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Mongiat M, Pascal G, Poletto E, Williams DM, Iozzo RV. Proteoglycans of basement membranes: Crucial controllers of angiogenesis, neurogenesis, and autophagy. PROTEOGLYCAN RESEARCH 2024; 2:e22. [PMID: 39184370 PMCID: PMC11340296 DOI: 10.1002/pgr2.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 06/02/2024] [Indexed: 08/27/2024]
Abstract
Anti-angiogenic therapy is an established method for the treatment of several cancers and vascular-related diseases. Most of the agents employed target the vascular endothelial growth factor A, the major cytokine stimulating angiogenesis. However, the efficacy of these treatments is limited by the onset of drug resistance. Therefore, it is of fundamental importance to better understand the mechanisms that regulate angiogenesis and the microenvironmental cues that play significant role and influence patient treatment and outcome. In this context, here we review the importance of the three basement membrane heparan sulfate proteoglycans (HSPGs), namely perlecan, agrin and collagen XVIII. These HSPGs are abundantly expressed in the vasculature and, due to their complex molecular architecture, they interact with multiple endothelial cell receptors, deeply affecting their function. Under normal conditions, these proteoglycans exert pro-angiogenic functions. However, in pathological conditions such as cancer and inflammation, extracellular matrix remodeling leads to the degradation of these large precursor molecules and the liberation of bioactive processed fragments displaying potent angiostatic activity. These unexpected functions have been demonstrated for the C-terminal fragments of perlecan and collagen XVIII, endorepellin and endostatin. These bioactive fragments can also induce autophagy in vascular endothelial cells which contributes to angiostasis. Overall, basement membrane proteoglycans deeply affect angiogenesis counterbalancing pro-angiogenic signals during tumor progression, and represent possible means to develop new prognostic biomarkers and novel therapeutic approaches for the treatment of solid tumors.
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Affiliation(s)
- Maurizio Mongiat
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy
| | - Gabriel Pascal
- Department of Pathology and Genomic Medicine, and the Translational Cellular Oncology Program, Sidney Kimmel Cancer Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Evelina Poletto
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy
| | - Davion M. Williams
- Department of Pathology and Genomic Medicine, and the Translational Cellular Oncology Program, Sidney Kimmel Cancer Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Renato V. Iozzo
- Department of Pathology and Genomic Medicine, and the Translational Cellular Oncology Program, Sidney Kimmel Cancer Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA
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Heiman MG, Bülow HE. Dendrite morphogenesis in Caenorhabditis elegans. Genetics 2024; 227:iyae056. [PMID: 38785371 PMCID: PMC11151937 DOI: 10.1093/genetics/iyae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/02/2024] [Indexed: 05/25/2024] Open
Abstract
Since the days of Ramón y Cajal, the vast diversity of neuronal and particularly dendrite morphology has been used to catalog neurons into different classes. Dendrite morphology varies greatly and reflects the different functions performed by different types of neurons. Significant progress has been made in our understanding of how dendrites form and the molecular factors and forces that shape these often elaborately sculpted structures. Here, we review work in the nematode Caenorhabditis elegans that has shed light on the developmental mechanisms that mediate dendrite morphogenesis with a focus on studies investigating ciliated sensory neurons and the highly elaborated dendritic trees of somatosensory neurons. These studies, which combine time-lapse imaging, genetics, and biochemistry, reveal an intricate network of factors that function both intrinsically in dendrites and extrinsically from surrounding tissues. Therefore, dendrite morphogenesis is the result of multiple tissue interactions, which ultimately determine the shape of dendritic arbors.
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Affiliation(s)
- Maxwell G Heiman
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Hannes E Bülow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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3
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Leonetti P, Dallera D, De Marchi D, Candito P, Pasotti L, Macovei A. Exploring the putative microRNAs cross-kingdom transfer in Solanum lycopersicum-Meloidogyne incognita interactions. FRONTIERS IN PLANT SCIENCE 2024; 15:1383986. [PMID: 38784062 PMCID: PMC11114104 DOI: 10.3389/fpls.2024.1383986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024]
Abstract
Introduction Plant-pathogen interaction is an inexhaustible source of information on how to sustainably control diseases that negatively affect agricultural production. Meloidogyne incognita is a root-knot nematode (RKN), representing a pest for many crops, including tomato (Solanum lycopersicum). RKNs are a global threat to agriculture, especially under climate change, and RNA technologies offer a potential alternative to chemical nematicides. While endogenous microRNAs have been identified in both S. lycopersicum and M. incognita, and their roles have been related to the regulation of developmental changes, no study has investigated the miRNAs cross-kingdom transfer during this interaction. Methods Here, we propose a bioinformatics pipeline to highlight potential miRNA-dependent cross-kingdom interactions between tomato and M. incognita. Results The obtained data show that nematode miRNAs putatively targeting tomato genes are mostly related to detrimental effects on plant development and defense. Similarly, tomato miRNAs putatively targeting M. incognita biological processes have negative effects on digestion, mobility, and reproduction. To experimentally test this hypothesis, an in vitro feeding assay was carried out using sly-miRNAs selected from the bioinformatics approach. The results show that two tomato miRNAs (sly-miRNA156a, sly-miR169f) soaked by juvenile larvae (J2s) affected their ability to infect plant roots and form galls. This was also coupled with a significant downregulation of predicted target genes (Minc11367, Minc00111), as revealed by a qRT-PCR analysis. Discussions Therefore, the current study expands the knowledge related to the cross-kingdom miRNAs involvement in host-parasite interactions and could pave the way for the application of exogenous plant miRNAs as tools to control nematode infection.
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Affiliation(s)
- Paola Leonetti
- Institute for Sustainable Plant Protection of the National Research Council, Unit of Bari, Bari, Italy
| | - Debora Dallera
- Laboratory of Bioinformatics, Mathematical Modelling, and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering - Centre for Health Technology, University of Pavia, Pavia, Italy
| | - Davide De Marchi
- Laboratory of Bioinformatics, Mathematical Modelling, and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering - Centre for Health Technology, University of Pavia, Pavia, Italy
| | - Pamela Candito
- Laboratory of Bioinformatics, Mathematical Modelling, and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering - Centre for Health Technology, University of Pavia, Pavia, Italy
| | - Lorenzo Pasotti
- Laboratory of Bioinformatics, Mathematical Modelling, and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering - Centre for Health Technology, University of Pavia, Pavia, Italy
| | - Anca Macovei
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
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4
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McIntyre DC, Nance J. Niche cells regulate primordial germ cell quiescence in response to basement membrane signaling. Development 2023; 150:dev201640. [PMID: 37497562 PMCID: PMC10445801 DOI: 10.1242/dev.201640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023]
Abstract
Stem cell quiescence, proliferation and differentiation are controlled by interactions with niche cells and a specialized extracellular matrix called basement membrane (BM). Direct interactions with adjacent BM are known to regulate stem cell quiescence; however, it is less clear how niche BM relays signals to stem cells that it does not contact. Here, we examine how niche BM regulates Caenorhabditis elegans primordial germ cells (PGCs). BM regulates PGC quiescence even though PGCs are enwrapped by somatic niche cells and do not contact the BM; this can be demonstrated by depleting laminin, which causes normally quiescent embryonic PGCs to proliferate. We show that following laminin depletion, niche cells relay proliferation-inducing signals from the gonadal BM to PGCs via integrin receptors. Disrupting the BM proteoglycan perlecan blocks PGC proliferation when laminin is depleted, indicating that laminin functions to inhibit a proliferation-inducing signal originating from perlecan. Reducing perlecan levels in fed larvae hampers germline growth, suggesting that BM signals regulate germ cell proliferation under physiological conditions. Our results reveal how BM signals can regulate stem cell quiescence indirectly, by activating niche cell integrin receptors.
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Affiliation(s)
- Daniel C. McIntyre
- Skirball Institute of Biomolecular Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
- University of Virginia, Department of Biology, 90 Geldard Drive, Physical Life Science Building Room 318, Charlottesville, VA 22904, USA
| | - Jeremy Nance
- Skirball Institute of Biomolecular Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
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5
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Guss EJ, Akbergenova Y, Cunningham KL, Littleton JT. Loss of the extracellular matrix protein Perlecan disrupts axonal and synaptic stability during Drosophila development. eLife 2023; 12:RP88273. [PMID: 37368474 PMCID: PMC10328508 DOI: 10.7554/elife.88273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Heparan sulfate proteoglycans (HSPGs) form essential components of the extracellular matrix (ECM) and basement membrane (BM) and have both structural and signaling roles. Perlecan is a secreted ECM-localized HSPG that contributes to tissue integrity and cell-cell communication. Although a core component of the ECM, the role of Perlecan in neuronal structure and function is less understood. Here, we identify a role for Drosophila Perlecan in the maintenance of larval motoneuron axonal and synaptic stability. Loss of Perlecan causes alterations in the axonal cytoskeleton, followed by axonal breakage and synaptic retraction of neuromuscular junctions. These phenotypes are not prevented by blocking Wallerian degeneration and are independent of Perlecan's role in Wingless signaling. Expression of Perlecan solely in motoneurons cannot rescue synaptic retraction phenotypes. Similarly, removing Perlecan specifically from neurons, glia, or muscle does not cause synaptic retraction, indicating the protein is secreted from multiple cell types and functions non-cell autonomously. Within the peripheral nervous system, Perlecan predominantly localizes to the neural lamella, a specialized ECM surrounding nerve bundles. Indeed, the neural lamella is disrupted in the absence of Perlecan, with axons occasionally exiting their usual boundary in the nerve bundle. In addition, entire nerve bundles degenerate in a temporally coordinated manner across individual hemi-segments throughout larval development. These observations indicate disruption of neural lamella ECM function triggers axonal destabilization and synaptic retraction of motoneurons, revealing a role for Perlecan in axonal and synaptic integrity during nervous system development.
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Affiliation(s)
- Ellen J Guss
- The Picower Institute for Learning and Memory, Department of Biology, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, United States
| | - Yulia Akbergenova
- The Picower Institute for Learning and Memory, Department of Biology, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, United States
| | - Karen L Cunningham
- The Picower Institute for Learning and Memory, Department of Biology, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, United States
| | - J Troy Littleton
- The Picower Institute for Learning and Memory, Department of Biology, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, United States
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Gianakas CA, Keeley DP, Ramos-Lewis W, Park K, Jayadev R, Kenny IW, Chi Q, Sherwood DR. Hemicentin-mediated type IV collagen assembly strengthens juxtaposed basement membrane linkage. J Cell Biol 2022; 222:213571. [PMID: 36282214 PMCID: PMC9597354 DOI: 10.1083/jcb.202112096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 08/16/2022] [Accepted: 09/26/2022] [Indexed: 01/07/2023] Open
Abstract
Basement membrane (BM) matrices surround and separate most tissues. However, through poorly understood mechanisms, BMs of adjacent tissue can also stably link to support organ structure and function. Using endogenous knock-in fluorescent proteins, conditional RNAi, optogenetics, and quantitative live imaging, we identified extracellular matrix proteins mediating a BM linkage (B-LINK) between the uterine utse and epidermal seam cell BMs in Caenorhabditis elegans that supports the uterus during egg-laying. We found that hemicentin is secreted by the utse and promotes fibulin-1 assembly to jointly initiate the B-LINK. During egg-laying, however, both proteins' levels decline and are not required for B-LINK maintenance. Instead, we discovered that hemicentin recruits ADAMTS9/20, which facilitates the assembly of high levels of type IV collagen that sustains the B-LINK during the mechanically active egg-laying period. This work reveals mechanisms underlying BM-BM linkage maturation and identifies a crucial function for hemicentin and fibulin-1 in initiating attachment and type IV collagen in strengthening this specialized form of tissue linkage.
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Affiliation(s)
- Claire A. Gianakas
- Department of Biology, Duke University, Durham, NC,Department of Pharmacology and Cancer Biology, Duke University, Durham, NC
| | | | | | - Kieop Park
- Department of Biology, Duke University, Durham, NC
| | | | | | - Qiuyi Chi
- Department of Biology, Duke University, Durham, NC
| | - David R. Sherwood
- Department of Biology, Duke University, Durham, NC,Department of Pharmacology and Cancer Biology, Duke University, Durham, NC,Correspondence to David R. Sherwood:
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Karengera A, Verburg I, Sterken MG, Riksen JAG, Murk AJ, Dinkla IJT. Determining Toxic Potencies of Water-Soluble Contaminants in Wastewater Influents and Effluent Using Gene Expression Profiling in C. elegans as a Bioanalytical Tool. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 83:284-294. [PMID: 36190544 PMCID: PMC9556352 DOI: 10.1007/s00244-022-00959-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
With chemical analysis, it is impossible to qualify and quantify the toxic potency of especially hydrophilic bioactive contaminants. In this study, we applied the nematode C. elegans as a model organism for detecting the toxic potency of whole influent wastewater samples. Gene expression in the nematode was used as bioanalytical tool to reveal the presence, type and potency of molecular pathways induced by 24-h exposure to wastewater from a hospital (H), nursing home (N), community (C), and influent (I) and treated effluent (E) from a local wastewater treatment plant. Exposure to influent water significantly altered expression of 464 genes, while only two genes were differentially expressed in nematodes treated with effluent. This indicates a significant decrease in bioactive pollutant-load after wastewater treatment. Surface water receiving the effluent did not induce any genes in exposed nematodes. A subset of 209 genes was differentially expressed in all untreated wastewaters, including cytochromes P450 and C-type lectins related to the nematode's xenobiotic metabolism and immune response, respectively. Different subsets of genes responded to particular waste streams making them candidates to fingerprint-specific wastewater sources. This study shows that gene expression profiling in C. elegans can be used for mechanism-based identification of hydrophilic bioactive compounds and fingerprinting of specific wastewaters. More comprehensive than with chemical analysis, it can demonstrate the effective overall removal of bioactive compounds through wastewater treatment. This bioanalytical tool can also be applied in the process of identification of the bioactive compounds via a process of toxicity identification evaluation.
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Affiliation(s)
- Antoine Karengera
- Department of Animal Sciences, Marine Animal Ecology Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Ilse Verburg
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Mark G. Sterken
- Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Joost A. G. Riksen
- Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Albertinka J. Murk
- Department of Animal Sciences, Marine Animal Ecology Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Inez J. T. Dinkla
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
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8
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Ochs ME, McWhirter RM, Unckless RL, Miller DM, Lundquist EA. Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration. BMC Genomics 2022; 23:13. [PMID: 34986795 PMCID: PMC8734324 DOI: 10.1186/s12864-021-08217-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/23/2021] [Indexed: 11/18/2022] Open
Abstract
Migration of neuroblasts and neurons from their birthplace is central to the formation of neural circuits and networks. ETR-1 is the Caenorhabditis elegans homolog of the CELF1 (CUGBP, ELAV-like family 1) RNA-processing factor involved in neuromuscular disorders. etr-1 regulates body wall muscle differentiation. Our previous work showed that etr-1 in muscle has a non-autonomous role in neuronal migration, suggesting that ETR-1 is involved in the production of a signal emanating from body wall muscle that controls neuroblast migration and that interacts with Wnt signaling. etr-1 is extensively alternatively-spliced, and we identified the viable etr-1(lq61) mutant, caused by a stop codon in alternatively-spliced exon 8 and only affecting etr-1 isoforms containing exon 8. We took advantage of viable etr-1(lq61) to identify potential RNA targets of ETR-1 in body wall muscle using a combination of fluorescence activated cell sorting (FACS) of body wall muscles from wild-type and etr-1(lq61) and subsequent RNA-seq. This analysis revealed genes whose splicing and transcript levels were controlled by ETR-1 exon 8 isoforms, and represented a broad spectrum of genes involved in muscle differentiation, myofilament lattice structure, and physiology. Genes with transcripts underrepresented in etr-1(lq61) included those involved in ribosome function and translation, similar to potential CELF1 targets identified in chick cardiomyocytes. This suggests that at least some targets of ETR-1 might be conserved in vertebrates, and that ETR-1 might generally stimulate translation in muscles. As proof-of-principle, a functional analysis of a subset of ETR-1 targets revealed genes involved in AQR and PQR neuronal migration. One such gene, lev-11/tropomyosin, requires ETR-1 for alternative splicing, and another, unc-52/perlecan, requires ETR-1 for the production of long isoforms containing 3' exons. In sum, these studies identified gene targets of ETR-1/CELF1 in muscles, which included genes involved in muscle development and physiology, and genes with novel roles in neuronal migration.
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Affiliation(s)
- Matthew E Ochs
- Program in Molecular, Cellular, and Developmental Biology, Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Rebecca M McWhirter
- Department of Cell and Developmental Biology and Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37203, USA
| | - Robert L Unckless
- Program in Molecular, Cellular, and Developmental Biology, Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - David M Miller
- Department of Cell and Developmental Biology and Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37203, USA
| | - Erik A Lundquist
- Program in Molecular, Cellular, and Developmental Biology, Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA.
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9
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Qiu Z, Park A, Wang L, Wilsey R, Lee M. The RGD (Arg-Gly-Asp) is a potential cell-binding motif of UNC-52/PERLECAN. Biochem Biophys Res Commun 2022; 586:143-149. [PMID: 34844120 DOI: 10.1016/j.bbrc.2021.11.083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/29/2022]
Abstract
UNC-52/perlecan is a basement membrane (BM) proteoglycan playing an essential role in the muscle cell attachment of C. elegans. The UNC-52 protein contains two RGD (Arg-Gly-Asp) motifs in domains III and IV, a well-characterized tripeptide known for binding to mammalian β integrin. To investigate the role of the RGD motif in UNC-52/perlecan, we created two mutations in the 2021RGD2023 motif: one mutation changed the RGD to an RGE, and the other deleted the RGD motif. The RGE2023 caused defective actin filaments and aberrant localization of PAT-3 β integrin and TLN-1/talin. Additionally, the in-frame deletion of RGD2023 resulted in a paralyzed and arrested at two-fold embryonic stages (Pat) phenotype, which is the identical phenotype of the pat-3 β integrin null allele. These results indicate that RGD2023 is a potential ligand for cell binding and is essential for development and survival. Furthermore, our analysis reveals that the RGD of an invertebrate BM molecule is a potential cell-binding motif, suggesting that the function of the RGD motif is conserved among species.
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Affiliation(s)
- Zhongqiang Qiu
- Department of Biology, Baylor University, Waco, TX, 76798, USA
| | - Aileen Park
- Department of Biology, Baylor University, Waco, TX, 76798, USA
| | - Lianzijun Wang
- Department of Biology, Baylor University, Waco, TX, 76798, USA
| | - Rachel Wilsey
- Department of Biology, Baylor University, Waco, TX, 76798, USA
| | - Myeongwoo Lee
- Department of Biology, Baylor University, Waco, TX, 76798, USA.
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10
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Abstract
Establishment of neural circuits requires reproducible and precise interactions between growing axons, dendrites and their tissue environment. Cell adhesion molecules and guidance factors are involved in the process, but how specificity is achieved remains poorly understood. Glycans are the third major class of biopolymers besides nucleic acids and proteins, and are usually covalently linked to proteins to form glycoconjugates. Common to most glycans is an extraordinary level of molecular diversity, making them attractive candidates to contribute specificity during neural development. Indeed, many genes important for neural development encode glycoproteins, or enzymes involved in synthesizing or modifying glycans. Glycoconjugates are classified based on both the types of glycans and type of attachment that link them to proteins. Here I discuss progress in understanding the function of glycans, glycan modifications and glycoconjugates during neural development in Caenorhabditis elegans. I will also highlight relevance to human disease and known roles of glycoconjugates in regeneration.
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Affiliation(s)
- Hannes E Bülow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States; Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States.
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11
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Kalichamy SS, Alcantara AV, Kim BS, Park J, Yoon KH, Lee JI. Muscle and epidermal contributions of the structural protein β-spectrin promote hypergravity-induced motor neuron axon defects in C. elegans. Sci Rep 2020; 10:21214. [PMID: 33273580 PMCID: PMC7713079 DOI: 10.1038/s41598-020-78414-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/23/2020] [Indexed: 11/09/2022] Open
Abstract
Biology is adapted to Earth's gravity force, and the long-term effects of varying gravity on the development of animals is unclear. Previously, we reported that high gravity, called hypergravity, increases defects in the development of motor neuron axons in the nematode Caenorhabditis elegans. Here, we show that a mutation in the unc-70 gene that encodes the cytoskeletal β-spectrin protein suppresses hypergravity-induced axon defects. UNC-70 expression is required in both muscle and epidermis to promote the axon defects in high gravity. We reveal that the location of axon defects is correlated to the size of the muscle cell that the axon traverses. We also show that mutations that compromise key proteins of hemidesmosomal structures suppress hypergravity-induced axon defects. These hemidesmosomal structures play a crucial role in coupling mechanical force between the muscle, epidermis and the external cuticle. We speculate a model in which the rigid organization of muscle, epidermal and cuticular layers under high gravity pressure compresses the narrow axon migration pathways in the extracellular matrix hindering proper axon pathfinding of motor neurons.
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Affiliation(s)
- Saraswathi S Kalichamy
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Mirae Campus 304, 1 Yonseidae-gil, Wonju, Gangwon-do, 26493, South Korea
| | - Alfredo V Alcantara
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Mirae Campus 304, 1 Yonseidae-gil, Wonju, Gangwon-do, 26493, South Korea
| | - Ban-Seok Kim
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Mirae Campus 304, 1 Yonseidae-gil, Wonju, Gangwon-do, 26493, South Korea
| | - Junsoo Park
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Mirae Campus 304, 1 Yonseidae-gil, Wonju, Gangwon-do, 26493, South Korea
| | - Kyoung-Hye Yoon
- Department of Physiology, Mitohormesis Research Center, Yonsei University Wonju College of Medicine, Wonju, Gangwon-do, 26426, South Korea.
| | - Jin I Lee
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Mirae Campus 304, 1 Yonseidae-gil, Wonju, Gangwon-do, 26493, South Korea.
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Wang C, Yang Y, Fu R, Zhu Y, Zhang H. Periodic subcellular structures undergo long-range synchronized reorganization during C. elegans epidermal development. J Cell Sci 2020; 133:jcs246793. [PMID: 33033182 PMCID: PMC10682509 DOI: 10.1242/jcs.246793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 10/01/2020] [Indexed: 01/22/2023] Open
Abstract
Periodic pattern formation on the cellular and tissue scale is an important process and has been extensively studied. However, periodic pattern formation at the subcellular level still remains poorly understood. The C. elegans epidermis displays a highly ordered parallel stripe pattern as part of its subcellular structure, making it an ideal model to study the formation and reorganization of periodic patterns within cells. Here, we show that the initial formation of periodic striped patterns in the C. elegans epidermis is dependent on actin and spectrin, and requires the apical membrane attachment structures for maintenance. The periodic subcellular structures do not accommodate cell growth by continuously making new stripes. Instead, they increase the number of stripes by going through one round of uniform duplication, which is independent of the increasing epidermal length or the developmental cycles. This long-range synchronized reorganization of subcellular structures is achieved by physical links established by extracellular collagens together with extension forces generated from epidermal cell growth. Our studies uncover a novel strategy employed by evenly spaced and interlinked subcellular structures to maintain their integrity and equidistribution during cell growth and tissue development.
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Affiliation(s)
- Chunxia Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Yuyan Yang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Rong Fu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Yi Zhu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Huimin Zhang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
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Fu R, Huang Z, Li H, Zhu Y, Zhang H. A Hemidesmosome-to-Cytoplasm Translocation of Small Heat Shock Proteins Provides Immediate Protection against Heat Stress. Cell Rep 2020; 33:108410. [DOI: 10.1016/j.celrep.2020.108410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/28/2020] [Accepted: 10/29/2020] [Indexed: 02/08/2023] Open
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14
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Kobaisi F, Fayyad N, Sulpice E, Badran B, Fayyad-Kazan H, Rachidi W, Gidrol X. High-throughput synthetic rescue for exhaustive characterization of suppressor mutations in human genes. Cell Mol Life Sci 2020; 77:4209-4222. [PMID: 32270227 PMCID: PMC7588364 DOI: 10.1007/s00018-020-03519-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/21/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023]
Abstract
Inherited or acquired mutations can lead to pathological outcomes. However, in a process defined as synthetic rescue, phenotypic outcome created by primary mutation is alleviated by suppressor mutations. An exhaustive characterization of these mutations in humans is extremely valuable to better comprehend why patients carrying the same detrimental mutation exhibit different pathological outcomes or different responses to treatment. Here, we first review all known suppressor mutations' mechanisms characterized by genetic screens on model species like yeast or flies. However, human suppressor mutations are scarce, despite some being discovered based on orthologue genes. Because of recent advances in high-throughput screening, developing an inventory of human suppressor mutations for pathological processes seems achievable. In addition, we review several screening methods for suppressor mutations in cultured human cells through knock-out, knock-down or random mutagenesis screens on large scale. We provide examples of studies published over the past years that opened new therapeutic avenues, particularly in oncology.
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Affiliation(s)
- Farah Kobaisi
- University of Grenoble Alpes, CEA, INSERM, IRIG-BGE U1038, 38000, Grenoble, France
- Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Hadath, Lebanon
- University of Grenoble Alpes, SYMMES/CIBEST UMR 5819 UGA-CNRS-CEA, IRIG/CEA-Grenoble, Grenoble, France
| | - Nour Fayyad
- University of Grenoble Alpes, SYMMES/CIBEST UMR 5819 UGA-CNRS-CEA, IRIG/CEA-Grenoble, Grenoble, France
| | - Eric Sulpice
- University of Grenoble Alpes, CEA, INSERM, IRIG-BGE U1038, 38000, Grenoble, France
| | - Bassam Badran
- Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Hadath, Lebanon
| | - Hussein Fayyad-Kazan
- Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Hadath, Lebanon
| | - Walid Rachidi
- University of Grenoble Alpes, SYMMES/CIBEST UMR 5819 UGA-CNRS-CEA, IRIG/CEA-Grenoble, Grenoble, France
| | - Xavier Gidrol
- University of Grenoble Alpes, CEA, INSERM, IRIG-BGE U1038, 38000, Grenoble, France.
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15
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Wilsey R, Hodge S, Kenney K, Wahl J, Jaffery R, Brau A, Qiu Z, Lee M. Two alleles of unc-52 locus disrupting potential cell-binding motif of UNC-52. MICROPUBLICATION BIOLOGY 2020; 2020. [PMID: 32550495 PMCID: PMC7252330 DOI: 10.17912/micropub.biology.000250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rachel Wilsey
- One Bear Place 97388, Department of Biology, Baylor University, Waco, TX 76798, U.S.A
| | - Sabrina Hodge
- One Bear Place 97388, Department of Biology, Baylor University, Waco, TX 76798, U.S.A
| | - Krysta Kenney
- One Bear Place 97388, Department of Biology, Baylor University, Waco, TX 76798, U.S.A
| | - Jacob Wahl
- One Bear Place 97388, Department of Biology, Baylor University, Waco, TX 76798, U.S.A
| | - Roshni Jaffery
- One Bear Place 97388, Department of Biology, Baylor University, Waco, TX 76798, U.S.A
| | - Avery Brau
- One Bear Place 97388, Department of Biology, Baylor University, Waco, TX 76798, U.S.A
| | - Zhongqiang Qiu
- One Bear Place 97388, Department of Biology, Baylor University, Waco, TX 76798, U.S.A
| | - Myeongwoo Lee
- One Bear Place 97388, Department of Biology, Baylor University, Waco, TX 76798, U.S.A
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16
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Warner AD, Gevirtzman L, Hillier LW, Ewing B, Waterston RH. The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution. Genome Res 2019; 29:1036-1045. [PMID: 31123079 PMCID: PMC6581053 DOI: 10.1101/gr.243394.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 03/11/2019] [Indexed: 12/22/2022]
Abstract
We have used RNA-seq in Caenorhabditis elegans to produce transcription profiles for seven specific embryonic cell populations from gastrulation to the onset of terminal differentiation. The expression data for these seven cell populations, covering major cell lineages and tissues in the worm, reveal the complex and dynamic changes in gene expression, both spatially and temporally. Also, within genes, start sites and exon usage can be highly differential, producing transcripts that are specific to developmental periods or cell lineages. We have also found evidence of novel exons and introns, as well as differential usage of SL1 and SL2 splice leaders. By combining this data set with the modERN ChIP-seq resource, we are able to support and predict gene regulatory relationships. The detailed information on differences and similarities between gene expression in cell lineages and tissues should be of great value to the community and provides a framework for the investigation of expression in individual cells.
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Affiliation(s)
- Adam D Warner
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Louis Gevirtzman
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - LaDeana W Hillier
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Brent Ewing
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Robert H Waterston
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA
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17
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Multiple Pathways Act Together To Establish Asymmetry of the Ventral Nerve Cord in Caenorhabditis elegans. Genetics 2019; 211:1331-1343. [PMID: 30792268 DOI: 10.1534/genetics.119.301999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/15/2019] [Indexed: 01/30/2023] Open
Abstract
The central nervous system of most animals is bilaterally symmetrical. Closer observation often reveals some functional or anatomical left-right asymmetries. In the nematode Caenorhabditis elegans, the most obvious asymmetry in the nervous system is found in the ventral nerve cord (VNC), where most axons are in the right axon tract. The asymmetry is established when axons entering the VNC from the brain switch from the left to the right side at the anterior end of the VNC. In genetic screens we identified several mutations compromising VNC asymmetry. This includes alleles of col-99 (encoding a transmembrane collagen), unc-52/perlecan and unc-34 (encoding the actin modulator Enabled/Vasodilator-stimulated phosphoproteins). In addition, we evaluated mutants in known axon guidance pathways for asymmetry defects and used genetic interaction studies to place the genes into genetic pathways. In total we identified four different pathways contributing to the establishment of VNC asymmetry, represented by UNC-6/netrin, SAX-3/Robo, COL-99, and EPI-1/laminin. The combined inactivation of these pathways in triple and quadruple mutants leads to highly penetrant VNC asymmetry defects, suggesting these pathways are important contributors to the establishment of VNC asymmetry in C. elegans.
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18
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Fu R, Zhu Y, Jiang X, Li Y, Zhu M, Dong M, Huang Z, Wang C, Labouesse M, Zhang H. CCAR-1 affects hemidesmosome biogenesis by regulating unc-52/perlecan alternative splicing in the C. elegans epidermis. J Cell Sci 2018; 131:jcs.214379. [PMID: 29748380 DOI: 10.1242/jcs.214379] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/02/2018] [Indexed: 12/31/2022] Open
Abstract
Hemidesmosomes are epithelial-specific attachment structures that maintain tissue integrity and resist tension. Despite their importance, how hemidesmosomes are regulated at the post-transcriptional level is poorly understood. Caenorhabditiselegans hemidesmosomes (CeHDs) have a similar structure and composition to their mammalian counterparts, making C. elegans an ideal model for studying hemidesmosomes. Here, we focus on the transcription regulator CCAR-1, identified in a previous genetic screen searching for enhancers of mutations in the conserved hemidesmosome component VAB-10A (known as plectin in mammals). Loss of CCAR-1 function in a vab-10(e698) background results in CeHD disruption and muscle detachment from the epidermis. CCAR-1 regulates CeHD biogenesis, not by controlling the transcription of CeHD-related genes, but by affecting the alternative splicing of unc-52 (known as perlecan or HSPG2 in mammals), the predicted basement extracellular matrix (ECM) ligand of CeHDs. CCAR-1 physically interacts with HRP-2 (hnRNPR in mammals), a splicing factor known to mediate unc-52 alternative splicing to control the proportions of different UNC-52 isoforms and stabilize CeHDs. Our discovery underlines the importance of post-transcriptional regulation in hemidesmosome reorganization. It also uncovers previously unappreciated roles of CCAR-1 in alternative splicing and hemidesmosome biogenesis, shedding new light on the mechanisms through which mammalian CCAR1 functions in tumorigenesis.
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Affiliation(s)
- Rong Fu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Yi Zhu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Xiaowan Jiang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Yuanbao Li
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Ming Zhu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Mengqiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhaohui Huang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Chunxia Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Michel Labouesse
- Institut de Biologie Paris Seine, Université Pierre et Marie Curie, Paris 75005, France
| | - Huimin Zhang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
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19
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Celestrin K, Díaz-Balzac CA, Tang LTH, Ackley BD, Bülow HE. Four specific immunoglobulin domains in UNC-52/Perlecan function with NID-1/Nidogen during dendrite morphogenesis in Caenorhabditis elegans. Development 2018; 145:dev.158881. [PMID: 29678816 DOI: 10.1242/dev.158881] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 04/11/2018] [Indexed: 12/21/2022]
Abstract
The extracellular matrix is essential for various aspects of nervous system patterning. For example, sensory dendrites in flies, worms and fish have been shown to rely on coordinated interactions of tissues with extracellular matrix proteins. Here we show that the conserved basement membrane protein UNC-52/Perlecan is required for establishing the correct number of the highly ordered dendritic trees in the somatosensory neuron PVD in Caenorhabditis elegans This function is dependent on four specific immunoglobulin domains, but independent of the known functions of UNC-52 in mediating muscle-skin attachment. Intriguingly, the four conserved immunoglobulin domains in UNC-52 are necessary to correctly localize the basement membrane protein NID-1/Nidogen. Genetic experiments further show that unc-52, nid-1 and genes of the netrin axon guidance signaling cassette share a common pathway to establish the correct number of somatosensory dendrites. Our studies suggest that, in addition to its role in mediating muscle-skin attachment, UNC-52 functions through immunoglobulin domains to establish an ordered lattice of basement membrane proteins, which may control the function of morphogens during dendrite patterning.
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Affiliation(s)
- Kevin Celestrin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Carlos A Díaz-Balzac
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Leo T H Tang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Brian D Ackley
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, KS 66045, USA
| | - Hannes E Bülow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA .,Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
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20
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Gotenstein JR, Koo CC, Ho TW, Chisholm AD. Genetic Suppression of Basement Membrane Defects in Caenorhabditis elegans by Gain of Function in Extracellular Matrix and Cell-Matrix Attachment Genes. Genetics 2018; 208:1499-1512. [PMID: 29440357 PMCID: PMC5887144 DOI: 10.1534/genetics.118.300731] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/05/2018] [Indexed: 11/18/2022] Open
Abstract
Basement membranes are extracellular matrices essential for embryonic development in animals. Peroxidasins are extracellular peroxidases implicated in the unique sulfilimine cross-links between type IV basement membrane collagens. Loss of function in the Caenorhabditis elegans peroxidasin PXN-2 results in fully penetrant embryonic or larval lethality. Using genetic suppressor screening, we find that the requirement for PXN-2 in development can be bypassed by gain of function in multiple genes encoding other basement membrane components, or proteins implicated in cell-matrix attachment. We identify multiple alleles of let-805, encoding the transmembrane protein myotactin, which suppress phenotypes of pxn-2 null mutants and of other basement membrane mutants such as F-spondin/spon-1 These let-805 suppressor alleles cause missense alterations in two pairs of FNIII repeats in the extracellular domain; they act dominantly and have no detectable phenotypes alone, suggesting they cause gain of function. We also identify suppressor missense mutations affecting basement membrane components type IV collagen (emb-9, let-2) and perlecan (unc-52), as well as a mutation affecting spectraplakin (vab-10), a component of the epidermal cytoskeleton. These suppressor alleles do not bypass the developmental requirement for core structural proteins of the basement membrane such as laminin or type IV collagen. In conclusion, putative gain-of-function alterations in matrix proteins or in cell-matrix receptors can overcome the requirement for certain basement membrane proteins in embryonic development, revealing previously unknown plasticity in the genetic requirements for the extracellular matrix.
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Affiliation(s)
- Jennifer R Gotenstein
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Cassidy C Koo
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Tiffany W Ho
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Andrew D Chisholm
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
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21
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MIP-MAP: High-Throughput Mapping of Caenorhabditis elegans Temperature-Sensitive Mutants via Molecular Inversion Probes. Genetics 2017; 207:447-463. [PMID: 28827289 PMCID: PMC5629315 DOI: 10.1534/genetics.117.300179] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/30/2017] [Indexed: 11/18/2022] Open
Abstract
Mutants remain a powerful means for dissecting gene function in model organisms such as Caenorhabditis elegans. Massively parallel sequencing has simplified the detection of variants after mutagenesis but determining precisely which change is responsible for phenotypic perturbation remains a key step. Genetic mapping paradigms in C. elegans rely on bulk segregant populations produced by crosses with the problematic Hawaiian wild isolate and an excess of redundant information from whole-genome sequencing (WGS). To increase the repertoire of available mutants and to simplify identification of the causal change, we performed WGS on 173 temperature-sensitive (TS) lethal mutants and devised a novel mapping method. The mapping method uses molecular inversion probes (MIP-MAP) in a targeted sequencing approach to genetic mapping, and replaces the Hawaiian strain with a Million Mutation Project strain with high genomic and phenotypic similarity to the laboratory wild-type strain N2. We validated MIP-MAP on a subset of the TS mutants using a competitive selection approach to produce TS candidate mapping intervals with a mean size < 3 Mb. MIP-MAP successfully uses a non-Hawaiian mapping strain and multiplexed libraries are sequenced at a fraction of the cost of WGS mapping approaches. Our mapping results suggest that the collection of TS mutants contains a diverse library of TS alleles for genes essential to development and reproduction. MIP-MAP is a robust method to genetically map mutations in both viable and essential genes and should be adaptable to other organisms. It may also simplify tracking of individual genotypes within population mixtures.
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22
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Gubbiotti MA, Neill T, Iozzo RV. A current view of perlecan in physiology and pathology: A mosaic of functions. Matrix Biol 2016; 57-58:285-298. [PMID: 27613501 DOI: 10.1016/j.matbio.2016.09.003] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/01/2016] [Indexed: 01/06/2023]
Abstract
Perlecan, a large basement membrane heparan sulfate proteoglycan, is expressed in a wide array of tissues where it regulates diverse cellular processes including bone formation, inflammation, cardiac development, and angiogenesis. Here we provide a contemporary review germane to the biology of perlecan encompassing its genetic regulation as well as an analysis of its modular protein structure as it pertains to function. As perlecan signaling from the extracellular matrix converges on master regulators of autophagy, including AMPK and mTOR, via a specific interaction with vascular endothelial growth factor receptor 2, we specifically focus on the mechanism of action of perlecan in autophagy and angiogenesis and contrast the role of endorepellin, the C-terminal fragment of perlecan, in these cellular and morphogenic events.
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Affiliation(s)
- Maria A Gubbiotti
- Department of Pathology, Anatomy, and Cell Biology and the Cancer Cell Biology and Signaling Program, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
| | - Thomas Neill
- Department of Pathology, Anatomy, and Cell Biology and the Cancer Cell Biology and Signaling Program, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
| | - Renato V Iozzo
- Department of Pathology, Anatomy, and Cell Biology and the Cancer Cell Biology and Signaling Program, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States.
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23
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Kumar J, Barhydt T, Awasthi A, Lithgow GJ, Killilea DW, Kapahi P. Zinc Levels Modulate Lifespan through Multiple Longevity Pathways in Caenorhabditis elegans. PLoS One 2016; 11:e0153513. [PMID: 27078872 PMCID: PMC4831763 DOI: 10.1371/journal.pone.0153513] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 03/30/2016] [Indexed: 12/22/2022] Open
Abstract
Zinc is an essential trace metal that has integral roles in numerous biological processes, including enzymatic function, protein structure, and cell signaling pathways. Both excess and deficiency of zinc can lead to detrimental effects on development and metabolism, resulting in abnormalities and disease. We altered the zinc balance within Caenorhabditis elegans to examine how changes in zinc burden affect longevity and healthspan in an invertebrate animal model. We found that increasing zinc levels in vivo with excess dietary zinc supplementation decreased the mean and maximum lifespan, whereas reducing zinc levels in vivo with a zinc-selective chelator increased the mean and maximum lifespan in C. elegans. We determined that the lifespan shortening effects of excess zinc required expression of DAF-16, HSF-1 and SKN-1 proteins, whereas the lifespan lengthening effects of the reduced zinc may be partially dependent upon this set of proteins. Furthermore, reducing zinc levels led to greater nuclear localization of DAF-16 and enhanced dauer formation compared to controls, suggesting that the lifespan effects of zinc are mediated in part by the insulin/IGF-1 pathway. Additionally, zinc status correlated with several markers of healthspan in worms, including proteostasis, locomotion and thermotolerance, with reduced zinc levels always associated with improvements in function. Taken together, these data support a role for zinc in regulating both development and lifespan in C. elegans, and that suggest that regulation of zinc homeostasis in the worm may be an example of antagonistic pleiotropy.
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Affiliation(s)
- Jitendra Kumar
- The Buck Institute for Research on Aging, Novato, California, United States of America
- DBT-PU-IPLS Programme, Department of Botany/Biotechnology, Patna University, Patna- 800005, Bihar, India
- * E-mail: (PK); (DWK); (JK)
| | - Tracy Barhydt
- The Buck Institute for Research on Aging, Novato, California, United States of America
| | - Anjali Awasthi
- Department of Biological Sciences, Birla Institute of Technology and Science, Rajasthan, India
| | - Gordon J. Lithgow
- The Buck Institute for Research on Aging, Novato, California, United States of America
| | - David W. Killilea
- Nutrition & Metabolism Center, Children’s Hospital of Oakland Research Institute, Oakland, California, United States of America
- * E-mail: (PK); (DWK); (JK)
| | - Pankaj Kapahi
- The Buck Institute for Research on Aging, Novato, California, United States of America
- * E-mail: (PK); (DWK); (JK)
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Rahmani P, Rogalski T, Moerman DG. The C. elegans UNC-23 protein, a member of the BCL-2-associated athanogene (BAG) family of chaperone regulators, interacts with HSP-1 to regulate cell attachment and maintain hypodermal integrity. WORM 2015; 4:e1023496. [PMID: 26435886 PMCID: PMC4590010 DOI: 10.1080/21624054.2015.1023496] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 02/11/2015] [Accepted: 02/20/2015] [Indexed: 11/19/2022]
Abstract
Mutations in the unc-23 gene in the free-living nematode, Caenorhabditis elegans result in detachment and dystrophy of the anterior body wall musculature and a bent-head phenotype when grown on solid substrate. We have determined that the unc-23 gene product is the nematode ortholog of the human BAG-2 protein, a member of the Bcl-2 associated athanogene (BAG) family of molecular chaperone regulators. We show that a functional GFP-tagged UNC-23 protein is expressed throughout development in several tissues of the animal, including body wall muscle and hypodermis, and associates with adhesion complexes and attachment structures within these 2 tissues. In humans, the BAG protein family consists of 6 members that all contain a conserved 45 amino acid BAG domain near their C-termini. These proteins bind to and modulate the activity of the ATPase domain of the heat shock cognate protein 70, Hsc70. We have isolated missense mutations in the ATPase domain of the C. elegans heat shock 70 protein, HSP-1 that suppress the phenotype exhibited by unc-23(e25) mutant hermaphrodites and we show that UNC-23 and HSP-1 interact in a yeast-2-hybrid system. The interaction of UNC-23 with HSP-1 defines a role for HSP-1 function in the maintenance of muscle attachment during development.
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Affiliation(s)
- Poupak Rahmani
- Department of Zoology; University of British Columbia ; Vancouver, British Columbia, Canada
| | - Teresa Rogalski
- Department of Zoology; University of British Columbia ; Vancouver, British Columbia, Canada
| | - Donald G Moerman
- Department of Zoology; University of British Columbia ; Vancouver, British Columbia, Canada
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25
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Basement Membranes in the Worm: A Dynamic Scaffolding that Instructs Cellular Behaviors and Shapes Tissues. CURRENT TOPICS IN MEMBRANES 2015; 76:337-71. [PMID: 26610919 DOI: 10.1016/bs.ctm.2015.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The nematode worm Caenorhabditis elegans has all the major basement membrane proteins found in vertebrates, usually with a smaller gene family encoding each component. With its powerful forward genetics, optical clarity, simple tissue organization, and the capability to functionally tag most basement membrane components with fluorescent proteins, C. elegans has facilitated novel insights into the assembly and function of basement membranes. Although basement membranes are generally thought of as static structures, studies in C. elegans have revealed their active properties and essential functions in tissue formation and maintenance. Here, we review discoveries from C. elegans development that highlight dynamic aspects of basement membrane assembly, function, and regulation during organ growth, tissue polarity, cell migration, cell invasion, and tissue attachment. These studies have helped transform our view of basement membranes from static support structures to dynamic scaffoldings that play broad roles in regulating tissue organization and cellular behavior that are essential for development and have important implications in human diseases.
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26
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Liang X, Dong X, Moerman DG, Shen K, Wang X. Sarcomeres Pattern Proprioceptive Sensory Dendritic Endings through UNC-52/Perlecan in C. elegans. Dev Cell 2015; 33:388-400. [PMID: 25982673 DOI: 10.1016/j.devcel.2015.03.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 01/18/2015] [Accepted: 03/06/2015] [Indexed: 12/31/2022]
Abstract
Sensory dendrites innervate peripheral tissues through cell-cell interactions that are poorly understood. The proprioceptive neuron PVD in C. elegans extends regular terminal dendritic branches between muscle and hypodermis. We found that the PVD branch pattern was instructed by adhesion molecule SAX-7/L1CAM, which formed regularly spaced stripes on the hypodermal cell. The regularity of the SAX-7 pattern originated from the repeated and regularly spaced dense body of the sarcomeres in the muscle. The extracellular proteoglycan UNC-52/Perlecan linked the dense body to the hemidesmosome on the hypodermal cells, which in turn instructed the SAX-7 stripes and PVD dendrites. Both UNC-52 and hemidesmosome components exhibited highly regular stripes that interdigitated with the SAX-7 stripe and PVD dendrites, reflecting the striking precision of subcellular patterning between muscle, hypodermis, and dendrites. Hence, the muscular contractile apparatus provides the instructive cues to pattern proprioceptive dendrites.
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Affiliation(s)
- Xing Liang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xintong Dong
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Donald G Moerman
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Kang Shen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| | - Xiangming Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China.
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Khare SM, Awasthi A, Venkataraman V, Koushika SP. Colored polydimethylsiloxane micropillar arrays for high throughput measurements of forces applied by genetic model organisms. BIOMICROFLUIDICS 2015; 9:014111. [PMID: 25713693 PMCID: PMC4312341 DOI: 10.1063/1.4906905] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
Measuring forces applied by multi-cellular organisms is valuable in investigating biomechanics of their locomotion. Several technologies have been developed to measure such forces, for example, strain gauges, micro-machined sensors, and calibrated cantilevers. We introduce an innovative combination of techniques as a high throughput screening tool to assess forces applied by multiple genetic model organisms. First, we fabricated colored Polydimethylsiloxane (PDMS) micropillars where the color enhances contrast making it easier to detect and track pillar displacement driven by the organism. Second, we developed a semi-automated graphical user interface to analyze the images for pillar displacement, thus reducing the analysis time for each animal to minutes. The addition of color reduced the Young's modulus of PDMS. Therefore, the dye-PDMS composite was characterized using Yeoh's hyperelastic model and the pillars were calibrated using a silicon based force sensor. We used our device to measure forces exerted by wild type and mutant Caenorhabditis elegans moving on an agarose surface. Wild type C. elegans exert an average force of ∼1 μN on an individual pillar and a total average force of ∼7.68 μN. We show that the middle of C. elegans exerts more force than its extremities. We find that C. elegans mutants with defective body wall muscles apply significantly lower force on individual pillars, while mutants defective in sensing externally applied mechanical forces still apply the same average force per pillar compared to wild type animals. Average forces applied per pillar are independent of the length, diameter, or cuticle stiffness of the animal. We also used the device to measure, for the first time, forces applied by Drosophila melanogaster larvae. Peristaltic waves occurred at 0.4 Hz applying an average force of ∼1.58 μN on a single pillar. Our colored microfluidic device along with its displacement tracking software allows us to measure forces applied by multiple model organisms that crawl or slither to travel through their environment.
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Affiliation(s)
- Siddharth M Khare
- Department of Physics, Indian Institute of Science , Bangalore 560012, India
| | | | - V Venkataraman
- Department of Physics, Indian Institute of Science , Bangalore 560012, India
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Yang Y, Lee WS, Tang X, Wadsworth WG. Extracellular matrix regulates UNC-6 (netrin) axon guidance by controlling the direction of intracellular UNC-40 (DCC) outgrowth activity. PLoS One 2014; 9:e97258. [PMID: 24824544 PMCID: PMC4019552 DOI: 10.1371/journal.pone.0097258] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/16/2014] [Indexed: 11/18/2022] Open
Abstract
How extracellular molecules influence the direction of axon guidance is poorly understood. The HSN axon of Caenorhabditis elegans is guided towards a ventral source of secreted UNC-6 (netrin). The axon's outgrowth response to UNC-6 is mediated by the UNC-40 (DCC) receptor. We have proposed that in response to the UNC-6 molecule the direction of UNC-40-mediated axon outgrowth is stochastically determined. The direction of guidance is controlled by asymmetric cues, including the gradient of UNC-6, that regulate the probability that UNC-40-mediated axon outgrowth is directed on average, over time, in a specific direction. Here we provide genetic evidence that a specialized extracellular matrix, which lies ventral to the HSN cell body, regulates the probability that UNC-40-mediated axon outgrowth will be directed ventrally towards the matrix. We show that mutations that disrupt the function of proteins associated with this matrix, UNC-52 (perlecan), UNC-112 (kindlin), VAB-19 (Kank), and UNC-97 (PINCH), decrease the probability of UNC-40-mediated axon outgrowth in the ventral direction, while increasing the probability of outgrowth in the anterior and posterior directions. Other results suggest that INA-1 (α integrin) and MIG-15 (NIK kinase) signaling mediate the response in HSN. Although the AVM axon also migrates through this matrix, the mutations have little effect on the direction of AVM axon outgrowth, indicating that responses to the matrix are cell-specific. Together, these results suggest that an extracellular matrix can regulate the direction of UNC-6 guidance by increasing the probability that UNC-40-mediated axon outgrowth activity will be oriented in a specific direction.
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Affiliation(s)
- Yong Yang
- Department of Pathology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Won Suk Lee
- Department of Pathology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Xia Tang
- Department of Pathology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - William G. Wadsworth
- Department of Pathology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
- * E-mail:
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Kuroyanagi H. Switch-like regulation of tissue-specific alternative pre-mRNA processing patterns revealed by customized fluorescence reporters. WORM 2013; 2:e23834. [PMID: 24778931 PMCID: PMC3875643 DOI: 10.4161/worm.23834] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 01/27/2013] [Accepted: 01/30/2013] [Indexed: 12/01/2022]
Abstract
Alternative processing of precursor mRNAs (pre-mRNAs), including alternative transcription start sites, alternative splicing and alternative polyadenylation, is the major source of protein diversity and plays crucial roles in development, differentiation and diseases in higher eukaryotes. It is estimated from microarray analyses and deep sequencing of mRNAs from synchronized worms that up to 25% of protein-coding genes in Caenorhabditis elegans undergo alternative pre-mRNA processing and that many of them are subject to developmental regulation. Recent progress in visualizing the alternative pre-mRNA processing patterns in living worms with custom-designed fluorescence reporters has enabled genetic analyses of the regulatory mechanisms for alternative processing events of interest in vivo. Expression of the tissue-specific isoforms of actin depolymerising factor (ADF)/cofilin, UNC-60A and UNC-60B, is regulated by a combination of alternative splicing and alternative polyadenylation of pre-mRNA from a single gene unc-60. We recently found that muscle-specific splicing regulators ASD-2 and SUP-12 cooperatively switch the pre-mRNA processing patterns of the unc-60 gene in body wall muscles. Here I summarize the bichromatic fluorescence reporter system utilized for visualizing the tissue-specific alternative processing patterns of the unc-60 pre-mRNA. I also discuss the model for the coordinated regulation of the UNC-60B-type pre-mRNA processing in body wall muscles by ASD-2 and SUP-12.
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Affiliation(s)
- Hidehito Kuroyanagi
- Laboratory of Gene Expression; Medical Research Institute; Tokyo Medical and Dental University; Tokyo, Japan
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Gysi S, Rhiner C, Flibotte S, Moerman DG, Hengartner MO. A network of HSPG core proteins and HS modifying enzymes regulates netrin-dependent guidance of D-type motor neurons in Caenorhabditis elegans. PLoS One 2013; 8:e74908. [PMID: 24066155 PMCID: PMC3774775 DOI: 10.1371/journal.pone.0074908] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 08/07/2013] [Indexed: 11/18/2022] Open
Abstract
Heparan sulfate proteoglycans (HSPGs) are proteins with long covalently attached sugar side chains of the heparan sulfate (HS) type. Depending on the cellular context HS chains carry multiple structural modifications such as sulfate residues or epimerized sugars allowing them to bind to a wide range of molecules. HSPGs have been found to play extremely diverse roles in animal development and were shown to interact with certain axon guidance molecules. In this study we describe the role of the Caenorhabditis elegans HSPG core proteins Syndecan (SDN-1) and Glypican (LON-2) and the HS modifying enzymes in the dorsal guidance of D-type motor axons, a process controlled mainly by the conserved axon guidance molecule UNC-6/Netrin. Our genetic analysis established the specific HS code relevant for this axon guidance event. Using two sensitized genetic backgrounds, we isolated novel components influencing D-type motor axon guidance with a link to HSPGs, as well as new alleles of several previously characterized axon guidance genes. Interestingly, the dorsal axon guidance defects induced by mutations in zfp-1 or lin-35 depended on the transgene oxIs12 used to visualize the D-type motor neurons. oxIs12 is a large multi-copy transgene that enlarges the X chromosome by approximately 20%. In a search for genes with a comparable phenotype we found that a mutation in the known dosage compensation gene dpy-21 showed similar axon guidance defects as zfp-1 or lin-35 mutants. Thus, derepression of genes on X, where many genes relevant for HS dependent axon guidance are located, might also influence axon guidance of D-type motor neurons.
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Affiliation(s)
- Stephan Gysi
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
| | - Christa Rhiner
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Stephane Flibotte
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Donald G. Moerman
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Michael O. Hengartner
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
- * E-mail:
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Farach-Carson MC, Warren CR, Harrington DA, Carson DD. Border patrol: insights into the unique role of perlecan/heparan sulfate proteoglycan 2 at cell and tissue borders. Matrix Biol 2013; 34:64-79. [PMID: 24001398 DOI: 10.1016/j.matbio.2013.08.004] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 08/16/2013] [Accepted: 08/17/2013] [Indexed: 12/11/2022]
Abstract
The extracellular matrix proteoglycan (ECM) perlecan, also known as heparan sulfate proteoglycan 2 or HSPG2, is one of the largest (>200 nm) and oldest (>550 M years) extracellular matrix molecules. In vertebrates, perlecan's five-domain structure contains numerous independently folding modules with sequence similarities to other ECM proteins, all connected like cars into one long, diverse complex train following a unique N-terminal domain I decorated with three long glycosaminoglycan chains, and an additional glycosaminoglycan attachment site in the C-terminal domain V. In lower invertebrates, perlecan is not typically a proteoglycan, possessing the majority of the core protein modules, but lacking domain I where the attachment sites for glycosaminoglycan chains are located. This suggests that uniting the heparan sulfate binding growth factor functions of domain I and the core protein functions of the rest of the molecule in domains II-V occurred later in evolution for a new functional purpose. In this review, we surveyed several decades of pertinent literature to ask a fundamental question: Why did nature design this protein uniquely as an extraordinarily long multifunctional proteoglycan with a single promoter regulating expression, rather than separating these functions into individual proteins that could be independently regulated? We arrived at the conclusion that the concentration of perlecan at functional borders separating tissues and tissue layers is an ancient key function of the core protein. The addition of the heparan sulfate chains in domain I likely occurred as an additional means of binding the core protein to other ECM proteins in territorial matrices and basement membranes, and as a means to reserve growth factors in an on-site depot to assist with rapid repair of those borders when compromised, such as would occur during wounding. We propose a function for perlecan that extends its role from that of an extracellular scaffold, as we previously suggested, to that of a critical agent for establishing and patrolling tissue borders in complex tissues in metazoans. We also propose that understanding these unique functions of the individual portions of the perlecan molecule can provide new insights and tools for engineering of complex multi-layered tissues including providing the necessary cues for establishing neotissue borders.
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Affiliation(s)
- Mary C Farach-Carson
- Department of Biochemistry and Cell Biology, Rice University W100 George R. Brown Hall P.O. Box 1892, MS-140, Houston, TX 77251-1892, United States.
| | - Curtis R Warren
- Department of Biochemistry and Cell Biology, Rice University W100 George R. Brown Hall P.O. Box 1892, MS-140, Houston, TX 77251-1892, United States
| | - Daniel A Harrington
- Department of Biochemistry and Cell Biology, Rice University W100 George R. Brown Hall P.O. Box 1892, MS-140, Houston, TX 77251-1892, United States
| | - Daniel D Carson
- Department of Biochemistry and Cell Biology, Rice University W100 George R. Brown Hall P.O. Box 1892, MS-140, Houston, TX 77251-1892, United States
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Abstract
Research on Caenorhabditis elegans has led to the discovery of the consequences of mutation in myosin, its associated proteins, and the extracellular matrix-membrane cytoskeleton complex. Key results include understanding thick filament structure and assembly, the regulation of sarcomeric protein turnover, and the organization of thick and thin filaments into ordered sarcomeres. These results are critical to studies of cardiovascular diseases such as the cardiomyopathies, congenital septal defects, aneurysms of the thoracic aorta, and cardiac remodeling in heart failure.
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Kihira S, Yu EJ, Cunningham J, Cram EJ, Lee M. A novel mutation in β integrin reveals an integrin-mediated interaction between the extracellular matrix and cki-1/p27KIP1. PLoS One 2012; 7:e42425. [PMID: 22879977 PMCID: PMC3412830 DOI: 10.1371/journal.pone.0042425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 07/09/2012] [Indexed: 01/20/2023] Open
Abstract
The cell-extracellular matrix (ECM) interaction plays an essential role in maintaining tissue shapes and regulates cell behaviors such as cell adhesion, differentiation and proliferation. The mechanism by which the ECM influences the cell cycle in vivo is poorly understood. Here we demonstrate that the β integrin PAT-3 regulates the localization and expression of CKI-1, a C. elegans homologue of the cyclin dependent kinase inhibitor p27(KIP1). In nematodes expressing wild type PAT-3, CKI-1::GFP localizes primarily to nucleoli in hypodermal cells, whereas in animals expressing mutant pat-3 with a defective splice junction, CKI-1::GFP appears clumped and disorganized in nucleoplasm. RNAi analysis links cell adhesion genes to the regulation of CKI-1. RNAi of unc-52/perlecan, ina-1/α integrin, pat-4/ILK, and unc-97/PINCH resulted in abnormal CKI-1::GFP localization. Additional RNAi experiments revealed that the SCF E3 ubiquitin-ligase complex genes, skpt-1/SKP2, cul-1/CUL1 and lin-23/F-box, are required for the proper localization and expression of CKI-1, suggesting that integrin signaling and SCF E3 ligase work together to regulate the cellular distribution of CKI-1. These data also suggest that integrin plays a major role in maintaining proper CKI-1/p27(KIP1) levels in the cell. Perturbed integrin signaling may lead to the inhibition of SCF ligase activity, mislocalization and elevation of CKI-1/p27(KIP1). These results suggest that adhesion signaling is crucial for cell cycle regulation in vivo.
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Affiliation(s)
- Shingo Kihira
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Eun Jeong Yu
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jessica Cunningham
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Erin J. Cram
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Myeongwoo Lee
- Department of Biology, Baylor University, Waco, Texas, United States of America
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Labouesse M. Role of the extracellular matrix in epithelial morphogenesis: a view from C. elegans. Organogenesis 2012; 8:65-70. [PMID: 22692230 DOI: 10.4161/org.20261] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The extracellular matrix (ECM) plays an essential role in organizing tissues, defining their shapes or in presenting growth factors. Their components have been well described in most species, but our understanding of the mechanisms that control ECM remodeling remains limited. Likewise, how the ECM contributes to cellular mechanical responses has been examined in few cases. Here, I review how studies performed in C. elegans have brought several significant advances on those topics. Focusing only on epithelial cells, I discuss basement membrane invasion by the anchor cell during vulva morphogenesis, a process that has greatly expanded our knowledge of ECM remodeling in vivo. I then discuss the ECM role in a novel mechanotransduction process, whereby muscle contractions stimulate the remodeling of hemidesmosome-like junctions in the epidermis, which highlights that these junctions are mechanosensitive. Finally, I discuss progress in defining the composition and potential roles of the apical ECM covering epidermal cells in embryos.
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Affiliation(s)
- Michel Labouesse
- Development and Stem Cells Program, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS (UMR 7104), INSERM (U964), Illkirch, France.
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Kovacevic I, Ho R, Cram EJ. CCDC-55 is required for larval development and distal tip cell migration in Caenorhabditis elegans. Mech Dev 2012; 128:548-59. [PMID: 22285439 DOI: 10.1016/j.mod.2012.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 01/10/2012] [Accepted: 01/11/2012] [Indexed: 01/19/2023]
Abstract
The Caenorhabditis elegans distal tip cells (DTCs) are an in vivo model for the study of developmentally regulated cell migration. In this study, we characterize a novel role for CCDC-55, a conserved coiled-coil domain containing protein, in DTC migration and larval development in C. elegans. Although animals homozygous for a probable null allele, ccdc-55(ok2851), display an early larval arrest, RNAi depletion experiments allow the analysis of later phenotypes and suggest that CCDC-55 is needed within the DTC for migration to cease at the end of larval morphogenesis. The ccdc-55 gene is found in an operon with rnf-121 and rnf-5, E3 ubiquitin ligases that target cell migration genes such as the β-integrin PAT-3. Genetic interaction studies using RNAi depletion and the deletion alleles rnf-121(ok848) and rnf-5(tm794) indicate that CCDC-55 and the RNF genes act at least partially in parallel to promote termination of cell migration in the adult DTC.
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Affiliation(s)
- Ismar Kovacevic
- Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave., Boston, MA 02115, United States
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Etheridge T, Oczypok EA, Lehmann S, Fields BD, Shephard F, Jacobson LA, Szewczyk NJ. Calpains mediate integrin attachment complex maintenance of adult muscle in Caenorhabditis elegans. PLoS Genet 2012; 8:e1002471. [PMID: 22253611 PMCID: PMC3257289 DOI: 10.1371/journal.pgen.1002471] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 11/23/2011] [Indexed: 11/23/2022] Open
Abstract
Two components of integrin containing attachment complexes, UNC-97/PINCH and UNC-112/MIG-2/Kindlin-2, were recently identified as negative regulators of muscle protein degradation and as having decreased mRNA levels in response to spaceflight. Integrin complexes transmit force between the inside and outside of muscle cells and signal changes in muscle size in response to force and, perhaps, disuse. We therefore investigated the effects of acute decreases in expression of the genes encoding these multi-protein complexes. We find that in fully developed adult Caenorhabditis elegans muscle, RNAi against genes encoding core, and peripheral, members of these complexes induces protein degradation, myofibrillar and mitochondrial dystrophies, and a movement defect. Genetic disruption of Z-line– or M-line–specific complex members is sufficient to induce these defects. We confirmed that defects occur in temperature-sensitive mutants for two of the genes: unc-52, which encodes the extra-cellular ligand Perlecan, and unc-112, which encodes the intracellular component Kindlin-2. These results demonstrate that integrin containing attachment complexes, as a whole, are required for proper maintenance of adult muscle. These defects, and collapse of arrayed attachment complexes into ball like structures, are blocked when DIM-1 levels are reduced. Degradation is also blocked by RNAi or drugs targeting calpains, implying that disruption of integrin containing complexes results in calpain activation. In wild-type animals, either during development or in adults, RNAi against calpain genes results in integrin muscle attachment disruptions and consequent sub-cellular defects. These results demonstrate that calpains are required for proper assembly and maintenance of integrin attachment complexes. Taken together our data provide in vivo evidence that a calpain-based molecular repair mechanism exists for dealing with attachment complex disruption in adult muscle. Since C. elegans lacks satellite cells, this mechanism is intrinsic to the muscles and raises the question if such a mechanism also exists in higher metazoans. Muscle is a dynamic tissue that grows in response to use and nutrition and shrinks in response to lack of use, poor nutrition, or disease. Loss of muscle mass is an important public health problem, but we understand little of the genes that regulate muscle shrinkage. We have found that, in adult worm muscle, attachment to the basement membrane is continuously required to prevent catastrophic sub-cellular defects that result in impaired ability of muscle to function. We have also identified a group of proteases that are activated when the attachment fails to be properly maintained. Conversely, when these proteases are lacking in adult muscle, the muscles fail to maintain attachment to the basement membrane. Thus, we have discovered a group of proteases that appear to act to maintain attachment to the basement membrane and therefore to maintain muscle itself. Because these worms lack satellite cells, this maintenance system is intrinsic to muscle, thus raising the question whether a similar or identical system also works in humans.
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Affiliation(s)
- Timothy Etheridge
- School of Graduate Entry Medicine and Health, University of Nottingham, Royal Derby Hospital, Derby, United Kingdom
| | - Elizabeth A. Oczypok
- School of Graduate Entry Medicine and Health, University of Nottingham, Royal Derby Hospital, Derby, United Kingdom
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Susann Lehmann
- School of Graduate Entry Medicine and Health, University of Nottingham, Royal Derby Hospital, Derby, United Kingdom
| | - Brandon D. Fields
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Freya Shephard
- School of Graduate Entry Medicine and Health, University of Nottingham, Royal Derby Hospital, Derby, United Kingdom
| | - Lewis A. Jacobson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nathaniel J. Szewczyk
- School of Graduate Entry Medicine and Health, University of Nottingham, Royal Derby Hospital, Derby, United Kingdom
- * E-mail:
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Giacomotto J, Ségalat L, Carre-Pierrat M, Gieseler K. Caenorhabditis elegans as a chemical screening tool for the study o f neuromuscular disorders. Manual and semi-automated methods. Methods 2011; 56:103-13. [PMID: 22041718 DOI: 10.1016/j.ymeth.2011.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 10/07/2011] [Accepted: 10/17/2011] [Indexed: 02/05/2023] Open
Abstract
We previously reported the use of the cheap and fast-growing nematode Caenorhabditis elegans to search for molecules, which reduce muscle degeneration in a model for Duchenne Muscular Dystrophy (DMD). We showed that Prednisone, a steroid that is generally prescribed as a palliative treatment to DMD patients, also reduced muscle degeneration in the C. elegans DMD model. We further showed that this strategy could lead to the discovery of new and unsuspected small molecules, which have been further validated in a mammalian model of DMD, i.e. the mdx mouse model. These proof-of-principles demonstrate that C. elegans can serve as a screening tool to search for drugs against neuromuscular disorders. Here, we report and discuss two methodologies used to screen chemical libraries for drugs against muscle disorders in C. elegans. We first describe a manual method used to find drugs against DMD. We further present a semi-automated method, which is currently in use for the search of drugs against the Schwartz-Jampel Syndrome (SJS). Both assays are simple to implement and can be readily transposed and/or adapted to screens against other muscle/neuromuscular diseases, which can be modeled in the worm. Finally we discuss, with respect to our experience and knowledge, the different parameters that have to be taken into account before choosing one or the other method.
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Affiliation(s)
- Jean Giacomotto
- Brain and Mind Research Institute, Sydney Medical School, University of Sydney, NSW 2050, Australia
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Mörck C, Vivekanand V, Jafari G, Pilon M. C. elegans ten-1 is synthetic lethal with mutations in cytoskeleton regulators, and enhances many axon guidance defective mutants. BMC DEVELOPMENTAL BIOLOGY 2010; 10:55. [PMID: 20497576 PMCID: PMC2887410 DOI: 10.1186/1471-213x-10-55] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Accepted: 05/24/2010] [Indexed: 12/24/2022]
Abstract
BACKGROUND Teneurins are transmembrane proteins that assist morphogenetic processes in many organisms. ten-1 is the C. elegans teneurin homolog with two transcripts, ten-1a and ten-1b, that respectively encode a long (TEN-1L) and short (TEN-1S) form of the protein. We previously isolated a C. elegans mutant where one pharyngeal neuron was frequently misplaced, and now show that it corresponds to a novel allele of ten-1. RESULTS The novel ten-1(et5) allele is a hypomorph since its post-embryonic phenotype is weaker than the null alleles ten-1(ok641) and ten-1(tm651). ten-1 mutants have defects in all pharyngeal neurons that we examined, and in vivo reporters show that only the long form of the ten-1 gene is expressed in the pharynx, specifically in six marginal cells and the M2 neurons. Defects in the pharyngeal M2 neurons were enhanced when the ten-1(ok641) mutation was combined with mutations in the following genes: mig-14, unc-5, unc-51, unc-52 and unc-129. None of the body neurons examined show any defects in the ten-1(ok641) mutant, but genetic interaction studies reveal that ten-1(ok641) is synthetic lethal with sax-3, unc-34 and unc-73, and examination of the hypodermal cells in embryos of the ten-1(ok641) mutant point to a role of ten-1 during hypodermal cell morphogenesis. CONCLUSIONS Our results are consistent with ten-1 normally providing a function complementary to the cytoskeletal remodeling processes that occur in migrating cells or cells undergoing morphogenesis. It is possible that ten-1 influences the composition/distribution of extracellular matrix.
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Affiliation(s)
- Catarina Mörck
- Department of Cell and Molecular Biology, University of Gothenburg S-405 30 Gothenburg, Sweden
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Zahreddine H, Zhang H, Diogon M, Nagamatsu Y, Labouesse M. CRT-1/Calreticulin and the E3 Ligase EEL-1/HUWE1 Control Hemidesmosome Maturation in C. elegans Development. Curr Biol 2010; 20:322-7. [DOI: 10.1016/j.cub.2009.12.061] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 12/08/2009] [Accepted: 12/08/2009] [Indexed: 11/30/2022]
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40
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Ma L, Horvitz HR. Mutations in the Caenorhabditis elegans U2AF large subunit UAF-1 alter the choice of a 3' splice site in vivo. PLoS Genet 2009; 5:e1000708. [PMID: 19893607 PMCID: PMC2762039 DOI: 10.1371/journal.pgen.1000708] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 10/05/2009] [Indexed: 11/18/2022] Open
Abstract
The removal of introns from eukaryotic RNA transcripts requires the activities of five multi-component ribonucleoprotein complexes and numerous associated proteins. The lack of mutations affecting splicing factors essential for animal survival has limited the study of the in vivo regulation of splicing. From a screen for suppressors of the Caenorhabditis elegans unc-93(e1500) rubberband Unc phenotype, we identified mutations in genes that encode the C. elegans orthologs of two splicing factors, the U2AF large subunit (UAF-1) and SF1/BBP (SFA-1). The uaf-1(n4588) mutation resulted in temperature-sensitive lethality and caused the unc-93 RNA transcript to be spliced using a cryptic 3′ splice site generated by the unc-93(e1500) missense mutation. The sfa-1(n4562) mutation did not cause the utilization of this cryptic 3′ splice site. We isolated four uaf-1(n4588) intragenic suppressors that restored the viability of uaf-1 mutants at 25°C. These suppressors differentially affected the recognition of the cryptic 3′ splice site and implicated a small region of UAF-1 between the U2AF small subunit-interaction domain and the first RNA recognition motif in affecting the choice of 3′ splice site. We constructed a reporter for unc-93 splicing and using site-directed mutagenesis found that the position of the cryptic splice site affects its recognition. We also identified nucleotides of the endogenous 3′ splice site important for recognition by wild-type UAF-1. Our genetic and molecular analyses suggested that the phenotypic suppression of the unc-93(e1500) Unc phenotype by uaf-1(n4588) and sfa-1(n4562) was likely caused by altered splicing of an unknown gene. Our observations provide in vivo evidence that UAF-1 can act in regulating 3′ splice-site choice and establish a system that can be used to investigate the in vivo regulation of RNA splicing in C. elegans. Eukaryotic genes contain intervening intronic sequences that must be removed from pre-mRNA transcripts by RNA splicing to generate functional messenger RNAs. While studying genes that encode and control a presumptive muscle potassium channel complex in the nematode Caenorhabditis elegans, we found that mutations in two splicing factors, the U2AF large subunit and SF1/BBP suppress the rubberband Unc phenotype caused by a rare missense mutation in the gene unc-93. Mutations affecting the U2AF large subunit caused the recognition of a cryptic 3′ splice site generated by the unc-93 mutation, providing in vivo evidence that the U2AF large subunit can affect splice-site selection. By contrast, an SF1/BBP mutation that suppressed the rubberband Unc phenotype did not cause splicing using this cryptic 3′ splice site. Our genetic studies identified a region of the U2AF large subunit important for its effect on 3′ splice-site choice. Our mutagenesis analysis of in vivo transgene splicing identified a positional effect on weak 3′ splice site selection and nucleotides of the endogenous 3′ splice site important for recognition. The system we have defined should facilitate future in vivo analyses of pre–mRNA splicing.
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Affiliation(s)
- Long Ma
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - H. Robert Horvitz
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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Krajacic P, Hermanowski J, Lozynska O, Khurana TS, Lamitina T. C. elegans dysferlin homolog fer-1 is expressed in muscle, and fer-1 mutations initiate altered gene expression of muscle enriched genes. Physiol Genomics 2009; 40:8-14. [PMID: 19755517 DOI: 10.1152/physiolgenomics.00106.2009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Mutations in the human dysferlin gene cause Limb Girdle Muscular Dystrophy 2B (LGMD2B). The Caenorhabditis elegans dysferlin homolog, fer-1, affects sperms development but is not known to be expressed in or have a functional roles outside of the male germline. Using several approaches, we show that fer-1 mRNA is present in C. elegans muscle cells but is absent from neurons. In mammals, loss of muscle-expressed dysferlin causes transcriptional deregulation of muscle expressed genes. To determine if similar alterations in gene expression are initiated in C. elegans due to loss of muscle-expressed fer-1, we performed whole genome Affymetrix microarray analysis of two loss-of-function fer-1 mutants. Both mutants gave rise to highly similar changes in gene expression and altered the expression of 337 genes. Using multiple analysis methods, we show that this gene set is enriched for genes known to regulate the structure and function of muscle. However, these transcriptional changes do not appear to be in response to gross sarcomeric damage, since genetically sensitized fer-1 mutants exhibit normal thin filament organization. Our data suggest that processes other than sarcomere stability may be affected by loss of fer-1 in C. elegans muscle. Therefore, C. elegans may be an attractive model system in which to explore new muscle-specific functions of the dysferlin protein and gain insights into the molecular pathogenesis of LGMD2B.
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Affiliation(s)
- Predrag Krajacic
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Kabat JL, Barberan-Soler S, Zahler AM. HRP-2, the Caenorhabditis elegans homolog of mammalian heterogeneous nuclear ribonucleoproteins Q and R, is an alternative splicing factor that binds to UCUAUC splicing regulatory elements. J Biol Chem 2009; 284:28490-7. [PMID: 19706616 DOI: 10.1074/jbc.m109.023101] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alternative splicing is regulated by cis sequences in the pre-mRNA that serve as binding sites for trans-acting alternative splicing factors. In a previous study, we used bioinformatics and molecular biology to identify and confirm that the intronic hexamer sequence UCUAUC is a nematode alternative splicing regulatory element. In this study, we used RNA affinity chromatography to identify trans factors that bind to this sequence. HRP-2, the Caenorhabditis elegans homolog of human heterogeneous nuclear ribonucleoproteins Q and R, binds to UCUAUC in the context of unc-52 intronic regulatory sequences as well as to RNAs containing tandem repeats of this sequence. The three Us in the hexamer are the most important determinants of this binding specificity. We demonstrate, using RNA interference, that HRP-2 regulates the alternative splicing of two genes, unc-52 and lin-10, both of which have cassette exons flanked by an intronic UCUAUC motif. We propose that HRP-2 is a protein responsible for regulating alternative splicing through binding interactions with the UCUAUC sequence.
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Affiliation(s)
- Jennifer L Kabat
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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Polanska UM, Fernig DG, Kinnunen T. Extracellular interactome of the FGF receptor-ligand system: complexities and the relative simplicity of the worm. Dev Dyn 2009; 238:277-93. [PMID: 18985724 DOI: 10.1002/dvdy.21757] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Fibroblast growth factors (FGFs) and their receptors (FGFRs) regulate a multitude of biological functions in embryonic development and in adult. A major question is how does one family of growth factors and their receptors control such a variety of functions? Classically, specificity was thought to be imparted by alternative splicing of the FGFRs, resulting in isoforms that bind specifically to a subset of the FGFs, and by different saccharide sequences in the heparan sulfate proteoglycan (HSPG) co-receptor. A growing number of noncanonical co-receptors such as integrins and neural cell adhesion molecule (NCAM) are now recognized as imparting additional complexity to classic FGFR signaling. This review will discuss the noncanonical FGFR ligands and speculate on the possibility that they provide additional and alternative means to determining the functional specificity of FGFR signaling. We will also discuss how invertebrate models such as C. elegans may advance our understanding of noncanonical FGFR signaling.
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Affiliation(s)
- Urszula M Polanska
- School of Biological Sciences, University of Liverpool, Liverpool, United Kingdom
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A genetic screen for suppressors of a mutated 5' splice site identifies factors associated with later steps of spliceosome assembly. Genetics 2009; 182:725-34. [PMID: 19380478 DOI: 10.1534/genetics.109.103473] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many alleles of human disease genes have mutations within splicing consensus sequences that activate cryptic splice sites. In Caenorhabditis elegans, the unc-73(e936) allele has a G-to-U mutation at the first base of the intron downstream of exon 15, which results in an uncoordinated phenotype. This mutation triggers cryptic splicing at the -1 and +23 positions and retains some residual splicing at the mutated wild-type (wt) position. We previously demonstrated that a mutation in sup-39, a U1 snRNA gene, suppresses e936 by increasing splicing at the wt splice site. We report here the results of a suppressor screen in which we identify three proteins that function in cryptic splice site choice. Loss-of-function mutations in the nonessential splicing factor smu-2 suppress e936 uncoordination through changes in splicing. SMU-2 binds SMU-1, and smu-1(RNAi) also leads to suppression of e936. A dominant mutation in the conserved C-terminal domain of the C. elegans homolog of the human tri-snRNP 27K protein, which we have named SNRP-27, suppresses e936 uncoordination through changes in splicing. We propose that SMU-2, SMU-1, and SNRP-27 contribute to the fidelity of splice site choice after the initial identification of 5' splice sites by U1 snRNP.
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Stum M, Girard E, Bangratz M, Bernard V, Herbin M, Vignaud A, Ferry A, Davoine CS, Echaniz-Laguna A, René F, Marcel C, Molgó J, Fontaine B, Krejci E, Nicole S. Evidence of a dosage effect and a physiological endplate acetylcholinesterase deficiency in the first mouse models mimicking Schwartz-Jampel syndrome neuromyotonia. Hum Mol Genet 2008; 17:3166-79. [PMID: 18647752 DOI: 10.1093/hmg/ddn213] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Schwartz-Jampel syndrome (SJS) is a recessive neuromyotonia with chondrodysplasia. It results from hypomorphic mutations of the gene encoding perlecan, leading to a decrease in the levels of this heparan sulphate proteoglycan in basement membranes (BMs). It has been suggested that SJS neuromyotonia may result from endplate acetylcholinesterase (AChE) deficiency, but this hypothesis has never been investigated in vivo due to the lack of an animal model for neuromyotonia. We used homologous recombination to generate a knock-in mouse strain with one missense substitution, corresponding to a human familial SJS mutation (p.C1532Y), in the perlecan gene. We derived two lines, one with the p.C1532Y substitution alone and one with p.C1532Y and the selectable marker Neo, to down-regulate perlecan gene activity and to test for a dosage effect of perlecan in mammals. These two lines mimicked SJS neuromyotonia with spontaneous activity on electromyogramm (EMG). An inverse correlation between disease severity and perlecan secretion in the BMs was observed at the macroscopic and microscopic levels, consistent with a dosage effect. Endplate AChE levels were low in both lines, due to synaptic perlecan deficiency rather than major myofibre or neuromuscular junction disorganization. Studies of muscle contractile properties showed muscle fatigability at low frequencies of nerve stimulation and suggested that partial endplate AChE deficiency might contribute to SJS muscle stiffness by potentiating muscle force. However, physiological endplate AChE deficiency was not associated with spontaneous activity at rest on EMG in the diaphragm, suggesting that additional changes are required to generate such activity characteristic of SJS.
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Bix G, Iozzo RV. Novel interactions of perlecan: unraveling perlecan's role in angiogenesis. Microsc Res Tech 2008; 71:339-48. [PMID: 18300285 DOI: 10.1002/jemt.20562] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Perlecan, a highly conserved and ubiquitous basement membrane heparan sulfate proteoglycan, is essential for life, inasmuch as its absence results in embryonic lethality in mice and C. elegans, and neonatal lethality in humans. Perlecan plays an essential role in vasculogenesis and chondrogenesis, as well as in pathological states where these processes are maladapted. Although a large body of evidence supports a pro-angiogenic role for perlecan, recent findings suggests that portions of the perlecan protein core can be antiangiogenic, requiring a further evaluation of the functioning of this complex molecule. This review is focused on the genetics of mammalian and nonmammalian perlecan, the elucidation of its novel interacting partners and its role in angiogenesis. By more fully understanding perlecan's functioning in angiogenesis, we may gain invaluable insight that could lead to therapeutic interventions in cancer and other pathologic states.
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Affiliation(s)
- Gregory Bix
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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Steinkraus KA, Smith ED, Davis C, Carr D, Pendergrass WR, Sutphin GL, Kennedy BK, Kaeberlein M. Dietary restriction suppresses proteotoxicity and enhances longevity by an hsf-1-dependent mechanism in Caenorhabditis elegans. Aging Cell 2008; 7:394-404. [PMID: 18331616 DOI: 10.1111/j.1474-9726.2008.00385.x] [Citation(s) in RCA: 188] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dietary restriction increases lifespan and slows the onset of age-associated disease in organisms from yeast to mammals. In humans, several age-related diseases are associated with aberrant protein folding or aggregation, including neurodegenerative disorders such as Alzheimer's, Parkinson's, and Huntington's diseases. We report here that dietary restriction dramatically suppresses age-associated paralysis in three nematode models of proteotoxicity. Similar to its longevity-enhancing properties, dietary restriction protects against proteotoxicity by a mechanism distinct from reduced insulin/IGF-1-like signaling. Instead, the heat shock transcription factor, hsf-1, is required for enhanced thermotolerance, suppression of proteotoxicity, and lifespan extension by dietary restriction. These findings demonstrate that dietary restriction confers a general protective effect against proteotoxicity and promotes longevity by a mechanism involving hsf-1.
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Axäng C, Rauthan M, Hall DH, Pilon M. Developmental genetics of the C. elegans pharyngeal neurons NSML and NSMR. BMC DEVELOPMENTAL BIOLOGY 2008; 8:38. [PMID: 18400083 PMCID: PMC2375884 DOI: 10.1186/1471-213x-8-38] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Accepted: 04/09/2008] [Indexed: 01/02/2023]
Abstract
BACKGROUND We are interested in understanding how the twenty neurons of the C. elegans pharynx develop in an intricate yet reproducible way within the narrow confines of the embryonic pharyngeal primordium. To complement an earlier study of the pharyngeal M2 motorneurons, we have now examined the effect of almost forty mutations on the morphology of a bilateral pair of pharyngeal neurosecretory-motor neurons, the NSMs. RESULTS A careful description of the NSM morphology led to the discovery of a third, hitherto unreported process originating from the NSM cell body and that is likely to play a proprioceptive function. We found that the three NSM processes are differently sensitive to mutations. The major dorsal branch was most sensitive to mutations that affect growth cone guidance and function (e.g. unc-6, unc-34, unc-73), while the major sub-ventral branch was more sensitive to mutations that affect components of the extracellular matrix (e.g. sdn-1). Of the tested mutations, only unc-101, which affects an adaptin, caused the loss of the newly described thin minor process. The major processes developed synaptic branches post-embryonically, and these exhibited activity-dependent plasticity. CONCLUSION By studying the effects of nearly forty different mutations we have learned that the different NSM processes require different genes for their proper guidance and use both growth cone dependent and growth cone independent mechanisms for establishing their proper trajectories. The two major NSM processes develop in a growth cone dependent manner, although the sub-ventral process relies more on substrate adhesion. The minor process also uses growth cones but uniquely develops using a mechanism that depends on the clathrin adaptor molecule UNC-101. Together with the guidance of the M2 neuron, this is the second case of a pharyngeal neuron establishing one of its processes using an unexpected mechanism.
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Affiliation(s)
- Claes Axäng
- Dept, Cell and Molecular Biology, Göteborg University, Box 462, S-405 30, Sweden.
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Broday L, Hauser CA, Kolotuev I, Ronai Z. Muscle-epidermis interactions affect exoskeleton patterning in Caenorhabditis elegans. Dev Dyn 2008; 236:3129-36. [PMID: 17937397 DOI: 10.1002/dvdy.21341] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The C. elegans hypodermis is a single epithelial cell layer separated from the musculature by a thin basement membrane on its basal surface. The hypodermis secretes the extracellular material of the cuticle from its apical surface. The regulation of cuticle synthesis and apical secretion is not well understood. UNC-95 is a component of the muscle dense bodies and M-lines, which are integrin-based adhesion complexes required for force transduction to the cuticle. Using gene expression profiling and in vivo assays, we show that, in unc-95 mutant worms, there is an increase in expression levels of a group of hypodermal and pharyngeal genes related to cuticle structure and molting. Moreover, the cuticle structure of unc-95 mutant adult is impaired. Our findings suggest that aberrant force transduction from the structurally impaired muscle attachments across the basement membrane to the underlying hypodermis elicits intercellular signaling that plays a role in regulating cuticle synthesis and patterning.
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Affiliation(s)
- Limor Broday
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Hrus A, Lau G, Hutter H, Schenk S, Ferralli J, Brown-Luedi M, Chiquet-Ehrismann R, Canevascini S. C. elegans agrin is expressed in pharynx, IL1 neurons and distal tip cells and does not genetically interact with genes involved in synaptogenesis or muscle function. PLoS One 2007; 2:e731. [PMID: 17710131 PMCID: PMC1939731 DOI: 10.1371/journal.pone.0000731] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 07/17/2007] [Indexed: 01/15/2023] Open
Abstract
Agrin is a basement membrane protein crucial for development and maintenance of the neuromuscular junction in vertebrates. The C. elegans genome harbors a putative agrin gene agr-1. We have cloned the corresponding cDNA to determine the primary structure of the protein and expressed its recombinant fragments to raise specific antibodies. The domain organization of AGR-1 is very similar to the vertebrate orthologues. C. elegans agrin contains a signal sequence for secretion, seven follistatin domains, three EGF-like repeats and two laminin G domains. AGR-1 loss of function mutants did not exhibit any overt phenotypes and did not acquire resistance to the acetylcholine receptor agonist levamisole. Furthermore, crossing them with various mutants for components of the dystrophin-glycoprotein complex with impaired muscle function did not lead to an aggravation of the phenotypes. Promoter-GFP translational fusion as well as immunostaining of worms revealed expression of agrin in buccal epithelium and the protein deposition in the basal lamina of the pharynx. Furthermore, dorsal and ventral IL1 head neurons and distal tip cells of the gonad arms are sources of agrin production, but no expression was detectable in body muscles or in the motoneurons innervating them. Recombinant worm AGR-1 fragment is able to cluster vertebrate dystroglycan in cultured cells, implying a conservation of this interaction, but since neither of these proteins is expressed in muscle of C. elegans, this interaction may be required in different tissues. The connections between muscle cells and the basement membrane, as well as neuromuscular junctions, are structurally distinct between vertebrates and nematodes.
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Affiliation(s)
- Ana Hrus
- Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel, Switzerland
| | - Gordon Lau
- Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel, Switzerland
| | - Harald Hutter
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Susanne Schenk
- Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel, Switzerland
| | - Jacqueline Ferralli
- Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel, Switzerland
| | - Marianne Brown-Luedi
- Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel, Switzerland
| | - Ruth Chiquet-Ehrismann
- Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel, Switzerland
- * To whom correspondence should be addressed. E-mail:
| | - Stefano Canevascini
- Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel, Switzerland
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