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Zhang W, Zhuang S, Guan H, Li F, Zou H, Li D. New insights into the anti-apoptotic mechanism of natural polyphenols in complex with Bax protein. J Biomol Struct Dyn 2024; 42:3081-3093. [PMID: 37184126 DOI: 10.1080/07391102.2023.2212066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/01/2023] [Indexed: 05/16/2023]
Abstract
Excessive apoptosis can kill normal cells and lead to liver damage, heart failure and neurodegenerative diseases. Polyphenols are secondary metabolites of plants that can interact with proteins to inhibit toxins and disease-related apoptosis. Bax is the major pro-apoptotic protein that disrupts the outer mitochondrial membrane to induce apoptosis, but limited studies have focused on the interaction between polyphenols and Bax and the associated anti-apoptotic mechanisms, especially at the atomic level. In this article, we collected 69 common polyphenols for active ingredient screening targeting Bax. Polyphenols with better and worse molecular docking scores were selected, and their anti-apoptosis effects were compared using the H2O2-induced HepG2 cell model. The interactions between the selected polyphenols and Bax protein were analyzed using molecular dynamics simulation to explore the molecular mechanism underlying the anti-apoptosis effect. Secoisolariciresinol diglucoside (SDG) and Epigallocatechin-3-gallate (EGCG) with the best affinity for Bax (-6.76 and -6.52 kcal/mol) reduced the expression of cytochrome c and caspase 3, decreasing the apoptosis rate from 52 to 11% and 12%. Molecular dynamics simulation results showed that Bim unfolded the α1-α2 loop of Bax, and disrupted the non-bond interactions between the loop (Pro-43, Glu-44 and Leu-45) and surface (Ile-133, Arg-134 and Met-137) residues, with binding free energy changed from -15.0 to 0 kJ/mol. The hydrogen bonds and van der Waals interactions formed between polyphenols and Bax prevented the unfolding of the loop. Taken together, our results proved that polyphenols can inhibit apoptosis by maintaining the unactivated conformation of Bax to reduce outer mitochondrial membrane damage.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wenyuan Zhang
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian, China
| | | | - Hui Guan
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian, China
| | - Feng Li
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian, China
| | - Hui Zou
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian, China
| | - Dapeng Li
- Qingdao Institute for Food and Drug Control, Qingdao, China
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2
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Faraji N, Daly NL, Arab SS, Khosroushahi AY. In silico design of potential Mcl-1 peptide-based inhibitors. J Mol Model 2024; 30:108. [PMID: 38499818 DOI: 10.1007/s00894-024-05901-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/10/2024] [Indexed: 03/20/2024]
Abstract
CONTEXT BIM (Bcl-2 interacting mediator of apoptosis)-derived peptides that specifically target over-expressed Mcl-1 (myeloid cell leukemia-1) protein and induce apoptosis are potentially anti-cancer agents. Since the helicity of BIM-derived peptides has a crucial role in their functionality, a range of strategies have been used to increase the helicity including the introduction of unnatural residues and stapling methods that have some drawbacks such as the accumulation in the liver. To avoid these drawbacks, this study aimed to design a more helical peptide by utilizing bioinformatics algorithms and molecular dynamics simulations without exploiting unnatural residues and stapling methods. MM-PBSA results showed that the mutations of A4fE and A2eE in analogue 5 demonstrate a preference towards binding with Mcl-1. As evidenced by Circular dichroism results, the helicity increases from 18 to 34%, these findings could enhance the potential of analogue 5 as an anti-cancer agent targeting Mcl-1. The applied strategies in this research could shed light on the in silico peptide design. Moreover, analogue 5 as a drug candidate can be evaluated in vitro and in vivo studies. METHODS The sequence of the lead peptide was determined using the ApInAPDB database and PRALINE program. Contact finder and PDBsum web server softwares were used to determine the contact involved amino acids in complex with Mcl-1. All identified salt bridge contributing residues were unaltered to preserve the binding affinity. After proposing novel analogues, their secondary structures were predicted by Cham finder web server software and GOR, Neural Network, and Chou-Fasman algorithms. Finally, molecular dynamics simulations run for 100 ns were done using the GROMACS, version 5.0.7, with the CHARMM36 force field. MM-PBSA was used to assess binding affinity specificity in targeting Mcl-1 and Bcl-xL (B-cell lymphoma extra-large).
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Affiliation(s)
- Naser Faraji
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Daneshgah Street, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Norelle L Daly
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, 4870, Australia
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Ahmad Yari Khosroushahi
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Daneshgah Street, Tabriz, Iran.
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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3
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Sakuragi T, Kanai R, Otani M, Kikkawa M, Toyoshima C, Nagata S. The role of the C-terminal tail region as a plug to regulate XKR8 lipid scramblase. J Biol Chem 2024; 300:105755. [PMID: 38364890 PMCID: PMC10938166 DOI: 10.1016/j.jbc.2024.105755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/27/2024] [Accepted: 02/10/2024] [Indexed: 02/18/2024] Open
Abstract
XK-related 8 (XKR8), in complex with the transmembrane glycoprotein basigin, functions as a phospholipid scramblase activated by the caspase-mediated cleavage or phosphorylation of its C-terminal tail. It carries a putative phospholipid translocation path of multiple hydrophobic and charged residues in the transmembrane region. It also has a crucial tryptophan at the exoplasmic end of the path that regulates its scrambling activity. We herein investigated the tertiary structure of the human XKR8-basigin complex embedded in lipid nanodiscs at an overall resolution of 3.66 Å. We found that the C-terminal tail engaged in intricate polar and van der Waals interactions with a groove at the cytoplasmic surface of XKR8. These interactions maintained the inactive state of XKR8. Point mutations to disrupt these interactions strongly enhanced the scrambling activity of XKR8, suggesting that the activation of XKR8 is mediated by releasing the C-terminal tail from the cytoplasmic groove. We speculate that the cytoplasmic tail region of XKR8 functions as a plug to prevent the scrambling of phospholipids.
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Affiliation(s)
- Takaharu Sakuragi
- Laboratory of Biochemistry and Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Ryuta Kanai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Mayumi Otani
- Laboratory of Biochemistry and Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Chikashi Toyoshima
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Shigekazu Nagata
- Laboratory of Biochemistry and Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
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4
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Liu T, Huang S, Zhang Q, Xia Y, Zhang M, Sun B. Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data. PLoS Comput Biol 2024; 20:e1011519. [PMID: 38324587 PMCID: PMC10878502 DOI: 10.1371/journal.pcbi.1011519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/20/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024] Open
Abstract
ASPP2 and iASPP bind to p53 through their conserved ANK-SH3 domains to respectively promote and inhibit p53-dependent cell apoptosis. While crystallography has indicated that these two proteins employ distinct surfaces of their ANK-SH3 domains to bind to p53, solution NMR data has suggested similar surfaces. In this study, we employed multi-scale molecular dynamics (MD) simulations combined with free energy calculations to reconcile the discrepancy in the binding modes. We demonstrated that the binding mode based solely on a single crystal structure does not enable iASPP's RT loop to engage with p53's C-terminal linker-a verified interaction. Instead, an ensemble of simulated iASPP-p53 complexes facilitates this interaction. We showed that the ensemble-average inter-protein contacting residues and NMR-detected interfacial residues qualitatively overlap on ASPP proteins, and the ensemble-average binding free energies better match experimental KD values compared to single crystallgarphy-determined binding mode. For iASPP, the sampled ensemble complexes can be grouped into two classes, resembling the binding modes determined by crystallography and solution NMR. We thus propose that crystal packing shifts the equilibrium of binding modes towards the crystallography-determined one. Lastly, we showed that the ensemble binding complexes are sensitive to p53's intrinsically disordered regions (IDRs), attesting to experimental observations that these IDRs contribute to biological functions. Our results provide a dynamic and ensemble perspective for scrutinizing these important cancer-related protein-protein interactions (PPIs).
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Affiliation(s)
- Te Liu
- Research Center for Pharmacoinformatics, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Sichao Huang
- Research Center for Pharmacoinformatics, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Qian Zhang
- Research Center for Pharmacoinformatics, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yu Xia
- Research Center for Pharmacoinformatics, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Manjie Zhang
- Research Center for Pharmacoinformatics, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Bin Sun
- Research Center for Pharmacoinformatics, College of Pharmacy, Harbin Medical University, Harbin, China
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5
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Afzal M, Alarifi A, Abduh NAY, Ayub A, Muddassir M. Identification of anti-cancer organometallic compounds by inhibition of BCL-2/Bax interactions. Comput Biol Med 2023; 167:107657. [PMID: 37931525 DOI: 10.1016/j.compbiomed.2023.107657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/21/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023]
Abstract
Apoptosis is regulated by the BCL-2 family, which includes the anti-apoptotic and pro-apoptotic proteins (Bax, Bok, Bak, etc.). These proteins often interact in dimers and act as apoptotic switches. Anti-apoptotic proteins, such as BCL-2, block the functions of these pro-apoptotic proteins. The pro-apoptotic and anti-apoptotic protein-protein interactions must be inhibited to prevent tumor cells from escaping apoptosis. This method has been used to develop anticancer drugs by inhibiting BCL-2 with both natural and synthetic compounds. Metal-containing compounds were used as pharmaceuticals for human cancer patients for a long time, and cisplatin was the first candidate of this class. Drug design, however, needs to pay more attention to metal complexes. We have studied the X-ray crystal structure of the BCL-2 protein in detail and identified the hydrophobic nature of the site with two less solvent-accessible sites. Based on the hydrophobic nature of the compounds, 74 organometallic compounds with X-ray crystallographically characterized bioactivity (including anticancer activity) were selected from the Cambridge crystallographic database. For testing, molecular docking was used to determine which compound was most effective against the BCL-2 protein. Organometallic compounds (benzene)-chloro-(1-{[(9H-fluoren-2-yl)imino]methyl}naphthalen-2-olato)-ruthenium (2), (1-((1,1'-biphenyl)-4-yl)-2,3,4,5-tetramethylcyclopentadienyl)-chloro-(4,4'-dimethyl-2,2'-bipyridine)-rhodium hexafluorophosphate (37), (μ-1,1'-(butane-1,4-diyl)bis(3-oxy-2-methylpyridin-4(1H)-one))-dichloro-bis(pentamethyl-cyclopentadienyl)-di-rhodium tetrahydrate (46), (μ-1,1'-(butane-1,4-diyl)bis(3-oxy-2-methylpyridin-4(1H)-one))-dichloro-bis(pentamethyl-cyclopentadienyl)-di-iridium (47) etc are found to be important compounds in this study. The capability of different types of complex interactions was identified using Hirshfeld surface analysis of the complexes. A NCI plot was conducted to understand the nature of the interaction between complex amino acids and active-site amino acids. A DFT study was conducted to examine the stability and chemical reactivity of the selected complexes. Using this study, one suitable hydrophobic lead anti-cancer organometallic pharmaceutical was found that binds at the less solvent-accessible hydrophobic site of BCL-2.
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Affiliation(s)
- Mohd Afzal
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
| | - Abdullah Alarifi
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Naaser A Y Abduh
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Arusha Ayub
- Department of Medicine and Health Sciences, University of Georgia, P.O. Box-0171, Tbilisi, Georgia
| | - Mohd Muddassir
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
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Aguilar F, Yu S, Grant RA, Swanson S, Ghose D, Su BG, Sarosiek KA, Keating AE. Peptides from human BNIP5 and PXT1 and non-native binders of pro-apoptotic BAK can directly activate or inhibit BAK-mediated membrane permeabilization. Structure 2023; 31:265-281.e7. [PMID: 36706751 PMCID: PMC9992319 DOI: 10.1016/j.str.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/24/2022] [Accepted: 01/02/2023] [Indexed: 01/27/2023]
Abstract
Apoptosis is important for development and tissue homeostasis, and its dysregulation can lead to diseases, including cancer. As an apoptotic effector, BAK undergoes conformational changes that promote mitochondrial outer membrane disruption, leading to cell death. This is termed "activation" and can be induced by peptides from the human proteins BID, BIM, and PUMA. To identify additional peptides that can regulate BAK, we used computational protein design, yeast surface display screening, and structure-based energy scoring to identify 10 diverse new binders. We discovered peptides from the human proteins BNIP5 and PXT1 and three non-native peptides that activate BAK in liposome assays and induce cytochrome c release from mitochondria. Crystal structures and binding studies reveal a high degree of similarity among peptide activators and inhibitors, ruling out a simple function-determining property. Our results shed light on the vast peptide sequence space that can regulate BAK function and will guide the design of BAK-modulating tools and therapeutics.
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Affiliation(s)
- Fiona Aguilar
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stacey Yu
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Program in Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA; John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sebastian Swanson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dia Ghose
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bonnie G Su
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kristopher A Sarosiek
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Program in Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA; John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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7
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Yi J, Kellner V, Joo H, Chien N, Patel S, Chaban Z, Tsai J. Characterizing the consensus residue specificity and surface of BCL-2 binding to BH3 ligands using the Knob-Socket model. PLoS One 2023; 18:e0281463. [PMID: 36795726 PMCID: PMC9934389 DOI: 10.1371/journal.pone.0281463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 01/24/2023] [Indexed: 02/17/2023] Open
Abstract
Cancer cells bypass cell death by changing the expression of the BCL-2 family of proteins, which are apoptotic pathway regulators. Upregulation of pro-survival BCL-2 proteins or downregulation of cell death effectors BAX and BAK interferes with the initiation of the intrinsic apoptotic pathway. In normal cells, apoptosis can occur through pro-apoptotic BH3-only proteins interacting and inhibiting pro-survival BCL-2 proteins. When cancer cells over-express pro-survival BCL-2 proteins, a potential remedy is the sequestration of these pro-survival proteins through a class of anti-cancer drugs called BH3 mimetics that bind in the hydrophobic groove of pro-survival BCL-2 proteins. To improve the design of these BH3 mimetics, the packing interface between BH3 domain ligands and pro-survival BCL-2 proteins was analyzed using the Knob-Socket model to identify the amino acid residues responsible for interaction affinity and specificity. A Knob-Socket analysis organizes all the residues in a binding interface into simple 4 residue units: 3-residue sockets defining surfaces on a protein that pack a 4th residue knob from the other protein. In this way, the position and composition of the knobs packing into sockets across the BH3/BCL-2 interface can be classified. A Knob-Socket analysis of 19 BCL-2 protein and BH3 helix co-crystals reveal multiple conserved binding patterns across protein paralogs. Conserved knob residues such as a Gly, Leu, Ala and Glu most likely define binding specificity in the BH3/BCL-2 interface, whereas other residues such as Asp, Asn, and Val are important for forming surface sockets that bind these knobs. These findings can be used to inform the design of BH3 mimetics that are specific to pro-survival BCL-2 proteins for cancer therapeutics.
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Affiliation(s)
- Jennifer Yi
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, California, United States of America
| | - Vivian Kellner
- Department of Chemistry, UC Davis, Davis, California, United States of America
| | - Hyun Joo
- Department of Chemistry, University of the Pacific, Stockton, California, United States of America
| | - Nathaniel Chien
- Computer Science Department, Stanford University, Stanford, California, United States of America
| | - Shivarni Patel
- Department of Chemistry, University of the Pacific, Stockton, California, United States of America
| | - Zaina Chaban
- Department of Chemistry, University of the Pacific, Stockton, California, United States of America
| | - Jerry Tsai
- Department of Chemistry, University of the Pacific, Stockton, California, United States of America
- * E-mail:
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8
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Vince MJK, Holub JM. Synthesis of Scyllatoxin-Based BH3 Domain Mimetics with Diverse Patterns of Native Disulfide Bonds. Curr Protoc 2022; 2:e526. [PMID: 35994574 DOI: 10.1002/cpz1.526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This article outlines the design and development of scyllatoxin (ScTx)-based BH3 domain mimetics with diverse patterns of native disulfide bonds. More specifically, this method summarizes the total chemical synthesis of ScTx-based peptides that contain zero, one, two, or three disulfide linkages, including techniques to generate variants with any combination of native disulfides. Each peptide reported herein is generated on solid-phase support using microwave-assisted coupling procedures, and all reaction parameters related to the peptide synthesis are described in detail. The various disulfide patterns of the ScTx-based constructs are established during peptide synthesis and are ultimately verified by mass analysis of trypsin-digested fragments. The BH3 domain mimetics developed herein were generated by transposing residues from the helical BH3 domain of the pro-apoptotic BCL2 protein Bax to the α-helix of wild-type ScTx. Interestingly, we found that the relative binding affinities of ScTx-Bax peptides for the anti-apoptotic BCL2 protein Bcl-2 (proper) were heavily influenced by the number and position of disulfide linkages within the ScTx-Bax sequence. As a consequence, we were able to utilize ScTx-Bax BH3 domain mimetics with varied patterns of disulfide bonds to survey how structural rigidity within the helical Bax BH3 domain affects binding to promiscuous anti-apoptotic BCL2 proteins. More broadly, the ability to generate ScTx-based molecules that contain any combination of native disulfide bonds expands the utility of such constructs as tools to study the molecular nature of protein-protein interactions. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Synthesis and characterization of ScTx-based Bax BH3 domain mimetics Basic Protocol 2: Oxidation of ScTx-Bax BH3 domain mimetics containing one, two, or three disulfide linkages Support Protocol: Mapping of disulfide linkages in oxidized ScTx-Bax BH3 domain mimetics.
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Affiliation(s)
- Matthew J K Vince
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio
- Institut für Bioanalytische Chemie, Fakultät für Chemie und Mineralogie, Universität Leipzig, Leipzig, Germany
- Biotechnologisch-Biomedizinisches Zentrum, Universität Leipzig, Leipzig, Germany
| | - Justin M Holub
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio
- Edison Biotechnology Institute, Ohio University, Athens, Ohio
- Molecular and Cellular Biology Program, Ohio University, Athens, Ohio
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Seraphim TV, Nano N, Cheung YWS, Aluksanasuwan S, Colleti C, Mao YQ, Bhandari V, Young G, Höll L, Phanse S, Gordiyenko Y, Southworth DR, Robinson CV, Thongboonkerd V, Gava LM, Borges JC, Babu M, Barbosa LRS, Ramos CHI, Kukura P, Houry WA. Assembly principles of the human R2TP chaperone complex reveal the presence of R2T and R2P complexes. Structure 2022; 30:156-171.e12. [PMID: 34492227 DOI: 10.1016/j.str.2021.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/16/2021] [Accepted: 08/10/2021] [Indexed: 11/18/2022]
Abstract
R2TP is a highly conserved chaperone complex formed by two AAA+ ATPases, RUVBL1 and RUVBL2, that associate with PIH1D1 and RPAP3 proteins. R2TP acts in promoting macromolecular complex formation. Here, we establish the principles of R2TP assembly. Three distinct RUVBL1/2-based complexes are identified: R2TP, RUVBL1/2-RPAP3 (R2T), and RUVBL1/2-PIH1D1 (R2P). Interestingly, we find that PIH1D1 does not bind to RUVBL1/RUVBL2 in R2TP and does not function as a nucleotide exchange factor; instead, RPAP3 is found to be the central subunit coordinating R2TP architecture and linking PIH1D1 and RUVBL1/2. We also report that RPAP3 contains an intrinsically disordered N-terminal domain mediating interactions with substrates whose sequences are primarily enriched for Armadillo repeat domains and other helical-type domains. Our work provides a clear and consistent model of R2TP complex structure and gives important insights into how a chaperone machine concerned with assembly of folded proteins into multisubunit complexes might work.
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Affiliation(s)
- Thiago V Seraphim
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada; Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Nardin Nano
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada
| | - Yiu Wing Sunny Cheung
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada
| | - Siripat Aluksanasuwan
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada; Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Carolina Colleti
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada; Center of Biological and Health Sciences, Federal University of São Carlos, São Carlos, SP 13560-970, Brazil
| | - Yu-Qian Mao
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada
| | - Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada
| | - Gavin Young
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Larissa Höll
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada; Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Yuliya Gordiyenko
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Daniel R Southworth
- Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158, USA
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Lisandra M Gava
- Center of Biological and Health Sciences, Federal University of São Carlos, São Carlos, SP 13560-970, Brazil
| | - Júlio C Borges
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP 13566-590, Brazil
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Leandro R S Barbosa
- Institute of Physics, University of São Paulo, São Paulo, SP 05508-090, Brazil; Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-100, Brazil
| | - Carlos H I Ramos
- Institute of Chemistry, University of Campinas (UNICAMP), Campinas, SP 13083-970, Brazil
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
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10
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Zurowska K, Alam A, Ganser-Pornillos BK, Pornillos O. Structural evidence that MOAP1 and PEG10 are derived from retrovirus/retrotransposon Gag proteins. Proteins 2022; 90:309-313. [PMID: 34357660 PMCID: PMC8671222 DOI: 10.1002/prot.26204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/06/2021] [Accepted: 07/28/2021] [Indexed: 01/03/2023]
Abstract
The Gag proteins of retroviruses play an essential role in virus particle assembly by forming a protein shell or capsid and thus generating the virion compartment. A variety of human proteins have now been identified with structural similarity to one or more of the major Gag domains. These human proteins are thought to have been evolved or "domesticated" from ancient integrations due to retroviral infections or retrotransposons. Here, we report that X-ray crystal structures of stably folded domains of MOAP1 (modulator of apoptosis 1) and PEG10 (paternally expressed gene 10) are highly similar to the C-terminal capsid (CA) domains of cognate Gag proteins. The structures confirm classification of MOAP1 and PEG10 as domesticated Gags, and suggest that these proteins may have preserved some of the key interactions that facilitated assembly of their ancestral Gags into capsids.
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Affiliation(s)
- Katarzyna Zurowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ayaan Alam
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
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11
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Abstract
Cell growth is dynamically regulated in response to external cues such as nutrient availability, growth factor signals, and stresses. Central to this adaptation process is the Target of Rapamycin Complex 1 (TORC1), an evolutionarily conserved kinase complex that fine-tunes an enormous number of cellular events. How upstream signals are sensed and transmitted to TORC1 has been intensively studied in major model organisms including the budding yeast Saccharomyces cerevisiae. This field recently saw a breakthrough: the identification of yeast phosphatidylInositol(3)-phosphate binding protein 2 (Pib2) protein as a critical regulator of TORC1. Although the study of Pib2 is still in its early days, multiple groups have provided important mechanistic insights on how Pib2 relays nutrient signals to TORC1. There remain, on the other hand, significant gaps in our knowledge and mysteries that warrant further investigations. This is the first dedicated review on Pib2 that summarizes major findings and outstanding questions around this emerging key player in cell growth regulation.
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Affiliation(s)
- Riko Hatakeyama
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
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12
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Luthold C, Lambert H, Guilbert SM, Rodrigue MA, Fuchs M, Varlet AA, Fradet-Turcotte A, Lavoie JN. CDK1-Mediated Phosphorylation of BAG3 Promotes Mitotic Cell Shape Remodeling and the Molecular Assembly of Mitotic p62 Bodies. Cells 2021; 10:cells10102638. [PMID: 34685619 PMCID: PMC8534064 DOI: 10.3390/cells10102638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 01/07/2023] Open
Abstract
The cochaperone BCL2-associated athanogene 3 (BAG3), in complex with the heat shock protein HSPB8, facilitates mitotic rounding, spindle orientation, and proper abscission of daughter cells. BAG3 and HSPB8 mitotic functions implicate the sequestosome p62/SQSTM1, suggesting a role for protein quality control. However, the interplay between this chaperone-assisted pathway and the mitotic machinery is not known. Here, we show that BAG3 phosphorylation at the conserved T285 is regulated by CDK1 and activates its function in mitotic cell shape remodeling. BAG3 phosphorylation exhibited a high dynamic at mitotic entry and both a non-phosphorylatable BAG3T285A and a phosphomimetic BAG3T285D protein were unable to correct the mitotic defects in BAG3-depleted HeLa cells. We also demonstrate that BAG3 phosphorylation, HSPB8, and CDK1 activity modulate the molecular assembly of p62/SQSTM1 into mitotic bodies containing K63 polyubiquitinated chains. These findings suggest the existence of a mitotically regulated spatial quality control mechanism for the fidelity of cell shape remodeling in highly dividing cells.
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Affiliation(s)
- Carole Luthold
- Centre de Recherche sur le Cancer, Université Laval, Quebec, QC G1R 3S3, Canada; (C.L.); (H.L.); (S.M.G.); (M.-A.R.); (M.F.); (A.-A.V.); (A.F.-T.)
- Oncology, Centre de Recherche du CHU de Québec-Université Laval, Hôtel-Dieu de Québec, Quebec, QC G1R 3S3, Canada
| | - Herman Lambert
- Centre de Recherche sur le Cancer, Université Laval, Quebec, QC G1R 3S3, Canada; (C.L.); (H.L.); (S.M.G.); (M.-A.R.); (M.F.); (A.-A.V.); (A.F.-T.)
- Oncology, Centre de Recherche du CHU de Québec-Université Laval, Hôtel-Dieu de Québec, Quebec, QC G1R 3S3, Canada
| | - Solenn M. Guilbert
- Centre de Recherche sur le Cancer, Université Laval, Quebec, QC G1R 3S3, Canada; (C.L.); (H.L.); (S.M.G.); (M.-A.R.); (M.F.); (A.-A.V.); (A.F.-T.)
- Oncology, Centre de Recherche du CHU de Québec-Université Laval, Hôtel-Dieu de Québec, Quebec, QC G1R 3S3, Canada
| | - Marc-Antoine Rodrigue
- Centre de Recherche sur le Cancer, Université Laval, Quebec, QC G1R 3S3, Canada; (C.L.); (H.L.); (S.M.G.); (M.-A.R.); (M.F.); (A.-A.V.); (A.F.-T.)
- Oncology, Centre de Recherche du CHU de Québec-Université Laval, Hôtel-Dieu de Québec, Quebec, QC G1R 3S3, Canada
| | - Margit Fuchs
- Centre de Recherche sur le Cancer, Université Laval, Quebec, QC G1R 3S3, Canada; (C.L.); (H.L.); (S.M.G.); (M.-A.R.); (M.F.); (A.-A.V.); (A.F.-T.)
- Oncology, Centre de Recherche du CHU de Québec-Université Laval, Hôtel-Dieu de Québec, Quebec, QC G1R 3S3, Canada
| | - Alice-Anaïs Varlet
- Centre de Recherche sur le Cancer, Université Laval, Quebec, QC G1R 3S3, Canada; (C.L.); (H.L.); (S.M.G.); (M.-A.R.); (M.F.); (A.-A.V.); (A.F.-T.)
- Oncology, Centre de Recherche du CHU de Québec-Université Laval, Hôtel-Dieu de Québec, Quebec, QC G1R 3S3, Canada
| | - Amélie Fradet-Turcotte
- Centre de Recherche sur le Cancer, Université Laval, Quebec, QC G1R 3S3, Canada; (C.L.); (H.L.); (S.M.G.); (M.-A.R.); (M.F.); (A.-A.V.); (A.F.-T.)
- Oncology, Centre de Recherche du CHU de Québec-Université Laval, Hôtel-Dieu de Québec, Quebec, QC G1R 3S3, Canada
- Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Quebec, QC G1V0A6, Canada
| | - Josée N. Lavoie
- Centre de Recherche sur le Cancer, Université Laval, Quebec, QC G1R 3S3, Canada; (C.L.); (H.L.); (S.M.G.); (M.-A.R.); (M.F.); (A.-A.V.); (A.F.-T.)
- Oncology, Centre de Recherche du CHU de Québec-Université Laval, Hôtel-Dieu de Québec, Quebec, QC G1R 3S3, Canada
- Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Quebec, QC G1V0A6, Canada
- Correspondence:
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13
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Kubagawa H, Skopnik CM, Al-Qaisi K, Calvert RA, Honjo K, Kubagawa Y, Teuber R, Aliabadi PM, Enghard P, Radbruch A, Sutton BJ. Differences between Human and Mouse IgM Fc Receptor (FcµR). Int J Mol Sci 2021; 22:ijms22137024. [PMID: 34209905 PMCID: PMC8267714 DOI: 10.3390/ijms22137024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 01/02/2023] Open
Abstract
Both non-immune "natural" and antigen-induced "immune" IgM are important for protection against pathogens and for regulation of immune responses to self-antigens. Since the bona fide IgM Fc receptor (FcµR) was identified in humans by a functional cloning strategy in 2009, the roles of FcµR in these IgM effector functions have begun to be explored. In this short essay, we describe the differences between human and mouse FcµRs in terms of their identification processes, cellular distributions and ligand binding activities with emphasis on our recent findings from the mutational analysis of human FcµR. We have identified at least three sites of human FcµR, i.e., Asn66 in the CDR2, Lys79 to Arg83 in the DE loop and Asn109 in the CDR3, responsible for its constitutive IgM-ligand binding. Results of computational structural modeling analysis are consistent with these mutational data and a model of the ligand binding, Ig-like domain of human FcµR is proposed. Serendipitously, substitution of Glu41 and Met42 in the CDR1 of human FcµR with mouse equivalents Gln and Leu, either single or more prominently in combination, enhances both the receptor expression and IgM binding. These findings would help in the future development of preventive and therapeutic interventions targeting FcµR.
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Affiliation(s)
- Hiromi Kubagawa
- Deutsches Rheuma-Forschungszentrum, 10117 Berlin, Germany; (C.M.S.); (K.A.-Q.); (R.T.); (P.M.A.); (A.R.)
- Correspondence: ; Tel.: +49-030-2846-0782
| | - Christopher M. Skopnik
- Deutsches Rheuma-Forschungszentrum, 10117 Berlin, Germany; (C.M.S.); (K.A.-Q.); (R.T.); (P.M.A.); (A.R.)
| | - Khlowd Al-Qaisi
- Deutsches Rheuma-Forschungszentrum, 10117 Berlin, Germany; (C.M.S.); (K.A.-Q.); (R.T.); (P.M.A.); (A.R.)
| | - Rosaleen A. Calvert
- Randall Centre for Cell and Molecular Biophysics, King’s College, London SE1 1UL, UK; (R.A.C.); (B.J.S.)
| | - Kazuhito Honjo
- Department of Pathology of University of Alabama at Birmingham, Birmingham, AL 35294, USA.; (K.H.); (Y.K.)
| | - Yoshiki Kubagawa
- Department of Pathology of University of Alabama at Birmingham, Birmingham, AL 35294, USA.; (K.H.); (Y.K.)
| | - Ruth Teuber
- Deutsches Rheuma-Forschungszentrum, 10117 Berlin, Germany; (C.M.S.); (K.A.-Q.); (R.T.); (P.M.A.); (A.R.)
| | - Pedram Mahmoudi Aliabadi
- Deutsches Rheuma-Forschungszentrum, 10117 Berlin, Germany; (C.M.S.); (K.A.-Q.); (R.T.); (P.M.A.); (A.R.)
| | - Philipp Enghard
- Department of Nephrology and Medical Intensive Care, Charité-Universitätmedizin, 10117 Berlin, Germany;
| | - Andreas Radbruch
- Deutsches Rheuma-Forschungszentrum, 10117 Berlin, Germany; (C.M.S.); (K.A.-Q.); (R.T.); (P.M.A.); (A.R.)
| | - Brian J. Sutton
- Randall Centre for Cell and Molecular Biophysics, King’s College, London SE1 1UL, UK; (R.A.C.); (B.J.S.)
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14
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Chen G, Li PH, He JY, Su YL, Chen HJ, Dong JD, Huang YH, Huang XH, Jiang YF, Qin QW, Sun HY. Molecular cloning, inducible expression with SGIV and Vibrio alginolyticus challenge, and function analysis of Epinephelus coioides PDCD4. Dev Comp Immunol 2021; 119:104013. [PMID: 33465381 DOI: 10.1016/j.dci.2021.104013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Programmed cell death 4 (PDCD4) in mammals, a gene closely associated with apoptosis, is involved in many biological processes, such as cell aging, differentiation, regulation of cell cycle, and inflammatory response. In this study, grouper Epinephelus coioides PDCD4, EcPDCD4-1 and EcPDCD4-2, were obtained. The open reading frame (ORF) of EcPDCD4-1 is 1413 bp encoding 470 amino acids with a molecular mass of 52.39 kDa and a theoretical pI of 5.33. The ORF of EcPDCD4-2 is 1410 bp encoding 469 amino acids with a molecular mass of 52.29 kDa and a theoretical pI of 5.29. Both EcPDCD4-1 and EcPDCD4-2 proteins contain two conserved MA3 domains, and their mRNA were detected in all eight tissues of E. coioides by quantitative real-time PCR (qRT-PCR) with the highest expression in liver. The expressions of two EcPDCD4s were significantly up-regulated after Singapore grouper iridovirus (SGIV) or Vibrio alginolyticus infection. In addition, over-expression of EcPDCD4-1 or EcPDCD4-2 can inhibit the activity of the nuclear factor-κB (NF-κB) and activator protein-1 (AP-1), and regulate SGIV-induced apoptosis. The results demonstrated that EcPDCD4s might play important roles in E. coioides tissues during pathogen-caused inflammation.
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Affiliation(s)
- Guo Chen
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China; Hainan Key Laboratory of Tropical Marine Biotechnology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Department of Laboratory, Jining No.1 People's Hospital; Postdoctoral Mobile Station of Shandong University of Traditional Chinese Medicine, Shandong, 272111, PR China; Life Sciences Institute, Zhejiang University, Zhejiang Province, 310058, PR China
| | - Pin-Hong Li
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Jia-Yang He
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Yu-Ling Su
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - He-Jia Chen
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Jun-De Dong
- Hainan Key Laboratory of Tropical Marine Biotechnology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
| | - You-Hua Huang
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Xiao-Hong Huang
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Yu-Feng Jiang
- Department of Laboratory, Jining No.1 People's Hospital; Postdoctoral Mobile Station of Shandong University of Traditional Chinese Medicine, Shandong, 272111, PR China.
| | - Qi-Wei Qin
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China.
| | - Hong-Yan Sun
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China.
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15
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Baeken MW, Behl C. On the origin of BAG(3) and its consequences for an expansion of BAG3's role in protein homeostasis. J Cell Biochem 2021; 123:102-114. [PMID: 33942360 DOI: 10.1002/jcb.29925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/02/2021] [Accepted: 03/24/2021] [Indexed: 11/07/2022]
Abstract
The B-cell CLL 2-associated athanogene (BAG) protein family in general and BAG3, in particular, are pivotal elements of cellular protein homeostasis, with BAG3 playing a major role in macroautophagy. In particular, in the contexts of senescence and degeneration, BAG3 has exhibited an essential role often related to its capabilities to organize and remove aggregated proteins. Exciting studies in different species ranging from human, murine, zebrafish, and plant samples have delivered vital insights into BAG3s' (and other BAG proteins') functions and their regulations. However, so far no studies have addressed neither BAG3's evolution nor its phylogenetic position in the BAG family.
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Affiliation(s)
- Marius W Baeken
- The Autophagy Lab, Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Christian Behl
- The Autophagy Lab, Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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16
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Han CW, Lee HN, Jeong MS, Park SY, Jang SB. Structural basis of the p53 DNA binding domain and PUMA complex. Biochem Biophys Res Commun 2021; 548:39-46. [PMID: 33631672 DOI: 10.1016/j.bbrc.2021.02.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/18/2022]
Abstract
PUMA (p53-upregulated modulator of apoptosis) is localized in mitochondria and a direct target in p53-mediated apoptosis. p53 elicits mitochondrial apoptosis via transcription-dependent and independent mechanisms. p53 is known to induce apoptosis via the transcriptional induction of PUMA, which encodes proapoptotic BH3-only members of the Bcl-2 protein family. However, the transcription-independent mechanisms of human PUMA remain poorly defined. For example, it is not known whether PUMA interacts directly with the DNA binding domain (DBD: residues 92-293) of p53 in vitro. Here, the structure of the complex between the DBD of p53 and PUMA peptide was elucidated by X-ray crystallography. Isothermal titration calorimetry showed that PUMA peptide binds strongly with p53 DBD, and the crystal structure of p53-PUMA peptide complex revealed it contains four molecules of p53 DBD and one PUMA peptide per asymmetric unit in space group P1. PUMA peptide bound to the N-terminal residues of p53 DBD. A cell proliferation assay demonstrated PUMA peptide inhibited the growth of a lung cancer cell line. These results contribute to understanding of the mechanism responsible for p53-mediated apoptosis.
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Affiliation(s)
- Chang Woo Han
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, 2Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Republic of Korea
| | - Han Na Lee
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, 2Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Republic of Korea
| | - Mi Suk Jeong
- Korea Nanobiotechnology Center, Pusan National University, 2,Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Republic of Korea
| | - So Young Park
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, 2Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Republic of Korea
| | - Se Bok Jang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, 2Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Republic of Korea.
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17
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Ye J, Zou G, Zhu R, Kong C, Miao C, Zhang M, Li J, Xiong W, Wang C. Structural basis of GABARAP-mediated GABA A receptor trafficking and functions on GABAergic synaptic transmission. Nat Commun 2021; 12:297. [PMID: 33436612 PMCID: PMC7803741 DOI: 10.1038/s41467-020-20624-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/04/2020] [Indexed: 01/07/2023] Open
Abstract
GABAA receptors (GABAARs) are the primary fast inhibitory ion channels in the central nervous system. Dysfunction of trafficking and localization of GABAARs to cell membranes is clinically associated with severe psychiatric disorders in humans. The GABARAP protein is known to support the stability of GABAARs in synapses, but the underlying molecular mechanisms remain to be elucidated. Here, we show that GABARAP/GABARAPL1 directly binds to a previously unappreciated region in the γ2 subunit of GABAAR. We demonstrate that GABARAP functions to stabilize GABAARs via promoting its trafficking pathway instead of blocking receptor endocytosis. The GABARAPL1-γ2-GABAAR crystal structure reveals the mechanisms underlying the complex formation. We provide evidence showing that phosphorylation of γ2-GABAAR differentially modulate the receptor's binding to GABARAP and the clathrin adaptor protein AP2. Finally, we demonstrate that GABAergic synaptic currents are reduced upon specific blockage of the GABARAP-GABAAR complex formation. Collectively, our results reveal that GABARAP/GABARAPL1, but not other members of the Atg8 family proteins, specifically regulates synaptic localization of GABAARs via modulating the trafficking of the receptor.
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Affiliation(s)
- Jin Ye
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027, Hefei, P.R. China
| | - Guichang Zou
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027, Hefei, P.R. China
| | - Ruichi Zhu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P.R. China
- Center of Systems Biology and Human Health, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P.R. China
| | - Chao Kong
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027, Hefei, P.R. China
| | - Chenjian Miao
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027, Hefei, P.R. China
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P.R. China
- Center of Systems Biology and Human Health, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P.R. China
| | - Jianchao Li
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, 510006, Guangzhou, P.R. China.
| | - Wei Xiong
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027, Hefei, P.R. China.
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 200031, Shanghai, P.R. China.
| | - Chao Wang
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027, Hefei, P.R. China.
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18
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Gong Q, Robinson K, Xu C, Huynh PT, Chong KHC, Tan EYJ, Zhang J, Boo ZZ, Teo DET, Lay K, Zhang Y, Lim JSY, Goh WI, Wright G, Zhong FL, Reversade B, Wu B. Structural basis for distinct inflammasome complex assembly by human NLRP1 and CARD8. Nat Commun 2021; 12:188. [PMID: 33420028 PMCID: PMC7794362 DOI: 10.1038/s41467-020-20319-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
Nod-like receptor (NLR) proteins activate pyroptotic cell death and IL-1 driven inflammation by assembling and activating the inflammasome complex. Closely related sensor proteins NLRP1 and CARD8 undergo unique auto-proteolysis-dependent activation and are implicated in auto-inflammatory diseases; however, their mechanisms of activation are not understood. Here we report the structural basis of how the activating domains (FIINDUPA-CARD) of NLRP1 and CARD8 self-oligomerize to assemble distinct inflammasome complexes. Recombinant FIINDUPA-CARD of NLRP1 forms a two-layered filament, with an inner core of oligomerized CARD surrounded by an outer ring of FIINDUPA. Biochemically, self-assembled NLRP1-CARD filaments are sufficient to drive ASC speck formation in cultured human cells-a process that is greatly enhanced by NLRP1-FIINDUPA which forms oligomers in vitro. The cryo-EM structures of NLRP1-CARD and CARD8-CARD filaments, solved here at 3.7 Å, uncover unique structural features that enable NLRP1 and CARD8 to discriminate between ASC and pro-caspase-1. In summary, our findings provide structural insight into the mechanisms of activation for human NLRP1 and CARD8 and reveal how highly specific signaling can be achieved by heterotypic CARD interactions within the inflammasome complexes.
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Affiliation(s)
- Qin Gong
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Kim Robinson
- Skin Research Institute (SRIS), Agency of Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore, Singapore
| | - Chenrui Xu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Phuong Thao Huynh
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technology University, 11 Mandalay Road, 308232, Singapore, Singapore
| | - Kelvin Han Chung Chong
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Eddie Yong Jun Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Jiawen Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Zhao Zhi Boo
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Daniel Eng Thiam Teo
- Institute of Molecular and Cell Biology, Agency of Science Technology and Research (A*STAR), 61 Biopolis Dr, 138673, Singapore, Singapore
| | - Kenneth Lay
- Institute of Molecular and Cell Biology, Agency of Science Technology and Research (A*STAR), 61 Biopolis Dr, 138673, Singapore, Singapore
| | - Yaming Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - John Soon Yew Lim
- Skin Research Institute (SRIS), Agency of Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore, Singapore
| | - Wah Ing Goh
- Skin Research Institute (SRIS), Agency of Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore, Singapore
| | - Graham Wright
- Institute of Molecular and Cell Biology, Agency of Science Technology and Research (A*STAR), 61 Biopolis Dr, 138673, Singapore, Singapore
| | - Franklin L Zhong
- Skin Research Institute (SRIS), Agency of Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technology University, 11 Mandalay Road, 308232, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Agency of Science Technology and Research (A*STAR), 61 Biopolis Dr, 138673, Singapore, Singapore.
| | - Bruno Reversade
- Institute of Molecular and Cell Biology, Agency of Science Technology and Research (A*STAR), 61 Biopolis Dr, 138673, Singapore, Singapore.
- Genome Institute of Singapore, Agency of Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore, Singapore.
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Dr, 117597, Singapore, Singapore.
- The Medical Genetics Department, School of Medicine (KUSoM), Koç University, 34010, Istanbul, Turkey.
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore.
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19
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Robert Hollingsworth L, David L, Li Y, Griswold AR, Ruan J, Sharif H, Fontana P, Orth-He EL, Fu TM, Bachovchin DA, Wu H. Mechanism of filament formation in UPA-promoted CARD8 and NLRP1 inflammasomes. Nat Commun 2021; 12:189. [PMID: 33420033 PMCID: PMC7794386 DOI: 10.1038/s41467-020-20320-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/26/2020] [Indexed: 01/29/2023] Open
Abstract
NLRP1 and CARD8 are related cytosolic sensors that upon activation form supramolecular signalling complexes known as canonical inflammasomes, resulting in caspase-1 activation, cytokine maturation and/or pyroptotic cell death. NLRP1 and CARD8 use their C-terminal (CT) fragments containing a caspase recruitment domain (CARD) and the UPA (conserved in UNC5, PIDD, and ankyrins) subdomain for self-oligomerization, which in turn form the platform to recruit the inflammasome adaptor ASC (apoptosis-associated speck-like protein containing a CARD) or caspase-1, respectively. Here, we report cryo-EM structures of NLRP1-CT and CARD8-CT assemblies, in which the respective CARDs form central helical filaments that are promoted by oligomerized, but flexibly linked, UPAs surrounding the filaments. Through biochemical and cellular approaches, we demonstrate that the UPA itself reduces the threshold needed for NLRP1-CT and CARD8-CT filament formation and signalling. Structural analyses provide insights on the mode of ASC recruitment by NLRP1-CT and the contrasting direct recruitment of caspase-1 by CARD8-CT. We also discover that subunits in the central NLRP1CARD filament dimerize with additional exterior CARDs, which roughly doubles its thickness and is unique among all known CARD filaments. Finally, we engineer and determine the structure of an ASCCARD-caspase-1CARD octamer, which suggests that ASC uses opposing surfaces for NLRP1, versus caspase-1, recruitment. Together these structures capture the architecture and specificity of the active NLRP1 and CARD8 inflammasomes in addition to key heteromeric CARD-CARD interactions governing inflammasome signalling.
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Affiliation(s)
- L Robert Hollingsworth
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, 02115, USA
| | - Liron David
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Andrew R Griswold
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jianbin Ruan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Humayun Sharif
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Pietro Fontana
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Elizabeth L Orth-He
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Tian-Min Fu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Biological Chemistry and Pharmacology, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Daniel A Bachovchin
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA.
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, 02115, USA.
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20
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Abstract
FANCM is involved in eukaryotic DNA-damage recognition and activates the Fanconi anemia (FA) pathway through complex formation. MHF is one of the FANCM-associating components and contains a histone-fold DNA-binding domain. Loss of the FANCM-MHF interaction compromises the activation of the FA pathway, resulting in chromosomal instability. Thus, formation of the FANCM-MHF complex is important for function, but its nature largely remains elusive. Here, the aim was to reveal the molecular and structural basis for the stability of the FANCM-MHF complex. A recombinant tripartite complex containing chicken FANCM (MHF interaction region), MHF1 and MHF2 was expressed and purified. The purified tripartite complex was crystallized under various conditions and three different crystals were obtained from similar crystallization conditions. Unexpectedly, structure determination revealed that one of the crystals contained the FANCM-MHF complex but that the other two contained the MHF complex without FANCM. How FANCM dissociates from MHF was further investigated and it was found that the presence of 2-methyl-2,4-pentanediol (MPD) and an oxidative environment may have promoted its release. However, under these conditions MHF retained its complexed form. FANCM-MHF interaction involves a mixture of hydrophobic/hydrophilic interactions, and chicken FANCM contains several nonconserved cysteines within this region which may lead to aggregation with other FANCM-MHF molecules. These results indicate an unexpected nature of the FANCM-MHF complex and the data can be used to improve the stability of the complex for biochemical and structural analyses.
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Affiliation(s)
- Sho Ito
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, 6-3-1 Niijyuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Tatsuya Nishino
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, 6-3-1 Niijyuku, Katsushika-ku, Tokyo 125-8585, Japan
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21
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Robinson KS, Teo DET, Tan KS, Toh GA, Ong HH, Lim CK, Lay K, Au BV, Lew TS, Chu JJH, Chow VTK, Wang DY, Zhong FL, Reversade B. Enteroviral 3C protease activates the human NLRP1 inflammasome in airway epithelia. Science 2020; 370:eaay2002. [PMID: 33093214 DOI: 10.1126/science.aay2002] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 02/11/2020] [Accepted: 10/08/2020] [Indexed: 12/17/2023]
Abstract
Immune sensor proteins are critical to the function of the human innate immune system. The full repertoire of cognate triggers for human immune sensors is not fully understood. Here, we report that human NACHT, LRR, and PYD domains-containing protein 1 (NLRP1) is activated by 3C proteases (3Cpros) of enteroviruses, such as human rhinovirus (HRV). 3Cpros directly cleave human NLRP1 at a single site between Glu130 and Gly131 This cleavage triggers N-glycine-mediated degradation of the autoinhibitory NLRP1 N-terminal fragment via the cullinZER1/ZYG11B complex, which liberates the activating C-terminal fragment. Infection of primary human airway epithelial cells by live human HRV triggers NLRP1-dependent inflammasome activation and interleukin-18 secretion. Our findings establish 3Cpros as a pathogen-derived trigger for the human NLRP1 inflammasome and suggest that NLRP1 may contribute to inflammatory diseases of the airway.
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Affiliation(s)
- Kim S Robinson
- Skin Research Institute of Singapore (SRIS), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Institute of Medical Biology, Agency of Science, Technological and Research, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Daniel Eng Thiam Teo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, 308232, Singapore
| | - Kai Sen Tan
- Department of Otolaryngology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 10 Medical Drive, 117597, Singapore
| | - Gee Ann Toh
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, 308232, Singapore
| | - Hsiao Hui Ong
- Department of Otolaryngology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 10 Medical Drive, 117597, Singapore
| | - Chrissie Kaishi Lim
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
| | - Kenneth Lay
- Institute of Medical Biology, Agency of Science, Technological and Research, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore
| | - Bijin Veonice Au
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
| | - Tian Sheng Lew
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 10 Medical Drive, 117597, Singapore
| | - Justin Jang Hann Chu
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 10 Medical Drive, 117597, Singapore
| | - Vincent Tak Kwong Chow
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 10 Medical Drive, 117597, Singapore
| | - De Yun Wang
- Department of Otolaryngology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 10 Medical Drive, 117597, Singapore
| | - Franklin L Zhong
- Skin Research Institute of Singapore (SRIS), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore.
- Institute of Medical Biology, Agency of Science, Technological and Research, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, 308232, Singapore
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
| | - Bruno Reversade
- Institute of Medical Biology, Agency of Science, Technological and Research, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore.
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
- Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 10 Medical Drive, 117597, Singapore
- The Medical Genetics Department, Koç University School of Medicine, 34010 Istanbul, Turkey
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22
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Wesch N, Kirkin V, Rogov VV. Atg8-Family Proteins-Structural Features and Molecular Interactions in Autophagy and Beyond. Cells 2020; 9:E2008. [PMID: 32882854 PMCID: PMC7564214 DOI: 10.3390/cells9092008] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/25/2022] Open
Abstract
Autophagy is a common name for a number of catabolic processes, which keep the cellular homeostasis by removing damaged and dysfunctional intracellular components. Impairment or misbalance of autophagy can lead to various diseases, such as neurodegeneration, infection diseases, and cancer. A central axis of autophagy is formed along the interactions of autophagy modifiers (Atg8-family proteins) with a variety of their cellular counter partners. Besides autophagy, Atg8-proteins participate in many other pathways, among which membrane trafficking and neuronal signaling are the most known. Despite the fact that autophagy modifiers are well-studied, as the small globular proteins show similarity to ubiquitin on a structural level, the mechanism of their interactions are still not completely understood. A thorough analysis and classification of all known mechanisms of Atg8-protein interactions could shed light on their functioning and connect the pathways involving Atg8-proteins. In this review, we present our views of the key features of the Atg8-proteins and describe the basic principles of their recognition and binding by interaction partners. We discuss affinity and selectivity of their interactions as well as provide perspectives for discovery of new Atg8-interacting proteins and therapeutic approaches to tackle major human diseases.
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Affiliation(s)
- Nicole Wesch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany;
| | - Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London, Sutton SM2 5NG, UK;
| | - Vladimir V. Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany;
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
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23
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Chen L, Li B, Hu S, Qiao R, Sun C, Yang D. A fas apoptotic inhibitory molecule from Ruditapes philippinarum: Investigation on molecular characterization and functional analysis. Fish Shellfish Immunol 2020; 104:133-140. [PMID: 32470512 DOI: 10.1016/j.fsi.2020.05.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/15/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
In the present study, a fas apoptotic inhibitory molecule (FAIM) was identified from Ruditapes philippinarum (designated as RpFAIM). Multiple alignments and phylogenetic analysis strongly suggested that RpFAIM was a new member of the FAIMs family. The RpFAIM transcripts were constitutively expressed in a wide range of tissues, and dominantly expressed in hemocytes. After V. anguillarum or M. luteus challenge, the expression level of RpFAIM transcripts was significantly induced and reached the maximum level at 6 h and 24 h, respectively. Knockdown of RpFAIM down-regulated the transcript levels of NF-κB signaling genes (e.g. RpIKK, RpIκB, RpNF-κB). The results were roughly similar to those under bacterial stimulation. Moreover, RpFAIM primarily localized in the cell cytoplasm, and its over-expression inhibited the apoptosis of HeLa cells. These results revealed that RpFAIM perhaps regulated the NF-κB signaling pathways positively, which provided a better understanding of RpFAIM in innate immunity.
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Affiliation(s)
- Lizhu Chen
- Shandong Marine Resource and Environment Research Institute, Yantai, 264006, PR China
| | - Bin Li
- Shandong Marine Resource and Environment Research Institute, Yantai, 264006, PR China
| | - Shunxin Hu
- Shandong Marine Resource and Environment Research Institute, Yantai, 264006, PR China
| | - Ruiguang Qiao
- Shandong Marine Resource and Environment Research Institute, Yantai, 264006, PR China
| | - Chunxiao Sun
- Shandong Marine Resource and Environment Research Institute, Yantai, 264006, PR China
| | - Dinglong Yang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Center for Ocean Mega-science, Chinese Academy of Sciences, Qingdao, Shandong, 266071, PR China; Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China.
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24
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Wang Q, Zhang T, Chang X, Lim DY, Wang K, Bai R, Wang T, Ryu J, Chen H, Yao K, Ma WY, Boardman LA, Bode AM, Dong Z. ARC Is a Critical Protector against Inflammatory Bowel Disease (IBD) and IBD-Associated Colorectal Tumorigenesis. Cancer Res 2020; 80:4158-4171. [PMID: 32816906 DOI: 10.1158/0008-5472.can-20-0469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 06/25/2020] [Accepted: 08/06/2020] [Indexed: 11/16/2022]
Abstract
The key functional molecules involved in inflammatory bowel disease (IBD) and IBD-induced colorectal tumorigenesis remain unclear. In this study, we found that the apoptosis repressor with caspase recruitment domain (ARC) protein plays critical roles in IBD. ARC-deficient mice exhibited substantially higher susceptibility to dextran sulfate sodium (DSS)-induced IBD compared with wild-type mice. The inflammatory burden induced in ARC-deficient conditions was inversely correlated with CCL5 and CXCL5 levels in immune cells, especially CD4-positive T cells. Pathologically, ARC expression in immune cells was significantly decreased in clinical biopsy specimens from patients with IBD compared with normal subjects. In addition, ARC levels inversely correlated with CCL5 and CXCL5 levels in human biopsy specimens. ARC interacted with TNF receptor associated factor (TRAF) 6, regulating ubiquitination of TRAF6, which was associated with NF-κB signaling. Importantly, we identified a novel ubiquitination site at lysine 461, which was critical in the function of ARC in IBD. ARC played a critical role in IBD and IBD-associated colon cancer in a bone marrow transplantation model and azoxymethane/DSS-induced colitis cancer mouse models. Overall, these findings reveal that ARC is critically involved in the maintenance of intestinal homeostasis and protection against IBD through its ubiquitination of TRAF6 and subsequent modulation of NF-κB activation in T cells. SIGNIFICANCE: This study uncovers a crucial role of ARC in the immune system and IBD, giving rise to a novel strategy for IBD and IBD-associated colon cancer therapy.
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Affiliation(s)
- Qiushi Wang
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Tianshun Zhang
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Xiaoyu Chang
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Do Young Lim
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Keke Wang
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Ruihua Bai
- The Hormel Institute, University of Minnesota, Austin, Minnesota
- The Henan Tumor Hospital, Zhengzhou, Henan, China
| | - Ting Wang
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Joohyun Ryu
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Hanyong Chen
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Ke Yao
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Wei-Ya Ma
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Lisa A Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin, Minnesota.
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, China
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25
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Bucholc K, Skrajna A, Adamska K, Yang XC, Krajewski K, Poznański J, Dadlez M, Domiński Z, Zhukov I. Structural Analysis of the SANT/Myb Domain of FLASH and YARP Proteins and Their Complex with the C-Terminal Fragment of NPAT by NMR Spectroscopy and Computer Simulations. Int J Mol Sci 2020; 21:ijms21155268. [PMID: 32722282 PMCID: PMC7432317 DOI: 10.3390/ijms21155268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 11/16/2022] Open
Abstract
FLICE-associated huge protein (FLASH), Yin Yang 1-Associated Protein-Related Protein (YARP) and Nuclear Protein, Ataxia-Telangiectasia Locus (NPAT) localize to discrete nuclear structures called histone locus bodies (HLBs) where they control various steps in histone gene expression. Near the C-terminus, FLASH and YARP contain a highly homologous domain that interacts with the C-terminal region of NPAT. Structural aspects of the FLASH-NPAT and YARP-NPAT complexes and their role in histone gene expression remain largely unknown. In this study, we used multidimensional NMR spectroscopy and in silico modeling to analyze the C-terminal domain in FLASH and YARP in an unbound form and in a complex with the last 31 amino acids of NPAT. Our results demonstrate that FLASH and YARP domains share the same fold of a triple α -helical bundle that resembles the DNA binding domain of Myb transcriptional factors and the SANT domain found in chromatin-modifying and remodeling complexes. The NPAT peptide contains a single α -helix that makes multiple contacts with α -helices I and III of the FLASH and YARP domains. Surprisingly, in spite of sharing a significant amino acid similarity, each domain likely binds NPAT using a unique network of interactions, yielding two distinct complexes. In silico modeling suggests that both complexes are structurally compatible with DNA binding, raising the possibility that they may function in identifying specific sequences within histone gene clusters, hence initiating the assembly of HLBs and regulating histone gene expression during cell cycle progression.
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Affiliation(s)
- Katarzyna Bucholc
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Aleksandra Skrajna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Kinga Adamska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Xiao-Cui Yang
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Zbigniew Domiński
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Correspondence: (Z.D.); (I.Z.); Tel.: +48-22-592-2038 (I.Z.)
| | - Igor Zhukov
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
- NanoBioMedical Centre, Adam Mickiewicz University, ul. Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland
- Correspondence: (Z.D.); (I.Z.); Tel.: +48-22-592-2038 (I.Z.)
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26
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Mikhailova A, Valle-Casuso JC, David A, Monceaux V, Volant S, Passaes C, Elfidha A, Müller-Trutwin M, Poyet JL, Sáez-Cirión A. Antiapoptotic Clone 11-Derived Peptides Induce In Vitro Death of CD4 + T Cells Susceptible to HIV-1 Infection. J Virol 2020; 94:e00611-20. [PMID: 32350074 PMCID: PMC7343195 DOI: 10.1128/jvi.00611-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 04/23/2020] [Indexed: 02/08/2023] Open
Abstract
HIV-1 successfully establishes long-term infection in its target cells despite viral cytotoxic effects. We have recently shown that cell metabolism is an important factor driving CD4+ T cell susceptibility to HIV-1 and the survival of infected cells. We show here that expression of antiapoptotic clone 11 (AAC-11), an antiapoptotic factor upregulated in many cancers, increased with progressive CD4+ T cell memory differentiation in association with the expression of cell cycle, activation, and metabolism genes and was correlated with susceptibility to HIV-1 infection. Synthetic peptides based on the LZ domain sequence of AAC-11, responsible for its interaction with molecular partners, were previously shown to be cytotoxic to cancer cells. Here, we observed that these peptides also blocked HIV-1 infection by inducing the death of HIV-1-susceptible primary CD4+ T cells across all T cell subsets. The peptides targeted metabolically active cells and had the greatest effect on effector and transitional CD4+ T cell memory subsets. Our results suggest that the AAC-11 survival pathway is potentially involved in the survival of HIV-1-infectible cells and provide proof of principle that some cellular characteristics can be targeted to eliminate the cells offering the best conditions to sustain HIV-1 replication.IMPORTANCE Although antiretroviral treatment efficiently blocks HIV multiplication, it cannot eliminate cells already carrying integrated proviruses. In the search for an HIV cure, the identification of new potential targets to selectively eliminate infected cells is of the outmost importance. We show here that peptides derived from antiapoptotic clone 11 (AAC-11), whose expression levels correlated with susceptibility to HIV-1 infection of CD4+ T cells, induced cytotoxicity in CD4+ T cells showing the highest levels of activation and metabolic activity, conditions known to favor HIV-1 infection. Accordingly, CD4+ T cells that survived the cytotoxic action of the AAC-11 peptides were resistant to HIV-1 replication. Our results identify a new potential molecular pathway to target HIV-1 infection.
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Affiliation(s)
- Anastassia Mikhailova
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
- Université Paris Diderot, Université de Paris, Paris, France
| | | | - Annie David
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
| | - Valérie Monceaux
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
| | - Stevenn Volant
- Institut Pasteur, Hub Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, Paris, France
| | - Caroline Passaes
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
| | - Amal Elfidha
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
- Université Paris Descartes, Université de Paris, Paris, France
| | | | - Jean-Luc Poyet
- INSERM UMRS976, Institut de Recherche Saint Louis, Hôpital Saint Louis, Paris, France
| | - Asier Sáez-Cirión
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
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Rodríguez CF, Llorca O. RPAP3 C-Terminal Domain: A Conserved Domain for the Assembly of R2TP Co-Chaperone Complexes. Cells 2020; 9:cells9051139. [PMID: 32384603 PMCID: PMC7290369 DOI: 10.3390/cells9051139] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/28/2020] [Accepted: 05/02/2020] [Indexed: 11/25/2022] Open
Abstract
The Rvb1-Rvb2-Tah1-Pih1 (R2TP) complex is a co-chaperone complex that works together with HSP90 in the activation and assembly of several macromolecular complexes, including RNA polymerase II (Pol II) and complexes of the phosphatidylinositol-3-kinase-like family of kinases (PIKKs), such as mTORC1 and ATR/ATRIP. R2TP is made of four subunits: RuvB-like protein 1 (RUVBL1) and RuvB-like 2 (RUVBL2) AAA-type ATPases, RNA polymerase II-associated protein 3 (RPAP3), and the Protein interacting with Hsp90 1 (PIH1) domain-containing protein 1 (PIH1D1). R2TP associates with other proteins as part of a complex co-chaperone machinery involved in the assembly and maturation of a growing list of macromolecular complexes. Recent progress in the structural characterization of R2TP has revealed an alpha-helical domain at the C-terminus of RPAP3 that is essential to bring the RUVBL1 and RUVBL2 ATPases to R2TP. The RPAP3 C-terminal domain interacts directly with RUVBL2 and it is also known as RUVBL2-binding domain (RBD). Several human proteins contain a region homologous to the RPAP3 C-terminal domain, and some are capable of assembling R2TP-like complexes, which could have specialized functions. Only the RUVBL1-RUVBL2 ATPase complex and a protein containing an RPAP3 C-terminal-like domain are found in all R2TP and R2TP-like complexes. Therefore, the RPAP3 C-terminal domain is one of few components essential for the formation of all R2TP and R2TP-like co-chaperone complexes.
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Affiliation(s)
| | - Oscar Llorca
- Correspondence: ; Tel.: +34-91-732-8000 (ext. 3000/3033)
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Huber J, Obata M, Gruber J, Akutsu M, Löhr F, Rogova N, Güntert P, Dikic I, Kirkin V, Komatsu M, Dötsch V, Rogov VV. An atypical LIR motif within UBA5 (ubiquitin like modifier activating enzyme 5) interacts with GABARAP proteins and mediates membrane localization of UBA5. Autophagy 2020; 16:256-270. [PMID: 30990354 PMCID: PMC6984602 DOI: 10.1080/15548627.2019.1606637] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 03/15/2019] [Accepted: 03/27/2019] [Indexed: 12/15/2022] Open
Abstract
Short linear motifs, known as LC3-interacting regions (LIRs), interact with mactoautophagy/autophagy modifiers (Atg8/LC3/GABARAP proteins) via a conserved universal mechanism. Typically, this includes the occupancy of 2 hydrophobic pockets on the surface of Atg8-family proteins by 2 specific aromatic and hydrophobic residues within the LIR motifs. Here, we describe an alternative mechanism of Atg8-family protein interaction with the non-canonical UBA5 LIR, an E1-like enzyme of the ufmylation pathway that preferentially interacts with GABARAP but not LC3 proteins. By solving the structures of both GABARAP and GABARAPL2 in complex with the UBA5 LIR, we show that in addition to the binding to the 2 canonical hydrophobic pockets (HP1 and HP2), a conserved tryptophan residue N-terminal of the LIR core sequence binds into a novel hydrophobic pocket on the surface of GABARAP proteins, which we term HP0. This mode of action is unique for UBA5 and accompanied by large rearrangements of key residues including the side chains of the gate-keeping K46 and the adjacent K/R47 in GABARAP proteins. Swapping mutations in LC3B and GABARAPL2 revealed that K/R47 is the key residue in the specific binding of GABARAP proteins to UBA5, with synergetic contributions of the composition and dynamics of the loop L3. Finally, we elucidate the physiological relevance of the interaction and show that GABARAP proteins regulate the localization and function of UBA5 on the endoplasmic reticulum membrane in a lipidation-independent manner.Abbreviations: ATG: AuTophaGy-related; EGFP: enhanced green fluorescent protein; GABARAP: GABA-type A receptor-associated protein; ITC: isothermal titration calorimetry; KO: knockout; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NMR: nuclear magnetic resonance; RMSD: root-mean-square deviation of atomic positions; TKO: triple knockout; UBA5: ubiquitin like modifier activating enzyme 5.
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Affiliation(s)
- Jessica Huber
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Miki Obata
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Jens Gruber
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Natalia Rogova
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
- Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Ivan Dikic
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany
- Institute of Biochemistry II, School of Medicine, Frankfurt am Main, Germany
| | - Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Masaaki Komatsu
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Vladimir V. Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
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Kønig SM, Rissler V, Terkelsen T, Lambrughi M, Papaleo E. Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level. PLoS Comput Biol 2019; 15:e1007485. [PMID: 31825969 PMCID: PMC6927658 DOI: 10.1371/journal.pcbi.1007485] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/23/2019] [Accepted: 10/12/2019] [Indexed: 12/11/2022] Open
Abstract
Apoptosis is an essential defensive mechanism against tumorigenesis. Proteins of the B-cell lymphoma-2 (Bcl-2) family regulate programmed cell death by the mitochondrial apoptosis pathway. In response to intracellular stress, the apoptotic balance is governed by interactions of three distinct subgroups of proteins; the activator/sensitizer BH3 (Bcl-2 homology 3)-only proteins, the pro-survival, and the pro-apoptotic executioner proteins. Changes in expression levels, stability, and functional impairment of pro-survival proteins can lead to an imbalance in tissue homeostasis. Their overexpression or hyperactivation can result in oncogenic effects. Pro-survival Bcl-2 family members carry out their function by binding the BH3 short linear motif of pro-apoptotic proteins in a modular way, creating a complex network of protein-protein interactions. Their dysfunction enables cancer cells to evade cell death. The critical role of Bcl-2 proteins in homeostasis and tumorigenesis, coupled with mounting insight in their structural properties, make them therapeutic targets of interest. A better understanding of gene expression, mutational profile, and molecular mechanisms of pro-survival Bcl-2 proteins in different cancer types, could help to clarify their role in cancer development and may guide advancement in drug discovery. Here, we shed light on the pro-survival Bcl-2 proteins in breast cancer using different bioinformatic approaches, linking -omics with structural data. We analyzed the changes in the expression of the Bcl-2 proteins and their BH3-containing interactors in breast cancer samples. We then studied, at the structural level, a selection of interactions, accounting for effects induced by mutations found in the breast cancer samples. We find two complexes between the up-regulated Bcl2A1 and two down-regulated BH3-only candidates (i.e., Hrk and Nr4a1) as targets associated with reduced apoptosis in breast cancer samples for future experimental validation. Furthermore, we predict L99R, M75R as damaging mutations altering protein stability, and Y120C as a possible allosteric mutation from an exposed surface to the BH3-binding site.
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Affiliation(s)
- Simon Mathis Kønig
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Vendela Rissler
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Thilde Terkelsen
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
- Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
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30
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Camacho-Jiménez L, Felix-Portillo M, Nuñez-Hernandez DM, Yepiz-Plascencia G. Molecular cloning and modeling of the Tp53-induced glycolysis and apoptotic regulator (TIGAR) from the Pacific white shrimp Litopenaeus vannamei and its expression in response to hypoxia. Fish Shellfish Immunol 2019; 93:484-491. [PMID: 31377432 DOI: 10.1016/j.fsi.2019.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Hypoxia is a common stressor for aquaculture species. The Pacific white shrimp Litopenaeus vannamei survives low dissolved oxygen (DO) conditions by adjusting its energy metabolism. In vertebrates, the transcription factor p53 regulates glucose metabolism under stress through diverse target genes like the Tp53-induced glycolysis and apoptotic regulator (TIGAR), a protein similar to fructose-2,6-bisphosphatase that has a pro-survival role in cells participating in the defense against oxidative damage. Until now, TIGAR has been not reported in any invertebrate species, including crustaceans. In this work, we report the molecular cloning of the white shrimp TIGAR. The cDNA sequence is 765 bp encoding a 254 amino acid protein. Bioinformatics analyses predicted that although the overall sequence identities of L. vannamei TIGAR and vertebrate proteins are not very high (33.61%-35.34%), they have a remarkable predicted structural similarity with full conservation of catalytic residues, secondary and three-dimensional structures. Gene expression analysis by RT-qPCR revealed that the mRNA abundance of TIGAR in white shrimp is tissue-specific under normal oxygen conditions, with higher expression in gills than hepatopancreas and muscle. Also, gene expression in gills and hepatopancreas is modified by environmental hypoxia, suggesting that TIGAR participates in the cellular tolerance of L. vannamei to this stressor.
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Affiliation(s)
- Laura Camacho-Jiménez
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C, Carretera Gustavo Enrique Astiazarán Rosas, no. 46, col La Victoria, Hermosillo, Sonora, C.P. 83304, Mexico
| | - Monserrath Felix-Portillo
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Periférico Francisco R. Almada, Km 1, Chihuahua, Chihuahua, 33820, Mexico
| | - Dahlia M Nuñez-Hernandez
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C, Carretera Gustavo Enrique Astiazarán Rosas, no. 46, col La Victoria, Hermosillo, Sonora, C.P. 83304, Mexico
| | - Gloria Yepiz-Plascencia
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C, Carretera Gustavo Enrique Astiazarán Rosas, no. 46, col La Victoria, Hermosillo, Sonora, C.P. 83304, Mexico.
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31
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Banjara S, Shimmon GL, Dixon LK, Netherton CL, Hinds MG, Kvansakul M. Crystal Structure of African Swine Fever Virus A179L with the Autophagy Regulator Beclin. Viruses 2019; 11:v11090789. [PMID: 31461953 PMCID: PMC6784060 DOI: 10.3390/v11090789] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/23/2019] [Accepted: 08/24/2019] [Indexed: 12/15/2022] Open
Abstract
Subversion of programmed cell death-based host defence systems is a prominent feature of infections by large DNA viruses. African swine fever virus (ASFV) is a large DNA virus and sole member of the Asfarviridae family that harbours the B-cell lymphoma 2 or Bcl-2 homolog A179L. A179L has been shown to bind to a range of cell death-inducing host proteins, including pro-apoptotic Bcl-2 proteins as well as the autophagy regulator Beclin. Here we report the crystal structure of A179L bound to the Beclin BH3 motif. A179L engages Beclin using the same canonical ligand-binding groove that is utilized to bind to pro-apoptotic Bcl-2 proteins. The mode of binding of Beclin to A179L mirrors that of Beclin binding to human Bcl-2 and Bcl-xL as well as murine γ-herpesvirus 68. The introduction of bulky hydrophobic residues into the A179L ligand-binding groove via site-directed mutagenesis ablates binding of Beclin to A179L, leading to a loss of the ability of A179L to modulate autophagosome formation in Vero cells during starvation. Our findings provide a mechanistic understanding for the potent autophagy inhibitory activity of A179L and serve as a platform for more detailed investigations into the role of autophagy during ASFV infection.
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Affiliation(s)
- Suresh Banjara
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | | | - Linda K Dixon
- Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK
| | | | - Mark G Hinds
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3050, Australia.
| | - Marc Kvansakul
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
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Crespo-Flores SL, Cabezas A, Hassan S, Wei Y. PEA-15 C-Terminal Tail Allosterically Modulates Death-Effector Domain Conformation and Facilitates Protein-Protein Interactions. Int J Mol Sci 2019; 20:ijms20133335. [PMID: 31284641 PMCID: PMC6651876 DOI: 10.3390/ijms20133335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/28/2019] [Accepted: 07/05/2019] [Indexed: 11/16/2022] Open
Abstract
Phosphoprotein enriched in astrocytes, 15 kDa (PEA-15) exerts its regulatory roles on several critical cellular pathways through protein–protein interactions depending on its phosphorylation states. It can either inhibit the extracellular signal-regulated kinase (ERK) activities when it is dephosphorylated or block the assembly of death-inducing signaling complex (DISC) and the subsequent activation of apoptotic initiator, caspase-8, when it is phosphorylated. Due to the important roles of PEA-15 in regulating these pathways that lead to opposite cellular outcomes (cell proliferation vs. cell death), we proposed a phosphostasis (phosphorylation homeostasis) model, in which the phosphorylation states of the protein are vigorously controlled and regulated to maintain a delicate balance. The phosphostasis gives rise to the protective cellular functions of PEA-15 to preserve optimum cellular conditions. In this article, using advanced multidimensional nuclear magnetic resonance (NMR) techniques combined with a novel chemical shift (CS)-Rosetta algorithm for de novo protein structural determination, we report a novel conformation of PEA-15 death-effector domain (DED) upon interacting with ERK2. This new conformation is modulated by the irregularly structured C-terminal tail when it first recognizes and binds to ERK2 at the d-peptide recruitment site (DRS) in an allosteric manner, and is facilitated by the rearrangement of the surface electrostatic and hydrogen-bonding interactions on the DED. In this ERK2-bound conformation, three of the six helices (α2, α3, and α4) comprising the DED reorient substantially in comparison to the free-form structure, exposing key residues on the other three helices that directly interact with ERK2 at the DEF-docking site (docking site for ERK, FxF) and the activation loop. Additionally, we provide evidence that the phosphorylation of the C-terminal tail leads to a distinct conformation of DED, allowing efficient interactions with Fas-associated death domain (FADD) protein at the DISC. Our results substantiate the allosteric regulatory roles of the C-terminal tail in modulating DED conformation and facilitating protein–protein interactions of PEA-15.
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Affiliation(s)
| | - Andres Cabezas
- Department of Chemistry, New Jersey City University, Jersey City, NJ 07305-1596, USA
| | - Sherouk Hassan
- Department of Chemistry, New Jersey City University, Jersey City, NJ 07305-1596, USA
| | - Yufeng Wei
- Department of Chemistry, New Jersey City University, Jersey City, NJ 07305-1596, USA.
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Xu H, Shi J, Gao H, Liu Y, Yang Z, Shao F, Dong N. The N-end rule ubiquitin ligase UBR2 mediates NLRP1B inflammasome activation by anthrax lethal toxin. EMBO J 2019; 38:e101996. [PMID: 31268597 PMCID: PMC6600268 DOI: 10.15252/embj.2019101996] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 11/09/2022] Open
Abstract
Anthrax lethal toxin (LT) is known to induce NLRP1B inflammasome activation and pyroptotic cell death in macrophages from certain mouse strains in its metalloprotease activity-dependent manner, but the underlying mechanism is unknown. Here, we establish a simple but robust cell system bearing dual-fluorescence reporters for LT-induced ASC specks formation and pyroptotic lysis. A genome-wide siRNA screen and a CRISPR-Cas9 knockout screen were applied to this system for identifying genes involved in LT-induced inflammasome activation. UBR2, an E3 ubiquitin ligase of the N-end rule degradation pathway, was found to be required for LT-induced NLRP1B inflammasome activation. LT is known to cleave NLRP1B after Lys44. The cleaved NLRP1B, bearing an N-terminal leucine, was targeted by UBR2-mediated ubiquitination and degradation. UBR2 partnered with an E2 ubiquitin-conjugating enzyme UBE2O in this process. NLRP1B underwent constitutive autocleavage before the C-terminal CARD domain. UBR2-mediated degradation of LT-cleaved NLRP1B thus triggered release of the noncovalent-bound CARD domain for subsequent caspase-1 activation. Our study illustrates a unique mode of inflammasome activation in cytosolic defense against bacterial insults.
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Affiliation(s)
- Hao Xu
- National Institute of Biological SciencesBeijingChina
- Present address:
Molecular Pathogenesis ProgramThe Kimmel Center for Biology and Medicine of the Skirball InstituteNew York University School of MedicineNew YorkNYUSA
| | - Jianjin Shi
- National Institute of Biological SciencesBeijingChina
- Present address:
Department of BiologyStanford UniversityStanfordCAUSA
| | - Hang Gao
- State Key Laboratory of Animal NutritionCollege of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Ying Liu
- State Key Laboratory of Animal NutritionCollege of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Zhenxiao Yang
- National Institute of Biological SciencesBeijingChina
| | - Feng Shao
- National Institute of Biological SciencesBeijingChina
- Tsinghua Institute of Multidisciplinary Biomedical ResearchTsinghua UniversityBeijingChina
| | - Na Dong
- National Institute of Biological SciencesBeijingChina
- State Key Laboratory of Animal NutritionCollege of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
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34
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Liu Q, Osterlund EJ, Chi X, Pogmore J, Leber B, Andrews DW. Bim escapes displacement by BH3-mimetic anti-cancer drugs by double-bolt locking both Bcl-XL and Bcl-2. eLife 2019; 8:e37689. [PMID: 30860026 PMCID: PMC6414199 DOI: 10.7554/elife.37689] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 01/16/2019] [Indexed: 01/07/2023] Open
Abstract
Tumor initiation, progression and resistance to chemotherapy rely on cancer cells bypassing programmed cell death by apoptosis. We report that unlike other pro-apoptotic proteins, Bim contains two distinct binding sites for the anti-apoptotic proteins Bcl-XL and Bcl-2. These include the BH3 sequence shared with other pro-apoptotic proteins and an unexpected sequence located near the Bim carboxyl-terminus (residues 181-192). Using automated Fluorescence Lifetime Imaging Microscopy - Fluorescence Resonance Energy Transfer (FLIM-FRET) we show that the two binding interfaces enable Bim to double-bolt lock Bcl-XL and Bcl-2 in complexes resistant to displacement by BH3-mimetic drugs currently in use or being evaluated for cancer therapy. Quantifying in live cells the contributions of individual amino acids revealed that residue L185 previously thought involved in binding Bim to membranes, instead contributes to binding to anti-apoptotic proteins. This double-bolt lock mechanism has profound implications for the utility of BH3-mimetics as drugs. .
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Affiliation(s)
- Qian Liu
- Biological SciencesSunnybrook Research InstituteTorontoCanada
| | - Elizabeth J Osterlund
- Biological SciencesSunnybrook Research InstituteTorontoCanada
- Department of BiochemistryUniversity of TorontoTorontoCanada
| | - Xiaoke Chi
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonCanada
| | - Justin Pogmore
- Department of BiochemistryUniversity of TorontoTorontoCanada
| | - Brian Leber
- Department of MedicineMcMaster UniversityHamiltonCanada
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35
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Huang Y, Liu S, Wu R, Zhang L, Zhang Y, Hong H, Zhang A, Xiao H, Liu Y, Wu Z, Zhu L, Kung HF. Synthesis and preliminary evaluation of a novel glutamine derivative: (2S,4S)4-[ 18F]FEBGln. Bioorg Med Chem Lett 2019; 29:1047-1050. [PMID: 30871772 DOI: 10.1016/j.bmcl.2019.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/04/2019] [Accepted: 03/10/2019] [Indexed: 12/22/2022]
Abstract
We report the preparation of a novel glutamine derivative, (2S,4S)-2,5-diamino-4-(4-(2-fluoroethoxy)benzyl)-5-oxopentanoic acid, (2S, 4S)4-[18F]FEBGln ([18F]4), through efficient organic and radiosyntheses. In vitro assays of [18F]4 using MCF-7 cells showed that it entered cells via multiple amino acid transporter systems including system L and ASC2 transporters but not through the system A transporter. [18F]4 showed promising properties for tumor imaging and may serve as a lead compound for further optimizing and targeting the system L transporter associated with enhanced glutamine metabolism in cancer cells.
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Affiliation(s)
- Yong Huang
- Beijing Institute of Brain Disorders, Capital Medical University, Beijing 100069, China
| | - Song Liu
- Beijing Institute of Brain Disorders, Capital Medical University, Beijing 100069, China
| | - Renbo Wu
- Beijing Institute of Brain Disorders, Capital Medical University, Beijing 100069, China
| | - Lifang Zhang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yan Zhang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Haiyan Hong
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Aili Zhang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hao Xiao
- Beijing Institute of Brain Disorders, Capital Medical University, Beijing 100069, China
| | - Yajing Liu
- Beijing Institute of Brain Disorders, Capital Medical University, Beijing 100069, China
| | - Zehui Wu
- Beijing Institute of Brain Disorders, Capital Medical University, Beijing 100069, China.
| | - Lin Zhu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hank F Kung
- Beijing Institute of Brain Disorders, Capital Medical University, Beijing 100069, China; Department of Radiology, University of Pennsylvania, Philadelphia 19104, United States.
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Zhang S, Zhang T, Liu C. Prediction of apoptosis protein subcellular localization via heterogeneous features and hierarchical extreme learning machine. SAR QSAR Environ Res 2019; 30:209-228. [PMID: 30806087 DOI: 10.1080/1062936x.2019.1576222] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/27/2019] [Indexed: 06/09/2023]
Abstract
Apoptosis is a fundamental process controlling normal tissue homeostasis by regulating a balance between cell proliferation and death. Predicting the subcellular location of apoptosis proteins is very helpful for understanding the mechanism of programmed cell death. Predicting protein subcellular localization with bioinformatic techniques provides quite a few opportunities in related fields. In this work, we propose the use of a hierarchical extreme learning machine (H-ELM) to make a classification of high-dimensional input data without demanding a dimension reduction process, which yields acceptable results. An attempt is made to extract features from different perspectives, and a feature fusion process is accomplished. Regarding the position-specific scoring matrix, the first type depicts the correlation within the sequence with the autocorrelation function for relatively random sections from the sequence; and the second type is the Kullback-Leibler (K-L) divergence of the two distributions formed by the amino acids' constitutuent proportions. It is illustrated in an experiment with features from different sources mixed by simple concatenation yielding a poor result, but the synthetical feature fused with stochastic nonlinear embedding (t-SNE) greatly improved the classification. Finally, the highest overall accuracy of ZD98 is 87.5% by adjusting the hyper-parameters of H-ELM, and of CL317 is 92.4%.
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Affiliation(s)
- S Zhang
- a School of Mathematics and Statistics, Xidian University , Xi'an , PR China
| | - T Zhang
- a School of Mathematics and Statistics, Xidian University , Xi'an , PR China
| | - C Liu
- b School of Electronic Engineering, Xidian University , Xi'an , PR China
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Lin KF, Hsu JY, Hsieh DL, Tsai MJ, Yeh CH, Chen CY. Crystal structure of the programmed cell death 5 protein from Sulfolobus solfataricus. Acta Crystallogr F Struct Biol Commun 2019; 75:73-79. [PMID: 30713157 PMCID: PMC6360439 DOI: 10.1107/s2053230x18017673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 12/13/2018] [Indexed: 11/10/2022] Open
Abstract
Programmed cell death 5 (PDCD5) is a vital signaling protein in the apoptosis pathway in eukaryotes. It is known that there are two dissociated N-terminal regions and a triple-helix core in eukaryotic PDCD5. Structural and functional studies of PDCD5 from hyperthermophilic archaea have been limited to date. Here, the PDCD5 homolog Sso0352 (SsoPDCD5) was identified in Sulfolobus solfataricus, the SsoPDCD5 protein was expressed and crystallized, and the phase was identified by single-wavelength anomalous diffraction. The native SsoPDCD5 crystal belonged to space group C2 and diffracted to 1.49 Å resolution. This is the first crystal structure of a PDCD5 homolog to be solved. SsoPDCD5 shares a similar triple-helix bundle with eukaryotic PDCD5 but has a long α-helix in the N-terminus. A structural search and biochemical data suggest that SsoPDCD5 may function as a DNA-binding protein.
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Affiliation(s)
- Kuan-Fu Lin
- Department of Life Sciences, National Central University, 300 Zhongda Road, Zhongli District, Taoyuan City 32001, Taiwan
| | - Jia-Yuan Hsu
- Department of Life Sciences, National Central University, 300 Zhongda Road, Zhongli District, Taoyuan City 32001, Taiwan
| | - Dong-Lin Hsieh
- Department of Life Sciences, National Central University, 300 Zhongda Road, Zhongli District, Taoyuan City 32001, Taiwan
| | - Meng-Ju Tsai
- Department of Life Sciences, National Central University, 300 Zhongda Road, Zhongli District, Taoyuan City 32001, Taiwan
| | - Ching-Hui Yeh
- Department of Life Sciences, National Central University, 300 Zhongda Road, Zhongli District, Taoyuan City 32001, Taiwan
| | - Chin-Yu Chen
- Department of Life Sciences, National Central University, 300 Zhongda Road, Zhongli District, Taoyuan City 32001, Taiwan
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Niture S, Dong X, Arthur E, Chimeh U, Niture SS, Zheng W, Kumar D. Oncogenic Role of Tumor Necrosis Factor α-Induced Protein 8 (TNFAIP8). Cells 2018; 8:cells8010009. [PMID: 30586922 PMCID: PMC6356598 DOI: 10.3390/cells8010009] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 12/19/2022] Open
Abstract
Tumor necrosis factor (TNF)-α-induced protein 8 (TNFAIP8) is a founding member of the TIPE family, which also includes TNFAIP8-like 1 (TIPE1), TNFAIP8-like 2 (TIPE2), and TNFAIP8-like 3 (TIPE3) proteins. Expression of TNFAIP8 is strongly associated with the development of various cancers including cancer of the prostate, liver, lung, breast, colon, esophagus, ovary, cervix, pancreas, and others. In human cancers, TNFAIP8 promotes cell proliferation, invasion, metastasis, drug resistance, autophagy, and tumorigenesis by inhibition of cell apoptosis. In order to better understand the molecular aspects, biological functions, and potential roles of TNFAIP8 in carcinogenesis, in this review, we focused on the expression, regulation, structural aspects, modifications/interactions, and oncogenic role of TNFAIP8 proteins in human cancers.
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Affiliation(s)
- Suryakant Niture
- Julius L. Chambers Biomedical Biotechnology Research Institute (BBRI), North Carolina Central University, Durham, NC 27707, USA.
| | - Xialan Dong
- Bio-manufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, NC 27707, USA.
| | - Elena Arthur
- Julius L. Chambers Biomedical Biotechnology Research Institute (BBRI), North Carolina Central University, Durham, NC 27707, USA.
| | - Uchechukwu Chimeh
- Julius L. Chambers Biomedical Biotechnology Research Institute (BBRI), North Carolina Central University, Durham, NC 27707, USA.
| | | | - Weifan Zheng
- Bio-manufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, NC 27707, USA.
| | - Deepak Kumar
- Julius L. Chambers Biomedical Biotechnology Research Institute (BBRI), North Carolina Central University, Durham, NC 27707, USA.
- Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC 27707, USA.
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39
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Clark AM, Ponniah K, Warden MS, Raitt EM, Yawn AC, Pascal SM. pH-Induced Folding of the Caspase-Cleaved Par-4 Tumor Suppressor: Evidence of Structure Outside of the Coiled Coil Domain. Biomolecules 2018; 8:biom8040162. [PMID: 30518159 PMCID: PMC6316887 DOI: 10.3390/biom8040162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 12/13/2022] Open
Abstract
Prostate apoptosis response-4 (Par-4) is a 38 kDa largely intrinsically disordered tumor suppressor protein that functions in cancer cell apoptosis. Par-4 down-regulation is often observed in cancer while up-regulation is characteristic of neurodegenerative conditions such as Alzheimer’s disease. Cleavage of Par-4 by caspase-3 activates tumor suppression via formation of an approximately 25 kDa fragment (cl-Par-4) that enters the nucleus and inhibits Bcl-2 and NF-ƙB, which function in pro-survival pathways. Here, we have investigated the structure of cl-Par-4 using biophysical techniques including circular dichroism (CD) spectroscopy, dynamic light scattering (DLS), and intrinsic tyrosine fluorescence. The results demonstrate pH-dependent folding of cl-Par-4, with high disorder and aggregation at neutral pH, but a largely folded, non-aggregated conformation at acidic pH.
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Affiliation(s)
- Andrea M Clark
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Komala Ponniah
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Meghan S Warden
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Emily M Raitt
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Andrea C Yawn
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Steven M Pascal
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
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Hiramoto E, Tsutsumi A, Suzuki R, Matsuoka S, Arai S, Kikkawa M, Miyazaki T. The IgM pentamer is an asymmetric pentagon with an open groove that binds the AIM protein. Sci Adv 2018; 4:eaau1199. [PMID: 30324136 PMCID: PMC6179379 DOI: 10.1126/sciadv.aau1199] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/31/2018] [Indexed: 05/09/2023]
Abstract
Soluble immunoglobulin M (IgM) forms a pentamer containing a joining (J) chain polypeptide. While IgM pentamer has various immune functions, it also behaves as a carrier of circulating apoptosis inhibitor of macrophage (AIM; also called CD5L) protein that facilitates repair during different diseases. AIM binds to the IgM pentamer solely in the presence of the J chain. Here, using a single-particle negative-stain electron microscopy, we found that the IgM pentamer exhibits an asymmetric pentagon containing one large gap, which is markedly different from the textbook symmetric pentagon model. A single AIM molecule specifically fits into the gap, cross-bridging two IgM-Fc that form the edges of the gap through a disulfide bond at one side and a charge-based interaction at the other side. The discovery of the bona fide shape of the IgM pentamer advances our structural understanding of the pentameric IgM and its binding mode with AIM.
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Affiliation(s)
- Emiri Hiramoto
- Laboratory of Molecular Biomedicine for Pathogenesis, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Akihisa Tsutsumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Risa Suzuki
- Laboratory of Molecular Biomedicine for Pathogenesis, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shigeru Matsuoka
- Laboratory of Molecular Biomedicine for Pathogenesis, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- Corresponding author. (T.M.); (S.A.)
| | - Satoko Arai
- Laboratory of Molecular Biomedicine for Pathogenesis, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- Corresponding author. (T.M.); (S.A.)
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Toru Miyazaki
- Laboratory of Molecular Biomedicine for Pathogenesis, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan
- Max Planck–The University of Tokyo Center for Integrative Inflammology, Tokyo, Japan
- Corresponding author. (T.M.); (S.A.)
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41
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Wang N, Zhan J, Guo C, Li C, Shen N, Gu X, Xie Y, Peng X, Yang G. Molecular Characterisation and Functions of Fis1 and PDCD6 Genes from Echinococcus granulosus. Int J Mol Sci 2018; 19:ijms19092669. [PMID: 30205566 PMCID: PMC6165261 DOI: 10.3390/ijms19092669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 08/22/2018] [Accepted: 09/05/2018] [Indexed: 11/16/2022] Open
Abstract
Cystic echinococcosis, a parasitic zoonosis that causes significant economic losses and poses a threat to public health, is caused by larvae of the tapeworm Echinococcus granulosus. Infection causes infertile cysts in intermediate hosts that cannot produce protoscoleces (PSCs) or complete the life cycle. Herein, we cloned, expressed, and characterised mitochondrial fission protein 1 (Eg-Fis1) and programmed cell death protein 6 (Eg-PDCD6) from E. granulosus, and explored their functions related to infertile cysts. Eg-Fis1 and Eg-PDCD6 encode putative 157 and 174 residue proteins, respectively, and Western blotting indicated good reactogenicity for both. Eg-Fis1 and Eg-PDCD6 were ubiquitously distributed in all stages of E. granulosus. Furthermore, mRNAs of Eg-Fis1 and Eg-PDCD6 were upregulated following H2O2 treatment which induced apoptosis in PSCs. To investigate the regulation of apoptosis in response to oxidative stress, RNA interference (RNAi) and terminal deoxynucleotidyl transferase dUTP nick-end labelling (TUNEL) assays were performed. The apoptotic rate of the Eg-Fis1 RNAi group was significantly lower than non-interference group, but there was no such difference for Eg-PDCD6. In conclusion, Eg-Fis1 promotes apoptosis induced by oxidative stress, whereas Eg-PDCD6 does not appear to be a key regulator of apoptosis.
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Affiliation(s)
- Ning Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin 644000, China.
| | - Jiafei Zhan
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
| | - Cheng Guo
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
| | - Chunyan Li
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
| | - Nengxing Shen
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xuerong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Chengdu 611130, China.
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
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42
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Cai J, Wei S, Lu Y, Wu Z, Qin Q, Jian J. Bax inhibitor-1 from orange spotted grouper, Epinephelus coioides involved in viral infection. Fish Shellfish Immunol 2018; 78:91-99. [PMID: 29679759 DOI: 10.1016/j.fsi.2018.04.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/05/2018] [Accepted: 04/07/2018] [Indexed: 06/08/2023]
Abstract
Bax inhibitor-1 (BI-1) is a conserved anti-apoptotic protein that suppresses endoplasmic reticulum (ER) stress-induced cell death. However, the function of fish BI-1 is not quite clear. In the present study, a bi-1 homolog (Ecbi-1) from orange spotted grouper, Epinephelus coioides was identified and its roles in viral infection were investigated. EcBI-1 encoded 237 amino acids protein, contained six transmembrane regions and a conservative C-terminus motif. Ecbi-1 predominantly expressed in kidney and spleen of healthy grouper. After SGIV stimulation, Ecbi-1 transcript was significantly increased in vitro. Subcellular localization analysis revealed that EcBI-1 was localized throughout the cytoplasm and co-localized with ER. Furthermore, overexpression of EcBI-1 suppressed SGIV infection induced cell death, caspase-3 activity and viral genes transcription. And C-terminus motif was critical for regulation roles of EcBI-1 during SGIV infection. In addition, EcBI-1 could interact with EcBNIP3 in vitro. Together, our data firstly demonstrated that fish BI-1 play important roles in response to viral infection.
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Affiliation(s)
- Jia Cai
- College of Fishery, Guangdong Ocean University, Zhanjiang 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang 524088, PR China
| | - Shina Wei
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China
| | - Yishan Lu
- College of Fishery, Guangdong Ocean University, Zhanjiang 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang 524088, PR China
| | - Zaohe Wu
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang 524088, PR China
| | - Qiwei Qin
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China.
| | - Jichang Jian
- College of Fishery, Guangdong Ocean University, Zhanjiang 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang 524088, PR China.
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43
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Zhang W, Yao F, Zhang H, Li N, Zou X, Sui L, Hou L. The Potential Roles of the Apoptosis-Related Protein PDRG1 in Diapause Embryo Restarting of Artemia sinica. Int J Mol Sci 2018; 19:E126. [PMID: 29301330 PMCID: PMC5796075 DOI: 10.3390/ijms19010126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 12/27/2017] [Accepted: 12/30/2017] [Indexed: 11/16/2022] Open
Abstract
High salinity and low temperatures can induce Artemia sinica to enter the diapause stage during embryonic development. Diapause embryos stop at the gastrula stage, allowing them to resist apoptosis and regulate cell cycle activity to guarantee normal development after diapause termination. P53 and DNA damage-regulated gene 1 (pdrg1) is involved in cellular physiological activities, such as apoptosis, DNA damage repair, cell cycle regulation, and promotion of programmed cell death. However, the role of pdrg1 in diapause and diapause termination in A. sinica remains unknown. Here, the full-length A. sinica pdrg1 cDNA (As-pdrg1) was obtained and found to contain 1119 nucleotides, including a 228 bp open reading frame (ORF), a 233 bp 5'-untranslated region (UTR), and a 658-bp 3'-UTR, which encodes a 75 amino acid protein. In situ hybridization showed no tissue specific expression of As-pdrg1. Quantitative real-time PCR and western blotting analyses of As-pdrg1 gene and protein expression showed high levels at 15-20 h of embryo development and a subsequent downward trend. Low temperatures upregulated As-pdrg1 expression. RNA interference for the pdrg1 gene in Artemia embryos caused significant developmental hysteresis. Thus, PDRG1 plays an important role in diapause termination and cell cycle regulation in early embryonic development of A. sinica.
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Affiliation(s)
- Wan Zhang
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China.
| | - Feng Yao
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China.
| | - Hong Zhang
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China.
| | - Na Li
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China.
| | - Xiangyang Zou
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China.
| | - Linlin Sui
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China.
| | - Lin Hou
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China.
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Templin AT, Samarasekera T, Meier DT, Hogan MF, Mellati M, Crow MT, Kitsis RN, Zraika S, Hull RL, Kahn SE. Apoptosis Repressor With Caspase Recruitment Domain Ameliorates Amyloid-Induced β-Cell Apoptosis and JNK Pathway Activation. Diabetes 2017; 66:2636-2645. [PMID: 28729244 PMCID: PMC5606321 DOI: 10.2337/db16-1352] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 07/13/2017] [Indexed: 12/28/2022]
Abstract
Islet amyloid is present in more than 90% of individuals with type 2 diabetes, where it contributes to β-cell apoptosis and insufficient insulin secretion. Apoptosis repressor with caspase recruitment domain (ARC) binds and inactivates components of the intrinsic and extrinsic apoptosis pathways and was recently found to be expressed in islet β-cells. Using a human islet amyloid polypeptide transgenic mouse model of islet amyloidosis, we show ARC knockdown increases amyloid-induced β-cell apoptosis and loss, while ARC overexpression decreases amyloid-induced apoptosis, thus preserving β-cells. These effects occurred in the absence of changes in islet amyloid deposition, indicating ARC acts downstream of amyloid formation. Because islet amyloid increases c-Jun N-terminal kinase (JNK) pathway activation, we investigated whether ARC affects JNK signaling in amyloid-forming islets. We found ARC knockdown enhances JNK pathway activation, whereas ARC overexpression reduces JNK, c-Jun phosphorylation, and c-Jun target gene expression (Jun and Tnf). Immunoprecipitation of ARC from mouse islet lysates showed ARC binds JNK, suggesting interaction between JNK and ARC decreases amyloid-induced JNK phosphorylation and downstream signaling. These data indicate that ARC overexpression diminishes amyloid-induced JNK pathway activation and apoptosis in the β-cell, a strategy that may reduce β-cell loss in type 2 diabetes.
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Affiliation(s)
- Andrew T Templin
- VA Puget Sound Health Care System and Department of Medicine, University of Washington, Seattle, WA
| | - Tanya Samarasekera
- VA Puget Sound Health Care System and Department of Medicine, University of Washington, Seattle, WA
| | - Daniel T Meier
- VA Puget Sound Health Care System and Department of Medicine, University of Washington, Seattle, WA
| | - Meghan F Hogan
- VA Puget Sound Health Care System and Department of Medicine, University of Washington, Seattle, WA
| | - Mahnaz Mellati
- VA Puget Sound Health Care System and Department of Medicine, University of Washington, Seattle, WA
| | - Michael T Crow
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Richard N Kitsis
- Departments of Medicine and Cell Biology and Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY
| | - Sakeneh Zraika
- VA Puget Sound Health Care System and Department of Medicine, University of Washington, Seattle, WA
| | - Rebecca L Hull
- VA Puget Sound Health Care System and Department of Medicine, University of Washington, Seattle, WA
| | - Steven E Kahn
- VA Puget Sound Health Care System and Department of Medicine, University of Washington, Seattle, WA
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Shao Y, Chen H, Lv M, Li C, Zhang W, Li Y, Zhao X, Bao Y. A novel TNFAIP8 gene mediates l-arginine metabolism in Apostichopus japonicus. Fish Shellfish Immunol 2017; 69:26-34. [PMID: 28797638 DOI: 10.1016/j.fsi.2017.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/04/2017] [Accepted: 08/04/2017] [Indexed: 06/07/2023]
Abstract
Tumor necrosis factor (TNF)-α-induced protein 8 (TNFAIP8) family is a newly identified protein with vital roles in maintaining immune homeostasis. In the current study, we first cloned and characterized a TNFAIP8 gene from the invertebrate sea cucumber Apostichopus japonicus. The gene was designated as AjTNFAIP8. The full-length cDNA of AjTNFAIP8 was 1455 bp long and encoded a matured protein of 201 amino acid residues. Structural analysis indicated that AjTNFAIP8 had a death effector domain (DED)-like domain and composed of six α-helices. Multiple sequence alignment and phylogenetic analysis supported that AjTNFAIP8 is a new member of the TNFAIP8 family. Analysis of basal transcription in five tissues revealed the constitutive expression of AjTNFAIP8 in the detected tissues with highest expression in the respiratory tree and minimum expression in the tentacle. Vibrio splendidus infection and LPS stimulation could significantly downregulate the mRNA expression of AjTNFAIP8. More importantly, the transcription of pro-inflammatory molecule NOS and its production of NO content were significantly increased after AjTNFAIP8 silencing, with the suppression of agmatinase transcript and arginase activity. These results clearly indicated that AjTNFAIP8 is an essential negative regulator in innate immunity. Basic information for further exploration of the functional mechanisms of TNFAIP8 family in other marine invertebrate is provided.
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Affiliation(s)
- Yina Shao
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Huahui Chen
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Miao Lv
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Chenghua Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China.
| | - Weiwei Zhang
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Ye Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Xuelin Zhao
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Yongbo Bao
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, Zhejiang Wanli University, Ningbo 315100, PR China.
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46
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Cai J, Wei S, Yu D, Song R, Lu Y, Wu Z, Qin Q, Jian J. BNIP3, a cell pro-apoptotic protein, involved in response to viral infection in orange spotted grouper, Epinephelus coioides. Fish Shellfish Immunol 2017; 64:407-413. [PMID: 28359943 DOI: 10.1016/j.fsi.2017.03.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/24/2017] [Accepted: 03/26/2017] [Indexed: 06/07/2023]
Abstract
BNIP3 is a kind of BH3-only protein that induces both cell death and autophagy. Here, a BNIP3 gene (EcBNIP3) was identified from orange spotted grouper, Epinephelus coioides. EcBNIP3 possessed 236 amino acids residues, contained a conservative BNIP3 domain and a transmembrane region. Besides, EcBNIP3 expressed at a relative high level in heart and spleen. EcBNIP3 transcript was up-regulated after SGIV infection in vitro. Subcellular localization analysis revealed that EcBNIP3 was predominantly localized in the cytoplasm and co-localized with mitochondria. In addition, overexpression EcBNIP3 accelerated SGIV infection induced cell death but inhibited viral genes transcription. Taken together, these results provided new evidence that fish BNIP3 might involved in response to virus infection.
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Affiliation(s)
- Jia Cai
- College of Fishery, Guangdong Ocean University, Zhanjiang 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang 524088, PR China
| | - Shina Wei
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Dapeng Yu
- College of Fishery, Guangdong Ocean University, Zhanjiang 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang 524088, PR China
| | - Rui Song
- Hunan Fisheries Science Institute, Changsha 410153, PR China
| | - Yishan Lu
- College of Fishery, Guangdong Ocean University, Zhanjiang 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang 524088, PR China
| | - Zaohe Wu
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang 524088, PR China
| | - Qiwei Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China; College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China.
| | - Jichang Jian
- College of Fishery, Guangdong Ocean University, Zhanjiang 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang 524088, PR China.
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Xia WL, Kang LH, Liu CB, Kang CJ. Death associated protein 1 (DAP 1) positively regulates virus replication and apoptosis of hemocytes in shrimp Marsupenaeus japonicus. Fish Shellfish Immunol 2017; 63:304-313. [PMID: 28212834 DOI: 10.1016/j.fsi.2017.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
Death-associated protein 1 (DAP1) is a small proline-rich cytoplasmic protein that functions both in the apoptosis and autophage process of mammalian and in the clinical cancer of human. However, little knowledge is known about the homologue gene of DAP1 and its roles in the physiological process of invertebrates. In this paper, we report a novel function of DAP1 in the antivirus immunity of shrimp. A homologue gene of DAP1 was cloned from Marsupenaeus japonicus and named as Mjdap-1. The full-length of Mjdap-1 was 1761 bp with a 309 bp open reading frame that encoded 102 amino acids. Reverse transcription-PCR results showed that Mjdap-1 was expressed in all tested tissues, including hemocytes, gills, intestines, stomach, heart, hepatopancreas, testes, and ovaries. In shrimp, Mjdap-1 transcripts were up-regulated by white spot syndrome virus (WSSV) infection; Mjdap-1 knockdown decreased the virus copy in vivo and the mortality of M. japonicus to WSSV challenge. Conversely, injecting the purified recombinant MjDAP1 protein promoted the amplification of virus in shrimp. Flow cytometric assay showed, the virus infection-induced apoptosis of hemocytes was enhanced by MjDAP1 protein injection and inhibited in MjDAP1 knockdown shrimp. Furthermore, the expression of apoptosis-inducing factor (AIF) was regulated by Mjdap-1, but the caspase transcripts were not affected. Our results suggested that MjDAP1 facilitated the amplification of virus in shrimp, which may be attributed to the promotion of hemocyte apoptosis in an AIF-dependent manner. These results provided a new insight into the function of this protein that may be used for virus disease control.
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Affiliation(s)
- Wen-Li Xia
- The Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100, China
| | - Li-Hua Kang
- The Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100, China
| | - Chang-Bin Liu
- The Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100, China
| | - Cui-Jie Kang
- The Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100, China.
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Chu WT, Clarke J, Shammas SL, Wang J. Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1. PLoS Comput Biol 2017; 13:e1005468. [PMID: 28369057 PMCID: PMC5400261 DOI: 10.1371/journal.pcbi.1005468] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/21/2017] [Accepted: 03/20/2017] [Indexed: 11/23/2022] Open
Abstract
PUMA, which belongs to the BH3-only protein family, is an intrinsically disordered protein (IDP). It binds to its cellular partner Mcl-1 through its BH3 motif, which folds upon binding into an α helix. We have applied a structure-based coarse-grained model, with an explicit Debye-Hückel charge model, to probe the importance of electrostatic interactions both in the early and the later stages of this model coupled folding and binding process. This model was carefully calibrated with the experimental data on helical content and affinity, and shown to be consistent with previously published experimental data on binding rate changes with respect to ionic strength. We find that intramolecular electrostatic interactions influence the unbound states of PUMA only marginally. Our results further suggest that intermolecular electrostatic interactions, and in particular non-native electrostatic interactions, are involved in formation of the initial encounter complex. We are able to reveal the binding mechanism in more detail than is possible using experimental data alone however, and in particular we uncover the role of non-native electrostatic interactions. We highlight the potential importance of such electrostatic interactions for describing the binding reactions of IDPs. Such approaches could be used to provide predictions for the results of mutational studies.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, United Kingdom
| | - Sarah L. Shammas
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, United Kingdom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, New York, United States of America
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Banjara S, Caria S, Dixon LK, Hinds MG, Kvansakul M. Structural Insight into African Swine Fever Virus A179L-Mediated Inhibition of Apoptosis. J Virol 2017; 91:e02228-16. [PMID: 28053104 PMCID: PMC5331815 DOI: 10.1128/jvi.02228-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 12/21/2016] [Indexed: 11/20/2022] Open
Abstract
Programmed cell death is a tightly controlled process critical for the removal of damaged or infected cells. Pro- and antiapoptotic proteins of the Bcl-2 family are pivotal mediators of this process. African swine fever virus (ASFV) is a large DNA virus, the only member of the Asfarviridae family, and harbors A179L, a putative Bcl-2 like protein. A179L has been shown to bind to several proapoptotic Bcl-2 proteins; however, the hierarchy of binding and the structural basis for apoptosis inhibition are currently not understood. We systematically evaluated the ability of A179L to bind proapoptotic Bcl-2 family members and show that A179L is the first antiapoptotic Bcl-2 protein to bind to all major death-inducing mammalian Bcl-2 proteins. We then defined the structural basis for apoptosis inhibition of A179L by determining the crystal structures of A179L bound to both Bid and Bax BH3 motifs. Our findings provide a mechanistic understanding for the potent antiapoptotic activity of A179L by identifying it as the first panprodeath Bcl-2 binder and serve as a platform for more-detailed investigations into the role of A179L during ASFV infection.IMPORTANCE Numerous viruses have acquired strategies to subvert apoptosis by encoding proteins capable of sequestering proapoptotic host proteins. African swine fever virus (ASFV), a large DNA virus and the only member of the Asfarviridae family, encodes the protein A179L, which functions to prevent apoptosis. We show that A179L is unusual among antiapoptotic Bcl-2 proteins in being able to physically bind to all core death-inducing mammalian Bcl-2 proteins. Currently, little is known regarding the molecular interactions between A179L and the proapoptotic Bcl-2 members. Using the crystal structures of A179L bound to two of the identified proapoptotic Bcl-2 proteins, Bid and Bax, we now provide a three-dimensional (3D) view of how A179L sequesters host proapoptotic proteins, which is crucial for subverting premature host cell apoptosis.
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Affiliation(s)
- Suresh Banjara
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sofia Caria
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | | | - Mark G Hinds
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Marc Kvansakul
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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Zheng J, Mao Y, Su Y, Wang J. Effects of nitrite stress on mRNA expression of antioxidant enzymes, immune-related genes and apoptosis-related proteins in Marsupenaeus japonicus. Fish Shellfish Immunol 2016; 58:239-252. [PMID: 27582290 DOI: 10.1016/j.fsi.2016.08.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/23/2016] [Accepted: 08/26/2016] [Indexed: 06/06/2023]
Abstract
Nitrite accumulation in aquaculture systems is a potential risk factor that may trigger stress responses in aquatic organisms. However, the mechanisms regulating the responses of shrimp to nitrite stress remain unclear. In this study, full-length cDNA sequences of two apoptosis-related genes, caspase-3 and defender against apoptotic death (DAD-1), were cloned from Marsupenaeus japonicus for the first time, and their expression levels and tissue distribution were analyzed by quantitative real-time PCR (qRT-PCR). The full lengths of Mjcaspase-3 and MjDAD-1 were 1203 bp and 640 bp respectively, with deduced amino acid (AA) sequences of 321 and 114 AA. Mjcaspase-3 was predominantly expressed in haemocytes and weakly expressed in the seven other tissues tested. MjDAD-1 was mainly expressed in the defense and digestive tissues, especially in the hepatopancreas and hemocytes. To explore the influence of nitrite stress on the genetic response of antioxidant enzymes, immune-related genes and apoptosis-related proteins, the mRNA expression profiles of MjCAT, MjMnSOD, Mj-ilys, Mj-sty, Mjcaspase-3 and MjDAD-1 in response to nitrite stress were analyzed by qRT-PCR. The mRNA levels of MjCAT, MjMnSOD, Mj-ilys, Mj-sty, Mjcaspase-3 and MjDAD-1 show both time- and dose-dependent changes in response to nitrite stress. The mRNA expression levels of MjCAT and MjSOD peaked at 6 h for all nitrite concentrations tested (p < 0.05) and the up-regulated of MjCAT and MjSOD exhibited a positive correlation with the nitrite concentration. The mRNA expression levels of Mj-ilys and Mj-sty gradually decreased during the experiment period. Mjcaspase-3 mRNA level reached a maximum at 6 h (p < 0.05), and MjDAD-1 reached its peak at 12 h and 48 h in 10 mg/L and 20 mg/L nitrite, respectively. In addition, CAT and SOD activity showed changes in response to nitrite stress that mirrored the induced expression of MjCAT and MjMnSOD, and prolonged nitrite exposure reduced the activity of CAT. This study provided basic data for further elucidating the responses of shrimp to nitrite stress at the molecular level.
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Affiliation(s)
- Jinbin Zheng
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yong Mao
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
| | - Yongquan Su
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Jun Wang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
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