Solution Structure of Apaf-1 CARD and Its Interaction with Caspase-9 CARD: a Structural Basis for Specific Adaptor͞caspase Interaction
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Α Are Regulated by Heat Shock Protein 90
The Levels of Retinoic Acid-Inducible Gene I Are Regulated by Heat Shock Protein 90- α Tomoh Matsumiya, Tadaatsu Imaizumi, Hidemi Yoshida, Kei Satoh, Matthew K. Topham and Diana M. Stafforini This information is current as of October 2, 2021. J Immunol 2009; 182:2717-2725; ; doi: 10.4049/jimmunol.0802933 http://www.jimmunol.org/content/182/5/2717 Downloaded from References This article cites 44 articles, 19 of which you can access for free at: http://www.jimmunol.org/content/182/5/2717.full#ref-list-1 Why The JI? Submit online. http://www.jimmunol.org/ • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average by guest on October 2, 2021 Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2009 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology The Levels of Retinoic Acid-Inducible Gene I Are Regulated by Heat Shock Protein 90-␣1 Tomoh Matsumiya,*‡ Tadaatsu Imaizumi,‡ Hidemi Yoshida,‡ Kei Satoh,‡ Matthew K. Topham,*† and Diana M. Stafforini2*† Retinoic acid-inducible gene I (RIG-I) is an intracellular pattern recognition receptor that plays important roles during innate immune responses to viral dsRNAs. -
MINI-REVIEW Programmed Cell Death Regulation
Leukemia (2000) 14, 1340–1344 2000 Macmillan Publishers Ltd All rights reserved 0887-6924/00 $15.00 www.nature.com/leu MINI-REVIEW Programmed cell death regulation: basic mechanisms and therapeutic opportunities DE Johnson Departments of Medicine and Pharmacology, University of Pittsburgh, and the University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA The molecular mechanisms responsible for induction or inhi- pH changes during apoptosis bition of apoptosis signal transduction have been intensively investigated during the past few years. Information gained from mechanistic studies and from structural analysis of apoptosis With respect to regulation of intracellular pH during regulatory proteins has provided considerable insight into the apoptosis, Dr Roberta Gottlieb reported that neutrophils pathways that determine whether a cell will live or die. Many deprived of G-CSF exhibit rapid cytosolic acidification, with of these advances were recently presented at the American cells typically reaching a pH of 6.6. Similar results were seen Association for Cancer Research Special Conference on ‘Pro- in Jurkat T leukemic cells undergoing Fas-mediated grammed Cell Death Regulation: Basic Mechanisms and Thera- apoptosis.1 Acidification was found to be concurrent with peutic Opportunities’. This mini-review will discuss the current state of knowledge regarding apoptosis signaling pathways phosphatidyl serine (PS) externalization, and it was proposed and the function of apoptosis regulatory proteins. Leukemia that the pH sensitivity of the enzyme responsible for flipping (2000) 14, 1340–1344. PS may account for this commonly observed apoptotic event. Keywords: apoptosis; mitochondria; Bcl-2; caspase; IAP; TRAIL Dr Gottlieb also observed that cytoplasmic acidification pre- cedes loss of mitochondrial membrane potential, and can be blocked by expression of Bcl-2. -
The Caenorhabditis Elegans Cell-Death Protein CED-3 Is a C.Y.Ste!Ne P.Rotease with Substrate Specl[Icltles S M Lar to Those of the Human CPP32 Protease
Downloaded from genesdev.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press The Caenorhabditis elegans cell-death protein CED-3 is a c.y.ste!ne p.rotease with substrate specl[iCltles s m lar to those of the human CPP32 protease Ding Xue, Shai Shaham, and H. Robert Horvitz Howard Hughes Medical Institute, Department of Biology, 68-425, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA The Caenorhabditis elegans cell-death gene ced-3 encodes a protein similar to mammalian interleukin-l[3-converting enzyme (ICE), a cysteine protease implicated in mammalian apoptosis. We show that the full-length CED-3 protein undergoes proteolytic activation to generate a CED-3 cysteine protease and that CED-3 protease activity is required for killing cells by programmed cell death in C. elegans. We developed an easy and general method for the purification of CED-3/ICE-Iike proteases and used this method to facilitate a comparison of the substrate specificities of four different purified cysteine proteases. We found that in its substrate preferences CED-3 was more similar to the mammalian CPP32 protease than to mammalian ICE or NEDD2/ICH-1 protease. Our results suggest that different mammalian CED-3/ICE-Iike proteases may have distinct roles in mammalian apoptosis and that CPP32 is a candidate for being a mammalian functional equivalent of CED-3. [Key Words: Programmed cell death; cysteine proteases; ced-3; C. elegans; substrate specificities] Received February 28, 1996; revised version accepted March 19, 1996. Programmed cell death is a fundamental cellular process tween ICE and CED-3 suggested that CED-3 may act as in the development and homeostasis of both vertebrates a protease to cause programmed cell death in C. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
New Tricks for Old Nods Eric M Pietras* and Genhong Cheng*†‡
Minireview New tricks for old NODs Eric M Pietras* and Genhong Cheng*†‡ Addresses: *Department of Microbiology, Immunology and Molecular Genetics, †Molecular Biology Institute, ‡Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA 90095, USA. Correspondence: Genhong Cheng. Email: [email protected] Published: 25 April 2008 Genome Biology 2008, 9:217 (doi:10.1186/gb-2008-9-4-217) The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2008/9/4/217 © 2008 BioMed Central Ltd Abstract Recent work has identified the human NOD-like receptor NLRX1 as a negative regulator of intracellular signaling leading to type I interferon production. Here we discuss these findings and the questions and implications they raise regarding the function of NOD-like receptors in the antiviral response. Upon infection with a pathogen, the host cell must recognize with a single amino-terminal CARD in the adaptor protein its presence, communicate this to neighboring cells and MAVS (also known as IPS-1, VISA or Cardif), which is tissues and initiate a biological response to limit the spread anchored to the outer mitochondrial membrane [4-7]. MAVS of infection and clear the pathogen. Recognition of invading complexes with the adaptor protein TRAF3, recruiting the microbes proceeds via specialized intracellular and extra- scaffold protein TANK and the IκB kinases (IKKs) TANK- cellular proteins termed pattern recognition receptors (PRRs), binding kinase 1 (TBK1) and IKKε, which activate the trans- which recognize conserved molecular motifs found on patho- cription factor IRF3. IRF3 activation leads to the trans- gens, known as pathogen-associated molecular patterns criptional activation of a number of antiviral genes, includ- (PAMPs). -
Regulation of Caspase-9 by Natural and Synthetic Inhibitors Kristen L
University of Massachusetts Amherst ScholarWorks@UMass Amherst Open Access Dissertations 5-2012 Regulation of Caspase-9 by Natural and Synthetic Inhibitors Kristen L. Huber University of Massachusetts Amherst, [email protected] Follow this and additional works at: https://scholarworks.umass.edu/open_access_dissertations Part of the Chemistry Commons Recommended Citation Huber, Kristen L., "Regulation of Caspase-9 by Natural and Synthetic Inhibitors" (2012). Open Access Dissertations. 554. https://doi.org/10.7275/jr9n-gz79 https://scholarworks.umass.edu/open_access_dissertations/554 This Open Access Dissertation is brought to you for free and open access by ScholarWorks@UMass Amherst. It has been accepted for inclusion in Open Access Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. REGULATION OF CASPASE-9 BY NATURAL AND SYNTHETIC INHIBITORS A Dissertation Presented by KRISTEN L. HUBER Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY MAY 2012 Chemistry © Copyright by Kristen L. Huber 2012 All Rights Reserved REGULATION OF CASPASE-9 BY NATURAL AND SYNTHETIC INHIBITORS A Dissertation Presented by KRISTEN L. HUBER Approved as to style and content by: _________________________________________ Jeanne A. Hardy, Chair _________________________________________ Lila M. Gierasch, Member _________________________________________ Robert M. Weis, -
Subcellular Localization and CARD-Dependent Oligomerization of the Death Adaptor RAIDD
Cell Death and Differentiation (2000) 7, 155 ± 165 ã 2000 Macmillan Publishers Ltd. All rights reserved 1350-9047/00 $15.00 www.nature.com/cdd Subcellular localization and CARD-dependent oligomerization of the death adaptor RAIDD 1 1 ,1, 2 LM Shearwin-Whyatt , NL Harvey and S Kumar* Introduction 1 Hanson Centre for Cancer Research, Institute of Medical and Veterinary The execution phase of apoptosis involves the activation of a Science, Frome Road, Adelaide, Australia family of cysteine proteases termed caspases.1±3 The fully 2 Department of Medicine, The University of Adelaide, Australia mature, catalytically active caspases are comprised of a * Corresponding author: S Kumar, Hanson Centre for Cancer Research, IMVS, heterotetramer made of two subunits derived from the PO Box 14, Rundle Mall, Adelaide, SA 5000, Australia. Tel: +61-8-8222-3738; proteolytic processing of the caspase precursors. In addition Fax: +61-8-8222-3139; E-mail: [email protected] to the region that gives rise to the two subunits of the active enzyme, procaspase molecules contain an amino terminal Received 7.7.99; revised 13.9.99; accepted 2.11.99 prodomain of varying length. Caspases have been subdivided Edited by S Martin into two classes on the basis of the length of their prodomains.4 Class I caspases, including caspase-2, -8, -9 and -10, contain long prodomains and class II caspases, Abstract including caspase-3, -6 and -7, lack or contain short prodomains. To some extent, this division also reflects a RAIDD, a caspase recruitment domain (CARD) containing functional hierarchy within the caspase family, with class I molecule, interacts with procaspase-2 in a CARD-dependent caspases lying upstream of class II caspases in the apoptotic manner. -
Sharmin Supple Legend 150706
Supplemental data Supplementary Figure 1 Generation of NPHS1-GFP iPS cells (A) TALEN activity tested in HEK 293 cells. The targeted region was PCR-amplified and cloned. Deletions in the NPHS1 locus were detected in four clones out of 10 that were sequenced. (B) PCR screening of human iPS cell homologous recombinants (C) Southern blot screening of human iPS cell homologous recombinants Supplementary Figure 2 Human glomeruli generated from NPHS1-GFP iPS cells (A) Morphological changes of GFP-positive glomeruli during differentiation in vitro. A different aggregate from the one shown in Figure 2 is presented. Lower panels: higher magnification of the areas marked by rectangles in the upper panels. Note the shape changes of the glomerulus (arrowheads). Scale bars: 500 µm. (B) Some, but not all, of the Bowman’s capsule cells were positive for nephrin (48E11 antibody: magenta) and GFP (green). Scale bars: 10 µm. Supplementary Figure 3 Histology of human podocytes generated in vitro (A) Transmission electron microscopy of the foot processes. Lower magnification of Figure 4H. Scale bars: 500 nm. (B) (C) The slit diaphragm between the foot processes. Higher magnification of the 1 regions marked by rectangles in panel A. Scale bar: 100 nm. (D) Absence of mesangial or vascular endothelial cells in the induced glomeruli. Anti-PDGFRβ and CD31 antibodies were used to detect the two lineages, respectively, and no positive signals were observed in the glomeruli. Podocytes are positive for WT1. Nuclei are counterstained with Nuclear Fast Red. Scale bars: 20 µm. Supplementary Figure 4 Cluster analysis of gene expression in various human tissues (A) Unbiased cluster analysis across various human tissues using the top 300 genes enriched in GFP-positive podocytes. -
The Death Domain Superfamily in Intracellular Signaling of Apoptosis and Inflammation
ANRV306-IY25-19 ARI 11 February 2007 12:51 The Death Domain Superfamily in Intracellular Signaling of Apoptosis and Inflammation Hyun Ho Park,1 Yu-Chih Lo,1 Su-Chang Lin,1 Liwei Wang,1 Jin Kuk Yang,1,2 and Hao Wu1 1Department of Biochemistry, Weill Medical College and Graduate School of Medical Sciences of Cornell University, New York, New York 10021; email: [email protected] 2Department of Chemistry, Soongsil University, Seoul 156-743, Korea Annu. Rev. Immunol. 2007. 25:561–86 Key Words First published online as a Review in Advance on death domain (DD), death effector domain (DED), tandem DED, January 2, 2007 caspase recruitment domain (CARD), pyrin domain (PYD), crystal The Annual Review of Immunology is online at structure, NMR structure immunol.annualreviews.org This article’s doi: Abstract 10.1146/annurev.immunol.25.022106.141656 The death domain (DD) superfamily comprising the death domain Copyright c 2007 by Annual Reviews. (DD) subfamily, the death effector domain (DED) subfamily, the Annu. Rev. Immunol. 2007.25:561-586. Downloaded from arjournals.annualreviews.org by CORNELL UNIVERSITY MEDICAL COLLEGE on 03/29/07. For personal use only. All rights reserved caspase recruitment domain (CARD) subfamily, and the pyrin do- 0732-0582/07/0423-0561$20.00 main (PYD) subfamily is one of the largest domain superfamilies. By mediating homotypic interactions within each domain subfam- ily, these proteins play important roles in the assembly and activation of apoptotic and inflammatory complexes. In this chapter, we review the molecular complexes assembled by these proteins, the structural and biochemical features of these domains, and the molecular in- teractions mediated by them. -
Mechanisms of Cell Death: Molecular Insights and Therapeutic Perspectives
Cell Death and Differentiation (2005) 12, 1449–1456 & 2005 Nature Publishing Group All rights reserved 1350-9047/05 $30.00 www.nature.com/cdd Meeting Report Mechanisms of cell death: molecular insights and therapeutic perspectives LF Dı´az1, M Chiong1, AFG Quest*,1, S Lavandero*,1 and A Stutzin*,1 1 Centro FONDAP de Estudios Moleculares de la Ce´lula, Facultades de Medicina y Ciencias Quı´micas y Farmace´uticas, Universidad de Chile, Independencia 1027, Santiago 838-0453, Chile * Corresponding authors: A Stutzin, AFG Quest, S Lavandero, Centro FONDAP de Estudios Moleculares de la Ce´lula, Facultad de Medicina Universidad de Chile, Independencia 1027, Santiago 838-0453, Chile. Tel: þ 56-2-6786494; Fax: þ 56-2-7376240; E-mail: [email protected], [email protected], [email protected] Cell Death and Differentiation (2005) 12, 1449–1456. doi:10.1038/sj.cdd.4401738; published online 29 July 2005 The International Symposium ‘Mechanisms of Cell Death: Molecular Insights and Therapeutic Perspectives’. Conference Town, Ren˜aca, Chile, 13–16 April 2005. The International Symposium ‘Mechanisms of Cell Death: The development of a function-based gene trapping Molecular Insights and Therapeutic Perspectives’, Confer- strategy based on the use of antisense cDNA libraries leads ence Town, Ren˜aca, Chile, 13–16 April 2005, was held at the to the identification of novel death-promoting (DAP) genes. beachside Conference Town resort of Ren˜aca, close to Galit Shohat and Adi Kimchi (Weizmann Institute of Science, Valparaı´so and some 100 km west from the capital city of Rehovot, Israel) discussed the family of DAP kinases (DAPk) Santiago. -
©Ferrata Storti Foundation
Original Articles T-cell/histiocyte-rich large B-cell lymphoma shows transcriptional features suggestive of a tolerogenic host immune response Peter Van Loo,1,2,3 Thomas Tousseyn,4 Vera Vanhentenrijk,4 Daan Dierickx,5 Agnieszka Malecka,6 Isabelle Vanden Bempt,4 Gregor Verhoef,5 Jan Delabie,6 Peter Marynen,1,2 Patrick Matthys,7 and Chris De Wolf-Peeters4 1Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium; 2Department of Human Genetics, K.U.Leuven, Leuven, Belgium; 3Bioinformatics Group, Department of Electrical Engineering, K.U.Leuven, Leuven, Belgium; 4Department of Pathology, University Hospitals K.U.Leuven, Leuven, Belgium; 5Department of Hematology, University Hospitals K.U.Leuven, Leuven, Belgium; 6Department of Pathology, The Norwegian Radium Hospital, University of Oslo, Oslo, Norway, and 7Department of Microbiology and Immunology, Rega Institute for Medical Research, K.U.Leuven, Leuven, Belgium Citation: Van Loo P, Tousseyn T, Vanhentenrijk V, Dierickx D, Malecka A, Vanden Bempt I, Verhoef G, Delabie J, Marynen P, Matthys P, and De Wolf-Peeters C. T-cell/histiocyte-rich large B-cell lymphoma shows transcriptional features suggestive of a tolero- genic host immune response. Haematologica. 2010;95:440-448. doi:10.3324/haematol.2009.009647 The Online Supplementary Tables S1-5 are in separate PDF files Supplementary Design and Methods One microgram of total RNA was reverse transcribed using random primers and SuperScript II (Invitrogen, Merelbeke, Validation of microarray results by real-time quantitative Belgium), as recommended by the manufacturer. Relative reverse transcriptase polymerase chain reaction quantification was subsequently performed using the compar- Ten genes measured by microarray gene expression profil- ative CT method (see User Bulletin #2: Relative Quantitation ing were validated by real-time quantitative reverse transcrip- of Gene Expression, Applied Biosystems). -
Caspases: a Decade of Death Research
Cell Death and Differentiation (1999) 6, 1023 ± 1027 ã 1999 Stockton Press All rights reserved 13509047/99 $15.00 http://www.stockton-press.co.uk/cdd Editorial Caspases: A decade of death research NA Thornberry*,1 the current thinking regarding the roles of these enzymes in cell death, and summarize some of the challenges that 1 Department of Enzymology and Protein Biochemistry, Merck Research remain for future research in this area. Laboratories, R80M-103, PO Box 2000, E. Lincoln Ave., Rahway, New Jersey 07065, USA * Corresponding author: NA Thornberry; Tel: +1 732-594-7120; Caspases and cell death Fax: +1 732-594-3664; E-mail: [email protected] As described in the overview of caspase structure and Edited by G Melino function by Nicholson, there are currently 11 human caspases. The precise biological functions of several of these enzymes remain to be established, but it is clear that they play pivitol and distinct roles in both inflammation and As the end of the millenium approaches, we reflect on the apoptosis, raising intriguing questions as to the evolutionary monumental advances in cell biology that have been relationships between these processes. The structural and in achieved, particularly in the last 50 years. Consider that vitro biochemical properties of these proteases are well proteins were first found to have precise amino acid understood; on several counts, these enzymes are perfectly sequences in 1953 by Sanger, about the same time that engineered to implement the highly coordinated and regulated Watson and Crick deduced the three-dimensional structure of events of apoptosis. DNA. In this context, it seems remarkable that we now have For example, the well ordered and specific cleavages of such an intimate understanding of at least some basic cellular proteins that are required to mediate apoptosis require a mechanisms, thanks largely to relatively recent advances in proteolytic machinery that is highly discriminatory.