1
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Falsztyn IB, Taylor SM, Baugh LR. Developmental and conditional regulation of DAF-2/INSR ubiquitination in Caenorhabditis elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595723. [PMID: 38854056 PMCID: PMC11160630 DOI: 10.1101/2024.05.24.595723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Insulin/IGF signaling (IIS) regulates developmental and metabolic plasticity. Conditional regulation of insulin-like peptide expression and secretion promotes different phenotypes in different environments. However, IIS can also be regulated by other, less-understood mechanisms. For example, stability of the only known insulin/IGF receptor in C. elegans, DAF-2/INSR, is regulated by CHIP-dependent ubiquitination. Disruption of chn-1/CHIP reduces longevity in C. elegans by increasing DAF-2/INSR abundance and IIS activity in adults. Likewise, mutation of a ubiquitination site causes daf-2(gk390525) to display gain-of-function phenotypes in adults. However, we show that this allele displays loss-of-function phenotypes in larvae, and that its effect on IIS activity transitions from negative to positive during development. In contrast, the allele acts like a gain-of-function in larvae cultured at high temperature, inhibiting temperature-dependent dauer formation. Disruption of chn-1/CHIP causes an increase in IIS activity in starved L1 larvae, unlike daf-2(gk390525). CHN-1/CHIP ubiquitinates DAF-2/INSR at multiple sites. These results suggest that the sites that are functionally relevant to negative regulation of IIS vary in larvae and adults, at different temperatures, and in nutrient-dependent fashion, revealing additional layers of IIS regulation.
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Affiliation(s)
| | - Seth M. Taylor
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - L. Ryan Baugh
- Department of Biology, Duke University, Durham, NC 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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2
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Erdmann EA, Forbes M, Becker M, Perez S, Hundley HA. ADR-2 regulates fertility and oocyte fate in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.01.565157. [PMID: 37961348 PMCID: PMC10635048 DOI: 10.1101/2023.11.01.565157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
RNA binding proteins play essential roles in coordinating germline gene expression and development in all organisms. Here, we report that loss of ADR-2, a member of the Adenosine DeAminase acting on RNA (ADAR) family of RNA binding proteins and the sole adenosine-to-inosine RNA editing enzyme in C. elegans, can improve fertility in multiple genetic backgrounds. First, we show that loss of RNA editing by ADR-2 restores normal embryo production to subfertile animals that transgenically express a vitellogenin (yolk protein) fusion to green fluorescent protein. Using this phenotype, a high-throughput screen was designed to identify RNA binding proteins that when depleted yield synthetic phenotypes with loss of adr-2. The screen uncovered a genetic interaction between ADR-2 and SQD-1, a member of the heterogenous nuclear ribonucleoprotein (hnRNP) family of RNA binding proteins. Microscopy, reproductive assays, and high-throughput sequencing reveal that sqd-1 is essential for the onset of oogenesis and oogenic gene expression in young adult animals, and that loss of adr-2 can counteract the effects of loss of sqd-1 on gene expression and rescue the switch from spermatogenesis to oogenesis. Together, these data demonstrate that ADR-2 can contribute to the suppression of fertility and suggest novel roles for both RNA editing-dependent and independent mechanisms in regulating embryogenesis.
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Affiliation(s)
- Emily A. Erdmann
- Genome, Cell and Developmental Biology Graduate Program, Indiana University, Bloomington IN, US 47405
| | - Melanie Forbes
- Department of Biology, Indiana University, Bloomington IN, US 47405
| | - Margaret Becker
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington IN, US 47405
| | - Sarina Perez
- Department of Biology, Indiana University, Bloomington IN, US 47405
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3
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Luo J, Bainbridge C, Miller RM, Barrios A, Portman DS. C. elegans males optimize mate-preference decisions via sex-specific responses to multimodal sensory cues. Curr Biol 2024; 34:1309-1323.e4. [PMID: 38471505 PMCID: PMC10965367 DOI: 10.1016/j.cub.2024.02.036] [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: 03/28/2023] [Revised: 12/07/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024]
Abstract
For sexually reproducing animals, selecting optimal mates is important for maximizing reproductive fitness. In the nematode C. elegans, populations reproduce largely by hermaphrodite self-fertilization, but the cross-fertilization of hermaphrodites by males also occurs. Males' ability to recognize hermaphrodites involves several sensory cues, but an integrated view of the ways males use these cues in their native context to assess characteristics of potential mates has been elusive. Here, we examine the mate-preference behavior of C. elegans males evoked by natively produced cues. We find that males use a combination of volatile sex pheromones (VSPs), ascaroside sex pheromones, surface-associated cues, and other signals to assess multiple features of potential mates. Specific aspects of mate preference are communicated by distinct signals: developmental stage and sex are signaled by ascaroside pheromones and surface cues, whereas the presence of a self-sperm-depleted hermaphrodite is likely signaled by VSPs. Furthermore, males prefer to interact with virgin over mated, and well-fed over food-deprived, hermaphrodites; these preferences are likely adaptive and are also mediated by ascarosides and other cues. Sex-typical mate-preference behavior depends on the sexual state of the nervous system, such that pan-neuronal genetic masculinization in hermaphrodites generates male-typical social behavior. We also identify an unexpected role for the sex-shared ASH sensory neurons in male attraction to ascaroside sex pheromones. Our findings lead to an integrated view in which the distinct physical properties of various mate-preference cues guide a flexible, stepwise behavioral program by which males assess multiple features of potential mates to optimize mate preference.
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Affiliation(s)
- Jintao Luo
- School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China; Department of Biomedical Genetics and Del Monte Institute for Neuroscience, University of Rochester, Rochester, NY 14642, USA
| | - Chance Bainbridge
- Department of Biomedical Genetics and Del Monte Institute for Neuroscience, University of Rochester, Rochester, NY 14642, USA
| | - Renee M Miller
- Department of Brain and Cognitive Sciences, University of Rochester, Rochester, NY 14620, USA
| | - Arantza Barrios
- Department of Cell and Developmental Biology, University College London, London WC1E 6DE, UK
| | - Douglas S Portman
- Department of Biomedical Genetics and Del Monte Institute for Neuroscience, University of Rochester, Rochester, NY 14642, USA.
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4
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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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5
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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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6
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Burton NO. A mother to offspring metabolic link. Nat Cell Biol 2023; 25:1083-1084. [PMID: 37537364 DOI: 10.1038/s41556-023-01189-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Affiliation(s)
- Nicholas O Burton
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
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7
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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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8
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Geens E, Van de Walle P, Caroti F, Jelier R, Steuwe C, Schoofs L, Temmerman L. Yolk-deprived Caenorhabditis elegans secure brood size at the expense of competitive fitness. Life Sci Alliance 2023; 6:e202201675. [PMID: 37059473 PMCID: PMC10105328 DOI: 10.26508/lsa.202201675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/16/2023] Open
Abstract
Oviparous animals support reproduction via the incorporation of yolk as a nutrient source into the eggs. In Caenorhabditis elegans, however, yolk proteins seem dispensable for fecundity, despite constituting the vast majority of the embryonic protein pool and acting as carriers for nutrient-rich lipids. Here, we used yolk protein-deprived C. elegans mutants to gain insight into the traits that may yet be influenced by yolk rationing. We show that massive yolk provisioning confers a temporal advantage during embryogenesis, while also increasing early juvenile body size and promoting competitive fitness. Opposite to species that reduce egg production under yolk deprivation, our results indicate that C. elegans relies on yolk as a fail-safe to secure offspring survival, rather than to maintain offspring numbers.
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Affiliation(s)
- Ellen Geens
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Francesca Caroti
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Rob Jelier
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Christian Steuwe
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
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9
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Luo J, Barrios A, Portman DS. C. elegans males optimize mate-choice decisions via sex-specific responses to multimodal sensory cues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.08.536021. [PMID: 37066192 PMCID: PMC10104232 DOI: 10.1101/2023.04.08.536021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
For sexually reproducing animals, selecting optimal mates is essential for maximizing reproductive fitness. Because the nematode C. elegans reproduces mostly by self-fertilization, little is known about its mate-choice behaviors. While several sensory cues have been implicated in males' ability to recognize hermaphrodites, achieving an integrated understanding of the ways males use these cues to assess relevant characteristics of potential mates has proven challenging. Here, we use a choice-based social-interaction assay to explore the ability of C. elegans males to make and optimize mate choices. We find that males use a combination of volatile sex pheromones (VSPs), ascaroside pheromones, surface-bound chemical cues, and other signals to robustly assess a variety of features of potential mates. Specific aspects of mate choice are communicated by distinct signals: the presence of a sperm-depleted, receptive hermaphrodite is likely signaled by VSPs, while developmental stage and sex are redundantly specified by ascaroside pheromones and surface-associated cues. Ascarosides also signal nutritional information, allowing males to choose well-fed over starved mates, while both ascarosides and surface-associated cues cause males to prefer virgin over previously mated hermaphrodites. The male-specificity of these behavioral responses is determined by both male-specific neurons and the male state of sex-shared circuits, and we reveal an unexpected role for the sex-shared ASH sensory neurons in male attraction to endogenously produced hermaphrodite ascarosides. Together, our findings lead to an integrated view of the signaling and behavioral mechanisms by which males use diverse sensory cues to assess multiple features of potential mates and optimize mate choice.
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Affiliation(s)
- Jintao Luo
- School of Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
- Department of Biomedical Genetics and Del Monte Institute for Neuroscience, University of Rochester, Rochester, NY 14642
| | - Arantza Barrios
- Department of Cell and Developmental Biology, University College London, London WC1E 6DE, UK
| | - Douglas S. Portman
- Department of Biomedical Genetics and Del Monte Institute for Neuroscience, University of Rochester, Rochester, NY 14642
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10
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Vogt MC, Hobert O. Starvation-induced changes in somatic insulin/IGF-1R signaling drive metabolic programming across generations. SCIENCE ADVANCES 2023; 9:eade1817. [PMID: 37027477 PMCID: PMC10081852 DOI: 10.1126/sciadv.ade1817] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 03/08/2023] [Indexed: 05/30/2023]
Abstract
Exposure to adverse nutritional and metabolic environments during critical periods of development can exert long-lasting effects on health outcomes of an individual and its descendants. Although such metabolic programming has been observed in multiple species and in response to distinct nutritional stressors, conclusive insights into signaling pathways and mechanisms responsible for initiating, mediating, and manifesting changes to metabolism and behavior across generations remain scarce. By using a starvation paradigm in Caenorhabditis elegans, we show that starvation-induced changes in dauer formation-16/forkhead box transcription factor class O (DAF-16/FoxO) activity, the main downstream target of insulin/insulin-like growth factor 1 (IGF-1) receptor signaling, are responsible for metabolic programming phenotypes. Tissue-specific depletion of DAF-16/FoxO during distinct developmental time points demonstrates that DAF-16/FoxO acts in somatic tissues, but not directly in the germline, to both initiate and manifest metabolic programming. In conclusion, our study deciphers multifaceted and critical roles of highly conserved insulin/IGF-1 receptor signaling in determining health outcomes and behavior across generations.
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11
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Jordan JM, Webster AK, Chen J, Chitrakar R, Ryan Baugh L. Early-life starvation alters lipid metabolism in adults to cause developmental pathology in Caenorhabditis elegans. Genetics 2023; 223:iyac172. [PMID: 36449523 PMCID: PMC9910403 DOI: 10.1093/genetics/iyac172] [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: 03/25/2022] [Revised: 03/25/2022] [Accepted: 10/31/2022] [Indexed: 12/02/2022] Open
Abstract
Early-life malnutrition increases adult disease risk in humans, but the causal changes in gene regulation, signaling, and metabolism are unclear. In the roundworm Caenorhabditis elegans, early-life starvation causes well-fed larvae to develop germline tumors and other gonad abnormalities as adults. Furthermore, reduced insulin/IGF signaling during larval development suppresses these starvation-induced abnormalities. How early-life starvation and insulin/IGF signaling affect adult pathology is unknown. We show that early-life starvation has pervasive effects on adult gene expression which are largely reversed by reduced insulin/IGF signaling following recovery from starvation. Early-life starvation increases adult fatty-acid synthetase fasn-1 expression in daf-2 insulin/IGF signaling receptor-dependent fashion, and fasn-1/FASN promotes starvation-induced abnormalities. Lipidomic analysis reveals increased levels of phosphatidylcholine in adults subjected to early-life starvation, and supplementation with unsaturated phosphatidylcholine during development suppresses starvation-induced abnormalities. Genetic analysis of fatty-acid desaturases reveals positive and negative effects of desaturation on development of starvation-induced abnormalities. In particular, the ω3 fatty-acid desaturase fat-1 and the Δ5 fatty-acid desaturase fat-4 inhibit and promote development of abnormalities, respectively. fat-4 is epistatic to fat-1, suggesting that arachidonic acid-containing lipids promote development of starvation-induced abnormalities, and supplementation with ARA enhanced development of abnormalities. This work shows that early-life starvation and insulin/IGF signaling converge on regulation of adult lipid metabolism, affecting stem-cell proliferation and tumor formation.
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Affiliation(s)
- James M Jordan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Amy K Webster
- Department of Biology, Duke University, Durham, NC 27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Jingxian Chen
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Rojin Chitrakar
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, NC 27708, USA
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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12
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Shaul NC, Jordan JM, Falsztyn IB, Ryan Baugh L. Insulin/IGF-dependent Wnt signaling promotes formation of germline tumors and other developmental abnormalities following early-life starvation in Caenorhabditis elegans. Genetics 2023; 223:iyac173. [PMID: 36449574 PMCID: PMC9910406 DOI: 10.1093/genetics/iyac173] [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: 03/25/2022] [Revised: 03/25/2022] [Accepted: 10/31/2022] [Indexed: 12/02/2022] Open
Abstract
The Developmental Origins of Health and Disease hypothesis postulates that early-life stressors can predispose people to disease later in life. In the roundworm Caenorhabditis elegans, prolonged early-life starvation causes germline tumors, uterine masses, and other gonad abnormalities to develop in well-fed adults. Reduction of insulin/insulin-like growth factor (IGF) signaling (IIS) during larval development suppresses these starvation-induced abnormalities. However, molecular mechanisms at play in formation and suppression of starvation-induced abnormalities are unclear. Here we describe mechanisms through which early-life starvation and reduced IIS affect starvation-induced abnormalities. Transcriptome sequencing revealed that expression of genes in the Wnt signaling pathway is upregulated in adults starved as young larvae, and that knockdown of the insulin/IGF receptor daf-2/InsR decreases their expression. Reduction of Wnt signaling through RNAi or mutation reduced starvation-induced abnormalities, and hyperactivation of Wnt signaling produced gonad abnormalities in worms that had not been starved. Genetic and reporter-gene analyses suggest that Wnt signaling acts downstream of IIS in the soma to cell-nonautonomously promote germline hyperproliferation. In summary, this work reveals that IIS-dependent transcriptional regulation of Wnt signaling promotes starvation-induced gonad abnormalities, illuminating signaling mechanisms that contribute to adult pathology following early-life starvation.
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Affiliation(s)
- Nathan C Shaul
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - James M Jordan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Ivan B Falsztyn
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, NC 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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13
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Zhai C, Zhang N, Li X, Chen X, Sun F, Dong M. Fusion and expansion of vitellogenin vesicles during Caenorhabditis elegans intestinal senescence. Aging Cell 2022; 21:e13719. [PMID: 36199214 PMCID: PMC9649609 DOI: 10.1111/acel.13719] [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: 02/11/2022] [Revised: 07/20/2022] [Accepted: 09/01/2022] [Indexed: 01/25/2023] Open
Abstract
Some of the most conspicuous aging phenotypes of C. elegans are related to post-reproductive production of vitellogenins (Vtg), which form yolk protein (YP) complexes after processing and lipid loading. Vtg/YP levels show huge increases with age, and inhibition of this extends lifespan, but how subcellular and organism-wide distribution of these proteins changes with age has not been systematically explored. Here, this has been done to understand how vitellogenesis promotes aging. The age-associated changes of intestinal vitellogenin vesicles (VVs), pseudocoelomic yolk patches (PYPs), and gonadal yolk organelles (YOs) have been characterized by immuno-electron microscopy. We find that from reproductive adult day 2 (AD 2) to post-reproductive AD 6 and AD 9, intestinal VVs expand from 0.2 to 3-4 μm in diameter or by >3000 times in volume, PYPs increase by >3 times in YP concentration and volume, while YOs in oocytes shrink slightly from 0.5 to 0.4 μm in diameter or by 49% in volume. In AD 6 and AD 9 worms, mislocalized YOs found in the hypodermis, uterine cells, and the somatic gonadal sheath can reach a size of 10 μm across in the former two tissues. This remarkable size increase of VVs and that of mislocalized YOs in post-reproductive worms are accompanied by extensive fusion between these Vtg/YP-containing vesicular structures in somatic cells. In contrast, no fusion is seen between YOs in oocytes. We propose that in addition to the continued production of Vtg, excessive fusion between VVs and mislocalized YOs in the soma worsen the aging pathologies seen in C. elegans.
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Affiliation(s)
- Chao Zhai
- School of Life SciencesPeking UniversityBeijingChina,National Institute of Biological SciencesBeijingChina
| | - Nan Zhang
- National Institute of Biological SciencesBeijingChina
| | - Xi‐Xia Li
- Center for Biological Imaging, Institute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Xi Chen
- Institute of AutomationChinese Academy of SciencesBeijingChina
| | - Fei Sun
- Center for Biological Imaging, Institute of BiophysicsChinese Academy of SciencesBeijingChina,National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of BiophysicsChinese Academy of SciencesBeijingChina,University of the Chinese Academy of SciencesBeijingChina
| | - Meng‐Qiu Dong
- National Institute of Biological SciencesBeijingChina
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14
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Wang Y, Guo K, Wang Q, Zhong G, Zhang W, Jiang Y, Mao X, Li X, Huang Z. Caenorhabditis elegans as an emerging model in food and nutrition research: importance of standardizing base diet. Crit Rev Food Sci Nutr 2022; 64:3167-3185. [PMID: 36200941 DOI: 10.1080/10408398.2022.2130875] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
As a model organism that has helped revolutionize life sciences, Caenorhabditis elegans has been increasingly used in nutrition research. Here we explore the tradeoffs between pros and cons of its use as a dietary model based primarily on literature review from the past decade. We first provide an overview of its experimental strengths as an animal model, focusing on lifespan and healthspan, behavioral and physiological phenotypes, and conservation of key nutritional pathways. We then summarize recent advances of its use in nutritional studies, e.g. food preference and feeding behavior, sugar status and metabolic reprogramming, lifetime and transgenerational nutrition tracking, and diet-microbiota-host interactions, highlighting cutting-edge technologies originated from or developed in C. elegans. We further review current challenges of using C. elegans as a nutritional model, followed by in-depth discussions on potential solutions. In particular, growth scales and throughputs, food uptake mode, and axenic culture of C. elegans are appraised in the context of food research. We also provide perspectives for future development of chemically defined nematode food ("NemaFood") for C. elegans, which is now widely accepted as a versatile and affordable in vivo model and has begun to show transformative potential to pioneer nutrition science.
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Affiliation(s)
- Yuqing Wang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
| | - Kaixin Guo
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Qiangqiang Wang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
| | - Guohuan Zhong
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Wenjun Zhang
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yiyi Jiang
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Xinliang Mao
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Xiaomin Li
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Zebo Huang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
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15
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Wei P, Li Y, Wang X, Feng Y, Zhang X. Morphometric changes of the pine wood nematode, Bursaphelenchus xylophilus (Steiner & Buhrer) Nickle, under different environmental conditions. NEMATOLOGY 2022. [DOI: 10.1163/15685411-bja10186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
The pathogen of pine wilt disease, Bursaphelenchus xylophilus, has caused serious damage to forest ecology and the forestry economy. As an invasive species, the reproduction ability of B. xylophilus is a significant factor that influences its pathogenicity. There are few reports on the morphometric changes to B. xylophilus in different environments. This paper describes our study of the effects of fungal species, B. xylophilus population density, and nutrition on the growth and development of B. xylophilus and the comparative fitness of different-sized eggs in this species. The results showed that B. xylophilus could feed on different fungal species, but there were differences in the sizes of adult females and eggs and the number of offspring. Adult female size, egg size and number of offspring of B. xylophilus decreased as the population densities increased or mycelium weight decreased. The results also showed that larger eggs had a fitness advantage over smaller eggs under the experimental treatment conditions.
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Affiliation(s)
- Pengfei Wei
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, P.R. China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, P.R. China
| | - Yongxia Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, P.R. China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, P.R. China
| | - Xuan Wang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, P.R. China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, P.R. China
| | - Yuqian Feng
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, P.R. China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, P.R. China
| | - Xingyao Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, P.R. China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, P.R. China
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16
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Webster AK, Chitrakar R, Powell M, Chen J, Fisher K, Tanny RE, Stevens L, Evans K, Wei A, Antoshechkin I, Andersen EC, Baugh LR. Using population selection and sequencing to characterize natural variation of starvation resistance in C. elegans. eLife 2022; 11:80204. [PMID: 35727141 PMCID: PMC9262388 DOI: 10.7554/elife.80204] [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: 05/11/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Starvation resistance is important to disease and fitness, but the genetic basis of its natural variation is unknown. Uncovering the genetic basis of complex, quantitative traits such as starvation resistance is technically challenging. We developed a synthetic-population (re)sequencing approach using molecular inversion probes (MIP-seq) to measure relative fitness during and after larval starvation in C. elegans. We applied this competitive assay to 100 genetically diverse, sequenced, wild strains, revealing natural variation in starvation resistance. We confirmed that the most starvation-resistant strains survive and recover from starvation better than the most starvation-sensitive strains using standard assays. We performed genome-wide association (GWA) with the MIP-seq trait data and identified three quantitative trait loci (QTL) for starvation resistance, and we created near isogenic lines (NILs) to validate the effect of these QTL on the trait. These QTL contain numerous candidate genes including several members of the Insulin/EGF Receptor-L Domain (irld) family. We used genome editing to show that four different irld genes have modest effects on starvation resistance. Natural variants of irld-39 and irld-52 affect starvation resistance, and increased resistance of the irld-39; irld-52 double mutant depends on daf-16/FoxO. DAF-16/FoxO is a widely conserved transcriptional effector of insulin/IGF signaling (IIS), and these results suggest that IRLD proteins modify IIS, though they may act through other mechanisms as well. This work demonstrates efficacy of using MIP-seq to dissect a complex trait and it suggests that irld genes are natural modifiers of starvation resistance in C. elegans.
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Affiliation(s)
- Amy K Webster
- Department of Biology, Duke University, Durham, United States
| | - Rojin Chitrakar
- Department of Biology, Duke University, Durham, United States
| | - Maya Powell
- Department of Biology, Duke University, Durham, United States
| | - Jingxian Chen
- Department of Biology, Duke University, Durham, United States
| | - Kinsey Fisher
- Department of Biology, Duke University, Durham, United States
| | - Robyn E Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Kathryn Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Angela Wei
- Department of Biology, Duke University, Durham, United States
| | - Igor Antoshechkin
- Division of Biology, California Institute of Technology, Pasadena, United States
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, United States
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17
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Moya A, Tejedor D, Manetti M, Clavijo A, Pagano E, Munarriz E, Kronberg MF. Reproductive toxicity by exposure to low concentrations of pesticides in Caenorhabditis elegans. Toxicology 2022; 475:153229. [PMID: 35697162 DOI: 10.1016/j.tox.2022.153229] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/20/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022]
Abstract
In view of the recurrent applications of pesticides in agricultural producing countries, the increased presence of these substances in the environment raise a demand for the evaluation of adverse effects on non-target organisms. This study assesses the impact of exposure to five pesticides suspected of being endocrine disruptors (atrazine, 2,4-dichlorophenoxyacetic acid, mancozeb, chlorpyrifos and cypermethrin) on the reproductive development of the nematode Caenorhabditis elegans. To this end, nematodes in the L4 larval stage were exposed to different concentrations of pesticides for 24 h and the consequences on brood size, percentage of gravid nematodes, expression of reproductive-related genes and vitellogenin trafficking and endocytosis were measured. Moreover, 17β-estradiol was used as an estrogenic control for endocrine disrupting compounds throughout the work. The results showed that all the pesticides disturbed to some extent one or more of the evaluated endpoints. Remarkably, we found that atrazine, 2,4-dichlorophenoxyacetic acid and chlorpyrifos produced comparable responses to 17β-estradiol suggesting that these pesticides may have estrogen-like endocrine disrupting activity. Atrazine and 17β-estradiol, as well as 2,4-dichlorophenoxyacetic acid and chlorpyrifos to a lesser extent, decreased the brood size, affected vitellogenin trafficking and endocytosis, and changed the expression of several reproductive-related genes. Conversely, mancozeb and cypermethrin had the least impact on the evaluated endpoint. Cypermethrin affected the brood size at the highest concentration tested and mancozeb altered the distribution of vitellogenin only in approximately 10% of the population. However, both products overexpressed hus-1 and vit-2 genes, indicating that an induction of stress could interfere with the normal development of the nematode. In conclusion, our work proved that C. elegans is a useful biological model to identify the effects of estrogen-like endocrine disruptor compounds, and the sublethal endpoints proposed may serve as an important contribution on evaluating environmental pollutants.
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Affiliation(s)
- Aldana Moya
- Cátedra de Protección vegetal, Facultad de Agronomía, Universidad de Buenos Aires, Avda. San Martín 4453, C1417DSE Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniela Tejedor
- Cátedra de Bioquímica, Facultad de Agronomía, Universidad de Buenos Aires, Avda. San Martín 4453, C1417DSE Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas, Avda. San Martín 4453, C1417DSE Ciudad Autónoma de Buenos Aires, Argentina
| | - Mariana Manetti
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas, Avda. San Martín 4453, C1417DSE Ciudad Autónoma de Buenos Aires, Argentina
| | - Araceli Clavijo
- Instituto de Investigaciones en Energía no Convencional, Universidad Nacional de Salta - Consejo Nacional de Investigaciones Científicas y Técnicas, Avda. Bolivia 5150, A4408FVY Ciudad de Salta, Argentina
| | - Eduardo Pagano
- Cátedra de Bioquímica, Facultad de Agronomía, Universidad de Buenos Aires, Avda. San Martín 4453, C1417DSE Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas, Avda. San Martín 4453, C1417DSE Ciudad Autónoma de Buenos Aires, Argentina
| | - Eliana Munarriz
- Cátedra de Bioquímica, Facultad de Agronomía, Universidad de Buenos Aires, Avda. San Martín 4453, C1417DSE Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas, Avda. San Martín 4453, C1417DSE Ciudad Autónoma de Buenos Aires, Argentina.
| | - María Florencia Kronberg
- Cátedra de Bioquímica, Facultad de Agronomía, Universidad de Buenos Aires, Avda. San Martín 4453, C1417DSE Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas, Avda. San Martín 4453, C1417DSE Ciudad Autónoma de Buenos Aires, Argentina.
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18
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Chen J, Tang LY, Powell ME, Jordan JM, Baugh LR. Genetic analysis of daf-18/PTEN missense mutants for starvation resistance and developmental regulation during Caenorhabditis elegans L1 arrest. G3 (BETHESDA, MD.) 2022; 12:jkac092. [PMID: 35451480 PMCID: PMC9157142 DOI: 10.1093/g3journal/jkac092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/14/2022] [Indexed: 02/06/2023]
Abstract
Mutations in the well-known tumor suppressor PTEN are observed in many cancers. PTEN is a dual-specificity phosphatase that harbors lipid and protein-phosphatase activities. The Caenorhabditis elegans PTEN ortholog is daf-18, which has pleiotropic effects on dauer formation, aging, starvation resistance, and development. Function of 3 daf-18 point-mutants, G174E, D137A, and C169S, had previously been investigated using high-copy transgenes in a daf-18 null background. These alleles were generated based on their mammalian counterparts and were treated as though they specifically disrupt lipid or protein-phosphatase activity, or both, respectively. Here, we investigated these alleles using genome editing of endogenous daf-18. We assayed 3 traits relevant to L1 starvation resistance, and we show that each point mutant is essentially as starvation-sensitive as a daf-18 null mutant. Furthermore, we show that G174E and D137A do not complement each other, suggesting overlapping effects on lipid and protein-phosphatase activity. We also show that each allele has strong effects on nucleocytoplasmic localization of DAF-16/FoxO and dauer formation, both of which are regulated by PI3K signaling, similar to a daf-18 null allele. In addition, each allele also disrupts M-cell quiescence during L1 starvation, though D137A has a weaker effect than the other alleles, including the null. Our results confirm that daf-18/PTEN is important for promoting starvation resistance and developmental arrest and that it is a potent regulator of PI3K signaling, and they highlight challenges of using genetic analysis to link specific DAF-18/PTEN enzymatic activities to particular phenotypes.
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Affiliation(s)
- Jingxian Chen
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Linda Y Tang
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Maya E Powell
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - James M Jordan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, NC 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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19
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Guo R, Li G, Lu L, Sun S, Liu T, Li M, Zheng Y, Walhout AJM, Wu J, Li H. The Plasmid pEX18Gm Indirectly Increases Caenorhabditis elegans Fecundity by Accelerating Bacterial Methionine Synthesis. Int J Mol Sci 2022; 23:5003. [PMID: 35563392 PMCID: PMC9102816 DOI: 10.3390/ijms23095003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 01/06/2023] Open
Abstract
Plasmids are mostly found in bacteria as extrachromosomal genetic elements and are widely used in genetic engineering. Exploring the mechanisms of plasmid-host interaction can provide crucial information for the application of plasmids in genetic engineering. However, many studies have generally focused on the influence of plasmids on their bacterial hosts, and the effects of plasmids on bacteria-feeding animals have not been explored in detail. Here, we use a "plasmid-bacteria-Caenorhabditis elegans" model to explore the impact of plasmids on their host bacteria and bacterivorous nematodes. First, the phenotypic responses of C. elegans were observed by feeding Escherichia coli OP50 harboring different types of plasmids. We found that E. coli OP50 harboring plasmid pEX18Gm unexpectedly increases the fecundity of C. elegans. Subsequently, we found that the plasmid pEX18Gm indirectly affects C. elegans fecundity via bacterial metabolism. To explore the underlying regulatory mechanism, we performed bacterial RNA sequencing and performed in-depth analysis. We demonstrated that the plasmid pEX18Gm upregulates the transcription of methionine synthase gene metH in the bacteria, which results in an increase in methionine that supports C. elegans fecundity. Additionally, we found that a pEX18Gm-induced increase in C. elegans can occur in different bacterial species. Our findings highlight the plasmid-bacteria-C. elegans model to reveal the mechanism of plasmids' effects on their host and provide a new pattern for systematically studying the interaction between plasmids and multi-species.
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Affiliation(s)
- Rui Guo
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.G.); (G.L.); (L.L.); (S.S.); (T.L.)
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA;
| | - Gen Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.G.); (G.L.); (L.L.); (S.S.); (T.L.)
| | - Leilei Lu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.G.); (G.L.); (L.L.); (S.S.); (T.L.)
| | - Shan Sun
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.G.); (G.L.); (L.L.); (S.S.); (T.L.)
| | - Ting Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.G.); (G.L.); (L.L.); (S.S.); (T.L.)
| | - Mengsha Li
- College of Science & Technology, Ningbo University, Cixi 315300, China;
| | - Yong Zheng
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China;
| | - Albertha J. M. Walhout
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA;
| | - Jun Wu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.G.); (G.L.); (L.L.); (S.S.); (T.L.)
| | - Huixin Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.G.); (G.L.); (L.L.); (S.S.); (T.L.)
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210014, China
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20
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Lister-Shimauchi EH, McCarthy B, Lippincott M, Ahmed S. Genetic and Epigenetic Inheritance at Telomeres. EPIGENOMES 2022; 6:9. [PMID: 35323213 PMCID: PMC8947350 DOI: 10.3390/epigenomes6010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/21/2022] [Accepted: 03/08/2022] [Indexed: 12/17/2022] Open
Abstract
Transgenerational inheritance can occur at telomeres in distinct contexts. Deficiency for telomerase or telomere-binding proteins in germ cells can result in shortened or lengthened chromosome termini that are transmitted to progeny. In human families, altered telomere lengths can result in stem cell dysfunction or tumor development. Genetic inheritance of altered telomeres as well as mutations that alter telomeres can result in progressive telomere length changes over multiple generations. Telomeres of yeast can modulate the epigenetic state of subtelomeric genes in a manner that is mitotically heritable, and the effects of telomeres on subtelomeric gene expression may be relevant to senescence or other human adult-onset disorders. Recently, two novel epigenetic states were shown to occur at C. elegans telomeres, where very low or high levels of telomeric protein foci can be inherited for multiple generations through a process that is regulated by histone methylation.Together, these observations illustrate that information relevant to telomere biology can be inherited via genetic and epigenetic mechanisms, although the broad impact of epigenetic inheritance to human biology remains unclear.
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Affiliation(s)
- Evan H. Lister-Shimauchi
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-3280, USA; (E.H.L.-S.); (B.M.); (M.L.)
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Benjamin McCarthy
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-3280, USA; (E.H.L.-S.); (B.M.); (M.L.)
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Michael Lippincott
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-3280, USA; (E.H.L.-S.); (B.M.); (M.L.)
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Shawn Ahmed
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-3280, USA; (E.H.L.-S.); (B.M.); (M.L.)
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
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21
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Gulyas L, Powell JR. Cold shock induces a terminal investment reproductive response in C. elegans. Sci Rep 2022; 12:1338. [PMID: 35079060 PMCID: PMC8789813 DOI: 10.1038/s41598-022-05340-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 12/08/2021] [Indexed: 12/04/2022] Open
Abstract
Challenges from environmental stressors have a profound impact on many life-history traits of an organism, including reproductive strategy. Examples across multiple taxa have demonstrated that maternal reproductive investment resulting from stress can improve offspring survival; a form of matricidal provisioning when death appears imminent is known as terminal investment. Here we report a reproductive response in the nematode Caenorhabditis elegans upon exposure to acute cold shock at 2 °C, whereby vitellogenic lipid movement from the soma to the germline appears to be massively upregulated at the expense of parental survival. This response is dependent on functional TAX-2; TAX-4 cGMP-gated channels that are part of canonical thermosensory mechanisms in worms and can be prevented in the presence of activated SKN-1/Nrf2, the master stress regulator. Increased maternal provisioning promotes improved embryonic cold shock survival, which is notably suppressed in animals with impaired vitellogenesis. These findings suggest that cold shock in C. elegans triggers terminal investment to promote progeny fitness at the expense of parental survival and may serve as a tractable model for future studies of stress-induced progeny plasticity.
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Affiliation(s)
- Leah Gulyas
- Department of Biology, Gettysburg College, Gettysburg, PA, 17325, USA.,Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94702, USA
| | - Jennifer R Powell
- Department of Biology, Gettysburg College, Gettysburg, PA, 17325, USA.
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22
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Molecular insights into transgenerational inheritance of stress memory. J Genet Genomics 2021; 49:89-95. [PMID: 34923165 DOI: 10.1016/j.jgg.2021.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/23/2022]
Abstract
There is accumulating evidence to show that environmental stressors can regulate a variety of phenotypes in descendants through germline-mediated epigenetic inheritance. Studies of model organisms exposed to environmental cues (e.g., diet, heat stress, toxins) indicate that altered DNA methylations, histone modifications, or non-coding RNAs in the germ cells are responsible for the transgenerational effects. In addition, it has also become evident that maternal provision could provide a mechanism for the transgenerational inheritance of stress adaptations that result from ancestral environmental cues. However, how the signal of environmentally-induced stress response transmits from the soma to the germline, which may influence offspring fitness, remains largely elusive. Small RNAs could serve as signaling molecules that transmit between tissues and even across generations. Furthermore, a recent study revealed that neuronal mitochondrial perturbations induce a transgenerational induction of the mitochondrial unfolded protein response mediated by a Wnt-dependent increase in mitochondrial DNA levels. Here, we review recent work on the molecular mechanism by which parental experience can affect future generations and the importance of soma-to-germline signaling for transgenerational inheritance.
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Maternal starvation primes progeny response to nutritional stress. PLoS Genet 2021; 17:e1009932. [PMID: 34843464 PMCID: PMC8659306 DOI: 10.1371/journal.pgen.1009932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 12/09/2021] [Accepted: 11/05/2021] [Indexed: 12/22/2022] Open
Abstract
Organisms adapt to environmental changes in order to survive. Mothers exposed to nutritional stresses can induce an adaptive response in their offspring. However, the molecular mechanisms behind such inheritable links are not clear. Here we report that in Drosophila, starvation of mothers primes the progeny against subsequent nutritional stress. We found that RpL10Ab represses TOR pathway activity by genetically interacting with TOR pathway components TSC2 and Rheb. In addition, starved mothers produce offspring with lower levels of RpL10Ab in the germline, which results in higher TOR pathway activity, conferring greater resistance to starvation-induced oocyte loss. The RpL10Ab locus encodes for the RpL10Ab mRNA and a stable intronic sequence RNA (sisR-8), which collectively repress RpL10Ab pre-mRNA splicing in a negative feedback mechanism. During starvation, an increase in maternally deposited RpL10Ab and sisR-8 transcripts leads to the reduction of RpL10Ab expression in the offspring. Our study suggests that the maternally deposited RpL10Ab and sisR-8 transcripts trigger a negative feedback loop that mediates intergenerational adaptation to nutritional stress as a starvation response. In the wild, animals need to adapt to frequent changes in the environment. Mothers who are exposed to nutritional stresses are known to produce offspring which are preconditioned to adapt to the mothers’ environment. However, it is unclear how such maternal “memory” is being passed on to the offspring. Here we show that Drosophila mothers exposed to starvation produce offspring which are more resistant to starvation during oogenesis. This process is mediated by maternally inherited RpL10Ab mRNA and a stable intronic sequence RNA (sisR-8), which collectively repress the splicing of RpL10Ab pre-mRNA, leading to lower RpL10Ab expression in the offspring ovaries. As a consequence, lower RpL10Ab expression results in higher TOR pathway activity, conferring greater resistance to starvation during oogenesis. Hence, maternally inherited transcripts may play a role as mediators in conferring intergenerational adaption to starvation.
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Burton NO, Willis A, Fisher K, Braukmann F, Price J, Stevens L, Baugh LR, Reinke A, Miska EA. Intergenerational adaptations to stress are evolutionarily conserved, stress-specific, and have deleterious trade-offs. eLife 2021; 10:e73425. [PMID: 34622777 PMCID: PMC8570697 DOI: 10.7554/elife.73425] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/27/2021] [Indexed: 12/24/2022] Open
Abstract
Despite reports of parental exposure to stress promoting physiological adaptations in progeny in diverse organisms, there remains considerable debate over the significance and evolutionary conservation of such multigenerational effects. Here, we investigate four independent models of intergenerational adaptations to stress in Caenorhabditis elegans - bacterial infection, eukaryotic infection, osmotic stress, and nutrient stress - across multiple species. We found that all four intergenerational physiological adaptations are conserved in at least one other species, that they are stress -specific, and that they have deleterious tradeoffs in mismatched environments. By profiling the effects of parental bacterial infection and osmotic stress exposure on progeny gene expression across species, we established a core set of 587 genes that exhibited a greater than twofold intergenerational change in expression in response to stress in C. elegans and at least one other species, as well as a set of 37 highly conserved genes that exhibited a greater than twofold intergenerational change in expression in all four species tested. Furthermore, we provide evidence suggesting that presumed adaptive and deleterious intergenerational effects are molecularly related at the gene expression level. Lastly, we found that none of the effects we detected of these stresses on C. elegans F1 progeny gene expression persisted transgenerationally three generations after stress exposure. We conclude that intergenerational responses to stress play a substantial and evolutionarily conserved role in regulating animal physiology and that the vast majority of the effects of parental stress on progeny gene expression are reversible and not maintained transgenerationally.
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Affiliation(s)
- Nicholas O Burton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
- Van Andel InstituteGrand RapidsUnited States
| | - Alexandra Willis
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Kinsey Fisher
- Department of Biology, Duke UniversityDurhamUnited States
| | - Fabian Braukmann
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
| | - Jonathan Price
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - L Ryan Baugh
- Department of Biology, Duke UniversityDurhamUnited States
- Center for Genomic and Computational Biology, Duke UniversityDurhamUnited States
| | - Aaron Reinke
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Eric A Miska
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
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25
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Burton NO, Greer EL. Multigenerational epigenetic inheritance: Transmitting information across generations. Semin Cell Dev Biol 2021; 127:121-132. [PMID: 34426067 DOI: 10.1016/j.semcdb.2021.08.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 01/07/2023]
Abstract
Inherited epigenetic information has been observed to regulate a variety of complex organismal phenotypes across diverse taxa of life. This continually expanding body of literature suggests that epigenetic inheritance plays a significant, and potentially fundamental, role in inheritance. Despite the important role these types of effects play in biology, the molecular mediators of this non-genetic transmission of information are just now beginning to be deciphered. Here we provide an intellectual framework for interpreting these findings and how they can interact with each other. We also define the different types of mechanisms that have been found to mediate epigenetic inheritance and to regulate whether epigenetic information persists for one or many generations. The field of epigenetic inheritance is entering an exciting phase, in which we are beginning to understand the mechanisms by which non-genetic information is transmitted to, and deciphered by, subsequent generations to maintain essential environmental information without permanently altering the genetic code. A more complete understanding of how and when epigenetic inheritance occurs will advance our understanding of numerous different aspects of biology ranging from how organisms cope with changing environments to human pathologies influenced by a parent's environment.
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Affiliation(s)
- Nicholas O Burton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
| | - Eric L Greer
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA.
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26
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The memory of neuronal mitochondrial stress is inherited transgenerationally via elevated mitochondrial DNA levels. Nat Cell Biol 2021; 23:870-880. [PMID: 34341532 DOI: 10.1038/s41556-021-00724-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 06/29/2021] [Indexed: 02/06/2023]
Abstract
The memory of stresses experienced by parents can be passed on to descendants as a forecast of the challenges to come. Here, we discovered that the neuronal mitochondrial perturbation-induced systemic mitochondrial unfolded protein response (UPRmt) in Caenorhabditis elegans can be transmitted to offspring over multiple generations. The transgenerational activation of UPRmt is mediated by maternal inheritance of elevated levels of mitochondrial DNA (mtDNA), which causes the proteostasis stress within mitochondria. Furthermore, results from intercrossing studies using wild C. elegans strains further support that maternal inheritance of higher levels of mtDNA can induce the UPRmt in descendants. The mitokine Wnt signalling pathway is required for the transmission of elevated mtDNA levels across generations, thereby conferring lifespan extension and stress resistance to offspring. Collectively, our results reveal that the nervous system can transmit stress signals across generations by increasing mtDNA in the germline, enabling descendants to better cope with anticipated challenges.
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27
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Wasson JA, Harris G, Keppler-Ross S, Brock TJ, Dar AR, Butcher RA, Fischer SEJ, Kagias K, Clardy J, Zhang Y, Mango SE. Neuronal control of maternal provisioning in response to social cues. SCIENCE ADVANCES 2021; 7:7/34/eabf8782. [PMID: 34417172 PMCID: PMC8378817 DOI: 10.1126/sciadv.abf8782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/30/2021] [Indexed: 05/03/2023]
Abstract
Mothers contribute cytoplasmic components to their progeny in a process called maternal provisioning. Provisioning is influenced by the parental environment, but the molecular pathways that transmit environmental cues between generations are not well understood. Here, we show that, in Caenorhabditis elegans, social cues modulate maternal provisioning to regulate gene silencing in offspring. Intergenerational signal transmission depends on a pheromone-sensing neuron and neuronal FMRFamide (Phe-Met-Arg-Phe)-like peptides. Parental FMRFamide-like peptide signaling dampens oxidative stress resistance and promotes the deposition of mRNAs for translational components in progeny, which, in turn, reduces gene silencing. This study identifies a previously unknown pathway for intergenerational communication that links neuronal responses to maternal provisioning. We suggest that loss of social cues in the parental environment represents an adverse environment that stimulates stress responses across generations.
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Affiliation(s)
| | - Gareth Harris
- Department of Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
- Department of Biology, California State University Channel Islands, Camarillo, CA, USA
| | | | | | - Abdul R Dar
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Rebecca A Butcher
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Sylvia E J Fischer
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Konstantinos Kagias
- Department of Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Cambridge, MA, USA
| | - Yun Zhang
- Department of Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA.
| | - Susan E Mango
- Biozentrum, University of Basel, Basel, Switzerland.
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Robles P, Turner A, Zuco G, Adams S, Paganopolou P, Winton M, Hill B, Kache V, Bateson C, Pires-daSilva A. Parental energy-sensing pathways control intergenerational offspring sex determination in the nematode Auanema freiburgensis. BMC Biol 2021; 19:102. [PMID: 34001117 PMCID: PMC8130380 DOI: 10.1186/s12915-021-01032-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/20/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Environmental stimuli experienced by the parental generation influence the phenotype of subsequent generations (Demoinet et al., Proc Natl Acad Sci U S A 114:E2689-E2698, 2017; Burton et al., Nat Cell Biol 19:252-257, 2017; Agrawal et al., Nature 401:60-63, 1999). The effects of these stimuli on the parental generation may be passed through the germline, but the mechanisms at the basis of this non-Mendelian type of inheritance, their level of conservation, how they lead to adaptive vs non-adaptive, and intergenerational vs transgenerational inheritance are poorly understood. Here we show that modulation of nutrient-sensing pathways in the parental generation of the nematode Auanema freiburgensis regulates phenotypic plasticity of its offspring. RESULTS In response to con-specific pheromones indicative of stress, AMP-activated protein kinase (AMPK), mechanistic target of rapamycin complex 1 (mTORC1), and insulin signaling regulate stress resistance and sex determination across one generation, and these effects can be mimicked by pathway modulators. The effectors of these pathways are closely associated with the chromatin, and their regulation affects the chromatin acetylation status in the germline. CONCLUSION These results suggest that highly conserved metabolic sensors regulate phenotypic plasticity through regulation of subcellular localization of their effectors, leading to changes in chromatin acetylation and epigenetic status of the germline.
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Affiliation(s)
- Pedro Robles
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Anisa Turner
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Giusy Zuco
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Sally Adams
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Michael Winton
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Beth Hill
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Vikas Kache
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Christine Bateson
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Andre Pires-daSilva
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA.
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29
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Hibshman JD, Webster AK, Baugh LR. Liquid-culture protocols for synchronous starvation, growth, dauer formation, and dietary restriction of Caenorhabditis elegans. STAR Protoc 2021; 2:100276. [PMID: 33490989 PMCID: PMC7811050 DOI: 10.1016/j.xpro.2020.100276] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Standard laboratory culture of Caenorhabditis elegans utilizes solid growth media with a bacterial food source. However, this culture method limits control of food availability and worm population density, factors that impact many life-history traits. Here, we describe liquid-culture protocols for precisely modulating bacterial food availability and population density, facilitating reliable production of arrested L1 larvae, dauer larvae, dietarily restricted worms, or well-fed worms. Worms can be grown in small quantities for standard assays or in the millions for other applications. For complete details on the use and execution of these protocols, please refer to Hibshman et al. (2016), Webster et al. (2018), and Jordan et al. (2019). A set of liquid-culture protocols for a variety of applications in C. elegans Stringent starvation-induced developmental arrest of L1-stage larvae Production of pure populations of dauer larvae without pheromone, mutants, or selection Dietary restriction based on bacterial dilution rather than mutants
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Affiliation(s)
| | - Amy K Webster
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, NC 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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30
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Ewe CK, Alok G, Rothman JH. Stressful development: integrating endoderm development, stress, and longevity. Dev Biol 2020; 471:34-48. [PMID: 33307045 DOI: 10.1016/j.ydbio.2020.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 10/22/2022]
Abstract
In addition to performing digestion and nutrient absorption, the intestine serves as one of the first barriers to the external environment, crucial for protecting the host from environmental toxins, pathogenic invaders, and other stress inducers. The gene regulatory network (GRN) governing embryonic development of the endoderm and subsequent differentiation and maintenance of the intestine has been well-documented in C. elegans. A key regulatory input that initiates activation of the embryonic GRN for endoderm and mesoderm in this animal is the maternally provided SKN-1 transcription factor, an ortholog of the vertebrate Nrf1 and 2, which, like C. elegans SKN-1, perform conserved regulatory roles in mediating a variety of stress responses across metazoan phylogeny. Other key regulatory factors in early gut development also participate in stress response as well as in innate immunity and aging and longevity. In this review, we discuss the intersection between genetic nodes that mediate endoderm/intestine differentiation and regulation of stress and homeostasis. We also consider how direct signaling from the intestine to the germline, in some cases involving SKN-1, facilitates heritable epigenetic changes, allowing transmission of adaptive stress responses across multiple generations. These connections between regulation of endoderm/intestine development and stress response mechanisms suggest that varying selective pressure exerted on the stress response pathways may influence the architecture of the endoderm GRN, thereby leading to genetic and epigenetic variation in early embryonic GRN regulatory events.
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Affiliation(s)
- Chee Kiang Ewe
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Geneva Alok
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Joel H Rothman
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA.
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31
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Mata-Cabana A, Pérez-Nieto C, Olmedo M. Nutritional control of postembryonic development progression and arrest in Caenorhabditis elegans. ADVANCES IN GENETICS 2020; 107:33-87. [PMID: 33641748 DOI: 10.1016/bs.adgen.2020.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Developmental programs are under strict genetic control that favors robustness of the process. In order to guarantee the same outcome in different environmental situations, development is modulated by input pathways, which inform about external conditions. In the nematode Caenorhabditis elegans, the process of postembryonic development involves a series of stereotypic cell divisions, the progression of which is controlled by the nutritional status of the animal. C. elegans can arrest development at different larval stages, leading to cell arrest of the relevant divisions of the stage. This means that studying the nutritional control of development in C. elegans we can learn about the mechanisms controlling cell division in an in vivo model. In this work, we reviewed the current knowledge about the nutrient sensing pathways that control the progression or arrest of development in response to nutrient availability, with a special focus on the arrest at the L1 stage.
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Affiliation(s)
- Alejandro Mata-Cabana
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avd. Reina Mercedes, Sevilla, Spain
| | - Carmen Pérez-Nieto
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avd. Reina Mercedes, Sevilla, Spain
| | - María Olmedo
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avd. Reina Mercedes, Sevilla, Spain.
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32
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Baugh LR, Hu PJ. Starvation Responses Throughout the Caenorhabditiselegans Life Cycle. Genetics 2020; 216:837-878. [PMID: 33268389 PMCID: PMC7768255 DOI: 10.1534/genetics.120.303565] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023] Open
Abstract
Caenorhabditis elegans survives on ephemeral food sources in the wild, and the species has a variety of adaptive responses to starvation. These features of its life history make the worm a powerful model for studying developmental, behavioral, and metabolic starvation responses. Starvation resistance is fundamental to life in the wild, and it is relevant to aging and common diseases such as cancer and diabetes. Worms respond to acute starvation at different times in the life cycle by arresting development and altering gene expression and metabolism. They also anticipate starvation during early larval development, engaging an alternative developmental program resulting in dauer diapause. By arresting development, these responses postpone growth and reproduction until feeding resumes. A common set of signaling pathways mediates systemic regulation of development in each context but with important distinctions. Several aspects of behavior, including feeding, foraging, taxis, egg laying, sleep, and associative learning, are also affected by starvation. A variety of conserved signaling, gene regulatory, and metabolic mechanisms support adaptation to starvation. Early life starvation can have persistent effects on adults and their descendants. With its short generation time, C. elegans is an ideal model for studying maternal provisioning, transgenerational epigenetic inheritance, and developmental origins of adult health and disease in humans. This review provides a comprehensive overview of starvation responses throughout the C. elegans life cycle.
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Affiliation(s)
- L Ryan Baugh
- Department of Biology, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708 and
| | - Patrick J Hu
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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Stuhr NL, Curran SP. Bacterial diets differentially alter lifespan and healthspan trajectories in C. elegans. Commun Biol 2020; 3:653. [PMID: 33159120 PMCID: PMC7648844 DOI: 10.1038/s42003-020-01379-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/14/2020] [Indexed: 01/21/2023] Open
Abstract
Diet is one of the more variable aspects in life due to the variety of options that organisms are exposed to in their natural habitats. In the laboratory, C. elegans are raised on bacterial monocultures, traditionally the E. coli B strain OP50, and spontaneously occurring microbial contaminants are removed to limit experimental variability because diet-including the presence of contaminants-can exert a potent influence over animal physiology. In order to diversify the menu available to culture C. elegans in the lab, we have isolated and cultured three such microbes: Methylobacterium, Xanthomonas, and Sphingomonas. The nutritional composition of these bacterial foods is unique, and when fed to C. elegans, can differentially alter multiple life history traits including development, reproduction, and metabolism. In light of the influence each food source has on specific physiological attributes, we comprehensively assessed the impact of these bacteria on animal health and devised a blueprint for utilizing different food combinations over the lifespan, in order to promote longevity. The expansion of the bacterial food options to use in the laboratory will provide a critical tool to better understand the complexities of bacterial diets and subsequent changes in physiology and gene expression.
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Affiliation(s)
- Nicole L Stuhr
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA, 90089, USA
- Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Sean P Curran
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA, 90089, USA.
- Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.
- Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Ave, Los Angeles, CA, 90033, USA.
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Baugh LR, Day T. Nongenetic inheritance and multigenerational plasticity in the nematode C. elegans. eLife 2020; 9:e58498. [PMID: 32840479 PMCID: PMC7447421 DOI: 10.7554/elife.58498] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
A rapidly growing body of literature in several organisms suggests that environmentally-induced adaptive changes in phenotype can be transmitted across multiple generations. Although within-generation plasticity has been well documented, multigenerational plasticity represents a significant departure from conventional evolutionary thought. Studies of C. elegans have been particularly influential because this species exhibits extensive phenotypic plasticity, it is often essentially isogenic, and it has well-documented molecular and cellular mechanisms through which nongenetic inheritance occurs. However, while experimentalists are eager to claim that nongenetic modes of inheritance characterized in this and other model systems enhance fitness, many biologists remain skeptical given the extraordinary nature of this claim. We establish three criteria to evaluate how compelling the evidence for adaptive multigenerational plasticity is, and we use these criteria to critically examine putative cases of it in C. elegans. We conclude by suggesting potentially fruitful avenues for future research.
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Affiliation(s)
- L Ryan Baugh
- Department of Biology, Center for Genomics and Computational Biology, Duke UniversityDurhamUnited States
| | - Troy Day
- Departments of Mathematics and Statistics, Department of Biology, Queens UniversityKingstonCanada
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35
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Natural cryptic variation in epigenetic modulation of an embryonic gene regulatory network. Proc Natl Acad Sci U S A 2020; 117:13637-13646. [PMID: 32482879 DOI: 10.1073/pnas.1920343117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Gene regulatory networks (GRNs) that direct animal embryogenesis must respond to varying environmental and physiological conditions to ensure robust construction of organ systems. While GRNs are evolutionarily modified by natural genomic variation, the roles of epigenetic processes in shaping plasticity of GRN architecture are not well understood. The endoderm GRN in Caenorhabditis elegans is initiated by the maternally supplied SKN-1/Nrf2 bZIP transcription factor; however, the requirement for SKN-1 in endoderm specification varies widely among distinct C. elegans wild isotypes, owing to rapid developmental system drift driven by accumulation of cryptic genetic variants. We report here that heritable epigenetic factors that are stimulated by transient developmental diapause also underlie cryptic variation in the requirement for SKN-1 in endoderm development. This epigenetic memory is inherited from the maternal germline, apparently through a nuclear, rather than cytoplasmic, signal, resulting in a parent-of-origin effect (POE), in which the phenotype of the progeny resembles that of the maternal founder. The occurrence and persistence of POE varies between different parental pairs, perduring for at least 10 generations in one pair. This long-perduring POE requires piwi-interacting RNA (piRNA) function and the germline nuclear RNA interference (RNAi) pathway, as well as MET-2 and SET-32, which direct histone H3K9 trimethylation and drive heritable epigenetic modification. Such nongenetic cryptic variation may provide a resource of additional phenotypic diversity through which adaptation may facilitate evolutionary changes and shape developmental regulatory systems.
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36
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Abstract
Epigenetic effects can be mediated by changes in chromatin state that are transmitted from parent to child via gametes, but support is gathering for maternal yolk, which is deposited into ooctyes, as an extranuclear epigenetic factor that can contribute to phenotypic plasticity across generations in Caenorhabditis elegans.
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Affiliation(s)
- Robert H Dowen
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Shawn Ahmed
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Ewe CK, Torres Cleuren YN, Rothman JH. Evolution and Developmental System Drift in the Endoderm Gene Regulatory Network of Caenorhabditis and Other Nematodes. Front Cell Dev Biol 2020; 8:170. [PMID: 32258041 PMCID: PMC7093329 DOI: 10.3389/fcell.2020.00170] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/02/2020] [Indexed: 01/17/2023] Open
Abstract
Developmental gene regulatory networks (GRNs) underpin metazoan embryogenesis and have undergone substantial modification to generate the tremendous variety of animal forms present on Earth today. The nematode Caenorhabditis elegans has been a central model for advancing many important discoveries in fundamental mechanistic biology and, more recently, has provided a strong base from which to explore the evolutionary diversification of GRN architecture and developmental processes in other species. In this short review, we will focus on evolutionary diversification of the GRN for the most ancient of the embryonic germ layers, the endoderm. Early embryogenesis diverges considerably across the phylum Nematoda. Notably, while some species deploy regulative development, more derived species, such as C. elegans, exhibit largely mosaic modes of embryogenesis. Despite the relatively similar morphology of the nematode gut across species, widespread variation has been observed in the signaling inputs that initiate the endoderm GRN, an exemplar of developmental system drift (DSD). We will explore how genetic variation in the endoderm GRN helps to drive DSD at both inter- and intraspecies levels, thereby resulting in a robust developmental system. Comparative studies using divergent nematodes promise to unveil the genetic mechanisms controlling developmental plasticity and provide a paradigm for the principles governing evolutionary modification of an embryonic GRN.
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Affiliation(s)
- Chee Kiang Ewe
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | | | - Joel H. Rothman
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
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Olmedo M, Mata‐Cabana A, Jesús Rodríguez‐Palero M, García‐Sánchez S, Fernández‐Yañez A, Merrow M, Artal‐Sanz M. Prolonged quiescence delays somatic stem cell-like divisions in Caenorhabditis elegans and is controlled by insulin signaling. Aging Cell 2020; 19:e13085. [PMID: 31852031 PMCID: PMC6996950 DOI: 10.1111/acel.13085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/30/2019] [Accepted: 11/13/2019] [Indexed: 01/05/2023] Open
Abstract
Cells can enter quiescence in adverse conditions and resume proliferation when the environment becomes favorable. Prolonged quiescence comes with a cost, reducing the subsequent speed and potential to return to proliferation. Here, we show that a similar process happens during Caenorhabditis elegans development, providing an in vivo model to study proliferative capacity after quiescence. Hatching under starvation provokes the arrest of blast cell divisions that normally take place during the first larval stage (L1). We have used a novel method to precisely quantify each stage of postembryonic development to analyze the consequences of prolonged L1 quiescence. We report that prolonged L1 quiescence delays the reactivation of blast cell divisions in C. elegans, leading to a delay in the initiation of postembryonic development. The transcription factor DAF-16/FOXO is necessary for rapid recovery after extended arrest, and this effect is independent from its role as a suppressor of cell proliferation. Instead, the activation of DAF-16 by decreased insulin signaling reduces the rate of L1 aging, increasing proliferative potential. We also show that yolk provisioning affects the proliferative potential after L1 arrest modulating the rate of L1 aging, providing a possible mechanistic link between insulin signaling and the maintenance of proliferative potential. Furthermore, variable yolk provisioning in embryos is one of the sources of interindividual variability in recovery after quiescence of genetically identical animals. Our results support the relevance of L1 arrest as an in vivo model to study stem cell-like aging and the mechanisms for maintenance of proliferation potential after quiescence.
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Affiliation(s)
- María Olmedo
- Departamento de GenéticaFacultad de BiologíaUniversidad de SevillaSevilleSpain
| | | | - María Jesús Rodríguez‐Palero
- Andalusian Center for Developmental BiologyConsejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de OlavideSevilleSpain
- Department of Molecular Biology and Biochemical EngineeringUniversidad Pablo de OlavideSevilleSpain
| | | | - Antonio Fernández‐Yañez
- Andalusian Center for Developmental BiologyConsejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de OlavideSevilleSpain
- Department of Molecular Biology and Biochemical EngineeringUniversidad Pablo de OlavideSevilleSpain
| | - Martha Merrow
- Institute of Medical PsychologyFaculty of MedicineLMU MunichMunichGermany
| | - Marta Artal‐Sanz
- Andalusian Center for Developmental BiologyConsejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de OlavideSevilleSpain
- Department of Molecular Biology and Biochemical EngineeringUniversidad Pablo de OlavideSevilleSpain
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39
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Van de Walle P, Geens E, Baggerman G, José Naranjo-Galindo F, Askjaer P, Schoofs L, Temmerman L. CEH-60/PBX regulates vitellogenesis and cuticle permeability through intestinal interaction with UNC-62/MEIS in Caenorhabditis elegans. PLoS Biol 2019; 17:e3000499. [PMID: 31675356 PMCID: PMC6824563 DOI: 10.1371/journal.pbio.3000499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 10/08/2019] [Indexed: 11/18/2022] Open
Abstract
The onset of sexual maturity involves dramatic changes in physiology and gene expression in many animals. These include abundant yolk protein production in egg-laying species, an energetically costly process under extensive transcriptional control. Here, we used the model organism Caenorhabditis elegans to provide evidence for the spatiotemporally defined interaction of two evolutionarily conserved transcription factors, CEH-60/PBX and UNC-62/MEIS, acting as a gateway to yolk protein production. Via proteomics, bimolecular fluorescence complementation (BiFC), and biochemical and functional readouts, we show that this interaction occurs in the intestine of animals at the onset of sexual maturity and suffices to support the reproductive program. Our electron micrographs and functional assays provide evidence that intestinal PBX/MEIS cooperation drives another process that depends on lipid mobilization: the formation of an impermeable epicuticle. Without this lipid-rich protective layer, mutant animals are hypersensitive to exogenous oxidative stress and are poor partners for mating. Dedicated communication between the hypodermis and intestine in C. elegans likely supports these physiological outcomes, and we propose a fundamental role for the conserved PBX/MEIS interaction in multicellular signaling networks that rely on lipid homeostasis.
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Affiliation(s)
- Pieter Van de Walle
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Ellen Geens
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Geert Baggerman
- Centre for Proteomics (CFP), University of Antwerp, Antwerpen, Belgium
- VITO, Mol, Belgium
| | | | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), Universidad Pablo de Olavide, Seville, Spain
| | - Liliane Schoofs
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
- * E-mail:
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40
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Webster AK, Hung A, Moore BT, Guzman R, Jordan JM, Kaplan REW, Hibshman JD, Tanny RE, Cook DE, Andersen E, Baugh LR. Population Selection and Sequencing of Caenorhabditis elegans Wild Isolates Identifies a Region on Chromosome III Affecting Starvation Resistance. G3 (BETHESDA, MD.) 2019; 9:3477-3488. [PMID: 31444297 PMCID: PMC6778785 DOI: 10.1534/g3.119.400617] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/21/2019] [Indexed: 12/18/2022]
Abstract
To understand the genetic basis of complex traits, it is important to be able to efficiently phenotype many genetically distinct individuals. In the nematode Caenorhabditis elegans, individuals have been isolated from diverse populations around the globe and whole-genome sequenced. As a result, hundreds of wild strains with known genome sequences can be used for genome-wide association studies (GWAS). However, phenotypic analysis of these strains can be laborious, particularly for quantitative traits requiring multiple measurements per strain. Starvation resistance is likely a fitness-proximal trait for nematodes, and it is related to metabolic disease risk in humans. However, natural variation in C. elegans starvation resistance has not been systematically characterized, and precise measurement of the trait is time-intensive. Here, we developed a population-selection-and-sequencing-based approach to phenotype starvation resistance in a pool of 96 wild strains. We used restriction site-associated DNA sequencing (RAD-seq) to infer the frequency of each strain among survivors in a mixed culture over time during starvation. We used manual starvation survival assays to validate the trait data, confirming that strains that increased in frequency over time are starvation-resistant relative to strains that decreased in frequency. Further, we found that variation in starvation resistance is significantly associated with variation at a region on chromosome III. Using a near-isogenic line (NIL), we showed the importance of this genomic interval for starvation resistance. This study demonstrates the feasibility of using population selection and sequencing in an animal model for phenotypic analysis of quantitative traits, documents natural variation of starvation resistance in C. elegans, and identifies a genomic region that contributes to such variation.
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Affiliation(s)
- Amy K Webster
- Department of Biology, Duke University, Durham, NC
- University Program in Genetics and Genomics, Duke University, Durham, NC, and
| | - Anthony Hung
- Department of Biology, Duke University, Durham, NC
| | - Brad T Moore
- Department of Biology, Duke University, Durham, NC
| | - Ryan Guzman
- Department of Biology, Duke University, Durham, NC
| | | | - Rebecca E W Kaplan
- Department of Biology, Duke University, Durham, NC
- University Program in Genetics and Genomics, Duke University, Durham, NC, and
| | - Jonathan D Hibshman
- Department of Biology, Duke University, Durham, NC
- University Program in Genetics and Genomics, Duke University, Durham, NC, and
| | - Robyn E Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
| | - Erik Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, NC
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Perez MF, Lehner B. Vitellogenins - Yolk Gene Function and Regulation in Caenorhabditis elegans. Front Physiol 2019; 10:1067. [PMID: 31551797 PMCID: PMC6736625 DOI: 10.3389/fphys.2019.01067] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/05/2019] [Indexed: 12/14/2022] Open
Abstract
Vitellogenins are a family of yolk proteins that are by far the most abundant among oviparous animals. In the model nematode Caenorhabditis elegans, the 6 vitellogenins are among the most highly expressed genes in the adult hermaphrodite intestine, which produces copious yolk to provision eggs. In this article we review what is known about the vitellogenin genes and proteins in C. elegans, in comparison with vitellogenins in other taxa. We argue that the primary purpose of abundant vitellogenesis in C. elegans is to support post-embryonic development and fertility, rather than embryogenesis, especially in harsh environments. Increasing vitellogenin provisioning underlies several post-embryonic phenotypic alterations associated with advancing maternal age, demonstrating that vitellogenins can act as an intergenerational signal mediating the influence of parental physiology on progeny. We also review what is known about vitellogenin regulation - how tissue-, sex- and stage-specificity of expression is achieved, how vitellogenins are regulated by major signaling pathways, how vitellogenin expression is affected by extra-intestinal tissues and how environmental experience affects vitellogenesis. Lastly, we speculate whether C. elegans vitellogenins may play other roles in worm physiology.
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Affiliation(s)
- Marcos Francisco Perez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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