1
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Lei M, Tan Y, Ke J, Wang M, He Z, Ou G, Tu H, Tan W. Loss of cilia in chemosensory neurons inhibits pathogen avoidance in Caenorhabditis elegans. Microbes Infect 2024:105370. [PMID: 38843949 DOI: 10.1016/j.micinf.2024.105370] [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: 02/11/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/16/2024]
Abstract
Pathogen avoidance is a crucial and evolutionarily conserved behavior that enhances survival by preventing infection in diverse species, including Caenorhabditis elegans (C. elegans). This behavior relies on multiple chemosensory neurons equipped with cilia that are exposed to the external environment. However, the specific role of neuronal cilia in pathogen avoidance has not been completely elucidated. Herein, we discovered that osm-3(p802) mutants, which lack chemosensory neuronal cilia, exhibit slower avoidance of the pathogen Pseudomonas aeruginosa PA14, but not Escherichia coli OP50. This observation was consistent when osm-3(p802) mutants were exposed to P. aeruginosa PAO1. Following an encounter with PA14, the pumping, thrashing, and defecation behaviors of osm-3 mutants were comparable to those of the wild-type. However, the osm-3 mutants demonstrated reduced intestinal colonization of PA14, suggesting that they have stronger intestinal clearance ability. We conducted RNA-seq to identify genes responding to external stimuli that were differentially expressed owing to the loss of osm-3 and PA14 infection. Using RNAi, we demonstrated that three of these genes were essential for normal pathogen avoidance. In conclusion, our findings demonstrate that the loss of chemosensory neuronal cilia reduces pathogen avoidance in C. elegans while delaying intestinal colonization.
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Affiliation(s)
- Ming Lei
- Academy of Medical Engineering and Translational Medicine, 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
| | - Jingyi Ke
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Mengqi Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan, China
| | - Zeyang He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan, China
| | - Guangshuo Ou
- School of Life Sciences, Tsinghua University, Beijing, 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, 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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2
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Cao S, Chen ZJ. Transgenerational epigenetic inheritance during plant evolution and breeding. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00112-2. [PMID: 38806375 DOI: 10.1016/j.tplants.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/12/2024] [Accepted: 04/25/2024] [Indexed: 05/30/2024]
Abstract
Plants can program and reprogram their genomes to create genetic variation and epigenetic modifications, leading to phenotypic plasticity. Although consequences of genetic changes are comprehensible, the basis for transgenerational inheritance of epigenetic variation is elusive. This review addresses contributions of external (environmental) and internal (genomic) factors to the establishment and maintenance of epigenetic memory during plant evolution, crop domestication, and modern breeding. Dynamic and pervasive changes in DNA methylation and chromatin modifications provide a diverse repertoire of epigenetic variation potentially for transgenerational inheritance. Elucidating and harnessing epigenetic inheritance will help us develop innovative breeding strategies and biotechnological tools to improve crop yield and resilience in the face of environmental challenges. Beyond plants, epigenetic principles are shared across sexually reproducing organisms including humans with relevance to medicine and public health.
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Affiliation(s)
- Shuai Cao
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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3
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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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4
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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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5
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Vuscan P, Kischkel B, Joosten LAB, Netea MG. Trained immunity: General and emerging concepts. Immunol Rev 2024; 323:164-185. [PMID: 38551324 DOI: 10.1111/imr.13326] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/11/2024] [Indexed: 05/18/2024]
Abstract
Over the past decade, compelling evidence has unveiled previously overlooked adaptive characteristics of innate immune cells. Beyond their traditional role in providing short, non-specific protection against pathogens, innate immune cells can acquire antigen-agnostic memory, exhibiting increased responsiveness to secondary stimulation. This long-term de-facto innate immune memory, also termed trained immunity, is mediated through extensive metabolic rewiring and epigenetic modifications. While the upregulation of trained immunity proves advantageous in countering immune paralysis, its overactivation contributes to the pathogenesis of autoinflammatory and autoimmune disorders. In this review, we present the latest advancements in the field of innate immune memory followed by a description of the fundamental mechanisms underpinning trained immunity generation and different cell types that mediate it. Furthermore, we explore its implications for various diseases and examine current limitations and its potential therapeutic targeting in immune-related disorders.
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Affiliation(s)
- Patricia Vuscan
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Brenda Kischkel
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department for Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
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6
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He C, Lin X, Li P, Hou J, Yang M, Sun Z, Zhang S, Yang K, Lin D. Nematode Uptake Preference toward Different Nanoplastics through Avoidance Behavior Regulation. ACS NANO 2024; 18:11323-11334. [PMID: 38635335 DOI: 10.1021/acsnano.4c00736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Expounding bioaccumulation pathways of nanoplastics in organisms is a prerequisite for assessing their ecological risks in the context of global plastic pollution. Invertebrate uptake preference toward nanoplastics is a key initial step of nanoplastic food chain transport that controls their global biosafety, while the biological regulatory mechanism remains unclear. Here, we reveal a preferential uptake mechanism involving active avoidance of nanoplastics by Caenorhabditis elegans and demonstrate the relationship between the uptake preference and nanoplastic characteristics. Nanoplastics with 100 nm in size or positive surface charges induce stronger avoidance due to higher toxicity, causing lower accumulation in nematodes, compared to the 500 nm-sized or negatively charged nanoplastics, respectively. Further evidence showed that nematodes did not actively ingest any types of nanoplastics, while different nanoplastics induced defense responses in a toxicity-dependent manner and distinctly stimulated the avoidance behavior of nematodes (ranged from 15.8 to 68.7%). Transcriptomics and validations using mutants confirmed that the insulin/IGF signaling (IIS) pathway is essential for the selective avoidance of nanoplastics. Specifically, the activation of DAF-16 promoted the IIS pathway-mediated defense against nanoplastics and stimulated the avoidance behavior, increasing the survival chances of nematodes. Considering the genetical universality of this defense response among invertebrates, such an uptake preference toward certain nanoplastics could lead to cascaded risks in the ecosystem.
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Affiliation(s)
- Caijiao He
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Xintong Lin
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong China
| | - Pei Li
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Jie Hou
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Meirui Yang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Ziyi Sun
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Shuang Zhang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Kun Yang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Daohui Lin
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang Ecological Civilization Academy, Anji 313300, China
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7
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Pliota P, Marvanova H, Koreshova A, Kaufman Y, Tikanova P, Krogull D, Hagmüller A, Widen SA, Handler D, Gokcezade J, Duchek P, Brennecke J, Ben-David E, Burga A. Selfish conflict underlies RNA-mediated parent-of-origin effects. Nature 2024; 628:122-129. [PMID: 38448590 PMCID: PMC10990930 DOI: 10.1038/s41586-024-07155-z] [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: 11/21/2022] [Accepted: 02/02/2024] [Indexed: 03/08/2024]
Abstract
Genomic imprinting-the non-equivalence of maternal and paternal genomes-is a critical process that has evolved independently in many plant and mammalian species1,2. According to kinship theory, imprinting is the inevitable consequence of conflictive selective forces acting on differentially expressed parental alleles3,4. Yet, how these epigenetic differences evolve in the first place is poorly understood3,5,6. Here we report the identification and molecular dissection of a parent-of-origin effect on gene expression that might help to clarify this fundamental question. Toxin-antidote elements (TAs) are selfish elements that spread in populations by poisoning non-carrier individuals7-9. In reciprocal crosses between two Caenorhabditis tropicalis wild isolates, we found that the slow-1/grow-1 TA is specifically inactive when paternally inherited. This parent-of-origin effect stems from transcriptional repression of the slow-1 toxin by the PIWI-interacting RNA (piRNA) host defence pathway. The repression requires PIWI Argonaute and SET-32 histone methyltransferase activities and is transgenerationally inherited via small RNAs. Remarkably, when slow-1/grow-1 is maternally inherited, slow-1 repression is halted by a translation-independent role of its maternal mRNA. That is, slow-1 transcripts loaded into eggs-but not SLOW-1 protein-are necessary and sufficient to counteract piRNA-mediated repression. Our findings show that parent-of-origin effects can evolve by co-option of the piRNA pathway and hinder the spread of selfish genes that require sex for their propagation.
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Affiliation(s)
- Pinelopi Pliota
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Hana Marvanova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Alevtina Koreshova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Yotam Kaufman
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Polina Tikanova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Daniel Krogull
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Andreas Hagmüller
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Sonya A Widen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Joseph Gokcezade
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Eyal Ben-David
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Alejandro Burga
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
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8
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Cooper JF, Nguyen K, Gates D, Wolfrum E, Capan C, Lee H, Williams D, Okoye C, Wojtovich AP, Burton NO. Oocyte mitochondria link maternal environment to offspring phenotype. RESEARCH SQUARE 2024:rs.3.rs-4087193. [PMID: 38585755 PMCID: PMC10996803 DOI: 10.21203/rs.3.rs-4087193/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
During maturation oocytes undergo a recently discovered mitochondrial proteome remodeling event in flies1, frogs1, and humans2. This oocyte mitochondrial remodeling, which includes substantial changes in electron transport chain (ETC) subunit abundance1,2, is regulated by maternal insulin signaling1. Why oocytes undergo mitochondrial remodeling is unknown, with some speculating that it might be an evolutionarily conserved mechanism to protect oocytes from genotoxic damage by reactive oxygen species (ROS)2. In Caenorhabditis elegans, we previously found that maternal exposure to osmotic stress drives a 50-fold increase in offspring survival in response to future osmotic stress3. Like mitochondrial remodeling, we found that this intergenerational adaptation is also regulated by insulin signaling to oocytes3. Here, we used proteomics and genetic manipulations to show that insulin signaling to oocytes regulates offspring's ability to adapt to future stress via a mechanism that depends on ETC composition in maternal oocytes. Specifically, we found that maternally expressed mutant alleles of nduf-7 (complex I subunit) or isp-1 (complex III subunit) altered offspring's response to osmotic stress at hatching independently of offspring genotype. Furthermore, we found that expressing wild-type isp-1 in germ cells (oocytes) was sufficient to restore offspring's normal response to osmotic stress. Chemical mutagenesis screens revealed that maternal ETC composition regulates offspring's response to stress by altering AMP kinase function in offspring which in turn regulates both ATP and glycerol metabolism in response to continued osmotic stress. To our knowledge, these data are the first to show that proper oocyte ETC composition is required to link a mother's environment to adaptive changes in offspring metabolism. The data also raise the possibility that the reason diverse animals exhibit insulin regulated remodeling of oocyte mitochondria is to tailor offspring metabolism to best match the environment of their mother.
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Affiliation(s)
- Jason F. Cooper
- Van Andel Research Institute, Department of Metabolism and Nutritional Programing, Grand Rapids, Michigan, USA, 49503
| | - Kim Nguyen
- Van Andel Research Institute, Department of Metabolism and Nutritional Programing, Grand Rapids, Michigan, USA, 49503
| | - Darrick Gates
- Van Andel Research Institute, Department of Metabolism and Nutritional Programing, Grand Rapids, Michigan, USA, 49503
| | - Emily Wolfrum
- Van Andel Research Institute, Grand Rapids, Michigan, USA, 49503
| | - Colt Capan
- Van Andel Research Institute, Grand Rapids, Michigan, USA, 49503
| | - Hyoungjoo Lee
- Van Andel Research Institute, Grand Rapids, Michigan, USA, 49503
| | - Devia Williams
- Van Andel Research Institute, Department of Metabolism and Nutritional Programing, Grand Rapids, Michigan, USA, 49503
| | - Chidozie Okoye
- University of Rochester Medical Center, Department of Anaesthesiology and Perioperative Medicine, 575 Elmwood Ave., Rochester, NY, 14642, Box 711/604, USA
| | - Andrew P Wojtovich
- University of Rochester Medical Center, Department of Anaesthesiology and Perioperative Medicine, 575 Elmwood Ave., Rochester, NY, 14642, Box 711/604, USA
| | - Nicholas O. Burton
- Van Andel Research Institute, Department of Metabolism and Nutritional Programing, Grand Rapids, Michigan, USA, 49503
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9
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Brissette B, Ficaro L, Li C, Jones DR, Ramanathan S, Ringstad N. Chemosensory detection of polyamine metabolites guides C. elegans to nutritive microbes. SCIENCE ADVANCES 2024; 10:eadj4387. [PMID: 38517971 PMCID: PMC10959419 DOI: 10.1126/sciadv.adj4387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
Much is known about molecular mechanisms by which animals detect pathogenic microbes, but how animals sense beneficial microbes remains poorly understood. The roundworm Caenorhabditis elegans is a microbivore that must distinguish nutritive microbes from pathogens. We characterized a neural circuit used by C. elegans to rapidly discriminate between nutritive bacteria and pathogens. Distinct sensory neuron populations responded to chemical cues from nutritive Escherichia coli and pathogenic Enterococcus faecalis, and these neural signals are decoded by downstream AIB interneurons. The polyamine metabolites cadaverine, putrescine, and spermidine produced by E. coli activate this neural circuit and elicit positive chemotaxis. Our study shows how polyamine odorants can be sensed by animals as proxies for microbe identity and suggests that, hence, polyamines might have widespread roles brokering host-microbe interactions.
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Affiliation(s)
- Benjamin Brissette
- Department of Cell Biology, Neuroscience and Physiology, Neuroscience Institute, NYU School of Medicine, New York, NY 10016, USA
| | - Lia Ficaro
- Department of Biochemistry and Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Chenguang Li
- Biophysics Program, Harvard University, Cambridge, MA 02138, USA
| | - Drew R. Jones
- Department of Biochemistry and Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Sharad Ramanathan
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Niels Ringstad
- Department of Cell Biology, Neuroscience and Physiology, Neuroscience Institute, NYU School of Medicine, New York, NY 10016, USA
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10
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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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11
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Tran TD, Luallen RJ. An organismal understanding of C. elegans innate immune responses, from pathogen recognition to multigenerational resistance. Semin Cell Dev Biol 2024; 154:77-84. [PMID: 36966075 PMCID: PMC10517082 DOI: 10.1016/j.semcdb.2023.03.005] [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] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/05/2023] [Accepted: 03/14/2023] [Indexed: 03/27/2023]
Abstract
The nematode Caenorhabditis elegans has been a model for studying infection since the early 2000s and many major discoveries have been made regarding its innate immune responses. C. elegans has been found to utilize some key conserved aspects of immune responses and signaling, but new interesting features of innate immunity have also been discovered in the organism that might have broader implications in higher eukaryotes such as mammals. Some of the distinctive features of C. elegans innate immunity involve the mechanisms this bacterivore uses to detect infection and mount specific immune responses to different pathogens, despite lacking putative orthologs of many important innate immune components, including cellular immunity, the inflammasome, complement, or melanization. Even when orthologs of known immune factors exist, there appears to be an absence of canonical functions, most notably the lack of pattern recognition by its sole Toll-like receptor. Instead, recent research suggests that C. elegans senses infection by specific pathogens through contextual information, including unique products produced by the pathogen or infection-induced disruption of host physiology, similar to the proposed detection of patterns of pathogenesis in mammalian systems. Interestingly, C. elegans can also transfer information of past infection to their progeny, providing robust protection for their offspring in face of persisting pathogens, in part through the RNAi pathway as well as potential new mechanisms that remain to be elucidated. Altogether, some of these strategies employed by C. elegans share key conceptual features with vertebrate adaptive immunity, as the animal can differentiate specific microbial features, as well as propagate a form of immune memory to their offspring.
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Affiliation(s)
- Tuan D Tran
- Department of Biology San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA
| | - Robert J Luallen
- Department of Biology San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA.
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12
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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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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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Ange JS, Weng Y, Stevenson ME, Kaletsky R, Moore RS, Zhou S, Murphy CT. Adult Single-nucleus Neuronal Transcriptomes of Insulin Signaling Mutants Reveal Regulators of Behavior and Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579364. [PMID: 38370779 PMCID: PMC10871314 DOI: 10.1101/2024.02.07.579364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The insulin/insulin-like signaling (IIS) pathway regulates many of C. elegans' adult functions, including learning and memory 1 . While whole-worm and tissue-specific transcriptomic analyses have identified IIS targets 2,3 , a higher-resolution single-cell approach is required to identify changes that confer neuron-specific improvements in the long-lived insulin receptor mutant, daf-2 . To understand how behaviors that are controlled by a small number of neurons change in daf-2 mutants, we used the deep resolution of single-nucleus RNA sequencing to define each neuron type's transcriptome in adult wild-type and daf-2 mutants. First, we found surprising differences between wild-type L4 larval neurons and young adult neurons in chemoreceptor expression, synaptic genes, and learning and memory genes. These Day 1 adult neuron transcriptomes allowed us to identify adult AWC-specific regulators of chemosensory function and to predict neuron-to-neuron peptide/receptor pairs. We then identified gene expression changes that correlate with daf-2's improved cognitive functions, particularly in the AWC sensory neuron that controls learning and associative memory 4 , and used behavioral assays to test their roles in cognitive function. Combining deep single-neuron transcriptomics, genetic manipulation, and behavioral analyses enabled us to identify genes that may function in a single adult neuron to control behavior, including conserved genes that function in learning and memory. One-Sentence Summary Single-nucleus sequencing of adult wild-type and daf-2 C. elegans neurons reveals functionally relevant transcriptional changes, including regulators of chemosensation, learning, and memory.
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Webster AK, Phillips PC. Heritable epigenetic variation facilitates long-term maintenance of epigenetic and genetic variation. G3 (BETHESDA, MD.) 2024; 14:jkad287. [PMID: 38113034 PMCID: PMC10849368 DOI: 10.1093/g3journal/jkad287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/03/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023]
Abstract
How genetic and phenotypic variation are maintained has long been one of the fundamental questions in population and quantitative genetics. A variety of factors have been implicated to explain the maintenance of genetic variation in some contexts (e.g. balancing selection), but the potential role of epigenetic regulation to influence population dynamics has been understudied. It is well recognized that epigenetic regulation, including histone methylation, small RNA expression, and DNA methylation, helps to define differences between cell types and facilitate phenotypic plasticity. In recent years, empirical studies have shown the potential for epigenetic regulation to also be heritable for at least a few generations without selection, raising the possibility that differences in epigenetic regulation can act alongside genetic variation to shape evolutionary trajectories. Heritable differences in epigenetic regulation that arise spontaneously are termed "epimutations." Epimutations differ from genetic mutations in 2 key ways-they occur at a higher rate and the loci at which they occur often revert back to their original state within a few generations. Here, we present an extension of the standard population genetic model with selection to incorporate epigenetic variation arising via epimutation. Our model assumes a diploid, sexually reproducing population with random mating. In addition to spontaneous genetic mutation, we included parameters for spontaneous epimutation and back-epimutation, allowing for 4 potential epialleles at a single locus (2 genetic alleles, each with 2 epigenetic states), each of which affect fitness. We then analyzed the conditions under which stable epialleles were maintained. Our results show that highly reversible epialleles can be maintained in long-term equilibrium under neutral conditions in a manner that depends on the epimutation and back-epimutation rates, which we term epimutation-back-epimutation equilibrium. On the other hand, epialleles that compensate for deleterious mutations cause deviations from the expectations of mutation-selection balance by a simple factor that depends on the epimutation and back-epimutation rates. We also numerically analyze several sets of fitness parameters for which large deviations from mutation-selection balance occur. Together, these results demonstrate that transient epigenetic regulation may be an important factor in the maintenance of both epigenetic and genetic variation in populations.
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Affiliation(s)
- Amy K Webster
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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16
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Hellmann JK, Keagy J, Carlson ER, Kempfer S, Bell AM. Predator-induced transgenerational plasticity of parental care behaviour in male three-spined stickleback fish across two generations. Proc Biol Sci 2024; 291:20232582. [PMID: 38196352 PMCID: PMC10777160 DOI: 10.1098/rspb.2023.2582] [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: 06/15/2023] [Accepted: 11/29/2023] [Indexed: 01/11/2024] Open
Abstract
Parental care is a critical determinant of offspring fitness, and parents adjust their care in response to ecological challenges, including predation risk. The experiences of both mothers and fathers can influence phenotypes of future generations (transgenerational plasticity). If it is adaptive for parents to alter parental care in response to predation risk, then we expect F1 and F2 offspring who receive transgenerational cues of predation risk to shift their parental care behaviour if these ancestral cues reliably predict a similarly risky environment as their F0 parents. Here, we used three-spined sticklebacks (Gasterosteus aculeatus) to understand how paternal exposure to predation risk prior to mating alters reproductive traits and parental care behaviour in unexposed F1 sons and F2 grandsons. Sons of predator-exposed fathers took more attempts to mate than sons of control fathers. F1 sons and F2 grandsons with two (maternal and paternal) predator-exposed grandfathers shifted their paternal care (fanning) behaviour in strikingly similar ways: they fanned less initially, but fanned more near egg hatching. This shift in fanning behaviour matches shifts observed in response to direct exposure to predation risk, suggesting a highly conserved response to pre-fertilization predator exposure that persists from the F0 to the F1 and F2 generations.
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Affiliation(s)
- Jennifer K. Hellmann
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Jason Keagy
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Erika R. Carlson
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Shayne Kempfer
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Alison M. Bell
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Program in Ecology, Evolution and Conservation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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17
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Dias BG. Legacies of salient environmental experiences-insights from chemosensation. Chem Senses 2024; 49:bjae002. [PMID: 38219073 PMCID: PMC10825851 DOI: 10.1093/chemse/bjae002] [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: 06/23/2023] [Indexed: 01/15/2024] Open
Abstract
Evidence for parental environments profoundly influencing the physiology, biology, and neurobiology of future generations has been accumulating in the literature. Recent efforts to understand this phenomenon and its underlying mechanisms have sought to use species like rodents and insects to model multi-generational legacies of parental experiences like stress and nutritional exposures. From these studies, we have come to appreciate that parental exposure to salient environmental experiences impacts the cadence of brain development, hormonal responses to stress, and the expression of genes that govern cellular responses to stress in offspring. Recent studies using chemosensory exposure have emerged as a powerful tool to shed new light on how future generations come to be influenced by environments to which parents are exposed. With a specific focus on studies that have leveraged such use of salient chemosensory experiences, this review synthesizes our current understanding of the concept, causes, and consequences of the inheritance of chemosensory legacies by future generations and how this field of inquiry informs the larger picture of how parental experiences can influence offspring biology.
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Affiliation(s)
- Brian G Dias
- Developmental Neuroscience and Neurogenetics Program, The Saban Research Institute, Los Angeles, CA, United States
- Division of Endocrinology, Diabetes and Metabolism, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Department of Pediatrics, Keck School of Medicine of USC, Los Angeles, CA, United States
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18
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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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Zhao Y, Zhong C, Li Y, Zhou W, Huang X. Novel Genes and Key Signaling Molecules Involved in the Repulsive Response of Meloidogyne incognita against Biocontrol Bacteria. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19445-19456. [PMID: 38033160 DOI: 10.1021/acs.jafc.3c06074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
The ability of the model organism, Caenorhabditis elegans, to distinguish and escape from pathogenic bacteria has been extensively studied; however, studies on the repulsive response of Meloidogyne incognita are still in their infancy. We have recently demonstrated that biocontrol bacteria induce a repulsive response in M. incognita via two classical signaling pathways. The present study aimed to identify the novel genes and signaling molecules of M. incognita that potentially contribute to its defense reaction. Analysis of the transcriptome data of M. incognita with and without a repulsive response against Bacillus nematocida B16 obtained 15 candidate genes, of which the novel genes Minc3s01748g26034 and Minc3s02548g30585 were found to regulate the aversive behavior of M. incognita, and their functions were further validated. To further confirm the neuronal localization of the two novel genes in M. incognita, in situ hybridization was conducted using the digoxin-labeled probes of ten tag genes, and preferentially profiled the localization of amphid sensory neurons of M. incognita. Analysis of the overviewed neuronal map suggested that Minc3s01748g26034 and Minc3s02548g30585 functioned in ASK/ASI and CEPD/V neurons, respectively. During their interactions, the volatile compounds 3-methyl-butyric acid and 2-methyl-butyric acid produced by the biocontrol bacteria were predicted as the primary signaling molecules that promoted the repulsive behavior of M. incognita against biocontrol bacteria. The findings provided novel insights into the mechanisms underlying the repulsive response of M. incognita that are different from the canonical molecular pathways previously found in C. elegans and can aid in developing novel strategies for controlling root-knot nematodes.
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Affiliation(s)
- Yanli Zhao
- School of Medicine, and State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China
| | - Chidi Zhong
- School of Medicine, and State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China
| | - Yixin Li
- School of Medicine, and State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China
| | - Wenhui Zhou
- School of Medicine, and State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China
| | - Xiaowei Huang
- School of Medicine, and State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China
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20
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Frézal L, Saglio M, Zhang G, Noble L, Richaud A, Félix MA. Genome-wide association and environmental suppression of the mortal germline phenotype of wild C. elegans. EMBO Rep 2023; 24:e58116. [PMID: 37983674 DOI: 10.15252/embr.202358116] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/19/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023] Open
Abstract
The animal germline lineage needs to be maintained along generations. However, some Caenorhabditis elegans wild isolates display a mortal germline phenotype, leading to sterility after several generations at 25°C. Using a genome-wide association approach, we detect a significant peak on chromosome III around 5 Mb, confirmed by introgressions. Thus, a seemingly deleterious genotype is maintained at intermediate frequency in the species. Environmental rescue is a likely explanation, and indeed associated bacteria and microsporidia suppress the phenotype of wild isolates as well as mutants in small RNA inheritance (nrde-2) and histone modifications (set-2). Escherichia coli strains of the K-12 lineage suppress the phenotype compared to B strains. By shifting a wild strain from E. coli K-12 to E. coli B, we find that memory of the suppressing condition is maintained over several generations. Thus, the mortal germline phenotype of wild C. elegans is in part revealed by laboratory conditions and may represent variation in epigenetic inheritance and environmental interactions. This study also points to the importance of non-genetic memory in the face of environmental variation.
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Affiliation(s)
- Lise Frézal
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Marie Saglio
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Gaotian Zhang
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Luke Noble
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Aurélien Richaud
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
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21
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Yeoh WJ, Krebs P. SHIP1 and its role for innate immune regulation-Novel targets for immunotherapy. Eur J Immunol 2023; 53:e2350446. [PMID: 37742135 DOI: 10.1002/eji.202350446] [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: 06/15/2023] [Revised: 08/03/2023] [Accepted: 09/21/2023] [Indexed: 09/25/2023]
Abstract
Phosphoinositide-3-kinase/AKT (PI3K/AKT) signaling plays key roles in the regulation of cellular activity in both health and disease. In immune cells, this PI3K/AKT pathway is critically regulated by the phosphoinositide phosphatase SHIP1, which has been reported to modulate the function of most immune subsets. In this review, we summarize our current knowledge of SHIP1 with a focus on innate immune cells, where we reflect on the most pertinent aspects described in the current literature. We also present several small-molecule agonists and antagonists of SHIP1 developed over the last two decades, which have led to improved outcomes in several preclinical models of disease. We outline these promising findings and put them in relation to human diseases with unmet medical needs, where we discuss the most attractive targets for immune therapies based on SHIP1 modulation.
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Affiliation(s)
- Wen Jie Yeoh
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Philippe Krebs
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
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22
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Vedor JE. Revisiting Carl Jung's archetype theory a psychobiological approach. Biosystems 2023; 234:105059. [PMID: 37832929 DOI: 10.1016/j.biosystems.2023.105059] [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: 08/09/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
This paper delves into the concept of archetypes, universal patterns of behavior and cognition, and proposes a novel tripartite model distinguishing between structural, regulatory, and representational archetypes. Drawing on insights from code biology, neuroscience, genetics, and epigenetics, the model provides a nuanced framework for understanding archetypes and their role in shaping cognition and behavior. The paper also explores the interplay between these elements to express representational archetypes. Furthermore, it addresses the informational capacity of the genome and its influence on post-natal development and the psyche. The paper concludes by discussing the future trajectory of psychology, emphasizing the need for an integrative approach that combines our understanding of social constructs with insights into our inherent organizational propensities or archetypes. This exploration holds the potential to advance our understanding of the human condition.
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23
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Marogi JG, Murphy CT, Myhrvold C, Gitai Z. P. aeruginosa controls both C. elegans attraction and pathogenesis by regulating nitrogen assimilation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569279. [PMID: 38077073 PMCID: PMC10705433 DOI: 10.1101/2023.11.29.569279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2024]
Abstract
Detecting chemical signals is important for identifying food sources and avoiding harmful agents. Like most animals, C. elegans use olfaction to chemotax towards their main food source, bacteria. However, little is known about the bacterial compounds governing C. elegans attraction to bacteria and the physiological importance of these compounds to bacteria. Here, we address these questions by investigating the function of a small RNA, P11, in the pathogen, Pseudomonas aeruginosa, that was previously shown to mediate learned pathogen avoidance. We discovered that this RNA also affects the attraction of untrained C. elegans to P. aeruginosa and does so by controlling production of ammonia, a volatile odorant produced during nitrogen assimilation. We untangle the complex regulation of P. aeruginosa nitrogen assimilation, which is mediated by a partner-switching mechanism involving environmental nitrates, sensor proteins, and P11. In addition to mediating C. elegans attraction, nitrogen assimilation is important for bacterial fitness and pathogenesis during C. elegans infection by P. aeruginosa . These studies define ammonia as a major mediator of trans-kingdom signaling, reveal the physiological importance of nitrogen assimilation for both bacteria and host organisms, and highlight how a bacterial metabolic pathway can either benefit or harm a host in different contexts.
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Tando Y, Matsui Y. Inheritance of environment-induced phenotypic changes through epigenetic mechanisms. ENVIRONMENTAL EPIGENETICS 2023; 9:dvad008. [PMID: 38094661 PMCID: PMC10719065 DOI: 10.1093/eep/dvad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 03/08/2024]
Abstract
Growing evidence suggests that epigenetic changes through various parental environmental factors alter the phenotypes of descendants in various organisms. Environmental factors, including exposure to chemicals, stress and abnormal nutrition, affect the epigenome in parental germ cells by different epigenetic mechanisms, such as DNA methylation, histone modification as well as small RNAs via metabolites. Some current remaining questions are the causal relationship between environment-induced epigenetic changes in germ cells and altered phenotypes of descendants, and the molecular basis of how the abnormal epigenetic changes escape reprogramming in germ cells. In this review, we introduce representative examples of intergenerational and transgenerational inheritance of phenotypic changes through parental environmental factors and the accompanied epigenetic and metabolic changes, with a focus on animal species. We also discuss the molecular mechanisms of epigenomic inheritance and their possible biological significance.
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Affiliation(s)
- Yukiko Tando
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 980-8575, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Yasuhisa Matsui
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 980-8575, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
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25
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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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26
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Huang X, Wang C, Zhang T, Li R, Chen L, Leung KL, Lakso M, Zhou Q, Zhang H, Wong G. PIWI-interacting RNA expression regulates pathogenesis in a Caenorhabditis elegans model of Lewy body disease. Nat Commun 2023; 14:6137. [PMID: 37783675 PMCID: PMC10545829 DOI: 10.1038/s41467-023-41881-8] [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: 01/16/2022] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that regulate gene expression, yet their molecular functions in neurobiology are unclear. While investigating neurodegeneration mechanisms using human α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg pan-neuronal overexpressing strains, we unexpectedly observed dysregulation of piRNAs. RNAi screening revealed that knock down of piRNA biogenesis genes improved thrashing behavior; further, a tofu-1 gene deletion ameliorated phenotypic deficits in α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg transgenic strains. piRNA expression was extensively downregulated and H3K9me3 marks were decreased after tofu-1 deletion in α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg strains. Dysregulated piRNAs targeted protein degradation genes suggesting that a decrease of piRNA expression leads to an increase of degradation ability in C. elegans. Finally, we interrogated piRNA expression in brain samples from PD patients. piRNAs were observed to be widely overexpressed at late motor stage. In this work, our results provide evidence that piRNAs are mediators in pathogenesis of Lewy body diseases and suggest a molecular mechanism for neurodegeneration in these and related disorders.
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Affiliation(s)
- Xiaobing Huang
- 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, China
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Changliang Wang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
- GMU-GIBH Joint School of Life Sciences, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, 510799, China
| | - Tianjiao Zhang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Rongzhen Li
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Liang Chen
- Department of Computer Science, College of Engineering, Shantou University, Shantou, 515063, China
| | - Ka Lai Leung
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Merja Lakso
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Qinghua Zhou
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
- Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, China
| | - Hongjie Zhang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Garry Wong
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China.
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Wibisono P, Sun J. Pathogen infection induces specific transgenerational modifications to gene expression and fitness in Caenorhabditis elegans. Front Physiol 2023; 14:1225858. [PMID: 37811492 PMCID: PMC10556243 DOI: 10.3389/fphys.2023.1225858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/12/2023] [Indexed: 10/10/2023] Open
Abstract
How pathogen infection in a parental generation affects response in future generations to the same pathogen via epigenetic modifications has been the topic of recent studies. These studies focused on changes attributed to transgenerational epigenetic inheritance and how these changes cause an observable difference in behavior or immune response in a population. However, we questioned if pathogen infection causes hidden epigenetic changes to fitness that are not observable at the population level. Using the nematode Caenorhabditis elegans as a model organism, we examined the generation-to-generation differences in survival of both an unexposed and primed lineage of animals against a human opportunistic pathogen Salmonella enterica. We discovered that training a lineage of C. elegans against a specific pathogen does not cause a significant change to overall survival, but rather narrows survival variability between generations. Quantification of gene expression revealed reduced variation of a specific member of the TFEB lipophagic pathway. We also provided the first report of a repeating pattern of survival times over the course of 12 generations in the control lineage of C. elegans. This repeating pattern indicates that the variability in survival between generations of the control lineage is not random but may be regulated by unknown mechanisms. Overall, our study indicates that pathogen infection can cause specific phenotypic changes due to epigenetic modifications, and a possible system of epigenetic regulation between generations.
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Affiliation(s)
- Phillip Wibisono
- Department of Translational Medicine and Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Jingru Sun
- Department of Translational Medicine and Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
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28
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Zhao M, Lin Z, Zheng Z, Yao D, Yang S, Zhao Y, Chen X, Aweya JJ, Zhang Y. The mechanisms and factors that induce trained immunity in arthropods and mollusks. Front Immunol 2023; 14:1241934. [PMID: 37744346 PMCID: PMC10513178 DOI: 10.3389/fimmu.2023.1241934] [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: 06/17/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023] Open
Abstract
Besides dividing the organism's immune system into adaptive and innate immunity, it has long been thought that only adaptive immunity can establish immune memory. However, many studies have shown that innate immunity can also build immunological memory through epigenetic reprogramming and modifications to resist pathogens' reinfection, known as trained immunity. This paper reviews the role of mitochondrial metabolism and epigenetic modifications and describes the molecular foundation in the trained immunity of arthropods and mollusks. Mitochondrial metabolism and epigenetic modifications complement each other and play a key role in trained immunity.
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Affiliation(s)
- Mingming Zhao
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Zhongyang Lin
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Zhihong Zheng
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Defu Yao
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Shen Yang
- College of Ocean Food and Biological Engineering, Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, Fujian, China
| | - Yongzhen Zhao
- Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, China
| | - Xiuli Chen
- Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, China
| | - Jude Juventus Aweya
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
- College of Ocean Food and Biological Engineering, Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, Fujian, China
| | - Yueling Zhang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
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29
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Yamamoto KK, Savage-Dunn C. TGF-β pathways in aging and immunity: lessons from Caenorhabditis elegans. Front Genet 2023; 14:1220068. [PMID: 37732316 PMCID: PMC10507863 DOI: 10.3389/fgene.2023.1220068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/23/2023] [Indexed: 09/22/2023] Open
Abstract
The Transforming Growth Factor-β (TGF-β) superfamily of signaling molecules plays critical roles in development, differentiation, homeostasis, and disease. Due to the conservation of these ligands and their signaling pathways, genetic studies in invertebrate systems including the nematode Caenorhabditis elegans have been instrumental in identifying signaling mechanisms. C. elegans is also a premier organism for research in longevity and healthy aging. Here we summarize current knowledge on the roles of TGF-β signaling in aging and immunity.
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Affiliation(s)
| | - Cathy Savage-Dunn
- Department of Biology, Queens College, and PhD Program in Biology, The Graduate Center, City University of New York, New York City, NY, United States
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30
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De-Souza EA, Thompson MA, Taylor RC. Olfactory chemosensation extends lifespan through TGF-β signaling and UPR activation. NATURE AGING 2023; 3:938-947. [PMID: 37500972 PMCID: PMC10432268 DOI: 10.1038/s43587-023-00467-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
Animals rely on chemosensory cues to survive in pathogen-rich environments. In Caenorhabditis elegans, pathogenic bacteria trigger aversive behaviors through neuronal perception and activate molecular defenses throughout the animal. This suggests that neurons can coordinate the activation of organism-wide defensive responses upon pathogen perception. In this study, we found that exposure to volatile pathogen-associated compounds induces activation of the endoplasmic reticulum unfolded protein response (UPRER) in peripheral tissues after xbp-1 splicing in neurons. This odorant-induced UPRER activation is dependent upon DAF-7/transforming growth factor beta (TGF-β) signaling and leads to extended lifespan and enhanced clearance of toxic proteins. Notably, rescue of the DAF-1 TGF-β receptor in RIM/RIC interneurons is sufficient to significantly recover UPRER activation upon 1-undecene exposure. Our data suggest that the cell non-autonomous UPRER rewires organismal proteostasis in response to pathogen detection, pre-empting proteotoxic stress. Thus, chemosensation of particular odors may be a route to manipulation of stress responses and longevity.
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Affiliation(s)
- Evandro A De-Souza
- Neurobiology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Maximillian A Thompson
- Neurobiology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Rebecca C Taylor
- Neurobiology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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31
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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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32
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Abay-Nørgaard S, Tapia MC, Zeijdner M, Kim JH, Won KJ, Porse B, Salcini AE. Inter and transgenerational impact of H3K4 methylation in neuronal homeostasis. Life Sci Alliance 2023; 6:e202301970. [PMID: 37225426 PMCID: PMC10209521 DOI: 10.26508/lsa.202301970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023] Open
Abstract
Epigenetic marks and associated traits can be transmitted for one or more generations, phenomena known respectively as inter- or transgenerational epigenetic inheritance. It remains unknown if genetically and conditionally induced aberrant epigenetic states can influence the development of the nervous system across generations. Here, we show, using Caenorhabditis elegans as a model system, that alteration of H3K4me3 levels in the parental generation, caused by genetic manipulation or changes in parental conditions, has, respectively, trans- and intergenerational effects on H3K4 methylome, transcriptome, and nervous system development. Thus, our study reveals the relevance of H3K4me3 transmission and maintenance in preventing long-lasting deleterious effects in nervous system homeostasis.
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Affiliation(s)
- Steffen Abay-Nørgaard
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marta Cecylia Tapia
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Mandoh Zeijdner
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeonghwan Henry Kim
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kyoung Jae Won
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bo Porse
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anna Elisabetta Salcini
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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33
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Silva-García CG. Devo-Aging: Intersections Between Development and Aging. GeroScience 2023; 45:2145-2159. [PMID: 37160658 PMCID: PMC10651630 DOI: 10.1007/s11357-023-00809-2] [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: 12/30/2022] [Accepted: 04/25/2023] [Indexed: 05/11/2023] Open
Abstract
There are two fundamental questions in developmental biology. How does a single fertilized cell give rise to a whole body? and how does this body later produce progeny? Synchronization of these embryonic and postembryonic developments ensures continuity of life from one generation to the next. An enormous amount of work has been done to unravel the molecular mechanisms behind these processes, but more recently, modern developmental biology has been expanded to study development in wider contexts, including regeneration, environment, disease, and even aging. However, we have just started to understand how the mechanisms that govern development also regulate aging. This review discusses examples of signaling pathways involved in development to elucidate how their regulation influences healthspan and lifespan. Therefore, a better knowledge of developmental signaling pathways stresses the possibility of using them as innovative biomarkers and targets for aging and age-related diseases.
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Affiliation(s)
- Carlos Giovanni Silva-García
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA.
- Center on the Biology of Aging, Brown University, Providence, RI, USA.
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34
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Deshe N, Eliezer Y, Hoch L, Itskovits E, Bokman E, Ben-Ezra S, Zaslaver A. Inheritance of associative memories and acquired cellular changes in C. elegans. Nat Commun 2023; 14:4232. [PMID: 37454110 PMCID: PMC10349803 DOI: 10.1038/s41467-023-39804-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 06/27/2023] [Indexed: 07/18/2023] Open
Abstract
Experiences have been shown to modulate behavior and physiology of future generations in some contexts, but there is limited evidence for inheritance of associative memory in different species. Here, we trained C. elegans nematodes to associate an attractive odorant with stressful starvation conditions and revealed that this associative memory was transmitted to the F1 progeny who showed odor-evoked avoidance behavior. Moreover, the F1 and the F2 descendants of trained animals exhibited odor-evoked cellular stress responses, manifested by the translocation of DAF-16/FOXO to cells' nuclei. Sperm, but not oocytes, transmitted these odor-evoked cellular stress responses which involved H3K9 and H3K36 methylations, the small RNA pathway machinery, and intact neuropeptide secretion. Activation of a single chemosensory neuron sufficed to induce a serotonin-mediated systemic stress response in both the parental trained generation and in its progeny. Moreover, inheritance of the cellular stress responses increased survival chances of the progeny as exposure to the training odorant allowed the animals to prepare in advance for an impending adversity. These findings suggest that in C. elegans associative memories and cellular changes may be transferred across generations.
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Affiliation(s)
- Noa Deshe
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Yifat Eliezer
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Lihi Hoch
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Eyal Itskovits
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Eduard Bokman
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Shachaf Ben-Ezra
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Alon Zaslaver
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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35
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Becerra D, Calixto A, Orio P. The Conscious Nematode: Exploring Hallmarks of Minimal Phenomenal Consciousness in Caenorhabditis Elegans. Int J Psychol Res (Medellin) 2023; 16:87-104. [PMID: 38106963 PMCID: PMC10723751 DOI: 10.21500/20112084.6487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/21/2022] [Accepted: 03/13/2023] [Indexed: 12/19/2023] Open
Abstract
While subcellular components of cognition and affectivity that involve the interaction between experience, environment, and physiology -such as learning, trauma, or emotion- are being identified, the physical mechanisms of phenomenal consciousness remain more elusive. We are interested in exploring whether ancient, simpler organisms such as nematodes have minimal consciousness. Is there something that feels like to be a worm? Or are worms blind machines? 'Simpler' models allow us to simultaneously extract data from multiple levels such as slow and fast neural dynamics, structural connectivity, molecular dynamics, behavior, decision making, etc., and thus, to test predictions of the current frameworks in dispute. In the present critical review, we summarize the current models of consciousness in order to reassess in light of the new evidence whether Caenorhabditis elegans, a nematode with a nervous system composed of 302 neurons, has minimal consciousness. We also suggest empirical paths to further advance consciousness research using C. elegans.
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Affiliation(s)
- Diego Becerra
- Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile.Universidad de ValparaísoUniversidad de ValparaísoValparaísoChile
- Doctorado en Ciencias, mención Biofísica y Biología Computacional, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile.Universidad de ValparaísoUniversidad de ValparaísoValparaísoChile
| | - Andrea Calixto
- Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile.Universidad de ValparaísoUniversidad de ValparaísoValparaísoChile
- Instituto de Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile.Universidad de ValparaísoUniversidad de ValparaísoValparaísoChile
| | - Patricio Orio
- Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile.Universidad de ValparaísoUniversidad de ValparaísoValparaísoChile
- Instituto de Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile.Universidad de ValparaísoUniversidad de ValparaísoValparaísoChile
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36
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Cabej NR. On the origin and nature of nongenetic information in eumetazoans. Ann N Y Acad Sci 2023. [PMID: 37154677 DOI: 10.1111/nyas.15001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nongenetic information implies all the forms of biological information not related to genes and DNA in general. Despite the deep scientific relevance of the concept, we currently lack reliable knowledge about its carriers and origins; hence, we still do not understand its true nature. Given that genes are the targets of nongenetic information, it appears that a parsimonious approach to find the ultimate source of that information is to trace back the sequential steps of the causal chain upstream of the target genes up to the ultimate link as the source of the nongenetic information. From this perspective, I examine seven nongenetically determined phenomena: placement of locus-specific epigenetic marks on DNA and histones, changes in snRNA expression patterns, neural induction of gene expression, site-specific alternative gene splicing, predator-induced morphological changes, and cultural inheritance. Based on the available evidence, I propose a general model of the common neural origin of all these forms of nongenetic information in eumetazoans.
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Affiliation(s)
- Nelson R Cabej
- Department of Biology, University of Tirana, Tirana, Albania
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Liu L, Wang X, Zhao W, Li Q, Li J, Chen H, Shan G. Systematic characterization of small RNAs associated with C. elegans Argonautes. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2304-8. [PMID: 37154856 DOI: 10.1007/s11427-022-2304-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/28/2022] [Indexed: 05/10/2023]
Abstract
Argonaute proteins generally play regulatory roles by forming complexes with the corresponding small RNAs (sRNAs). An expanded Argonaute family with 20 potentially functional members has been identified in Caenorhabditis elegans. Canonical sRNAs in C. elegans are miRNAs, small interfering RNAs including 22G-RNAs and 26G-RNAs, and 21U-RNAs, which are C. elegans piRNAs. Previous studies have only covered some of these Argonautes for their sRNA partners, and thus, a systematic study is needed to reveal the comprehensive regulatory networks formed by C. elegans Argonautes and their associated sRNAs. We obtained in situ knockin (KI) strains of all C. elegans Argonautes with fusion tags by CRISPR/Cas9 technology. RNA immunoprecipitation against these endogenously expressed Argonautes and high-throughput sequencing acquired the sRNA profiles of individual Argonautes. The sRNA partners for each Argonaute were then analyzed. We found that there were 10 Argonautes enriched miRNAs, 17 Argonautes bound to 22G-RNAs, 8 Argonautes bound to 26G-RNAs, and 1 Argonaute PRG-1 bound to piRNAs. Uridylated 22G-RNAs were bound by four Argonautes HRDE-1, WAGO-4, CSR-1, and PPW-2. We found that all four Argonautes played a role in transgenerational epigenetic inheritance. Regulatory roles of the corresponding Argonaute-sRNA complex in managing levels of long transcripts and interspecies regulation were also demonstrated. In this study, we portrayed the sRNAs bound to each functional Argonaute in C. elegans. Bioinformatics analyses together with experimental investigations provided perceptions in the overall view of the regulatory network formed by C. elegans Argonautes and sRNAs. The sRNA profiles bound to individual Argonautes reported here will be valuable resources for further studies.
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Affiliation(s)
- Lei Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Xiaolin Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Wenfang Zhao
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Qiqi Li
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Jingxin Li
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - He Chen
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Anhui University, Hefei, 230601, China
| | - Ge Shan
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China.
- Department of Pulmonary and Critical Care Medicine, Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
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Kachhawaha AS, Mishra S, Tiwari AK. Epigenetic control of heredity. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:25-60. [PMID: 37225323 DOI: 10.1016/bs.pmbts.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Epigenetics is the field of science that deals with the study of changes in gene function that do not involve changes in DNA sequence and are heritable while epigenetics inheritance is the process of transmission of epigenetic modifications to the next generation. It can be transient, intergenerational, or transgenerational. There are various epigenetic modifications involving mechanisms such as DNA methylation, histone modification, and noncoding RNA expression, all of which are inheritable. In this chapter, we summarize the information on epigenetic inheritance, its mechanism, inheritance studies on various organisms, factors affecting epigenetic modifications and their inheritance, and the role of epigenetic inheritance in the heritability of diseases.
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Affiliation(s)
- Akanksha Singh Kachhawaha
- Laboratory of Forensic Chemistry & Toxicology, School of Forensic Sciences, National Forensic Sciences University (NFSU), Gandhinagar, Gujarat, India
| | - Sarita Mishra
- Laboratory of Forensic Chemistry & Toxicology, School of Forensic Sciences, National Forensic Sciences University (NFSU), Gandhinagar, Gujarat, India
| | - Anand Krishna Tiwari
- Genetics & Developmental Biology Laboratory, Department of Biotechnology & Bioengineering, Institute of Advanced Research, Gandhinagar, Gujarat, India.
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Santilli F, Boskovic A. Mechanisms of transgenerational epigenetic inheritance: lessons from animal model organisms. Curr Opin Genet Dev 2023; 79:102024. [PMID: 36893483 DOI: 10.1016/j.gde.2023.102024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/24/2022] [Accepted: 01/26/2023] [Indexed: 03/09/2023]
Abstract
Epigenetic inheritance is a phenomenon whereby stochastic or signal-induced changes to parental germline epigenome modulate phenotypic output in one or more subsequent generations, independently of mutations in the genomic DNA. While the number of reported epigenetic inheritance phenomena across phyla is exponentially growing, much remains to be elucidated about their mechanistic underpinnings, and their significance for organismal homeostasis and adaptation. Here, we review the most recent epigenetic inheritance examples in animal models, outlining molecular details behind environmental sensing by the germline, and the functional relationships connecting epigenetic mechanisms and phenotypic traits after fertilization. We touch upon the experimental challenges associated with studying the scope of environmental input on phenotypic outcomes between generations. Finally, we discuss the implications of mechanistic findings from model organisms for the emergent examples of parental effects in human populations.
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Affiliation(s)
- Flavio Santilli
- European Molecular Biology Laboratory Epigenetics & Neurobiology Unit, Monterotondo, RM, Italy. https://twitter.com/@santilli_flavio
| | - Ana Boskovic
- European Molecular Biology Laboratory Epigenetics & Neurobiology Unit, Monterotondo, RM, Italy.
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40
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Croft JC, Colunga A, Solh L, Dillon MK, Lee TWS. Pharyngeal pumping rate does not reflect lifespan extension in C. elegans transgenerational longevity mutants. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000719. [PMID: 36793895 PMCID: PMC9923420 DOI: 10.17912/micropub.biology.000719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 02/17/2023]
Abstract
Epigenetic modifications must be reprogrammed with each new generation. In Caenorhabditis elegans , defects in histone methylation reprogramming allow for the transgenerational acquisition of longevity. For example, mutations in the putative H3K9 demethylase JHDM-1 extend lifespan after six to ten generations. We noticed that long-lived jhdm-1 mutants appear healthier than wild-type animals from the same generation. To quantify health, we compared the common metric of pharyngeal pumping rate at specific adult ages between early-gen populations with normal lifespans and late-gen populations with long lifespans. Longevity did not affect pumping rate, but long-lived mutants stop pumping at a younger age, suggesting a possible conservation of energy to extend lifespan.
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Affiliation(s)
- Jaime C. Croft
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
| | - Arthur Colunga
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
| | - Lea Solh
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
| | - Michaela K. Dillon
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
| | - Teresa Wei-sy Lee
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
,
Correspondence to: Teresa Wei-sy Lee (
)
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41
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Seroussi U, Lugowski A, Wadi L, Lao RX, Willis AR, Zhao W, Sundby AE, Charlesworth AG, Reinke AW, Claycomb JM. A comprehensive survey of C. elegans argonaute proteins reveals organism-wide gene regulatory networks and functions. eLife 2023; 12:e83853. [PMID: 36790166 PMCID: PMC10101689 DOI: 10.7554/elife.83853] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/14/2023] [Indexed: 02/16/2023] Open
Abstract
Argonaute (AGO) proteins associate with small RNAs to direct their effector function on complementary transcripts. The nematode Caenorhabditis elegans contains an expanded family of 19 functional AGO proteins, many of which have not been fully characterized. In this work, we systematically analyzed every C. elegans AGO using CRISPR-Cas9 genome editing to introduce GFP::3xFLAG tags. We have characterized the expression patterns of each AGO throughout development, identified small RNA binding complements, and determined the effects of ago loss on small RNA populations and developmental phenotypes. Our analysis indicates stratification of subsets of AGOs into distinct regulatory modules, and integration of our data led us to uncover novel stress-induced fertility and pathogen response phenotypes due to ago loss.
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Affiliation(s)
- Uri Seroussi
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Andrew Lugowski
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Lina Wadi
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Robert X Lao
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | | | - Winnie Zhao
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Adam E Sundby
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | | | - Aaron W Reinke
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Julie M Claycomb
- Department of Molecular Genetics, University of TorontoTorontoCanada
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Wang X, Ramat A, Simonelig M, Liu MF. Emerging roles and functional mechanisms of PIWI-interacting RNAs. Nat Rev Mol Cell Biol 2023; 24:123-141. [PMID: 36104626 DOI: 10.1038/s41580-022-00528-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 02/02/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that associate with proteins of the PIWI clade of the Argonaute family. First identified in animal germ line cells, piRNAs have essential roles in germ line development. The first function of PIWI-piRNA complexes to be described was the silencing of transposable elements, which is crucial for maintaining the integrity of the germ line genome. Later studies provided new insights into the functions of PIWI-piRNA complexes by demonstrating that they regulate protein-coding genes. Recent studies of piRNA biology, including in new model organisms such as golden hamsters, have deepened our understanding of both piRNA biogenesis and piRNA function. In this Review, we discuss the most recent advances in our understanding of piRNA biogenesis, the molecular mechanisms of piRNA function and the emerging roles of piRNAs in germ line development mainly in flies and mice, and in infertility, cancer and neurological diseases in humans.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Anne Ramat
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Martine Simonelig
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France.
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China. .,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.
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43
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Ding AJ, Zhang WM, Tao J, Chen B, Liu XC, Dong Y, Ma HJ, Pan SD, He JB, Zeng WK. Salmonella enterica serovar Paratyphi A-induced immune response in Caenorhabditis elegans depends on MAPK pathways and DAF-16. Front Immunol 2023; 14:1118003. [PMID: 37122724 PMCID: PMC10132459 DOI: 10.3389/fimmu.2023.1118003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Salmonella enterica serovar Paratyphi A (S. Paratyphi A) is a pathogen that can cause enteric fever. According to the recent epidemic trends of typhoid fever, S. Paratyphi A has been the major important causative factor in paratyphoid fever. An effective vaccine for S. Paratyphi A has not been developed, which made it a tricky public health concern. Until now, how S. Paratyphi A interacts with organisms remain unknown. Here using lifespan assay, we found that S. Paratyphi A could infect Caenorhabditis elegans (C. elegans) at 25°C, and attenuate thermotolerance. The immune response of C. elegans was mediated by tir-1, nsy-1, sek-1, pmk-1, mpk-1, skn-1, daf-2 and daf-16, suggesting that S. Paratyphi A could regulate the MAPK and insulin pathways. Furthermore, we observed several phenotypical changes when C. elegans were fed S. Paratyphi A, including an accelerated decline in body movement, reduced the reproductive capacity, shortened spawning cycle, strong preference for OP50, arrested pharyngeal pumping and colonization of the intestinal lumen. The virulence of S. Paratyphi A requires living bacteria and is not mediated by secreting toxin. Using hydrogen peroxide analysis and quantitative RT-PCR, we discovered that S. Paratyphi A could increase oxidative stress and regulate the immune response in C. elegans. Our results sheds light on the infection mechanisms of S. Paratyphi A and lays a foundation for drugs and vaccine development.
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44
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Zhao Y, Chen J, Wang R, Pu X, Wang D. A review of transgenerational and multigenerational toxicology in the in vivo model animal Caenorhabditis elegans. J Appl Toxicol 2023; 43:122-145. [PMID: 35754092 DOI: 10.1002/jat.4360] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/09/2022] [Accepted: 06/24/2022] [Indexed: 11/09/2022]
Abstract
A large number of pollutants existing in the environment can last for a long time, and their potential toxic effects can transfer from parents to their offspring. Thus, it is necessary to investigate the toxicity of environmental pollutants across multigenerations and the underlying mechanisms in organisms. Due to its short life cycle and sensitivity to environmental exposures, Caenorhabditis elegans is an important animal model for toxicity assessment of environmental pollutants across multigenerations. In this review, we introduced the transgenerational and multigenerational toxicity caused by various environmental pollutants in C. elegans. Moreover, we discussed the underlying mechanisms for the observed transgenerational and multigenerational toxicity of environmental contaminants in C. elegans.
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Affiliation(s)
- Yunli Zhao
- Medical School, Southeast University, Nanjing, China.,School of Public Health, Bengbu Medical College, Bengbu, China
| | - Jingya Chen
- School of Public Health, Bengbu Medical College, Bengbu, China
| | - Rui Wang
- School of Public Health, Bengbu Medical College, Bengbu, China
| | - Xiaoxiao Pu
- School of Public Health, Bengbu Medical College, Bengbu, China
| | - Dayong Wang
- Medical School, Southeast University, Nanjing, China
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45
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Rodriguez JD, Katz DJ. Lineage Tracing and Single-Cell RNA-seq in C. elegans to Analyze Transgenerational Epigenetic Phenotypes Inherited from Germ Cells. Methods Mol Biol 2023; 2677:61-79. [PMID: 37464235 DOI: 10.1007/978-1-0716-3259-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The last several years have seen an increasing number of examples of transgenerational epigenetic inheritance, in which phenotypes are inherited for three or more generations without changes to the underlying DNA sequence. One model system that has been particularly useful for studying transgenerational epigenetic inheritance is C. elegans. Their short generation time and hermaphroditic reproduction have allowed multiple transgenerational phenotypes to be identified, including aging, fertility, and behavior. However, it is still not clear how transgenerational epigenetic inheritance from the germline affects embryogenesis. Fortunately, the C. elegans embryo has a unique property that makes it ideal for addressing this question: they develop via an invariant lineage, with each cell undergoing stereotypical cell divisions to adopt the same cell fate in every individual embryo. Because of this invariant cell lineage, automated lineage tracing and single-cell RNA-seq can be employed to determine how transgenerational epigenetic inheritance from the germline affects developmental timing and cell fate. Unfortunately, difficulties with these techniques have severely limited their adoption in the community. Here, we provide a practical guide to automated lineage tracing coupled with single-cell RNA-seq to facilitate their use in studying transgenerational epigenetic inheritance in C. elegans embryos.
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Affiliation(s)
- Juan D Rodriguez
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - David J Katz
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.
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46
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Wang SY, Kim K, O'Brown ZK, Levan A, Dodson AE, Kennedy SG, Chernoff C, Greer EL. Hypoxia induces transgenerational epigenetic inheritance of small RNAs. Cell Rep 2022; 41:111800. [PMID: 36516753 PMCID: PMC9847139 DOI: 10.1016/j.celrep.2022.111800] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 09/23/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022] Open
Abstract
Animals sense and adapt to decreased oxygen availability, but whether and how hypoxia exposure in ancestors can elicit phenotypic consequences in normoxia-reared descendants are unclear. We show that hypoxia educes an intergenerational reduction in lipids and a transgenerational reduction in fertility in the nematode Caenorhabditis elegans. The transmission of these epigenetic phenotypes is dependent on repressive histone-modifying enzymes and the argonaute HRDE-1. Feeding naive C. elegans small RNAs extracted from hypoxia-treated worms is sufficient to induce a fertility defect. Furthermore, the endogenous small interfering RNA F44E5.4/5 is upregulated intergenerationally in response to hypoxia, and soaking naive normoxia-reared C. elegans with F44E5.4/5 double-stranded RNA (dsRNA) is sufficient to induce an intergenerational fertility defect. Finally, we demonstrate that labeled F44E5.4/5 dsRNA is itself transmitted from parents to children. Our results suggest that small RNAs respond to the environment and are sufficient to transmit non-genetic information from parents to their naive children.
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Affiliation(s)
- Simon Yuan Wang
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Kathleen Kim
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Zach Klapholz O'Brown
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Aileen Levan
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Anne Elizabeth Dodson
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Scott G Kennedy
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Chaim Chernoff
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Eric Lieberman Greer
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
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Hu S, Xiang D, Zhang X, Zhang L, Wang S, Jin K, You L, Huang J. The mechanisms and cross-protection of trained innate immunity. Virol J 2022; 19:210. [PMID: 36482472 PMCID: PMC9733056 DOI: 10.1186/s12985-022-01937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
In recent years, the traditional cognition of immunological memory being specific to adaptive immunity has been challenged. Innate immunity can mount enhanced responsiveness upon secondary stimulation, and a phenomenon is termed trained innate immunity. Trained innate immunity is orchestrated by distinct metabolic and epigenetic reprogramming in both circulating myeloid cells and myeloid progenitor cells in bone marrow, leading to long-term resistance to related and non-related pathogens infections. The induction of trained innate immunity can also polarize innate immune cells towards a hyperresponsive phenotype in the tumor microenvironment to exert antitumor effects. This review will discuss the current understanding of innate immune memory and the mechanisms during the induction of innate immunity, including signaling pathways, metabolic changes, and epigenetic rewriting. We also provide an overview of cross-protection against infectious diseases and cancers based on trained innate immunity.
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Affiliation(s)
- Shiwei Hu
- grid.13402.340000 0004 1759 700XDepartment of Hematology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Yiwu, Zhejiang China ,Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang China
| | - Danhong Xiang
- grid.13402.340000 0004 1759 700XDepartment of Hematology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Yiwu, Zhejiang China ,Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang China
| | - Xinlu Zhang
- grid.13402.340000 0004 1759 700XDepartment of Hematology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Yiwu, Zhejiang China ,Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang China
| | - Lan Zhang
- grid.13402.340000 0004 1759 700XDepartment of Hematology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Yiwu, Zhejiang China ,Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang China
| | - Shengjie Wang
- grid.13402.340000 0004 1759 700XDepartment of Hematology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Yiwu, Zhejiang China ,Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang China
| | - Keyi Jin
- grid.13402.340000 0004 1759 700XDepartment of Hematology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Yiwu, Zhejiang China ,Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang China
| | - Liangshun You
- grid.13402.340000 0004 1759 700XDepartment of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang China ,Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang China
| | - Jian Huang
- grid.13402.340000 0004 1759 700XDepartment of Hematology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Yiwu, Zhejiang China ,grid.13402.340000 0004 1759 700XDepartment of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang China ,Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang China
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PRETTY: A Parallel Transgenerational Learning-Assisted Evolutionary Algorithm for Computationally Expensive Multi-Objective Optimization. Inf Sci (N Y) 2022. [DOI: 10.1016/j.ins.2022.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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49
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Santiago E, Moreno DF, Acar M. Phenotypic plasticity as a facilitator of microbial evolution. ENVIRONMENTAL EPIGENETICS 2022; 8:dvac020. [PMID: 36465837 PMCID: PMC9709823 DOI: 10.1093/eep/dvac020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/27/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Tossed about by the tides of history, the inheritance of acquired characteristics has found a safe harbor at last in the rapidly expanding field of epigenetics. The slow pace of genetic variation and high opportunity cost associated with maintaining a diverse genetic pool are well-matched by the flexibility of epigenetic traits, which can enable low-cost exploration of phenotypic space and reactive tuning to environmental pressures. Aiding in the generation of a phenotypically plastic population, epigenetic mechanisms often provide a hotbed of innovation for countering environmental pressures, while the potential for genetic fixation can lead to strong epigenetic-genetic evolutionary synergy. At the level of cells and cellular populations, we begin this review by exploring the breadth of mechanisms for the storage and intergenerational transmission of epigenetic information, followed by a brief review of common and exotic epigenetically regulated phenotypes. We conclude by offering an in-depth coverage of recent papers centered around two critical issues: the evolvability of epigenetic traits through Baldwinian adaptive phenotypic plasticity and the potential for synergy between epigenetic and genetic evolution.
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Affiliation(s)
- Emerson Santiago
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA
| | - David F Moreno
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Murat Acar
- *Correspondence address. Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA. Tel: +90 (543) 304-0388; E-mail:
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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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