1
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Sundaram MV, Pujol N. The Caenorhabditis elegans cuticle and precuticle: a model for studying dynamic apical extracellular matrices in vivo. Genetics 2024; 227:iyae072. [PMID: 38995735 PMCID: PMC11304992 DOI: 10.1093/genetics/iyae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/25/2024] [Indexed: 07/14/2024] Open
Abstract
Apical extracellular matrices (aECMs) coat the exposed surfaces of animal bodies to shape tissues, influence social interactions, and protect against pathogens and other environmental challenges. In the nematode Caenorhabditis elegans, collagenous cuticle and zona pellucida protein-rich precuticle aECMs alternately coat external epithelia across the molt cycle and play many important roles in the worm's development, behavior, and physiology. Both these types of aECMs contain many matrix proteins related to those in vertebrates, as well as some that are nematode-specific. Extensive differences observed among tissues and life stages demonstrate that aECMs are a major feature of epithelial cell identity. In addition to forming discrete layers, some cuticle components assemble into complex substructures such as ridges, furrows, and nanoscale pillars. The epidermis and cuticle are mechanically linked, allowing the epidermis to sense cuticle damage and induce protective innate immune and stress responses. The C. elegans model, with its optical transparency, facilitates the study of aECM cell biology and structure/function relationships and all the myriad ways by which aECM can influence an organism.
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Affiliation(s)
- Meera V Sundaram
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Nathalie Pujol
- Aix Marseille University, INSERM, CNRS, CIML, Turing Centre for Living Systems, 13009 Marseille, France
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2
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Hu Q, Xu Y, Song M, Dai Y, Antebi A, Shen Y. BLMP-1 is a critical temporal regulator of dietary-restriction-induced response in Caenorhabditis elegans. Cell Rep 2024; 43:113959. [PMID: 38483903 DOI: 10.1016/j.celrep.2024.113959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 02/07/2024] [Accepted: 02/28/2024] [Indexed: 04/02/2024] Open
Abstract
The extrinsic diet and the intrinsic developmental programs are intertwined. Although extensive research has been conducted on how nutrition regulates development, whether and how developmental programs control the timing of nutritional responses remain barely known. Here, we report that a developmental timing regulator, BLMP-1/BLIMP1, governs the temporal response to dietary restriction (DR). At the end of larval development, BLMP-1 is induced and interacts with DR-activated PHA-4/FOXA, a key transcription factor responding to the reduced nutrition. By integrating temporal and nutritional signaling, the DR response regulates many development-related genes, including gska-3/GSK3β, through BLMP-1-PHA-4 at the onset of adulthood. Upon DR, a precocious activation of BLMP-1 in early larval stages impairs neuronal development through gska-3, whereas the increase of gska-3 by BLMP-1-PHA-4 at the last larval stage suppresses WNT signaling in adulthood for DR-induced longevity. Our findings reveal a temporal checkpoint of the DR response that protects larval development and promotes adult health.
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Affiliation(s)
- Qingyuan Hu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunpeng Xu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengjiao Song
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yumin Dai
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674 Cologne, Germany
| | - Yidong Shen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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3
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Adams JRG, Pooranachithra M, Jyo EM, Zheng SL, Goncharov A, Crew JR, Kramer JM, Jin Y, Ernst AM, Chisholm AD. Nanoscale patterning of collagens in C. elegans apical extracellular matrix. Nat Commun 2023; 14:7506. [PMID: 37980413 PMCID: PMC10657453 DOI: 10.1038/s41467-023-43058-9] [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: 02/05/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
Apical extracellular matrices (aECMs) are complex extracellular compartments that form important interfaces between animals and their environment. In the adult C. elegans cuticle, layers are connected by regularly spaced columnar structures known as struts. Defects in struts result in swelling of the fluid-filled medial cuticle layer ('blistering', Bli). Here we show that three cuticle collagens BLI-1, BLI-2, and BLI-6, play key roles in struts. BLI-1 and BLI-2 are essential for strut formation whereas activating mutations in BLI-6 disrupt strut formation. BLI-1, BLI-2, and BLI-6 precisely colocalize to arrays of puncta in the adult cuticle, corresponding to struts, initially deposited in diffuse stripes adjacent to cuticle furrows. They eventually exhibit tube-like morphology, with the basal ends of BLI-containing struts contact regularly spaced holes in the cuticle. Genetic interaction studies indicate that BLI strut patterning involves interactions with other cuticle components. Our results reveal strut formation as a tractable example of precise aECM patterning at the nanoscale.
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Affiliation(s)
- Jennifer R G Adams
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Murugesan Pooranachithra
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Erin M Jyo
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sherry Li Zheng
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alexandr Goncharov
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jennifer R Crew
- Northwestern University School of Medicine, Department of Cell and Molecular Biology, Chicago, IL, 60611, USA
| | - James M Kramer
- Northwestern University School of Medicine, Department of Cell and Molecular Biology, Chicago, IL, 60611, USA
| | - Yishi Jin
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andreas M Ernst
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andrew D Chisholm
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
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4
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Reich H, Savage-Dunn C. Signaling circuits and the apical extracellular matrix in aging: connections identified in the nematode Caenorhabditis elegans. Am J Physiol Cell Physiol 2023; 325:C1201-C1211. [PMID: 37721005 PMCID: PMC10861026 DOI: 10.1152/ajpcell.00195.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/24/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
Numerous conserved signaling pathways play critical roles in aging, including insulin/IGF-1, TGF-β, and Wnt pathways. Some of these pathways also play prominent roles in the formation and maintenance of the extracellular matrix. The nematode Caenorhabditis elegans has been an enduringly productive system for the identification of conserved mechanisms of biological aging. Recent studies in C. elegans highlight the regulatory circuits between conserved signaling pathways and the extracellular matrix, revealing a bidirectional relationship between these factors and providing a platform to address how regulation of and by the extracellular matrix can impact lifespan and organismal health during aging. These discoveries provide new opportunities for clinical advances and novel therapeutic strategies.
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Affiliation(s)
- Hannah Reich
- Department of Biology, Queens College, City University of New York, Flushing, New York, United States
| | - Cathy Savage-Dunn
- Department of Biology, Queens College, City University of New York, Flushing, New York, United States
- PhD Program in Biology, The Graduate Center, City University of New York, New York, New York, United States
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5
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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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6
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Barbulescu R, Mestre G, Oliveira AL, Silveira LM. Learning the dynamics of realistic models of C. elegans nervous system with recurrent neural networks. Sci Rep 2023; 13:467. [PMID: 36627317 PMCID: PMC9832137 DOI: 10.1038/s41598-022-25421-w] [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: 06/23/2022] [Accepted: 11/29/2022] [Indexed: 01/12/2023] Open
Abstract
Given the inherent complexity of the human nervous system, insight into the dynamics of brain activity can be gained from studying smaller and simpler organisms. While some of the potential target organisms are simple enough that their behavioural and structural biology might be well-known and understood, others might still lead to computationally intractable models that require extensive resources to simulate. Since such organisms are frequently only acting as proxies to further our understanding of underlying phenomena or functionality, often one is not interested in the detailed evolution of every single neuron in the system. Instead, it is sufficient to observe the subset of neurons that capture the effect that the profound nonlinearities of the neuronal system have in response to different stimuli. In this paper, we consider the well-known nematode Caenorhabditis elegans and seek to investigate the possibility of generating lower complexity models that capture the system's dynamics with low error using only measured or simulated input-output information. Such models are often termed black-box models. We show how the nervous system of C. elegans can be modelled and simulated with data-driven models using different neural network architectures. Specifically, we target the use of state-of-the-art recurrent neural network architectures such as Long Short-Term Memory and Gated Recurrent Units and compare these architectures in terms of their properties and their accuracy (Root Mean Square Error), as well as the complexity of the resulting models. We show that Gated Recurrent Unit models with a hidden layer size of 4 are able to accurately reproduce the system response to very different stimuli. We furthermore explore the relative importance of their inputs as well as scalability to more scenarios.
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Affiliation(s)
| | - Gonçalo Mestre
- grid.14647.300000 0001 0279 8114INESC-ID Lisboa, Rua Alves Redol 9, Lisbon, 1000-029 Portugal ,grid.9983.b0000 0001 2181 4263IST Técnico Lisboa, Universidade de Lisboa, Av. Rovisco Pais 1, Lisbon, 1049-001 Portugal
| | - Arlindo L. Oliveira
- grid.14647.300000 0001 0279 8114INESC-ID Lisboa, Rua Alves Redol 9, Lisbon, 1000-029 Portugal ,grid.9983.b0000 0001 2181 4263IST Técnico Lisboa, Universidade de Lisboa, Av. Rovisco Pais 1, Lisbon, 1049-001 Portugal
| | - Luís Miguel Silveira
- grid.14647.300000 0001 0279 8114INESC-ID Lisboa, Rua Alves Redol 9, Lisbon, 1000-029 Portugal ,grid.9983.b0000 0001 2181 4263IST Técnico Lisboa, Universidade de Lisboa, Av. Rovisco Pais 1, Lisbon, 1049-001 Portugal
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7
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Yücel D. Ketamine induces apical extracellular matrix modifications in Caenorhabditis elegans. Sci Rep 2022; 12:22122. [PMID: 36543791 PMCID: PMC9772317 DOI: 10.1038/s41598-022-24632-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
Ketamine is a widely used anesthetic agent since 1960s and has recently been exploited for its rapid antidepressant action at subanesthetic doses. It has been demonstrated that ketamine induces alterations in extracellular matrix (ECM) in rodent models which in part plays a role in its anti-depressant action. The nematode Caenorhabditis elegans serves as a powerful tool for understanding mechanisms of drug action with its short life cycle, genetic amenability and conserved cellular processes. Further investigation is required particularly in in vivo systems to gain broader understanding of ketamine's actions. In this study, we aimed to decipher ketamine-mediated alterations using C. elegans as a model. We show that ketamine specifically induces apical extracellular matrix modifications (aECM) in the vulva and the cuticle. Ketamine treatment phenocopies neuronal migration and vulval invagination defects of chondroitin mutants despite wild-type like chondroitin staining pattern. Normal vulval expansion and defective vulval eversion phenotypes of ketamine-treated animals are suggestive of alterations in the network of aECM factors which do not impinge on chondroitin. Ketamine ameliorates impaired movement of a group of roller mutants characterised with collagen defects in the cuticle and RNA-seq identifies that 30% of the cuticular collagens are upregulated in response to ketamine. Ketamine alters aECM, neuronal migration and collagen expression in C. elegans. We propose C. elegans as a putative animal model to investigate ketamine-mediated ECM modifications.
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Affiliation(s)
- Duygu Yücel
- grid.411739.90000 0001 2331 2603Genome and Stem Cell Center (GENKOK), Erciyes University, 38039 Melikgazi, Kayseri Turkey
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8
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Hayat R, Manzoor M, Hussain A. Wnt Signaling Pathway: A Comprehensive Review. Cell Biol Int 2022; 46:863-877. [PMID: 35297539 DOI: 10.1002/cbin.11797] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/10/2022] [Accepted: 03/07/2022] [Indexed: 11/09/2022]
Abstract
Wnt signaling is an evolutionary cell-to-cell coordination mechanism and it is highly critical for a variety of physiological processes of an organism's body, including stem cell regeneration, proliferation, division, migration, polarity of a cell, determining fate of the cell and specification of neural crest, neural symmetry and morphogenesis. Wnts are extracellular secreted glycol proteins, consisted of a family of 19 human proteins that represent the complex nature of the regulatory structure and physiological efficiency of signaling. Moreover, a Wnt/β-catenin-dependent pathway and the β-catenin-independent pathway that is further classified into the Planar Cell Polarity and Wnt/Ca2+ pathways have been established as key signaling nodes downstream of the frizzled (Fz/Fzd) receptor, and these nodes are extensively analyzed at biochemical and molecular levels. Genetic and epigenetic activities that ultimately characterize the pathway and its subsequent responses contribute to Wnt-β-catenin signaling pathway hypo or hyper-activation and is associated with the variety of human disorders progression most significantly cancers. Recognizing how this mechanism operates is crucial to the advancement of cancer prevention therapies or regenerative medicine methods. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Rabia Hayat
- Institute of Evolution and Marine Biodiversity, Ocean university of China, Qingdao
| | - Maleeha Manzoor
- Department of Zoology, Government College University, Faisalabad
| | - Ali Hussain
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore
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9
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Sang Y, Ren J, Aballay A. The transcription factor HLH-26 controls probiotic-mediated protection against intestinal infection through up-regulation of the Wnt/BAR-1 pathway. PLoS Biol 2022; 20:e3001581. [PMID: 35263319 PMCID: PMC8936500 DOI: 10.1371/journal.pbio.3001581] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 03/21/2022] [Accepted: 02/23/2022] [Indexed: 12/31/2022] Open
Abstract
Probiotics play a critical role in the control of host intestinal microbial balance, protecting the host from gastrointestinal pathogens, modulating the host immune response, and decreasing host susceptibility to infection. To understand the mechanism underlying the protective effect of probiotics against infections through immune regulation, we examined protection against Salmonella enterica infection following exposure to nonpathogenic Enterococcus faecium in the nematode Caenorhabditis elegans. We found that the transcription factor HLH-26, a REF-1 family member of basic helix-loop-helix transcription factors, was required in the intestine for E. faecium-mediated protection of C. elegans against a lethal S. enterica infection. In addition, we uncovered that defense response genes controlled by the canonical Wnt/BAR-1 pathway were activated upon exposure to E. faecium in an HLH-26-dependent manner. Our findings highlight a role for REF-1/HLH-26 in the control of the Wnt/BAR-1 pathway in probiotic-mediated protection against gut infection.
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Affiliation(s)
- Yu Sang
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Jie Ren
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Alejandro Aballay
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
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10
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Mishra N, Mallick S, Negi VD. Salmonella Typhimurium infection causes defects and fastening of Caenorhabditis elegans developmental stages. Microbes Infect 2021; 24:104894. [PMID: 34756991 DOI: 10.1016/j.micinf.2021.104894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/03/2021] [Accepted: 10/22/2021] [Indexed: 01/12/2023]
Affiliation(s)
- Neha Mishra
- Laboratory of Infection Immunology, Department of Life Science National Institute of Technology, Rourkela 769008, Odisha, India.
| | - Swarupa Mallick
- Laboratory of Infection Immunology, Department of Life Science National Institute of Technology, Rourkela 769008, Odisha, India.
| | - Vidya Devi Negi
- Laboratory of Infection Immunology, Department of Life Science National Institute of Technology, Rourkela 769008, Odisha, India.
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11
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Mesbahi H, Pho KB, Tench AJ, Leon Guerrero VL, MacNeil LT. Cuticle Collagen Expression Is Regulated in Response to Environmental Stimuli by the GATA Transcription Factor ELT-3 in Caenorhabditis elegans. Genetics 2020; 215:483-495. [PMID: 32229533 PMCID: PMC7268988 DOI: 10.1534/genetics.120.303125] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 03/23/2020] [Indexed: 12/21/2022] Open
Abstract
The nematode Caenorhabditis elegans is protected from the environment by the cuticle, an extracellular collagen-based matrix that encloses the animal. Over 170 cuticular collagens are predicted in the C. elegans genome, but the role of each individual collagen is unclear. Stage-specific specialization of the cuticle explains the need for some collagens; however, the large number of collagens suggests that specialization of the cuticle may also occur in response to other environmental triggers. Missense mutations in many collagen genes can disrupt cuticle morphology, producing a helically twisted body causing the animal to move in a stereotypical pattern described as rolling. We find that environmental factors, including diet, early developmental arrest, and population density can differentially influence the penetrance of rolling in these mutants. These effects are in part due to changes in collagen gene expression that are mediated by the GATA family transcription factor ELT-3 We propose a model by which ELT-3 regulates collagen gene expression in response to environmental stimuli to promote the assembly of a cuticle specialized to a given environment.
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Affiliation(s)
- Hiva Mesbahi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Kim B Pho
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Andrea J Tench
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Victoria L Leon Guerrero
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Lesley T MacNeil
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
- Farncombe Family Digestive Health Research Institute, McMaster University, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8S 4K1
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12
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Hintze M, Koneru SL, Gilbert SPR, Katsanos D, Lambert J, Barkoulas M. A Cell Fate Switch in the Caenorhabditis elegans Seam Cell Lineage Occurs Through Modulation of the Wnt Asymmetry Pathway in Response to Temperature Increase. Genetics 2020; 214:927-939. [PMID: 31988193 PMCID: PMC7153939 DOI: 10.1534/genetics.119.302896] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/24/2020] [Indexed: 12/20/2022] Open
Abstract
Populations often display consistent developmental phenotypes across individuals despite inevitable biological stochasticity. Nevertheless, developmental robustness has limits, and systems can fail upon change in the environment or the genetic background. We use here the seam cells, a population of epidermal stem cells in Caenorhabditis elegans, to study the influence of temperature change and genetic variation on cell fate. Seam cell development has mostly been studied so far in the laboratory reference strain (N2), grown at 20° temperature. We demonstrate that an increase in culture temperature to 25° introduces variability in the wild-type seam cell lineage, with a proportion of animals showing an increase in seam cell number. We map this increase to lineage-specific symmetrization events of normally asymmetric cell divisions at the fourth larval stage, leading to the retention of seam cell fate in both daughter cells. Using genetics and single-molecule imaging, we demonstrate that this symmetrization occurs via changes in the Wnt asymmetry pathway, leading to aberrant Wnt target activation in anterior cell daughters. We find that intrinsic differences in the Wnt asymmetry pathway already exist between seam cells at 20° and this may sensitize cells toward a cell fate switch at increased temperature. Finally, we demonstrate that wild isolates of C. elegans display variation in seam cell sensitivity to increased culture temperature, although their average seam cell number is comparable at 20°. Our results highlight how temperature can modulate cell fate decisions in an invertebrate model of stem cell patterning.
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Affiliation(s)
- Mark Hintze
- Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Sneha L Koneru
- Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | | | | | - Julien Lambert
- Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
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13
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Madaan U, Faure L, Chowdhury A, Ahmed S, Ciccarelli EJ, Gumienny TL, Savage-Dunn C. Feedback regulation of BMP signaling by Caenorhabditis elegans cuticle collagens. Mol Biol Cell 2020; 31:825-832. [PMID: 32049594 PMCID: PMC7185965 DOI: 10.1091/mbc.e19-07-0390] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Cellular responsiveness to environment, including changes in extracellular matrix (ECM), is critical for normal processes such as development and wound healing, but can go awry, as in oncogenesis and fibrosis. One type of molecular pathway contributing to this responsiveness is the BMP signaling pathway. Owing to their broad and potent functions, BMPs and their pathways are regulated at multiple levels. In Caenorhabditis elegans, the BMP ligand DBL-1 is a regulator of body size. We previously showed that DBL-1/BMP signaling determines body size through transcriptional regulation of cuticle collagen genes. We now identify feedback regulation of DBL-1/BMP through analysis of four DBL-1–regulated collagen genes. Inactivation of any of these genes reduces DBL-1/BMP signaling, measured by a pathway activity reporter. Furthermore, depletion of these collagens reduces GFP::DBL-1 fluorescence and acts unexpectedly at the level of dbl-1 transcription. We conclude that cuticle, a specialized ECM, impinges on DBL-1/BMP expression and signaling. Interestingly, the feedback regulation of DBL-1/BMP signaling by collagens is likely to be contact independent due to physical separation of the cuticle from DBL-1–expressing cells in the ventral nerve cord. Our results provide an entry point into a novel regulatory mechanism for BMP signaling, with broader implications for mechanical regulation of gene expression.
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Affiliation(s)
- Uday Madaan
- Department of Biology, Queens College, City University of New York, Flushing, NY 11367.,PhD Program in Biology, The Graduate Center, City University of New York, NY 10016
| | - Lionel Faure
- Department of Biology, Texas Woman's University, Denton, TX 76204
| | - Albar Chowdhury
- Department of Biology, Queens College, City University of New York, Flushing, NY 11367
| | - Shahrear Ahmed
- Department of Biology, Queens College, City University of New York, Flushing, NY 11367
| | - Emma J Ciccarelli
- Department of Biology, Queens College, City University of New York, Flushing, NY 11367.,PhD Program in Biology, The Graduate Center, City University of New York, NY 10016
| | - Tina L Gumienny
- Department of Biology, Texas Woman's University, Denton, TX 76204
| | - Cathy Savage-Dunn
- Department of Biology, Queens College, City University of New York, Flushing, NY 11367.,PhD Program in Biology, The Graduate Center, City University of New York, NY 10016
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14
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Abete-Luzi P, Fukushige T, Yun S, Krause MW, Eisenmann DM. New Roles for the Heterochronic Transcription Factor LIN-29 in Cuticle Maintenance and Lipid Metabolism at the Larval-to-Adult Transition in Caenorhabditis elegans. Genetics 2020; 214:669-690. [PMID: 31974205 PMCID: PMC7054012 DOI: 10.1534/genetics.119.302860] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/21/2020] [Indexed: 11/18/2022] Open
Abstract
Temporal regulation of gene expression is a crucial aspect of metazoan development. In the roundworm Caenorhabditis elegans, the heterochronic pathway controls multiple developmental events in a time-specific manner. The most downstream effector of this pathway, the zinc-finger transcription factor LIN-29, acts in the last larval stage (L4) to regulate elements of the larval-to-adult switch. Here, we explore new LIN-29 targets and their implications for this developmental transition. We used RNA-sequencing to identify genes differentially expressed between animals misexpressing LIN-29 at an early time point and control animals. Among 230 LIN-29-activated genes, we found that genes encoding cuticle collagens were overrepresented. Interestingly, expression of lin-29 and some of these collagens was increased in adults with cuticle damage, suggesting a previously unknown function for LIN-29 in adult cuticle maintenance. On the other hand, genes involved in fat metabolism were enriched among 350 LIN-29-downregulated targets. We used mass spectrometry to assay lipid content in animals overexpressing LIN-29 and observed reduced fatty acid levels. Many LIN-29-repressed genes are normally expressed in the intestine, suggesting cell-nonautonomous regulation. We identified several LIN-29 upregulated genes encoding signaling molecules that may act as mediators in the regulation of intestinally expressed genes encoding fat metabolic enzymes and vitellogenins. Overall, our results support the model of LIN-29 as a major regulator of adult cuticle synthesis and integrity, and as the trigger for metabolic changes that take place at the important transition from rapid growth during larval life to slower growth and offspring production during adulthood.
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Affiliation(s)
- Patricia Abete-Luzi
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250
| | - Tetsunari Fukushige
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Sijung Yun
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Michael W Krause
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - David M Eisenmann
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250
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15
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Zhao Y, Dong S, Kong Y, Rui Q, Wang D. Molecular basis of intestinal canonical Wnt/β-catenin BAR-1 in response to simulated microgravity in Caenorhabditis elegans. Biochem Biophys Res Commun 2020; 522:198-204. [DOI: 10.1016/j.bbrc.2019.11.082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 12/29/2022]
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16
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Lakdawala MF, Madhu B, Faure L, Vora M, Padgett RW, Gumienny TL. Genetic interactions between the DBL-1/BMP-like pathway and dpy body size-associated genes in Caenorhabditis elegans. Mol Biol Cell 2019; 30:3151-3160. [PMID: 31693440 PMCID: PMC6938244 DOI: 10.1091/mbc.e19-09-0500] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/22/2019] [Accepted: 11/01/2019] [Indexed: 12/14/2022] Open
Abstract
Bone morphogenetic protein (BMP) signaling pathways control many developmental and homeostatic processes, including cell size and extracellular matrix remodeling. An understanding of how this pathway itself is controlled remains incomplete. To identify novel regulators of BMP signaling, we performed a forward genetic screen in Caenorhabditis elegans for genes involved in body size regulation, a trait under the control of BMP member DBL-1. We isolated mutations that suppress the long phenotype of lon-2, a gene that encodes a negative regulator that sequesters DBL-1. This screen was effective because we isolated alleles of several core components of the DBL-1 pathway, demonstrating the efficacy of the screen. We found additional alleles of previously identified but uncloned body size genes. Our screen also identified widespread involvement of extracellular matrix proteins in DBL-1 regulation of body size. We characterized interactions between the DBL-1 pathway and extracellular matrix and other genes that affect body morphology. We discovered that loss of some of these genes affects the DBL-1 pathway, and we provide evidence that DBL-1 signaling affects many molecular and cellular processes associated with body size. We propose a model in which multiple body size factors are controlled by signaling through the DBL-1 pathway and by DBL-1-independent processes.
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Affiliation(s)
| | - Bhoomi Madhu
- Department of Biology, Texas Woman’s University, Denton, TX 76204-5799
| | - Lionel Faure
- Department of Biology, Texas Woman’s University, Denton, TX 76204-5799
| | - Mehul Vora
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854-8020
| | - Richard W. Padgett
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854-8020
- Waksman Institute of Microbiology Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854-8020
- Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ 08854-8020
| | - Tina L. Gumienny
- Department of Biology, Texas Woman’s University, Denton, TX 76204-5799
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17
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Xu Y, He Z, Song M, Zhou Y, Shen Y. A microRNA switch controls dietary restriction-induced longevity through Wnt signaling. EMBO Rep 2019; 20:embr.201846888. [PMID: 30872315 DOI: 10.15252/embr.201846888] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 01/31/2019] [Accepted: 02/12/2019] [Indexed: 12/29/2022] Open
Abstract
Dietary restriction (DR) is known to have a potent and conserved longevity effect, yet its underlying molecular mechanisms remain elusive. DR modulates signaling pathways in response to nutrient status, a process that also regulates animal development. Here, we show that the suppression of Wnt signaling, a key pathway controlling development, is required for DR-induced longevity in Caenorhabditis elegans We find that DR induces the expression of mir-235, which inhibits cwn-1/WNT4 expression by binding to the 3'-UTR The "switch-on" of mir-235 by DR occurs at the onset of adulthood, thereby minimizing potential disruptions in development. Our results therefore implicate that DR controls the adult lifespan by using a temporal microRNA switch to modulate Wnt signaling.
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Affiliation(s)
- Yunpeng Xu
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China
| | - Zhidong He
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China
| | - Mengjiao Song
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China
| | - Yifei Zhou
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China
| | - Yidong Shen
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China
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18
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Ding X, Rui Q, Wang D. Functional disruption in epidermal barrier enhances toxicity and accumulation of graphene oxide. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 163:456-464. [PMID: 30075448 DOI: 10.1016/j.ecoenv.2018.07.102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/22/2018] [Accepted: 07/24/2018] [Indexed: 06/08/2023]
Abstract
In Caenorhabditis elegans, mutation of mlt-7 causes the deficits in epidermal barrier. Using the nematodes with epidermal-specific RNA interference (RNAi) knockdown of mlt-7 as a genetic tool, we found that epidermal-specific RNAi knockdown of mlt-7 resulted in a susceptibility to graphene oxide (GO) toxicity, and enhanced GO accumulation in the body. Epidermal-development related proteins of BLI-1 and IFB-1 acted as downstream targets of MLT-7, and mediated the function of MLT-7 in maintaining the epidermal barrier. Antimicrobial proteins of NLP-30 and CNC-2 also acted as downstream targets of MLT-7 in the regulation of GO toxicity. Epidermal-specific RNAi knockdown of nlp-30 or cnc-2 enhanced GO toxicity and accumulation in bli-1(RNAi) or ifb-1(RNAi) nematodes. Our data highlights the importance of maintaining normal epidermal barrier for nematodes against the GO toxicity.
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Affiliation(s)
- Xuecheng Ding
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China
| | - Qi Rui
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Dayong Wang
- Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China.
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19
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PRY-1/Axin signaling regulates lipid metabolism in Caenorhabditis elegans. PLoS One 2018; 13:e0206540. [PMID: 30403720 PMCID: PMC6221325 DOI: 10.1371/journal.pone.0206540] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/15/2018] [Indexed: 02/02/2023] Open
Abstract
The nematode Caenorhabditis elegans constitutes a leading animal model to study how signaling pathway components function in conserved biological processes. Here, we describe the role of an Axin family member, PRY-1, in lipid metabolism. Axins are scaffolding proteins that play crucial roles in signal transduction pathways by physically interacting with multiple factors and coordinating the assembly of protein complexes. Genome-wide transcriptome profiling of a pry-1 mutant revealed differentially regulated genes that are associated with lipid metabolism such as vitellogenins (yolk lipoproteins), fatty acid desaturases, lipases, and fatty acid transporters. Consistent with these categorizations, we found that pry-1 is crucial for the maintenance of lipid levels. Knockdowns of vit genes in a pry-1 mutant background restored lipid levels, suggesting that vitellogenins contribute to PRY-1 function in lipid metabolic processes. Additionally, lowered expression of desaturases and lipidomic analysis provided evidence that fatty acid synthesis is reduced in pry-1 mutants. Accordingly, an exogenous supply of oleic acid restored depleted lipids in somatic tissues of worms. Overall, our findings demonstrate that PRY-1/Axin signaling is essential for lipid metabolism and involves the regulation of yolk proteins.
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20
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Zhao L, Kong J, Krasteva N, Wang D. Deficit in the epidermal barrier induces toxicity and translocation of PEG modified graphene oxide in nematodes. Toxicol Res (Camb) 2018; 7:1061-1070. [PMID: 30510679 PMCID: PMC6220715 DOI: 10.1039/c8tx00136g] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/02/2018] [Indexed: 01/01/2023] Open
Abstract
The developmental basis for the epidermal barrier against the translocation of nanomaterials is still largely unclear in organisms. We here investigated the effect of deficits in the epidermal barrier on the translocation and toxicity of PEG modified graphene oxide (GO-PEG) in Caenorhabditis elegans. In wild-type or NR222 nematodes, GO-PEG exposure did not cause toxicity and affect the expression of epidermal-development related genes. However, GO-PEG exposure resulted in toxicity in mlt-7(RNAi) nematodes with deficit in the function of epidermal barrier. Epidermal RNAi knockdown of mlt-7 allowed GO-PEG accumulation and translocation into targeted organs through the epidermal barrier. Epidermal-development related proteins of BLI-1 and IFB-1 were identified as targets for MLT-7 in the regulation of GO-PEG toxicity and accounted for MLT-7 function in maintaining the epidermal barrier. AAK-2, a catalytic α subunit of AMP-activated protein kinase, was identified as another target for MLT-7 in the regulation of GO-PEG toxicity. AAK-2 functioned synergistically with BLI-1 or IFB-1 in the regulation of GO-PEG toxicity. Our data provide the molecular basis for the role of epidermal barrier against the toxicity and translocation of nanomaterials in organisms.
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Affiliation(s)
- Li Zhao
- Key Laboratory of Environmental Medicine Engineering in Ministry of Education , Medical School , Southeast University , Nanjing 210009 , China .
| | - Jingting Kong
- Key Laboratory of Environmental Medicine Engineering in Ministry of Education , Medical School , Southeast University , Nanjing 210009 , China .
| | - Natalia Krasteva
- Institute of Biophysics and Biomedical Engineering , Bulgarian Academy of Science , Sofia 1113 , Bulgaria
| | - Dayong Wang
- Key Laboratory of Environmental Medicine Engineering in Ministry of Education , Medical School , Southeast University , Nanjing 210009 , China .
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21
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BMP Signaling Determines Body Size via Transcriptional Regulation of Collagen Genes in Caenorhabditis elegans. Genetics 2018; 210:1355-1367. [PMID: 30274988 DOI: 10.1534/genetics.118.301631] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/25/2018] [Indexed: 01/10/2023] Open
Abstract
Body size is a tightly regulated phenotype in metazoans that depends on both intrinsic and extrinsic factors. While signaling pathways are known to control organ and body size, the downstream effectors that mediate their effects remain poorly understood. In the nematode Caenorhabditis elegans, a Bone Morphogenetic Protein (BMP)-related signaling pathway is the major regulator of growth and body size. We investigated the transcriptional network through which the BMP pathway regulates body size and identified cuticle collagen genes as major effectors of growth control. We demonstrate that cuticle collagens can act as positive regulators (col-41), negative regulators (col-141), or dose-sensitive regulators (rol-6) of body size. Moreover, we find a requirement of BMP signaling for stage-specific expression of cuticle collagen genes. We show that the Smad signal transducers directly bind conserved Smad-binding elements in regulatory regions of col-141 and col-142, but not of col-41 Hence, cuticle collagen genes may be directly and indirectly regulated via the BMP pathway. Our work thus connects a conserved signaling pathway with its critical downstream effectors, advancing insight into how body size is specified. Since collagen mutations and misregulation are implicated in numerous human genetic disorders and injury sequelae, understanding how collagen gene expression is regulated has broad implications.
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22
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Grainger S, Willert K. Mechanisms of Wnt signaling and control. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2018; 10:e1422. [PMID: 29600540 PMCID: PMC6165711 DOI: 10.1002/wsbm.1422] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 02/14/2018] [Accepted: 02/22/2018] [Indexed: 01/17/2023]
Abstract
The Wnt signaling pathway is a highly conserved system that regulates complex biological processes across all metazoan species. At the cellular level, secreted Wnt proteins serve to break symmetry and provide cells with positional information that is critical to the patterning of the entire body plan. At the organismal level, Wnt signals are employed to orchestrate fundamental developmental processes, including the specification of the anterior-posterior body axis, induction of the primitive streak and ensuing gastrulation movements, and the generation of cell and tissue diversity. Wnt functions extend into adulthood where they regulate stem cell behavior, tissue homeostasis, and damage repair. Disruption of Wnt signaling activity during embryonic development or in adults results in a spectrum of abnormalities and diseases, including cancer. The molecular mechanisms that underlie the myriad of Wnt-regulated biological effects have been the subject of intense research for over three decades. This review is intended to summarize our current understanding of how Wnt signals are generated and interpreted. This article is categorized under: Biological Mechanisms > Cell Signaling Developmental Biology > Stem Cell Biology and Regeneration.
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Affiliation(s)
- Stephanie Grainger
- Department of Cellular and Molecular Medicine University of California San Diego La Jolla California
| | - Karl Willert
- Department of Cellular and Molecular Medicine University of California San Diego La Jolla California
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23
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Zhang Q, Wu X, Chen P, Liu L, Xin N, Tian Y, Dillin A. The Mitochondrial Unfolded Protein Response Is Mediated Cell-Non-autonomously by Retromer-Dependent Wnt Signaling. Cell 2018; 174:870-883.e17. [PMID: 30057120 DOI: 10.1016/j.cell.2018.06.029] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/18/2018] [Accepted: 06/13/2018] [Indexed: 12/15/2022]
Abstract
The mitochondrial unfolded protein response (UPRmt) can be triggered in a cell-non-autonomous fashion across multiple tissues in response to mitochondrial dysfunction. The ability to communicate information about the presence of mitochondrial stress enables a global response that can ultimately better protect an organism from local mitochondrial challenges. We find that animals use retromer-dependent Wnt signaling to propagate mitochondrial stress signals from the nervous system to peripheral tissues. Specifically, the polyQ40-triggered activation of mitochondrial stress or reduction of cco-1 (complex IV subunit) in neurons of C. elegans results in the Wnt-dependent induction of cell-non-autonomous UPRmt in peripheral cells. Loss-of-function mutations of retromer complex components that are responsible for recycling the Wnt secretion-factor/MIG-14 prevent Wnt secretion and thereby suppress cell-non-autonomous UPRmt. Neuronal expression of the Wnt ligand/EGL-20 is sufficient to induce cell-non-autonomous UPRmt in a retromer complex-, Wnt signaling-, and serotonin-dependent manner, clearly implicating Wnt signaling as a strong candidate for the "mitokine" signal.
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Affiliation(s)
- Qian Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xueying Wu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Peng Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Limeng Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Nan Xin
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, and The Paul F. Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ye Tian
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China.
| | - Andrew Dillin
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, and The Paul F. Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720, USA.
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24
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Xia T, Horton ER, Salcini AE, Pocock R, Cox TR, Erler JT. Proteomic Characterization of Caenorhabditis elegans Larval Development. Proteomics 2017; 18. [PMID: 29178193 DOI: 10.1002/pmic.201700238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/03/2017] [Indexed: 11/06/2022]
Abstract
The nematode Caenorhabditis elegans is widely used as a model organism to study cell and developmental biology. Quantitative proteomics of C. elegans is still in its infancy and, so far, most studies have been performed on adult worm samples. Here, we used quantitative mass spectrometry to characterize protein level changes across the four larval developmental stages (L1-L4) of C. elegans. In total, we identified 4130 proteins, and quantified 1541 proteins that were present across all four stages in three biological replicates from independent experiments. Using hierarchical clustering and functional ontological analyses, we identified 21 clusters containing proteins with similar protein profiles across the four stages, and highlighted the most overrepresented biological functions in each of these protein clusters. In addition, we used the dataset to identify putative larval stage-specific proteins in each individual developmental stage, as well as in the early and late developmental stages. In summary, this dataset provides system-wide analysis of protein level changes across the four C. elegans larval developmental stages, which serves as a useful resource for the C. elegans research community. MS data were deposited in ProteomeXchange (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the primary accession identifier PXD006676.
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Affiliation(s)
- Tian Xia
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Edward R Horton
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Roger Pocock
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Thomas R Cox
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Cancer Division, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Janine T Erler
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
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25
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Blazie SM, Geissel HC, Wilky H, Joshi R, Newbern J, Mangone M. Alternative Polyadenylation Directs Tissue-Specific miRNA Targeting in Caenorhabditis elegans Somatic Tissues. Genetics 2017; 206:757-774. [PMID: 28348061 PMCID: PMC5499184 DOI: 10.1534/genetics.116.196774] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 03/02/2017] [Indexed: 01/03/2023] Open
Abstract
mRNA expression dynamics promote and maintain the identity of somatic tissues in living organisms; however, their impact in post-transcriptional gene regulation in these processes is not fully understood. Here, we applied the PAT-Seq approach to systematically isolate, sequence, and map tissue-specific mRNA from five highly studied Caenorhabditis elegans somatic tissues: GABAergic and NMDA neurons, arcade and intestinal valve cells, seam cells, and hypodermal tissues, and studied their mRNA expression dynamics. The integration of these datasets with previously profiled transcriptomes of intestine, pharynx, and body muscle tissues, precisely assigns tissue-specific expression dynamics for 60% of all annotated C. elegans protein-coding genes, providing an important resource for the scientific community. The mapping of 15,956 unique high-quality tissue-specific polyA sites in all eight somatic tissues reveals extensive tissue-specific 3'untranslated region (3'UTR) isoform switching through alternative polyadenylation (APA) . Almost all ubiquitously transcribed genes use APA and harbor miRNA targets in their 3'UTRs, which are commonly lost in a tissue-specific manner, suggesting widespread usage of post-transcriptional gene regulation modulated through APA to fine tune tissue-specific protein expression. Within this pool, the human disease gene C. elegans orthologs rack-1 and tct-1 use APA to switch to shorter 3'UTR isoforms in order to evade miRNA regulation in the body muscle tissue, resulting in increased protein expression needed for proper body muscle function. Our results highlight a major positive regulatory role for APA, allowing genes to counteract miRNA regulation on a tissue-specific basis.
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Affiliation(s)
- Stephen M Blazie
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, Arizona 85281
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona 85281
| | - Heather C Geissel
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, Arizona 85281
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona 85281
| | - Henry Wilky
- Barrett Honors College, Arizona State University, Tempe, Arizona 85281
| | - Rajan Joshi
- College of Letters and Sciences, Interdisciplinary Studies, Biological Sciences and Informatics, Arizona State University, Tempe, Arizona 85281
| | - Jason Newbern
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, Arizona 85281
- Barrett Honors College, Arizona State University, Tempe, Arizona 85281
| | - Marco Mangone
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, Arizona 85281
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona 85281
- Barrett Honors College, Arizona State University, Tempe, Arizona 85281
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26
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Chatterjee N, Kim Y, Yang J, Roca CP, Joo SW, Choi J. A systems toxicology approach reveals the Wnt-MAPK crosstalk pathway mediated reproductive failure in Caenorhabditis elegans exposed to graphene oxide (GO) but not to reduced graphene oxide (rGO). Nanotoxicology 2016; 11:76-86. [DOI: 10.1080/17435390.2016.1267273] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Youngho Kim
- School of Environmental Engineering, University of Seoul, Seoul, Korea
| | - Jisu Yang
- School of Environmental Engineering, University of Seoul, Seoul, Korea
| | - Carlos P. Roca
- Department of Chemical Engineering, Universitat Rovira i Virgili, Tarragona, Spain
- Department of Bioscience, Aarhus University, Silkeborg, Denmark
| | - Sang-Woo Joo
- Department of Information Communication, Materials, and Chemistry Convergence Technology, Soongsil University, Seoul, Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, Seoul, Korea
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27
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Asymmetric Wnt Pathway Signaling Facilitates Stem Cell-Like Divisions via the Nonreceptor Tyrosine Kinase FRK-1 in Caenorhabditis elegans. Genetics 2015; 201:1047-60. [PMID: 26358719 DOI: 10.1534/genetics.115.181412] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/05/2015] [Indexed: 11/18/2022] Open
Abstract
Asymmetric cell division is critical during development, as it influences processes such as cell fate specification and cell migration. We have characterized FRK-1, a homolog of the mammalian Fer nonreceptor tyrosine kinase, and found it to be required for differentiation and maintenance of epithelial cell types, including the stem cell-like seam cells of the hypodermis. A genomic knockout of frk-1, allele ok760, results in severely uncoordinated larvae that arrest at the L1 stage and have an excess number of lateral hypodermal cells that appear to have lost asymmetry in the stem cell-like divisions of the seam cell lineage. frk-1(ok760) mutants show that there are excess lateral hypodermal cells that are abnormally shaped and smaller in size compared to wild type, a defect that could be rescued only in a manner dependent on the kinase activity of FRK-1. Additionally, we observed a significant change in the expression of heterochronic regulators in frk-1(ok760) mutants. However, frk-1(ok760) mutants do not express late, nonseam hypodermal GFP markers, suggesting the seam cells do not precociously differentiate as adult-hyp7 cells. Finally, our data also demonstrate a clear role for FRK-1 in seam cell proliferation, as eliminating FRK-1 during the L3-L4 transition results in supernumerary seam cell nuclei that are dependent on asymmetric Wnt signaling. Specifically, we observe aberrant POP-1 and WRM-1 localization that is dependent on the presence of FRK-1 and APR-1. Overall, our data suggest a requirement for FRK-1 in maintaining the identity and proliferation of seam cells primarily through an interaction with the asymmetric Wnt pathway.
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28
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Gorrepati L, Krause MW, Chen W, Brodigan TM, Correa-Mendez M, Eisenmann DM. Identification of Wnt Pathway Target Genes Regulating the Division and Differentiation of Larval Seam Cells and Vulval Precursor Cells in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2015; 5:1551-66. [PMID: 26048561 PMCID: PMC4528312 DOI: 10.1534/g3.115.017715] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/18/2015] [Indexed: 12/29/2022]
Abstract
The evolutionarily conserved Wnt/β-catenin signaling pathway plays a fundamental role during metazoan development, regulating numerous processes including cell fate specification, cell migration, and stem cell renewal. Wnt ligand binding leads to stabilization of the transcriptional effector β-catenin and upregulation of target gene expression to mediate a cellular response. During larval development of the nematode Caenorhabditis elegans, Wnt/β-catenin pathways act in fate specification of two hypodermal cell types, the ventral vulval precursor cells (VPCs) and the lateral seam cells. Because little is known about targets of the Wnt signaling pathways acting during larval VPC and seam cell differentiation, we sought to identify genes regulated by Wnt signaling in these two hypodermal cell types. We conditionally activated Wnt signaling in larval animals and performed cell type-specific "mRNA tagging" to enrich for VPC and seam cell-specific mRNAs, and then used microarray analysis to examine gene expression compared to control animals. Two hundred thirty-nine genes activated in response to Wnt signaling were identified, and we characterized 50 genes further. The majority of these genes are expressed in seam and/or vulval lineages during normal development, and reduction of function for nine genes caused defects in the proper division, fate specification, fate execution, or differentiation of seam cells and vulval cells. Therefore, the combination of these techniques was successful at identifying potential cell type-specific Wnt pathway target genes from a small number of cells and at increasing our knowledge of the specification and behavior of these C. elegans larval hypodermal cells.
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Affiliation(s)
- Lakshmi Gorrepati
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250
| | | | - Weiping Chen
- Intramural Research Program, NIDDK, Bethesda, Maryland 20814
| | | | - Margarita Correa-Mendez
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250
| | - David M Eisenmann
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250
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Yin J, Madaan U, Park A, Aftab N, Savage-Dunn C. Multiple cis elements and GATA factors regulate a cuticle collagen gene in Caenorhabditis elegans. Genesis 2015; 53:278-84. [PMID: 25711168 DOI: 10.1002/dvg.22847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 01/05/2023]
Abstract
The cuticle of the nematode Caenorhabditis elegans is a specialized extracellular matrix whose major component is collagen. Cuticle collagens are encoded by a large multigene family consisting of more than 150 members. Cuticle collagen genes are expressed in epidermis (hypodermis) and may be stage-specific or cyclically expressed. We identified cuticle collagen genes as transcriptional targets of the DBL-1 TGF-β-related signaling pathway. These studies prompted us to investigate the cis-regulatory sequences required for transcription of one of the target genes, col-41. We generated reporter constructs that reproduce stage- and tissue-specific expression of fluorescent markers. We identify four conserved sequence elements that are required for transcription of reporters. Finally, we provide evidence that col-41 expression is controlled by a sequence element containing two GATA sites and by the epidermal GATA transcription factors ELT-1 and ELT-3.
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Affiliation(s)
- Jianghua Yin
- Department of Biology, Queens College, CUNY, Flushing, New York; The Graduate Center, CUNY, New York, New York
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Gorrepati L, Eisenmann DM. The C. elegans embryonic fate specification factor EGL-18 (GATA) is reutilized downstream of Wnt signaling to maintain a population of larval progenitor cells. WORM 2015; 4:e996419. [PMID: 26430560 PMCID: PMC4588385 DOI: 10.1080/23723556.2014.996419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 11/20/2014] [Accepted: 12/04/2014] [Indexed: 10/23/2022]
Abstract
In metazoans, stem cells in developing and adult tissues can divide asymmetrically to give rise to a daughter that differentiates and a daughter that retains the progenitor fate. Although the short-lived nematode C. elegans does not possess adult somatic stem cells, the lateral hypodermal seam cells behave in a similar manner: they divide once per larval stage to generate an anterior daughter that adopts a non-dividing differentiated fate and a posterior daughter that retains the seam fate and the ability to divide further. Wnt signaling pathway is known to regulate the asymmetry of these divisions and maintain the progenitor cell fate in one daughter, but how activation of the Wnt pathway accomplished this was unknown. We describe here our recent work that identified the GATA transcription factor EGL-18 as a downstream target of Wnt signaling necessary for maintenance of a progenitor population of larval seam cells. EGL-18 was previously shown to act in the initial specification of the seam cells in the embryo. Thus the acquisition of a Wnt-responsive cis-regulatory module allows an embryonic fate specification factor to be reutilized later in life downstream of a different regulator (Wnt signaling) to maintain a progenitor cell population. These results support the use of seam cell development in C. elegans as a simple model system for studying stem and progenitor cell biology.
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Affiliation(s)
- Lakshmi Gorrepati
- Carnegie Institution for Science; Department of Embryology; Baltimore, MD USA
| | - David M Eisenmann
- Department of Biological Sciences; University of Maryland Baltimore County; Baltimore, MD USA
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Posnien N, Zeng V, Schwager EE, Pechmann M, Hilbrant M, Keefe JD, Damen WGM, Prpic NM, McGregor AP, Extavour CG. A comprehensive reference transcriptome resource for the common house spider Parasteatoda tepidariorum. PLoS One 2014; 9:e104885. [PMID: 25118601 PMCID: PMC4132015 DOI: 10.1371/journal.pone.0104885] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/17/2014] [Indexed: 12/12/2022] Open
Abstract
Parasteatoda tepidariorum is an increasingly popular model for the study of spider development and the evolution of development more broadly. However, fully understanding the regulation and evolution of P. tepidariorum development in comparison to other animals requires a genomic perspective. Although research on P. tepidariorum has provided major new insights, gene analysis to date has been limited to candidate gene approaches. Furthermore, the few available EST collections are based on embryonic transcripts, which have not been systematically annotated and are unlikely to contain transcripts specific to post-embryonic stages of development. We therefore generated cDNA from pooled embryos representing all described embryonic stages, as well as post-embryonic stages including nymphs, larvae and adults, and using Illumina HiSeq technology obtained a total of 625,076,514 100-bp paired end reads. We combined these data with 24,360 ESTs available in GenBank, and 1,040,006 reads newly generated from 454 pyrosequencing of a mixed-stage embryo cDNA library. The combined sequence data were assembled using a custom de novo assembly strategy designed to optimize assembly product length, number of predicted transcripts, and proportion of raw reads incorporated into the assembly. The de novo assembly generated 446,427 contigs with an N50 of 1,875 bp. These sequences obtained 62,799 unique BLAST hits against the NCBI non-redundant protein data base, including putative orthologs to 8,917 Drosophila melanogaster genes based on best reciprocal BLAST hit identity compared with the D. melanogaster proteome. Finally, we explored the utility of the transcriptome for RNA-Seq studies, and showed that this resource can be used as a mapping scaffold to detect differential gene expression in different cDNA libraries. This resource will therefore provide a platform for future genomic, gene expression and functional approaches using P. tepidariorum.
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Affiliation(s)
- Nico Posnien
- Johann-Friedrich-Blumenbach-Institute for Zoology and Anthropology, Department of Developmental Biology, Georg-August-University Göttingen, GZMB Ernst-Caspari-Haus, Göttingen, Germany
- * E-mail: (NP); (CGE)
| | - Victor Zeng
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Evelyn E. Schwager
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Matthias Pechmann
- Cologne Biocenter, Institute of Developmental Biology, University of Cologne, Cologne, Germany
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Joseph D. Keefe
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Wim G. M. Damen
- Department of Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Nikola-Michael Prpic
- Johann-Friedrich-Blumenbach-Institute for Zoology and Anthropology, Department of Developmental Biology, Georg-August-University Göttingen, GZMB Ernst-Caspari-Haus, Göttingen, Germany
| | - Alistair P. McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Cassandra G. Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail: (NP); (CGE)
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