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Gordon KL, Payne SG, Linden-High LM, Pani AM, Goldstein B, Hubbard EJA, Sherwood DR. Ectopic Germ Cells Can Induce Niche-like Enwrapment by Neighboring Body Wall Muscle. Curr Biol 2019; 29:823-833.e5. [PMID: 30799241 DOI: 10.1016/j.cub.2019.01.056] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/18/2019] [Accepted: 01/23/2019] [Indexed: 12/20/2022]
Abstract
Niche cell enwrapment of stem cells and their differentiating progeny is common and provides a specialized signaling and protective environment. Elucidating the mechanisms underlying enwrapment behavior has important basic and clinical significance in not only understanding how niches are formed and maintained but also how they can be engineered and how they are misregulated in human pathologies, such as cancer. Previous work in C. elegans found that, when germ cells, which are enwrapped by somatic gonadal niche cells, are freed into the body cavity, they embed into other tissues. We investigated this phenomenon using live-cell imaging and discovered that ectopic germ cells preferentially induce body-wall muscle to extend cellular processes that enwrap the germ cells, the extent of which was strikingly similar to the distal tip cell (DTC)-germ stem cell niche. Enwrapment was specific for escaped germ cells, and genetic analysis revealed it did not depend on pathways that control cell death and engulfment or muscle arm extension. Instead, using a large-scale RNAi screen and GFP knockin strains, we discovered that the enwrapping behavior of muscle relied upon the same suite of cell-cell adhesion molecules that functioned in the endogenous niche: the C. elegans E-cadherin HMR-1, its intracellular associates α-catenin (HMP-1) and β-catenin (HMP-2), and the L1CAM protein SAX-7. This ectopic niche-like behavior resembles the seed-and-soil model of cancer metastasis and offers a new model to understand factors regulating ectopic niche formation.
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Affiliation(s)
- Kacy L Gordon
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Sara G Payne
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Ariel M Pani
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - E Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Departments of Cell Biology and Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - David R Sherwood
- Department of Biology, Duke University, Durham, NC 27708, USA; Regeneration Next, Duke University, Durham, NC 27708, USA.
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102
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Yang B, Xu X, Russell L, Sullenberger MT, Yanowitz JL, Maine EM. A DNA repair protein and histone methyltransferase interact to promote genome stability in the Caenorhabditis elegans germ line. PLoS Genet 2019; 15:e1007992. [PMID: 30794539 PMCID: PMC6402707 DOI: 10.1371/journal.pgen.1007992] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 03/06/2019] [Accepted: 01/28/2019] [Indexed: 12/29/2022] Open
Abstract
Histone modifications regulate gene expression and chromosomal events, yet how histone-modifying enzymes are targeted is poorly understood. Here we report that a conserved DNA repair protein, SMRC-1, associates with MET-2, the C. elegans histone methyltransferase responsible for H3K9me1 and me2 deposition. We used molecular, genetic, and biochemical methods to investigate the biological role of SMRC-1 and to explore its relationship with MET-2. SMRC-1, like its mammalian ortholog SMARCAL1, provides protection from DNA replication stress. SMRC-1 limits accumulation of DNA damage and promotes germline and embryonic viability. MET-2 and SMRC-1 localize to mitotic and meiotic germline nuclei, and SMRC-1 promotes an increase in MET-2 abundance in mitotic germline nuclei upon replication stress. In the absence of SMRC-1, germline H3K9me2 generally decreases after multiple generations at high culture temperature. Genetic data are consistent with MET-2 and SMRC-1 functioning together to limit replication stress in the germ line and in parallel to promote other germline processes. We hypothesize that loss of SMRC-1 activity causes chronic replication stress, in part because of insufficient recruitment of MET-2 to nuclei.
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Affiliation(s)
- Bing Yang
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Xia Xu
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Logan Russell
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | | | - Judith L. Yanowitz
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Eleanor M. Maine
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
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103
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Neumann B, Linton C, Giordano-Santini R, Hilliard MA. Axonal fusion: An alternative and efficient mechanism of nerve repair. Prog Neurobiol 2018; 173:88-101. [PMID: 30500382 DOI: 10.1016/j.pneurobio.2018.11.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 02/07/2023]
Abstract
Injuries to the nervous system can cause lifelong morbidity due to the disconnect that occurs between nerve cells and their cellular targets. Re-establishing these lost connections is the ultimate goal of endogenous regenerative mechanisms, as well as those induced by exogenous manipulations in a laboratory or clinical setting. Reconnection between severed neuronal fibers occurs spontaneously in some invertebrate species and can be induced in mammalian systems. This process, known as axonal fusion, represents a highly efficient means of repair after injury. Recent progress has greatly enhanced our understanding of the molecular control of axonal fusion, demonstrating that the machinery required for the engulfment of apoptotic cells is repurposed to mediate the reconnection between severed axon fragments, which are subsequently merged by fusogen proteins. Here, we review our current understanding of naturally occurring axonal fusion events, as well as those being ectopically produced with the aim of achieving better clinical outcomes.
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Affiliation(s)
- Brent Neumann
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne VIC 3800, Australia.
| | - Casey Linton
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rosina Giordano-Santini
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Massimo A Hilliard
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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104
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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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105
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Mishra N, Wei H, Conradt B. Caenorhabditis elegans ced-3 Caspase Is Required for Asymmetric Divisions That Generate Cells Programmed To Die. Genetics 2018; 210:983-998. [PMID: 30194072 PMCID: PMC6218217 DOI: 10.1534/genetics.118.301500] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 09/04/2018] [Indexed: 01/30/2023] Open
Abstract
Caspases have functions other than in apoptosis. Here, we report that Caenorhabditis elegans CED-3 caspase regulates asymmetric cell division. Many of the 131 cells that are "programmed" to die during C. elegans development are the smaller daughter of a neuroblast that divides asymmetrically by size and fate. We have previously shown that CED-3 caspase is activated in such neuroblasts, and that before neuroblast division, a gradient of CED-3 caspase activity is formed in a ced-1 MEGF10 ( m ultiple EGF -like domains 10 )-dependent manner. This results in the nonrandom segregation of active CED-3 caspase or "apoptotic potential" into the smaller daughter. We now show that CED-3 caspase is necessary for the ability of neuroblasts to divide asymmetrically by size. In addition, we provide evidence that a pig-1 MELK (maternal embryonic leucine zipper kinase)-dependent reciprocal gradient of "mitotic potential" is formed in the QL.p neuroblast, and that CED-3 caspase antagonizes this mitotic potential. Based on these findings, we propose that CED-3 caspase plays a critical role in the asymmetric division by size and fate of neuroblasts, and that this contributes to the reproducibility and robustness with which the smaller daughter cell is produced and adopts the apoptotic fate. Finally, the function of CED-3 caspase in this context is dependent on its activation through the conserved egl-1 BH3-only, ced-9 Bcl-2, and ced-4 Apaf-1 pathway. In mammals, caspases affect various aspects of stem cell lineages. We speculate that the new nonapoptotic function of C. elegans CED-3 caspase in asymmetric neuroblast division is relevant to the function(s) of mammalian caspases in stem cells.
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Affiliation(s)
- Nikhil Mishra
- Faculty of Biology, Center for Integrated Protein Science Munich, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Hai Wei
- Faculty of Biology, Center for Integrated Protein Science Munich, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Barbara Conradt
- Faculty of Biology, Center for Integrated Protein Science Munich, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
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106
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Ni JZ, Kalinava N, Mendoza SG, Gu SG. The spatial and temporal dynamics of nuclear RNAi-targeted retrotransposon transcripts in Caenorhabditis elegans. Development 2018; 145:dev167346. [PMID: 30254142 PMCID: PMC6215403 DOI: 10.1242/dev.167346] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 09/17/2018] [Indexed: 02/03/2023]
Abstract
Nuclear RNA interference provides a unique approach to the study of RNA-mediated transgenerational epigenetic inheritance. A paradox in the field is that expression of target loci is necessary for the initiation and maintenance of their silencing. How expression and repression are coordinated during animal development is poorly understood. To resolve this gap, we took imaging, deep-sequencing and genetic approaches towards delineating the developmental regulation and subcellular localization of RNA transcripts of two representative endogenous targets, the LTR retrotransposons Cer3 and Cer8. By examining wild-type worms and a collection of mutant strains, we found that the expression and silencing cycle of Cer3 and Cer8 is coupled with embryonic and germline development. Strikingly, endogenous targets exhibit a hallmark of nuclear enrichment of their RNA transcripts. In addition, germline and somatic repressions of Cer3 have different genetic requirements for three heterochromatin enzymes, MET-2, SET-25 and SET-32, in conjunction with the nuclear Argonaute protein HRDE-1. These results provide the first comprehensive cellular and developmental characterization of nuclear RNAi activities throughout the animal reproductive cycle.
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Affiliation(s)
- Julie Zhouli Ni
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Natallia Kalinava
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sofia Galindo Mendoza
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sam Guoping Gu
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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107
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Li Y, Maine EM. The balance of poly(U) polymerase activity ensures germline identity, survival and development in Caenorhabditis elegans. Development 2018; 145:145/19/dev165944. [PMID: 30305273 DOI: 10.1242/dev.165944] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/29/2018] [Indexed: 12/21/2022]
Abstract
Poly(U) polymerases (PUPs) catalyze 3' uridylation of mRNAs and small RNAs, a modification often correlating with decreased RNA stability. We have investigated the importance of three proteins with in vitro PUP activity, PUP-1/CDE-1, PUP-2 and PUP-3, in C. elegans germline development. Genetic analysis indicates that PUP-1/CDE-1 and PUP-2 are developmentally redundant under conditions of temperature stress during which they ensure germline viability and development. Multiple lines of evidence indicate that pup-1/-2 double mutant germ cells fail to maintain their identity as distinct from soma. Consistent with phenotypic data, PUP-1 and PUP-2 are expressed in embryonic germ cell precursors and throughout germline development. The developmental importance of PUP activity is presumably in regulating gene expression as both a direct and indirect consequence of modifying target RNAs. PUP-3 is significantly overexpressed in the pup-1/-2 germline, and loss of pup-3 function partially suppresses pup-1/-2 germline defects. We conclude that one major function of PUP-1/-2 is to limit PUP-3 expression. Overall, the balance of PUP-1, PUP-2 and PUP-3 activities appears to ensure proper germline development.
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Affiliation(s)
- Yini Li
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - Eleanor M Maine
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
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108
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Mohankumar A, Shanmugam G, Kalaiselvi D, Levenson C, Nivitha S, Thiruppathi G, Sundararaj P. East Indian sandalwood ( Santalum album L.) oil confers neuroprotection and geroprotection in Caenorhabditis elegans via activating SKN-1/Nrf2 signaling pathway. RSC Adv 2018; 8:33753-33774. [PMID: 30319772 PMCID: PMC6171454 DOI: 10.1039/c8ra05195j] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 09/18/2018] [Indexed: 02/06/2023] Open
Abstract
East Indian Sandalwood Oil (EISO) has diverse beneficial effects and has been used for thousands of years in traditional folk-medicine for treatment of different human ailments. However, there has been no in-depth scientific investigation to decipher the neuroprotective and geroprotective mechanism of EISO and its principle components, α- and β-santalol. Hence the current study was undertaken to assess the protective effects of EISO, and α- and β-santalol against neurotoxic (6-OHDA/6-hydroxydopamine) and proteotoxic (α-synuclein) stresses in a Caenorhabditis elegans model. Initially, we found that EISO and its principle components exerted an excellent antioxidant and antiapoptotic activity as it was able to extend the lifespan, and inhibit the ROS generation, and germline cell apoptosis in 6-OHDA-intoxicated C. elegans. Further, we showed that supplementation of EISO, and α- and β-santalol reduced the 6-OHDA and α-synuclein-induced Parkinson's disease associated pathologies and improved the physiological functions. The genetic and reporter gene expression analysis revealed that an EISO, or α- and β-santalol-mediated protective effect does not appear to rely on DAF-2/DAF-16, but selectively regulates SKN-1 and its downstream targets involved in antioxidant defense and geroprotective processes. Together, our findings indicated that EISO and its principle components are worth exploring further as a candidate redox-based neuroprotectant for the prevention and management of age-related neurological disorders.
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Affiliation(s)
- A Mohankumar
- Unit of Nematology, Department of Zoology, Bharathiar University, Coimbatore, Tamilnadu-641046, India. ; ; ; Tel: +91-9943340405; Tel: +91-9677667720
| | - G Shanmugam
- Unit of Nematology, Department of Zoology, Bharathiar University, Coimbatore, Tamilnadu-641046, India. ; ; ; Tel: +91-9943340405; Tel: +91-9677667720
| | - D Kalaiselvi
- Unit of Nematology, Department of Zoology, Bharathiar University, Coimbatore, Tamilnadu-641046, India. ; ; ; Tel: +91-9943340405; Tel: +91-9677667720
| | - C Levenson
- Santalis Pharmaceuticals Inc., 18618 Tuscany Stone, Suite 100, San Antonio, Texas 78258, USA
| | - S Nivitha
- College of Science, Northeastern University, Boston, Massachusetts 02115, USA
| | - G Thiruppathi
- Unit of Nematology, Department of Zoology, Bharathiar University, Coimbatore, Tamilnadu-641046, India. ; ; ; Tel: +91-9943340405; Tel: +91-9677667720
| | - P Sundararaj
- Unit of Nematology, Department of Zoology, Bharathiar University, Coimbatore, Tamilnadu-641046, India. ; ; ; Tel: +91-9943340405; Tel: +91-9677667720
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109
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Harders RH, Morthorst TH, Lande AD, Hesselager MO, Mandrup OA, Bendixen E, Stensballe A, Olsen A. Dynein links engulfment and execution of apoptosis via CED-4/Apaf1 in C. elegans. Cell Death Dis 2018; 9:1012. [PMID: 30262881 PMCID: PMC6160458 DOI: 10.1038/s41419-018-1067-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/21/2018] [Accepted: 09/10/2018] [Indexed: 12/14/2022]
Abstract
Apoptosis ensures removal of damaged cells and helps shape organs during development by removing excessive cells. To prevent the intracellular content of the apoptotic cells causing damage to surrounding cells, apoptotic cells are quickly cleared by engulfment. Tight regulation of apoptosis and engulfment is needed to prevent several pathologies such as cancer, neurodegenerative and autoimmune diseases. There is increasing evidence that the engulfment machinery can regulate the execution of apoptosis. However, the underlying molecular mechanisms are poorly understood. We show that dynein mediates cell non-autonomous cross-talk between the engulfment and apoptotic programs in the Caenorhabditis elegans germline. Dynein is an ATP-powered microtubule-based molecular motor, built from several subunits. Dynein has many diverse functions including transport of cargo around the cell. We show that both dynein light chain 1 (DLC-1) and dynein heavy chain 1 (DHC-1) localize to the nuclear membrane inside apoptotic germ cells in C. elegans. Strikingly, lack of either DLC-1 or DHC-1 at the nuclear membrane inhibits physiological apoptosis specifically in mutants defective in engulfment. This suggests that a cell fate determining dialogue takes place between engulfing somatic sheath cells and apoptotic germ cells. The underlying mechanism involves the core apoptotic protein CED-4/Apaf1, as we find that DLC-1 and the engulfment protein CED-6/GULP are required for the localization of CED-4 to the nuclear membrane of germ cells. A better understanding of the communication between the engulfment machinery and the apoptotic program is essential for identifying novel therapeutic targets in diseases caused by inappropriate engulfment or apoptosis.
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Affiliation(s)
- Rikke Hindsgaul Harders
- Department of Chemistry and Biosciences, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, DK-9220, Denmark
| | - Tine Hørning Morthorst
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus C, DK-8000, Denmark
| | - Anna Dippel Lande
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus C, DK-8000, Denmark
| | | | - Ole Aalund Mandrup
- Department of Engineering, Aarhus University, Gustav Wieds Vej 10C, Aarhus C, DK-8000, Denmark
| | - Emøke Bendixen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus C, DK-8000, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 7E, Aalborg, DK-9220, Denmark
| | - Anders Olsen
- Department of Chemistry and Biosciences, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, DK-9220, Denmark.
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110
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Ulicna L, Rohozkova J, Hozak P. Multiple Aspects of PIP2 Involvement in C. elegans Gametogenesis. Int J Mol Sci 2018; 19:ijms19092679. [PMID: 30201859 PMCID: PMC6163852 DOI: 10.3390/ijms19092679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/28/2018] [Accepted: 09/05/2018] [Indexed: 12/20/2022] Open
Abstract
One of the most studied phosphoinositides is phosphatidylinositol 4,5-bisphosphate (PIP2), which localizes to the plasma membrane, nuclear speckles, small foci in the nucleoplasm, and to the nucleolus in mammalian cells. Here, we show that PIP2 also localizes to the nucleus in prophase I, during the gametogenesis of C. elegans hermaphrodite. The depletion of PIP2 by type I PIP kinase (PPK-1) kinase RNA interference results in an altered chromosome structure and leads to various defects during meiotic progression. We observed a decreased brood size and aneuploidy in progeny, defects in synapsis, and crossover formation. The altered chromosome structure is reflected in the increased transcription activity of a tightly regulated process in prophase I. To elucidate the involvement of PIP2 in the processes during the C. elegans development, we identified the PIP2-binding partners, leucine-rich repeat (LRR-1) protein and proteasome subunit beta 4 (PBS-4), pointing to its involvement in the ubiquitin–proteasome pathway.
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Affiliation(s)
- Livia Ulicna
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prague 142 20, Czech Republic.
| | - Jana Rohozkova
- Department of Epigenetics of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Division BIOCEV, Vestec 252 50, Czech Republic.
| | - Pavel Hozak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prague 142 20, Czech Republic.
- Department of Epigenetics of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Division BIOCEV, Vestec 252 50, Czech Republic.
- Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prague 142 20, Czech Republic.
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111
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Williamson AP, Vale RD. Spatial control of Draper receptor signaling initiates apoptotic cell engulfment. J Cell Biol 2018; 217:3977-3992. [PMID: 30139739 PMCID: PMC6219719 DOI: 10.1083/jcb.201711175] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/25/2018] [Accepted: 07/30/2018] [Indexed: 01/20/2023] Open
Abstract
Clearance of apoptotic cells is essential for tissue maintenance and initiated by recognition of “eat-me” ligands on the dead cells. Using a simplified cellular reconstitution system, Williamson and Vale report that the Drosophila melanogaster engulfment receptor Draper (CED-1/Megf10) is triggered in a manner similar to mammalian immune receptors. The engulfment of apoptotic cells is essential for tissue homeostasis and recovering from damage. Engulfment is mediated by receptors that recognize ligands exposed on apoptotic cells such as phosphatidylserine (PS). In this study, we convert Drosophila melanogaster S2 cells into proficient phagocytes by transfecting the Draper engulfment receptor and replacing apoptotic cells with PS-coated beads. Similar to the T cell receptor (TCR), PS-ligated Draper forms dynamic microclusters that recruit cytosolic effector proteins and exclude a bulky transmembrane phosphatase, consistent with a kinetic segregation-based triggering mechanism. However, in contrast with the TCR, localized signaling at Draper microclusters results in time-dependent depletion of actin filaments, which facilitates engulfment. The Draper–PS extracellular module can be replaced with FRB and FKBP, respectively, resulting in a rapamycin-inducible engulfment system that can be programmed toward defined targets. Collectively, our results reveal mechanistic similarities and differences between the receptors involved in apoptotic corpse clearance and mammalian immunity and demonstrate that engulfment can be reprogrammed toward nonnative targets.
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Affiliation(s)
- Adam P Williamson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA .,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA
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112
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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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113
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Gut AM, Vasiljevic T, Yeager T, Donkor ON. Salmonella infection - prevention and treatment by antibiotics and probiotic yeasts: a review. MICROBIOLOGY-SGM 2018; 164:1327-1344. [PMID: 30136920 DOI: 10.1099/mic.0.000709] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Global Salmonella infection, especially in developing countries, is a health and economic burden. The use of antibiotic drugs in treating the infection is proving less effective due to the alarming rise of antibiotic-resistant strains of Salmonella, the effects of antibiotics on normal gut microflora and antibiotic-associated diarrhoea, all of which bring a growing need for alternative treatments, including the use of probiotic micro-organisms. However, there are issues with probiotics, including their potential to be opportunistic pathogens and antibiotic-resistant carriers, and their antibiotic susceptibility if used as complementary therapy. Clinical trials, animal trials and in vitro investigations into the prophylactic and therapeutic efficacies of probiotics have demonstrated antagonistic properties against Salmonella and other enteropathogenic bacteria. Nonetheless, there is a need for further studies into the potential mechanisms, efficacy and mode of delivery of yeast probiotics in Salmonella infections. This review discusses Salmonella infections and treatment using antibiotics and probiotics.
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Affiliation(s)
- Abraham Majak Gut
- 1Institute for Sustainable Industries and Livable Cities, College of Health and Biomedicine, Victoria University, Werribee Campus, PO Box 14428, Melbourne, Victoria 8001, Australia
| | - Todor Vasiljevic
- 1Institute for Sustainable Industries and Livable Cities, College of Health and Biomedicine, Victoria University, Werribee Campus, PO Box 14428, Melbourne, Victoria 8001, Australia
| | - Thomas Yeager
- 2Institute for Sustainable Industries and Livable Cities, College of Engineering and Science, Victoria University, Werribee Campus, PO Box 14428, Melbourne, Victoria 8001, Australia
| | - Osaana N Donkor
- 1Institute for Sustainable Industries and Livable Cities, College of Health and Biomedicine, Victoria University, Werribee Campus, PO Box 14428, Melbourne, Victoria 8001, Australia
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114
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Çelen İ, Doh JH, Sabanayagam CR. Effects of liquid cultivation on gene expression and phenotype of C. elegans. BMC Genomics 2018; 19:562. [PMID: 30064382 PMCID: PMC6069985 DOI: 10.1186/s12864-018-4948-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/19/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Liquid cultures have been commonly used in space, toxicology, and pharmacology studies of Caenorhabditis elegans. However, the knowledge about transcriptomic alterations caused by liquid cultivation remains limited. Moreover, the impact of different genotypes in rapid adaptive responses to environmental changes (e.g., liquid cultivation) is often overlooked. Here, we report the transcriptomic and phenotypic responses of laboratory N2 and the wild-isolate AB1 strains after culturing P0 worms on agar plates, F1 in liquid cultures, and F2 back on agar plates. RESULTS Significant variations were found in the gene expressions between the N2 and AB1 strains in response to liquid cultivation. The results demonstrated that 8-34% of the environmental change-induced transcriptional responses are transmitted to the subsequent generation. By categorizing the gene expressions for genotype, environment, and genotype-environment interactions, we identified that the genotype has a substantial impact on the adaptive responses. Functional analysis of the transcriptome showed correlation with phenotypical changes. For example, the N2 strain exhibited alterations in both phenotype and gene expressions for germline and cuticle in axenic liquid cultivation. We found transcript evidence to approximately 21% of the computationally predicted genes in C. elegans by exposing the worms to environmental changes. CONCLUSIONS The presented study reveals substantial differences between N2 and AB1 strains for transcriptomic and phenotypical responses to rapid environmental changes. Our data can provide standard controls for future studies for the liquid cultivation of C. elegans and enable the discovery of condition-specific genes.
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Affiliation(s)
- İrem Çelen
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711 USA
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711 USA
| | - Jung H. Doh
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711 USA
| | - Chandran R. Sabanayagam
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711 USA
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115
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Membrane Fluidity Is Regulated Cell Nonautonomously by Caenorhabditis elegans PAQR-2 and Its Mammalian Homolog AdipoR2. Genetics 2018; 210:189-201. [PMID: 29997234 PMCID: PMC6116961 DOI: 10.1534/genetics.118.301272] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/09/2018] [Indexed: 01/24/2023] Open
Abstract
The properties of cell membranes are determined mostly by the types of fatty acids that they contain. Bodhicharla et al. report that a key regulator of membrane fluidity, the PAQR-2/IGLR-2 protein complex... Maintenance of membrane properties is an essential aspect of cellular homeostasis of which the regulatory mechanisms remain mostly uncharacterized. In Caenorhabditis elegans, the PAQR-2 and IGLR-2 proteins act together as a plasma membrane sensor that responds to decreased fluidity by promoting fatty acid desaturation, hence restoring membrane fluidity. Here, we used mosaic analysis for paqr-2 and iglr-2, and tissue-specific paqr-2 expression, to show that membrane homeostasis is achieved cell nonautonomously. Specifically, we found that expression of paqr-2 in the hypodermis, gonad sheath cells, or intestine is sufficient to suppress systemic paqr-2 mutant phenotypes, including tail tip morphology, membrane fluidity in intestinal cells, cold and glucose intolerance, vitellogenin transport to the germline, germ cell development, and brood size. Finally, we show that the cell nonautonomous regulation of membrane homeostasis is conserved in human cells: HEK293 cells that express AdipoR2, a homolog of paqr-2, are able to normalize membrane fluidity in distant cells where AdipoR2 has been silenced. Finally, using C. elegans mutants and small interfering RNA against Δ9 stearoyl-CoA desaturase in HEK293 cells, we show that Δ9 desaturases are essential for the cell nonautonomous maintenance of membrane fluidity. We conclude that cells are able to share membrane components even when they are not in direct contact with each other, and that this contributes to the maintenance of membrane homeostasis in C. elegans and human cells.
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116
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Kumar S, Calianese D, Birge RB. Efferocytosis of dying cells differentially modulate immunological outcomes in tumor microenvironment. Immunol Rev 2018; 280:149-164. [PMID: 29027226 DOI: 10.1111/imr.12587] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Programmed cell death (apoptosis) is an integral part of tissue homeostasis in complex organisms, allowing for tissue turnover, repair, and renewal while simultaneously inhibiting the release of self antigens and danger signals from apoptotic cell-derived constituents that can result in immune activation, inflammation, and autoimmunity. Unlike cells in culture, the physiological fate of cells that die by apoptosis in vivo is their rapid recognition and engulfment by phagocytic cells (a process called efferocytosis). To this end, apoptotic cells express specific eat-me signals, such as externalized phosphatidylserine (PS), that are recognized in a specific context by receptors to initiate signaling pathways for engulfment. The importance of carefully regulated recognition and clearance pathways is evident in the spectrum of inflammatory and autoimmune disorders caused by defects in PS receptors and signaling molecules. However, in recent years, several additional cell death pathways have emerged, including immunogenic cell death, necroptosis, pyroptosis, and netosis that interweave different cell death pathways with distinct innate and adaptive responses from classical apoptosis that can shape long-term host immunity. In this review, we discuss the role of different cell death pathways in terms of their immune potential outcomes specifically resulting in specific cell corpse/phagocyte interactions (phagocytic synapses) that impinge on host immunity, with a main emphasis on tolerance and cancer immunotherapy.
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Affiliation(s)
- Sushil Kumar
- New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, Newark, NJ, USA
| | - David Calianese
- New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, Newark, NJ, USA
| | - Raymond B Birge
- New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, Newark, NJ, USA
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Abstract
Cell death is a perpetual feature of tissue microenvironments; each day under homeostatic conditions, billions of cells die and must be swiftly cleared by phagocytes. However, cell death is not limited to this natural turnover-apoptotic cell death can be induced by infection, inflammation, or severe tissue injury. Phagocytosis of apoptotic cells is thus coupled to specific functions, from the induction of growth factors that can stimulate the replacement of dead cells to the promotion of tissue repair or tissue remodeling in the affected site. In this review, we outline the mechanisms by which phagocytes sense apoptotic cell death and discuss how phagocytosis is integrated with environmental cues to drive appropriate responses.
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Affiliation(s)
- Lidia Bosurgi
- I. Medizinische Klinik und Poliklinik, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.,Bernard-Nocht-Institut für Tropenmedizin, Hamburg, Germany
| | - Lindsey D Hughes
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Carla V Rothlin
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA.,Department of Pharmacology, School of Medicine, Yale University, New Haven, CT, USA
| | - Sourav Ghosh
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT, USA.,Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
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118
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Scholtes C, Bellemin S, Martin E, Carre-Pierrat M, Mollereau B, Gieseler K, Walter L. DRP-1-mediated apoptosis induces muscle degeneration in dystrophin mutants. Sci Rep 2018; 8:7354. [PMID: 29743663 PMCID: PMC5943356 DOI: 10.1038/s41598-018-25727-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/03/2018] [Indexed: 02/08/2023] Open
Abstract
Mitochondria are double-membrane subcellular organelles with highly conserved metabolic functions including ATP production. Mitochondria shapes change continually through the combined actions of fission and fusion events rendering mitochondrial network very dynamic. Mitochondria are largely implicated in pathologies and mitochondrial dynamics is often disrupted upon muscle degeneration in various models. Currently, the exact roles of mitochondria in the molecular mechanisms that lead to muscle degeneration remain poorly understood. Here we report a role for DRP-1 in regulating apoptosis induced by dystrophin-dependent muscle degeneration. We found that: (i) dystrophin-dependent muscle degeneration was accompanied by a drastic increase in mitochondrial fragmentation that can be rescued by genetic manipulations of mitochondrial dynamics (ii) the loss of function of the fission gene drp-1 or the overexpression of the fusion genes eat-3 and fzo-1 provoked a reduction of muscle degeneration and an improved mobility of dystrophin mutant worms (iii) the functions of DRP-1 in apoptosis and of others apoptosis executors are important for dystrophin-dependent muscle cell death (iv) DRP-1-mediated apoptosis is also likely to induce age-dependent loss of muscle cell. Collectively, our findings point toward a mechanism involving mitochondrial dynamics to respond to trigger(s) of muscle degeneration via apoptosis in Caenorhabditis elegans.
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Affiliation(s)
- Charlotte Scholtes
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, UMS 3444 Biosciences Lyon Gerland, Universite de Lyon, Lyon, 69007, France.,NeuroMyoGene Institute (INMG), Universite Lyon 1, CNRS UMR 5310, INSERM U1217, Lyon 69008, France
| | - Stéphanie Bellemin
- NeuroMyoGene Institute (INMG), Universite Lyon 1, CNRS UMR 5310, INSERM U1217, Lyon 69008, France
| | - Edwige Martin
- NeuroMyoGene Institute (INMG), Universite Lyon 1, CNRS UMR 5310, INSERM U1217, Lyon 69008, France
| | - Maïté Carre-Pierrat
- Biology of Caenorhabditis elegans facility, Universite Lyon 1, UMS3421, Lyon 69008, France
| | - Bertrand Mollereau
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, UMS 3444 Biosciences Lyon Gerland, Universite de Lyon, Lyon, 69007, France
| | - Kathrin Gieseler
- NeuroMyoGene Institute (INMG), Universite Lyon 1, CNRS UMR 5310, INSERM U1217, Lyon 69008, France.
| | - Ludivine Walter
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, UMS 3444 Biosciences Lyon Gerland, Universite de Lyon, Lyon, 69007, France.
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SCARF1: a multifaceted, yet largely understudied, scavenger receptor. Inflamm Res 2018; 67:627-632. [PMID: 29725698 PMCID: PMC6028831 DOI: 10.1007/s00011-018-1154-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND As is a prerequisite of belonging to the scavenger receptor super family, SCARF1 (scavenger receptor class F, member 1) is known to play a key role in the binding and endocytosis of a wide range of endogenous and exogenous ligands. FINDINGS Unlike most scavenger receptors, SCARF1 is an essential protein, as SCARF1-deficient mice exhibit a severe resting phenotype in which they develop systemic lupus erythematosus (SLE)-like disease, thus highlighting the importance of SCARF1-mediated clearance of apoptotic host cells in homeostasis. In addition, a number of other roles in homeostasis and disease pathology have also been suggested, including roles in both innate and adaptive immunity; however, the majority of these studies have utilised transfected cell lines engineered to ectopically express SCARF1 and very few have utilised in vivo or ex vivo approaches. CONCLUSION This review summarises our current knowledge on SCARF1 biology and reflects on future directions for research on this multifaceted, yet largely understudied, scavenger receptor.
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120
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Hernandez MR, Davis MB, Jiang J, Brouhard EA, Severson AF, Csankovszki G. Condensin I protects meiotic cohesin from WAPL-1 mediated removal. PLoS Genet 2018; 14:e1007382. [PMID: 29768402 PMCID: PMC5973623 DOI: 10.1371/journal.pgen.1007382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 05/29/2018] [Accepted: 04/27/2018] [Indexed: 11/22/2022] Open
Abstract
Condensin complexes are key determinants of higher-order chromatin structure and are required for mitotic and meiotic chromosome compaction and segregation. We identified a new role for condensin in the maintenance of sister chromatid cohesion during C. elegans meiosis. Using conventional and stimulated emission depletion (STED) microscopy we show that levels of chromosomally-bound cohesin were significantly reduced in dpy-28 mutants, which lack a subunit of condensin I. SYP-1, a component of the synaptonemal complex central region, was also diminished, but no decrease in the axial element protein HTP-3 was observed. Surprisingly, the two key meiotic cohesin complexes of C. elegans were both depleted from meiotic chromosomes following the loss of condensin I, and disrupting condensin I in cohesin mutants increased the frequency of detached sister chromatids. During mitosis and meiosis in many organisms, establishment of cohesion is antagonized by cohesin removal by Wapl, and we found that condensin I binds to C. elegans WAPL-1 and counteracts WAPL-1-dependent cohesin removal. Our data suggest that condensin I opposes WAPL-1 to promote stable binding of cohesin to meiotic chromosomes, thereby ensuring linkages between sister chromatids in early meiosis.
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Affiliation(s)
- Margarita R. Hernandez
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Michael B. Davis
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Jianhao Jiang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Elizabeth A. Brouhard
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Aaron F. Severson
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, United States of America
| | - Györgyi Csankovszki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States of America
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Papaluca A, Wagner JR, Saragovi HU, Ramotar D. UNG-1 and APN-1 are the major enzymes to efficiently repair 5-hydroxymethyluracil DNA lesions in C. elegans. Sci Rep 2018; 8:6860. [PMID: 29717169 PMCID: PMC5931555 DOI: 10.1038/s41598-018-25124-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/13/2018] [Indexed: 11/16/2022] Open
Abstract
In Caenorhabditis elegans, two DNA glycosylases, UNG-1 and NTH-1, and two AP endonucleases, APN-1 and EXO-3, have been characterized from the base-excision repair (BER) pathway that repairs oxidatively modified DNA bases. UNG-1 removes uracil, while NTH-1 can remove 5-hydroxymethyluracil (5-hmU), an oxidation product of thymine, as well as other lesions. Both APN-1 and EXO-3 can incise AP sites and remove 3′-blocking lesions at DNA single strand breaks, and only APN-1 possesses 3′- to 5′-exonulease and nucleotide incision repair activities. We used C. elegans mutants to study the role of the BER pathway in processing 5-hmU. We observe that ung-1 mutants exhibited a decrease in brood size and lifespan, and an elevated level of germ cell apoptosis when challenged with 5-hmU. These phenotypes were exacerbated by RNAi downregulation of apn-1 in the ung-1 mutant. The nth-1 or exo-3 mutants displayed wild type phenotypes towards 5-hmU. We show that partially purified UNG-1 can act on 5-hmU lesion in vitro. We propose that UNG-1 removes 5-hmU incorporated into the genome and the resulting AP site is cleaved by APN-1 or EXO-3. In the absence of UNG-1, the 5-hmU is removed by NTH-1 creating a genotoxic 3′-blocking lesion that requires the action of APN-1.
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Affiliation(s)
- Arturo Papaluca
- Maisonneuve-Rosemont Hospital, Research Center, Université de Montréal, Department of Medicine, 5415 Boul. de l'Assomption, Montréal, Québec, H1T2M4, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Department of Pharmacology and Therapeutics, McGill University, Department of Pharmacology and Therapeutics, 3755 Chemin de la Côte Sainte-Catherine, Québec, Montréal, H3T1E2, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12 Avenue Nord, Sherbrooke, Québec, J1H5N4, Canada
| | - H Uri Saragovi
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Department of Pharmacology and Therapeutics, McGill University, Department of Pharmacology and Therapeutics, 3755 Chemin de la Côte Sainte-Catherine, Québec, Montréal, H3T1E2, Canada
| | - Dindial Ramotar
- Maisonneuve-Rosemont Hospital, Research Center, Université de Montréal, Department of Medicine, 5415 Boul. de l'Assomption, Montréal, Québec, H1T2M4, Canada.
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122
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King SD, Gray CF, Song L, Nechushtai R, Gumienny TL, Mittler R, Padilla PA. The cisd gene family regulates physiological germline apoptosis through ced-13 and the canonical cell death pathway in Caenorhabditis elegans. Cell Death Differ 2018; 26:162-178. [PMID: 29666474 PMCID: PMC6294797 DOI: 10.1038/s41418-018-0108-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 02/13/2018] [Accepted: 03/05/2018] [Indexed: 11/09/2022] Open
Abstract
Programmed cell death, which occurs through a conserved core molecular pathway, is important for fundamental developmental and homeostatic processes. The human iron-sulfur binding protein NAF-1/CISD2 binds to Bcl-2 and its disruption in cells leads to an increase in apoptosis. Other members of the CDGSH iron sulfur domain (CISD) family include mitoNEET/CISD1 and Miner2/CISD3. In humans, mutations in CISD2 result in Wolfram syndrome 2, a disease in which the patients display juvenile diabetes, neuropsychiatric disorders and defective platelet aggregation. The C. elegans genome contains three previously uncharacterized cisd genes that code for CISD-1, which has homology to mitoNEET/CISD1 and NAF-1/CISD2, and CISD-3.1 and CISD-3.2, both of which have homology to Miner2/CISD3. Disrupting the function of the cisd genes resulted in various germline abnormalities including distal tip cell migration defects and a significant increase in the number of cell corpses within the adult germline. This increased germ cell death is blocked by a gain-of-function mutation of the Bcl-2 homolog CED-9 and requires functional caspase CED-3 and the APAF-1 homolog CED-4. Furthermore, the increased germ cell death is facilitated by the pro-apoptotic, CED-9-binding protein CED-13, but not the related EGL-1 protein. This work is significant because it places the CISD family members as regulators of physiological germline programmed cell death acting through CED-13 and the core apoptotic machinery.
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Affiliation(s)
- Skylar D King
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Chipo F Gray
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Luhua Song
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Rachel Nechushtai
- Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem, 91904, Israel
| | - Tina L Gumienny
- Department of Biology, Texas Woman's University, Denton, TX, 76204, USA
| | - Ron Mittler
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Pamela A Padilla
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA.
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123
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Gibson CL, Balbona JT, Niedzwiecki A, Rodriguez P, Nguyen KCQ, Hall DH, Blakely RD. Glial loss of the metallo β-lactamase domain containing protein, SWIP-10, induces age- and glutamate-signaling dependent, dopamine neuron degeneration. PLoS Genet 2018; 14:e1007269. [PMID: 29590100 PMCID: PMC5891035 DOI: 10.1371/journal.pgen.1007269] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/09/2018] [Accepted: 02/22/2018] [Indexed: 12/24/2022] Open
Abstract
Across phylogeny, glutamate (Glu) signaling plays a critical role in regulating neural excitability, thus supporting many complex behaviors. Perturbed synaptic and extrasynaptic Glu homeostasis in the human brain has been implicated in multiple neuropsychiatric and neurodegenerative disorders including Parkinson's disease, where theories suggest that excitotoxic insults may accelerate a naturally occurring process of dopamine (DA) neuron degeneration. In C. elegans, mutation of the glial expressed gene, swip-10, results in Glu-dependent DA neuron hyperexcitation that leads to elevated DA release, triggering DA signaling-dependent motor paralysis. Here, we demonstrate that swip-10 mutations induce premature and progressive DA neuron degeneration, with light and electron microscopy studies demonstrating the presence of dystrophic dendritic processes, as well as shrunken and/or missing cell soma. As with paralysis, DA neuron degeneration in swip-10 mutants is rescued by glial-specific, but not DA neuron-specific expression of wildtype swip-10, consistent with a cell non-autonomous mechanism. Genetic studies implicate the vesicular Glu transporter VGLU-3 and the cystine/Glu exchanger homolog AAT-1 as potential sources of Glu signaling supporting DA neuron degeneration. Degeneration can be significantly suppressed by mutations in the Ca2+ permeable Glu receptors, nmr-2 and glr-1, in genes that support intracellular Ca2+ signaling and Ca2+-dependent proteolysis, as well as genes involved in apoptotic cell death. Our studies suggest that Glu stimulation of nematode DA neurons in early larval stages, without the protective actions of SWIP-10, contributes to insults that ultimately drive DA neuron degeneration. The swip-10 model may provide an efficient platform for the identification of molecular mechanisms that enhance risk for Parkinson's disease and/or the identification of agents that can limit neurodegenerative disease progression.
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Affiliation(s)
- Chelsea L. Gibson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, United States of America
| | - Joseph T. Balbona
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
| | - Ashlin Niedzwiecki
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
| | - Peter Rodriguez
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, United States of America
| | - Ken C. Q. Nguyen
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - David H. Hall
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Randy D. Blakely
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, United States of America
- Department of Psychiatry, Vanderbilt University, Nashville, TN, United States of America
- The Brain Institute, Florida Atlantic University, Jupiter, FL, United States of America
- * E-mail:
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Ghose P, Rashid A, Insley P, Trivedi M, Shah P, Singhal A, Lu Y, Bao Z, Shaham S. EFF-1 fusogen promotes phagosome sealing during cell process clearance in Caenorhabditis elegans. Nat Cell Biol 2018; 20:393-399. [PMID: 29556089 PMCID: PMC5876135 DOI: 10.1038/s41556-018-0068-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 02/16/2018] [Indexed: 12/21/2022]
Abstract
Phagocytosis of dying cells is critical in development and immunity1–3. While proteins for recognition and engulfment of cellular debris following cell death are known4,5, proteins that directly mediate phagosome sealing are uncharacterized. Furthermore, whether all phagocytic targets are cleared using the same machinery is unclear. Degeneration of morphologically-complex cells, such as neurons, glia, and melanocytes, produces phagocytic targets of various shapes and sizes located in different microenvironments6,7. Such cells, therefore, offer unique settings to explore engulfment program mechanisms and specificity. Here we report that dismantling and clearance of a morphologically-complex C. elegans epithelial cell requires separate cell-soma, proximal-, and distal-process programs. Similar compartment-specific events govern elimination of a C. elegans neuron. While canonical engulfment proteins drive cell-soma clearance, these are not required for process removal. We find that EFF-1, a protein previously implicated in cell-cell fusion8, specifically promotes distal-process phagocytosis. EFF-1 localizes to phagocyte pseudopod tips, and acts exoplasmically to drive phagosome sealing. eff-1 mutations result in phagocytosis arrest with unsealed phagosomes. Our studies suggest universal mechanisms for dismantling morphologically-complex cells, and uncover a phagosome sealing component promoting cell-process clearance.
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Affiliation(s)
- Piya Ghose
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY, USA
| | - Alina Rashid
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY, USA
| | - Peter Insley
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY, USA
| | - Meera Trivedi
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY, USA
| | - Pavak Shah
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Anupriya Singhal
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY, USA
| | - Yun Lu
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY, USA.
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125
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The ABC Transporter Eato Promotes Cell Clearance in the Drosophila melanogaster Ovary. G3-GENES GENOMES GENETICS 2018; 8:833-843. [PMID: 29295819 PMCID: PMC5844305 DOI: 10.1534/g3.117.300427] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The clearance of dead cells is a fundamental process in the maintenance of tissue homeostasis. Genetic studies in Drosophila melanogaster, Caenorhabditis elegans, and mammals have identified two evolutionarily conserved signaling pathways that act redundantly to regulate this engulfment process: the ced-1/-6/-7 and ced-2/-5/-12 pathways. Of these engulfment genes, only the ced-7/ABCA1 ortholog remains to be identified in D. melanogaster Homology searches have revealed a family of putative ced-7/ABCA1 homologs encoding ATP-binding cassette (ABC) transporters in D. melanogaster To determine which of these genes functions similarly to ced-7/ABCA1, we analyzed mutants for engulfment phenotypes in oogenesis, during which nurse cells (NCs) in each egg chamber undergo programmed cell death (PCD) and are removed by neighboring phagocytic follicle cells (FCs). Our genetic analyses indicate that one of the ABC transporter genes, which we have named Eato (Engulfment ABC Transporter in the ovary), is required for NC clearance in the ovary and acts in the same pathways as drpr, the ced-1 ortholog, and in parallel to Ced-12 in the FCs. Additionally, we show that Eato acts in the FCs to promote accumulation of the transmembrane receptor Drpr, and promote membrane extensions around the NCs for their clearance. Since ABCA class transporters, such as CED-7 and ABCA1, are known to be involved in lipid trafficking, we propose that Eato acts to transport membrane material to the growing phagocytic cup for cell corpse clearance. Our work presented here identifies Eato as the ced-7/ABCA1 ortholog in D. melanogaster, and demonstrates a role for Eato in Drpr accumulation and phagocytic membrane extensions during NC clearance in the ovary.
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Turcotte CA, Sloat SA, Rigothi JA, Rosenkranse E, Northrup AL, Andrews NP, Checchi PM. Maintenance of Genome Integrity by Mi2 Homologs CHD-3 and LET-418 in Caenorhabditis elegans. Genetics 2018; 208:991-1007. [PMID: 29339410 PMCID: PMC5844346 DOI: 10.1534/genetics.118.300686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/10/2018] [Indexed: 02/06/2023] Open
Abstract
Meiotic recombination depends upon the tightly coordinated regulation of chromosome dynamics and is essential for the production of haploid gametes. Central to this process is the formation and repair of meiotic double-stranded breaks (DSBs), which must take place within the constraints of a specialized chromatin architecture. Here, we demonstrate a role for the nucleosome remodeling and deacetylase (NuRD) complex in orchestrating meiotic chromosome dynamics in Caenorhabditis elegans Our data reveal that the conserved Mi2 homologs Chromodomain helicase DNA-binding protein (CHD-3) and its paralog LET-418 facilitate meiotic progression by ensuring faithful repair of DSBs through homologous recombination. We discovered that loss of either CHD-3 or LET-418 results in elevated p53-dependent germ line apoptosis, which relies on the activation of the conserved checkpoint kinase CHK-1 Consistent with these findings, chd-3 and let-418 mutants produce a reduced number of offspring, indicating a role for Mi2 in forming viable gametes. When Mi2 function is compromised, persisting recombination intermediates are detected in late pachytene nuclei, indicating a failure in the timely repair of DSBs. Intriguingly, our data indicate that in Mi2 mutant germ lines, a subset of DSBs are repaired by nonhomologous end joining, which manifests as chromosomal fusions. We find that meiotic defects are exacerbated in Mi2 mutants lacking CKU-80, as evidenced by increased recombination intermediates, corpses, and defects in chromosomal integrity. Taken together, our findings support a model wherein the C. elegans Mi2 complex maintains genomic integrity through reinforcement of a chromatin landscape suitable for homology-driven repair mechanisms.
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Affiliation(s)
| | - Solomon A Sloat
- Department of Biology, Marist College, Poughkeepsie, New York 12601
| | - Julia A Rigothi
- Department of Biology, Marist College, Poughkeepsie, New York 12601
| | | | | | | | - Paula M Checchi
- Department of Biology, Marist College, Poughkeepsie, New York 12601
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Myers TR, Amendola PG, Lussi YC, Salcini AE. JMJD-1.2 controls multiple histone post-translational modifications in germ cells and protects the genome from replication stress. Sci Rep 2018; 8:3765. [PMID: 29491442 PMCID: PMC5830613 DOI: 10.1038/s41598-018-21914-9] [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: 07/14/2017] [Accepted: 02/13/2018] [Indexed: 01/29/2023] Open
Abstract
Post-translational modifications of histones, constitutive components of chromatin, regulate chromatin compaction and control all DNA-based cellular processes. C. elegans JMJD-1.2, a member of the KDM7 family, is a demethylase active towards several lysine residues on Histone 3 (H3), but its contribution in regulating histone methylation in germ cells has not been fully investigated. Here, we show that jmjd-1.2 is expressed abundantly in the germline where it controls the level of histone 3 lysine 9, lysine 23 and lysine 27 di-methylation (H3K9/K23/K27me2) both in mitotic and meiotic cells. Loss of jmjd-1.2 is not associated with major defects in the germ cells in animals grown under normal conditions or after DNA damage induced by UV or ionizing irradiation. However, jmjd-1.2 mutants are more sensitive to replication stress and the progeny of mutant animals exposed to hydroxyurea show increased embryonic lethality and mutational rate, compared to wild-type. Thus, our results suggest a role for jmjd-1.2 in the maintenance of genome integrity after replication stress and emphasize the relevance of the regulation of histone methylation in genomic stability.
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Affiliation(s)
- Toshia R Myers
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Pier Giorgio Amendola
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Yvonne C Lussi
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Anna Elisabetta Salcini
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark.
- Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark.
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128
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Abstract
Germ cells are unique in their ability to transfer traits and genetic information from one generation to the next. The proper development and integrity of their genome are therefore of utmost importance for the health of organisms and survival of species. Many features of mammalian germ cells, including their long development span and difficulty of access, present challenges for their study in the context of toxicity assays. In light of these barriers, the model system Caenorhabditis elegans shows great potential given its ease of manipulation and genetic tractability which can be easily adapted for high-throughput analysis. In this chapter, we discuss the advantages of examining germ cell processes in C. elegans, and describe three functional germline assays for the examination of chemical impact on germline maintenance and function including assays probing germ cell differentiation, germline apoptosis, and germline epigenetic regulation.
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129
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Serizier SB, McCall K. Scrambled Eggs: Apoptotic Cell Clearance by Non-Professional Phagocytes in the Drosophila Ovary. Front Immunol 2017; 8:1642. [PMID: 29238344 PMCID: PMC5712531 DOI: 10.3389/fimmu.2017.01642] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/09/2017] [Indexed: 01/20/2023] Open
Abstract
For half of a century, it has been known that non-professional phagocytes, such as fibroblasts, endothelial, and epithelial cells, are capable of efferocytosis (engulfment of apoptotic cells). Non-professional phagocytes differ from professional phagocytes in the range and efficiency of engulfment. Much of the recognition and underlying signaling machinery between non-professional and professional phagocytes is the same, but it is not known how the engulfment capacity of non-professional phagocytes is controlled. Moreover, the signaling networks involved in cell corpse recognition, engulfment, and phagosome maturation are only partially understood. The Drosophila ovary provides an excellent system to investigate the regulation of phagocytic activity by epithelial cells, a major class of non-professional phagocytes. During Drosophila oogenesis, mid-stage egg chambers undergo apoptosis of the germline in response to nutrient deprivation. Epithelial follicle cells then undergo major cell shape changes and concomitantly engulf the germline material. Our previous work has established that Draper and the integrin α-PS3/β-PS heterodimer are required in follicle cells for germline cell clearance. In addition, we have characterized phagosome maturation pathways, and found that the JNK pathway amplifies the engulfment response. In this review, we discuss recent advances on the interplay between engulfment pathways in the follicular epithelium for cell clearance in the Drosophila ovary. We also provide a comparison to apoptotic cell clearance mechanisms in C. elegans and mammals, illustrating strong conservation of efferocytosis mechanisms by non-professional phagocytes.
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Affiliation(s)
- Sandy B Serizier
- Department of Biology, Boston University, Boston, MA, United States.,Graduate Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA, United States
| | - Kimberly McCall
- Department of Biology, Boston University, Boston, MA, United States
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130
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Villanueva-Chimal E, Salinas LS, Fernández-Cardenas LP, Huelgas-Morales G, Cabrera-Wrooman A, Navarro RE. DPFF-1 transcription factor deficiency causes the aberrant activation of MPK-1 and meiotic defects in the Caenorhabditis elegans germline. Genesis 2017; 55. [PMID: 28940692 DOI: 10.1002/dvg.23072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 09/15/2017] [Accepted: 09/20/2017] [Indexed: 12/19/2022]
Abstract
The d4 family of transcription factors consists of three members in mammals. DPF1/neuro-d4 is expressed mainly in neurons and the peripheral nervous system, and is important for brain development. DPF2/requiem/ubi-d4 is expressed ubiquitously and presumably functions as an apoptotic factor, especially during the deprivation of trophic factors. DPF3/cer-d4 is expressed in neurons and in the heart, and is important for heart development and function in zebrafish. In Drosophila, there is only one member, dd4, whose function is still unknown, but it is expressed in many tissues and is particularly abundant in the brain of developing embryos and in adults. Here, we present DPFF-1, the only member of this family of proteins in the nematode C. elegans. DPFF-1 is similar to its mammalian homolog DPF2/requiem/ubi-d4 because it is ubiquitously expressed during embryogenesis and in adult tissues, and because it is important for the induction of germ cell apoptosis during stress. Here, we show that dpff-1 null mutant animals produce less progeny than wild-type nematodes, presumably due to meiotic defects. Gonads of dpff-1 deficient animals showed more germ cells in pachytene and overexpressed the P-MPK-1 signal. Additionally, these animals presented higher levels of p53-induced germ cell apoptosis than wild-type animals. Furthermore, we observed that dpff-1 deficient animals are more sensitive to heat shock. This is the first report showing that the d4 family of transcription factors could be involved in meiosis and stress protection.
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Affiliation(s)
- Emmanuel Villanueva-Chimal
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D.F., México
| | - Laura S Salinas
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D.F., México
| | - Laura P Fernández-Cardenas
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D.F., México
| | - Gabriela Huelgas-Morales
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D.F., México
| | - Alejandro Cabrera-Wrooman
- Laboratorio de Tejido Conjuntivo, Centro Nacional de Investigación y Atención de Quemados, Instituto Nacional de Rehabilitación "Luis Guillermo Ibarra Ibarra,", México, D.F, México
| | - Rosa E Navarro
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D.F., México
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131
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Herbette M, Mercier M, Michal F, Cluet D, Burny C, Yvert G, Robert V, Palladino F. The C. elegans SET-2/SET1 histone H3 Lys4 (H3K4) methyltransferase preserves genome stability in the germline. DNA Repair (Amst) 2017; 57:139-150. [DOI: 10.1016/j.dnarep.2017.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/13/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
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132
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Boateng R, Nguyen KCQ, Hall DH, Golden A, Allen AK. Novel functions for the RNA-binding protein ETR-1 in Caenorhabditis elegans reproduction and engulfment of germline apoptotic cell corpses. Dev Biol 2017; 429:306-320. [PMID: 28648844 PMCID: PMC5603194 DOI: 10.1016/j.ydbio.2017.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 06/01/2017] [Accepted: 06/08/2017] [Indexed: 01/31/2023]
Abstract
RNA-binding proteins (RBPs) are essential regulators of gene expression that act through a variety of mechanisms to ensure the proper post-transcriptional regulation of their target RNAs. RBPs in multiple species have been identified as playing crucial roles during development and as having important functions in various adult organ systems, including the heart, nervous, muscle, and reproductive systems. ETR-1, a highly conserved ELAV-Type RNA-binding protein belonging to the CELF/Bruno protein family, has been previously reported to be involved in C. elegans muscle development. Animals depleted of ETR-1 have been previously characterized as arresting at the two-fold stage of embryogenesis. In this study, we show that ETR-1 is expressed in the hermaphrodite somatic gonad and germ line, and that reduction of ETR-1 via RNA interference (RNAi) results in reduced hermaphrodite fecundity. Detailed characterization of this fertility defect indicates that ETR-1 is required in both the somatic tissue and the germ line to ensure wild-type reproductive levels. Additionally, the ability of ETR-1 depletion to suppress the published WEE-1.3-depletion infertility phenotype is dependent on ETR-1 being reduced in the soma. Within the germline of etr-1(RNAi) hermaphrodite animals, we observe a decrease in average oocyte size and an increase in the number of germline apoptotic cell corpses as evident by an increased number of CED-1::GFP and acridine orange positive apoptotic germ cells. Transmission Electron Microscopy (TEM) studies confirm the significant increase in apoptotic cells in ETR-1-depleted animals, and reveal a failure of the somatic gonadal sheath cells to properly engulf dying germ cells in etr-1(RNAi) animals. Through investigation of an established engulfment pathway in C. elegans, we demonstrate that co-depletion of CED-1 and ETR-1 suppresses both the reduced fecundity and the increase in the number of apoptotic cell corpses observed in etr-1(RNAi) animals. Combined, this data identifies a novel role for ETR-1 in hermaphrodite gametogenesis and in the process of engulfment of germline apoptotic cell corpses.
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Affiliation(s)
- Ruby Boateng
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - Ken C Q Nguyen
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - David H Hall
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Andy Golden
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna K Allen
- Department of Biology, Howard University, Washington, DC 20059, USA
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133
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Sanders J, Scholz M, Merutka I, Biron D. Distinct unfolded protein responses mitigate or mediate effects of nonlethal deprivation of C. elegans sleep in different tissues. BMC Biol 2017; 15:67. [PMID: 28844202 PMCID: PMC5572162 DOI: 10.1186/s12915-017-0407-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/24/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Disrupting sleep during development leads to lasting deficits in chordates and arthropods. To address lasting impacts of sleep deprivation in Caenorhabditis elegans, we established a nonlethal deprivation protocol. RESULTS Deprivation triggered protective insulin-like signaling and two unfolded protein responses (UPRs): the mitochondrial (UPRmt) and the endoplasmic reticulum (UPRER) responses. While the latter is known to be triggered by sleep deprivation in rodent and insect brains, the former was not strongly associated with sleep deprivation previously. We show that deprivation results in a feeding defect when the UPRmt is deficient and in UPRER-dependent germ cell apoptosis. In addition, when the UPRER is deficient, deprivation causes excess twitching in vulval muscles, mirroring a trend caused by loss of egg-laying command neurons. CONCLUSIONS These data show that nonlethal deprivation of C. elegans sleep causes proteotoxic stress. Unless mitigated, distinct types of deprivation-induced proteotoxicity can lead to anatomically and genetically separable lasting defects. The relative importance of different UPRs post-deprivation likely reflects functional, developmental, and genetic differences between the respective tissues and circuits.
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Affiliation(s)
- Jarred Sanders
- Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.
| | - Monika Scholz
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Ilaria Merutka
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - David Biron
- Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.,Department of Physics, The University of Chicago, Chicago, IL, 60637, USA
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134
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The Core Molecular Machinery Used for Engulfment of Apoptotic Cells Regulates the JNK Pathway Mediating Axon Regeneration in Caenorhabditis elegans. J Neurosci 2017; 36:9710-21. [PMID: 27629720 DOI: 10.1523/jneurosci.0453-16.2016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 07/25/2016] [Indexed: 02/04/2023] Open
Abstract
UNLABELLED The mechanisms that govern the ability of specific neurons to regenerate their axons after injury are not well understood. In Caenorhabditis elegans, the initiation of axon regeneration is positively regulated by the JNK-MAPK pathway. In this study, we identify two components functioning upstream of the JNK pathway: the Ste20-related protein kinase MAX-2 and the Rac-type GTPase CED-10. CED-10, when bound by GTP, interacts with MAX-2 and functions as its upstream regulator in axon regeneration. CED-10, in turn, is activated by axon injury via signals initiated from the integrin α-subunit INA-1 and the nonreceptor tyrosine kinase SRC-1 and transmitted via the signaling module CED-2/CrkII-CED-5/Dock180-CED-12/ELMO. This module is also known to regulate the engulfment of apoptotic cells during development. Our findings thus reveal that the molecular machinery used for engulfment of apoptotic cells also promotes axon regeneration through activation of the JNK pathway. SIGNIFICANCE STATEMENT The molecular mechanisms of axon regeneration after injury remain poorly understood. In Caenorhabditis elegans, the initiation of axon regeneration is positively regulated by the JNK-MAPK pathway. In this study, we show that integrin, Rac-GTPase, and several other molecules, all of which are known to regulate engulfment of apoptotic cells during development, also regulate axon regeneration. This signaling module activates the JNK-MAPK cascade via MAX-2, a PAK-like protein kinase that binds Rac. Our findings thus reveal that the molecular machinery used for engulfment of apoptotic cells also promotes axon regeneration through activation of the JNK pathway.
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135
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Purice MD, Ray A, Münzel EJ, Pope BJ, Park DJ, Speese SD, Logan MA. A novel Drosophila injury model reveals severed axons are cleared through a Draper/MMP-1 signaling cascade. eLife 2017; 6. [PMID: 28825401 PMCID: PMC5565368 DOI: 10.7554/elife.23611] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 07/25/2017] [Indexed: 02/06/2023] Open
Abstract
Neural injury triggers swift responses from glia, including glial migration and phagocytic clearance of damaged neurons. The transcriptional programs governing these complex innate glial immune responses are still unclear. Here, we describe a novel injury assay in adult Drosophila that elicits widespread glial responses in the ventral nerve cord (VNC). We profiled injury-induced changes in VNC gene expression by RNA sequencing (RNA-seq) and found that responsive genes fall into diverse signaling classes. One factor, matrix metalloproteinase-1 (MMP-1), is induced in Drosophila ensheathing glia responding to severed axons. Interestingly, glial induction of MMP-1 requires the highly conserved engulfment receptor Draper, as well as AP-1 and STAT92E. In MMP-1 depleted flies, glia do not properly infiltrate neuropil regions after axotomy and, as a consequence, fail to clear degenerating axonal debris. This work identifies Draper-dependent activation of MMP-1 as a novel cascade required for proper glial clearance of severed axons.
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Affiliation(s)
- Maria D Purice
- Jungers Center for Neurosciences Research, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Arpita Ray
- Jungers Center for Neurosciences Research, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Eva Jolanda Münzel
- Jungers Center for Neurosciences Research, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Bernard J Pope
- Melbourne Informatics, The University of Melbourne, Melbourne, Australia
| | - Daniel J Park
- Melbourne Informatics, The University of Melbourne, Melbourne, Australia
| | - Sean D Speese
- Jungers Center for Neurosciences Research, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Mary A Logan
- Jungers Center for Neurosciences Research, Department of Neurology, Oregon Health and Science University, Portland, United States
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136
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Lin L, Rodrigues FSLM, Kary C, Contet A, Logan M, Baxter RHG, Wood W, Baehrecke EH. Complement-Related Regulates Autophagy in Neighboring Cells. Cell 2017; 170:158-171.e8. [PMID: 28666117 DOI: 10.1016/j.cell.2017.06.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 03/07/2017] [Accepted: 06/13/2017] [Indexed: 11/25/2022]
Abstract
Autophagy degrades cytoplasmic components and is important for development and human health. Although autophagy is known to be influenced by systemic intercellular signals, the proteins that control autophagy are largely thought to function within individual cells. Here, we report that Drosophila macroglobulin complement-related (Mcr), a complement ortholog, plays an essential role during developmental cell death and inflammation by influencing autophagy in neighboring cells. This function of Mcr involves the immune receptor Draper, suggesting a relationship between autophagy and the control of inflammation. Interestingly, Mcr function in epithelial cells is required for macrophage autophagy and migration to epithelial wounds, a Draper-dependent process. This study reveals, unexpectedly, that complement-related from one cell regulates autophagy in neighboring cells via an ancient immune signaling program.
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Affiliation(s)
- Lin Lin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, MD 21218, USA
| | - Frederico S L M Rodrigues
- School of Cellular and Molecular Medicine, Faculty of Biomedical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Christina Kary
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Alicia Contet
- Department of Chemistry and Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Mary Logan
- Junger's Center for Neurosciences Research, Department of Neurology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Richard H G Baxter
- Department of Chemistry and Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Will Wood
- School of Cellular and Molecular Medicine, Faculty of Biomedical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Eric H Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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137
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Presumptive TRP channel CED-11 promotes cell volume decrease and facilitates degradation of apoptotic cells in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2017; 114:8806-8811. [PMID: 28760991 PMCID: PMC5565440 DOI: 10.1073/pnas.1705084114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Apoptotic cells undergo a series of morphological changes. These changes are dependent on caspase cleavage of downstream targets, but which targets are significant and how they facilitate the death process are not well understood. In Caenorhabditis elegans an increase in the refractility of the dying cell is a hallmark morphological change that is caspase dependent. We identify a presumptive transient receptor potential (TRP) cation channel, CED-11, that acts in the dying cell to promote the increase in apoptotic cell refractility. CED-11 is required for multiple other morphological changes during apoptosis, including an increase in electron density as visualized by electron microscopy and a decrease in cell volume. In ced-11 mutants, the degradation of apoptotic cells is delayed. Mutation of ced-11 does not cause an increase in cell survival but can enhance cell survival in other cell-death mutants, indicating that ced-11 facilitates the death process. In short, ced-11 acts downstream of caspase activation to promote the shrinkage, death, and degradation of apoptotic cells.
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138
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Sung M, Kawasaki I, Shim YH. Depletion of cdc-25.3, a Caenorhabditis elegans orthologue of cdc25, increases physiological germline apoptosis. FEBS Lett 2017. [PMID: 28627101 DOI: 10.1002/1873-3468.12717] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In Caenorhabditis elegans hermaphrodites, physiological germline apoptosis is higher in cdc-25.3 mutants than in wild-type. The elevated germline apoptosis in cdc-25.3 mutants seems to be induced by accumulation of double-stranded DNA breaks (DSBs). Both DNA damage and synapsis checkpoint genes are required to increase the germline apoptosis. Notably, the number of germ cells that lose P-granule components, PGL-1 and PGL-3, increase in cdc-25.3 mutants, and the increase in germline apoptosis requires the activity of SIR-2.1, a Sirtuin orthologue. These results suggest that elevation of germline apoptosis in cdc-25.3 mutants is induced by accumulation of DSBs, leading to a loss of PGL-1 and PGL-3 in germ cells, which promotes cytoplasmic translocation of SIR-2.1, and finally activates the core apoptotic machinery.
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Affiliation(s)
- Minhee Sung
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
| | - Ichiro Kawasaki
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
| | - Yhong-Hee Shim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
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139
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Megf10 Is a Receptor for C1Q That Mediates Clearance of Apoptotic Cells by Astrocytes. J Neurosci 2017; 36:5185-92. [PMID: 27170117 DOI: 10.1523/jneurosci.3850-15.2016] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 03/31/2016] [Indexed: 11/21/2022] Open
Abstract
UNLABELLED Multiple EGF-like domains 10 (Megf10) is a class F scavenger receptor (SR-F3) expressed on astrocytes and myosatellite cells, and recessive mutations in humans result in early-onset myopathy, areflexia, respiratory distress, and dysphagia (EMARDD). Here we report that Megf10-deficient mice have increased apoptotic cells in the developing cerebellum and have impaired phagocytosis of apoptotic cells by astrocytes ex vivo We also report that cells transfected with Megf10 gain the ability to phagocytose apoptotic neurons and that Megf10 binds with high affinity to C1q, an eat-me signal for apoptotic cells. In contrast, cells expressing Megf10 with EMARDD mutations have impaired apoptotic cell clearance and impaired binding to C1q. Our studies reveal that Megf10 is a receptor for C1q and identify a novel role for Megf10 in clearance of apoptotic cells in the mammalian developing brain with potential relevance to EMARDD patients and other CNS disorders. SIGNIFICANCE STATEMENT Apoptosis is a universal homeostatic process and occurs in many disease conditions. Multiple EGF-like domains 10 (Megf10) is emerging as an essential receptor for synaptic pruning, clearance of neuronal debris, and for muscle differentiation. Here we define a novel Megf10-dependent pathway for apoptotic cell clearance and show that Megf10 is a receptor for C1q, an eat-me signal, that binds phosphatidylserine expressed on the surface of apoptotic cells. Understanding the pathways by which apoptotic cells are cleared in the CNS is relevant to many physiological and pathological conditions of the CNS.
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140
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Rieckher M, Bujarrabal A, Doll MA, Soltanmohammadi N, Schumacher B. A simple answer to complex questions: Caenorhabditis elegans as an experimental model for examining the DNA damage response and disease genes. J Cell Physiol 2017; 233:2781-2790. [PMID: 28463453 DOI: 10.1002/jcp.25979] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 04/28/2017] [Indexed: 01/31/2023]
Abstract
The genetic information is constantly challenged by genotoxic attacks. DNA repair mechanisms evolved early in evolution and recognize and remove the various lesions. A complex network of DNA damage responses (DDR) orchestrates a variety of physiological adaptations to the presence of genome instability. Erroneous repair or malfunctioning of the DDR causes cancer development and the accumulation of DNA lesions drives the aging process. For understanding the complex DNA repair and DDR mechanisms it is pivotal to employ simple metazoan as model systems. The nematode Caenorhabditis elegans has become a well-established and popular experimental organism that allows dissecting genome stability mechanisms in dynamic and differentiated tissues and under physiological conditions. We provide an overview of the distinct advantages of the nematode system for studying DDR and provide a range of currently applied methodologies.
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Affiliation(s)
- Matthias Rieckher
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), and Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Arturo Bujarrabal
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), and Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Markus A Doll
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), and Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Najmeh Soltanmohammadi
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), and Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), and Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
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141
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Genetic variants in the transcription regulatory region of MEGF10 are associated with autism in Chinese Han population. Sci Rep 2017; 7:2292. [PMID: 28536440 PMCID: PMC5442155 DOI: 10.1038/s41598-017-02348-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/10/2017] [Indexed: 12/27/2022] Open
Abstract
Multiple epidermal growth factor-like-domains 10 (MEGF10), a critical member of the apoptotic engulfment pathway, mediates axon pruning and synapse elimination during brain development. Previous studies indicated that synaptic pruning deficit was associated with autism-related phenotypes. However, the relationship between MEGF10 and autism remains poorly understood. Disease-associated variants are significantly enriched in the transcription regulatory regions. These include the transcription start site (TSS) and its cis-regulatory elements. To investigate the role of MEGF10 variants with putative transcription regulatory function in the etiology of autism, we performed a family-based association study in 410 Chinese Han trios. Our results indicate that three single nucleotide polymorphisms (SNPs), rs4836316, rs2194079 and rs4836317 near the TSS are significantly associated with autism following Bonferroni correction (p = 0.0011, p = 0.0088, and p = 0.0023, respectively). Haplotype T-A-G (rs4836316-rs2194079-rs4836317) was preferentially transmitted from parents to affected offspring (p permutation = 0.0055). Consistently, functional exploration further verified that the risk allele and haplotype might influence its binding with transcription factors, resulting in decreased transcriptional activity of MEGF10. Our findings indicated that the risk alleles and haplotype near the MEGF10 TSS might modulate transcriptional activity and increase the susceptibility to autism.
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142
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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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143
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Nonaka S, Ando Y, Kanetani T, Hoshi C, Nakai Y, Nainu F, Nagaosa K, Shiratsuchi A, Nakanishi Y. Signaling pathway for phagocyte priming upon encounter with apoptotic cells. J Biol Chem 2017; 292:8059-8072. [PMID: 28325838 DOI: 10.1074/jbc.m116.769745] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/12/2017] [Indexed: 12/18/2022] Open
Abstract
The phagocytic elimination of cells undergoing apoptosis is an evolutionarily conserved innate immune mechanism for eliminating unnecessary cells. Previous studies showed an increase in the level of engulfment receptors in phagocytes after the phagocytosis of apoptotic cells, which leads to the enhancement of their phagocytic activity. However, precise mechanisms underlying this phenomenon require further clarification. We found that the pre-incubation of a Drosophila phagocyte cell line with the fragments of apoptotic cells enhanced the subsequent phagocytosis of apoptotic cells, accompanied by an augmented expression of the engulfment receptors Draper and integrin αPS3. The DNA-binding activity of the transcription repressor Tailless was transiently raised in those phagocytes, depending on two partially overlapping signal-transduction pathways for the induction of phagocytosis as well as the occurrence of engulfment. The RNAi knockdown of tailless in phagocytes abrogated the enhancement of both phagocytosis and engulfment receptor expression. Furthermore, the hemocyte-specific RNAi of tailless reduced apoptotic cell clearance in Drosophila embryos. Taken together, we propose the following mechanism for the activation of Drosophila phagocytes after an encounter with apoptotic cells: two partially overlapping signal-transduction pathways for phagocytosis are initiated; transcription repressor Tailless is activated; expression of engulfment receptors is stimulated; and phagocytic activity is enhanced. This phenomenon most likely ensures the phagocytic elimination of apoptotic cells by stimulated phagocytes and is thus considered as a mechanism to prime phagocytes in innate immunity.
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Affiliation(s)
- Saori Nonaka
- From the Graduate School of Medical Sciences and
| | - Yuki Ando
- From the Graduate School of Medical Sciences and
| | | | - Chiharu Hoshi
- School of Pharmacy, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Yuji Nakai
- the Institute for Food Sciences, Hirosaki University, Aomori, Aomori 038-0012, Japan, and
| | - Firzan Nainu
- From the Graduate School of Medical Sciences and.,the Faculty of Pharmacy, Hasanuddin University, Makassar, South Sulawesi 90245, Indonesia
| | - Kaz Nagaosa
- the Institute for Food Sciences, Hirosaki University, Aomori, Aomori 038-0012, Japan, and
| | | | - Yoshinobu Nakanishi
- From the Graduate School of Medical Sciences and .,School of Pharmacy, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
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144
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McMurchy AN, Stempor P, Gaarenstroom T, Wysolmerski B, Dong Y, Aussianikava D, Appert A, Huang N, Kolasinska-Zwierz P, Sapetschnig A, Miska EA, Ahringer J. A team of heterochromatin factors collaborates with small RNA pathways to combat repetitive elements and germline stress. eLife 2017; 6:e21666. [PMID: 28294943 PMCID: PMC5395297 DOI: 10.7554/elife.21666] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 03/10/2017] [Indexed: 12/26/2022] Open
Abstract
Repetitive sequences derived from transposons make up a large fraction of eukaryotic genomes and must be silenced to protect genome integrity. Repetitive elements are often found in heterochromatin; however, the roles and interactions of heterochromatin proteins in repeat regulation are poorly understood. Here we show that a diverse set of C. elegans heterochromatin proteins act together with the piRNA and nuclear RNAi pathways to silence repetitive elements and prevent genotoxic stress in the germ line. Mutants in genes encoding HPL-2/HP1, LIN-13, LIN-61, LET-418/Mi-2, and H3K9me2 histone methyltransferase MET-2/SETDB1 also show functionally redundant sterility, increased germline apoptosis, DNA repair defects, and interactions with small RNA pathways. Remarkably, fertility of heterochromatin mutants could be partially restored by inhibiting cep-1/p53, endogenous meiotic double strand breaks, or the expression of MIRAGE1 DNA transposons. Functional redundancy among factors and pathways underlies the importance of safeguarding the genome through multiple means.
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Affiliation(s)
- Alicia N McMurchy
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Przemyslaw Stempor
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Tessa Gaarenstroom
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Brian Wysolmerski
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Yan Dong
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Darya Aussianikava
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Alex Appert
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ni Huang
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Alexandra Sapetschnig
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Eric A Miska
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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145
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C. elegans neurons jettison protein aggregates and mitochondria under neurotoxic stress. Nature 2017; 542:367-371. [PMID: 28178240 PMCID: PMC5336134 DOI: 10.1038/nature21362] [Citation(s) in RCA: 259] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 01/03/2017] [Indexed: 12/12/2022]
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146
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Axon degeneration induces glial responses through Draper-TRAF4-JNK signalling. Nat Commun 2017; 8:14355. [PMID: 28165006 PMCID: PMC5303877 DOI: 10.1038/ncomms14355] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/20/2016] [Indexed: 12/31/2022] Open
Abstract
Draper/Ced-1/MEGF-10 is an engulfment receptor that promotes clearance of cellular debris in C. elegans, Drosophila and mammals. Draper signals through an evolutionarily conserved Src family kinase cascade to drive cytoskeletal rearrangements and target engulfment through Rac1. Glia also alter gene expression patterns in response to axonal injury but pathways mediating these responses are poorly defined. We show Draper is cell autonomously required for glial activation of transcriptional reporters after axonal injury. We identify TNF receptor associated factor 4 (TRAF4) as a novel Draper binding partner that is required for reporter activation and phagocytosis of axonal debris. TRAF4 and misshapen (MSN) act downstream of Draper to activate c-Jun N-terminal kinase (JNK) signalling in glia, resulting in changes in transcriptional reporters that are dependent on Drosophila AP-1 (dAP-1) and STAT92E. Our data argue injury signals received by Draper at the membrane are important regulators of downstream transcriptional responses in reactive glia.
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147
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Teuliere J, Garriga G. Size Matters: How C. elegans Asymmetric Divisions Regulate Apoptosis. Results Probl Cell Differ 2017; 61:141-163. [PMID: 28409303 DOI: 10.1007/978-3-319-53150-2_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Apoptosis is a form of programmed cell death used by metazoans to eliminate abnormal cells, control cell number, and shape the development of organs. The use of the nematode Caenorhabditis elegans as a model for the study of apoptosis has led to important insights into how cells die and how their corpses are removed. Eighty percent of these apoptotic cell deaths occur during nervous system development and in daughters of neuroblasts that divide asymmetrically. Pioneering work defined a conserved apoptosis pathway that is initiated in C. elegans by the BH3-only protein EGL-1 and that leads to the activation of the caspase CED-3. While the execution of the apoptotic fate is well understood, much less is known about the mechanisms that specify the apoptotic fate of particular cells. In some cells fated to die, this regulation occurs at the level of the egl-1 gene transcription, and investigators have identified several lineage-specific transcription factors that both positively and negatively regulate egl-1. In this review, we focus on a second set of molecules that appear to influence apoptosis by controlling the position of the cleavage plane in divisions that produce apoptotic cells.
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Affiliation(s)
- Jerome Teuliere
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
| | - Gian Garriga
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA.
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148
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Nonaka S, Shiratsuchi A, Nagaosa K, Nakanishi Y. Mechanisms and Significance of Phagocytic Elimination of Cells Undergoing Apoptotic Death. Biol Pharm Bull 2017; 40:1819-1827. [DOI: 10.1248/bpb.b17-00478] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Saori Nonaka
- Graduate School of Medical Sciences, Kanazawa University
| | | | - Kaz Nagaosa
- Graduate School of Medical Sciences, Kanazawa University
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149
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Gao Y, Xu D, Zhao L, Sun Y. The DNA damage response of C. elegans affected by gravity sensing and radiosensitivity during the Shenzhou-8 spaceflight. Mutat Res 2017; 795:15-26. [PMID: 28088539 DOI: 10.1016/j.mrfmmm.2017.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/06/2016] [Accepted: 01/04/2017] [Indexed: 06/06/2023]
Abstract
Space radiation and microgravity are recognized as primary and inevitable risk factors for humans traveling in space, but the reports regarding their synergistic effects remain inconclusive and vary across studies due to differences in the environmental conditions and intrinsic biological sensitivity. Thus, we studied the synergistic effects on transcriptional changes in the global genome and DNA damage response (DDR) by using dys-1 mutant and ced-1 mutant of C. elegans, which respectively presented microgravity-insensitivity and radiosensitivity when exposure to spaceflight condition (SF) and space radiation (SR). The dys-1 mutation induced similar transcriptional changes under both conditions, including the transcriptional distribution and function of altered genes. The majority of alterations were related to metabolic shift under both conditions, including transmembrane transport, lipid metabolic processes and proteolysis. Under SF and SR conditions, 12/14 and 10/13 altered pathways, respectively, were both grouped in the metabolism category. Out of the 778 genes involved in DDR, except eya-1 and ceh-34, 28 altered genes in dys-1 mutant showed no predicted protein interactions, or anti-correlated miRNAs during spaceflight. The ced-1 mutation induced similar changes under SF and SR; however, these effects were stronger than those of the dys-1 mutant. The additional genes identified were related to phosphorous/phosphate metabolic processes and growth rather than, metabolism, especially for environmental information processing under SR. Although the DDR profiles were significantly changed under both conditions, the ced-1 mutation favored DNA repair under SF and apoptosis under SR. Notably, 37 miRNAs were predicted to be involved in the DDR. Our study indicates that, the dys-1 mutation reduced the transcriptional response to SF, and the ced-1 mutation increased the response to SR, when compared with the wild type C. elegans. Although some effects were due to radiosensitivity, microgravity, depending on the dystrophin, exerts predominant effects on transcription in C. elegans during short-duration spaceflight.
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Affiliation(s)
- Ying Gao
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Shushanhu Road 350, Hefei 230031, China; Cancer Hospital, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Shushanhu Road 350, Hefei 230031, China
| | - Dan Xu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Linghai Road 1, Dalian 116026, China
| | - Lei Zhao
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Linghai Road 1, Dalian 116026, China
| | - Yeqing Sun
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Linghai Road 1, Dalian 116026, China.
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150
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Cheng S, Liu K, Yang C, Wang X. Dissecting Phagocytic Removal of Apoptotic Cells in Caenorhabditis elegans. Methods Mol Biol 2017; 1519:265-284. [PMID: 27815886 DOI: 10.1007/978-1-4939-6581-6_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The unique features of programmed cell death during C. elegans development provide an outstanding system to decipher the mechanisms governing phagocytic removal of apoptotic cells. Like in many other organisms, phagocytosis in C. elegans involves several essential events, including exposure of eat-me signals on the cell corpse surface, cell corpse recognition and engulfment by phagocytes, and maturation of phagosomes for cell corpse destruction. Forward or reverse genetic approaches, microscopy-based cell biological methods, and biochemical assays have successfully been employed to identify key factors that control different steps of phagocytosis and to understand their functions in these cellular events. In this chapter, we mainly describe how to apply genetic and cell biological approaches to dissect cell corpse removal by phagocytosis in C. elegans.
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Affiliation(s)
- Shiya Cheng
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China
| | - Kai Liu
- 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
| | - 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.
| | - Xiaochen Wang
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China.
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