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Ragle JM, Turzo A, Levenson MT, Jonnalagadda K, Jackson A, Vo AA, Pham VT, Ward JD. MLT-11 is a transient apical extracellular matrix component required for cuticle patterning and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593762. [PMID: 38766248 PMCID: PMC11100798 DOI: 10.1101/2024.05.12.593762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Apical extracellular matrices (aECMs) are associated with all epithelia and form a protective layer against biotic and abiotic threats in the environment. Despite their importance, we lack a deep understanding of their structure and dynamics in development and disease. C. elegans molting offers a powerful entry point to understanding developmentally programmed aECM remodeling. A transient matrix is formed in embryos and at the end of each larval stage, presumably to pattern the new cuticle. Focusing on targets of NHR-23, a key transcription factor which drives molting, we identified the Kunitz family protease inhibitor gene mlt-11 as an NHR-23 target. We identified NHR-23-binding sites that are necessary and sufficient for epithelial expression. mlt-11 is necessary to pattern every layer of the adult cuticle, suggesting a broad patterning role prior to the formation of the mature cuticle. MLT-11::mNeonGreen::3xFLAG transiently localized to the aECM in the cuticle and embryo. It was also detected in lining openings to the exterior (vulva, rectum, mouth). Reduction of mlt-11 function disrupted the barrier function of the cuticle. Tissue-specific RNAi suggested mlt-11 activity is primarily necessary in seam cells and we observed alae and seam cell fusion defects upon mlt-11 inactivation. Predicted mlt-11 null mutations caused fully penetrant embryonic lethality and elongation defects suggesting mlt-11 also plays an important role in patterning the embryonic sheath. Finally, we found that mlt-11 inactivation suppressed the blistered cuticle phenotype of mutants of bli-4 mutants, a subtilisin protease gene but did not affect BLI-4::sfGFP expression. These data could suggest that MLT-11 may be necessary to assure proper levels of BLI-4 activity.
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Affiliation(s)
- James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ariela Turzo
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Max T. Levenson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Keya Jonnalagadda
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Anton Jackson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - An A. Vo
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Vivian T. Pham
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jordan D. Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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2
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Patil G, van Zon JS. Timers, variability, and body-wide coordination: C. elegans as a model system for whole-animal developmental timing. Curr Opin Genet Dev 2024; 85:102172. [PMID: 38432125 DOI: 10.1016/j.gde.2024.102172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Successful development requires both precise timing of cellular processes, such as division and differentiation, and tight coordination of timing between tissues and organs. Yet, how time information is encoded with high precision and synchronized between tissues, despite inherent molecular noise, is unsolved. Here, we propose the nematode C. elegans as a unique model system for studying body-wide control of developmental timing. Recent studies combining genetics, quantitative analysis, and simulations have 1) mapped core timers controlling larval development, indicating temporal gradients as an underlying mechanism, and 2) elucidated general principles that make timing insensitive to inherent fluctuations and variation in environmental conditions. As the molecular regulators of C. elegans developmental timing are broadly conserved, these mechanisms likely apply also to higher organisms.
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3
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Binti S, Edeen PT, Fay DS. Loss of the Na + /K + cation pump CATP-1 suppresses nekl -associated molting defects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585189. [PMID: 38559007 PMCID: PMC10979969 DOI: 10.1101/2024.03.15.585189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The conserved C. elegans protein kinases NEKL-2 and NEKL-3 regulate multiple steps of membrane trafficking and are required for larval molting. Through a forward genetic screen we identified a loss-of-function mutation in catp-1 as a suppressor of molting defects in synthetically lethal nekl-2; nekl-3 double mutants. catp-1 is predicted to encode a membrane- associated P4-type ATPase involved in Na + -K + exchange. Moreover, a mutation predicted to abolish CATP-1 ion-pump activity also suppressed nekl-2; nekl-3 mutants. Endogenously tagged CATP-1 was primarily expressed in epidermal (hypodermal) cells within punctate structures located at or near the apical plasma membrane. Through whole genome sequencing, we identified two additional nekl-2; nekl-3 suppressor strains containing coding-altering mutations in catp-1 but found that neither mutation, when introduced into nekl-2; nekl-3 mutants using CRISPR methods, was sufficient to elicit robust suppression of molting defects. Our data also suggested that the two catp-1 isoforms, catp-1a and catp-1b , may in some contexts be functionally redundant. On the basis of previously published studies, we tested the hypothesis that loss of catp-1 may suppress nekl -associated defects by inducing partial entry into the dauer pathway. Contrary to expectations, however, we failed to obtain evidence that loss of catp-1 suppresses nekl-2; nekl-3 defects through a dauer-associated mechanism or that loss of catp-1 leads to entry into the pre-dauer L2d stage. As such, loss of catp-1 may suppress nekl- associated molting and membrane trafficking defects by altering electrochemical gradients within membrane-bound compartments.
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4
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Binti S, Linder AG, Edeen PT, Fay DS. A conserved protein tyrosine phosphatase, PTPN-22, functions in diverse developmental processes in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584557. [PMID: 38559252 PMCID: PMC10980042 DOI: 10.1101/2024.03.12.584557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Protein tyrosine phosphatases non-receptor type (PTPNs) have been studied extensively in the context of the adaptive immune system; however, their roles beyond immunoregulation are less well explored. Here we identify novel functions for the conserved C. elegans phosphatase PTPN-22, establishing its role in nematode molting, cell adhesion, and cytoskeletal regulation. Through a non-biased genetic screen, we found that loss of PTPN-22 phosphatase activity suppressed molting defects caused by loss-of-function mutations in the conserved NIMA-related kinases NEKL-2 (human NEK8/NEK9) and NEKL-3 (human NEK6/NEK7), which act at the interface of membrane trafficking and actin regulation. To better understand the functions of PTPN-22, we carried out proximity labeling studies to identify candidate interactors of PTPN-22 during development. Through this approach we identified the CDC42 guanine-nucleotide exchange factor DNBP-1 (human DNMBP) as an in vivo partner of PTPN-22. Consistent with this interaction, loss of DNBP-1 also suppressed nekl-associated molting defects. Genetic analysis, co-localization studies, and proximity labeling revealed roles for PTPN-22 in several epidermal adhesion complexes, including C. elegans hemidesmosomes, suggesting that PTPN-22 plays a broad role in maintaining the structural integrity of tissues. Localization and proximity labeling also implicated PTPN-22 in functions connected to nucleocytoplasmic transport and mRNA regulation, particularly within the germline, as nearly one-third of proteins identified by PTPN-22 proximity labeling are known P granule components. Collectively, these studies highlight the utility of combined genetic and proteomic approaches for identifying novel gene functions.
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Affiliation(s)
- Shaonil Binti
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming
| | - Adison G Linder
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming
| | - Philip T Edeen
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming
| | - David S Fay
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, 1000 E. University Ave., Laramie, Wyoming
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5
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Sullivan LF, Barker MS, Felix PC, Vuong RQ, White BH. Neuromodulation and the toolkit for behavioural evolution: can ecdysis shed light on an old problem? FEBS J 2024; 291:1049-1079. [PMID: 36223183 PMCID: PMC10166064 DOI: 10.1111/febs.16650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/06/2022] [Accepted: 10/12/2022] [Indexed: 05/10/2023]
Abstract
The geneticist Thomas Dobzhansky famously declared: 'Nothing in biology makes sense except in the light of evolution'. A key evolutionary adaptation of Metazoa is directed movement, which has been elaborated into a spectacularly varied number of behaviours in animal clades. The mechanisms by which animal behaviours have evolved, however, remain unresolved. This is due, in part, to the indirect control of behaviour by the genome, which provides the components for both building and operating the brain circuits that generate behaviour. These brain circuits are adapted to respond flexibly to environmental contingencies and physiological needs and can change as a function of experience. The resulting plasticity of behavioural expression makes it difficult to characterize homologous elements of behaviour and to track their evolution. Here, we evaluate progress in identifying the genetic substrates of behavioural evolution and suggest that examining adaptive changes in neuromodulatory signalling may be a particularly productive focus for future studies. We propose that the behavioural sequences used by ecdysozoans to moult are an attractive model for studying the role of neuromodulation in behavioural evolution.
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Affiliation(s)
- Luis F Sullivan
- Section on Neural Function, Laboratory of Molecular Biology, National Institute of Mental Health, Bethesda, MD, USA
| | - Matthew S Barker
- Section on Neural Function, Laboratory of Molecular Biology, National Institute of Mental Health, Bethesda, MD, USA
| | - Princess C Felix
- Section on Neural Function, Laboratory of Molecular Biology, National Institute of Mental Health, Bethesda, MD, USA
| | - Richard Q Vuong
- Section on Neural Function, Laboratory of Molecular Biology, National Institute of Mental Health, Bethesda, MD, USA
| | - Benjamin H White
- Section on Neural Function, Laboratory of Molecular Biology, National Institute of Mental Health, Bethesda, MD, USA
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6
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Hiroki S, Yoshitane H. Ror homolog nhr-23 is essential for both developmental clock and circadian clock in C. elegans. Commun Biol 2024; 7:243. [PMID: 38418700 PMCID: PMC10902330 DOI: 10.1038/s42003-024-05894-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Animals have internal clocks that generate biological rhythms. In mammals, clock genes such as Period form the circadian clock to generate approximately 24-h biological rhythms. In C. elegans, the clock gene homologs constitute the "developmental clock", which has an 8-h period during larval development to determine the timing of molting. Thus, the ancestral circadian clock has been believed to evolve into the oscillator with a shorter period in C. elegans. However, circadian rhythms have also been observed in adult C. elegans, albeit relatively weak. This prompts the question: if the clock gene homologs drive the developmental rhythm with 8-h period, which genes generate the circadian rhythms in C. elegans? In this study, we discovered that nhr-23, a homolog of the mammalian circadian clock gene Ror, is essential for circadian transcriptional rhythms in adult C. elegans. Interestingly, nhr-23 was also known to be essential for the molting clock. The bilaterian ancestral circadian clock genes might have evolved to function over multiple periods depending on developmental contexts rather than a single 8-h period in C. elegans.
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Affiliation(s)
- Shingo Hiroki
- Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan.
| | - Hikari Yoshitane
- Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan.
- Department of Biological Sciences, School of Science, University of Tokyo, Tokyo, Japan.
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7
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Egan BM, Pohl F, Anderson X, Williams SC, Gregory Adodo I, Hunt P, Wang Z, Chiu CH, Scharf A, Mosley M, Kumar S, Schneider DL, Fujiwara H, Hsu FF, Kornfeld K. The ACE inhibitor captopril inhibits ACN-1 to control dauer formation and aging. Development 2024; 151:dev202146. [PMID: 38284547 PMCID: PMC10911126 DOI: 10.1242/dev.202146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024]
Abstract
The renin-angiotensin-aldosterone system (RAAS) plays a well-characterized role regulating blood pressure in mammals. Pharmacological and genetic manipulation of the RAAS has been shown to extend lifespan in Caenorhabditis elegans, Drosophila and rodents, but its mechanism is not well defined. Here, we investigate the angiotensin-converting enzyme (ACE) inhibitor drug captopril, which extends lifespan in worms and mice. To investigate the mechanism, we performed a forward genetic screen for captopril-hypersensitive mutants. We identified a missense mutation that causes a partial loss of function of the daf-2 receptor tyrosine kinase gene, a powerful regulator of aging. The homologous mutation in the human insulin receptor causes Donohue syndrome, establishing these mutant worms as an invertebrate model of this disease. Captopril functions in C. elegans by inhibiting ACN-1, the worm homolog of ACE. Reducing the activity of acn-1 via captopril or RNA interference promoted dauer larvae formation, suggesting that acn-1 is a daf gene. Captopril-mediated lifespan extension was abrogated by daf-16(lf) and daf-12(lf) mutations. Our results indicate that captopril and acn-1 influence lifespan by modulating dauer formation pathways. We speculate that this represents a conserved mechanism of lifespan control.
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Affiliation(s)
- Brian M. Egan
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Franziska Pohl
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xavier Anderson
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shoshana C. Williams
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Patrick Hunt
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zuoxu Wang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chen-Hao Chiu
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrea Scharf
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, MO 65409, USA
| | - Matthew Mosley
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sandeep Kumar
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniel L. Schneider
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hideji Fujiwara
- Division of Endocrinology, Metabolism & Lipid Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Fong-Fu Hsu
- Division of Endocrinology, Metabolism & Lipid Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kerry Kornfeld
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
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8
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Aarthy M, Pandiyan GN, Paramasivan R, Kumar A, Gupta B. Identification and prioritisation of potential vaccine candidates using subtractive proteomics and designing of a multi-epitope vaccine against Wuchereria bancrofti. Sci Rep 2024; 14:1970. [PMID: 38263422 PMCID: PMC10806236 DOI: 10.1038/s41598-024-52457-x] [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: 06/26/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024] Open
Abstract
This study employed subtractive proteomics and immunoinformatics to analyze the Wuchereria bancrofti proteome and identify potential therapeutic targets, with a focus on designing a vaccine against the parasite species. A comprehensive bioinformatics analysis of the parasite's proteome identified 51 probable therapeutic targets, among which "Kunitz/bovine pancreatic trypsin inhibitor domain-containing protein" was identified as the most promising vaccine candidate. The candidate protein was used to design a multi-epitope vaccine, incorporating B-cell and T-cell epitopes identified through various tools. The vaccine construct underwent extensive analysis of its antigenic, physical, and chemical features, including the determination of secondary and tertiary structures. Docking and molecular dynamics simulations were performed with HLA alleles, Toll-like receptor 4 (TLR4), and TLR3 to assess its potential to elicit the human immune response. Immune simulation analysis confirmed the predicted vaccine's strong binding affinity with immunoglobulins, indicating its potential efficacy in generating an immune response. However, experimental validation and testing of this multi-epitope vaccine construct would be needed to assess its potential against W. bancrofti and even for a broader range of lymphatic filarial infections given the similarities between W. bancrofti and Brugia.
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Affiliation(s)
- Murali Aarthy
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India
| | - G Navaneetha Pandiyan
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India
| | - R Paramasivan
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India
| | - Ashwani Kumar
- ICMR-Vector Control Research Centre (VCRC), Puducherry, India
- Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Tandhalam, Chennai, Tamil Nadu, 602105, India
| | - Bhavna Gupta
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India.
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9
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Summers KM. Genetic models of fibrillinopathies. Genetics 2024; 226:iyad189. [PMID: 37972149 PMCID: PMC11021029 DOI: 10.1093/genetics/iyad189] [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: 09/01/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023] Open
Abstract
The fibrillinopathies represent a group of diseases in which the 10-12 nm extracellular microfibrils are disrupted by genetic variants in one of the genes encoding fibrillin molecules, large glycoproteins of the extracellular matrix. The best-known fibrillinopathy is Marfan syndrome, an autosomal dominant condition affecting the cardiovascular, ocular, skeletal, and other systems, with a prevalence of around 1 in 3,000 across all ethnic groups. It is caused by variants of the FBN1 gene, encoding fibrillin-1, which interacts with elastin to provide strength and elasticity to connective tissues. A number of mouse models have been created in an attempt to replicate the human phenotype, although all have limitations. There are also natural bovine models and engineered models in pig and rabbit. Variants in FBN2 encoding fibrillin-2 cause congenital contractural arachnodactyly and mouse models for this condition have also been produced. In most animals, including birds, reptiles, and amphibians, there is a third fibrillin, fibrillin-3 (FBN3 gene) for which the creation of models has been difficult as the gene is degenerate and nonfunctional in mice and rats. Other eukaryotes such as the nematode C. elegans and zebrafish D. rerio have a gene with some homology to fibrillins and models have been used to discover more about the function of this family of proteins. This review looks at the phenotype, inheritance, and relevance of the various animal models for the different fibrillinopathies.
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Affiliation(s)
- Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba QLD 4102, Australia
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10
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Kamal M, Tokmakjian L, Knox J, Han D, Moshiri H, Magomedova L, Nguyen KCQ, Zheng H, Burns AR, Cooke B, Lacoste J, Yeo M, Hall DH, Cummins CL, Roy PJ. PGP-14 establishes a polar lipid permeability barrier within the C. elegans pharyngeal cuticle. PLoS Genet 2023; 19:e1011008. [PMID: 37930961 PMCID: PMC10653525 DOI: 10.1371/journal.pgen.1011008] [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: 03/05/2023] [Revised: 11/16/2023] [Accepted: 10/05/2023] [Indexed: 11/08/2023] Open
Abstract
The cuticles of ecdysozoan animals are barriers to material loss and xenobiotic insult. Key to this barrier is lipid content, the establishment of which is poorly understood. Here, we show that the p-glycoprotein PGP-14 functions coincidently with the sphingomyelin synthase SMS-5 to establish a polar lipid barrier within the pharyngeal cuticle of the nematode C. elegans. We show that PGP-14 and SMS-5 are coincidentally expressed in the epithelium that surrounds the anterior pharyngeal cuticle where PGP-14 localizes to the apical membrane. pgp-14 and sms-5 also peak in expression at the time of new cuticle synthesis. Loss of PGP-14 and SMS-5 dramatically reduces pharyngeal cuticle staining by Nile Red, a key marker of polar lipids, and coincidently alters the nematode's response to a wide-range of xenobiotics. We infer that PGP-14 exports polar lipids into the developing pharyngeal cuticle in an SMS-5-dependent manner to safeguard the nematode from environmental insult.
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Affiliation(s)
- Muntasir Kamal
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Levon Tokmakjian
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Jessica Knox
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Duhyun Han
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Houtan Moshiri
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Lilia Magomedova
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Ken CQ Nguyen
- Department of Neuroscience, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Hong Zheng
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Andrew R. Burns
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Brittany Cooke
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jessica Lacoste
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - May Yeo
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - David H. Hall
- Department of Neuroscience, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Carolyn L. Cummins
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Peter J. Roy
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
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11
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Birnbaum SK, Cohen JD, Belfi A, Murray JI, Adams JRG, Chisholm AD, Sundaram MV. The proprotein convertase BLI-4 promotes collagen secretion prior to assembly of the Caenorhabditis elegans cuticle. PLoS Genet 2023; 19:e1010944. [PMID: 37721936 PMCID: PMC10538796 DOI: 10.1371/journal.pgen.1010944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/28/2023] [Accepted: 08/30/2023] [Indexed: 09/20/2023] Open
Abstract
Some types of collagens, including transmembrane MACIT collagens and C. elegans cuticle collagens, are N-terminally cleaved at a dibasic site that resembles the consensus for furin or other proprotein convertases of the subtilisin/kexin (PCSK) family. Such cleavage may release transmembrane collagens from the plasma membrane and affect extracellular matrix assembly or structure. However, the functional consequences of such cleavage are unclear and evidence for the role of specific PCSKs is lacking. Here, we used endogenous collagen fusions to fluorescent proteins to visualize the secretion and assembly of the first collagen-based cuticle in C. elegans and then tested the role of the PCSK BLI-4 in these processes. Unexpectedly, we found that cuticle collagens SQT-3 and DPY-17 are secreted into the extraembryonic space several hours before cuticle matrix assembly. Furthermore, this early secretion depends on BLI-4/PCSK; in bli-4 and cleavage-site mutants, SQT-3 and DPY-17 are not efficiently secreted and instead form large intracellular puncta. Their later assembly into cuticle matrix is reduced but not entirely blocked. These data reveal a role for collagen N-terminal processing in intracellular trafficking and the control of matrix assembly in vivo. Our observations also prompt a revision of the classic model for C. elegans cuticle matrix assembly and the pre-cuticle-to-cuticle transition, suggesting that cuticle layer assembly proceeds via a series of regulated steps and not simply by sequential secretion and deposition.
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Affiliation(s)
- Susanna K. Birnbaum
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jennifer D. Cohen
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Alexandra Belfi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - John I. Murray
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jennifer R. G. Adams
- Departments of Neurobiology and Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Andrew D. Chisholm
- Departments of Neurobiology and Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Meera V. Sundaram
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
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12
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Lim DS, Kim J, Kim W, Kim N, Lee SH, Lee D, Lee J. daf-42 is an evolutionarily young gene essential for dauer development in Caenorhabditis elegans. Genetics 2023; 224:iyad097. [PMID: 37216205 DOI: 10.1093/genetics/iyad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023] Open
Abstract
Under adverse environmental conditions, nematodes arrest into dauer, an alternative developmental stage for diapause. Dauer endures unfavorable environments and interacts with host animals to access favorable environments, thus playing a critical role in survival. Here, we report that in Caenorhabditis elegans, daf-42 is essential for development into the dauer stage, as the null mutant of daf-42 exhibited a "no viable dauer" phenotype in which no viable dauers were obtained in any dauer-inducing conditions. Long-term time lapse microscopy of synchronized larvae revealed that daf-42 is involved in developmental changes from the pre-dauer L2d stage to the dauer stage. daf-42 encodes large, disordered proteins of various sizes that are expressed in and secreted from the seam cells within a narrow time window shortly before the molt into dauer stage. Transcriptome analysis showed that the transcription of genes involved in larval physiology and dauer metabolism is highly affected by the daf-42 mutation. Contrary to the notion that essential genes that control the life and death of an organism may be well conserved across diverse species, daf-42 is an evolutionarily young gene conserved only in the Caenorhabditis genus. Our study shows that dauer formation is a vital process that is controlled not only by conserved genes but also by newly emerged genes, providing important insights into evolutionary mechanisms.
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Affiliation(s)
- Daisy S Lim
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Jun Kim
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
- Department of Convergent Bioscience and Informatics, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Wonjoo Kim
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Nari Kim
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Hee Lee
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
- Korea Basic Science Institute, Ochang, Cheongju, Chungbuk 28119, Republic of Korea
| | - Daehan Lee
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
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13
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Ewald CY, Nyström A. Mechanotransduction through hemidesmosomes during aging and longevity. J Cell Sci 2023; 136:jcs260987. [PMID: 37522320 DOI: 10.1242/jcs.260987] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023] Open
Abstract
Hemidesmosomes are structural protein complexes localized at the interface of tissues with high mechanical demand and shear forces. Beyond tissue anchoring, hemidesmosomes have emerged as force-modulating structures important for translating mechanical cues into biochemical and transcriptional adaptation (i.e. mechanotransduction) across tissues. Here, we discuss the recent insights into the roles of hemidesmosomes in age-related tissue regeneration and aging in C. elegans, mice and humans. We highlight the emerging concept of preserved dynamic mechanoregulation of hemidesmosomes in tissue maintenance and healthy aging.
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Affiliation(s)
- Collin Y Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Zürich, Schwerzenbach CH-8603, Switzerland
| | - Alexander Nyström
- Department of Dermatology, Medical Faculty, Medical Center - University of Freiburg, Freiburg DE-79104, Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albertstraße 19, Freiburg im Breisgau DE-79104, Germany
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14
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Egan BM, Pohl F, Anderson X, Williams SC, Adodo IG, Hunt P, Wang Z, Chiu CH, Scharf A, Mosley M, Kumar S, Schneider DL, Fujiwara H, Hsu FF, Kornfeld K. The ACE-inhibitor drug captopril inhibits ACN-1 to control dauer formation and aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549402. [PMID: 37502959 PMCID: PMC10370070 DOI: 10.1101/2023.07.17.549402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The renin-angiotensin-aldosterone system (RAAS) plays a well-characterized role regulating blood pressure in mammals. Pharmacological and genetic manipulation of the RAAS has been shown to extend lifespan in C. elegans , Drosophila , and rodents, but its mechanism is not well defined. Here we investigate the angiotensin-converting enzyme (ACE) inhibitor drug captopril, which extends lifespan in worms and mice. To investigate the mechanism, we performed a forward genetic screen for captopril hypersensitive mutants. We identified a missense mutation that causes a partial loss-of-function of the daf-2 receptor tyrosine kinase gene, a powerful regulator of aging. The homologous mutation in the human insulin receptor causes Donohue syndrome, establishing these mutant worms as an invertebrate model of this disease. Captopril functions in C. elegans by inhibiting ACN-1, the worm homolog of ACE. Reducing the activity of acn-1 via captopril or RNAi promoted dauer larvae formation, suggesting acn-1 is a daf gene. Captopril-mediated lifespan extension xwas abrogated by daf-16(lf) and daf-12(lf) mutations. Our results indicate that captopril and acn-1 control aging by modulating dauer formation pathways. We speculate that this represents a conserved mechanism of lifespan control. Summary Statement Captopril and acn-1 control aging. By demonstrating they regulate dauer formation and interact with daf genes, including a new DAF-2(A261V) mutant corresponding to a human disease variant, we clarified the mechanism.
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Balasubramaniam B, Topalidou I, Kelley M, Meadows SM, Funk O, Ailion M, Fay DS. Effectors of anterior morphogenesis in C. elegans embryos. Biol Open 2023; 12:bio059982. [PMID: 37345480 PMCID: PMC10339035 DOI: 10.1242/bio.059982] [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: 04/23/2023] [Accepted: 06/19/2023] [Indexed: 06/23/2023] Open
Abstract
During embryogenesis the nascent Caenorhabditis elegans epidermis secretes an apical extracellular matrix (aECM) that serves as an external stabilizer, preventing deformation of the epidermis by mechanical forces exerted during morphogenesis. At present, the factors that contribute to aECM function are mostly unknown, including the aECM components themselves, their posttranslational regulators, and the pathways required for their secretion. Here we showed that two proteins previously linked to aECM function, SYM-3/FAM102A and SYM-4/WDR44, colocalize to intracellular and membrane-associated puncta and likely function in a complex. Proteomics experiments also suggested potential roles for SYM-3/FAM102A and SYM-4/WDR44 family proteins in intracellular trafficking. Nonetheless, we found no evidence to support a critical function for SYM-3 or SYM-4 in the apical deposition of two aECM components, NOAH-1 and FBN-1. Moreover, loss of a key splicing regulator of fbn-1, MEC-8/RBPMS2, had surprisingly little effect on the abundance or deposition of FBN-1. Using a focused screening approach, we identified 32 additional proteins that likely contribute to the structure and function of the embryonic aECM. We also characterized morphogenesis defects in embryos lacking mir-51 microRNA family members, which display a similar phenotype to mec-8; sym double mutants. Collectively, these findings add to our knowledge of factors controlling embryonic morphogenesis.
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Affiliation(s)
- Boopathi Balasubramaniam
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
| | - Irini Topalidou
- Department of Biochemistry, University of Washington, Seattle 98195-7350, WA, USA
| | - Melissa Kelley
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
| | - Sarina M. Meadows
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
| | - Owen Funk
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle 98195-7350, WA, USA
| | - David S. Fay
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
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16
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Birnbaum SK, Cohen JD, Belfi A, Murray JI, Adams JRG, Chisholm AD, Sundaram MV. The proprotein convertase BLI-4 promotes collagen secretion during assembly of the Caenorhabditis elegans cuticle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.542650. [PMID: 37333289 PMCID: PMC10274747 DOI: 10.1101/2023.06.06.542650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Some types of collagens, including transmembrane MACIT collagens and C. elegans cuticle collagens, are N-terminally cleaved at a dibasic site that resembles the consensus for furin or other proprotein convertases of the subtilisin/kexin (PCSK) family. Such cleavage may release transmembrane collagens from the plasma membrane and affect extracellular matrix assembly or structure. However, the functional consequences of such cleavage are unclear and evidence for the role of specific PCSKs is lacking. Here, we used endogenous collagen fusions to fluorescent proteins to visualize the secretion and assembly of the first collagen-based cuticle in C. elegans and then tested the role of the PCSK BLI-4 in these processes. Unexpectedly, we found that cuticle collagens SQT-3 and DPY-17 are secreted into the extraembryonic space several hours before cuticle matrix assembly. Furthermore, this early secretion depends on BLI-4/PCSK; in bli-4 and cleavage-site mutants, SQT-3 and DPY-17 are not efficiently secreted and instead form large intracellular aggregates. Their later assembly into cuticle matrix is reduced but not entirely blocked. These data reveal a role for collagen N-terminal processing in intracellular trafficking and in the spatial and temporal restriction of matrix assembly in vivo . Our observations also prompt a revision of the classic model for C. elegans cuticle matrix assembly and the pre-cuticle-to-cuticle transition, suggesting that cuticle layer assembly proceeds via a series of regulated steps and not simply by sequential secretion and deposition.
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Affiliation(s)
- Susanna K Birnbaum
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
| | - Jennifer D Cohen
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
| | - Alexandra Belfi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
| | - John I Murray
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
| | - Jennifer R G Adams
- Departments of Neurobiology and Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego CA
| | - Andrew D Chisholm
- Departments of Neurobiology and Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego CA
| | - Meera V Sundaram
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
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17
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Johnson LC, Vo AA, Clancy JC, Myles KM, Pooranachithra M, Aguilera J, Levenson MT, Wohlenberg C, Rechtsteiner A, Ragle JM, Chisholm AD, Ward JD. NHR-23 activity is necessary for C. elegans developmental progression and apical extracellular matrix structure and function. Development 2023; 150:dev201085. [PMID: 37129010 PMCID: PMC10233720 DOI: 10.1242/dev.201085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Nematode molting is a remarkable process where animals must repeatedly build a new apical extracellular matrix (aECM) beneath a previously built aECM that is subsequently shed. The nuclear hormone receptor NHR-23 (also known as NR1F1) is an important regulator of C. elegans molting. NHR-23 expression oscillates in the epidermal epithelium, and soma-specific NHR-23 depletion causes severe developmental delay and death. Tissue-specific RNAi suggests that nhr-23 acts primarily in seam and hypodermal cells. NHR-23 coordinates the expression of factors involved in molting, lipid transport/metabolism and remodeling of the aECM. NHR-23 depletion causes dampened expression of a nas-37 promoter reporter and a loss of reporter oscillation. The cuticle collagen ROL-6 and zona pellucida protein NOAH-1 display aberrant annular localization and severe disorganization over the seam cells after NHR-23 depletion, while the expression of the adult-specific cuticle collagen BLI-1 is diminished and frequently found in patches. Consistent with these localization defects, the cuticle barrier is severely compromised when NHR-23 is depleted. Together, this work provides insight into how NHR-23 acts in the seam and hypodermal cells to coordinate aECM regeneration during development.
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Affiliation(s)
- Londen C. Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - An A. Vo
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - John C. Clancy
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Krista M. Myles
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Murugesan Pooranachithra
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joseph Aguilera
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Max T. Levenson
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Chloe Wohlenberg
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andreas Rechtsteiner
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andrew D. Chisholm
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jordan D. Ward
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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18
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Boopathi B, Topalidou I, Kelley M, Meadows SM, Funk O, Ailion M, Fay DS. Pathways that affect anterior morphogenesis in C. elegans embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.23.537986. [PMID: 37163004 PMCID: PMC10168279 DOI: 10.1101/2023.04.23.537986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
During embryogenesis the nascent Caenorhabditis elegans epidermis secretes an apical extracellular matrix (aECM) that serves as an external stabilizer, preventing deformation of the epidermis by mechanical forces exerted during morphogenesis. We showed that two conserved proteins linked to this process, SYM-3/FAM102A and SYM-4/WDR44, colocalize to intracellular and membrane-associated puncta and likely function together in a complex. Proteomics data also suggested potential roles for FAM102A and WDR44 family proteins in intracellular trafficking, consistent with their localization patterns. Nonetheless, we found no evidence to support a clear function for SYM-3 or SYM-4 in the apical deposition of two aECM components, FBN-1 and NOAH. Surprisingly, loss of MEC-8/RBPMS2, a conserved splicing factor and regulator of fbn-1 , had little effect on the abundance or deposition of FBN-1 to the aECM. Using a focused screening approach, we identified 32 additional proteins that likely contribute to the structure and function of the embryonic aECM. Lastly, we examined morphogenesis defects in embryos lacking mir-51 microRNA family members, which display a related embryonic phenotype to mec-8; sym double mutants. Collectively, our findings add to our knowledge of pathways controlling embryonic morphogenesis. SUMMARY STATEMENT We identify new proteins in apical ECM biology in C. elegans and provide evidence that SYM-3/FAM102A and SYM-4/WDR44 function together in trafficking but do not regulate apical ECM protein deposition.
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Affiliation(s)
- Balasubramaniam Boopathi
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Irini Topalidou
- Department of Biochemistry, University of Washington, Seattle, United States of America
| | - Melissa Kelley
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Sarina M Meadows
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Owen Funk
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle, United States of America
| | - David S Fay
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
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19
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Clancy JC, Vo AA, Myles KM, Levenson MT, Ragle JM, Ward JD. Experimental considerations for study of C. elegans lysosomal proteins. G3 (BETHESDA, MD.) 2023; 13:jkad032. [PMID: 36748711 PMCID: PMC10085801 DOI: 10.1093/g3journal/jkad032] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 06/20/2022] [Accepted: 01/27/2023] [Indexed: 02/08/2023]
Abstract
Lysosomes are an important organelle required for the degradation of a range of cellular components. Lysosome function is critical for development and homeostasis as dysfunction can lead to inherited genetic disorders, cancer, and neurodegenerative and metabolic diseases. The acidic and protease-rich environment of lysosomes poses experimental challenges. Many fluorescent proteins are quenched or degraded, while specific red fluorescent proteins can be cleaved from translational fusion partners and accumulate. While studying MLT-11, a Caenorhabditis elegans molting factor that localizes to lysosomes and the cuticle, we sought to optimize several experimental parameters. We found that, in contrast to mNeonGreen fusions, mScarlet fusions to MLT-11 missed cuticular and rectal epithelial localization. Rapid sample lysis and denaturation were critical for preventing MLT-11 fragmentation while preparing lysates for western blots. Using a model lysosomal substrate (NUC-1), we found that rigid polyproline linkers and truncated mCherry constructs do not prevent cleavage of mCherry from NUC-1. We provide evidence that extended localization in lysosomal environments prevents the detection of FLAG epitopes in western blots. Finally, we optimize an acid-tolerant green fluorescent protein (Gamillus) for use in C. elegans. These experiments provide important experimental considerations and new reagents for the study of C. elegans lysosomal proteins.
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Affiliation(s)
- John C Clancy
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - An A Vo
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Krista M Myles
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Max T Levenson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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20
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Kawano T, Kashiwagi M, Kanuka M, Chen CK, Yasugaki S, Hatori S, Miyazaki S, Tanaka K, Fujita H, Nakajima T, Yanagisawa M, Nakagawa Y, Hayashi Y. ER proteostasis regulators cell-non-autonomously control sleep. Cell Rep 2023; 42:112267. [PMID: 36924492 DOI: 10.1016/j.celrep.2023.112267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 01/17/2023] [Accepted: 02/28/2023] [Indexed: 03/17/2023] Open
Abstract
Sleep is regulated by peripheral tissues under fatigue. The molecular pathways in peripheral cells that trigger systemic sleep-related signals, however, are unclear. Here, a forward genetic screen in C. elegans identifies 3 genes that strongly affect sleep amount: sel-1, sel-11, and mars-1. sel-1 and sel-11 encode endoplasmic reticulum (ER)-associated degradation components, whereas mars-1 encodes methionyl-tRNA synthetase. We find that these machineries function in non-neuronal tissues and that the ER unfolded protein response components inositol-requiring enzyme 1 (IRE1)/XBP1 and protein kinase R-like ER kinase (PERK)/eukaryotic initiation factor-2α (eIF2α)/activating transcription factor-4 (ATF4) participate in non-neuronal sleep regulation, partly by reducing global translation. Neuronal epidermal growth factor receptor (EGFR) signaling is also required. Mouse studies suggest that this mechanism is conserved in mammals. Considering that prolonged wakefulness increases ER proteostasis stress in peripheral tissues, our results suggest that peripheral ER proteostasis factors control sleep homeostasis. Moreover, based on our results, peripheral tissues likely cope with ER stress not only by the well-established cell-autonomous mechanisms but also by promoting the individual's sleep.
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Affiliation(s)
- Taizo Kawano
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan
| | - Mitsuaki Kashiwagi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan; Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mika Kanuka
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan
| | - Chung-Kuan Chen
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan; Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Shinnosuke Yasugaki
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan; Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Sena Hatori
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan; PhD Program in Humanics, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Shinichi Miyazaki
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan; PhD Program in Humanics, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Kaeko Tanaka
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan
| | - Hidetoshi Fujita
- Department of Biomedical Engineering, Osaka Institute of Technology, Osaka 535-8585, Japan
| | - Toshiro Nakajima
- Institute of Medical Science, Tokyo Medical University, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan; Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba 305-8575, Japan; Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yoshimi Nakagawa
- Department of Complex Biosystem Research, Institute of Natural Medicine, University of Toyama, Toyama, Toyama 930-0194, Japan
| | - Yu Hayashi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan; Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
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21
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Meeuse MWM, Hauser YP, Nahar S, Smith AAT, Braun K, Azzi C, Rempfler M, Großhans H. C. elegans molting requires rhythmic accumulation of the Grainyhead/LSF transcription factor GRH-1. EMBO J 2023; 42:e111895. [PMID: 36688410 PMCID: PMC9929640 DOI: 10.15252/embj.2022111895] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 01/24/2023] Open
Abstract
C. elegans develops through four larval stages that are rhythmically terminated by molts, that is, the synthesis and shedding of a cuticular exoskeleton. Each larval cycle involves rhythmic accumulation of thousands of transcripts, which we show here relies on rhythmic transcription. To uncover the responsible gene regulatory networks (GRNs), we screened for transcription factors that promote progression through the larval stages and identified GRH-1, BLMP-1, NHR-23, NHR-25, MYRF-1, and BED-3. We further characterize GRH-1, a Grainyhead/LSF transcription factor, whose orthologues in other animals are key epithelial cell-fate regulators. We find that GRH-1 depletion extends molt durations, impairs cuticle integrity and shedding, and causes larval death. GRH-1 is required for, and accumulates prior to, each molt, and preferentially binds to the promoters of genes expressed during this time window. Binding to the promoters of additional genes identified in our screen furthermore suggests that we have identified components of a core molting-clock GRN. Since the mammalian orthologues of GRH-1, BLMP-1 and NHR-23, have been implicated in rhythmic homeostatic skin regeneration in mouse, the mechanisms underlying rhythmic C. elegans molting may apply beyond nematodes.
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Affiliation(s)
- Milou W M Meeuse
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- University of BaselBaselSwitzerland
| | - Yannick P Hauser
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- University of BaselBaselSwitzerland
| | - Smita Nahar
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
| | | | - Kathrin Braun
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
| | - Chiara Azzi
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- University of BaselBaselSwitzerland
| | - Markus Rempfler
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- University of BaselBaselSwitzerland
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22
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Burkhardt RN, Artyukhin AB, Aprison EZ, Curtis BJ, Fox BW, Ludewig AH, Palomino DF, Luo J, Chaturbedi A, Panda O, Wrobel CJJ, Baumann V, Portman DS, Lee SS, Ruvinsky I, Schroeder FC. Sex-specificity of the C. elegans metabolome. Nat Commun 2023; 14:320. [PMID: 36658169 PMCID: PMC9852247 DOI: 10.1038/s41467-023-36040-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Recent studies of animal metabolism have revealed large numbers of novel metabolites that are involved in all aspects of organismal biology, but it is unclear to what extent metabolomes differ between sexes. Here, using untargeted comparative metabolomics for the analysis of wildtype animals and sex determination mutants, we show that C. elegans hermaphrodites and males exhibit pervasive metabolomic differences. Several hundred small molecules are produced exclusively or in much larger amounts in one sex, including a host of previously unreported metabolites that incorporate building blocks from nucleoside, carbohydrate, lipid, and amino acid metabolism. A subset of male-enriched metabolites is specifically associated with the presence of a male germline, whereas enrichment of other compounds requires a male soma. Further, we show that one of the male germline-dependent metabolites, an unusual dipeptide incorporating N,N-dimethyltryptophan, increases food consumption, reduces lifespan, and accelerates the last stage of larval development in hermaphrodites. Our results serve as a foundation for mechanistic studies of how the genetic sex of soma and germline shape the C. elegans metabolome and provide a blueprint for the discovery of sex-dependent metabolites in other animals.
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Affiliation(s)
- Russell N Burkhardt
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Alexander B Artyukhin
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
- Chemistry Department, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
| | - Erin Z Aprison
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Brian J Curtis
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Bennett W Fox
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Andreas H Ludewig
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Diana Fajardo Palomino
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jintao Luo
- Department of Biomedical Genetics, University of Rochester, Rochester, NY, 14642, USA
- School of Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Amaresh Chaturbedi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Oishika Panda
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Chester J J Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Victor Baumann
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Douglas S Portman
- Department of Biomedical Genetics, University of Rochester, Rochester, NY, 14642, USA
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Ilya Ruvinsky
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
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23
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Greiffer L, Liebau E, Herrmann FC, Spiegler V. Condensed tannins act as anthelmintics by increasing the rigidity of the nematode cuticle. Sci Rep 2022; 12:18850. [PMID: 36344622 PMCID: PMC9640668 DOI: 10.1038/s41598-022-23566-2] [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: 09/02/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Tannins and tanniferous plant extracts have been discussed as sustainable means for helminth control in the past two decades in response to a dramatic increase of resistances towards standard anthelmintics. While their bioactivities have been broadly investigated in vitro and in vivo, less is known about their mode of action in nematodes, apart from their protein binding properties. In the current study we therefore investigated the impact of a phytochemically well characterized plant extract from Combretum mucronatum, known to contain procyanidins as the active compounds, on the model organism Caenorhabditis elegans. By different microscopic techniques, the cuticle was identified as the main binding site for tannins, whereas underlying tissues did not seem to be affected. In addition to disruptions of the cuticle structure, molting defects occurred at all larval stages. Finally, an increased rigidity of the nematodes' cuticle due to binding of tannins was confirmed by force spectroscopic measurements. This could be a key finding to explain several anthelmintic activities reported for tannins, especially impairment of molting or exsheathment as well as locomotion.
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Affiliation(s)
- Luise Greiffer
- grid.5949.10000 0001 2172 9288Institute for Pharmaceutical Biology and Phytochemistry, University of Münster, Münster, Germany
| | - Eva Liebau
- grid.5949.10000 0001 2172 9288Institute of Integrative Cell Biology and Physiology, University of Münster, Münster, Germany
| | - Fabian C. Herrmann
- grid.5949.10000 0001 2172 9288Institute for Pharmaceutical Biology and Phytochemistry, University of Münster, Münster, Germany
| | - Verena Spiegler
- grid.5949.10000 0001 2172 9288Institute for Pharmaceutical Biology and Phytochemistry, University of Münster, Münster, Germany
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24
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Kamal M, Tokmakjian L, Knox J, Mastrangelo P, Ji J, Cai H, Wojciechowski JW, Hughes MP, Takács K, Chu X, Pei J, Grolmusz V, Kotulska M, Forman-Kay JD, Roy PJ. A spatiotemporal reconstruction of the C. elegans pharyngeal cuticle reveals a structure rich in phase-separating proteins. eLife 2022; 11:e79396. [PMID: 36259463 PMCID: PMC9629831 DOI: 10.7554/elife.79396] [Citation(s) in RCA: 4] [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: 04/11/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022] Open
Abstract
How the cuticles of the roughly 4.5 million species of ecdysozoan animals are constructed is not well understood. Here, we systematically mine gene expression datasets to uncover the spatiotemporal blueprint for how the chitin-based pharyngeal cuticle of the nematode Caenorhabditis elegans is built. We demonstrate that the blueprint correctly predicts expression patterns and functional relevance to cuticle development. We find that as larvae prepare to molt, catabolic enzymes are upregulated and the genes that encode chitin synthase, chitin cross-linkers, and homologs of amyloid regulators subsequently peak in expression. Forty-eight percent of the gene products secreted during the molt are predicted to be intrinsically disordered proteins (IDPs), many of which belong to four distinct families whose transcripts are expressed in overlapping waves. These include the IDPAs, IDPBs, and IDPCs, which are introduced for the first time here. All four families have sequence properties that drive phase separation and we demonstrate phase separation for one exemplar in vitro. This systematic analysis represents the first blueprint for cuticle construction and highlights the massive contribution that phase-separating materials make to the structure.
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Affiliation(s)
- Muntasir Kamal
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Levon Tokmakjian
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
- Department of Pharmacology and Toxicology, University of TorontoTorontoCanada
| | - Jessica Knox
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Peter Mastrangelo
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Jingxiu Ji
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Hao Cai
- Molecular Medicine Program, The Hospital for Sick ChildrenTorontoCanada
| | - Jakub W Wojciechowski
- Wroclaw University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical EngineeringWroclawPoland
| | - Michael P Hughes
- Department of Cell and Molecular Biology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Kristóf Takács
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös UniversityBudapestHungary
| | - Xiaoquan Chu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Jianfeng Pei
- Department of Computer Science and Technology, Tsinghua UniversityBeijingChina
| | - Vince Grolmusz
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös UniversityBudapestHungary
| | - Malgorzata Kotulska
- Wroclaw University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical EngineeringWroclawPoland
| | - Julie Deborah Forman-Kay
- Molecular Medicine Program, The Hospital for Sick ChildrenTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
| | - Peter J Roy
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
- Department of Pharmacology and Toxicology, University of TorontoTorontoCanada
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25
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Patel R, Galagali H, Kim JK, Frand AR. Feedback between a retinoid-related nuclear receptor and the let-7 microRNAs controls the pace and number of molting cycles in C. elegans. eLife 2022; 11:e80010. [PMID: 35968765 PMCID: PMC9377799 DOI: 10.7554/elife.80010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Animal development requires coordination among cyclic processes, sequential cell fate specifications, and once-a-lifetime morphogenic events, but the underlying timing mechanisms are not well understood. Caenorhabditis elegans undergoes four molts at regular 8 to 10 hour intervals. The pace of the cycle is governed by PERIOD/lin-42 and other as-yet unknown factors. Cessation of the cycle in young adults is controlled by the let-7 family of microRNAs and downstream transcription factors in the heterochronic pathway. Here, we characterize a negative feedback loop between NHR-23, the worm homolog of mammalian retinoid-related orphan receptors (RORs), and the let-7 family of microRNAs that regulates both the frequency and finite number of molts. The molting cycle is decelerated in nhr-23 knockdowns and accelerated in let-7(-) mutants, but timed similarly in let-7(-) nhr-23(-) double mutants and wild-type animals. NHR-23 binds response elements (ROREs) in the let-7 promoter and activates transcription. In turn, let-7 dampens nhr-23 expression across development via a complementary let-7-binding site (LCS) in the nhr-23 3' UTR. The molecular interactions between NHR-23 and let-7 hold true for other let-7 family microRNAs. Either derepression of nhr-23 transcripts by LCS deletion or high gene dosage of nhr-23 leads to protracted behavioral quiescence and extra molts in adults. NHR-23 and let-7 also coregulate scores of genes required for execution of the molts, including lin-42. In addition, ROREs and LCSs isolated from mammalian ROR and let-7 genes function in C. elegans, suggesting conservation of this feedback mechanism. We propose that this feedback loop unites the molting timer and the heterochronic gene regulatory network, possibly by functioning as a cycle counter.
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Affiliation(s)
- Ruhi Patel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Himani Galagali
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - John K Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Alison R Frand
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
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26
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Joseph BB, Edeen PT, Meadows S, Binti S, Fay DS. An unexpected role for the conserved ADAM-family metalloprotease ADM-2 in Caenorhabditis elegans molting. PLoS Genet 2022; 18:e1010249. [PMID: 35639786 PMCID: PMC9187072 DOI: 10.1371/journal.pgen.1010249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/10/2022] [Accepted: 05/11/2022] [Indexed: 11/18/2022] Open
Abstract
Molting is a widespread developmental process in which the external extracellular matrix (ECM), the cuticle, is remodeled to allow for organismal growth and environmental adaptation. Studies in the nematode Caenorhabditis elegans have identified a diverse set of molting-associated factors including signaling molecules, intracellular trafficking regulators, ECM components, and ECM-modifying enzymes such as matrix metalloproteases. C. elegans NEKL-2 and NEKL-3, two conserved members of the NEK family of protein kinases, are essential for molting and promote the endocytosis of environmental steroid-hormone precursors by the epidermis. Steroids in turn drive the cyclic induction of many genes required for molting. Here we report a role for the sole C. elegans ADAM–meltrin metalloprotease family member, ADM-2, as a mediator of molting. Loss of adm-2, including mutations that disrupt the metalloprotease domain, led to the strong suppression of molting defects in partial loss-of-function nekl mutants. ADM-2 is expressed in the epidermis, and its trafficking through the endo-lysosomal network was disrupted after NEKL depletion. We identified the epidermally expressed low-density lipoprotein receptor–related protein, LRP-1, as a candidate target of ADM-2 regulation. Whereas loss of ADM-2 activity led to the upregulation of apical epidermal LRP-1, ADM-2 overexpression caused a reduction in LRP-1 levels. Consistent with this, several mammalian ADAMs, including the meltrin ADAM12, have been shown to regulate mammalian LRP1 via proteolysis. In contrast to mammalian homologs, however, the regulation of LRP-1 by ADM-2 does not appear to involve the metalloprotease function of ADM-2, nor is proteolytic processing of LRP-1 strongly affected in adm-2 mutants. Our findings suggest a noncanonical role for an ADAM family member in the regulation of a lipoprotein-like receptor and lead us to propose that endocytic trafficking may be important for both the internalization of factors that promote molting as well as the removal of proteins that can inhibit the process. The molecular and cellular features of molting in nematodes share many similarities with cellular and developmental processes that occur in mammals. This includes the degradation and reorganization of extracellular matrix materials that surround cells, as well as the intracellular machineries that allow cells to sample and modify their environments. In the current study, we found an unexpected function for a conserved protein that cleaves other proteins on the external surface of cells. Rather than promoting molting through extracellular matrix reorganization, however, the ADM-2 protease appears to function as a negative regulator of molting. This observation can be explained in part by data showing that ADM-2 negatively regulates a cell surface receptor required for molting. Surprisingly, it appears to do so through a mechanism that does not involve proteolysis. Our data provide insights into the mechanisms controlling molting and link several conserved proteins to show how they function together during development.
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Affiliation(s)
- Braveen B. Joseph
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Phillip T. Edeen
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Sarina Meadows
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Shaonil Binti
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - David S. Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
- * E-mail:
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27
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Wu YZ, Jiang HS, Han HF, Li PH, Lu MR, Tsai IJ, Wu YC. C. elegans BLMP-1 controls apical epidermal cell morphology by repressing expression of mannosyltransferase bus-8 and molting signal mlt-8. Dev Biol 2022; 486:96-108. [DOI: 10.1016/j.ydbio.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/17/2022] [Accepted: 03/29/2022] [Indexed: 11/26/2022]
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28
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Binti S, Melinda RV, Joseph BB, Edeen PT, Miller SD, Fay DS. A life cycle alteration can correct molting defects in Caenorhabditis elegans. Dev Biol 2022; 483:143-156. [PMID: 35038442 PMCID: PMC8867747 DOI: 10.1016/j.ydbio.2022.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 11/28/2022]
Abstract
Molting is a widespread feature in the development of many invertebrates, including nematodes and arthropods. In Caenorhabditis elegans, the highly conserved protein kinases NEKL-2/NEK8/9 and NEKL-3/NEK6/7 (NEKLs) promote molting through their involvement in the uptake and intracellular trafficking of epidermal cargos. We found that the relative requirements for NEKL-2 and NEKL-3 differed at different life-cycle stages and under different environmental conditions. Most notably, the transition from the second to the third larval stage (L2→L3 molt) required a higher level of NEKL function than during several other life stages or when animals had experienced starvation at the L1 stage. Specifically, larvae that entered the pre-dauer L2d stage could escape molting defects when transiting to the (non-dauer) L3 stage. Consistent with this, mutations that promote entry into L2d suppressed nekl-associated molting defects, whereas mutations that inhibit L2d entry reduced starvation-mediated suppression. We further showed that loss or reduction of NEKL functions led to defects in the transcription of cyclically expressed molting genes, many of which are under the control of systemic steroid hormone regulation. Moreover, the timing and severity of these transcriptional defects correlated closely with the strength of nekl alleles and with their stage of arrest. Interestingly, transit through L2d rescued nekl-associated expression defects in suppressed worms, providing an example of how life-cycle decisions can impact subsequent developmental events. Given that NEKLs are implicated in the uptake of sterols by the epidermis, we propose that loss of NEKLs leads to a physiological reduction in steroid-hormone signaling and consequent defects in the transcription of genes required for molting.
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Affiliation(s)
- Shaonil Binti
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - Rosa V Melinda
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - Braveen B Joseph
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - Phillip T Edeen
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - Sam D Miller
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - David S Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA.
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29
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Mallick A, Jhaveri N, Jeon J, Chang Y, Shah K, Hosein H, Gupta BP. Genetic analysis of Caenorhabditis elegans pry-1/Axin suppressors identifies genes involved in reproductive structure development, stress responses, and aging. G3 GENES|GENOMES|GENETICS 2022; 12:6462200. [PMID: 35100345 PMCID: PMC9210326 DOI: 10.1093/g3journal/jkab430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/22/2021] [Indexed: 01/15/2023]
Abstract
Abstract
The Axin family of scaffolding proteins regulates a wide array of developmental and post-developmental processes in eukaryotes. Studies in the nematode Caenorhabditis elegans have shown that the Axin homolog PRY-1 plays essential roles in multiple tissues. To understand the genetic network of pry-1, we focused on a set of genes that are differentially expressed in the pry-1-mutant transcriptome and are linked to reproductive structure development. Knocking down eight of the genes (spp-1, clsp-1, ard-1, rpn-7, cpz-1, his-7, cdk-1, and rnr-1) via RNA interference efficiently suppressed the multivulva phenotype of pry-1 mutants. In all cases, the ectopic induction of P3.p vulval precursor cell was also inhibited. The suppressor genes are members of known gene families in eukaryotes and perform essential functions. Our genetic interaction experiments revealed that in addition to their role in vulval development, these genes participate in one or more pry-1-mediated biological events. Whereas four of them (cpz-1, his-7, cdk-1, and rnr-1) function in both stress response and aging, two (spp-1 and ard-1) are specific to stress response. Altogether, these findings demonstrate the important role of pry-1 suppressors in regulating developmental and post-developmental processes in C. elegans. Given that the genes described in this study are conserved, future investigations of their interactions with Axin and their functional specificity promises to uncover the genetic network of Axin in metazoans.
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Affiliation(s)
- Avijit Mallick
- Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada
| | - Nikita Jhaveri
- Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada
| | - Jihae Jeon
- Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada
| | - Yvonne Chang
- Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada
| | - Krupali Shah
- Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada
| | - Hannah Hosein
- Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada
| | - Bhagwati P Gupta
- Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada
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30
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Rich MS, Nix P, Jorgensen EM. The C. elegans mapping locus rol-9 is encoded by a gain-of-function mutation in mlt-11. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000506. [PMID: 35005481 PMCID: PMC8733821 DOI: 10.17912/micropub.biology.000506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 11/06/2022]
Abstract
We mapped rol-9 to the mlt-11 locus (encoded by the gene W01F3.3) on the far-right end of chromosome V. The canonical allele of rol-9, sc148, is an in-frame deletion in a conserved exon of the protein that creates a gain-of-function roller phenotype. sc148 deletes a short peptide of unknown function conserved in nematodes.
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Affiliation(s)
- Matthew S Rich
- School of Biological Sciences, Howard Hughes Medical Institute, University of Utah, USA
| | - Paola Nix
- School of Biological Sciences, Howard Hughes Medical Institute, University of Utah, USA
| | - Erik M Jorgensen
- School of Biological Sciences, Howard Hughes Medical Institute, University of Utah, USA
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31
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Zhou Z, Eichner C, Nilsen F, Jonassen I, Dondrup M. A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis). BMC Genomics 2021; 22:832. [PMID: 34789144 PMCID: PMC8600823 DOI: 10.1186/s12864-021-08054-7] [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: 05/03/2021] [Accepted: 10/04/2021] [Indexed: 11/25/2022] Open
Abstract
Background The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required. Methods Three weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages. Results Eight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with a RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like transcription factor obtained highest scores in the regulatory impact factor calculation. Conclusions We propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirm the effectiveness of our approach and demonstrated the indispensable role of a RAB1A-like gene in the development of the salmon louse. We propose that our approach could be generalized to identify important genes associated with a phenotype of interest in other organisms. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-08054-7).
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Affiliation(s)
- Zhaoran Zhou
- Department of Informatics & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008, Norway
| | - Christiane Eichner
- Department of Biological Sciences & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008, Norway
| | - Frank Nilsen
- Department of Biological Sciences & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008, Norway
| | - Inge Jonassen
- Department of Informatics & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008, Norway
| | - Michael Dondrup
- Department of Informatics & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008, Norway.
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32
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Yang FJ, Chen CN, Chang T, Cheng TW, Chang NC, Kao CY, Lee CC, Huang YC, Hsu JC, Li J, Lu MJ, Chan SP, Wang J. phiC31 integrase for recombination mediated single copy insertion and genome manipulation in C. elegans. Genetics 2021; 220:6428549. [PMID: 34791215 DOI: 10.1093/genetics/iyab206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 11/02/2021] [Indexed: 11/14/2022] Open
Abstract
C. elegans benefits from a large set of tools for genome manipulation. Yet, the precise single-copy insertion of very large DNA constructs (>10 kb) and the generation of inversions are still challenging. Here, we adapted the phiC31 integrase system for C. elegans. We generated an integrated phiC31 integrase expressing strain flanked by attP sites that serves as a landing pad for integration of transgenes by recombination mediated cassette exchange (RCME). This strain is unc-119(-) so RMCE integrants can be produced simply by injection of a plasmid carrying attB sites flanking unc-119(+) and the gene(s) of interest. Additionally, phiC31 integrase is removed concomitantly with integration, eliminating the need to outcross away the integrase. Integrations were obtained for insert sizes up to ∼33.4 kb. Taking advantage of this integration method we establish a dual color fluorescent operon reporter system able to study post-transcriptional regulation of mRNA. Last, we show that large chromosomal segments can be inverted using phiC31 integrase. Thus, the phiC31 integrase system should be a useful addition to the C. elegans toolkit.
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Affiliation(s)
- Fang-Jung Yang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chiao-Nung Chen
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Tiffany Chang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Ting-Wei Cheng
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Ni-Chen Chang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Yi Kao
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Chi Lee
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Ching Huang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jung-Chen Hsu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jengyi Li
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Meiyeh J Lu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Shih-Peng Chan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
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Weadick CJ. Molecular Evolutionary Analysis of Nematode Zona Pellucida (ZP) Modules Reveals Disulfide-Bond Reshuffling and Standalone ZP-C Domains. Genome Biol Evol 2021; 12:1240-1255. [PMID: 32426804 PMCID: PMC7456536 DOI: 10.1093/gbe/evaa095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2020] [Indexed: 12/11/2022] Open
Abstract
Zona pellucida (ZP) modules mediate extracellular protein-protein interactions and contribute to important biological processes including syngamy and cellular morphogenesis. Although some biomedically relevant ZP modules are well studied, little is known about the protein family's broad-scale diversity and evolution. The increasing availability of sequenced genomes from "nonmodel" systems provides a valuable opportunity to address this issue and to use comparative approaches to gain new insights into ZP module biology. Here, through phylogenetic and structural exploration of ZP module diversity across the nematode phylum, I report evidence that speaks to two important aspects of ZP module biology. First, I show that ZP-C domains-which in some modules act as regulators of ZP-N domain-mediated polymerization activity, and which have never before been found in isolation-can indeed be found as standalone domains. These standalone ZP-C domain proteins originated in independent (paralogous) lineages prior to the diversification of extant nematodes, after which they evolved under strong stabilizing selection, suggesting the presence of ZP-N domain-independent functionality. Second, I provide a much-needed phylogenetic perspective on disulfide bond variability, uncovering evidence for both convergent evolution and disulfide-bond reshuffling. This result has implications for our evolutionary understanding and classification of ZP module structural diversity and highlights the usefulness of phylogenetics and diverse sampling for protein structural biology. All told, these findings set the stage for broad-scale (cross-phyla) evolutionary analysis of ZP modules and position Caenorhabditis elegans and other nematodes as important experimental systems for exploring the evolution of ZP modules and their constituent domains.
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Huang Y, Wu J, Chen X, Tong D, Zhou J, Wu F, Zhang H, Yang Y, Ma G, Du A. A Zinc Metalloprotease nas-33 Is Required for Molting and Survival in Parasitic Nematode Haemonchus contortus. Front Cell Dev Biol 2021; 9:695003. [PMID: 34327203 PMCID: PMC8313830 DOI: 10.3389/fcell.2021.695003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/17/2021] [Indexed: 12/04/2022] Open
Abstract
Molting is of great importance for the survival and development of nematodes. Nematode astacins (NAS), a large family of zinc metalloproteases, have been proposed as novel anthelmintic targets due to their multiple roles in biological processes of parasitic nematodes. In this study, we report a well conserved nas-33 gene in nematodes of clade V and elucidate how this gene is involved in the molting process of the free-living nematode Caenorhabditis elegans and the parasitic nematode Haemonchus contortus. A predominant transcription of nas-33 is detected in the larval stages of these worms, particularly in the molting process. Knockdown of this gene results in marked molecular changes of genes involved in cuticle synthesis and ecdysis, compromised shedding of the old cuticle, and reduced worm viability in H. contortus. The crucial role of nas-33 in molting is closely associated with a G protein beta subunit (GPB-1). Suppression of both nas-33 and gpb-1 blocks shedding of the old cuticle, compromises the connection between the cuticle and hypodermis, and leads to an increased number of sick and dead worms, indicating essentiality of this module in nematode development and survival. These findings reveal the functional role of nas-33 in nematode molting process and identify astacins as novel anthelmintic targets for parasitic nematodes of socioeconomic significance.
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Affiliation(s)
- Yan Huang
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Jie Wu
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Xueqiu Chen
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Danni Tong
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Jingru Zhou
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Fei Wu
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Hui Zhang
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Yi Yang
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Guangxu Ma
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Aifang Du
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
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Faerberg DF, Gurarie V, Ruvinsky I. Inferring temporal organization of postembryonic development from high-content behavioral tracking. Dev Biol 2021; 475:54-64. [PMID: 33636188 PMCID: PMC8107144 DOI: 10.1016/j.ydbio.2021.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 11/22/2022]
Abstract
Understanding temporal regulation of development remains an important challenge. Whereas average, species-typical timing of many developmental processes has been established, less is known about inter-individual variability and correlations in timing of specific events. We addressed these questions in the context of postembryonic development in Caenorhabditis elegans. Based on patterns of locomotor activity of freely moving animals, we inferred durations of four larval stages (L1-L4) in over 100 individuals. Analysis of these data supports several conclusions. Individuals have consistently faster or slower rates of development because durations of L1 through L3 stages are positively correlated. The last larval stage, the L4, is less variable than the earlier stages and its duration is largely independent of the rate of early larval development, implying existence of two distinct larval epochs. We describe characteristic patterns of variation and correlation, as well as the fact that stage durations tend to scale relative to total developmental time. This scaling relationship suggests that each larval stage is not limited by an absolute duration, but is instead terminated when a subset of events that must occur prior to adulthood have been completed. The approach described here offers a scalable platform that will facilitate the study of temporal regulation of postembryonic development.
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Affiliation(s)
- Denis F Faerberg
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Victor Gurarie
- Department of Physics, University of Colorado, Boulder, CO, 80309, USA
| | - Ilya Ruvinsky
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
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Doenier J, Lynch TR, Kimble J, Aoki ST. An improved in vivo tethering assay with single molecule FISH reveals that a nematode Nanos enhances reporter expression and mRNA stability. RNA (NEW YORK, N.Y.) 2021; 27:643-652. [PMID: 33727224 PMCID: PMC8127996 DOI: 10.1261/rna.078693.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Robust methods are critical for testing the in vivo regulatory mechanism of RNA binding proteins. Here we report improvement of a protein-mRNA tethering assay to probe the function of an RNA binding protein in its natural context within the C. elegans adult germline. The assay relies on a dual reporter expressing two mRNAs from a single promoter and resolved by trans-splicing. The gfp reporter 3'UTR harbors functional binding elements for λN22 peptide, while the mCherry reporter 3'UTR carries mutated nonfunctional elements. This strategy enables internally controlled quantitation of reporter protein by immunofluorescence and mRNA by smFISH. To test the new system, we analyzed a C. elegans Nanos protein, NOS-3, which serves as a post-transcriptional regulator of germ cell fate. Unexpectedly, tethered NOS-3 enhanced reporter expression. We confirmed this enhancement activity with a second reporter engineered at an endogenous germline gene. NOS-3 enhancement of reporter expression was associated with its amino-terminal intrinsically disordered region, not its carboxy-terminal zinc fingers. RNA quantitation revealed that tethered NOS-3 enhances stability of the reporter mRNA. We suggest that this direct NOS-3 enhancement activity may explain a paradox: Classically Nanos proteins are expected to repress RNA, but nos-3 had been found to promote gld-1 expression, an effect that could be direct. Regardless, the new dual reporter dramatically improves in situ quantitation of reporter expression after RNA binding protein tethering to determine its molecular mechanism in a multicellular tissue.
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Affiliation(s)
- Jonathan Doenier
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Tina R Lynch
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Scott T Aoki
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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37
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Chiyoda H, Kume M, del Castillo CC, Kontani K, Spang A, Katada T, Fukuyama M. Caenorhabditis elegans PTR/PTCHD PTR-18 promotes the clearance of extracellular hedgehog-related protein via endocytosis. PLoS Genet 2021; 17:e1009457. [PMID: 33872306 PMCID: PMC8104386 DOI: 10.1371/journal.pgen.1009457] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 05/07/2021] [Accepted: 03/01/2021] [Indexed: 01/25/2023] Open
Abstract
Spatiotemporal restriction of signaling plays a critical role in animal development and tissue homeostasis. All stem and progenitor cells in newly hatched C. elegans larvae are quiescent and capable of suspending their development until sufficient food is supplied. Here, we show that ptr-18, which encodes the evolutionarily conserved patched-related (PTR)/patched domain-containing (PTCHD) protein, temporally restricts the availability of extracellular hedgehog-related protein to establish the capacity of progenitor cells to maintain quiescence. We found that neural progenitor cells exit from quiescence in ptr-18 mutant larvae even when hatched under starved conditions. This unwanted reactivation depended on the activity of a specific set of hedgehog-related grl genes including grl-7. Unexpectedly, neither PTR-18 nor GRL-7 were expressed in newly hatched wild-type larvae. Instead, at the late embryonic stage, both PTR-18 and GRL-7 proteins were first localized around the apical membrane of hypodermal and neural progenitor cells and subsequently targeted for lysosomal degradation before hatching. Loss of ptr-18 caused a significant delay in GRL-7 clearance, causing this protein to be retained in the extracellular space in newly hatched ptr-18 mutant larvae. Furthermore, the putative transporter activity of PTR-18 was shown to be required for the appropriate function of the protein. These findings not only uncover a previously undescribed role of PTR/PTCHD in the clearance of extracellular hedgehog-related proteins via endocytosis-mediated degradation but also illustrate that failure to temporally restrict intercellular signaling during embryogenesis can subsequently compromise post-embryonic progenitor cell function.
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Affiliation(s)
- Hirohisa Chiyoda
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Masahiko Kume
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Kenji Kontani
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Anne Spang
- Biozentrum, University of Basel, Basel, Switzerland
| | - Toshiaki Katada
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Masamitsu Fukuyama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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38
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An Epigenetic Priming Mechanism Mediated by Nutrient Sensing Regulates Transcriptional Output during C. elegans Development. Curr Biol 2020; 31:809-826.e6. [PMID: 33357451 DOI: 10.1016/j.cub.2020.11.060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/07/2020] [Accepted: 11/23/2020] [Indexed: 11/23/2022]
Abstract
Although precise tuning of gene expression levels is critical for most developmental pathways, the mechanisms by which the transcriptional output of dosage-sensitive molecules is established or modulated by the environment remain poorly understood. Here, we provide a mechanistic framework for how the conserved transcription factor BLMP-1/Blimp1 operates as a pioneer factor to decompact chromatin near its target loci during embryogenesis (hours prior to major transcriptional activation) and, by doing so, regulates both the duration and amplitude of subsequent target gene transcription during post-embryonic development. This priming mechanism is genetically separable from the mechanisms that establish the timing of transcriptional induction and functions to canalize aspects of cell-fate specification, animal size regulation, and molting. A key feature of the BLMP-1-dependent transcriptional priming mechanism is that chromatin decompaction is initially established during embryogenesis and maintained throughout larval development by nutrient sensing. This anticipatory mechanism integrates transcriptional output with environmental conditions and is essential for resuming normal temporal patterning after animals exit nutrient-mediated developmental arrests.
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39
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Tsiairis C, Großhans H. Gene expression oscillations in C. elegans underlie a new developmental clock. Curr Top Dev Biol 2020; 144:19-43. [PMID: 33992153 DOI: 10.1016/bs.ctdb.2020.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
During C. elegans larval development, thousands of genes, accounting for >20% of the transcriptome, exhibit oscillatory expression with large amplitudes. The time of peaking varies for different genes, but expression generally peaks once per larval stage, with both the oscillation period and larval stage duration varying in concert with temperature. This and other evidence support the existence of a gene expression oscillator that functions as a developmental clock. In this article, we review what is known about the biology, architecture and possible mechanisms of this clock. We compare it to other oscillators, and highlight tools and approaches suited to its study. Finally, we point out implications of these wide-spread and dynamic changes of gene expression on any type of gene expression profiling experiment in C. elegans larvae and how such experiments need to be controlled.
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Affiliation(s)
- Charisios Tsiairis
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland; University of Basel, Basel, Switzerland.
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40
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Galford KF, Jose AM. The FDA-approved drugs ticlopidine, sertaconazole, and dexlansoprazole can cause morphological changes in C. elegans. CHEMOSPHERE 2020; 261:127756. [PMID: 32731027 PMCID: PMC7606649 DOI: 10.1016/j.chemosphere.2020.127756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Urgent need for treatments limit studies of therapeutic drugs before approval by regulatory agencies. Analyses of drugs after approval can therefore improve our understanding of their mechanism of action and enable better therapies. We screened a library of 1443 Food and Drug Administration (FDA)-approved drugs using a simple assay in the nematode C. elegans and found three compounds that caused morphological changes. While the anticoagulant ticlopidine and the antifungal sertaconazole caused both accumulations that resulted in distinct distortions of pharyngeal anatomy and lethality upon acute exposure, the proton-pump inhibitor dexlansoprazole caused molting defects and required exposure during larval development. Such easily detectable defects in a powerful genetic model system advocate the continued exploration of current medicines using a variety of model organisms to better understand drugs already prescribed to millions of patients.
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Affiliation(s)
- Kyle F Galford
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
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41
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Ragle JM, Aita AL, Morrison KN, Martinez-Mendez R, Saeger HN, Ashley GA, Johnson LC, Schubert KA, Shakes DC, Ward JD. The conserved molting/circadian rhythm regulator NHR-23/NR1F1 serves as an essential co-regulator of C. elegans spermatogenesis. Development 2020; 147:dev193862. [PMID: 33060131 PMCID: PMC7710015 DOI: 10.1242/dev.193862] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/12/2020] [Indexed: 12/21/2022]
Abstract
In sexually reproducing metazoans, spermatogenesis is the process by which uncommitted germ cells give rise to haploid sperm. Work in model systems has revealed mechanisms controlling commitment to the sperm fate, but how this fate is subsequently executed remains less clear. While studying the well-established role of the conserved nuclear hormone receptor transcription factor, NHR-23/NR1F1, in regulating C. elegans molting, we discovered that NHR-23/NR1F1 is also constitutively expressed in developing primary spermatocytes and is a critical regulator of spermatogenesis. In this novel role, NHR-23/NR1F1 functions downstream of the canonical sex-determination pathway. Degron-mediated depletion of NHR-23/NR1F1 within hermaphrodite or male germlines causes sterility due to an absence of functional sperm, as depleted animals produce arrested primary spermatocytes rather than haploid sperm. These spermatocytes arrest in prometaphase I and fail to either progress to anaphase or attempt spermatid-residual body partitioning. They make sperm-specific membranous organelles but fail to assemble their major sperm protein into fibrous bodies. NHR-23/NR1F1 appears to function independently of the known SPE-44 gene regulatory network, revealing the existence of an NHR-23/NR1F1-mediated module that regulates the spermatogenesis program.
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Affiliation(s)
- James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Abigail L Aita
- Department of Biology, William & Mary, Williamsburg, VA 23187, USA
| | | | - Raquel Martinez-Mendez
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hannah N Saeger
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Guinevere A Ashley
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Londen C Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Katherine A Schubert
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Diane C Shakes
- Department of Biology, William & Mary, Williamsburg, VA 23187, USA
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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42
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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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43
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Cohen JD, Sundaram MV. C. elegans Apical Extracellular Matrices Shape Epithelia. J Dev Biol 2020; 8:E23. [PMID: 33036165 PMCID: PMC7712855 DOI: 10.3390/jdb8040023] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Apical extracellular matrices (aECMs) coat exposed surfaces of epithelia to shape developing tissues and protect them from environmental insults. Despite their widespread importance for human health, aECMs are poorly understood compared to basal and stromal ECMs. The nematode Caenorhabditis elegans contains a variety of distinct aECMs, some of which share many of the same types of components (lipids, lipoproteins, collagens, zona pellucida domain proteins, chondroitin glycosaminoglycans and proteoglycans) with mammalian aECMs. These aECMs include the eggshell, a glycocalyx-like pre-cuticle, both collagenous and chitin-based cuticles, and other understudied aECMs of internal epithelia. C. elegans allows rapid genetic manipulations and live imaging of fluorescently-tagged aECM components, and is therefore providing new insights into aECM structure, trafficking, assembly, and functions in tissue shaping.
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Affiliation(s)
| | - Meera V. Sundaram
- Department of Genetics, University of Pennsylvania Perelman School of Medicine 415 Curie Blvd, Philadelphia, PA 19104-6145, USA;
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44
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Wickramatunga PGTS, Gunawardene YINS, Wijesinghe KJ, Ellepola ANB, Dassanayake RS. RNAi-mediated silencing of ARV1 in Setaria digitata impairs in-vitro microfilariae release, embryogenesis and adult parasite viability. Vet Parasitol 2020; 284:109189. [PMID: 32739751 DOI: 10.1016/j.vetpar.2020.109189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 02/01/2023]
Abstract
Setaria digitata is a nematode that resides in the peritoneal cavity of ruminants causing cerebrospinal nematodiasis disease affecting livestock and inflicting significant economic forfeitures in Asia. Further, this nematode can infect humans, causing abscesses, allergic reactions, enlarged lymph nodes, eye lesions and inflammation of the lungs. The 'ARE2 required for viability1' (ARV1) encodes for putative lipid transporter localized in the endoplasmic reticulum (ER) and Golgi complex membrane in humans and yeast. In the present study, the functional role of S. digitata ARV1 (SD-ARV1) was investigated using RNA interference (RNAi) reverse genetic tool. The targeted silencing SD-ARV1 transcripts by siRNA mediated RNAi resulted in a dramatic reduction of SD-ARV1 gene and protein expressions in S. digitata, which in turn modulated the parasitic motility, its production of eggs and microfilaria viability. Further, the same silencing caused severe phenotypic deformities such as distortion of eggs and embryonic development arrest in the intrauterine stages of adult female S. digitata. These results suggest that SD-ARV1 plays a pivotal role in worm embryogenesis, adult parasite motility and microfilariae viability. Finally, the ubiquitous presence of ARV1 in human filarial nematodes, its crucial functional roles in nematode biology and its remarkable diversity in primary protein structure compared to homologues in their hosts warrants further investigations to ascertain its candidacy in anthelmintic drug development.
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Affiliation(s)
| | | | - Kaveesha Jayani Wijesinghe
- Department of Chemistry, Faculty of Science, University of Colombo, PO 1490, Kumaratunga Munidasa Mawatha, Colombo, 00300, Sri Lanka
| | - Arjuna N B Ellepola
- Division of Oral Microbiology, Faculty of Dentistry, Health Sciences Center, Kuwait University, Kuwait
| | - Ranil Samantha Dassanayake
- Department of Chemistry, Faculty of Science, University of Colombo, PO 1490, Kumaratunga Munidasa Mawatha, Colombo, 00300, Sri Lanka.
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Meeuse MWM, Hauser YP, Morales Moya LJ, Hendriks G, Eglinger J, Bogaarts G, Tsiairis C, Großhans H. Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans. Mol Syst Biol 2020; 16:e9498. [PMID: 32687264 PMCID: PMC7370751 DOI: 10.15252/msb.20209498] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 11/26/2022] Open
Abstract
Gene expression oscillators can structure biological events temporally and spatially. Different biological functions benefit from distinct oscillator properties. Thus, finite developmental processes rely on oscillators that start and stop at specific times, a poorly understood behavior. Here, we have characterized a massive gene expression oscillator comprising > 3,700 genes in Caenorhabditis elegans larvae. We report that oscillations initiate in embryos, arrest transiently after hatching and in response to perturbation, and cease in adults. Experimental observation of the transitions between oscillatory and non-oscillatory states at high temporal resolution reveals an oscillator operating near a Saddle Node on Invariant Cycle (SNIC) bifurcation. These findings constrain the architecture and mathematical models that can represent this oscillator. They also reveal that oscillator arrests occur reproducibly in a specific phase. Since we find oscillations to be coupled to developmental processes, including molting, this characteristic of SNIC bifurcations endows the oscillator with the potential to halt larval development at defined intervals, and thereby execute a developmental checkpoint function.
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Affiliation(s)
- Milou WM Meeuse
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- University of BaselBaselSwitzerland
| | - Yannick P Hauser
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- University of BaselBaselSwitzerland
| | | | - Gert‐Jan Hendriks
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- University of BaselBaselSwitzerland
| | - Jan Eglinger
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
| | | | - Charisios Tsiairis
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- University of BaselBaselSwitzerland
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46
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Jasmer DP, Rosa BA, Tyagi R, Bulman CA, Beerntsen B, Urban JF, Sakanari J, Mitreva M. De novo identification of toxicants that cause irreparable damage to parasitic nematode intestinal cells. PLoS Negl Trop Dis 2020; 14:e0007942. [PMID: 32453724 PMCID: PMC7274465 DOI: 10.1371/journal.pntd.0007942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 06/05/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023] Open
Abstract
Efforts to identify new drugs for therapeutic and preventive treatments against parasitic nematodes have gained increasing interest with expanding pathogen omics databases and drug databases from which new anthelmintic compounds might be identified. Here, a novel approach focused on integrating a pan-Nematoda multi-omics data targeted to a specific nematode organ system (the intestinal tract) with evidence-based filtering and chemogenomic screening was undertaken. Based on de novo computational target prioritization of the 3,564 conserved intestine genes in A. suum, exocytosis was identified as a high priority pathway, and predicted inhibitors of exocytosis were tested using the large roundworm (Ascaris suum larval stages), a filarial worm (Brugia pahangi adult and L3), a whipworm (Trichuris muris adult), and the non-parasitic nematode Caenorhabditis elegans. 10 of 13 inhibitors were found to cause rapid immotility in A. suum L3 larvae, and five inhibitors were effective against the three phylogenetically diverse parasitic nematode species, indicating potential for a broad spectrum anthelmintics. Several distinct pathologic phenotypes were resolved related to molting, motility, or intestinal cell and tissue damage using conventional and novel histologic methods. Pathologic profiles characteristic for each inhibitor will guide future research to uncover mechanisms of the anthelmintic effects and improve on drug designs. This progress firmly validates the focus on intestinal cell biology as a useful resource to develop novel anthelmintic strategies.
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Affiliation(s)
- Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Bruce A Rosa
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rahul Tyagi
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Christina A Bulman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Brenda Beerntsen
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
| | - Joseph F Urban
- U.S. Department of Agriculture, Northeast Area, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasite Diseases Laboratory and Beltsville Human Nutrition Research Center, Diet Genomics and Immunology Laboratory, Beltsville, Maryland, United States of America
| | - Judy Sakanari
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
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47
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Fong HT, Hagen T, Inoue T. LDB1 and the SWI/SNF complex participate in both transcriptional activation and repression by Caenorhabditis elegans BLIMP1/PRDM1. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194577. [PMID: 32417234 DOI: 10.1016/j.bbagrm.2020.194577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 01/05/2023]
Abstract
Transcription factors of the BLIMP1/PRDM1 family are important regulators of development. BLIMP1/PRDM1 can both activate and repress gene expression, however, the mechanism of activation is not well understood. Therefore, we looked for factors involved in gene activation by C. elegans BLMP-1, the ortholog of BLIMP1/PRDM1. BLMP-1 activates the expression of bed-3, a gene involved in vulval development. By screening nuclear proteins that function in vulval development, we identified two proteins (LDB-1 and HAM-3) required for BLMP-1 dependent bed-3 expression. LDB-1 is the sole C. elegans member of the LIM Binding Protein (LDB) family, whereas HAM-3 is an accessory subunit of the SWI/SNF complex (ortholog of human SMARCD3/BAF60C). A core SWI/SNF subunit SWSN-1 (ortholog of human SMARCC1/BAF155) is also involved. We found that LDB-1 and HAM-3 bind to BLMP-1, suggesting that BLMP-1 recruits LDB-1 and the SWI/SNF complex to activate bed-3 expression. Interestingly, LDB-1 and HAM-3 are involved in both transcriptional activation and repression. In particular, BLMP-1, LDB-1 and HAM-3 co-regulate a set of hypodermal genes including bed-3 (activated), col-124 (activated) and lin-29 (repressed). On the other hand, LDB-1 and HAM-3 are not required for activation or repression of some genes regulated by BLMP-1 (e.g. T09D3.8, nas-10). We also found that human LDB1, SMARCD3/BAF60C and SMARCC1/BAF155 all physically interact with human BLIMP1/PRDM1 in vitro and are closely associated with BLIMP1/PRDM1 in vivo. Taken together, these results identify LDB1 and SWI/SNF as likely conserved cofactors of BLIMP1/PRDM1, which participate in activation and repression of a subset of BLIMP1/PRDM1-regulated genes.
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Affiliation(s)
- Hei Tung Fong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Thilo Hagen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore.
| | - Takao Inoue
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore.
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48
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Xie J, Sang M, Song X, Zhang S, Kim D, Veenstra JA, Park Y, Li B. A new neuropeptide insect parathyroid hormone iPTH in the red flour beetle Tribolium castaneum. PLoS Genet 2020; 16:e1008772. [PMID: 32365064 PMCID: PMC7224569 DOI: 10.1371/journal.pgen.1008772] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 05/14/2020] [Accepted: 04/09/2020] [Indexed: 12/15/2022] Open
Abstract
In the postgenomics era, comparative genomics have advanced the understanding of evolutionary processes of neuropeptidergic signaling systems. The evolutionary origin of many neuropeptidergic signaling systems can be traced date back to early metazoan evolution based on the conserved sequences. Insect parathyroid hormone receptor (iPTHR) was previously described as an ortholog of vertebrate PTHR that has a well-known function in controlling bone remodeling. However, there was no sequence homologous to PTH sequence in insect genomes, leaving the iPTHR as an orphan receptor. Here, we identified the authentic ligand insect PTH (iPTH) for the iPTHR. The taxonomic distribution of iPTHR, which is lacking in Diptera and Lepidoptera, provided a lead for identifying the authentic ligand. We found that a previously described orphan ligand known as PXXXamide (where X is any amino acid) described in the cuttlefish Sepia officinalis has a similar taxonomic distribution pattern as iPTHR. Tests of this peptide, iPTH, in functional reporter assays confirmed the interaction of the ligand-receptor pair. Study of a model beetle, Tribolium castaneum, was used to investigate the function of the iPTH signaling system by RNA interference followed by RNA sequencing and phenotyping. The results suggested that the iPTH system is likely involved in the regulation of cuticle formation that culminates with a phenotype of defects in wing exoskeleton maturation at the time of adult eclosion. Moreover, RNAi of iPTHRs also led to significant reductions in egg numbers and hatching rates after parental RNAi. Vertebrate parathyroid hormone (PTH) and its receptors have been extensively studied with respect to their function in bone remodeling and calcium metabolism. Insect parathyroid hormone receptors (iPTHRs) have been previously described as counterparts of vertebrate PTHRs, however, they are still orphan receptors for which the authentic ligands and biological functions remain unknown. We describe an insect form of parathyroid hormone (iPTH) by analyzing its interactions with iPTHRs. Identification of this new insect peptidergic system proved that the PTH system is an ancestral signaling system dating back to the evolutionary time before the divergence of protostomes and deuterostomes. We also investigated the functions of the iPTH system in a model beetle Tribolium castaneum by using RNA interference. RNA interference of iPTHR resulted in defects in wing exoskeleton maturation and fecundity. Based on the differential gene expression patterns and the phenotype induced by RNAi, we propose that the iPTH system is likely involved in the regulation of exoskeletal cuticle formation and fecundity in insects.
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Affiliation(s)
- Jia Xie
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- Department of Entomology, Kansas State University, Manhattan, KS, United States of America
| | - Ming Sang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaowen Song
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Sisi Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Donghun Kim
- Department of Entomology, Kansas State University, Manhattan, KS, United States of America
- Department of Applied Biology, Kyungpook National University, Sangju, Korea
| | - Jan A. Veenstra
- INCIA UMR 5287 CNRS, University of Bordeaux, Pessac, France
- * E-mail: (JAV); (YP); (BL)
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS, United States of America
- * E-mail: (JAV); (YP); (BL)
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- * E-mail: (JAV); (YP); (BL)
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Sandhof CA, Hoppe SO, Druffel-Augustin S, Gallrein C, Kirstein J, Voisine C, Nussbaum-Krammer C. Reducing INS-IGF1 signaling protects against non-cell autonomous vesicle rupture caused by SNCA spreading. Autophagy 2020; 16:878-899. [PMID: 31354022 PMCID: PMC7144869 DOI: 10.1080/15548627.2019.1643657] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 07/02/2019] [Accepted: 07/11/2019] [Indexed: 01/28/2023] Open
Abstract
Aging is associated with a gradual decline of cellular proteostasis, giving rise to devastating protein misfolding diseases, such as Alzheimer disease (AD) or Parkinson disease (PD). These diseases often exhibit a complex pathology involving non-cell autonomous proteotoxic effects, which are still poorly understood. Using Caenorhabditis elegans we investigated how local protein misfolding is affecting neighboring cells and tissues showing that misfolded PD-associated SNCA/α-synuclein is accumulating in highly dynamic endo-lysosomal vesicles. Irrespective of whether being expressed in muscle cells or dopaminergic neurons, accumulated proteins were transmitted into the hypodermis with increasing age, indicating that epithelial cells might play a role in remote degradation when the local endo-lysosomal degradation capacity is overloaded. Cell biological and genetic approaches revealed that inter-tissue dissemination of SNCA was regulated by endo- and exocytosis (neuron/muscle to hypodermis) and basement membrane remodeling (muscle to hypodermis). Transferred SNCA conformers were, however, inefficiently cleared and induced endo-lysosomal membrane permeabilization. Remarkably, reducing INS (insulin)-IGF1 (insulin-like growth factor 1) signaling provided protection by maintaining endo-lysosomal integrity. This study suggests that the degradation of lysosomal substrates is coordinated across different tissues in metazoan organisms. Because the chronic dissemination of poorly degradable disease proteins into neighboring tissues exerts a non-cell autonomous toxicity, this implies that restoring endo-lysosomal function not only in cells with pathological inclusions, but also in apparently unaffected cell types might help to halt disease progression.Abbreviations: AD: Alzheimer disease; BM: basement membrane; BWM: body wall muscle; CEP: cephalic sensilla; CLEM: correlative light and electron microscopy; CTNS-1: cystinosin (lysosomal protein) homolog; DA: dopaminergic; DAF-2: abnormal dauer formation; ECM: extracellular matrix; FLIM: fluorescence lifetime imaging microscopy; fps: frames per second; GFP: green fluorescent protein; HPF: high pressure freezing; IGF1: insulin-like growth factor 1; INS: insulin; KD: knockdown; LMP: lysosomal membrane permeabilization; MVB: multivesicular body; NOC: nocodazole; PD: Parkinson disease; RFP: red fluorescent protein; RNAi: RNA interference; sfGFP: superfolder GFP; SNCA: synuclein alpha; TEM: transmission electron microscopy; TNTs: tunneling nanotubes; TCSPC: time correlated single photon counting; YFP: yellow fluorescent protein.
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Affiliation(s)
- Carl Alexander Sandhof
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Simon Oliver Hoppe
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Silke Druffel-Augustin
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Christian Gallrein
- Department of Molecular Physiology and Cell Biology, Leibniz-Institute for Molecular Pharmacology (FMP) im Forschungsverbund Berlin e.V, Berlin, Germany
| | - Janine Kirstein
- Department of Molecular Physiology and Cell Biology, Leibniz-Institute for Molecular Pharmacology (FMP) im Forschungsverbund Berlin e.V, Berlin, Germany
| | - Cindy Voisine
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Carmen Nussbaum-Krammer
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
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50
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Joseph BB, Wang Y, Edeen P, Lažetić V, Grant BD, Fay DS. Control of clathrin-mediated endocytosis by NIMA family kinases. PLoS Genet 2020; 16:e1008633. [PMID: 32069276 PMCID: PMC7048319 DOI: 10.1371/journal.pgen.1008633] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/28/2020] [Accepted: 01/28/2020] [Indexed: 12/16/2022] Open
Abstract
Endocytosis, the process by which cells internalize plasma membrane and associated cargo, is regulated extensively by posttranslational modifications. Previous studies suggested the potential involvement of scores of protein kinases in endocytic control, of which only a few have been validated in vivo. Here we show that the conserved NIMA-related kinases NEKL-2/NEK8/9 and NEKL-3/NEK6/7 (the NEKLs) control clathrin-mediated endocytosis in C. elegans. Loss of NEKL-2 or NEKL-3 activities leads to penetrant larval molting defects and to the abnormal localization of trafficking markers in arrested larvae. Using an auxin-based degron system, we also find that depletion of NEKLs in adult-stage C. elegans leads to gross clathrin mislocalization and to a dramatic reduction in clathrin mobility at the apical membrane. Using a non-biased genetic screen to identify suppressors of nekl molting defects, we identified several components and regulators of AP2, the major clathrin adapter complex acting at the plasma membrane. Strikingly, reduced AP2 activity rescues both nekl mutant molting defects as well as associated trafficking phenotypes, whereas increased levels of active AP2 exacerbate nekl defects. Moreover, in a unique example of mutual suppression, NEKL inhibition alleviates defects associated with reduced AP2 activity, attesting to the tight link between NEKL and AP2 functions. We also show that NEKLs are required for the clustering and internalization of membrane cargo required for molting. Notably, we find that human NEKs can rescue molting and trafficking defects in nekl mutant worms, suggesting that the control of intracellular trafficking is an evolutionarily conserved function of NEK family kinases. In order to function properly, cells must continually import materials from the outside. This process, termed endocytosis, is necessary for the uptake of nutrients and for interpreting signals coming from the external environment or from within the body. These signals are critical during animal development but also affect many types of cell behaviors throughout life. In our current work, we show that several highly conserved proteins in the nematode Caenorhabditis elegans, NEKL-2 and NEKL-3, regulate endocytosis. The human counterparts of NEKL-2 and NEKL-3 have been implicated in cardiovascular and renal diseases as well as many types of cancers. However, their specific functions within cells is incompletely understood and very little is known about their role in endocytosis or how this role might impact disease processes. Here we use several complementary approaches to characterize the specific functions of C. elegans NEKL-2 and NEKL-3 in endocytosis and show that their human counterparts likely have very similar functions. This work paves the way to a better understanding of fundamental biological processes and to determining the cellular functions of proteins connected to human diseases.
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Affiliation(s)
- Braveen B. Joseph
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Yu Wang
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Phil Edeen
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Vladimir Lažetić
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Barth D. Grant
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - David S. Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
- * E-mail:
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