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Ha HJ, Park HH. Molecular basis of apoptotic DNA fragmentation by DFF40. Cell Death Dis 2022; 13:198. [PMID: 35236824 PMCID: PMC8891305 DOI: 10.1038/s41419-022-04662-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/03/2022] [Accepted: 02/16/2022] [Indexed: 11/09/2022]
Abstract
AbstractAlthough the functions of CIDE domain-containing proteins, including DFF40, DFF45, CIDE-A, CIDE-B, and FSP27, in apoptotic DNA fragmentation and lipid homeostasis have been studied extensively in mammals, the functions of four CIDE domain-containing proteins identified in the fly, namely DREP1, 2, 3, and 4, have not been explored much. Recent structural study of DREP4, a fly orthologue of mammalian DFF40 (an endonuclease involved in apoptotic DNA fragmentation), showed that the CIDE domain of DREP4 (and DFF40) forms filament-like assembly, which is critical for the corresponding function. The current study aimed to investigate the mechanism of filament formation of DREP4 CIDE and to characterize the same. DREP4 CIDE was shown to specifically bind to histones H1 and H2, an event important for the nuclease activity of DREP4. Based on the current experimental results, we proposed the mechanism underlying the process of apoptotic DNA fragmentation.
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2
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Lee SY, Kwon S, Ha HJ, Lee SH, Park HH. Helical filament structure of the DREP3 CIDE domain reveals a unified mechanism of CIDE-domain assembly. Acta Crystallogr D Struct Biol 2021; 77:1543-1553. [PMID: 34866610 PMCID: PMC8647176 DOI: 10.1107/s2059798321010767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/18/2021] [Indexed: 12/04/2022] Open
Abstract
The cell-death-inducing DFF45-like effector (CIDE) domain is a protein-interaction module comprising ∼80 amino acids and was initially identified in several apoptotic nucleases and their regulators. CIDE-domain-containing proteins were subsequently identified among proteins involved in lipid metabolism. Given the involvement of CIDE-domain-containing proteins in cell death and lipid homeostasis, their structure and function have been intensively studied. Here, the head-to-tail helical filament structure of the CIDE domain of DNA fragmentation factor-related protein 3 (DREP3) is presented. The helical filament structure was formed by opposing positively and negatively charged interfaces of the domain and was assembled depending on protein and salt concentrations. Although conserved filament structures are observed in CIDE family members, the structure elucidated in this study and its comparison with previous structures indicated that the size and the number of molecules used in one turn vary. These findings suggest that this charged-surface-based head-to-tail helical filament structure represents a unified mechanism of CIDE-domain assembly and provides insight into the function of various forms of the filament structure of the CIDE domain in higher-order assembly for apoptotic DNA fragmentation and control of lipid-droplet size.
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Affiliation(s)
- So Yeon Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sunghark Kwon
- Department of Biotechnology, Konkuk University, Chungju, Chungbuk 27478, Republic of Korea
| | - Hyun Ji Ha
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sung Hoon Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
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3
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Crystal structure and mutation analysis revealed that DREP2 CIDE forms a filament-like structure with features differing from those of DREP4 CIDE. Sci Rep 2018; 8:17810. [PMID: 30546036 PMCID: PMC6292858 DOI: 10.1038/s41598-018-36253-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/16/2018] [Indexed: 11/26/2022] Open
Abstract
Cell death-inducing DFF45-like effect (CIDE) domain-containing proteins, DFF40, DFF45, CIDE-A, CIDE-B, and FSP27, play important roles in apoptotic DNA fragmentation and lipid homeostasis. The function of DFF40/45 in apoptotic DNA fragmentation is mediated by CIDE domain filament formation. Although our recent structural study of DREP4 CIDE revealed the first filament-like structure of the CIDE domain and its functional importance, the filament structure of DREP2 CIDE is unclear because this structure was not helical in the asymmetric unit. In this study, we present the crystal structure and mutagenesis analysis of the DREP2 CIDE mutant, which confirmed that DREP2 CIDE also forms a filament-like structure with features differing from those of DREP4 CIDE.
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Kim CM, Jeon SH, Choi JH, Lee JH, Park HH. Interaction mode of CIDE family proteins in fly: DREP1 and DREP3 acidic surfaces interact with DREP2 and DREP4 basic surfaces. PLoS One 2017; 12:e0189819. [PMID: 29240809 PMCID: PMC5730196 DOI: 10.1371/journal.pone.0189819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 12/01/2017] [Indexed: 11/19/2022] Open
Abstract
Cell death-inducing DNA fragmentation factor 45 (DFF45)-like effector (CIDE) domains were initially identified as protein interaction modules in apoptotic nucleases and are now known to form a highly conserved family with diverse functions that range from cell death to lipid homeostasis. In the fly, four CIDE domain-containing proteins (DFF-related protein [DREP]-1–4) and their functions, including interaction relationships, have been identified. In this study, we introduced and investigated acidic side-disrupted mutants of DREP1, DREP2, and DREP3. We discovered that the acidic surface patches of DREP1 and DREP3 are critical for the homo-dimerization. In addition, we found that the acidic surface sides of DREP1 and DREP3 interact with the basic surface sides of DREP2 and DREP4. Our current study provides clear evidence demonstrating the mechanism of the interactions between four DREP proteins in the fly.
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Affiliation(s)
- Chang Min Kim
- School of Natural Science, Department of Chemistry and Biochemistry and Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
| | - Sun Hee Jeon
- School of Natural Science, Department of Chemistry and Biochemistry and Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
| | - Jun-Hyuk Choi
- Department of Metrology for Quality of Life, Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Inchon, Republic of Korea
| | - Hyun Ho Park
- School of Natural Science, Department of Chemistry and Biochemistry and Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
- * E-mail:
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5
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CIDE domains form functionally important higher-order assemblies for DNA fragmentation. Proc Natl Acad Sci U S A 2017; 114:7361-7366. [PMID: 28652364 DOI: 10.1073/pnas.1705949114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cell death-inducing DFF45-like effector (CIDE) domains, initially identified in apoptotic nucleases, form a family with diverse functions ranging from cell death to lipid homeostasis. Here we show that the CIDE domains of Drosophila and human apoptotic nucleases Drep2, Drep4, and DFF40 all form head-to-tail helical filaments. Opposing positively and negatively charged interfaces mediate the helical structures, and mutations on these surfaces abolish nuclease activation for apoptotic DNA fragmentation. Conserved filamentous structures are observed in CIDE family members involved in lipid homeostasis, and mutations on the charged interfaces compromise lipid droplet fusion, suggesting that CIDE domains represent a scaffold for higher-order assembly in DNA fragmentation and other biological processes such as lipid homeostasis.
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Zhang K, Luo L, Chen X, Hu M, Hu Q, Gong L, Weng Q. Molecular Effects of Irradiation (Cobalt-60) on the Control of Panonychus citri (Acari: Tetranychidae). Int J Mol Sci 2015; 16:26964-77. [PMID: 26569230 PMCID: PMC4661862 DOI: 10.3390/ijms161126004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/21/2015] [Accepted: 11/02/2015] [Indexed: 11/16/2022] Open
Abstract
The effective dose of irradiation to control pest mites in quarantine has been studied extensively, but the molecular mechanisms underlying the effects of the irradiation on mites are largely unknown. In this study, exposure to 400 Gy of γ rays had significant (p < 0.05) effects on the adult survival, fecundity and egg viability of Panonychus citri. The irradiation caused the degradation of the DNA of P. citri adults and damaged the plasma membrane system of the egg, which led to condensed nucleoli and gathered yolk. Additionally, the transcriptomes and gene expression profiles between irradiated and non-irradiated mites were compared, and three digital gene expression libraries were assembled and analyzed. The differentially expressed genes were putatively involved in apoptosis, cell death and the cell cycle. Finally, the expression profiles of some related genes were studied using quantitative real-time PCR. Our study provides valuable information on the changes in the transcriptome of irradiated P. citri, which will facilitate a better understanding of the molecular mechanisms that cause the sterility induced by irradiation.
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Affiliation(s)
- Ke Zhang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education of China, South China Agricultural University, Guangzhou 510642, China.
| | - Lingyan Luo
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education of China, South China Agricultural University, Guangzhou 510642, China.
| | - Xieting Chen
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education of China, South China Agricultural University, Guangzhou 510642, China.
| | - Meiying Hu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education of China, South China Agricultural University, Guangzhou 510642, China.
| | - Qiongbo Hu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education of China, South China Agricultural University, Guangzhou 510642, China.
| | - Liang Gong
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Qunfang Weng
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education of China, South China Agricultural University, Guangzhou 510642, China.
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8
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Andlauer TFM, Scholz-Kornehl S, Tian R, Kirchner M, Babikir HA, Depner H, Loll B, Quentin C, Gupta VK, Holt MG, Dipt S, Cressy M, Wahl MC, Fiala A, Selbach M, Schwärzel M, Sigrist SJ. Drep-2 is a novel synaptic protein important for learning and memory. eLife 2014; 3. [PMID: 25392983 PMCID: PMC4229683 DOI: 10.7554/elife.03895] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/13/2014] [Indexed: 12/16/2022] Open
Abstract
CIDE-N domains mediate interactions between the DNase Dff40/CAD and its inhibitor Dff45/ICAD. In this study, we report that the CIDE-N protein Drep-2 is a novel synaptic protein important for learning and behavioral adaptation. Drep-2 was found at synapses throughout the Drosophila brain and was strongly enriched at mushroom body input synapses. It was required within Kenyon cells for normal olfactory short- and intermediate-term memory. Drep-2 colocalized with metabotropic glutamate receptors (mGluRs). Chronic pharmacological stimulation of mGluRs compensated for drep-2 learning deficits, and drep-2 and mGluR learning phenotypes behaved non-additively, suggesting that Drep 2 might be involved in effective mGluR signaling. In fact, Drosophila fragile X protein mutants, shown to benefit from attenuation of mGluR signaling, profited from the elimination of drep-2. Thus, Drep-2 is a novel regulatory synaptic factor, probably intersecting with metabotropic signaling and translational regulation. DOI:http://dx.doi.org/10.7554/eLife.03895.001 Synapses are specialized structures that connect nerve cells to one another and allow information to be transmitted between the cells. Synapses are essential for learning and storing memories. Many proteins that regulate how signals are transmitted at synapses have already been studied. In this manner, much has been learned about their function in learning and memory. Cells can commit suicide by a process called apoptosis, also known as programmed cell death. Apoptosis is not only triggered in damaged cells but is also necessary for an organism to develop correctly. In fruit flies, the protein Drep-2 is a member of a family of proteins that degrade the DNA of cells that undergo apoptosis. Andlauer et al. found no evidence that Drep-2 plays a role in apoptosis, but have now found Drep-2 at the synapses of the brain of the fruit fly Drosophila. Drep-2 could be observed in close proximity to another type of protein called metabotropic glutamate receptors. Metabotropic glutamate receptors and their signaling pathways are important for regulating certain changes to the synapses that mediate learning processes. Indeed, Andlauer et al. found that flies that have lost the gene that produces Drep-2 were unable to remember smells when these were paired with a punishment. Stimulating the regulatory glutamate receptors with drugs helped to overcome learning deficits that result from the lack of Drep-2. Alterations in the production of a protein called FMRP cause fragile X syndrome in humans, the most common form of hereditary mental disability originating from a single gene defect. Flies lacking the FMRP protein show learning deficits that are very similar to the ones seen in flies that cannot produce Drep-2. However, Andlauer et al. observed that flies lacking both Drep-2 and FMRP can learn normally. Exactly how Drep-2 works in synapses to help with memory formation remains to be discovered, although there are indications that it boosts the effects of signaling from the glutamate receptors and counteracts FMRP. Further research will be needed to establish whether the mammalian proteins related to Drep-2 perform similar roles in the brains of mammals. DOI:http://dx.doi.org/10.7554/eLife.03895.002
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Affiliation(s)
- Till F M Andlauer
- Genetics, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | | | - Rui Tian
- Genetics, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Marieluise Kirchner
- Department of Cell Signalling and Mass Spectrometry, Max-Delbrück-Centrum für Molekulare Medizin, Berlin-Buch, Germany
| | - Husam A Babikir
- Genetics, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Harald Depner
- Genetics, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Bernhard Loll
- Institute of Chemistry and Biochemisty, Freie Universität Berlin, Berlin, Germany
| | - Christine Quentin
- Genetics, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Varun K Gupta
- Genetics, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Matthew G Holt
- Department Laboratory of Glia Biology, Vlaams Instituut voor Biotechnologie (VIB) Center for the Biology of Disease, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Shubham Dipt
- Department of Molecular Neurobiology of Behavior, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Michael Cressy
- Department of Neuroscience, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Markus C Wahl
- Institute of Chemistry and Biochemisty, Freie Universität Berlin, Berlin, Germany
| | - André Fiala
- Department of Molecular Neurobiology of Behavior, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Matthias Selbach
- Department of Cell Signalling and Mass Spectrometry, Max-Delbrück-Centrum für Molekulare Medizin, Berlin-Buch, Germany
| | - Martin Schwärzel
- Genetics, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Stephan J Sigrist
- Genetics, Institute of Biology, Freie Universität Berlin, Berlin, Germany
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Abstract
CIDE domain containing proteins are involved in apoptosis and lipid metabolism, and four CIDE containing proteins, Drep1, Drep2, Drep3, and Drep4, have been identified in fly. In this study, we found that Drep3 interacts with Drep4 via the CIDE domain specifically, which completes the interaction map of Drep system in fly, cyclic interactions: Drep1–Drep2–Drep3–Drep4–Drep1. In addition, we analyzed the dynamic stoichiometry changes of Drep proteins upon binding to their binding partners. Our current studies will help us to understand Drep system in fly as well as CIDE domain for protein–protein interactions.
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10
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Lee SM, Jang TH, Park HH. Molecular basis for homo-dimerization of the CIDE domain revealed by the crystal structure of the CIDE-N domain of FSP27. Biochem Biophys Res Commun 2013; 439:564-9. [PMID: 24025675 DOI: 10.1016/j.bbrc.2013.09.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 09/03/2013] [Indexed: 12/12/2022]
Abstract
FSP27 (CIDE-3 in humans) plays critical roles in lipid metabolism and apoptosis and is known to be involved in regulation of lipid droplet (LD) size and lipid storage and apoptotic DNA fragmentation. Given that CIDE-containing proteins including FSP27 are associated with many human diseases including cancer, aging, diabetes, and obesity, studies of FSP27 and other CIDE-containing proteins are of great biological importance. As a first step toward elucidating the molecular mechanisms of FSP27-mediated lipid droplet growth and apoptosis, we report the crystal structure of the CIDE-N domain of FSP27 at a resolution of 2.0 Å. The structure revealed a possible biologically important homo-dimeric interface similar to that formed by the hetero-dimeric complex, CAD/ICAD. Comparison with other structural homologues revealed that the PB1 domain of BEM1P, ubiquitin-like domain of BAG6 and ubiquitin are structurally similar proteins. Our homo-dimeric structure of the CIDE-N domain of FSP27 will provide important information that will enable better understanding of the function of FSP27.
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Affiliation(s)
- Seung Mi Lee
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan, South Korea
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