101
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Maroilley T, Li X, Oldach M, Jean F, Stasiuk SJ, Tarailo-Graovac M. Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing. Sci Rep 2021; 11:18258. [PMID: 34521941 PMCID: PMC8440550 DOI: 10.1038/s41598-021-97764-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
Genomic rearrangements cause congenital disorders, cancer, and complex diseases in human. Yet, they are still understudied in rare diseases because their detection is challenging, despite the advent of whole genome sequencing (WGS) technologies. Short-read (srWGS) and long-read WGS approaches are regularly compared, and the latter is commonly recommended in studies focusing on genomic rearrangements. However, srWGS is currently the most economical, accurate, and widely supported technology. In Caenorhabditis elegans (C. elegans), such variants, induced by various mutagenesis processes, have been used for decades to balance large genomic regions by preventing chromosomal crossover events and allowing the maintenance of lethal mutations. Interestingly, those chromosomal rearrangements have rarely been characterized on a molecular level. To evaluate the ability of srWGS to detect various types of complex genomic rearrangements, we sequenced three balancer strains using short-read Illumina technology. As we experimentally validated the breakpoints uncovered by srWGS, we showed that, by combining several types of analyses, srWGS enables the detection of a reciprocal translocation (eT1), a free duplication (sDp3), a large deletion (sC4), and chromoanagenesis events. Thus, applying srWGS to decipher real complex genomic rearrangements in model organisms may help designing efficient bioinformatics pipelines with systematic detection of complex rearrangements in human genomes.
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Affiliation(s)
- Tatiana Maroilley
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Xiao Li
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Matthew Oldach
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Francesca Jean
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Susan J Stasiuk
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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102
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Vuong-Brender TT, Flynn S, Vallis Y, de Bono M. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife 2021; 10:68238. [PMID: 34499028 PMCID: PMC8428840 DOI: 10.7554/elife.68238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/28/2021] [Indexed: 01/18/2023] Open
Abstract
The ubiquitous Ca2+ sensor calmodulin (CaM) binds and regulates many proteins, including ion channels, CaM kinases, and calcineurin, according to Ca2+-CaM levels. What regulates neuronal CaM levels, is, however, unclear. CaM-binding transcription activators (CAMTAs) are ancient proteins expressed broadly in nervous systems and whose loss confers pleiotropic behavioral defects in flies, mice, and humans. Using Caenorhabditis elegans and Drosophila, we show that CAMTAs control neuronal CaM levels. The behavioral and neuronal Ca2+ signaling defects in mutants lacking camt-1, the sole C. elegans CAMTA, can be rescued by supplementing neuronal CaM. CAMT-1 binds multiple sites in the CaM promoter and deleting these sites phenocopies camt-1. Our data suggest CAMTAs mediate a conserved and general mechanism that controls neuronal CaM levels, thereby regulating Ca2+ signaling, physiology, and behavior.
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Affiliation(s)
- Thanh Thi Vuong-Brender
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.,Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Sean Flynn
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Yvonne Vallis
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Mario de Bono
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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103
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Campos TL, Korhonen PK, Hofmann A, Gasser RB, Young ND. Harnessing model organism genomics to underpin the machine learning-based prediction of essential genes in eukaryotes - Biotechnological implications. Biotechnol Adv 2021; 54:107822. [PMID: 34461202 DOI: 10.1016/j.biotechadv.2021.107822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022]
Abstract
The availability of high-quality genomes and advances in functional genomics have enabled large-scale studies of essential genes in model eukaryotes, including the 'elegant worm' (Caenorhabditis elegans; Nematoda) and the 'vinegar fly' (Drosophila melanogaster; Arthropoda). However, this is not the case for other, much less-studied organisms, such as socioeconomically important parasites, for which functional genomic platforms usually do not exist. Thus, there is a need to develop innovative techniques or approaches for the prediction, identification and investigation of essential genes. A key approach that could enable the prediction of such genes is machine learning (ML). Here, we undertake an historical review of experimental and computational approaches employed for the characterisation of essential genes in eukaryotes, with a particular focus on model ecdysozoans (C. elegans and D. melanogaster), and discuss the possible applicability of ML-approaches to organisms such as socioeconomically important parasites. We highlight some recent results showing that high-performance ML, combined with feature engineering, allows a reliable prediction of essential genes from extensive, publicly available 'omic data sets, with major potential to prioritise such genes (with statistical confidence) for subsequent functional genomic validation. These findings could 'open the door' to fundamental and applied research areas. Evidence of some commonality in the essential gene-complement between these two organisms indicates that an ML-engineering approach could find broader applicability to ecdysozoans such as parasitic nematodes or arthropods, provided that suitably large and informative data sets become/are available for proper feature engineering, and for the robust training and validation of algorithms. This area warrants detailed exploration to, for example, facilitate the identification and characterisation of essential molecules as novel targets for drugs and vaccines against parasitic diseases. This focus is particularly important, given the substantial impact that such diseases have worldwide, and the current challenges associated with their prevention and control and with drug resistance in parasite populations.
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Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Bioinformatics Core Facility, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
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104
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Sauvola CW, Littleton JT. SNARE Regulatory Proteins in Synaptic Vesicle Fusion and Recycling. Front Mol Neurosci 2021; 14:733138. [PMID: 34421538 PMCID: PMC8377282 DOI: 10.3389/fnmol.2021.733138] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/20/2021] [Indexed: 01/01/2023] Open
Abstract
Membrane fusion is a universal feature of eukaryotic protein trafficking and is mediated by the soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) family. SNARE proteins embedded in opposing membranes spontaneously assemble to drive membrane fusion and cargo exchange in vitro. Evolution has generated a diverse complement of SNARE regulatory proteins (SRPs) that ensure membrane fusion occurs at the right time and place in vivo. While a core set of SNAREs and SRPs are common to all eukaryotic cells, a specialized set of SRPs within neurons confer additional regulation to synaptic vesicle (SV) fusion. Neuronal communication is characterized by precise spatial and temporal control of SNARE dynamics within presynaptic subdomains specialized for neurotransmitter release. Action potential-elicited Ca2+ influx at these release sites triggers zippering of SNAREs embedded in the SV and plasma membrane to drive bilayer fusion and release of neurotransmitters that activate downstream targets. Here we discuss current models for how SRPs regulate SNARE dynamics and presynaptic output, emphasizing invertebrate genetic findings that advanced our understanding of SRP regulation of SV cycling.
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Affiliation(s)
- Chad W Sauvola
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - J Troy Littleton
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
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105
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Emerson S, Hay M, Smith M, Granger R, Blauch D, Snyder N, El Bejjani R. Acetylcholine signaling genes are required for cocaine-stimulated egg laying in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2021; 11:jkab143. [PMID: 33914087 PMCID: PMC8763240 DOI: 10.1093/g3journal/jkab143] [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: 03/27/2021] [Accepted: 04/20/2021] [Indexed: 11/23/2022]
Abstract
The toxicity and addictive liability associated with cocaine abuse are well-known. However, its mode of action is not completely understood, and effective pharmacotherapeutic interventions remain elusive. The cholinergic effects of cocaine on acetylcholine receptors, synthetic enzymes, and degradative enzymes have been the focus of relatively little empirical investigation. Due to its genetic tractability and anatomical simplicity, the egg laying circuit of the hermaphroditic nematode, Caenorhabditis elegans, is a powerful model system to precisely examine the genetic and molecular targets of cocaine in vivo. Here, we report a novel cocaine-induced behavioral phenotype in C. elegans, cocaine-stimulated egg laying. In addition, we present the results of an in vivo candidate suppression screen of synthetic enzymes, receptors, degradative enzymes, and downstream components of the intracellular signaling cascades of the main neurotransmitter systems that control C. elegans egg laying. Our results show that cocaine-stimulated egg laying is dependent on acetylcholine synthesis and synaptic release, functional nicotinic acetylcholine receptors, and the C. elegans acetylcholinesterases.
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Affiliation(s)
- Soren Emerson
- Neuroscience Interdisciplinary Program, Davidson College, Davidson, NC 28035, USA
| | - Megan Hay
- Biology Department, Davidson College, Davidson, NC 28035, USA
| | - Mark Smith
- Neuroscience Interdisciplinary Program, Davidson College, Davidson, NC 28035, USA
- Psychology Department, Davidson College, Davidson, NC 28035, USA
| | - Ricky Granger
- Biology Department, Davidson College, Davidson, NC 28035, USA
| | - David Blauch
- Chemistry Department, Davidson College, Davidson, NC 28035 USA
| | - Nicole Snyder
- Chemistry Department, Davidson College, Davidson, NC 28035 USA
| | - Rachid El Bejjani
- Neuroscience Interdisciplinary Program, Davidson College, Davidson, NC 28035, USA
- Biology Department, Davidson College, Davidson, NC 28035, USA
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106
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Prosée RF, Wenda JM, Özdemir I, Gabus C, Delaney K, Schwager F, Gotta M, Steiner FA. Transgenerational inheritance of centromere identity requires the CENP-A N-terminal tail in the C. elegans maternal germ line. PLoS Biol 2021; 19:e3000968. [PMID: 34228701 PMCID: PMC8259991 DOI: 10.1371/journal.pbio.3000968] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 05/28/2021] [Indexed: 12/15/2022] Open
Abstract
Centromere protein A (CENP-A) is a histone H3 variant that defines centromeric chromatin and is essential for centromere function. In most eukaryotes, CENP-A-containing chromatin is epigenetically maintained, and centromere identity is inherited from one cell cycle to the next. In the germ line of the holocentric nematode Caenorhabditis elegans, this inheritance cycle is disrupted. CENP-A is removed at the mitosis-to-meiosis transition and is reestablished on chromatin during diplotene of meiosis I. Here, we show that the N-terminal tail of CENP-A is required for the de novo establishment of centromeres, but then its presence becomes dispensable for centromere maintenance during development. Worms homozygous for a CENP-A tail deletion maintain functional centromeres during development but give rise to inviable offspring because they fail to reestablish centromeres in the maternal germ line. We identify the N-terminal tail of CENP-A as a critical domain for the interaction with the conserved kinetochore protein KNL-2 and argue that this interaction plays an important role in setting centromere identity in the germ line. We conclude that centromere establishment and maintenance are functionally distinct in C. elegans.
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Affiliation(s)
- Reinier F. Prosée
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Joanna M. Wenda
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Isa Özdemir
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Caroline Gabus
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Kamila Delaney
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Francoise Schwager
- Department of Cell Physiology and Metabolism and Institute of Genetics and Genomics in Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Monica Gotta
- Department of Cell Physiology and Metabolism and Institute of Genetics and Genomics in Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Florian A. Steiner
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
- * E-mail:
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107
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Sando SR, Bhatla N, Lee EL, Horvitz HR. An hourglass circuit motif transforms a motor program via subcellularly localized muscle calcium signaling and contraction. eLife 2021; 10:59341. [PMID: 34212858 PMCID: PMC8331187 DOI: 10.7554/elife.59341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/26/2021] [Indexed: 12/27/2022] Open
Abstract
Neural control of muscle function is fundamental to animal behavior. Many muscles can generate multiple distinct behaviors. Nonetheless, individual muscle cells are generally regarded as the smallest units of motor control. We report that muscle cells can alter behavior by contracting subcellularly. We previously discovered that noxious tastes reverse the net flow of particles through the C. elegans pharynx, a neuromuscular pump, resulting in spitting. We now show that spitting results from the subcellular contraction of the anterior region of the pm3 muscle cell. Subcellularly localized calcium increases accompany this contraction. Spitting is controlled by an ‘hourglass’ circuit motif: parallel neural pathways converge onto a single motor neuron that differentially controls multiple muscles and the critical subcellular muscle compartment. We conclude that subcellular muscle units enable modulatory motor control and propose that subcellular muscle contraction is a fundamental mechanism by which neurons can reshape behavior.
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Affiliation(s)
- Steven R Sando
- Howard Hughes Medical Institute, Department of Biology, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Nikhil Bhatla
- Howard Hughes Medical Institute, Department of Biology, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States.,Miller Institute, Helen Wills Neuroscience Institute, Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, United States.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, United States
| | - Eugene Lq Lee
- Howard Hughes Medical Institute, Department of Biology, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, United States
| | - H Robert Horvitz
- Howard Hughes Medical Institute, Department of Biology, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States
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108
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van der Woude M, Lans H. C. elegans survival assays to discern global and transcription-coupled nucleotide excision repair. STAR Protoc 2021; 2:100586. [PMID: 34151304 PMCID: PMC8192855 DOI: 10.1016/j.xpro.2021.100586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Global genome nucleotide excision repair (GG-NER) and transcription-coupled nucleotide excision repair (TC-NER) protect cells against a variety of helix-distorting DNA lesions. In C. elegans, GG-NER primarily acts in proliferative germ cells and embryos, while TC-NER acts in post-mitotic somatic cells to maintain transcription. We leverage this difference to distinguish whether proteins function in GG-NER and/or TC-NER by straightforward UV survival assays. Here, we detail a protocol for these assays, using GG-NER factor xpc-1 and TC-NER factor csb-1 as examples. For complete details on the use and execution of this protocol, please refer to Sabatella et al. (2021).
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Affiliation(s)
- Melanie van der Woude
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
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109
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Ravi B, Zhao J, Chaudhry I, Signorelli R, Bartole M, Kopchock RJ, Guijarro C, Kaplan JM, Kang L, Collins KM. Presynaptic Gαo (GOA-1) signals to depress command neuron excitability and allow stretch-dependent modulation of egg laying in Caenorhabditis elegans. Genetics 2021; 218:6284136. [PMID: 34037773 DOI: 10.1093/genetics/iyab080] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/18/2021] [Indexed: 12/29/2022] Open
Abstract
Egg laying in the nematode worm Caenorhabditis elegans is a two-state behavior modulated by internal and external sensory input. We have previously shown that homeostatic feedback of embryo accumulation in the uterus regulates bursting activity of the serotonergic HSN command neurons that sustains the egg-laying active state. How sensory feedback of egg release signals to terminate the egg-laying active state is less understood. We find that Gαo, a conserved Pertussis Toxin-sensitive G protein, signals within HSN to inhibit egg-laying circuit activity and prevent entry into the active state. Gαo signaling hyperpolarizes HSN, reducing HSN Ca2+ activity and input onto the postsynaptic vulval muscles. Loss of inhibitory Gαo signaling uncouples presynaptic HSN activity from a postsynaptic, stretch-dependent homeostat, causing precocious entry into the egg-laying active state when only a few eggs are present in the uterus. Feedback of vulval opening and egg release activates the uv1 neuroendocrine cells which release NLP-7 neuropeptides which signal to inhibit egg laying through Gαo-independent mechanisms in the HSNs and Gαo-dependent mechanisms in cells other than the HSNs. Thus, neuropeptide and inhibitory Gαo signaling maintains a bi-stable state of electrical excitability that dynamically controls circuit activity in response to both external and internal sensory input to drive a two-state behavior output.
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Affiliation(s)
- Bhavya Ravi
- Neuroscience Program, University of Miami Miller School of Medicine, Miami, FL USA 33136.,Department of Biology, University of Miami, Coral Gables, FL USA 33146
| | - Jian Zhao
- Department of Neuroscience, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA 02114
| | - I Chaudhry
- Department of Biology, University of Miami, Coral Gables, FL USA 33146
| | | | - Mattingly Bartole
- Neuroscience Program, University of Miami Miller School of Medicine, Miami, FL USA 33136.,Department of Biology, University of Miami, Coral Gables, FL USA 33146
| | | | | | - Joshua M Kaplan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA 02114
| | - Lijun Kang
- Department of Neuroscience, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kevin M Collins
- Neuroscience Program, University of Miami Miller School of Medicine, Miami, FL USA 33136.,Department of Biology, University of Miami, Coral Gables, FL USA 33146
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110
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Wani KA, Goswamy D, Taubert S, Ratnappan R, Ghazi A, Irazoqui JE. NHR-49/PPAR-α and HLH-30/TFEB cooperate for C. elegans host defense via a flavin-containing monooxygenase. eLife 2021; 10:62775. [PMID: 33978570 PMCID: PMC8139828 DOI: 10.7554/elife.62775] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 04/29/2021] [Indexed: 12/26/2022] Open
Abstract
The model organism Caenorhabditis elegans mounts transcriptional defense responses against intestinal bacterial infections that elicit overlapping starvation and infection responses, the regulation of which is not well understood. Direct comparison of C. elegans that were starved or infected with Staphylococcus aureus revealed a large infection-specific transcriptional signature, which was almost completely abrogated by deletion of transcription factor hlh-30/TFEB, except for six genes including a flavin-containing monooxygenase (FMO) gene, fmo-2/FMO5. Deletion of fmo-2/FMO5 severely compromised infection survival, thus identifying the first FMO with innate immunity functions in animals. Moreover, fmo-2/FMO5 induction required the nuclear hormone receptor, NHR-49/PPAR-α, which controlled host defense cell non-autonomously. These findings reveal an infection-specific host response to S. aureus, identify HLH-30/TFEB as its main regulator, reveal FMOs as important innate immunity effectors in animals, and identify the mechanism of FMO regulation through NHR-49/PPAR-α during S. aureus infection, with implications for host defense and inflammation in higher organisms.
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Affiliation(s)
- Khursheed A Wani
- Department of Microbiology and Physiological Systems, UMass Medical School, Worcester, United States
| | - Debanjan Goswamy
- Department of Microbiology and Physiological Systems, UMass Medical School, Worcester, United States
| | - Stefan Taubert
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Ramesh Ratnappan
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, United States.,Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States.,Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States.,Department of Physiology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Arjumand Ghazi
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, United States.,Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States.,Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States.,Department of Physiology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Javier E Irazoqui
- Department of Microbiology and Physiological Systems, UMass Medical School, Worcester, United States
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111
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Abbasi S, Parmar G, Kelly RD, Balasuriya N, Schild-Poulter C. The Ku complex: recent advances and emerging roles outside of non-homologous end-joining. Cell Mol Life Sci 2021; 78:4589-4613. [PMID: 33855626 PMCID: PMC11071882 DOI: 10.1007/s00018-021-03801-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/29/2021] [Accepted: 02/24/2021] [Indexed: 12/15/2022]
Abstract
Since its discovery in 1981, the Ku complex has been extensively studied under multiple cellular contexts, with most work focusing on Ku in terms of its essential role in non-homologous end-joining (NHEJ). In this process, Ku is well-known as the DNA-binding subunit for DNA-PK, which is central to the NHEJ repair process. However, in addition to the extensive study of Ku's role in DNA repair, Ku has also been implicated in various other cellular processes including transcription, the DNA damage response, DNA replication, telomere maintenance, and has since been studied in multiple contexts, growing into a multidisciplinary point of research across various fields. Some advances have been driven by clarification of Ku's structure, including the original Ku crystal structure and the more recent Ku-DNA-PKcs crystallography, cryogenic electron microscopy (cryoEM) studies, and the identification of various post-translational modifications. Here, we focus on the advances made in understanding the Ku heterodimer outside of non-homologous end-joining, and across a variety of model organisms. We explore unique structural and functional aspects, detail Ku expression, conservation, and essentiality in different species, discuss the evidence for its involvement in a diverse range of cellular functions, highlight Ku protein interactions and recent work concerning Ku-binding motifs, and finally, we summarize the clinical Ku-related research to date.
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Affiliation(s)
- Sanna Abbasi
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Gursimran Parmar
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Rachel D Kelly
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Nileeka Balasuriya
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Caroline Schild-Poulter
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada.
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112
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Willis AR, Zhao W, Sukhdeo R, Wadi L, El Jarkass HT, Claycomb JM, Reinke AW. A parental transcriptional response to microsporidia infection induces inherited immunity in offspring. SCIENCE ADVANCES 2021; 7:7/19/eabf3114. [PMID: 33952520 PMCID: PMC8099193 DOI: 10.1126/sciadv.abf3114] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 03/17/2021] [Indexed: 05/05/2023]
Abstract
Parental infection can result in the production of offspring with enhanced immunity phenotypes. Critically, the mechanisms underlying inherited immunity are poorly understood. Here, we show that Caenorhabditis elegans infected with the intracellular microsporidian parasite N. parisii produce progeny that are resistant to microsporidia infection. We determine the kinetics of the response and show that intergenerational immunity prevents host-cell invasion by Nematocida parisii and enhances survival to the bacterial pathogen Pseudomonas aeruginosa We demonstrate that immunity is induced by the parental transcriptional response to infection, which can be mimicked through maternal somatic depletion of PALS-22 and the retinoblastoma protein ortholog, LIN-35. We find that other biotic and abiotic stresses (viral infection and cadmium exposure) that induce a similar transcriptional response as microsporidia also induce immunity in progeny. Together, our results reveal how a parental transcriptional signal can be induced by distinct stimuli and protect offspring against multiple classes of pathogens.
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Affiliation(s)
- Alexandra R Willis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Winnie Zhao
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ronesh Sukhdeo
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Lina Wadi
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Aaron W Reinke
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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113
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A complement factor H homolog, heparan sulfation, and syndecan maintain inversin compartment boundaries in C. elegans cilia. Proc Natl Acad Sci U S A 2021; 118:2016698118. [PMID: 33859044 DOI: 10.1073/pnas.2016698118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Age-related macular degeneration (AMD) is a leading cause of blindness among the elderly. Canonical disease models suggest that defective interactions between complement factor H (CFH) and cell surface heparan sulfate (HS) result in increased alternative complement pathway activity, cytolytic damage, and tissue inflammation in the retina. Although these factors are thought to contribute to increased disease risk, multiple studies indicate that noncanonical mechanisms that result from defective CFH and HS interaction may contribute to the progression of AMD as well. A total of 60 ciliated sensory neurons in the nematode Caenorhabditis elegans detect chemical, olfactory, mechanical, and thermal cues in the environment. Here, we find that a C. elegans CFH homolog localizes on CEP mechanosensory neuron cilia where it has noncanonical roles in maintaining inversin/NPHP-2 within its namesake proximal compartment and preventing inversin/NPHP-2 accumulation in distal cilia compartments in aging adults. CFH localization and maintenance of inversin/NPHP-2 compartment integrity depend on the HS 3-O sulfotransferase HST-3.1 and the transmembrane proteoglycan syndecan/SDN-1. Defective inversin/NPHP-2 localization in mouse and human photoreceptors with CFH mutations indicates that these functions and interactions may be conserved in vertebrate sensory neurons, suggesting that previously unappreciated defects in cilia structure may contribute to the progressive photoreceptor dysfunction associated with CFH loss-of-function mutations in some AMD patients.
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114
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Bradner JM, Kalia V, Lau FK, Sharma M, Bucher ML, Johnson M, Chen M, Walker DI, Jones DP, Miller GW. Genetic or Toxicant-Induced Disruption of Vesicular Monoamine Storage and Global Metabolic Profiling in Caenorhabditis elegans. Toxicol Sci 2021; 180:313-324. [PMID: 33538833 PMCID: PMC8041460 DOI: 10.1093/toxsci/kfab011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The proper storage and release of monoamines contributes to a wide range of neuronal activity. Here, we examine the effects of altered vesicular monoamine transport in the nematode Caenorhabditis elegans. The gene cat-1 is responsible for the encoding of the vesicular monoamine transporter (VMAT) in C. elegans and is analogous to the mammalian vesicular monoamine transporter 2 (VMAT2). Our laboratory has previously shown that reduced VMAT2 activity confers vulnerability on catecholamine neurons in mice. The purpose of this article was to determine whether this function is conserved and to determine the impact of reduced VMAT activity in C. elegans. Here we show that deletion of cat-1/VMAT increases sensitivity to the neurotoxicant 1-methyl-4-phenylpyridinium (MPP+) as measured by enhanced degeneration of dopamine neurons. Reduced cat-1/VMAT also induces changes in dopamine-mediated behaviors. High-resolution mass spectrometry-based metabolomics in the whole organism reveals changes in amino acid metabolism, including tyrosine metabolism in the cat-1/VMAT mutants. Treatment with MPP+ disrupted tryptophan metabolism. Both conditions altered glycerophospholipid metabolism, suggesting a convergent pathway of neuronal dysfunction. Our results demonstrate the evolutionarily conserved nature of monoamine function in C. elegans and further suggest that high-resolution mass spectrometry-based metabolomics can be used in this model to study environmental and genetic contributors to complex human disease.
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Affiliation(s)
- Joshua M Bradner
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, USA
| | - Vrinda Kalia
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, USA
| | - Fion K Lau
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, USA
| | - Monica Sharma
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, USA
| | - Meghan L Bucher
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, USA
| | - Michelle Johnson
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, USA
| | - Merry Chen
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, USA
| | - Douglas I Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Dean P Jones
- Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia 30303, USA
| | - Gary W Miller
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, USA
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115
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Suehiro Y, Yoshina S, Motohashi T, Iwata S, Dejima K, Mitani S. Efficient collection of a large number of mutations by mutagenesis of DNA damage response defective animals. Sci Rep 2021; 11:7630. [PMID: 33828169 PMCID: PMC8027614 DOI: 10.1038/s41598-021-87226-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/24/2021] [Indexed: 02/01/2023] Open
Abstract
With the development of massive parallel sequencing technology, it has become easier to establish new model organisms that are ideally suited to the specific biological phenomena of interest. Considering the history of research using classical model organisms, we believe that the efficient construction and sharing of gene mutation libraries will facilitate the progress of studies using these new model organisms. Using C. elegans, we applied the TMP/UV mutagenesis method to animals lacking function in the DNA damage response genes atm-1 and xpc-1. This method produces genetic mutations three times more efficiently than mutagenesis of wild-type animals. Furthermore, we confirmed that the use of next-generation sequencing and the elimination of false positives through machine learning could automate the process of mutation identification with an accuracy of over 95%. Eventually, we sequenced the whole genomes of 488 strains and isolated 981 novel mutations generated by the present method; these strains have been made available to anyone who wants to use them. Since the targeted DNA damage response genes are well conserved and the mutagens used in this study are also effective in a variety of species, we believe that our method is generally applicable to a wide range of animal species.
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Affiliation(s)
- Yuji Suehiro
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Sawako Yoshina
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Tomoko Motohashi
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Satoru Iwata
- Chubu University Center for Education in Laboratory Animal Research, Kasugai, Aichi, Japan
| | - Katsufumi Dejima
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Shohei Mitani
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan.
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Shinjuku, Tokyo, Japan.
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116
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Pees B, Yang W, Kloock A, Petersen C, Peters L, Fan L, Friedrichsen M, Butze S, Zárate-Potes A, Schulenburg H, Dierking K. Effector and regulator: Diverse functions of C. elegans C-type lectin-like domain proteins. PLoS Pathog 2021; 17:e1009454. [PMID: 33793670 PMCID: PMC8051790 DOI: 10.1371/journal.ppat.1009454] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 04/16/2021] [Accepted: 03/05/2021] [Indexed: 11/22/2022] Open
Abstract
In C. elegans, 283 clec genes encode a highly diverse family of C-type lectin-like domain (CTLD) proteins. Since vertebrate CTLD proteins have characterized functions in defense responses against pathogens and since expression of C. elegans clec genes is pathogen-dependent, it is generally assumed that clec genes function in C. elegans immune defenses. However, little is known about the relative contribution and exact function of CLEC proteins in C. elegans immunity. Here, we focused on the C. elegans clec gene clec-4, whose expression is highly upregulated by pathogen infection, and its paralogs clec-41 and clec-42. We found that, while mutation of clec-4 resulted in enhanced resistance to the Gram-positive pathogen Bacillus thuringiensis MYBt18247 (Bt247), inactivation of clec-41 and clec-42 by RNAi enhanced susceptibility to Bt247. Further analyses revealed that enhanced resistance of clec-4 mutants to Bt247 was due to an increase in feeding cessation on the pathogen and consequently a decrease in pathogen load. Moreover, clec-4 mutants exhibited feeding deficits also on non-pathogenic bacteria that were in part reflected in the clec-4 gene expression profile, which overlapped with gene sets affected by starvation or mutation in nutrient sensing pathways. However, loss of CLEC-4 function only mildly affected life-history traits such as fertility, indicating that clec-4 mutants are not subjected to dietary restriction. While CLEC-4 function appears to be associated with the regulation of feeding behavior, we show that CLEC-41 and CLEC-42 proteins likely function as bona fide immune effector proteins that have bacterial binding and antimicrobial capacities. Together, our results exemplify functional diversification within clec gene paralogs. C-type lectin-like domain (CTLD) containing proteins fulfill various and fundamental tasks in the human and mouse immune system. Genes encoding CTLD proteins are present in all animal genomes, in some cases in very large numbers and highly diversified. While the function of several vertebrate CTLD proteins is well characterized, experimental evidence of an immune function of most invertebrate CTLD proteins is missing, although their role in immunity is usually assumed. We here explore the immune function of three related CTLD proteins in the model nematode Caenorhabditis elegans. We find that they play diverse roles in C. elegans immunity, functioning as antimicrobial immune effector proteins that are important for defense against pathogen infection and probably directly interact with bacteria, but also regulators of feeding behavior that more indirectly affect C. elegans pathogen resistance. Such insight into the functional consequence of invertebrate CTLD protein diversification contributes to our understanding of the evolution of innate and invertebrate immune systems.
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Affiliation(s)
- Barbara Pees
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Department of Comparative Immunobiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Wentao Yang
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Anke Kloock
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Carola Petersen
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Department of Comparative Immunobiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Lena Peters
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Li Fan
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Meike Friedrichsen
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Sabrina Butze
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Alejandra Zárate-Potes
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Katja Dierking
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- * E-mail:
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117
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Cho JY, Choi TW, Kim SH, Ahnn J, Lee SK. Morphological Characterization of small, dumpy, and long Phenotypes in Caenorhabditis elegans. Mol Cells 2021; 44:160-167. [PMID: 33692220 PMCID: PMC8019597 DOI: 10.14348/molcells.2021.2236] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 11/27/2022] Open
Abstract
The determinant factors of an organism's size during animal development have been explored from various angles but remain partially understood. In Caenorhabditis elegans, many genes affecting cuticle structure, cell growth, and proliferation have been identified to regulate the worm's overall morphology, including body size. While various mutations in those genes directly result in changes in the morphological phenotypes, there is still a need for established, clear, and distinct standards to determine the apparent abnormality in a worm's size and shape. In this study, we measured the body length, body width, terminal bulb length, and head size of mutant worms with reported Dumpy (Dpy), Small (Sma) or Long (Lon) phenotypes by plotting and comparing their respective ratios of various parameters. These results show that the Sma phenotypes are proportionally smaller overall with mild stoutness, and Dpy phenotypes are significantly stouter and have disproportionally small head size. This study provides a standard platform for determining morphological phenotypes designating and annotating mutants that exhibit body shape variations, defining the morphological phenotype of previously unexamined mutants.
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Affiliation(s)
- Joshua Young Cho
- Department of Life Science, School of Natural Sciences, Hanyang University, Seoul 04763, Korea
- BK21 PLUS Life Science for BDR Team, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Present address: Doctor of Dental Surgery Program, University of the Pacific, Arthur A. Dugoni School of Dentistry, San Francisco, CA 94103, USA
| | - Tae-Woo Choi
- Department of Life Science, School of Natural Sciences, Hanyang University, Seoul 04763, Korea
- BK21 PLUS Life Science for BDR Team, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Present address: Macrogen Inc., Seoul 08511, Korea
| | - Seung Hyun Kim
- Department of Life Science, School of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Joohong Ahnn
- Department of Life Science, School of Natural Sciences, Hanyang University, Seoul 04763, Korea
- BK21 PLUS Life Science for BDR Team, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Sun-Kyung Lee
- Department of Life Science, School of Natural Sciences, Hanyang University, Seoul 04763, Korea
- BK21 PLUS Life Science for BDR Team, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
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118
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Hammerquist AM, Escorcia W, Curran SP. Maf1 regulates intracellular lipid homeostasis in response to DNA damage response activation. Mol Biol Cell 2021; 32:1086-1093. [PMID: 33788576 PMCID: PMC8351542 DOI: 10.1091/mbc.e20-06-0378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Surveillance of DNA damage and maintenance of lipid metabolism are critical factors for general cellular homeostasis. We discovered that in response to DNA damage–inducing UV light exposure, intact Caenorhabditis elegans accumulate intracellular lipids in a dose-dependent manner. The increase in intracellular lipids in response to exposure to UV light utilizes mafr-1, a negative regulator of RNA polymerase III and the apical kinases atm-1 and atl-1 of the DNA damage response (DDR) pathway. In the absence of exposure to UV light, the genetic ablation of mafr-1 results in the activation of the DDR, including increased intracellular lipid accumulation, phosphorylation of ATM/ATR target proteins, and expression of the Bcl-2 homology region genes, egl-1 and ced-13. Taken together, our results reveal mafr-1 as a component the DDR pathway response to regulating lipid homeostasis following exposure to UV genotoxic stress.
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Affiliation(s)
- Amy M Hammerquist
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089.,Molecular and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089
| | - Wilber Escorcia
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089.,Department of Biology, Xavier University, Cincinnati, OH 45207
| | - Sean P Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089.,Molecular and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
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119
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Raiders S, Black EC, Bae A, MacFarlane S, Klein M, Shaham S, Singhvi A. Glia actively sculpt sensory neurons by controlled phagocytosis to tune animal behavior. eLife 2021; 10:63532. [PMID: 33759761 PMCID: PMC8079151 DOI: 10.7554/elife.63532] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/23/2021] [Indexed: 02/07/2023] Open
Abstract
Glia in the central nervous system engulf neuron fragments to remodel synapses and recycle photoreceptor outer segments. Whether glia passively clear shed neuronal debris or actively prune neuron fragments is unknown. How pruning of single-neuron endings impacts animal behavior is also unclear. Here, we report our discovery of glia-directed neuron pruning in Caenorhabditis elegans. Adult C. elegans AMsh glia engulf sensory endings of the AFD thermosensory neuron by repurposing components of the conserved apoptotic corpse phagocytosis machinery. The phosphatidylserine (PS) flippase TAT-1/ATP8A functions with glial PS-receptor PSR-1/PSR and PAT-2/α-integrin to initiate engulfment. This activates glial CED-10/Rac1 GTPase through the ternary GEF complex of CED-2/CrkII, CED-5/DOCK180, CED-12/ELMO. Execution of phagocytosis uses the actin-remodeler WSP-1/nWASp. This process dynamically tracks AFD activity and is regulated by temperature, the AFD sensory input. Importantly, glial CED-10 levels regulate engulfment rates downstream of neuron activity, and engulfment-defective mutants exhibit altered AFD-ending shape and thermosensory behavior. Our findings reveal a molecular pathway underlying glia-dependent engulfment in a peripheral sense-organ and demonstrate that glia actively engulf neuron fragments, with profound consequences on neuron shape and animal sensory behavior. Neurons are tree-shaped cells that receive information through endings connected to neighbouring cells or the environment. Controlling the size, number and location of these endings is necessary to ensure that circuits of neurons get precisely the right amount of input from their surroundings. Glial cells form a large portion of the nervous system, and they are tasked with supporting, cleaning and protecting neurons. In humans, part of their duties is to ‘eat’ (or prune) unnecessary neuron endings. In fact, this role is so important that defects in glial pruning are associated with conditions such as Alzheimer’s disease. Yet it is still unknown how pruning takes place, and in particular whether it is the neuron or the glial cell that initiates the process. To investigate this question, Raiders et al. enlisted the common laboratory animal Caenorhabditis elegans, a tiny worm with a simple nervous system where each neuron has been meticulously mapped out. First, the experiments showed that glial cells in C. elegans actually prune the endings of sensory neurons. Focusing on a single glia-neuron pair then revealed that the glial cell could trim the endings of a living neuron by redeploying the same molecular machinery it uses to clear dead cell debris. Compared to this debris-clearing activity, however, the glial cell takes a more nuanced approach to pruning: specifically, it can adjust the amount of trimming based on the activity load of the neuron. When Raiders et al. disrupted the glial pruning for a single temperature-sensing neuron, the worm lost its normal temperature preferences; this demonstrated how the pruning activity of a single glial cell can be linked to behavior. Taken together the experiments showcase how C. elegans can be used to study glial pruning. Further work using this model could help to understand how disease emerges when glial cells cannot perform their role, and to spot the genetic factors that put certain individuals at increased risk for neurological and sensory disorders.
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Affiliation(s)
- Stephan Raiders
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, United States
| | - Erik Calvin Black
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Andrea Bae
- Laboratory of Developmental Genetics, The Rockefeller University, New York, United States.,Cellular Imaging Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Stephen MacFarlane
- Department of Physics and Department of Biology, University of Miami, Coral Gables, United States
| | - Mason Klein
- Department of Physics and Department of Biology, University of Miami, Coral Gables, United States
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, New York, United States
| | - Aakanksha Singhvi
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, United States.,Department of Biological Structure, University of Washington School of Medicine, Seattle, United States.,Brotman Baty Institute for Precision Medicine, Seattle, United States
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120
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Dubois C, Gupta S, Mugler A, Félix MA. Temporally regulated cell migration is sensitive to variation in body size. Development 2021; 148:dev196949. [PMID: 33593818 PMCID: PMC10683003 DOI: 10.1242/dev.196949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/14/2021] [Indexed: 12/15/2022]
Abstract
Few studies have measured the robustness to perturbations of the final position of a long-range migrating cell. In the nematode Caenorhabditis elegans, the QR neuroblast migrates anteriorly, while undergoing three division rounds. We study the final position of two of its great-granddaughters, the end of migration of which was previously shown to depend on a timing mechanism. We find that the variance in their final position is similar to that of other long-range migrating neurons. As expected from the timing mechanism, the position of QR descendants depends on body size, which we varied by changing maternal age or using body size mutants. Using a mathematical model, we show that body size variation is partially compensated for. Applying environmental perturbations, we find that the variance in final position increased following starvation at hatching. The mean position is displaced upon a temperature shift. Finally, highly significant variation was found among C. elegans wild isolates. Overall, this study reveals that the final position of these neurons is quite robust to stochastic variation, shows some sensitivity to body size and to external perturbations, and varies in the species.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Clément Dubois
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, 75005 Paris, France
| | - Shivam Gupta
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Andrew Mugler
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, 75005 Paris, France
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121
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Taylor SKB, Minhas MH, Tong J, Selvaganapathy PR, Mishra RK, Gupta BP. C. elegans electrotaxis behavior is modulated by heat shock response and unfolded protein response signaling pathways. Sci Rep 2021; 11:3115. [PMID: 33542359 PMCID: PMC7862228 DOI: 10.1038/s41598-021-82466-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/18/2021] [Indexed: 01/30/2023] Open
Abstract
The nematode C. elegans is a leading model to investigate the mechanisms of stress-induced behavioral changes coupled with biochemical mechanisms. Our group has previously characterized C. elegans behavior using a microfluidic-based electrotaxis device, and showed that worms display directional motion in the presence of a mild electric field. In this study, we describe the effects of various forms of genetic and environmental stress on the electrotactic movement of animals. Using exposure to chemicals, such as paraquat and tunicamycin, as well as mitochondrial and endoplasmic reticulum (ER) unfolded protein response (UPR) mutants, we demonstrate that chronic stress causes abnormal movement. Additionally, we report that pqe-1 (human RNA exonuclease 1 homolog) is necessary for the maintenance of multiple stress response signaling and electrotaxis behavior of animals. Further, exposure of C. elegans to several environmental stress-inducing conditions revealed that while chronic heat and dietary restriction caused electrotaxis speed deficits due to prolonged stress, daily exercise had a beneficial effect on the animals, likely due to improved muscle health and transient activation of UPR. Overall, these data demonstrate that the electrotaxis behavior of worms is susceptible to cytosolic, mitochondrial, and ER stress, and that multiple stress response pathways contribute to its preservation in the face of stressful stimuli.
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Affiliation(s)
- Shane K. B. Taylor
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
| | - Muhammad H. Minhas
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
| | - Justin Tong
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
| | - P. Ravi Selvaganapathy
- grid.25073.330000 0004 1936 8227Department of Mechanical Engineering, McMaster University, Hamilton, ON Canada
| | - Ram K. Mishra
- grid.25073.330000 0004 1936 8227Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON Canada
| | - Bhagwati P. Gupta
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
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122
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Ahier A, Suman SK, Jarriault S. Gene bashing of ceh-6 locus identifies genomic regions important for ceh-6 rectal cell expression and rescue of its mutant lethality. MICROPUBLICATION BIOLOGY 2020; 2020. [PMID: 33364555 PMCID: PMC7753896 DOI: 10.17912/micropub.biology.000339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Strong loss-of-function or null mutants can sometimes lead to a penetrant early lethality, impairing the study of these genes’ function. This is the case for the ceh-6 null mutant, which exhibits 100% penetrant lethality. Here, we describe how we used gene bashing to identify distinct regulatory regions in the ceh-6 locus. This allowed us to generate a ceh-6 null strain that is viable and still displays ceh-6 mutant Y-to-PDA transdifferentiation phenotype. Such strategy can be applied to many other mutants impacting viability.
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Affiliation(s)
- Arnaud Ahier
- IGBMC, Development and Stem Cells Department, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch CU Strasbourg, 67404 France.,current address: Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Shashi Kumar Suman
- IGBMC, Development and Stem Cells Department, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch CU Strasbourg, 67404 France
| | - Sophie Jarriault
- IGBMC, Development and Stem Cells Department, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch CU Strasbourg, 67404 France
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123
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Oswald M, Hulsey-Vincent H, Dahlberg C(L. Mutations in two ERAD E3 ubiquitin ligase enzymes reduce spontaneous reversal frequency in Caenorhabditis elegans. MICROPUBLICATION BIOLOGY 2020; 2020:10.17912/micropub.biology.000329. [PMID: 33274327 PMCID: PMC7704257 DOI: 10.17912/micropub.biology.000329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Mackenzi Oswald
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | - Heino Hulsey-Vincent
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | - Caroline (Lina) Dahlberg
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA,
Correspondence to: Caroline (Lina) Dahlberg ()
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van der Burght SN, Rademakers S, Johnson JL, Li C, Kremers GJ, Houtsmuller AB, Leroux MR, Jansen G. Ciliary Tip Signaling Compartment Is Formed and Maintained by Intraflagellar Transport. Curr Biol 2020; 30:4299-4306.e5. [DOI: 10.1016/j.cub.2020.08.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 07/13/2020] [Accepted: 08/07/2020] [Indexed: 02/07/2023]
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125
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Lee K, Escobar I, Jang Y, Kim W, Ausubel FM, Mylonakis E. In the Model Host Caenorhabditis elegans, Sphingosine-1-Phosphate-Mediated Signaling Increases Immunity toward Human Opportunistic Bacteria. Int J Mol Sci 2020; 21:ijms21217813. [PMID: 33105563 PMCID: PMC7672543 DOI: 10.3390/ijms21217813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 12/25/2022] Open
Abstract
Sphingosine-1-phophate (S1P) is a sphingolipid-derived signaling molecule that controls diverse cellular functions including cell growth, homeostasis, and stress responses. In a variety of metazoans, cytosolic S1P is transported into the extracellular space where it activates S1P receptors in a concentration-dependent manner. In the free-living nematode Caenorhabditis elegans, the spin-2 gene, which encodes a S1P transporter, is activated during Gram-positive or Gram-negative bacterial infection of the intestine. However, the role during infection of spin-2 and three additional genes in the C. elegans genome encoding other putative S1P transporters has not been elucidated. Here, we report an evolutionally conserved function for S1P and a non-canonical role for S1P transporters in the C. elegans immune response to bacterial pathogens. We found that mutations in the sphingosine kinase gene (sphk-1) or in the S1P transporter genes spin-2 or spin-3 decreased nematode survival after infection with Pseudomonas aeruginosa or Enterococcus faecalis. In contrast to spin-2 and spin-3, mutating spin-1 leads to an increase in resistance to P. aeruginosa. Consistent with these results, when wild-type C. elegans were supplemented with extracellular S1P, we found an increase in their lifespan when challenged with P. aeruginosa and E. faecalis. In comparison, spin-2 and spin-3 mutations suppressed the ability of S1P to rescue the worms from pathogen-mediated killing, whereas the spin-1 mutation had no effect on the immune-enhancing activity of S1P. S1P demonstrated no antimicrobial activity toward P. aeruginosa and Escherichia coli and only minimal activity against E. faecalis MMH594 (40 µM). These data suggest that spin-2 and spin-3, on the one hand, and spin-1, on the other hand, transport S1P across cellular membranes in opposite directions. Finally, the immune modulatory effect of S1P was diminished in C. eleganssek-1 and pmk-1 mutants, suggesting that the immunomodulatory effects of S1P are mediated by the p38 MAPK signaling pathway.
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Affiliation(s)
- Kiho Lee
- Division of Infectious Diseases, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA; (K.L.); (I.E.); (Y.J.)
| | - Iliana Escobar
- Division of Infectious Diseases, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA; (K.L.); (I.E.); (Y.J.)
| | - Yeeun Jang
- Division of Infectious Diseases, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA; (K.L.); (I.E.); (Y.J.)
| | - Wooseong Kim
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea;
| | - Frederick M. Ausubel
- Department of Genetics, Harvard Medical School and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA;
| | - Eleftherios Mylonakis
- Division of Infectious Diseases, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA; (K.L.); (I.E.); (Y.J.)
- Correspondence: ; Tel.: +1-401-444-7856
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Mathies LD, Lindsay JH, Handal AP, Blackwell GG, Davies AG, Bettinger JC. SWI/SNF complexes act through CBP-1 histone acetyltransferase to regulate acute functional tolerance to alcohol. BMC Genomics 2020; 21:646. [PMID: 32957927 PMCID: PMC7507291 DOI: 10.1186/s12864-020-07059-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 09/10/2020] [Indexed: 01/19/2023] Open
Abstract
Background SWI/SNF chromatin remodeling genes are required for normal acute responses to alcohol in C. elegans and are associated with alcohol use disorder in two human populations. In an effort to discover the downstream genes that are mediating this effect, we identified SWI/SNF-regulated genes in C. elegans. Results To identify SWI/SNF-regulated genes in adults, we compared mRNA expression in wild type and swsn-1(os22ts) worms under conditions that produce inactive swsn-1 in mature cells. To identify SWI/SNF-regulated genes in neurons, we compared gene expression in swsn-9(ok1354) null mutant worms that harbor a neuronal rescue or a control construct. RNA sequencing was performed to an average depth of 25 million reads per sample using 50-base, paired-end reads. We found that 6813 transcripts were significantly differentially expressed between swsn-1(os22ts) mutants and wild-type worms and 2412 transcripts were significantly differentially expressed between swsn-9(ok1354) mutants and swsn-9(ok1354) mutants with neuronal rescue. We examined the intersection between these two datasets and identified 603 genes that were differentially expressed in the same direction in both comparisons; we defined these as SWI/SNF-regulated genes in neurons and in adults. Among the differentially expressed genes was cbp-1, a C. elegans homolog of the mammalian CBP/p300 family of histone acetyltransferases. CBP has been implicated in the epigenetic regulation in response to alcohol in animal models and a polymorphism in the human CBP gene, CREBBP, has been associated with alcohol-related phenotypes. We found that cbp-1 is required for the development of acute functional tolerance to alcohol in C. elegans. Conclusions We identified 603 transcripts that were regulated by two different SWI/SNF complex subunits in adults and in neurons. The SWI/SNF-regulated genes were highly enriched for genes involved in membrane rafts, suggesting an important role for this membrane microdomain in the acute alcohol response. Among the differentially expressed genes was cbp-1; CBP-1 homologs have been implicated in alcohol responses across phyla and we found that C. elegans cbp-1 was required for the acute alcohol response in worms.
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Affiliation(s)
- Laura D Mathies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA.
| | - Jonathan H Lindsay
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
| | - Amal P Handal
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
| | - GinaMari G Blackwell
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
| | - Andrew G Davies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
| | - Jill C Bettinger
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
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PIG-1 MELK-dependent phosphorylation of nonmuscle myosin II promotes apoptosis through CES-1 Snail partitioning. PLoS Genet 2020; 16:e1008912. [PMID: 32946434 PMCID: PMC7527206 DOI: 10.1371/journal.pgen.1008912] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/30/2020] [Accepted: 07/29/2020] [Indexed: 01/06/2023] Open
Abstract
The mechanism(s) through which mammalian kinase MELK promotes tumorigenesis is not understood. We find that the C. elegans orthologue of MELK, PIG-1, promotes apoptosis by partitioning an anti-apoptotic factor. The C. elegans NSM neuroblast divides to produce a larger cell that differentiates into a neuron and a smaller cell that dies. We find that in this context, PIG-1 MELK is required for partitioning of CES-1 Snail, a transcriptional repressor of the pro-apoptotic gene egl-1 BH3-only. pig-1 MELK is controlled by both a ces-1 Snail- and par-4 LKB1-dependent pathway, and may act through phosphorylation and cortical enrichment of nonmuscle myosin II prior to neuroblast division. We propose that pig-1 MELK-induced local contractility of the actomyosin network plays a conserved role in the acquisition of the apoptotic fate. Our work also uncovers an auto-regulatory loop through which ces-1 Snail controls its own activity through the formation of a gradient of CES-1 Snail protein. Apoptosis is critical for the elimination of ‘unwanted’ cells. What distinguishes wanted from unwanted cells in developing animals is poorly understood. We report that in the C. elegans NSM neuroblast lineage, the level of CES-1, a Snail-family member and transcriptional repressor of the pro-apoptotic gene egl-1, contributes to this process. In addition, we demonstrate that C. elegans PIG-1, the orthologue of mammalian proto-oncoprotein MELK, plays a critical role in controlling CES-1Snail levels. Specifically, during NSM neuroblast division, PIG-1MELK controls partitioning of CES-1Snail into one but not the other daughter cell thereby promoting the making of one wanted and one unwanted cell. Furthermore, we present evidence that PIG-1MELK acts prior to NSM neuroblast division by locally activating the actomyosin network.
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128
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cnd-1/NeuroD1 Functions with the Homeobox Gene ceh-5/Vax2 and Hox Gene ceh-13/labial To Specify Aspects of RME and DD Neuron Fate in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2020; 10:3071-3085. [PMID: 32601060 PMCID: PMC7466980 DOI: 10.1534/g3.120.401515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Identifying the mechanisms behind neuronal fate specification are key to understanding normal neural development in addition to neurodevelopmental disorders such as autism and schizophrenia. In vivo cell fate specification is difficult to study in vertebrates. However, the nematode Caenorhabditis elegans, with its invariant cell lineage and simple nervous system of 302 neurons, is an ideal organism to explore the earliest stages of neural development. We used a comparative transcriptome approach to examine the role of cnd-1/NeuroD1 in C. elegans nervous system development and function. This basic helix-loop-helix transcription factor is deeply conserved across phyla and plays a crucial role in cell fate specification in both the vertebrate nervous system and pancreas. We find that cnd-1 controls expression of ceh-5, a Vax2-like homeobox class transcription factor, in the RME head motorneurons and PVQ tail interneurons. We also show that cnd-1 functions redundantly with the Hox gene ceh-13/labial in defining the fate of DD1 and DD2 embryonic ventral nerve cord motorneurons. These data highlight the utility of comparative transcriptomes for identifying transcription factor targets and understanding gene regulatory networks.
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129
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Treinin M, Jin Y. Cholinergic transmission in C. elegans: Functions, diversity, and maturation of ACh-activated ion channels. J Neurochem 2020; 158:1274-1291. [PMID: 32869293 DOI: 10.1111/jnc.15164] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/13/2020] [Accepted: 08/21/2020] [Indexed: 02/06/2023]
Abstract
Acetylcholine is an abundant neurotransmitter in all animals. Effects of acetylcholine are excitatory, inhibitory, or modulatory depending on the receptor and cell type. Research using the nematode C. elegans has made ground-breaking contributions to the mechanistic understanding of cholinergic transmission. Powerful genetic screens for behavioral mutants or for responses to pharmacological reagents identified the core cellular machinery for synaptic transmission. Pharmacological reagents that perturb acetylcholine-mediated processes led to the discovery and also uncovered the composition and regulators of acetylcholine-activated channels and receptors. From a combination of electrophysiological and molecular cellular studies, we have gained a profound understanding of cholinergic signaling at the levels of synapses, neural circuits, and animal behaviors. This review will begin with a historical overview, then cover in-depth current knowledge on acetylcholine-activated ionotropic receptors, mechanisms regulating their functional expression and their functions in regulating locomotion.
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Affiliation(s)
- Millet Treinin
- Department of Medical Neurobiology, Hadassah Medical school - Hebrew University, Jerusalem, Israel
| | - Yishi Jin
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
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130
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Willis AR, Sukhdeo R, Reinke AW. Remembering your enemies: mechanisms of within-generation and multigenerational immune priming in Caenorhabditis elegans. FEBS J 2020; 288:1759-1770. [PMID: 32767821 DOI: 10.1111/febs.15509] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/17/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022]
Abstract
Pathogens are abundant and drive evolution of host immunity. Whilst immune memory is classically associated with adaptive immunity, studies in diverse species now show that priming of innate immune defences can also protect against secondary infection. Remarkably, priming may also be passed on to progeny to enhance pathogen resistance and promote survival in future generations. Phenotypic changes that occur independent of DNA sequence underlie both 'within-generation' priming and 'multigenerational' priming. However, the molecular mechanisms responsible for these phenomena are still poorly understood. Caenorhabditis elegans is a simple and genetically tractable model organism that has enabled key advances in immunity and environmental epigenetics. Using both natural and human pathogens, researchers have uncovered numerous examples of innate immune priming in this animal. Viral infection models have provided key evidence for a conserved antiviral RNA silencing mechanism that is inherited in progeny. Bacterial infection models have explored mechanisms of within-generation and multigenerational priming that span chromatin modification and transcriptional changes, small RNA pathways, maternal provisioning and pathogen avoidance strategies. Together, these studies are providing novel insight into the immune reactivity of the genome and have important consequences for our understanding of health and evolution. In this review, we present the current evidence for learned protection against pathogens in C. elegans, discuss the significance and limitations of these findings and highlight important avenues of future investigation.
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Affiliation(s)
| | - Ronesh Sukhdeo
- Department of Molecular Genetics, University of Toronto, ON, Canada
| | - Aaron W Reinke
- Department of Molecular Genetics, University of Toronto, ON, Canada
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131
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Gordon KL, Zussman JW, Li X, Miller C, Sherwood DR. Stem cell niche exit in C. elegans via orientation and segregation of daughter cells by a cryptic cell outside the niche. eLife 2020; 9:e56383. [PMID: 32692313 PMCID: PMC7467730 DOI: 10.7554/elife.56383] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/17/2020] [Indexed: 12/17/2022] Open
Abstract
Stem cells reside in and rely upon their niche to maintain stemness but must balance self-renewal with the production of daughters that leave the niche to differentiate. We discovered a mechanism of stem cell niche exit in the canonical C. elegans distal tip cell (DTC) germ stem cell niche mediated by previously unobserved, thin, membranous protrusions of the adjacent somatic gonad cell pair (Sh1). A disproportionate number of germ cell divisions were observed at the DTC-Sh1 interface. Stem-like and differentiating cell fates segregated across this boundary. Spindles polarized, pairs of daughter cells oriented between the DTC and Sh1, and Sh1 grew over the Sh1-facing daughter. Impeding Sh1 growth by RNAi to cofilin and Arp2/3 perturbed the DTC-Sh1 interface, reduced germ cell proliferation, and shifted a differentiation marker. Because Sh1 membrane protrusions eluded detection for decades, it is possible that similar structures actively regulate niche exit in other systems.
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Affiliation(s)
- Kacy L Gordon
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Jay W Zussman
- Department of Biology, Duke UniversityDurhamUnited States
| | - Xin Li
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Camille Miller
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - David R Sherwood
- Department of Biology, Duke UniversityDurhamUnited States
- Regeneration Next, Duke UniversityDurhamUnited States
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132
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LaBella ML, Hujber EJ, Moore KA, Rawson RL, Merrill SA, Allaire PD, Ailion M, Hollien J, Bastiani MJ, Jorgensen EM. Casein Kinase 1δ Stabilizes Mature Axons by Inhibiting Transcription Termination of Ankyrin. Dev Cell 2020; 52:88-103.e18. [PMID: 31910362 DOI: 10.1016/j.devcel.2019.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/09/2019] [Accepted: 12/10/2019] [Indexed: 01/19/2023]
Abstract
After axon outgrowth and synapse formation, the nervous system transitions to a stable architecture. In C. elegans, this transition is marked by the appearance of casein kinase 1δ (CK1δ) in the nucleus. In CK1δ mutants, neurons continue to sprout growth cones into adulthood, leading to a highly ramified nervous system. Nervous system architecture in these mutants is completely restored by suppressor mutations in ten genes involved in transcription termination. CK1δ prevents termination by phosphorylating and inhibiting SSUP-72. SSUP-72 would normally remodel the C-terminal domain of RNA polymerase in anticipation of termination. The antitermination activity of CK1δ establishes the mature state of a neuron by promoting the expression of the long isoform of a single gene, the cytoskeleton protein Ankyrin.
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Affiliation(s)
- Matthew L LaBella
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Edward J Hujber
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Kristin A Moore
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Randi L Rawson
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Sean A Merrill
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Patrick D Allaire
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Julie Hollien
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | | | - Erik M Jorgensen
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA.
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133
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Mesbahi H, Pho KB, Tench AJ, Leon Guerrero VL, MacNeil LT. Cuticle Collagen Expression Is Regulated in Response to Environmental Stimuli by the GATA Transcription Factor ELT-3 in Caenorhabditis elegans. Genetics 2020; 215:483-495. [PMID: 32229533 PMCID: PMC7268988 DOI: 10.1534/genetics.120.303125] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 03/23/2020] [Indexed: 12/21/2022] Open
Abstract
The nematode Caenorhabditis elegans is protected from the environment by the cuticle, an extracellular collagen-based matrix that encloses the animal. Over 170 cuticular collagens are predicted in the C. elegans genome, but the role of each individual collagen is unclear. Stage-specific specialization of the cuticle explains the need for some collagens; however, the large number of collagens suggests that specialization of the cuticle may also occur in response to other environmental triggers. Missense mutations in many collagen genes can disrupt cuticle morphology, producing a helically twisted body causing the animal to move in a stereotypical pattern described as rolling. We find that environmental factors, including diet, early developmental arrest, and population density can differentially influence the penetrance of rolling in these mutants. These effects are in part due to changes in collagen gene expression that are mediated by the GATA family transcription factor ELT-3 We propose a model by which ELT-3 regulates collagen gene expression in response to environmental stimuli to promote the assembly of a cuticle specialized to a given environment.
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Affiliation(s)
- Hiva Mesbahi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Kim B Pho
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Andrea J Tench
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Victoria L Leon Guerrero
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Lesley T MacNeil
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
- Farncombe Family Digestive Health Research Institute, McMaster University, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8S 4K1
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A Multimodal Genotoxic Anticancer Drug Characterized by Pharmacogenetic Analysis in Caenorhabditis elegans. Genetics 2020; 215:609-621. [PMID: 32414869 PMCID: PMC7337070 DOI: 10.1534/genetics.120.303169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/08/2020] [Indexed: 01/05/2023] Open
Abstract
New anticancer therapeutics require extensive in vivo characterization to identify endogenous and exogenous factors affecting efficacy, to measure toxicity and mutagenicity, and to determine genotypes that result in therapeutic sensitivity or resistance. We used Caenorhabditis elegans as a platform with which to characterize properties of the anticancer therapeutic CX-5461. To understand the processes that respond to CX-5461-induced damage, we generated pharmacogenetic profiles for a panel of C. elegans DNA replication and repair mutants with common DNA-damaging agents for comparison with the profile of CX-5461. We found that multiple repair pathways, including homology-directed repair, microhomology-mediated end joining, nucleotide excision repair, and translesion synthesis, were needed for CX-5461 tolerance. To determine the frequency and spectrum of CX-5461-induced mutations, we used a genetic balancer to capture CX-5461-induced mutations. We found that CX-5461 is mutagenic, resulting in both large copy number variations and a high frequency of single-nucleotide variations (SNVs), which are consistent with the pharmacogenetic profile for CX-5461. Whole-genome sequencing of CX-5461-exposed animals found that CX-5461-induced SNVs exhibited a distinct mutational signature. We also phenocopied the CX-5461 photoreactivity observed in clinical trials and demonstrated that CX-5461 generates reactive oxygen species when exposed to UVA radiation. Together, the data from C. elegans demonstrate that CX-5461 is a multimodal DNA-damaging anticancer agent.
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135
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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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136
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Weaver BP, Weaver YM, Omi S, Yuan W, Ewbank JJ, Han M. Non-Canonical Caspase Activity Antagonizes p38 MAPK Stress-Priming Function to Support Development. Dev Cell 2020; 53:358-369.e6. [PMID: 32302544 PMCID: PMC7641037 DOI: 10.1016/j.devcel.2020.03.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/15/2019] [Accepted: 03/15/2020] [Indexed: 02/02/2023]
Abstract
Recent studies have revealed non-canonical activities of apoptotic caspases involving specific modulation of gene expression, such as limiting asymmetric divisions of stem-like cell types. Here we report that CED-3 caspase negatively regulates an epidermal p38 stress-responsive MAPK pathway to promote larval development in C. elegans. We show that PMK-1 (p38 MAPK) primes animals for encounters with hostile environments at the expense of retarding post-embryonic development. CED-3 counters this function by directly cleaving PMK-1 to promote development. Moreover, we found that CED-3 and PMK-1 oppose each other to balance developmental and stress-responsive gene expression programs. Specifically, expression of more than 300 genes is inversely regulated by CED-3 and PMK-1. Analyses of these genes showed enrichment for epidermal stress-responsive factors, including the fatty acid synthase FASN-1, anti-microbial peptides, and genes involved in lethargus states. Our findings demonstrate a non-canonical role for a caspase in promoting development by limiting epidermal stress response programs.
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Affiliation(s)
- Benjamin P Weaver
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder and Howard Hughes Medical Institute, Boulder, CO 80309, USA.
| | - Yi M Weaver
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder and Howard Hughes Medical Institute, Boulder, CO 80309, USA
| | - Shizue Omi
- Aix Marseille University, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France
| | - Wang Yuan
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jonathan J Ewbank
- Aix Marseille University, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France
| | - Min Han
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder and Howard Hughes Medical Institute, Boulder, CO 80309, USA
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137
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Després PC, Dubé AK, Seki M, Yachie N, Landry CR. Perturbing proteomes at single residue resolution using base editing. Nat Commun 2020; 11:1871. [PMID: 32313011 PMCID: PMC7170841 DOI: 10.1038/s41467-020-15796-7] [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: 07/18/2019] [Accepted: 03/27/2020] [Indexed: 01/18/2023] Open
Abstract
Base editors derived from CRISPR-Cas9 systems and DNA editing enzymes offer an unprecedented opportunity for the precise modification of genes, but have yet to be used at a genome-scale throughput. Here, we test the ability of the Target-AID base editor to systematically modify genes genome-wide by targeting yeast essential genes. We mutate around 17,000 individual sites in parallel across more than 1500 genes. We identify over 700 sites at which mutations have a significant impact on fitness. Using previously determined and preferred Target-AID mutational outcomes, we find that gRNAs with significant effects on fitness are enriched in variants predicted to be deleterious based on residue conservation and predicted protein destabilization. We identify key features influencing effective gRNAs in the context of base editing. Our results show that base editing is a powerful tool to identify key amino acid residues at the scale of proteomes.
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Affiliation(s)
- Philippe C Després
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Alexandre K Dubé
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Motoaki Seki
- Research Center for Advanced Science and Technology, Synthetic Biology Division, University of Tokyo, Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Japan
| | - Nozomu Yachie
- Research Center for Advanced Science and Technology, Synthetic Biology Division, University of Tokyo, Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Japan.
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan.
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
| | - Christian R Landry
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada.
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada.
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada.
- Département de Biologie, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada.
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138
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Liu F, Zhang Y, Zhang M, Luo Q, Cao X, Cui C, Lin K, Huang K. Toxicological assessment and underlying mechanisms of tetrabromobisphenol A exposure on the soil nematode Caenorhabditis elegans. CHEMOSPHERE 2020; 242:125078. [PMID: 31704520 DOI: 10.1016/j.chemosphere.2019.125078] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 10/04/2019] [Accepted: 10/07/2019] [Indexed: 05/19/2023]
Abstract
The widespread use of tetrabromobisphenol A (TBBPA) in industries has resulted in its frequent detection in environmental matrices, and the mechanisms of its associated hazards need further investigation. In this study, the nematode Caenorhabditis elegans (C. elegans) was exposed to environmentally relevant concentrations of TBBPA (0, 0.1, 1, 10, 100, 200 μg/L) to determine its effects. At TBBPA concentrations above 1 μg/L, the number of head thrashes, as the most sensitive physiological indicator, decreased significantly. Using the Illumina HiSeq™ 2000 sequencer, differentially expressed genes (DEGs) were determined, and 52 were down regulated and 105 were up regulated in the 200 μg/L TBBPA treatment group versus the control group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database analysis demonstrated that dorso-ventral axis formation is related to neurotoxicity; metabolism of xenobiotics by Cytochrome P450 (CYP450) and glutathione-S-transferase (GST) was found to be the vital metabolic mechanisms and were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR). GST was ascribed to the augmentation because mutations in cyp-13A7 were constrained under TBBPA exposure. Additionally, oxidative stress indicators accumulated in a dose-dependent relationship. These results will help understand the molecular basis for TBBPA-induced toxicity in C. elegans and open novel avenues for facilitating the exploration of more efficient strategies against TBBPA toxicity.
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Affiliation(s)
- Fuwen Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ying Zhang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Meng Zhang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Qishi Luo
- Branch of Shanghai, Yonker Environmental Protection Co., Ltd, Shanghai, 200051, China
| | - Xue Cao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Kuangfei Lin
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Kai Huang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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139
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Kroll JR, Tsiaxiras J, van Zon JS. Variability in β-catenin pulse dynamics in a stochastic cell fate decision in C. elegans. Dev Biol 2020; 461:110-123. [PMID: 32032579 PMCID: PMC7203549 DOI: 10.1016/j.ydbio.2020.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 11/30/2022]
Abstract
During development, cell fate decisions are often highly stochastic, but with the frequency of the different possible fates tightly controlled. To understand how signaling networks control the cell fate frequency of such random decisions, we studied the stochastic decision of the Caenorhabditis elegans P3.p cell to either fuse to the hypodermis or assume vulva precursor cell fate. Using time-lapse microscopy to measure the single-cell dynamics of two key inhibitors of cell fusion, the Hox gene LIN-39 and Wnt signaling through the β-catenin BAR-1, we uncovered significant variability in the dynamics of LIN-39 and BAR-1 levels. Most strikingly, we observed that BAR-1 accumulated in a single, 1–4 h pulse at the time of the P3.p cell fate decision, with strong variability both in pulse slope and time of pulse onset. We found that the time of BAR-1 pulse onset was delayed relative to the time of cell fusion in mutants with low cell fusion frequency, linking BAR-1 pulse timing to cell fate outcome. Overall, a model emerged where animal-to-animal variability in LIN-39 levels and BAR-1 pulse dynamics biases cell fate by modulating their absolute level at the time cell fusion is induced. Our results highlight that timing of cell signaling dynamics, rather than its average level or amplitude, could play an instructive role in determining cell fate. The fate of the C. elegans P3.p cell is stochastic. β-catenin (BAR-1) accumulated in P3.p at the time of the cell fate decision. There is variability in dynamics of Hox and β-catenin levels during the decision. BAR-1 accumulated with variable pulse slope and time of pulse onset. Pulse dynamics bias cell fate at the time of the cell fate decision.
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Affiliation(s)
- Jason R Kroll
- Department of Living Matter, AMOLF, 1098 XG, Amsterdam, the Netherlands
| | - Jasonas Tsiaxiras
- Department of Living Matter, AMOLF, 1098 XG, Amsterdam, the Netherlands
| | - Jeroen S van Zon
- Department of Living Matter, AMOLF, 1098 XG, Amsterdam, the Netherlands.
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140
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Voss L, Foster OK, Harper L, Morris C, Lavoy S, Brandt JN, Peloza K, Handa S, Maxfield A, Harp M, King B, Eichten V, Rambo FM, Hermann GJ. An ABCG Transporter Functions in Rab Localization and Lysosome-Related Organelle Biogenesis in Caenorhabditis elegans. Genetics 2020; 214:419-445. [PMID: 31848222 PMCID: PMC7017009 DOI: 10.1534/genetics.119.302900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/11/2019] [Indexed: 12/20/2022] Open
Abstract
ABC transporters couple ATP hydrolysis to the transport of substrates across cellular membranes. This protein superfamily has diverse activities resulting from differences in their cargo and subcellular localization. Our work investigates the role of the ABCG family member WHT-2 in the biogenesis of gut granules, a Caenorhabditis elegans lysosome-related organelle. In addition to being required for the accumulation of birefringent material within gut granules, WHT-2 is necessary for the localization of gut granule proteins when trafficking pathways to this organelle are partially disrupted. The role of WHT-2 in gut granule protein targeting is likely linked to its function in Rab GTPase localization. We show that WHT-2 promotes the gut granule association of the Rab32 family member GLO-1 and the endolysosomal RAB-7, identifying a novel function for an ABC transporter. WHT-2 localizes to gut granules where it could play a direct role in controlling Rab localization. Loss of CCZ-1 and GLO-3, which likely function as a guanine nucleotide exchange factor (GEF) for GLO-1, lead to similar disruption of GLO-1 localization. We show that CCZ-1, like GLO-3, is localized to gut granules. WHT-2 does not direct the gut granule association of the GLO-1 GEF and our results point to WHT-2 functioning differently than GLO-3 and CCZ-1 Point mutations in WHT-2 that inhibit its transport activity, but not its subcellular localization, lead to the loss of GLO-1 from gut granules, while other WHT-2 activities are not completely disrupted, suggesting that WHT-2 functions in organelle biogenesis through transport-dependent and transport-independent activities.
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Affiliation(s)
- Laura Voss
- Department of Biology, Lewis & Clark College, Portland, Oregon
| | - Olivia K Foster
- Department of Biology, Lewis & Clark College, Portland, Oregon
| | - Logan Harper
- Department of Biology, Lewis & Clark College, Portland, Oregon
| | - Caitlin Morris
- Department of Biology, Lewis & Clark College, Portland, Oregon
| | - Sierra Lavoy
- Department of Biology, Lewis & Clark College, Portland, Oregon
| | - James N Brandt
- Department of Biology, Lewis & Clark College, Portland, Oregon
| | - Kimberly Peloza
- Department of Biology, Lewis & Clark College, Portland, Oregon
| | - Simran Handa
- Department of Biology, Lewis & Clark College, Portland, Oregon
| | - Amanda Maxfield
- Department of Biology, Lewis & Clark College, Portland, Oregon
| | - Marie Harp
- Department of Biology, Lewis & Clark College, Portland, Oregon
| | - Brian King
- Department of Biology, Lewis & Clark College, Portland, Oregon
| | | | - Fiona M Rambo
- Department of Biology, Lewis & Clark College, Portland, Oregon
| | - Greg J Hermann
- Department of Biology, Lewis & Clark College, Portland, Oregon
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141
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ATP13A2 deficiency disrupts lysosomal polyamine export. Nature 2020; 578:419-424. [PMID: 31996848 DOI: 10.1038/s41586-020-1968-7] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 12/02/2019] [Indexed: 02/07/2023]
Abstract
ATP13A2 (PARK9) is a late endolysosomal transporter that is genetically implicated in a spectrum of neurodegenerative disorders, including Kufor-Rakeb syndrome-a parkinsonism with dementia1-and early-onset Parkinson's disease2. ATP13A2 offers protection against genetic and environmental risk factors of Parkinson's disease, whereas loss of ATP13A2 compromises lysosomes3. However, the transport function of ATP13A2 in lysosomes remains unclear. Here we establish ATP13A2 as a lysosomal polyamine exporter that shows the highest affinity for spermine among the polyamines examined. Polyamines stimulate the activity of purified ATP13A2, whereas ATP13A2 mutants that are implicated in disease are functionally impaired to a degree that correlates with the disease phenotype. ATP13A2 promotes the cellular uptake of polyamines by endocytosis and transports them into the cytosol, highlighting a role for endolysosomes in the uptake of polyamines into cells. At high concentrations polyamines induce cell toxicity, which is exacerbated by ATP13A2 loss due to lysosomal dysfunction, lysosomal rupture and cathepsin B activation. This phenotype is recapitulated in neurons and nematodes with impaired expression of ATP13A2 or its orthologues. We present defective lysosomal polyamine export as a mechanism for lysosome-dependent cell death that may be implicated in neurodegeneration, and shed light on the molecular identity of the mammalian polyamine transport system.
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142
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Novakovic S, Molesworth LW, Gourley TE, Boag PR, Davis GM. Zinc transporters maintain longevity by influencing insulin/IGF-1 activity in Caenorhabditis elegans. FEBS Lett 2020; 594:1424-1432. [PMID: 31883120 DOI: 10.1002/1873-3468.13725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/05/2019] [Accepted: 12/11/2019] [Indexed: 12/12/2022]
Abstract
Adequate dietary intake of essential metals such as zinc is important for maintaining homeostasis. Abnormal zinc intake in Caenorhabditis elegans has been shown to increase or decrease normal lifespan by influencing the insulin/IGF-1 pathway. Distribution of zinc is achieved by a family of highly conserved zinc transport proteins (ZIPT in C. elegans). This study investigated the role of the zipt family of genes and showed that depletion of individual zipt genes results in a decreased lifespan. Moreover, zipt-16 and zipt-17 mutants synthetically interact with the insulin/IGF cofactors daf-16 and skn-1, and cause abnormal localisation of DAF-16. This study suggests that the zipt family of genes are required for maintaining normal lifespan through influencing the insulin/IGF-1 pathway.
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Affiliation(s)
- Stevan Novakovic
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - Luke W Molesworth
- School of Health and Life Sciences, Federation University, Churchill, VIC, Australia
| | - Taylin E Gourley
- School of Health and Life Sciences, Federation University, Churchill, VIC, Australia
| | - Peter R Boag
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - Gregory M Davis
- School of Health and Life Sciences, Federation University, Churchill, VIC, Australia
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143
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Serrano-Saiz E, Vogt MC, Levy S, Wang Y, Kaczmarczyk KK, Mei X, Bai G, Singson A, Grant BD, Hobert O. SLC17A6/7/8 Vesicular Glutamate Transporter Homologs in Nematodes. Genetics 2020; 214:163-178. [PMID: 31776169 PMCID: PMC6944403 DOI: 10.1534/genetics.119.302855] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/24/2019] [Indexed: 01/04/2023] Open
Abstract
Members of the superfamily of solute carrier (SLC) transmembrane proteins transport diverse substrates across distinct cellular membranes. Three SLC protein families transport distinct neurotransmitters into synaptic vesicles to enable synaptic transmission in the nervous system. Among them is the SLC17A6/7/8 family of vesicular glutamate transporters, which endows specific neuronal cell types with the ability to use glutamate as a neurotransmitter. The genome of the nematode Caenorhabditis elegans encodes three SLC17A6/7/8 family members, one of which, eat-4/VGLUT, has been shown to be involved in glutamatergic neurotransmission. Here, we describe our analysis of the two remaining, previously uncharacterized SLC17A6/7/8 family members, vglu-2 and vglu-3 These two genes directly neighbor one another and are the result of a recent gene duplication event in C. elegans, but not in other Caenorhabditis species. Compared to EAT-4, the VGLU-2 and VGLU-3 protein sequences display a more distant similarity to canonical, vertebrate VGLUT proteins. We tagged both genomic loci with gfp and detected no expression of vglu-3 at any stage of development in any cell type of both C. elegans sexes. In contrast, vglu-2::gfp is dynamically expressed in a restricted set of distinct cell types. Within the nervous system, vglu-2::gfp is exclusively expressed in a single interneuron class, AIA, where it localizes to vesicular structures in the soma, but not along the axon, suggesting that VGLU-2 may not be involved in synaptic transport of glutamate. Nevertheless, vglu-2 mutants are partly defective in the function of the AIA neuron in olfactory behavior. Outside the nervous system, VGLU-2 is expressed in collagen secreting skin cells where VGLU-2 most prominently localizes to early endosomes, and to a lesser degree to apical clathrin-coated pits, the trans-Golgi network, and late endosomes. On early endosomes, VGLU-2 colocalizes most strongly with the recycling promoting factor SNX-1, a retromer component. Loss of vglu-2 affects the permeability of the collagen-containing cuticle of the worm, and based on the function of a vertebrate VGLUT1 protein in osteoclasts, we speculate that vglu-2 may have a role in collagen trafficking in the skin. We conclude that C. elegans SLC17A6/7/8 family members have diverse functions within and outside the nervous system.
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Affiliation(s)
- Esther Serrano-Saiz
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, New York 10027
- Centro de Biologia Molecular Severo Ochoa/Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Merly C Vogt
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, New York 10027
| | - Sagi Levy
- Rockefeller University, New York, New York 10065
| | - Yu Wang
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Karolina K Kaczmarczyk
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, New York 10027
| | - Xue Mei
- Waksman Institute, Rutgers University, Piscataway, New Jersey 08854
| | - Ge Bai
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Andrew Singson
- Waksman Institute, Rutgers University, Piscataway, New Jersey 08854
- Department of Genetics, Rutgers University, Piscataway, New Jersey 08854
| | - Barth D Grant
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, New York 10027
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144
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Hertz MI, Glaessner PM, Rush A, Budge PJ. Brugia malayi galectin 2 is a tandem-repeat type galectin capable of binding mammalian polysaccharides. Mol Biochem Parasitol 2019; 235:111233. [PMID: 31738955 DOI: 10.1016/j.molbiopara.2019.111233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022]
Abstract
Galectins are among the most abundant excretory/secretory (ES) products of filarial worms, but their role in filarial biology is poorly understood. Galectin-2 (Lec-2), a major component of Brugia malayi extracellular vesicles, is released by filarial worms, and was recently identified in the serum of persons with loiasis. We therefore sought to clone and characterize Lec-2, and to develop reagents to examine its potential as a biomarker and its role in parasite biology. We cloned and expressed recombinant B. malayi Lec-2 (rBmLec-2), generated a Lec-2-specific monoclonal antibody (4B4), and used it to confirm the presence of Lec-2 in B. malayi ES products and whole worm lysate. We show that Lec-2 is absent in B. malayi oocytes, and increases in concentration as embryos mature. Recombinant BmLec-2 hemagglutinates rabbit red blood cells at concentrations less than 1 μg/mL, and this is abrogated by single amino acid substitutions in the predicted carbohydrate recognition domains. rBmLec-2 binds multiple LacNAc oligosaccharides on a mammalian carbohydrate array. Sera from 17/23 (78 %) persons with microfilaremic loiasis and 4/10 (40 %) persons with bancroftian filariasis had detectable antibody to Lec-2 by western blot. Our studies confirm the functionality of BmLec-2 and indicate anti-Lec-2 antibody responses are common in persons with filariasis. These studies set the stage for further examination of the role of Lec-2 in filarial biology and in filarial-host interactions.
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Affiliation(s)
- Marla I Hertz
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States.
| | - Philip M Glaessner
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Amy Rush
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Philip J Budge
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
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145
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Zhao Y, Wang H, Poole RJ, Gems D. A fln-2 mutation affects lethal pathology and lifespan in C. elegans. Nat Commun 2019; 10:5087. [PMID: 31704915 PMCID: PMC6841690 DOI: 10.1038/s41467-019-13062-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 10/15/2019] [Indexed: 12/12/2022] Open
Abstract
Differences in genetic background in model organisms can have complex effects on phenotypes of interest. We previously reported a difference in hermaphrodite lifespan between two wild-type lines widely used by C. elegans researchers (N2 hermaphrodite and male stocks). Here, using pathology-based approaches and genome sequencing, we identify the cause of this difference as a nonsense mutation in the filamin gene fln-2 in the male stock, which reduces early mortality caused by pharyngeal infection. We show how fln-2 variation explains previous discrepancies involving effects of sir-2.1 (sirtuin deacetylase) on ageing, and show that in a fln-2(+) background, sir-2.1 over-expression causes an FUDR (DNA synthesis inhibitor)-dependent reduction in pharyngeal infection and increase in lifespan. In addition we show how fln-2 variation confounds effects on lifespan of daf-2 (insulin/IGF-1 signalling), daf-12 (steroid hormone signalling), and eat-2 (putative dietary restriction). These findings underscore the importance of identifying and controlling genetic background variation.
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Affiliation(s)
- Yuan Zhao
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Hongyuan Wang
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Richard J Poole
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - David Gems
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
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146
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Bhan P, Muthaiyan Shanmugam M, Wang D, Bayansan O, Chen C, Wagner OI. Characterization of TAG‐63 and its role on axonal transport inC.elegans. Traffic 2019; 21:231-249. [DOI: 10.1111/tra.12706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 10/13/2019] [Accepted: 10/13/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Prerana Bhan
- Department of Life ScienceNational Tsing Hua University, Institute of Molecular and Cellular Biology Hsinchu Taiwan, ROC
- Research Center for Healthy AgingChina Medical University Taichung Taiwan, ROC
| | - Muniesh Muthaiyan Shanmugam
- Department of Life ScienceNational Tsing Hua University, Institute of Molecular and Cellular Biology Hsinchu Taiwan, ROC
| | - Ding Wang
- Department of Life ScienceNational Tsing Hua University, Institute of Molecular and Cellular Biology Hsinchu Taiwan, ROC
| | - Odvogmed Bayansan
- Department of Life ScienceNational Tsing Hua University, Institute of Molecular and Cellular Biology Hsinchu Taiwan, ROC
| | - Chih‐Wei Chen
- Department of Life ScienceNational Tsing Hua University, Institute of Molecular and Cellular Biology Hsinchu Taiwan, ROC
| | - Oliver I. Wagner
- Department of Life ScienceNational Tsing Hua University, Institute of Molecular and Cellular Biology Hsinchu Taiwan, ROC
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147
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Sellegounder D, Liu Y, Wibisono P, Chen CH, Leap D, Sun J. Neuronal GPCR NPR-8 regulates C. elegans defense against pathogen infection. SCIENCE ADVANCES 2019; 5:eaaw4717. [PMID: 31799388 PMCID: PMC6867885 DOI: 10.1126/sciadv.aaw4717] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 09/17/2019] [Indexed: 05/18/2023]
Abstract
Increasing evidence indicates that infection-triggered host defenses are regulated by the nervous system. However, the precise mechanisms of this regulation are not well understood. Here, we demonstrate that neuronal G protein-coupled receptor NPR-8 negatively regulates Caenorhabditis elegans defense against pathogen infection by suppressing cuticular collagen expression. NPR-8 controls the dynamics of cuticle structure in response to infection, likely through its regulation of cuticular collagen genes which, in turn, affects the nematode's defense. We further show that the defense activity of NPR-8 is confined to amphid sensory neurons AWB, ASJ, and AWC. It is generally believed that physical barrier defenses are not a response to infections but are part of the body's basic innate defense against pathogens. Our results challenge this view by showing not only that C. elegans cuticle structure dynamically changes in response to infection but also that the cuticle barrier defense is regulated by the nervous system.
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Affiliation(s)
- Durai Sellegounder
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Yiyong Liu
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
- Genomics Core, Washington State University, Spokane, WA, USA
| | - Phillip Wibisono
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Chia-Hui Chen
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - David Leap
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Jingru Sun
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
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148
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Abstract
Using neXtProt release 2019-01-11, we manually curated a list of 1837 functionally uncharacterized human proteins. Using OrthoList 2, we found that 270 of them have homologues in Caenorhabditis elegans, including 60 with a one-to-one orthology relationship. According to annotations extracted from WormBase, the vast majority of these 60 worm genes have RNAi experimental data or mutant alleles, but manual inspection shows that only 15% have phenotypes that could be interpreted in terms of a specific function. One third of the worm orthologs have protein-protein interaction data, and two of these interactions are conserved in humans. The combination of phenotypic, protein-protein interaction, and gene expression data provides functional hypotheses for 8 uncharacterized human proteins. Experimental validation in human or orthologs is necessary before they can be considered for annotation.
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Affiliation(s)
- Paula Duek
- CALIPHO Group , SIB-Swiss Institute of Bioinformatics, CMU , Michel-Servet 1 , 1211 Geneva 4 , Switzerland
| | - Lydie Lane
- CALIPHO Group , SIB-Swiss Institute of Bioinformatics, CMU , Michel-Servet 1 , 1211 Geneva 4 , Switzerland.,Department of Microbiology and Molecular Medicine, Faculty of Medicine , University of Geneva, CMU , Michel-Servet 1 , 1211 Geneva 4 , Switzerland
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149
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Zullo JM, Drake D, Aron L, O'Hern P, Dhamne SC, Davidsohn N, Mao CA, Klein WH, Rotenberg A, Bennett DA, Church GM, Colaiácovo MP, Yankner BA. Regulation of lifespan by neural excitation and REST. Nature 2019; 574:359-364. [PMID: 31619788 PMCID: PMC6893853 DOI: 10.1038/s41586-019-1647-8] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 09/18/2019] [Indexed: 12/27/2022]
Abstract
The mechanisms that extend lifespan in humans are poorly understood. Here we show that extended longevity in humans is associated with a distinct transcriptome signature in the cerebral cortex that is characterized by downregulation of genes related to neural excitation and synaptic function. In Caenorhabditis elegans, neural excitation increases with age and inhibition of excitation globally, or in glutamatergic or cholinergic neurons, increases longevity. Furthermore, longevity is dynamically regulated by the excitatory-inhibitory balance of neural circuits. The transcription factor REST is upregulated in humans with extended longevity and represses excitation-related genes. Notably, REST-deficient mice exhibit increased cortical activity and neuronal excitability during ageing. Similarly, loss-of-function mutations in the C. elegans REST orthologue genes spr-3 and spr-4 elevate neural excitation and reduce the lifespan of long-lived daf-2 mutants. In wild-type worms, overexpression of spr-4 suppresses excitation and extends lifespan. REST, SPR-3, SPR-4 and reduced excitation activate the longevity-associated transcription factors FOXO1 and DAF-16 in mammals and worms, respectively. These findings reveal a conserved mechanism of ageing that is mediated by neural circuit activity and regulated by REST.
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Affiliation(s)
- Joseph M Zullo
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Derek Drake
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Liviu Aron
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Patrick O'Hern
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sameer C Dhamne
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Noah Davidsohn
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chai-An Mao
- Department of Ophthalmology and Visual Science, The University of Texas McGovern Medical School, Houston, TX, USA
| | - William H Klein
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander Rotenberg
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Bruce A Yankner
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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150
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Meneely PM, Dahlberg CL, Rose JK. Working with Worms:Caenorhabditis elegansas a Model Organism. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/cpet.35] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | | | - Jacqueline K. Rose
- Behavioral Neuroscience Program, Department of PsychologyWestern Washington University Bellingham Washington
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