive SKN-1 activation drives pathogen apathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579755. [PMID: 38405962 PMCID: PMC10888766 DOI: 10.1101/2024.02.10.579755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
When an organism encounters a pathogen, the host innate immune system activates to defend against pathogen colonization and toxic xenobiotics produced. C. elegans employ multiple defense systems to ensure survival when exposed to Pseudomonas aeruginosa including activation of the cytoprotective transcription factor SKN-1/NRF2. Although wildtype C. elegans quickly learn to avoid pathogens, here we describe a peculiar apathy-like behavior towards PA14 in animals with constitutive activation of SKN-1, whereby animals choose not to leave and continue to feed on the pathogen even when a non-pathogenic and healthspan-promoting food option is available. Although lacking the urgency to escape the infectious environment, animals with constitutive SKN-1 activity are not oblivious to the presence of the pathogen and display the typical pathogen-induced intestinal distension and eventual demise. SKN-1 activation, specifically in neurons and intestinal tissues, orchestrates a unique transcriptional program which leads to defects in serotonin signaling that is required from both neurons and non-neuronal tissues. Serotonin depletion from SKN-1 activation limits pathogen defense capacity, drives the pathogen-associated apathy behaviors and induces a synthetic sensitivity to selective serotonin reuptake inhibitors. Taken together, our work reveals new insights into how animals perceive environmental pathogens and subsequently alter behavior and cellular programs to promote survival. KEY POINTS Identify an apathy-like behavioral response for pathogens resulting from the constitutive activation of the cytoprotective transcription factor SKN-1.Uncover the obligate role for serotonin synthesis in both neuronal and non-neuronal cells for the apathy-like state and ability of serotonin treatment to restore normal behaviors.Characterize the timing and tissue specificity of SKN-1 nuclear localization in neurons and intestinal cells in response to pathogen exposure.Define the unique and context-specific transcriptional signatures of animals with constitutive SKN-1 activation when exposed to pathogenic environments.Reveal necessity for both neuronal and non-neuronal serotonin signaling in host survival from pathogen infection.
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15
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Tung A, Sperry MM, Clawson W, Pavuluri A, Bulatao S, Yue M, Flores RM, Pai VP, McMillen P, Kuchling F, Levin M. Embryos assist morphogenesis of others through calcium and ATP signaling mechanisms in collective teratogen resistance. Nat Commun 2024; 15:535. [PMID: 38233424 PMCID: PMC10794468 DOI: 10.1038/s41467-023-44522-2] [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: 06/22/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024] Open
Abstract
Information for organismal patterning can come from a variety of sources. We investigate the possibility that instructive influences for normal embryonic development are provided not only at the level of cells within the embryo, but also via interactions between embryos. To explore this, we challenge groups of embryos with disruptors of normal development while varying group size. Here, we show that Xenopus laevis embryos are much more sensitive to a diverse set of chemical and molecular-biological perturbations when allowed to develop alone or in small groups, than in large groups. Keeping per-embryo exposure constant, we find that increasing the number of exposed embryos in a cohort increases the rate of survival while incidence of defects decreases. This inter-embryo assistance effect is mediated by short-range diffusible signals and involves the P2 ATP receptor. Our data and computational model emphasize that morphogenesis is a collective phenomenon not only at the level of cells, but also of whole bodies, and that cohort size is a crucial variable in studies of ecotoxicology, teratogenesis, and developmental plasticity.
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Affiliation(s)
- Angela Tung
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Megan M Sperry
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Wesley Clawson
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Ananya Pavuluri
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Sydney Bulatao
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Michelle Yue
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Ramses Martinez Flores
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Vaibhav P Pai
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Patrick McMillen
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Franz Kuchling
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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16
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Ow MC, Hall SE. Inheritance of Stress Responses via Small Non-Coding RNAs in Invertebrates and Mammals. EPIGENOMES 2023; 8:1. [PMID: 38534792 DOI: 10.3390/epigenomes8010001] [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: 10/06/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 03/28/2024] Open
Abstract
While reports on the generational inheritance of a parental response to stress have been widely reported in animals, the molecular mechanisms behind this phenomenon have only recently emerged. The booming interest in epigenetic inheritance has been facilitated in part by the discovery that small non-coding RNAs are one of its principal conduits. Discovered 30 years ago in the Caenorhabditis elegans nematode, these small molecules have since cemented their critical roles in regulating virtually all aspects of eukaryotic development. Here, we provide an overview on the current understanding of epigenetic inheritance in animals, including mice and C. elegans, as it pertains to stresses such as temperature, nutritional, and pathogenic encounters. We focus on C. elegans to address the mechanistic complexity of how small RNAs target their cohort mRNAs to effect gene expression and how they govern the propagation or termination of generational perdurance in epigenetic inheritance. Presently, while a great amount has been learned regarding the heritability of gene expression states, many more questions remain unanswered and warrant further investigation.
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Affiliation(s)
- Maria C Ow
- Department of Biology, Syracuse University, Syracuse, NY 13210, USA
| | - Sarah E Hall
- Department of Biology and Program in Neuroscience, Syracuse University, Syracuse, NY 13210, USA
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17
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Pandey T, Kalluraya CA, Wang B, Xu T, Huang X, Guang S, Daugherty MD, Ma DK. Acquired stress resilience through bacteria-to-nematode interdomain horizontal gene transfer. EMBO J 2023; 42:e114835. [PMID: 37953666 PMCID: PMC10711659 DOI: 10.15252/embj.2023114835] [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: 06/24/2023] [Revised: 09/24/2023] [Accepted: 10/02/2023] [Indexed: 11/14/2023] Open
Abstract
Natural selection drives the acquisition of organismal resilience traits to protect against adverse environments. Horizontal gene transfer (HGT) is an important evolutionary mechanism for the acquisition of novel traits, including metazoan acquisitions in immunity, metabolic, and reproduction function via interdomain HGT (iHGT) from bacteria. Here, we report that the nematode gene rml-3 has been acquired by iHGT from bacteria and that it enables exoskeleton resilience and protection against environmental toxins in Caenorhabditis elegans. Phylogenetic analysis reveals that diverse nematode RML-3 proteins form a single monophyletic clade most similar to bacterial enzymes that biosynthesize L-rhamnose, a cell-wall polysaccharide component. C. elegans rml-3 is highly expressed during larval development and upregulated in developing seam cells upon heat stress and during the stress-resistant dauer stage. rml-3 deficiency impairs cuticle integrity, barrier functions, and nematode stress resilience, phenotypes that can be rescued by exogenous L-rhamnose. We propose that interdomain HGT of an ancient bacterial rml-3 homolog has enabled L-rhamnose biosynthesis in nematodes, facilitating cuticle integrity and organismal resilience to environmental stressors during evolution. These findings highlight a remarkable contribution of iHGT on metazoan evolution conferred by the domestication of a bacterial gene.
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Affiliation(s)
- Taruna Pandey
- Cardiovascular Research Institute and Department of PhysiologyUniversity of California San FranciscoSan FranciscoCAUSA
| | | | - Bingying Wang
- Cardiovascular Research Institute and Department of PhysiologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Ting Xu
- Division of Life Sciences and Medicine, Department of Obstetrics and Gynecology, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, The First Affiliated Hospital of USTC, Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | - Xinya Huang
- Division of Life Sciences and Medicine, Department of Obstetrics and Gynecology, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, The First Affiliated Hospital of USTC, Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | - Shouhong Guang
- Division of Life Sciences and Medicine, Department of Obstetrics and Gynecology, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, The First Affiliated Hospital of USTC, Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | | | - Dengke K Ma
- Cardiovascular Research Institute and Department of PhysiologyUniversity of California San FranciscoSan FranciscoCAUSA
- Innovative Genomics InstituteUniversity of CaliforniaBerkeleyCAUSA
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18
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Sengupta T, St. Ange J, Moore R, Kaletsky R, Marogi J, Myhrvold C, Gitai Z, Murphy CT. A natural bacterial pathogen of C. elegans uses a small RNA to induce transgenerational inheritance of learned avoidance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.20.549962. [PMID: 37503135 PMCID: PMC10370180 DOI: 10.1101/2023.07.20.549962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Previously, we discovered that a small RNA from a clinical isolate of Pseudomonas aeruginosa, PA14, induces learned avoidance and its transgenerational inheritance in C. elegans. Pseudomonas aeruginosa is an important human pathogen, and there are other Pseudomonads in C. elegans' natural habitat, but it is unclear whether C. elegans ever encounters PA14-like bacteria in the wild. Thus, it is not known if small RNAs from bacteria found in C. elegans' natural habitat can also regulate host behavior and produce heritable behavioral effects. Here we found that a pathogenic Pseudomonas vranovensis strain isolated from the C. elegans microbiota, GRb0427, like PA14, regulates worm behavior: worms learn to avoid this pathogenic bacterium following exposure to GRb0427, and this learned avoidance is inherited for four generations. The learned response is entirely mediated by bacterially-produced small RNAs, which induce avoidance and transgenerational inheritance, providing further support that such mechanisms of learning and inheritance exist in the wild. Using bacterial small RNA sequencing, we identified Pv1, a small RNA from GRb0427, that matches the sequence of C. elegans maco-1. We find that Pv1 is both necessary and sufficient to induce learned avoidance of Grb0427. However, Pv1 also results in avoidance of a beneficial microbiome strain, P. mendocina; this potentially maladaptive response may favor reversal of the transgenerational memory after a few generations. Our findings suggest that bacterial small RNA-mediated regulation of host behavior and its transgenerational inheritance are functional in C. elegans' natural environment, and that different bacterial small RNA-mediated regulation systems evolved independently but define shared molecular features of bacterial small RNAs that produce transgenerationally-inherited effects.
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Affiliation(s)
- Titas Sengupta
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jonathan St. Ange
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Rebecca Moore
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Rachel Kaletsky
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jacob Marogi
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Coleen T. Murphy
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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19
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Yang J, Tang R, Chen S, Chen Y, Yuan K, Huang R, Wang L. Exposure to high-sugar diet induces transgenerational changes in sweet sensitivity and feeding behavior via H3K27me3 reprogramming. eLife 2023; 12:e85365. [PMID: 37698486 PMCID: PMC10558205 DOI: 10.7554/elife.85365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 09/11/2023] [Indexed: 09/13/2023] Open
Abstract
Human health is facing a host of new threats linked to unbalanced diets, including high-sugar diet (HSD), which contributes to the development of both metabolic and behavioral disorders. Studies have shown that diet-induced metabolic dysfunctions can be transmitted to multiple generations of offspring and exert long-lasting health burden. Meanwhile, whether and how diet-induced behavioral abnormalities can be transmitted to the offspring remains largely unclear. Here, we showed that ancestral HSD exposure suppressed sweet sensitivity and feeding behavior in the offspring in Drosophila. These behavioral deficits were transmitted through the maternal germline and companied by the enhancement of H3K27me3 modifications. PCL-PRC2 complex, a major driver of H3K27 trimethylation, was upregulated by ancestral HSD exposure, and disrupting its activity eliminated the transgenerational inheritance of sweet sensitivity and feeding behavior deficits. Elevated H3K27me3 inhibited the expression of a transcriptional factor Cad and suppressed sweet sensitivity of the sweet-sensing gustatory neurons, reshaping the sweet perception and feeding behavior of the offspring. Taken together, we uncovered a novel molecular mechanism underlying behavioral abnormalities spanning multiple generations of offspring upon ancestral HSD exposure, which would contribute to the further understanding of long-term health risk of unbalanced diet.
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Affiliation(s)
- Jie Yang
- Life Sciences Institute, Zhejiang UniversityHangzhouChina
| | - Ruijun Tang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Neurosurgery, Xiangya Hospital, and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Shiye Chen
- Life Sciences Institute, Zhejiang UniversityHangzhouChina
| | - Yinan Chen
- Life Sciences Institute, Zhejiang UniversityHangzhouChina
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Neurosurgery, Xiangya Hospital, and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
- The Biobank of Xiangya Hospital, Xiangya Hospital, Central South UniversityChangshaChina
| | - Rui Huang
- Center for Neurointelligence, School of Medicine, Chongqing UniversityChongqingChina
- Institute of Molecular Physiology, Shenzhen Bay LaboratoryShenzhenChina
| | - Liming Wang
- Institute of Molecular Physiology, Shenzhen Bay LaboratoryShenzhenChina
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20
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Pandey T, Kalluraya C, Wang B, Xu T, Huang X, Guang S, Daugherty MD, Ma DK. Acquired stress resilience through bacteria-to-nematode horizontal gene transfer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.20.554039. [PMID: 37662235 PMCID: PMC10473587 DOI: 10.1101/2023.08.20.554039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Natural selection drives acquisition of organismal resilience traits to protect against adverse environments. Horizontal gene transfer (HGT) is an important evolutionary mechanism for the acquisition of novel traits, including metazoan acquisition of functions in immunity, metabolism, and reproduction via interdomain HGT (iHGT) from bacteria. We report that the nematode gene rml-3, which was acquired by iHGT from bacteria, enables exoskeleton resilience and protection against environmental toxins in C. elegans. Phylogenetic analysis reveals that diverse nematode RML-3 proteins form a single monophyletic clade most highly similar to bacterial enzymes that biosynthesize L-rhamnose to build cell wall polysaccharides. C. elegans rml-3 is regulated in developing seam cells by heat stress and stress-resistant dauer stage. Importantly, rml-3 deficiency impairs cuticle integrity, barrier functions and organismal stress resilience, phenotypes that are rescued by exogenous L-rhamnose. We propose that iHGT of an ancient bacterial rml-3 homolog enables L-rhamnose biosynthesis in nematodes that facilitates cuticle integrity and organismal resilience in adaptation to environmental stresses during evolution. These findings highlight the remarkable contribution of iHGT on metazoan evolution that is conferred by the domestication of bacterial genes.
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Affiliation(s)
- Taruna Pandey
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, USA
| | - Chinmay Kalluraya
- Department of Molecular Biology, University of California, San Diego, San Diego, USA
| | - Bingying Wang
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, USA
| | - Ting Xu
- The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, China
| | - Xinya Huang
- The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, China
| | - Shouhong Guang
- The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, China
| | - Matthew D. Daugherty
- Department of Molecular Biology, University of California, San Diego, San Diego, USA
| | - Dengke K. Ma
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, USA
- Innovative Genomics Institute, University of California, Berkeley, USA
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21
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Guskjolen A, Cembrowski MS. Engram neurons: Encoding, consolidation, retrieval, and forgetting of memory. Mol Psychiatry 2023; 28:3207-3219. [PMID: 37369721 PMCID: PMC10618102 DOI: 10.1038/s41380-023-02137-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
Tremendous strides have been made in our understanding of the neurobiological substrates of memory - the so-called memory "engram". Here, we integrate recent progress in the engram field to illustrate how engram neurons transform across the "lifespan" of a memory - from initial memory encoding, to consolidation and retrieval, and ultimately to forgetting. To do so, we first describe how cell-intrinsic properties shape the initial emergence of the engram at memory encoding. Second, we highlight how these encoding neurons preferentially participate in synaptic- and systems-level consolidation of memory. Third, we describe how these changes during encoding and consolidation guide neural reactivation during retrieval, and facilitate memory recall. Fourth, we describe neurobiological mechanisms of forgetting, and how these mechanisms can counteract engram properties established during memory encoding, consolidation, and retrieval. Motivated by recent experimental results across these four sections, we conclude by proposing some conceptual extensions to the traditional view of the engram, including broadening the view of cell-type participation within engrams and across memory stages. In collection, our review synthesizes general principles of the engram across memory stages, and describes future avenues to further understand the dynamic engram.
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Affiliation(s)
- Axel Guskjolen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
| | - Mark S Cembrowski
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada.
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22
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Sun B, Kim H, Mello CC, Priess JR. The CERV protein of Cer1, a C. elegans LTR retrotransposon, is required for nuclear export of viral genomic RNA and can form giant nuclear rods. PLoS Genet 2023; 19:e1010804. [PMID: 37384599 PMCID: PMC10309623 DOI: 10.1371/journal.pgen.1010804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Retroviruses and closely related LTR retrotransposons export full-length, unspliced genomic RNA (gRNA) for packaging into virions and to serve as the mRNA encoding GAG and POL polyproteins. Because gRNA often includes splice acceptor and donor sequences used to splice viral mRNAs, retroelements must overcome host mechanisms that retain intron-containing RNAs in the nucleus. Here we examine gRNA expression in Cer1, an LTR retrotransposon in C. elegans which somehow avoids silencing and is highly expressed in germ cells. Newly exported Cer1 gRNA associates rapidly with the Cer1 GAG protein, which has structural similarity with retroviral GAG proteins. gRNA export requires CERV (C. elegans regulator of viral expression), a novel protein encoded by a spliced Cer1 mRNA. CERV phosphorylation at S214 is essential for gRNA export, and phosphorylated CERV colocalizes with nuclear gRNA at presumptive sites of transcription. By electron microscopy, tagged CERV proteins surround clusters of distinct, linear fibrils that likely represent gRNA molecules. Single fibrils, or groups of aligned fibrils, also localize near nuclear pores. During the C. elegans self-fertile period, when hermaphrodites fertilize oocytes with their own sperm, CERV concentrates in two nuclear foci that are coincident with gRNA. However, as hermaphrodites cease self-fertilization, and can only produce cross-progeny, CERV undergoes a remarkable transition to form giant nuclear rods or cylinders that can be up to 5 microns in length. We propose a novel mechanism of rod formation, in which stage-specific changes in the nucleolus induce CERV to localize to the nucleolar periphery in flattened streaks of protein and gRNA; these streaks then roll up into cylinders. The rods are a widespread feature of Cer1 in wild strains of C. elegans, but their function is not known and might be limited to cross-progeny. We speculate that the adaptive strategy Cer1 uses for the identical self-progeny of a host hermaphrodite might differ for heterozygous cross-progeny sired by males. For example, mating introduces male chromosomes which can have different, or no, Cer1 elements.
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Affiliation(s)
- Bing Sun
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester,United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Haram Kim
- Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Craig C. Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester,United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - James R. Priess
- Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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23
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Harris JC, Trigg NA, Goshu B, Yokoyama Y, Dohnalová L, White EK, Harman A, Thaiss CA, Grice EA, Conine CC, Kambayashi T. The microbiota and immune system non-genetically affect offspring phenotypes transgenerationally. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535940. [PMID: 37066207 PMCID: PMC10104111 DOI: 10.1101/2023.04.06.535940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The host-microbiota relationship has evolved to shape mammalian processes, including immunity, metabolism, and development 1-3 . Host phenotypes change in direct response to microbial exposures by the individual. Here we show that the microbiota induces phenotypic change not only in the individual but also in their succeeding generations of progeny. We found that germ-free mice exhibit a robust sebum secretion defect and transcriptional changes in various organs, persisting across multiple generations despite microbial colonization and breeding with conventional mice. Host-microbe interactions could be involved in this process, since T cell-deficient mice, which display defective sebum secretion 4 , also transgenerationally transmit their phenotype to progeny. These phenotypes are inherited by progeny conceived during in vitro fertilization using germ-free sperm and eggs, demonstrating that epigenetic information in the gametes is required for phenotypic transmission. Accordingly, small non-coding RNAs that can regulate embryonic gene expression 5 were strikingly and similarly altered in gametes of germ-free and T cell-deficient mice. Thus, we have uncovered a novel mechanism whereby the microbiota and immune system induce phenotypic changes in successive generations of offspring. This epigenetic form of inheritance could be advantageous for host adaptation to environmental perturbation, where phenotypic diversity can be introduced more rapidly than by genetic mutation.
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24
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Ewe CK, Rechavi O. The third barrier to transgenerational inheritance in animals: somatic epigenetic resetting. EMBO Rep 2023; 24:e56615. [PMID: 36862326 PMCID: PMC10074133 DOI: 10.15252/embr.202256615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/02/2023] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
After early controversy, it is now increasingly clear that acquired responses to environmental factors may perpetuate across multiple generations-a phenomenon termed transgenerational epigenetic inheritance (TEI). Experiments with Caenorhabditis elegans, which exhibits robust heritable epigenetic effects, demonstrated small RNAs as key factors of TEI. Here, we discuss three major barriers to TEI in animals, two of which, the "Weismann barrier" and germline epigenetic reprogramming, have been known for decades. These are thought to effectively prevent TEI in mammals but not to the same extent in C. elegans. We argue that a third barrier-that we termed "somatic epigenetic resetting"-may further inhibit TEI and, unlike the other two, restricts TEI in C. elegans as well. While epigenetic information can overcome the Weismann barrier and transmit from the soma to the germline, it usually cannot "travel back" directly from the germline to the soma in subsequent generations. Nevertheless, heritable germline memory may still influence the animal's physiology by indirectly modifying gene expression in somatic tissues.
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Affiliation(s)
- Chee Kiang Ewe
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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25
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The molecular memory code and synaptic plasticity: A synthesis. Biosystems 2023; 224:104825. [PMID: 36610586 DOI: 10.1016/j.biosystems.2022.104825] [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: 10/14/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023]
Abstract
The most widely accepted view of memory in the brain holds that synapses are the storage sites of memory, and that memories are formed through associative modification of synapses. This view has been challenged on conceptual and empirical grounds. As an alternative, it has been proposed that molecules within the cell body are the storage sites of memory, and that memories are formed through biochemical operations on these molecules. This paper proposes a synthesis of these two views, grounded in a computational model of memory. Synapses are conceived as storage sites for the parameters of an approximate posterior probability distribution over latent causes. Intracellular molecules are conceived as storage sites for the parameters of a generative model. The model stipulates how these two components work together as part of an integrated algorithm for learning and inference.
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26
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Shi C, Murphy CT. piRNAs regulate a Hedgehog germline-to-soma pro-aging signal. NATURE AGING 2023; 3:47-63. [PMID: 37118518 PMCID: PMC10154208 DOI: 10.1038/s43587-022-00329-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/03/2022] [Indexed: 04/30/2023]
Abstract
The reproductive system regulates somatic aging through competing anti- and pro-aging signals. Germline removal extends somatic lifespan through conserved pathways including insulin and mammalian target-of-rapamycin signaling, while germline hyperactivity shortens lifespan through unknown mechanisms. Here we show that mating-induced germline hyperactivity downregulates piRNAs, in turn desilencing their targets, including the Hedgehog-like ligand-encoding genes wrt-1 and wrt-10, ultimately causing somatic collapse and death. Germline-produced Hedgehog signals require PTR-6 and PTR-16 receptors for mating-induced shrinking and death. Our results reveal an unconventional role of the piRNA pathway in transcriptional regulation of Hedgehog signaling and a new role of Hedgehog signaling in the regulation of longevity and somatic maintenance: Hedgehog signaling is controlled by the tunable piRNA pathway to encode the previously unknown germline-to-soma pro-aging signal. Mating-induced piRNA downregulation in the germline and subsequent Hedgehog signaling to the soma enable the animal to tune somatic resource allocation to germline needs, optimizing reproductive timing and survival.
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Affiliation(s)
- Cheng Shi
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, USA.
| | - Coleen T Murphy
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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27
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Guzman DM, Chakka K, Shi T, Marron A, Fiorito AE, Rahman NS, Ro S, Sucich DG, Pierce JT. Transgenerational effects of alcohol on behavioral sensitivity to alcohol in Caenorhabditis elegans. PLoS One 2022; 17:e0271849. [PMID: 36256641 PMCID: PMC9578632 DOI: 10.1371/journal.pone.0271849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022] Open
Abstract
Alcohol abuse and dependence have a substantial heritable component. Although the genome has been considered the sole vehicle of heritable phenotypes, recent studies suggest that drug or alcohol exposure may induce alterations in gene expression that are transmitted across generations. Still, the transgenerational impact of alcohol use (and abuse) remains largely unexplored in part because multigenerational studies using rodent models present challenges for time, sample size, and genetic heterogeneity. Here, we took advantage of the extremely short generation time, large broods, and clonal form of reproduction of the nematode Caenorhabditis elegans. We developed a model of pre-fertilization parental alcohol exposure to test alterations in behavioral responses to acute alcohol treatment (referred to in short as intoxication) in subsequent F1, F2 and F3 generations. We found that chronic and intermittent alcohol-treatment paradigms resulted in opposite changes to intoxication sensitivity of F3 progeny that were only apparent when controlling for yoked trials. Chronic alcohol-treatment paradigm in the parental generation resulted in alcohol-naïve F3 progeny displaying moderate resistance to intoxication. Intermittent treatment resulted in alcohol-naïve F3 progeny displaying moderate hypersensitivity to intoxication. Further study of these phenomena using this new C. elegans model may yield mechanistic insights into how transgenerational effects may occur in other animals.
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Affiliation(s)
- Dawn M. Guzman
- Department of Neuroscience, Waggoner Center for Alcohol and Addiction Research, Center for Learning and Memory, University of Texas at Austin, Austin, Texas, United States of America
| | - Keerthana Chakka
- Department of Neuroscience, Waggoner Center for Alcohol and Addiction Research, Center for Learning and Memory, University of Texas at Austin, Austin, Texas, United States of America
| | - Ted Shi
- Department of Neuroscience, Waggoner Center for Alcohol and Addiction Research, Center for Learning and Memory, University of Texas at Austin, Austin, Texas, United States of America
| | - Alyssa Marron
- Department of Neuroscience, Waggoner Center for Alcohol and Addiction Research, Center for Learning and Memory, University of Texas at Austin, Austin, Texas, United States of America
| | - Ansley E. Fiorito
- Department of Neuroscience, Waggoner Center for Alcohol and Addiction Research, Center for Learning and Memory, University of Texas at Austin, Austin, Texas, United States of America
| | - Nima S. Rahman
- Department of Neuroscience, Waggoner Center for Alcohol and Addiction Research, Center for Learning and Memory, University of Texas at Austin, Austin, Texas, United States of America
| | - Stephanie Ro
- Department of Neuroscience, Waggoner Center for Alcohol and Addiction Research, Center for Learning and Memory, University of Texas at Austin, Austin, Texas, United States of America
| | - Dylan G. Sucich
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jonathan T. Pierce
- Department of Neuroscience, Waggoner Center for Alcohol and Addiction Research, Center for Learning and Memory, University of Texas at Austin, Austin, Texas, United States of America
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28
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Merchant M, Mata CP, Liu Y, Zhai H, Protasio AV, Modis Y. A bioactive phlebovirus-like envelope protein in a hookworm endogenous virus. SCIENCE ADVANCES 2022; 8:eabj6894. [PMID: 35544562 PMCID: PMC9094657 DOI: 10.1126/sciadv.abj6894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 03/25/2022] [Indexed: 05/02/2023]
Abstract
Endogenous viral elements (EVEs), accounting for 15% of our genome, serve as a genetic reservoir from which new genes can emerge. Nematode EVEs are particularly diverse and informative of virus evolution. We identify Atlas virus-an intact retrovirus-like EVE in the human hookworm Ancylostoma ceylanicum, with an envelope protein genetically related to GN-GC glycoproteins from the family Phenuiviridae. A cryo-EM structure of Atlas GC reveals a class II viral membrane fusion protein fold not previously seen in retroviruses. Atlas GC has the structural hallmarks of an active fusogen. Atlas GC trimers insert into membranes with endosomal lipid compositions and low pH. When expressed on the plasma membrane, Atlas GC has cell-cell fusion activity. With its preserved biological activities, Atlas GC has the potential to acquire a cellular function. Our work reveals structural plasticity in reverse-transcribing RNA viruses.
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Affiliation(s)
- Monique Merchant
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge CB2 0AW, UK
| | - Carlos P. Mata
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge CB2 0AW, UK
| | - Yangci Liu
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge CB2 0AW, UK
| | - Haoming Zhai
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge CB2 0AW, UK
| | - Anna V. Protasio
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
- Christ’s College, University of Cambridge, St Andrew’s Street, Cambridge, CB2 3BU, UK
| | - Yorgo Modis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge CB2 0AW, UK
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29
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Quarato P, Singh M, Bourdon L, Cecere G. Inheritance and maintenance of small RNA-mediated epigenetic effects. Bioessays 2022; 44:e2100284. [PMID: 35338497 DOI: 10.1002/bies.202100284] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/04/2022] [Accepted: 03/15/2022] [Indexed: 11/08/2022]
Abstract
Heritable traits are predominantly encoded within genomic DNA, but it is now appreciated that epigenetic information is also inherited through DNA methylation, histone modifications, and small RNAs. Several examples of transgenerational epigenetic inheritance of traits have been documented in plants and animals. These include even the inheritance of traits acquired through the soma during the life of an organism, implicating the transfer of epigenetic information via the germline to the next generation. Small RNAs appear to play a significant role in carrying epigenetic information across generations. This review focuses on how epigenetic information in the form of small RNAs is transmitted from the germline to the embryos through the gametes. We also consider how inherited epigenetic information is maintained across generations in a small RNA-dependent and independent manner. Finally, we discuss how epigenetic traits acquired from the soma can be inherited through small RNAs.
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Affiliation(s)
- Piergiuseppe Quarato
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Meetali Singh
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Loan Bourdon
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Germano Cecere
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
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30
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Wan QL, Meng X, Wang C, Dai W, Luo Z, Yin Z, Ju Z, Fu X, Yang J, Ye Q, Zhang ZH, Zhou Q. Histone H3K4me3 modification is a transgenerational epigenetic signal for lipid metabolism in Caenorhabditis elegans. Nat Commun 2022; 13:768. [PMID: 35140229 PMCID: PMC8828817 DOI: 10.1038/s41467-022-28469-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/20/2022] [Indexed: 11/09/2022] Open
Abstract
As a major risk factor to human health, obesity presents a massive burden to people and society. Interestingly, the obese status of parents can cause progeny's lipid accumulation through epigenetic inheritance in multiple species. To date, many questions remain as to how lipid accumulation leads to signals that are transmitted across generations. In this study, we establish a nematode model of C. elegans raised on a high-fat diet (HFD) that leads to measurable lipid accumulation, which can transmit the lipid accumulation signal to their multigenerational progeny. Using this model, we find that transcription factors DAF-16/FOXO and SBP-1/SREBP, nuclear receptors NHR-49 and NHR-80, and delta-9 desaturases (fat-5, fat-6, and fat-7) are required for transgenerational lipid accumulation. Additionally, histone H3K4 trimethylation (H3K4me3) marks lipid metabolism genes and increases their transcription response to multigenerational obesogenic effects. In summary, this study establishes an interaction between a network of lipid metabolic genes and chromatin modifications, which work together to achieve transgenerational epigenetic inheritance of obesogenic effects.
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Affiliation(s)
- Qin-Li Wan
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China.,Department of Pathogen Biology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Xiao Meng
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Chongyang Wang
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Wenyu Dai
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Zhenhuan Luo
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Zhinan Yin
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regeneration Medicine, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Xiaodie Fu
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Jing Yang
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Qunshan Ye
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Zhan-Hui Zhang
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Qinghua Zhou
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China. .,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China.
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31
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Molecular insights into transgenerational inheritance of stress memory. J Genet Genomics 2021; 49:89-95. [PMID: 34923165 DOI: 10.1016/j.jgg.2021.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/23/2022]
Abstract
There is accumulating evidence to show that environmental stressors can regulate a variety of phenotypes in descendants through germline-mediated epigenetic inheritance. Studies of model organisms exposed to environmental cues (e.g., diet, heat stress, toxins) indicate that altered DNA methylations, histone modifications, or non-coding RNAs in the germ cells are responsible for the transgenerational effects. In addition, it has also become evident that maternal provision could provide a mechanism for the transgenerational inheritance of stress adaptations that result from ancestral environmental cues. However, how the signal of environmentally-induced stress response transmits from the soma to the germline, which may influence offspring fitness, remains largely elusive. Small RNAs could serve as signaling molecules that transmit between tissues and even across generations. Furthermore, a recent study revealed that neuronal mitochondrial perturbations induce a transgenerational induction of the mitochondrial unfolded protein response mediated by a Wnt-dependent increase in mitochondrial DNA levels. Here, we review recent work on the molecular mechanism by which parental experience can affect future generations and the importance of soma-to-germline signaling for transgenerational inheritance.
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32
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Pujol N, Ewbank JJ. C. elegans: out on an evolutionary limb. Immunogenetics 2021; 74:63-73. [PMID: 34761293 DOI: 10.1007/s00251-021-01231-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
The natural environment of the free-living nematode Caenorhabditis elegans is rich in pathogenic microbes. There is now ample evidence to indicate that these pathogens exert a strong selection pressure on C. elegans, and have shaped its genome, physiology, and behaviour. In this short review, we concentrate on how C. elegans stands out from other animals in terms of its immune repertoire and innate immune signalling pathways. We discuss how C. elegans often detects pathogens because of their effects on essential cellular processes, or organelle integrity, in addition to direct microbial recognition. We illustrate the extensive molecular plasticity that is characteristic of immune defences in C. elegans and highlight some remarkable instances of lineage-specific innovation in innate immune mechanisms.
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Affiliation(s)
- Nathalie Pujol
- Aix Marseille Univ, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France.
| | - Jonathan J Ewbank
- Aix Marseille Univ, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France
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33
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An integrated view of innate immune mechanisms in C. elegans. Biochem Soc Trans 2021; 49:2307-2317. [PMID: 34623403 DOI: 10.1042/bst20210399] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022]
Abstract
The simple notion 'infection causes an immune response' is being progressively refined as it becomes clear that immune mechanisms cannot be understood in isolation, but need to be considered in a more global context with other cellular and physiological processes. In part, this reflects the deployment by pathogens of virulence factors that target diverse cellular processes, such as translation or mitochondrial respiration, often with great molecular specificity. It also reflects molecular cross-talk between a broad range of host signalling pathways. Studies with the model animal C. elegans have uncovered a range of examples wherein innate immune responses are intimately connected with different homeostatic mechanisms, and can influence reproduction, ageing and neurodegeneration, as well as various other aspects of its biology. Here we provide a short overview of a number of such connections, highlighting recent discoveries that further the construction of a fully integrated view of innate immunity.
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34
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Gowri V, Monteiro A. Inheritance of Acquired Traits in Insects and Other Animals and the Epigenetic Mechanisms That Break the Weismann Barrier. J Dev Biol 2021; 9:41. [PMID: 34698204 PMCID: PMC8544363 DOI: 10.3390/jdb9040041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/21/2021] [Accepted: 10/01/2021] [Indexed: 01/29/2023] Open
Abstract
The credibility of the Weismann barrier has come into question. Several studies in various animal systems, from mice to worms, have shown that novel environmental stimuli can generate an altered developmental or behavioral trait that can be transmitted to offspring of the following generation. Recently, insects have become ideal models to study the inheritance of acquired traits. This is because insects can be reared in high numbers at low cost, they have short generation times and produce abundant offspring. Numerous studies have shown that an insect can modify its phenotype in response to a novel stimulus to aid its survival, and also that this modified phenotypic trait can be inherited by its offspring. Epigenetic mechanisms are likely at play but, most studies do not address the mechanisms that underlie the inheritance of acquired traits in insects. Here we first review general epigenetic mechanisms such as DNA methylation, histone acetylation and small noncoding RNAs that have been implicated in the transmission of acquired traits in animals, then we focus on the few insect studies in which these mechanisms have been investigated.
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Affiliation(s)
- V. Gowri
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore;
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore;
- Science Division, Yale-NUS College, Singapore 138609, Singapore
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Rahmani A, Chew YL. Investigating the molecular mechanisms of learning and memory using Caenorhabditis elegans. J Neurochem 2021; 159:417-451. [PMID: 34528252 DOI: 10.1111/jnc.15510] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/15/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022]
Abstract
Learning is an essential biological process for survival since it facilitates behavioural plasticity in response to environmental changes. This process is mediated by a wide variety of genes, mostly expressed in the nervous system. Many studies have extensively explored the molecular and cellular mechanisms underlying learning and memory. This review will focus on the advances gained through the study of the nematode Caenorhabditis elegans. C. elegans provides an excellent system to study learning because of its genetic tractability, in addition to its invariant, compact nervous system (~300 neurons) that is well-characterised at the structural level. Importantly, despite its compact nature, the nematode nervous system possesses a high level of conservation with mammalian systems. These features allow the study of genes within specific sensory-, inter- and motor neurons, facilitating the interrogation of signalling pathways that mediate learning via defined neural circuits. This review will detail how learning and memory can be studied in C. elegans through behavioural paradigms that target distinct sensory modalities. We will also summarise recent studies describing mechanisms through which key molecular and cellular pathways are proposed to affect associative and non-associative forms of learning.
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Affiliation(s)
- Aelon Rahmani
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Yee Lian Chew
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
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