1
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Singh N, Zhang P, Li KJ, Gordon KL. The Rac pathway prevents cell fragmentation in a nonprotrusively migrating leader cell during C. elegans gonad organogenesis. Curr Biol 2024; 34:2387-2402.e5. [PMID: 38776905 DOI: 10.1016/j.cub.2024.04.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/22/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The C. elegans hermaphrodite distal tip cell (DTC) leads gonadogenesis. Loss-of-function mutations in a C. elegans ortholog of the Rac1 GTPase (ced-10) and its GEF complex (ced-5/DOCK180, ced-2/CrkII, ced-12/ELMO) cause gonad migration defects related to directional sensing; we discovered an additional defect class of gonad bifurcation in these mutants. Using genetic approaches, tissue-specific and whole-body RNAi, and in vivo imaging of endogenously tagged proteins and marked cells, we find that loss of Rac1 or its regulators causes the DTC to fragment as it migrates. Both products of fragmentation-the now-smaller DTC and the membranous patch of cellular material-localize important stem cell niche signaling (LAG-2 ligand) and migration (INA-1/integrin subunit alpha) factors to their membranes, but only one retains the DTC nucleus and therefore the ability to maintain gene expression over time. The enucleate patch can lead a bifurcating branch off the gonad arm that grows through germ cell proliferation. Germ cells in this branch differentiate as the patch loses LAG-2 expression. While the nucleus is surprisingly dispensable for aspects of leader cell function, it is required for stem cell niche activity long term. Prior work found that Rac1-/-;Rac2-/- mouse erythrocytes fragment; in this context, our new findings support the conclusion that maintaining a cohesive but deformable cell is a conserved function of this important cytoskeletal regulator.
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Affiliation(s)
- Noor Singh
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pu Zhang
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen Jian Li
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kacy Lynn Gordon
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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2
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Yarychkivska O, Sharmin R, Elkhalil A, Ghose P. Apoptosis and beyond: A new era for programmed cell death in Caenorhabditis elegans. Semin Cell Dev Biol 2024; 154:14-22. [PMID: 36792437 DOI: 10.1016/j.semcdb.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023]
Abstract
Programmed cell death (PCD) is crucial for normal development and homeostasis. Our first insights into the genetic regulation of apoptotic cell death came from in vivo studies in the powerful genetic model system of C. elegans. More recently, novel developmental cell death programs occurring both embryonically and post-embryonically, and sex-specifically, have been elucidated. Recent studies in the apoptotic setting have also shed new light on the intricacies of phagocytosis in particular. This review provides a brief historical perspective of the origins of PCD studies in C. elegans, followed by a more detailed description of non-canonical apoptotic and non-apoptotic death programs. We conclude by posing open questions and commenting on our outlook on the future of PCD studies in C. elegans, highlighting the importance of advanced imaging tools and the continued leveraging of C. elegans genetics both with classical and modern cutting-edge approaches.
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Affiliation(s)
| | | | | | - Piya Ghose
- The University of Texas at Arlington, USA.
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3
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Singh N, Jian Li K, Lynn Gordon K. Getting there in one piece: The Rac pathway prevents cell fragmentation in a nonprotrusively migrating leader cell during organogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569642. [PMID: 38106045 PMCID: PMC10723291 DOI: 10.1101/2023.12.01.569642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The C. elegans hermaphrodite distal tip cell (DTC) leads gonadogenesis. Loss-of-function mutations in a C. elegans ortholog of the Rac1 GTPase (ced-10) and its GEF complex (ced-5/DOCK180, ced-2/CrkII, ced-12/ELMO) cause gonad migration defects related to directional sensing; we discovered an additional defect class of gonad bifurcation in these mutants. Using genetic approaches, tissue-specific and whole-body RNAi, and in vivo imaging of endogenously tagged proteins and marked cells, we find that loss of Rac1 or its regulators causes the DTC to fragment as it migrates. Both products of fragmentation-the now-smaller DTC and the membranous patch of cellular material-localize important stem cell niche signaling (LAG-2/DSL ligand) and migration (INA-1/integrin subunit alpha) factors to their membranes, but only one retains the DTC nucleus and therefore the ability to maintain gene expression over time. The enucleate patch can lead a bifurcating branch off the gonad arm that grows through germ cell proliferation. Germ cells in this branch differentiate as the patch loses LAG-2 expression. While the nucleus is surprisingly dispensable for aspects of leader cell function, it is required for stem cell niche activity long-term. Prior work found that Rac1-/-;Rac2-/- mouse erythrocytes fragment; in this context, our new findings support the conclusion that maintaining a cohesive but deformable cell is a conserved function of this important cytoskeletal regulator.
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Affiliation(s)
- Noor Singh
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Karen Jian Li
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Kacy Lynn Gordon
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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4
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Venkatachalam T, Mannimala S, Soto MC. CED-5/CED-12 (DOCK/ELMO) can promote and inhibit F-actin formation via distinct motifs that target different GTPases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.04.560868. [PMID: 37873140 PMCID: PMC10592980 DOI: 10.1101/2023.10.04.560868] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Coordinated activation and inhibition of F-actin supports the movements of morphogenesis. Understanding the proteins that regulate F-actin is important, since these proteins are mis-regulated in diseases like cancer. Our studies of C. elegans embryonic epidermal morphogenesis identified the GTPase CED-10/Rac1 as an essential activator of F-actin. However, we need to identify the GEF, or Guanine-nucleotide Exchange Factor, that activates CED-10/Rac1 during embryonic cell migrations. The two-component GEF, CED-5/CED-12, is known to activate CED-10/Rac1 to promote cell movements that result in the engulfment of dying cells during embryogenesis, and a later cell migration of the larval Distal Tip Cell. It is believed that CED-5/CED-12 powers cellular movements of corpse engulfment and DTC migration by promoting F-actin formation. Therefore, we tested if CED-5/CED-12 was involved in embryonic migrations, and got a contradictory result. CED-5/CED-12 definitely support embryonic migrations, since their loss led to embryos that died due to failed epidermal cell migrations. However, CED-5/CED-12 inhibited F-actin in the migrating epidermis, the opposite of what was expected for a CED-10 GEF. To address how CED-12/CED-5 could have two opposing effects on F-actin, during corpse engulfment and cell migration, we investigated if CED-12 harbors GAP (GTPase Activating Protein) functions. A candidate GAP region in CED-12 faces away from the CED-5 GEF catalytic region. Mutating a candidate catalytic Arginine in the CED-12 GAP region (R537A) altered the epidermal cell migration function, and not the corpse engulfment function. A candidate GEF region on CED-5 faces towards Rac1/CED-10. Mutating Serine-Arginine in CED-5/DOCK predicted to bind and stabilize Rac1 for catalysis, resulted in loss of both ventral enclosure and corpse engulfment. Genetic and expression studies showed the GEF and GAP functions act on different GTPases. Thus, we propose CED-5/CED-12 support the cycling of multiple GTPases, by using distinct domains, to both promote and inhibit F-actin nucleation.
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Affiliation(s)
- Thejasvi Venkatachalam
- Department of Pathology and Laboratory Medicine, Rutgers – Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Sushma Mannimala
- Department of Pathology and Laboratory Medicine, Rutgers – Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Martha C. Soto
- Department of Pathology and Laboratory Medicine, Rutgers – Robert Wood Johnson Medical School, Piscataway, NJ, USA
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5
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Dobbelaere J, Su TY, Erdi B, Schleiffer A, Dammermann A. A phylogenetic profiling approach identifies novel ciliogenesis genes in Drosophila and C. elegans. EMBO J 2023; 42:e113616. [PMID: 37317646 PMCID: PMC10425847 DOI: 10.15252/embj.2023113616] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/22/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023] Open
Abstract
Cilia are cellular projections that perform sensory and motile functions in eukaryotic cells. A defining feature of cilia is that they are evolutionarily ancient, yet not universally conserved. In this study, we have used the resulting presence and absence pattern in the genomes of diverse eukaryotes to identify a set of 386 human genes associated with cilium assembly or motility. Comprehensive tissue-specific RNAi in Drosophila and mutant analysis in C. elegans revealed signature ciliary defects for 70-80% of novel genes, a percentage similar to that for known genes within the cluster. Further characterization identified different phenotypic classes, including a set of genes related to the cartwheel component Bld10/CEP135 and two highly conserved regulators of cilium biogenesis. We propose this dataset defines the core set of genes required for cilium assembly and motility across eukaryotes and presents a valuable resource for future studies of cilium biology and associated disorders.
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Affiliation(s)
- Jeroen Dobbelaere
- Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
| | - Tiffany Y Su
- Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Balazs Erdi
- Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC)ViennaAustria
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6
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Actin Up: An Overview of the Rac GEF Dock1/Dock180 and Its Role in Cytoskeleton Rearrangement. Cells 2022; 11:cells11223565. [PMID: 36428994 PMCID: PMC9688060 DOI: 10.3390/cells11223565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Dock1, originally Dock180, was the first identified member of the Dock family of GTPase Exchange Factors. Early biochemical and genetic studies of Dock180 elucidated the functions and regulation of Dock180 and informed our understanding of all Dock family members. Dock180 activates Rac to stimulate actin polymerization in response to signals initiated by a variety of receptors. Dock180 dependent Rac activation is essential for processes such as apoptotic cell engulfment, myoblast fusion, and cell migration during development and homeostasis. Inappropriate Dock180 activity has been implicated in cancer invasion and metastasis and in the uptake of bacterial pathogens. Here, we give an overview of the history and current understanding of the activity, regulation, and impacts of Dock180.
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7
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Boger M, Bennewitz K, Wohlfart DP, Hausser I, Sticht C, Poschet G, Kroll J. Comparative Morphological, Metabolic and Transcriptome Analyses in elmo1−/−, elmo2−/−, and elmo3−/− Zebrafish Mutants Identified a Functional Non-Redundancy of the Elmo Proteins. Front Cell Dev Biol 2022; 10:918529. [PMID: 35874819 PMCID: PMC9304559 DOI: 10.3389/fcell.2022.918529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
The ELMO protein family consists of the homologues ELMO1, ELMO2 and ELMO3. Several studies have shown that the individual ELMO proteins are involved in a variety of cellular and developmental processes. However, it has poorly been understood whether the Elmo proteins show similar functions and act redundantly. To address this question, elmo1−/−, elmo2−/− and elmo3−/− zebrafish were generated and a comprehensive comparison of the phenotypic changes in organ morphology, transcriptome and metabolome was performed in these mutants. The results showed decreased fasting and increased postprandial blood glucose levels in adult elmo1−/−, as well as a decreased vascular formation in the adult retina in elmo1−/−, but an increased vascular formation in the adult elmo3−/− retina. The phenotypical comparison provided few similarities, as increased Bowman space areas in adult elmo1−/− and elmo2−/− kidneys, an increased hyaloid vessel diameter in elmo1−/− and elmo3−/− and a transcriptional downregulation of the vascular development in elmo1−/−, elmo2−/−, and elmo3−/− zebrafish larvae. Besides this, elmo1−/−, elmo2−/−, and elmo3−/− zebrafish exhibited several distinct changes in the vascular and glomerular structure and in the metabolome and the transcriptome. Especially, elmo3−/− zebrafish showed extensive differences in the larval transcriptome and an impaired survivability. Together, the data demonstrated that the three zebrafish Elmo proteins regulate not only similar but also divergent biological processes and mechanisms and show a low functional redundancy.
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Affiliation(s)
- Mike Boger
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Katrin Bennewitz
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - David Philipp Wohlfart
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ingrid Hausser
- Institute of Pathology IPH, EM Lab, Heidelberg University Hospital, Heidelberg, Germany
| | - Carsten Sticht
- NGS Core Facility, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Gernot Poschet
- Metabolomics Core Technology Platform, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Jens Kroll
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- *Correspondence: Jens Kroll,
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8
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Juanez K, Ghose P. Repurposing the Killing Machine: Non-canonical Roles of the Cell Death Apparatus in Caenorhabditis elegans Neurons. Front Cell Dev Biol 2022; 10:825124. [PMID: 35237604 PMCID: PMC8882910 DOI: 10.3389/fcell.2022.825124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/31/2022] [Indexed: 12/29/2022] Open
Abstract
Here we highlight the increasingly divergent functions of the Caenorhabditis elegans cell elimination genes in the nervous system, beyond their well-documented roles in cell dismantling and removal. We describe relevant background on the C. elegans nervous system together with the apoptotic cell death and engulfment pathways, highlighting pioneering work in C. elegans. We discuss in detail the unexpected, atypical roles of cell elimination genes in various aspects of neuronal development, response and function. This includes the regulation of cell division, pruning, axon regeneration, and behavioral outputs. We share our outlook on expanding our thinking as to what cell elimination genes can do and noting their versatility. We speculate on the existence of novel genes downstream and upstream of the canonical cell death pathways relevant to neuronal biology. We also propose future directions emphasizing the exploration of the roles of cell death genes in pruning and guidance during embryonic development.
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9
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Taban Q, Mumtaz PT, Masoodi KZ, Haq E, Ahmad SM. Scavenger receptors in host defense: from functional aspects to mode of action. Cell Commun Signal 2022; 20:2. [PMID: 34980167 PMCID: PMC8721182 DOI: 10.1186/s12964-021-00812-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/27/2021] [Indexed: 12/17/2022] Open
Abstract
Scavenger receptors belong to a superfamily of proteins that are structurally heterogeneous and encompass the miscellaneous group of transmembrane proteins and soluble secretory extracellular domain. They are functionally diverse as they are involved in various disorders and biological pathways and their major function in innate immunity and homeostasis. Numerous scavenger receptors have been discovered so far and are apportioned in various classes (A-L). Scavenger receptors are documented as pattern recognition receptors and known to act in coordination with other co-receptors such as Toll-like receptors in generating the immune responses against a repertoire of ligands such as microbial pathogens, non-self, intracellular and modified self-molecules through various diverse mechanisms like adhesion, endocytosis and phagocytosis etc. Unlike, most of the scavenger receptors discussed below have both membrane and soluble forms that participate in scavenging; the role of a potential scavenging receptor Angiotensin-Converting Enzyme-2 has also been discussed whereby only its soluble form might participate in preventing the pathogen entry and replication, unlike its membrane-bound form. This review majorly gives an insight on the functional aspect of scavenger receptors in host defence and describes their mode of action extensively in various immune pathways involved with each receptor type. Video abstract.
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Affiliation(s)
- Qamar Taban
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e- Kashmir University of Agricultural Sciences and Technology - Kashmir, Shuhama, 190006, India.,Department of Biotechnology, University of Kashmir, Hazratbal Srinagar, Kashmir, India
| | | | - Khalid Z Masoodi
- Division of Plant Biotechnology, Transcriptomics Laboratory, SKUAST-K, Shalimar, India
| | - Ehtishamul Haq
- Department of Biotechnology, University of Kashmir, Hazratbal Srinagar, Kashmir, India
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e- Kashmir University of Agricultural Sciences and Technology - Kashmir, Shuhama, 190006, India.
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10
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Ghose P, Wehman AM. The developmental and physiological roles of phagocytosis in Caenorhabditis elegans. Curr Top Dev Biol 2020; 144:409-432. [PMID: 33992160 DOI: 10.1016/bs.ctdb.2020.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Phagocytosis is an essential process by which cellular debris and pathogens are cleared from the environment. Cells extend their plasma membrane to engulf objects and contain them within a limiting membrane for isolation from the cytosol or for intracellular degradation in phagolysosomes. The basic mechanisms of phagocytosis and intracellular clearance are well conserved between animals. Indeed, much of our understanding is derived from studies on the nematode worm, Caenorhabditis elegans. Here, we review the latest progress in understanding the mechanisms and functions of phagocytic clearance from C. elegans studies. In particular, we highlight new insights into phagocytic signaling pathways, phagosome formation and phagolysosome resolution, as well as the challenges in studying these cyclic processes.
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Affiliation(s)
- Piya Ghose
- Department of Biology, University of Texas, Arlington, TX, United States.
| | - Ann M Wehman
- Department of Biological Sciences, University of Denver, Denver, CO, United States.
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11
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Chang L, Yang J, Jo CH, Boland A, Zhang Z, McLaughlin SH, Abu-Thuraia A, Killoran RC, Smith MJ, Côté JF, Barford D. Structure of the DOCK2-ELMO1 complex provides insights into regulation of the auto-inhibited state. Nat Commun 2020; 11:3464. [PMID: 32651375 PMCID: PMC7351999 DOI: 10.1038/s41467-020-17271-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 06/17/2020] [Indexed: 12/29/2022] Open
Abstract
DOCK (dedicator of cytokinesis) proteins are multidomain guanine nucleotide exchange factors (GEFs) for RHO GTPases that regulate intracellular actin dynamics. DOCK proteins share catalytic (DOCKDHR2) and membrane-associated (DOCKDHR1) domains. The structurally-related DOCK1 and DOCK2 GEFs are specific for RAC, and require ELMO (engulfment and cell motility) proteins for function. The N-terminal RAS-binding domain (RBD) of ELMO (ELMORBD) interacts with RHOG to modulate DOCK1/2 activity. Here, we determine the cryo-EM structures of DOCK2-ELMO1 alone, and as a ternary complex with RAC1, together with the crystal structure of a RHOG-ELMO2RBD complex. The binary DOCK2-ELMO1 complex adopts a closed, auto-inhibited conformation. Relief of auto-inhibition to an active, open state, due to a conformational change of the ELMO1 subunit, exposes binding sites for RAC1 on DOCK2DHR2, and RHOG and BAI GPCRs on ELMO1. Our structure explains how up-stream effectors, including DOCK2 and ELMO1 phosphorylation, destabilise the auto-inhibited state to promote an active GEF.
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Affiliation(s)
- Leifu Chang
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Jing Yang
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Chang Hwa Jo
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3T 1J4, Canada
| | - Andreas Boland
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
- Department of Molecular Biology, Science III, University of Geneva, Geneva, Switzerland
| | - Ziguo Zhang
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | - Afnan Abu-Thuraia
- Montreal Institute of Clinical Research (IRCM), Montréal, QC, H2W 1R7, Canada
| | - Ryan C Killoran
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3T 1J4, Canada
| | - Matthew J Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3T 1J4, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Jean-Francois Côté
- Montreal Institute of Clinical Research (IRCM), Montréal, QC, H2W 1R7, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC, H3A 0C7, Canada
| | - David Barford
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
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12
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Haley R, Zhou Z. The small GTPase RAB-35 facilitates the initiation of phagosome maturation and acts as a robustness factor for apoptotic cell clearance. Small GTPases 2019; 12:188-201. [PMID: 31607221 DOI: 10.1080/21541248.2019.1680066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
We recently identified the novel function of the small GTPase RAB-35 in apoptotic cell clearance in Caenorhabditis elegans, a process in which dying cells are engulfed and degraded inside phagosomes. We have found that RAB-35 functions in two separate steps of cell corpse clearance, cell corpse recognition and the initiation of phagosome maturation. During the latter process, RAB-35 facilitates the removal of phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) from the membranes of nascent phagosomes and the simultaneous production of phosphatidylinositol-3-P (PI(3)P) on these same membranes, a process that we have coined the PI(4,5)P2 to PI(3)P shift. RAB-35 also promotes the recruitment of the small GTPase RAB-5 to the phagosomal surface. During these processes, the activity of RAB-35 is controlled by the candidate GTPase-activating protein (GAP) TBC-10 and the candidate guanine nucleotide exchange factor (GEF) FLCN-1. Overall, RAB-35 leads a third pathway during cell corpse clearance that functions in parallel to the two known pathways, one led by the phagocytic receptor CED-1 and the other led by the CED-10/Rac1 GTPase. Here, we further report that RAB-35 acts as a robustness factor that maintains the clearance activity and embryonic viability under conditions of heat stress. Moreover, we obtained additional evidence suggesting that RAB-35 acts upstream of RAB-5 and RAB-7. To establish a precise temporal pattern for its own dissociation from phagosomal surfaces, RAB-35 controls the removal of its own GAP. We propose that RAB-35 defines a largely unexplored initial phase of phagosome maturation.
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Affiliation(s)
- Ryan Haley
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Zheng Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
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13
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Chiu H, Zou Y, Suzuki N, Hsieh YW, Chuang CF, Wu YC, Chang C. Engulfing cells promote neuronal regeneration and remove neuronal debris through distinct biochemical functions of CED-1. Nat Commun 2018; 9:4842. [PMID: 30451835 PMCID: PMC6242819 DOI: 10.1038/s41467-018-07291-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/22/2018] [Indexed: 11/25/2022] Open
Abstract
Two important biological events happen coincidently soon after nerve injury in the peripheral nervous system in C. elegans: removal of axon debris and initiation of axon regeneration. But, it is not known how these two events are co-regulated. Mutants of ced-1, a homolog of Draper and MEGF10, display defects in both events. One model is that those events could be related. But our data suggest that they are actually separable. CED-1 functions in the muscle-type engulfing cells in both events and is enriched in muscle protrusions in close contact with axon debris and regenerating axons. Its two functions occur through distinct biochemical mechanisms; extracellular domain-mediated adhesion for regeneration and extracellular domain binding-induced intracellular domain signaling for debris removal. These studies identify CED-1 in engulfing cells as a receptor in debris removal but as an adhesion molecule in neuronal regeneration, and have important implications for understanding neural circuit repair after injury.
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Affiliation(s)
- Hui Chiu
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, 60607, USA
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 10617, Taiwan
- Division of Biology and Biological Engineering and HHMI, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Yan Zou
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, 60607, USA
- School of Life Science, ShanghaiTech University, Shanghai, 200031, China
| | - Nobuko Suzuki
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, 60607, USA
| | - Yi-Wen Hsieh
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, 60607, USA
| | - Chiou-Fen Chuang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, 60607, USA
| | - Yi-Chun Wu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 10617, Taiwan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Chieh Chang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, 60607, USA.
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14
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Nørgaard S, Deng S, Cao W, Pocock R. Distinct CED-10/Rac1 domains confer context-specific functions in development. PLoS Genet 2018; 14:e1007670. [PMID: 30265669 PMCID: PMC6179291 DOI: 10.1371/journal.pgen.1007670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/10/2018] [Accepted: 08/30/2018] [Indexed: 11/18/2022] Open
Abstract
Rac GTPases act as master switches to coordinate multiple interweaved signaling pathways. A major function for Rac GTPases is to control neurite development by influencing downstream effector molecules and pathways. In Caenorhabditis elegans, the Rac proteins CED-10, RAC-2 and MIG-2 act in parallel to control axon outgrowth and guidance. Here, we have identified a single glycine residue in the CED-10/Rac1 Switch 1 region that confers a non-redundant function in axon outgrowth but not guidance. Mutation of this glycine to glutamic acid (G30E) reduces GTP binding and inhibits axon outgrowth but does not affect other canonical CED-10 functions. This demonstrates previously unappreciated domain-specific functions within the CED-10 protein. Further, we reveal that when CED-10 function is diminished, the adaptor protein NAB-1 (Neurabin) and its interacting partner SYD-1 (Rho-GAP-like protein) can act as inhibitors of axon outgrowth. Together, we reveal that specific domains and residues within Rac GTPases can confer context-dependent functions during animal development. Brain development requires that neurite outgrowth and guidance are precisely regulated. Previous studies have shown that molecular switch proteins called Rac GTPases perform redundant functions in controlling neurite development. Using a pair of bilateral neurons in the nematode Caenorhabditis elegans to model neurite development, we found that a single amino acid in a conserved domain of the Rac GTPase CED-10 is crucial for controlling neurite outgrowth in a partially non-redundant manner. Further, we revealed that lesions in discrete domains in the CED-10 protein lead to distinct developmental defects. Therefore, our in vivo study proposes that regulation of distinct signalling pathways through Rac GTPase protein domains can drive different developmental outcomes.
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Affiliation(s)
- Steffen Nørgaard
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Shuer Deng
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
| | - Wei Cao
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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15
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Haley R, Wang Y, Zhou Z. The small GTPase RAB-35 defines a third pathway that is required for the recognition and degradation of apoptotic cells. PLoS Genet 2018; 14:e1007558. [PMID: 30138370 PMCID: PMC6107108 DOI: 10.1371/journal.pgen.1007558] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/12/2018] [Indexed: 01/18/2023] Open
Abstract
In metazoans, apoptotic cells are swiftly engulfed by phagocytes and degraded inside phagosomes. Multiple small GTPases in the Rab family are known to function in phagosome maturation by regulating vesicle trafficking. We discovered rab-35 as a new gene important for apoptotic cell clearance from a genetic screen targeting putative Rab GTPases in Caenorhabditis elegans. We further identified TBC-10 as a putative GTPase-activating protein (GAP), and FLCN-1 and RME-4 as two putative Guanine Nucleotide Exchange Factors (GEFs), for RAB-35. We found that RAB-35 was required for the efficient incorporation of early endosomes to phagosomes and for the timely degradation of apoptotic cell corpses. More specifically, RAB-35 promotes two essential events that initiate phagosome maturation: the switch of phagosomal membrane phosphatidylinositol species from PtdIns(4,5)P2 to PtdIns(3)P, and the recruitment of the small GTPase RAB-5 to phagosomal surfaces. These functions of RAB-35 were previously unknown. Remarkably, although the phagocytic receptor CED-1 regulates these same events, RAB-35 and CED-1 appear to function independently. Upstream of degradation, RAB-35 also facilitates the recognition of apoptotic cells independently of the known CED-1 and CED-5 pathways. RAB-35 localizes to extending pseudopods and is further enriched on nascent phagosomes, consistent with its dual roles in regulating apoptotic cell-recognition and phagosome maturation. Epistasis analyses indicate that rab-35 acts in parallel to both of the canonical ced-1/6/7 and ced-2/5/10/12 clearance pathways. We propose that RAB-35 acts as a robustness factor, defining a novel pathway that aids these canonical pathways in both the recognition and degradation of apoptotic cells.
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Affiliation(s)
- Ryan Haley
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Ying Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Zheng Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
- * E-mail:
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16
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Li W, Sun J, Ling J, Li J, He C, Liu Y, Chen H, Men M, Niu Z, Deng Y, Li M, Li T, Wen J, Sang S, Li H, Wan Z, Richard EM, Chapagain P, Yan D, Liu XZ, Mei L, Feng Y. ELMOD3, a novel causative gene, associated with human autosomal dominant nonsyndromic and progressive hearing loss. Hum Genet 2018; 137:329-342. [PMID: 29713870 DOI: 10.1007/s00439-018-1885-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/16/2018] [Indexed: 11/26/2022]
Abstract
Autosomal dominant nonsyndromic hearing loss (ADNSHL) is a highly genetically heterogeneous disorder. Up to date only approximately 37 ADNSHL-causing genes have been identified. The goal of this study was to determine the causative gene in a five-generation Chinese family with ADNSHL. A Chinese family was ascertained. Simultaneously, two affected individuals and one normal hearing control from the family were analyzed by whole exome capture sequencing. To assess the functional effect of the identified variant, in-vitro studies were performed. novel missense variant, c.512A>G (p.His171Arg) in exon 8 of the ELMO domain-containing 3 (ELMOD3) gene, was identified as a causative variant in this family affected by late-onset and progressive ADNSHL. The variant was validated by Sanger sequencing and found to co-segregate with the phenotype within the pedigree and was absent in 500 ethnically matched unrelated normal hearing control subjects. To our knowledge, this is the first report of a family with ADNSHL caused by ELMOD3 mutation. Western blots and immunofluorescence staining demonstrated that p.His171Arg resulted in abnormal expression levels of ELMOD3 and abnormal subcellular localization. Furthermore, the analysis of the stability of the wild-type (WT) and mutant ELMOD3 protein shows that the decay of p.His171Arg is faster than that of the WT, suggesting a shorter halflife of the c.512A > G variant. A novel variant in the ELMOD3 gene, encoding a member of the engulfment and cell motility (ELMO) family of GTPase-activating proteins, was identified for the first time as responsible for ADNSHL.
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Affiliation(s)
- Wu Li
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Jie Sun
- Department of Otolaryngology, The Eight Affiliated Hospital, Sun Yat-sen University, 3025 Shennan Middle Road, Shenzhen, Guangdong, China
| | - Jie Ling
- Institute of Precision Medicine, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
| | - Jiada Li
- Center for Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan, China
- School of Life Sciences, Central South University of China, 110 Xiangya Road, Changsha, Hunan, China
| | - Chufeng He
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Yalan Liu
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Hongsheng Chen
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Meichao Men
- Health Management Center, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
| | - Zhijie Niu
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Yuyuan Deng
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Meng Li
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Taoxi Li
- Center for Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan, China
- School of Life Sciences, Central South University of China, 110 Xiangya Road, Changsha, Hunan, China
| | - Jie Wen
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Shushan Sang
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Haibo Li
- Department of Ophthalmology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
| | - Zhengqing Wan
- Center for Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan, China
- School of Life Sciences, Central South University of China, 110 Xiangya Road, Changsha, Hunan, China
| | - Elodie M Richard
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, Florida, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, USA
| | - Xue Zhong Liu
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Lingyun Mei
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China.
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China.
| | - Yong Feng
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China.
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China.
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17
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Programmed Cell Death During Caenorhabditis elegans Development. Genetics 2017; 203:1533-62. [PMID: 27516615 DOI: 10.1534/genetics.115.186247] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/22/2016] [Indexed: 12/21/2022] Open
Abstract
Programmed cell death is an integral component of Caenorhabditis elegans development. Genetic and reverse genetic studies in C. elegans have led to the identification of many genes and conserved cell death pathways that are important for the specification of which cells should live or die, the activation of the suicide program, and the dismantling and removal of dying cells. Molecular, cell biological, and biochemical studies have revealed the underlying mechanisms that control these three phases of programmed cell death. In particular, the interplay of transcriptional regulatory cascades and networks involving multiple transcriptional regulators is crucial in activating the expression of the key death-inducing gene egl-1 and, in some cases, the ced-3 gene in cells destined to die. A protein interaction cascade involving EGL-1, CED-9, CED-4, and CED-3 results in the activation of the key cell death protease CED-3, which is tightly controlled by multiple positive and negative regulators. The activation of the CED-3 caspase then initiates the cell disassembly process by cleaving and activating or inactivating crucial CED-3 substrates; leading to activation of multiple cell death execution events, including nuclear DNA fragmentation, mitochondrial elimination, phosphatidylserine externalization, inactivation of survival signals, and clearance of apoptotic cells. Further studies of programmed cell death in C. elegans will continue to advance our understanding of how programmed cell death is regulated, activated, and executed in general.
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18
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Penberthy KK, Ravichandran KS. Apoptotic cell recognition receptors and scavenger receptors. Immunol Rev 2016; 269:44-59. [PMID: 26683144 DOI: 10.1111/imr.12376] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Phosphatidylserine recognition receptors are a highly diverse set of receptors grouped by their ability to recognize the 'eat-me' signal phosphatidylserine on apoptotic cells. Most of the phosphatidylserine recognition receptors dampen inflammation by inducing the production of anti-inflammatory mediators during the phagocytosis of apoptotic corpses. However, many phosphatidylserine receptors are also capable of recognizing other ligands, with some receptors being categorized as scavenger receptors. It is now appreciated that these receptors can elicit different downstream events for particular ligands. Therefore, how phosphatidylserine recognition receptors mediate specific signals during recognition of apoptotic cells versus other ligands, and how this might help regulate the inflammatory state of a tissue is an important question that is not fully understood. Here, we revisit the work on signaling downstream of the phosphatidylserine recognition receptor BAI1, and evaluate how these and other signaling modules mediate signaling downstream from other receptors, including Stabilin-2, MerTK, and αvβ5. We also propose the concept that phosphatidylserine recognition receptors could be viewed as a subset of scavenger receptors that are capable of eliciting anti-inflammatory responses to apoptotic cells.
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Affiliation(s)
- Kristen K Penberthy
- Department of Microbiology, Immunology, and Cancer Biology, Center for Cell Clearance, University of Virginia, Charlottesville, VA, USA
| | - Kodi S Ravichandran
- Department of Microbiology, Immunology, and Cancer Biology, Center for Cell Clearance, University of Virginia, Charlottesville, VA, USA
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19
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Wang X, Yang C. Programmed cell death and clearance of cell corpses in Caenorhabditis elegans. Cell Mol Life Sci 2016; 73:2221-36. [PMID: 27048817 PMCID: PMC11108496 DOI: 10.1007/s00018-016-2196-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 03/18/2016] [Indexed: 01/01/2023]
Abstract
Programmed cell death is critical to the development of diverse animal species from C. elegans to humans. In C. elegans, the cell death program has three genetically distinguishable phases. During the cell suicide phase, the core cell death machinery is activated through a protein interaction cascade. This activates the caspase CED-3, which promotes numerous pro-apoptotic activities including DNA degradation and exposure of the phosphatidylserine "eat me" signal on the cell corpse surface. Specification of the cell death fate involves transcriptional activation of the cell death initiator EGL-1 or the caspase CED-3 by coordinated actions of specific transcription factors in distinct cell types. In the cell corpse clearance stage, recognition of cell corpses by phagocytes triggers several signaling pathways to induce phagocytosis of apoptotic cell corpses. Cell corpse-enclosing phagosomes ultimately fuse with lysosomes for digestion of phagosomal contents. This article summarizes our current knowledge about programmed cell death and clearance of cell corpses in C. elegans.
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Affiliation(s)
- Xiaochen Wang
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China.
| | - Chonglin Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.
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20
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Lee J, Moon B, Lee DH, Lee G, Park D. Identification of a novel protein interaction between Elmo1 and Cdc27. Biochem Biophys Res Commun 2016; 471:497-502. [PMID: 26882976 DOI: 10.1016/j.bbrc.2016.02.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 02/12/2016] [Indexed: 11/24/2022]
Abstract
Elmo has no intrinsic catalytic activity but coordinate multiple cellular processes via their interactions with other proteins. Studies thus have been focused on identifying Elmo binding partners, but the number of characterized Elmo-interacting proteins remains limited. Here, we report Cdc27 as a novel Elmo1-interacting protein. In yeast and mammalian cells, Cdc27 specifically interacted with the C-terminal region of Elmo1 essential for Dock1 association and function. The interaction of Elmo1 with Dock1 abrogated binding between Elmo1 and Cdc27, but the Dock1-Elmo1 interaction was unaffected by Cdc27. Similarly, cellular phagocytotic functions mediated by the Elmo1-Dock1-Rac module were unaffected by Cdc27 levels. In summary, a novel binding partner, Cdc27, was identified for Elmo1 and they appear to be independent of Elmo-Dock1-Rac-mediated processes.
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Affiliation(s)
- Juyeon Lee
- School of Life Sciences and Bio Imaging Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea; Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Byeongjin Moon
- School of Life Sciences and Bio Imaging Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Dae-Hee Lee
- Department of Surgery and Pharmacology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gwangrog Lee
- School of Life Sciences and Bio Imaging Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Daeho Park
- School of Life Sciences and Bio Imaging Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea; Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 120-750, Republic of Korea.
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21
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Ismail OZ, Zhang X, Bonventre JV, Gunaratnam L. G protein α 12 (Gα 12) is a negative regulator of kidney injury molecule-1-mediated efferocytosis. Am J Physiol Renal Physiol 2015; 310:F607-F620. [PMID: 26697979 DOI: 10.1152/ajprenal.00169.2015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 12/22/2015] [Indexed: 01/01/2023] Open
Abstract
Kidney injury molecule-1 (KIM-1) is a receptor for the "eat me" signal, phosphatidylserine, on apoptotic cells. The specific upregulation of KIM-1 by injured tubular epithelial cells (TECs) enables them to clear apoptotic cells (also known as efferocytosis), thereby protecting from acute kidney injury. Recently, we uncovered that KIM-1 binds directly to the α-subunit of heterotrimeric G12 protein (Gα12) and inhibits its activation by reactive oxygen species during renal ischemia-reperfusion injury (Ismail OZ, Zhang X, Wei J, Haig A, Denker BM, Suri RS, Sener A, Gunaratnam L. Am J Pathol 185: 1207-1215, 2015). Here, we investigated the role that Gα12 plays in KIM-1-mediated efferocytosis by TECs. We showed that KIM-1 remains bound to Gα12 and suppresses its activity during phagocytosis. When we silenced Gα12 expression using small interefering RNA, KIM-1-mediated engulfment of apoptotic cells was increased significantly; in contrast overexpression of constitutively active Gα12 (QLGα12) resulted in inhibition of efferocytosis. Inhibition of RhoA, a key effector of Gα12, using a chemical inhibitor or expression of dominant-negative RhoA, had the same effect as inhibition of Gα12 on efferocytosis. Consistent with this, silencing Gα12 suppressed active RhoA in KIM-1-expressing cells. Finally, using primary TECs from Kim-1+/+ and Kim-1-/- mice, we confirmed that engulfment of apoptotic cells requires KIM-1 expression and that silencing Gα12 enhanced efferocytosis by primary TECs. Our data reveal a previously unknown role for Gα12 in regulating efferocytosis and that renal TECs require KIM-1 to mediate this process. These results may have therapeutic implications given the known harmful role of Gα12 in acute kidney injury.
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Affiliation(s)
- Ola Z Ismail
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada.,Matthew Mailing Centre for Translational Transplant Studies, Lawson Health Research Institute, London, Ontario, Canada
| | - Xizhong Zhang
- Matthew Mailing Centre for Translational Transplant Studies, Lawson Health Research Institute, London, Ontario, Canada
| | - Joseph V Bonventre
- Renal Division and Biomedical Engineering Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; and
| | - Lakshman Gunaratnam
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada; .,Matthew Mailing Centre for Translational Transplant Studies, Lawson Health Research Institute, London, Ontario, Canada.,Division of Nephrology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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22
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Abstract
Cell death is a common and important feature of animal development, and cell death defects underlie many human disease states. The nematode Caenorhabditis elegans has proven fertile ground for uncovering molecular and cellular processes controlling programmed cell death. A core pathway consisting of the conserved proteins EGL-1/BH3-only, CED-9/BCL2, CED-4/APAF1, and CED-3/caspase promotes most cell death in the nematode, and a conserved set of proteins ensures the engulfment and degradation of dying cells. Multiple regulatory pathways control cell death onset in C. elegans, and many reveal similarities with tumor formation pathways in mammals, supporting the idea that cell death plays key roles in malignant progression. Nonetheless, a number of observations suggest that our understanding of developmental cell death in C. elegans is incomplete. The interaction between dying and engulfing cells seems to be more complex than originally appreciated, and it appears that key aspects of cell death initiation are not fully understood. It has also become apparent that the conserved apoptotic pathway is dispensable for the demise of the C. elegans linker cell, leading to the discovery of a previously unexplored gene program promoting cell death. Here, we review studies that formed the foundation of cell death research in C. elegans and describe new observations that expand, and in some cases remodel, this edifice. We raise the possibility that, in some cells, more than one death program may be needed to ensure cell death fidelity.
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Affiliation(s)
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, New York, USA.
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23
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Levy-Strumpf N, Krizus M, Zheng H, Brown L, Culotti JG. The Wnt Frizzled Receptor MOM-5 Regulates the UNC-5 Netrin Receptor through Small GTPase-Dependent Signaling to Determine the Polarity of Migrating Cells. PLoS Genet 2015; 11:e1005446. [PMID: 26292279 PMCID: PMC4546399 DOI: 10.1371/journal.pgen.1005446] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 07/15/2015] [Indexed: 01/28/2023] Open
Abstract
Wnt and Netrin signaling regulate diverse essential functions. Using a genetic approach combined with temporal gene expression analysis, we found a regulatory link between the Wnt receptor MOM-5/Frizzled and the UNC-6/Netrin receptor UNC-5. These two receptors play key roles in guiding cell and axon migrations, including the migration of the C. elegans Distal Tip Cells (DTCs). DTCs migrate post-embryonically in three sequential phases: in the first phase along the Antero-Posterior (A/P) axis, in the second, along the Dorso-Ventral (D/V) axis, and in the third, along the A/P axis. Loss of MOM-5/Frizzled function causes third phase A/P polarity reversals of the migrating DTCs. We show that an over-expression of UNC-5 causes similar DTC A/P polarity reversals and that unc-5 deficits markedly suppress the A/P polarity reversals caused by mutations in mom-5/frizzled. This implicates MOM-5/Frizzled as a negative regulator of unc-5. We provide further evidence that small GTPases mediate MOM-5's regulation of unc-5 such that one outcome of impaired function of small GTPases like CED-10/Rac and MIG-2/RhoG is an increase in unc-5 function. The work presented here demonstrates the existence of cross talk between components of the Netrin and Wnt signaling pathways and provides further insights into the way guidance signaling mechanisms are integrated to orchestrate directed cell migration.
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Affiliation(s)
- Naomi Levy-Strumpf
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- * E-mail:
| | - Meghan Krizus
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Hong Zheng
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Louise Brown
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Joseph G. Culotti
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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24
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Nakaya M. [Research on Molecular Mechanisms of Engulfment of Apoptotic Cells]. YAKUGAKU ZASSHI 2015; 135:949-54. [PMID: 26234352 DOI: 10.1248/yakushi.15-00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Apoptotic cells generated during development and immune responses in animals are rapidly engulfed by phagocytes, such as macrophages and dendritic cells. When the engulfment process malfunctions, the apoptotic cells undergo secondary necrosis, which results in the release of noxious cellular components into the extracellular space. Thus, the efficient clearance of apoptotic cells is indispensable for the maintenance of tissue homeostasis; however, the molecular mechanisms underlying the engulfment of apoptotic cells remain largely unknown. To identify the molecules that are involved in this process, we developed a functional screening strategy using a retrovirus cDNA library. Using this assay, we isolated cDNA clones encoding RhoG and Rab5 which enhanced the engulfment of apoptotic cells. In addition, we found that Rac1, which is very similar to RhoG, and Rab5 are necessary for engulfment; their activities were successfully visualized by a combination of fluorescence resonance energy transfer technology with time-lapse imaging techniques. We further determined that G protein-coupled receptor kinase 6 (GRK6), originally identified as a kinase responsible for the desensitization and downregulation of G-protein-coupled receptors, activates Rac1 independent of the two known intracellular engulfment pathways in phagocytes. GRK6-deficient macrophages exhibited impaired phagocytosis of apoptotic cells. Consequently, GRK6-deficient mice developed autoimmune phenotypes such as an increase in the amount of anti-dsDNA in serum and the deposition of immune complexes in the kidney. Thus, our findings contributed to the understanding of the molecular mechanisms that regulate apoptotic engulfment in phagocytes.
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Affiliation(s)
- Michio Nakaya
- Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University
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25
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Makino Y, Tsuda M, Ohba Y, Nishihara H, Sawa H, Nagashima K, Tanaka S. Tyr724 phosphorylation of ELMO1 by Src is involved in cell spreading and migration via Rac1 activation. Cell Commun Signal 2015. [PMID: 26205662 PMCID: PMC4513707 DOI: 10.1186/s12964-015-0113-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The complex of Dock180/ELMO1 that functions as a bipartite guanine nucleotide exchange factor for Rac is essential for diverse physiological and pathological processes of cells such as cell migration, phagocytosis, and invasion of cancer cells. Among the Src-family tyrosine kinases (SFKs), it has been reported that Hck directly phosphorylates ELMO1, regulating phagocytosis by promoting activation of Rac1; however, the involvement of other SFKs in ELMO1 phosphorylation has remained unknown. Here, we identified novel tyrosine (Y) residues of ELMO1 phosphorylated by SFKs, and examined the effects on Rac1 activity, cell adhesion, spreading, and cell motility on extracellular matrix (ECM). RESULTS In this study, we unveiled that Src and Fyn can induce tyrosine phosphorylation of ELMO1 in in vivo and in vitro phosphorylation assays. Mutational analyses identified both Y720 and Y724 residues of ELMO1 as Src-mediated phosphorylation sites, preferentially on Y724. Single substitution of Y724 to Phe abrogated Rac1 activation triggered by Src. To elucidate the biological function of pY724, we established NIH3T3 cells stably expressing wild-type ELMO1 or its Y724F mutant together with Dock180. Among them, Y724-deficient cells exhibited a depletion of Rac1 activity with diminished phosphorylation of ELMO1 even upon the ECM-stimulation. It is noteworthy that NIH3T3 cells with ELMO1 Y724F were strikingly defective to promote cell spreading on fibronectin-coated dish, concomitantly exhibiting immature assemblies of actin stress fibers and focal adhesions. Eventually, ELMO1 Y724F significantly impaired cell migration. CONCLUSION These results define that Src-mediated Y724 phosphorylation in ELMO1 plays a critical role for cell spreading via activation of Rac1, leading to promotion of cell migration. As the overexpression and/or hyperactivation of Src have been shown in a wide variety of human cancers, Src-mediated phosphorylation of Y724 in ELMO1 may regulate cancer cell adhesion to the ECM, invasion into surrounding tissues, and subsequent distant metastasis.
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Affiliation(s)
- Yoshinori Makino
- Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, N15, W7, Kita-ku, Sapporo, 060-8638, Japan. .,Laboratory of Pathology and Development, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.
| | - Masumi Tsuda
- Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, N15, W7, Kita-ku, Sapporo, 060-8638, Japan.
| | - Yusuke Ohba
- Department of Cell Physiology, Hokkaido University Graduate School of Medicine, N15, W7, Kita-ku, Sapporo, 060-8638, Japan.
| | - Hiroshi Nishihara
- Department of Translational Pathology, Hokkaido University Graduate School of Medicine, N15, W7, Kita-ku, Sapporo, 060-8638, Japan.
| | - Hirofumi Sawa
- Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, N15, W7, Kita-ku, Sapporo, 060-8638, Japan. .,Hokkaido University Research Center for Zoonosis Control, Sapporo, 001-0020, Japan.
| | - Kazuo Nagashima
- Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, N15, W7, Kita-ku, Sapporo, 060-8638, Japan. .,Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan.
| | - Shinya Tanaka
- Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, N15, W7, Kita-ku, Sapporo, 060-8638, Japan. .,Department of Translational Pathology, Hokkaido University Graduate School of Medicine, N15, W7, Kita-ku, Sapporo, 060-8638, Japan.
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26
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Yang H, Chen YZ, Zhang Y, Wang X, Zhao X, Godfroy JI, Liang Q, Zhang M, Zhang T, Yuan Q, Ann Royal M, Driscoll M, Xia NS, Yin H, Xue D. A lysine-rich motif in the phosphatidylserine receptor PSR-1 mediates recognition and removal of apoptotic cells. Nat Commun 2015; 6:5717. [PMID: 25564762 PMCID: PMC4306451 DOI: 10.1038/ncomms6717] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 10/31/2014] [Indexed: 02/02/2023] Open
Abstract
The conserved phosphatidylserine receptor (PSR) was first identified as a receptor for phosphatidylserine, an "eat-me" signal exposed by apoptotic cells. However, several studies suggest that PSR may also act as an arginine demethylase, a lysyl hydroxylase, or an RNA binding protein through its N-terminal JmjC domain. How PSR might execute drastically different biochemical activities, and whether they are physiologically significant, remain unclear. Here we report that a lysine-rich motif in the extracellular domain of PSR-1, the Caenorhabditis elegans PSR, mediates specific phosphatidylserine binding in vitro and clearance of apoptotic cells in vivo. This motif also mediates phosphatidylserine-induced oligomerization of PSR-1, suggesting a mechanism by which PSR-1 activates phagocytosis. Mutations in the phosphatidylserine-binding motif, but not in its Fe(II) binding site critical for the JmjC activity, abolish PSR-1 phagocytic function. Moreover, PSR-1 enriches and clusters around apoptotic cells during apoptosis. These results establish that PSR-1 is a conserved, phosphatidylserine-recognizing phagocyte receptor.
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Affiliation(s)
- Hengwen Yang
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Yu-Zen Chen
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Yi Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohui Wang
- Department of Chemistry &Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Xiang Zhao
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - James I Godfroy
- Department of Chemistry &Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Qian Liang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Man Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tianying Zhang
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Quan Yuan
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Mary Ann Royal
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Monica Driscoll
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Ning-Shao Xia
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Hang Yin
- 1] Department of Chemistry &Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA [2] Center of Basic Molecular Science and Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Ding Xue
- 1] Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA [2] School of Life Sciences, Tsinghua University, Beijing 100084, China
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27
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Neukomm LJ, Kinchen JM. SRGP-1 regulation, targets, and contribution to cell killing in C. elegans. Small GTPases 2014; 2:177-181. [PMID: 21776421 DOI: 10.4161/sgtp.2.3.16700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 05/25/2011] [Accepted: 05/30/2011] [Indexed: 11/19/2022] Open
Abstract
The engulfment of apoptotic cell corpses is an evolutionary conserved process used by multicellular systems to remove cells with inappropriate potential (e.g., self-reactive T-cells, potentially cancerous cells). Neighboring or specialized phagocytic cells remove cell corpses through distinct steps: they first recognize the cell on the verge of death, then reorchestrate their cellular architecture toward it, actively contribute to cell killing, and eventually engulf the corpse. Thus engulfment signaling must be tightly controlled to maintain tissue homeostasis. Signaling cascades mediating cell corpse clearance likely converge at the level of the small GTPase CED-10 (Rac1); given this key position, CED-10 must be subject to a tight regulatory mechanism to prevent inappropriate phagocytic events. Here, we discuss recent work characterizing srgp-1 (nematode ortholog of mammalian srGAP), a candidate GTPase activating protein (GAP) for CED-10 involved in cell corpse clearance and "sick" cell killing in C. elegans. We additionally discuss several possible determinants of SRGP-1 function, contributing to either SRGP-1 localization and/or activation. We also survey other potential candidate GTPases that might contribute to cell corpse clearance in C. elegans, and eventually recapitulate the role of engulfment during cell killing.
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Affiliation(s)
- Lukas Jakob Neukomm
- Institute of Molecular Life Science; University of Zürich; Zürich, Switzerland
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28
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Mulinari S, Häcker U. Rho-guanine nucleotide exchange factors during development: Force is nothing without control. Small GTPases 2014; 1:28-43. [PMID: 21686118 DOI: 10.4161/sgtp.1.1.12672] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Revised: 05/31/2010] [Accepted: 06/14/2010] [Indexed: 01/04/2023] Open
Abstract
The development of multicellular organisms is associated with extensive rearrangements of tissues and cell sheets. The driving force for these rearrangements is generated mostly by the actin cytoskeleton. In order to permit the reproducible development of a specific body plan, dynamic reorganization of the actin cytoskeleton must be precisely coordinated in space and time. GTP-exchange factors that activate small GTPases of the Rho family play an important role in this process. Here we review the role of this class of cytoskeletal regulators during important developmental processes such as epithelial morphogenesis, cytokinesis, cell migration, cell polarity, neuronal growth cone extension and phagocytosis in different model systems.
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Affiliation(s)
- Shai Mulinari
- Department of Experimental Medical Science; Lund Strategic Research Center for Stem Cell Biology and Cell Therapy; Lund University; Lund, Sweden
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29
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Morishita K, Ozasa F, Eguchi K, Yoshioka Y, Yoshida H, Hiai H, Yamaguchi M. Drosophila DOCK family protein sponge regulates the JNK pathway during thorax development. Cell Struct Funct 2014; 39:113-24. [PMID: 25311449 DOI: 10.1247/csf.14008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The dedicator of cytokinesis (DOCK) family proteins that are conserved in a wide variety of species are known as DOCK1-DOCK11 in mammals. The Sponge (Spg) is a Drosophila counterpart to the mammalian DOCK3. Specific knockdown of spg by pannir-GAL4 or apterous-GAL4 driver in wing discs induced split thorax phenotype in adults. Reduction of the Drosophila c-Jun N-terminal kinase (JNK), basket (bsk) gene dose enhanced the spg knockdown-induced phenotype. Conversely, overexpression of bsk suppressed the split thorax phenotype. Monitoring JNK activity in the wing imaginal discs by immunostaining with anti-phosphorylated JNK (anti-pJNK) antibody together with examination of lacZ expression in a puckered-lacZ enhancer trap line revealed the strong reduction of the JNK activity in the spg knockdown clones. This was further confirmed by Western immunoblot analysis of extracts from wing discs of spg knockdown fly with anti-pJNK antibody. Furthermore, the Duolink in situ Proximity Ligation Assay method detected interaction signals between Spg and Rac1 in the wing discs. Taken together, these results indicate Spg positively regulates JNK pathway that is required for thorax development and the regulation is mediated by interaction with Rac1.
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30
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Xu M, Liu Y, Zhao L, Gan Q, Wang X, Yang C. The lysosomal cathepsin protease CPL-1 plays a leading role in phagosomal degradation of apoptotic cells in Caenorhabditis elegans. Mol Biol Cell 2014; 25:2071-83. [PMID: 24829385 PMCID: PMC4072580 DOI: 10.1091/mbc.e14-01-0015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In Caenorhabditis elegans, the lysosomal cathepsin protease CPL-1 is indispensable for clearance of apoptotic cells by playing a leading role in destruction of cell corpses in phagolysosomes. During programmed cell death, the clearance of apoptotic cells is achieved by their phagocytosis and delivery to lysosomes for destruction in engulfing cells. However, the role of lysosomal proteases in cell corpse destruction is not understood. Here we report the identification of the lysosomal cathepsin CPL-1 as an indispensable protease for apoptotic cell removal in Caenorhabditis elegans. We find that loss of cpl-1 function leads to strong accumulation of germ cell corpses, which results from a failure in degradation rather than engulfment. CPL-1 is expressed in a variety of cell types, including engulfment cells, and its mutation does not affect the maturation of cell corpse–containing phagosomes, including phagosomal recruitment of maturation effectors and phagosome acidification. Of importance, we find that phagosomal recruitment and incorporation of CPL-1 occurs before digestion of cell corpses, which depends on factors required for phagolysosome formation. Using RNA interference, we further examine the role of other candidate lysosomal proteases in cell corpse clearance but find that they do not obviously affect this process. Collectively, these findings establish CPL-1 as the leading lysosomal protease required for elimination of apoptotic cells in C. elegans.
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Affiliation(s)
- Meng Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, ChinaGraduate University of Chinese Academy of Sciences, Beijing 100109, China
| | - Yubing Liu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Liyuan Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, ChinaGraduate University of Chinese Academy of Sciences, Beijing 100109, China
| | - Qiwen Gan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, ChinaGraduate University of Chinese Academy of Sciences, Beijing 100109, China
| | - Xiaochen Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Chonglin Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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31
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Small GTPase CDC-42 promotes apoptotic cell corpse clearance in response to PAT-2 and CED-1 in C. elegans. Cell Death Differ 2014; 21:845-53. [PMID: 24632947 PMCID: PMC4013519 DOI: 10.1038/cdd.2014.23] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 11/27/2013] [Accepted: 12/17/2013] [Indexed: 12/26/2022] Open
Abstract
The rapid clearance of dying cells is important for the well-being of multicellular organisms. In C. elegans, cell corpse removal is mainly mediated by three parallel engulfment signaling cascades. These pathways include two small GTPases, MIG-2/RhoG and CED-10/Rac1. Here we present the identification and characterization of CDC-42 as a third GTPase involved in the regulation of cell corpse clearance. Genetic analyses performed by both loss of cdc-42 function and cdc-42 overexpression place cdc-42 in parallel to the ced-2/5/12 signaling module, in parallel to or upstream of the ced-10 module, and downstream of the ced-1/6/7 module. CDC-42 accumulates in engulfing cells at membranes surrounding apoptotic corpses. The formation of such halos depends on the integrins PAT-2/PAT-3, UNC-112 and the GEF protein UIG-1, but not on the canonical ced-1/6/7 or ced-2/5/12 signaling modules. Together, our results suggest that the small GTPase CDC-42 regulates apoptotic cell engulfment possibly upstream of the canonical Rac GTPase CED-10, by polarizing the engulfing cell toward the apoptotic corpse in response to integrin signaling and ced-1/6/7 signaling in C. elegans.
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32
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Tasdemir-Yilmaz OE, Freeman MR. Astrocytes engage unique molecular programs to engulf pruned neuronal debris from distinct subsets of neurons. Genes Dev 2013; 28:20-33. [PMID: 24361692 PMCID: PMC3894410 DOI: 10.1101/gad.229518.113] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Neural circuit assembly involves an initial overproduction of neurons and synaptic connections, followed by their selective elimination. Tasdemir-Yilmaz and Freeman show that Drosophila larval astrocytes are the primary phagocytic cell type in the pupal CNS neuropil. MB γ neuron axons are engulfed by astrocytes using the Draper and Crk/Mbc/dCed-12 signaling pathways, while Crk/Mbc/dCed-12, but not Draper, mediates the elimination of vCrz+ neurites. Eliminating Draper signaling delays early vCrz+ neurite degeneration, suggesting that glial cells promote neurite destruction through engulfment signaling. Precise neural circuit assembly is achieved by initial overproduction of neurons and synapses, followed by refinement through elimination of exuberant neurons and synapses. Glial cells are the primary cells responsible for clearing neuronal debris, but the cellular and molecular basis of glial pruning is poorly defined. Here we show that Drosophila larval astrocytes transform into phagocytes through activation of a cell-autonomous, steroid-dependent program at the initiation of metamorphosis and are the primary phagocytic cell type in the pupal neuropil. We examined the developmental elimination of two neuron populations—mushroom body (MB) γ neurons and vCrz+ neurons (expressing Corazonin [Crz] neuropeptide in the ventral nerve cord [VNC])—where only neurites are pruned or entire cells are eliminated, respectively. We found that MB γ axons are engulfed by astrocytes using the Draper and Crk/Mbc/dCed-12 signaling pathways in a partially redundant manner. In contrast, while elimination of vCrz+ cell bodies requires Draper, elimination of vCrz+ neurites is mediated by Crk/Mbc/dCed-12 but not Draper. Intriguingly, we also found that elimination of Draper delayed vCrz+ neurite degeneration, suggesting that glia promote neurite destruction through engulfment signaling. This study identifies a novel role for astrocytes in the clearance of synaptic and neuronal debris and for Crk/Mbc/dCed-12 as a new glial pathway mediating pruning and reveals, unexpectedly, that the engulfment signaling pathways engaged by glia depend on whether neuronal debris was generated through cell death or local pruning.
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Affiliation(s)
- Ozge E Tasdemir-Yilmaz
- Department of Neurobiology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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33
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Shen Q, He B, Lu N, Conradt B, Grant BD, Zhou Z. Phagocytic receptor signaling regulates clathrin and epsin-mediated cytoskeletal remodeling during apoptotic cell engulfment in C. elegans. Development 2013; 140:3230-43. [PMID: 23861060 PMCID: PMC3931732 DOI: 10.1242/dev.093732] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The engulfment and subsequent degradation of apoptotic cells by phagocytes is an evolutionarily conserved process that efficiently removes dying cells from animal bodies during development. Here, we report that clathrin heavy chain (CHC-1), a membrane coat protein well known for its role in receptor-mediated endocytosis, and its adaptor epsin (EPN-1) play crucial roles in removing apoptotic cells in Caenorhabditis elegans. Inactivating epn-1 or chc-1 disrupts engulfment by impairing actin polymerization. This defect is partially suppressed by inactivating UNC-60, a cofilin ortholog and actin server/depolymerization protein, further indicating that EPN-1 and CHC-1 regulate actin assembly during pseudopod extension. CHC-1 is enriched on extending pseudopods together with EPN-1, in an EPN-1-dependent manner. Epistasis analysis places epn-1 and chc-1 in the same cell-corpse engulfment pathway as ced-1, ced-6 and dyn-1. CED-1 signaling is necessary for the pseudopod enrichment of EPN-1 and CHC-1. CED-1, CED-6 and DYN-1, like EPN-1 and CHC-1, are essential for the assembly and stability of F-actin underneath pseudopods. We propose that in response to CED-1 signaling, CHC-1 is recruited to the phagocytic cup through EPN-1 and acts as a scaffold protein to organize actin remodeling. Our work reveals novel roles of clathrin and epsin in apoptotic-cell internalization, suggests a Hip1/R-independent mechanism linking clathrin to actin assembly, and ties the CED-1 pathway to cytoskeleton remodeling.
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Affiliation(s)
- Qian Shen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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34
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Morthorst TH, Olsen A. Cell-nonautonomous inhibition of radiation-induced apoptosis by dynein light chain 1 in Caenorhabditis elegans. Cell Death Dis 2013; 4:e799. [PMID: 24030151 PMCID: PMC3789177 DOI: 10.1038/cddis.2013.319] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 06/18/2013] [Accepted: 07/30/2013] [Indexed: 11/09/2022]
Abstract
The evolutionarily conserved process of programmed cell death, apoptosis, is essential for development of multicellular organisms and is also a protective mechanism against cellular damage. We have identified dynein light chain 1 (DLC-1) as a new regulator of germ cell apoptosis in Caenorhabditis elegans. The DLC-1 protein is highly conserved across species and is a part of the dynein motor complex. There is, however, increasing evidence for dynein-independent functions of DLC-1, and our data describe a novel dynein-independent role. In mammalian cells, DLC-1 is important for cellular transport, cell division and regulation of protein activity, and it has been implicated in cancer. In C. elegans, we find that knockdown of dlc-1 by RNA interference (RNAi) induces excessive apoptosis in the germline but not in somatic cells during development. We show that DLC-1 mediates apoptosis through the genes lin-35, egl-1 and ced-13, which are all involved in the response to ionising radiation (IR)-induced apoptosis. In accordance with this, we show that IR cannot further induce apoptosis in dlc-1(RNAi) animals. Furthermore, we find that DLC-1 is functioning cell nonautonomously through the same pathway as kri-1 in response to IR-induced apoptosis and that DLC-1 regulates the levels of KRI-1. Our results strengthen the notion of a highly dynamic communication between somatic cells and germ cells in regulating the apoptotic process.
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Affiliation(s)
- T H Morthorst
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus C DK-8000, Denmark
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35
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Eguchi K, Yoshioka Y, Yoshida H, Morishita K, Miyata S, Hiai H, Yamaguchi M. The Drosophila DOCK family protein sponge is involved in differentiation of R7 photoreceptor cells. Exp Cell Res 2013; 319:2179-95. [DOI: 10.1016/j.yexcr.2013.05.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/16/2013] [Accepted: 05/18/2013] [Indexed: 01/17/2023]
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36
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Gómez-Orte E, Sáenz-Narciso B, Moreno S, Cabello J. Multiple functions of the noncanonical Wnt pathway. Trends Genet 2013; 29:545-53. [PMID: 23846023 DOI: 10.1016/j.tig.2013.06.003] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/29/2013] [Accepted: 06/07/2013] [Indexed: 01/11/2023]
Abstract
Thirty years after the identification of WNTs, understanding of their signal transduction pathways continues to expand. Here, we review recent advances in characterizing the Wnt-dependent signaling pathways in Caenorhabditis elegans linking polar signals to rearrangements of the cytoskeleton in different developmental processes, such as proper mitotic spindle orientation, cell migration, and engulfment of apoptotic corpses. In addition to the well-described transcriptional outputs of the canonical and noncanonical Wnt pathways, new branches regulating nontranscriptional outputs that control RAC (Ras related GTPase) activity are also discussed. These findings suggest that Wnt signaling is a master regulator not only of development, but also of cell polarization.
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Affiliation(s)
- Eva Gómez-Orte
- Center for Biomedical Research of La Rioja (CIBIR), C/Piqueras 98, 26006 Logroño, Spain
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37
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Hochreiter-Hufford A, Ravichandran KS. Clearing the dead: apoptotic cell sensing, recognition, engulfment, and digestion. Cold Spring Harb Perspect Biol 2013; 5:a008748. [PMID: 23284042 DOI: 10.1101/cshperspect.a008748] [Citation(s) in RCA: 368] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Clearance of apoptotic cells is the final stage of programmed cell death. Uncleared corpses can become secondarily necrotic, promoting inflammation and autoimmunity. Remarkably, even in tissues with high cellular turnover, apoptotic cells are rarely seen because of efficient clearance mechanisms in healthy individuals. Recently, significant progress has been made in understanding the steps involved in prompt cell clearance in vivo. These include the sensing of corpses via "find me" signals, the recognition of corpses via "eat me" signals and their cognate receptors, the signaling pathways that regulate cytoskeletal rearrangement necessary for engulfment, and the responses of the phagocyte that keep cell clearance events "immunologically silent." This study focuses on our understanding of these steps.
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Affiliation(s)
- Amelia Hochreiter-Hufford
- Department of Microbiology, Immunology and Cancer Biology, Center for Cell Clearance and Beirne Carter Center for Immunology Research, University of Virginia, Charlottesville, VA 22908, USA
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38
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Li Z, Lu N, He X, Zhou Z. Monitoring the clearance of apoptotic and necrotic cells in the nematode Caenorhabditis elegans. Methods Mol Biol 2013; 1004:183-202. [PMID: 23733578 DOI: 10.1007/978-1-62703-383-1_14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The nematode Caenorhabditis elegans is an excellent model organism for studying the mechanisms -controlling cell death, including apoptosis, a cell suicide event, and necrosis, pathological cell deaths caused by environmental insults or genetic alterations. C. elegans has also been established as a model for understanding how dying cells are cleared from animal bodies. In particular, the transparent nature of worm bodies and eggshells make C. elegans particularly amenable for live-cell microscopy. Here we describe methods for identifying apoptotic and necrotic cells in living C. elegans embryos, larvae, and adults and for monitoring their clearance during development. We further discuss specific methods to distinguish engulfed from unengulfed apoptotic cells, and methods to monitor cellular and molecular events occurring during phagosome maturation. These methods are based on Differential Interference Contrast (DIC) microscopy or fluorescence microscopy using GFP-based reporters.
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Affiliation(s)
- Zao Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
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39
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Huang J, Wang H, Chen Y, Wang X, Zhang H. Residual body removal during spermatogenesis in C. elegans requires genes that mediate cell corpse clearance. Development 2012; 139:4613-22. [PMID: 23172915 PMCID: PMC3509724 DOI: 10.1242/dev.086769] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2012] [Indexed: 12/20/2022]
Abstract
Generation of spermatozoa involves segregation of most of the cytoplasm into residual bodies, which are detached from spermatids and eliminated in mammals. However, the molecular and cellular mechanism underlying the removal of residual bodies remains largely unknown. Here, we demonstrate that during C. elegans spermatogenesis residual bodies are engulfed and degraded by gonadal sheath cells, a process that uses the same set of genes underlying apoptotic cell removal. The two partially redundant engulfment pathways that clear cell corpses also mediate phagocytosis of residual bodies, possibly by recognizing the 'eat me' signal phosphatidylserine exposed on the surface. The residual body-containing phagosome undergoes a maturation process involving sequential steps including dynamic coating with PtdIns(3)P and association of RAB small GTPases. The genetic hierarchy of residual body removal in hermaphrodites is similar to that of cell corpse clearance, but male residual body removal involves a distinct hierarchy, with differential use of the engulfment genes. Efficient removal of residual bodies regulates the number of spermatids and effective transfer of spermatids during male matings. Our results indicate that a similar molecular mechanism is employed for the removal of residual bodies and apoptotic cell corpses in C. elegans.
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Affiliation(s)
- Jie Huang
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, P.R. China
- Key Laboratory of Medical Immunology, Ministry of Health, Peking University Health Science Center, Beijing, 100191, P.R. China
| | - Haibin Wang
- College of Life Sciences, China Agricultural University, Beijing, 100094, P.R. China
- National Institute of Biological Sciences, Beijing, 102206, P.R. China
| | - Yingyu Chen
- Key Laboratory of Medical Immunology, Ministry of Health, Peking University Health Science Center, Beijing, 100191, P.R. China
| | - Xiaochen Wang
- National Institute of Biological Sciences, Beijing, 102206, P.R. China
| | - Hong Zhang
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, P.R. China
- National Institute of Biological Sciences, Beijing, 102206, P.R. China
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40
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Pinto SM, Hengartner MO. Cleaning up the mess: cell corpse clearance in Caenorhabditis elegans. Curr Opin Cell Biol 2012. [PMID: 23206434 DOI: 10.1016/j.ceb.2012.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genetic and cell biology studies have led to the identification in Caenorhabditis elegans of a set of evolutionary conserved cellular mechanisms responsible for the clearance of apoptotic cells. Based on the phenotype of cell corpse clearance mutants, corpse clearance can be divided into three distinct, but linked steps: corpse recognition, corpse internalization, and corpse degradation. Work in recent years has led to a better understanding of the molecular pathways that mediate each of these steps. Here, we review recent developments in our understanding of in vivo cell corpse clearance in this simple but most elegant model organism.
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Affiliation(s)
- Sérgio Morgado Pinto
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; Graduate Program in Areas of Basic and Applied Biology (GABBA), Universidade do Porto, Porto, Portugal
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41
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Margaron Y, Fradet N, Côté JF. ELMO recruits actin cross-linking family 7 (ACF7) at the cell membrane for microtubule capture and stabilization of cellular protrusions. J Biol Chem 2012. [PMID: 23184944 DOI: 10.1074/jbc.m112.431825] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
ELMO and DOCK180 proteins form an evolutionarily conserved module controlling Rac GTPase signaling during cell migration, phagocytosis, and myoblast fusion. Here, we identified the microtubule and actin-binding spectraplakin ACF7 as a novel ELMO-interacting partner. A C-terminal polyproline segment in ELMO and the last spectrin repeat of ACF7 mediate a direct interaction between these proteins. Co-expression of ELMO1 with ACF7 promoted the formation of long membrane protrusions during integrin-mediated cell spreading. Quantification of membrane dynamics established that coupling of ELMO and ACF7 increases the persistence of the protruding activity. Mechanistically, we uncovered a role for ELMO in the recruitment of ACF7 to the membrane to promote microtubule capture and stability. Functionally, these effects of ELMO and ACF7 on cytoskeletal dynamics required the Rac GEF DOCK180. In conclusion, our findings support a role for ELMO in protrusion stability by acting at the interface between the actin cytoskeleton and the microtubule network.
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Affiliation(s)
- Yoran Margaron
- Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
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42
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Huang S, Jia K, Wang Y, Zhou Z, Levine B. Autophagy genes function in apoptotic cell corpse clearance during C. elegans embryonic development. Autophagy 2012; 9:138-49. [PMID: 23108454 DOI: 10.4161/auto.22352] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Efficient apoptotic corpse clearance is essential for metazoan development and adult tissue homeostasis. Several autophagy proteins have been previously shown to function in apoptotic cell clearance; however, it remains unknown whether autophagy genes are essential for efficient apoptotic corpse clearance in the developing embryo. Here we show that, in Caenorhabditis elegans embryos, loss-of-function mutations in several autophagy genes that act at distinct steps in the autophagy pathway resulted in increased numbers of cell corpses and delayed cell corpse clearance. Further analysis of embryos with a null mutation in bec- 1, the C. elegans ortholog of yeast VPS30/ATG6/mammalian beclin 1 (BECN1), revealed normal phosphatidylserine exposure on dying cells. Moreover, the corpse clearance defects of bec- 1(ok691) embryos were rescued by BEC-1 expression in engulfing cells, and bec- 1(ok691) enhanced corpse clearance defects in nematodes with simultaneous mutations in the engulfment genes, ced- 1, ced- 6 or ced- 12. Together, these data demonstrate that autophagy proteins play an important role in cell corpse clearance during nematode embryonic development, and likely function in parallel to known pathways involved in corpse removal.
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Affiliation(s)
- Shuyi Huang
- Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
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43
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East MP, Bowzard JB, Dacks JB, Kahn RA. ELMO domains, evolutionary and functional characterization of a novel GTPase-activating protein (GAP) domain for Arf protein family GTPases. J Biol Chem 2012; 287:39538-53. [PMID: 23014990 DOI: 10.1074/jbc.m112.417477] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human family of ELMO domain-containing proteins (ELMODs) consists of six members and is defined by the presence of the ELMO domain. Within this family are two subclassifications of proteins, based on primary sequence conservation, protein size, and domain architecture, deemed ELMOD and ELMO. In this study, we used homology searching and phylogenetics to identify ELMOD family homologs in genomes from across eukaryotic diversity. This demonstrated not only that the protein family is ancient but also that ELMOs are potentially restricted to the supergroup Opisthokonta (Metazoa and Fungi), whereas proteins with the ELMOD organization are found in diverse eukaryotes and thus were likely the form present in the last eukaryotic common ancestor. The segregation of the ELMO clade from the larger ELMOD group is consistent with their contrasting functions as unconventional Rac1 guanine nucleotide exchange factors and the Arf family GTPase-activating proteins, respectively. We used unbiased, phylogenetic sorting and sequence alignments to identify the most highly conserved residues within the ELMO domain to identify a putative GAP domain within the ELMODs. Three independent but complementary assays were used to provide an initial characterization of this domain. We identified a highly conserved arginine residue critical for both the biochemical and cellular GAP activity of ELMODs. We also provide initial evidence of the function of human ELMOD1 as an Arf family GAP at the Golgi. These findings provide the basis for the future study of the ELMOD family of proteins and a new avenue for the study of Arf family GTPases.
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Affiliation(s)
- Michael P East
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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44
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Wong MC, Schwarzbauer JE. Gonad morphogenesis and distal tip cell migration in the Caenorhabditis elegans hermaphrodite. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2012; 1:519-31. [PMID: 23559979 PMCID: PMC3614366 DOI: 10.1002/wdev.45] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell migration and morphogenesis are key events in tissue development and organogenesis. In Caenorhabditis elegans, the migratory path of the distal tip cells determines the morphology of the hermaphroditic gonad. The distal tip cells undergo a series of migratory phases interspersed with turns to form the gonad. A wide variety of genes have been identified as crucial to this process, from genes that encode components and modifiers of the extracellular matrix to signaling proteins and transcriptional regulators. The connections between extracellular and transmembrane protein functions and intracellular pathways are essential for distal tip cell migration, and the integration of this information governs gonad morphogenesis and determines gonad size and shape.
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Affiliation(s)
- Ming-Ching Wong
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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45
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Distinct molecular pathways mediate glial activation and engulfment of axonal debris after axotomy. Nat Neurosci 2012; 15:979-87. [PMID: 22706267 PMCID: PMC4976689 DOI: 10.1038/nn.3135] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 05/11/2012] [Indexed: 12/16/2022]
Abstract
Glial cells efficiently recognize and clear cellular debris after nervous system injury to maintain brain homeostasis, but pathways governing glial responses to neural injury remain poorly defined. We identify the Drosophila guanine-nucleotide exchange factor (GEF) complex Crk/Mbc/dCed-12, and the small GTPase Rac1 as novel modulators of glial clearance of axonal debris. We show Crk/Mbc/dCed-12 and Rac1 function in a non-redundant fashion with the Draper pathway—loss of either pathway fully suppresses clearance of axonal debris. Draper signaling is required early during glial responses, promoting glial activation, which includes increased Draper and dCed-6 expression and extension of glial membranes to degenerating axons. In contrast, the Crk/Mbc/dCed-12 complex functions at later phases promoting glial phagocytosis of axonal debris. Our work identifies new components of the glial engulfment machinery and shows that glial activation, phagocytosis of axonal debris, and termination of responses to injury are genetically separable events mediated by distinct signaling pathways.
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46
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Florey O, Overholtzer M. Autophagy proteins in macroendocytic engulfment. Trends Cell Biol 2012; 22:374-80. [PMID: 22608991 DOI: 10.1016/j.tcb.2012.04.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 04/11/2012] [Accepted: 04/12/2012] [Indexed: 10/28/2022]
Abstract
Eukaryotic cells must constantly degrade both intracellular and extracellular material to maintain cellular and organismal homeostasis. Two engulfment pathways, autophagy and phagocytosis, contribute to the turnover of intracellular and extracellular substrates by delivering material to the lysosome. Historically these are thought to be separate pathways, but recent studies have revealed the direct participation of autophagy proteins in phagocytosis. Autophagy proteins lipidate LC3 onto phagosomes and other macroendocytic vacuole membranes, and are required for lysosomal degradation of engulfed cargo, demonstrating an autophagosome-independent role for autophagy proteins in mediating the turnover of extracellular substrates. This review discusses the biological systems in which autophagy proteins have been found to regulate lysosome fusion to non-autophagic membranes.
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Affiliation(s)
- Oliver Florey
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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47
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Hsieh HH, Hsu TY, Jiang HS, Wu YC. Integrin α PAT-2/CDC-42 signaling is required for muscle-mediated clearance of apoptotic cells in Caenorhabditis elegans. PLoS Genet 2012; 8:e1002663. [PMID: 22615577 PMCID: PMC3355063 DOI: 10.1371/journal.pgen.1002663] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 03/06/2012] [Indexed: 11/25/2022] Open
Abstract
Clearance of apoptotic cells by engulfment plays an important role in the homeostasis and development of multicellular organisms. Despite the fact that the recognition of apoptotic cells by engulfment receptors is critical in inducing the engulfment process, the molecular mechanisms are still poorly understood. Here, we characterize a novel cell corpse engulfment pathway mediated by the integrin α subunit PAT-2 in Caenorhabditis elegans and show that it specifically functions in muscle-mediated engulfment during embryogenesis. Inactivation of pat-2 results in a defect in apoptotic cell internalization. The PAT-2 extracellular region binds to the surface of apoptotic cells in vivo, and the intracellular region may mediate signaling for engulfment. We identify essential roles of small GTPase CDC-42 and its activator UIG-1, a guanine-nucleotide exchange factor, in PAT-2–mediated cell corpse removal. PAT-2 and CDC-42 both function in muscle cells for apoptotic cell removal and are co-localized in growing muscle pseudopods around apoptotic cells. Our data suggest that PAT-2 functions through UIG-1 for CDC-42 activation, which in turn leads to cytoskeletal rearrangement and apoptotic cell internalization by muscle cells. Moreover, in contrast to PAT-2, the other integrin α subunit INA-1 and the engulfment receptor CED-1, which signal through the conserved signaling molecules CED-5 (DOCK180)/CED-12 (ELMO) or CED-6 (GULP) respectively, preferentially act in epithelial cells to mediate cell corpse removal during mid-embryogenesis. Our results show that different engulfing cells utilize distinct repertoires of receptors for engulfment at the whole organism level. When cells undergo apoptosis, their corpses are quickly recognized and phagocytosed by engulfing cells. Although many cell types, such as muscle cells and epithelial cells, possess the ability to remove apoptotic cells, little is known about the receptors and signaling pathways used for apoptotic cell uptake by these “amateur” phagocytes. We show that, in Caenorhabditis elegans, integrin PAT-2/PAT-3 functions as an engulfment receptor in muscle cells. The integrin α subunit PAT-2 mediates both the recognition and subsequent phagocytosis of apoptotic cells. PAT-2 signals through UIG-1 for CDC-42 activation, leading to the cytoskeletal reorganization as the engulfing muscle cell extends pseudopods around the apoptotic cell. Furthermore, in contrast to PAT-2, the other integrin α subunit INA-1 and the engulfment receptor CED-1, both of which appear to act upstream of small GTPase CED-10 (RAC1), predominantly function in epithelial cells to mediate cell corpse removal. Therefore, epithelial cells and muscle cells employ different engulfment receptors for apoptotic cell recognition, downstream signaling, and specific GTPase activation during apoptotic cell removal.
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Affiliation(s)
- Hsiao-Han Hsieh
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Tsung-Yuan Hsu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Hang-Shiang Jiang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Yi-Chun Wu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
- Center for Systems Biology, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
- * E-mail:
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48
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Johnson KR, Longo-Guess CM, Gagnon LH. Mutations of the mouse ELMO domain containing 1 gene (Elmod1) link small GTPase signaling to actin cytoskeleton dynamics in hair cell stereocilia. PLoS One 2012; 7:e36074. [PMID: 22558334 PMCID: PMC3338648 DOI: 10.1371/journal.pone.0036074] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 03/25/2012] [Indexed: 11/18/2022] Open
Abstract
Stereocilia, the modified microvilli projecting from the apical surfaces of the sensory hair cells of the inner ear, are essential to the mechanoelectrical transduction process underlying hearing and balance. The actin-filled stereocilia on each hair cell are tethered together by fibrous links to form a highly patterned hair bundle. Although many structural components of hair bundles have been identified, little is known about the signaling mechanisms that regulate their development, morphology, and maintenance. Here, we describe two naturally occurring, allelic mutations that result in hearing and balance deficits in mice, named roundabout (rda) and roundabout-2J (rda(2J)). Positional cloning identified both as mutations of the mouse ELMO domain containing 1 gene (Elmod1), a poorly characterized gene with no previously reported mutant phenotypes. The rda mutation is a 138 kb deletion that includes exons 1-5 of Elmod1, and rda(2J) is an intragenic duplication of exons 3-8 of Elmod1. The deafness associated with these mutations is caused by cochlear hair cell dysfunction, as indicated by conspicuous elongations and fusions of inner hair cell stereocilia and progressive degeneration of outer hair cell stereocilia. Mammalian ELMO-family proteins are known to be involved in complexes that activate small GTPases to regulate the actin cytoskeleton during phagocytosis and cell migration. ELMOD1 and ELMOD2 recently were shown to function as GTPase-activating proteins (GAPs) for the Arf family of small G proteins. Our finding connecting ELMOD1 deficiencies with stereocilia dysmorphologies thus establishes a link between the Ras superfamily of small regulatory GTPases and the actin cytoskeleton dynamics of hair cell stereocilia.
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49
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Van Goethem E, Silva EA, Xiao H, Franc NC. The Drosophila TRPP cation channel, PKD2 and Dmel/Ced-12 act in genetically distinct pathways during apoptotic cell clearance. PLoS One 2012; 7:e31488. [PMID: 22347485 PMCID: PMC3275576 DOI: 10.1371/journal.pone.0031488] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 01/09/2012] [Indexed: 11/18/2022] Open
Abstract
Apoptosis, a genetically programmed cell death, allows for homeostasis and tissue remodelling during development of all multi-cellular organisms. Phagocytes swiftly recognize, engulf and digest apoptotic cells. Yet, to date the molecular mechanisms underlying this phagocytic process are still poorly understood. To delineate the molecular mechanisms of apoptotic cell clearance in Drosophila, we have carried out a deficiency screen and have identified three overlapping phagocytosis-defective mutants, which all delete the fly homologue of the ced-12 gene, known as Dmel\ced12. As anticipated, we have found that Dmel\ced-12 is required for apoptotic cell clearance, as for its C. elegans and mammalian homologues, ced-12 and elmo, respectively. However, the loss of Dmel\ced-12 did not solely account for the phenotypes of all three deficiencies, as zygotic mutations and germ line clones of Dmel\ced-12 exhibited weaker phenotypes. Using a nearby genetically interacting deficiency, we have found that the polycystic kidney disease 2 gene, pkd2, which encodes a member of the TRPP channel family, is also required for phagocytosis of apoptotic cells, thereby demonstrating a novel role for PKD2 in this process. We have also observed genetic interactions between pkd2, simu, drpr, rya-r44F, and retinophilin (rtp), also known as undertaker (uta), a gene encoding a MORN-repeat containing molecule, which we have recently found to be implicated in calcium homeostasis during phagocytosis. However, we have not found any genetic interaction between Dmel\ced-12 and simu. Based on these genetic interactions and recent reports demonstrating a role for the mammalian pkd-2 gene product in ER calcium release during store-operated calcium entry, we propose that PKD2 functions in the DRPR/RTP pathway to regulate calcium homeostasis during this process. Similarly to its C. elegans homologue, Dmel\Ced-12 appears to function in a genetically distinct pathway.
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Affiliation(s)
- Emeline Van Goethem
- Medical Research Council Cell Biology Unit, MRC Laboratory for Molecular Cell Biology and Anatomy and Developmental Biology Department, University College London, London, United Kingdom
| | - Elizabeth A. Silva
- Medical Research Council Cell Biology Unit, MRC Laboratory for Molecular Cell Biology and Anatomy and Developmental Biology Department, University College London, London, United Kingdom
| | - Hui Xiao
- The Department of Genetics, Affiliated to the Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, United States of America
| | - Nathalie C. Franc
- The Department of Genetics, Affiliated to the Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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50
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Sévajol M, Reiser JB, Chouquet A, Pérard J, Ayala I, Gans P, Kleman JP, Housset D. The C-terminal polyproline-containing region of ELMO contributes to an increase in the life-time of the ELMO-DOCK complex. Biochimie 2011; 94:823-8. [PMID: 22177965 DOI: 10.1016/j.biochi.2011.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 11/29/2011] [Indexed: 10/14/2022]
Abstract
The eukaryotic Engulfment and CellMotility (ELMO) proteins form an evolutionary conserved family of key regulators which play a central role in Rho-dependent biological processes such as engulfment and cell motility/migration. ELMO proteins interact with a subset of Downstream of Crk (DOCK) family members, a new type of guanine exchange factors (GEF) for Rac and cdc42 GTPases. The physiological function of DOCK is to facilitate actin remodeling, a process which occurs only in presence of ELMO. Several studies have determined that the last 200 C-terminal residues of ELMO1 and the first 180 N-terminal residues of DOCK180 are responsible for the ELMO-DOCK interaction. However, the precise role of the different domains and motifs identified in these regions has remained elusive. Divergent functional, biochemical and structural data have been reported regarding the contribution of the C-terminal end of ELMO, comprising its polyproline motif, and of the DOCK SH3 domain. In the present study, we have investigated the contribution of the C-terminal end of ELMO1 to the interaction between ELMO1 and the SH3 domain of DOCK180 using nuclear magnetic resonance spectroscopy and surface plasmon resonance. Our data presented here demonstrate the ability of the SH3 domain of DOCK180 to interact with ELMO1, regardless of the presence of the polyproline-containing C-terminal end. However, the presence of the polyproline region leads to a significant increase in the half-life of the ELMO1-DOCK180 complex, along with a moderate increase on the affinity.
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Affiliation(s)
- Marion Sévajol
- Immune response to pathogens and altered-self group, Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, Université Joseph Fourier-Grenoble 1, 41, rue Jules Horowitz, F-38027 Grenoble, France
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