title: A systems biology analysis of apoptosome formation and apoptosis execution supports allosteric procaspase-9 activation.
abstract: The protease caspase-9 is activated on the apoptosome, a multiprotein signal transduction platform that assembles in response to mitochondria-dependent apoptosis initiation. Despite extensive molecular research, the assembly of the holo-apoptosome and the process of caspase-9 activation remain incompletely understood. Here, we therefore integrated quantitative data on the molecular interactions and proteolytic processes during apoptosome formation and apoptosis execution and conducted mathematical simulations to investigate the resulting biochemical signaling, quantitatively and kinetically. Interestingly, when implementing the homodimerization of procaspase-9 as a prerequisite for activation, the calculated kinetics of apoptosis execution and the efficacy of caspase-3 activation failed to replicate experimental data. In contrast, assuming a scenario in which procaspase-9 is activated allosterically upon binding to the apoptosome backbone, the mathematical simulations quantitatively and kinetically reproduced all experimental data. These data included a XIAP threshold concentration at which apoptosis execution is suppressed in HeLa cervical cancer cells, half-times of procaspase-9 processing, as well as the molecular timer function of the apoptosome. Our study therefore provides novel mechanistic insight into apoptosome-dependent apoptosis execution and suggests that caspase-9 is activated allosterically by binding to the apoptosome backbone. Our findings challenge the currently prevailing dogma that all initiator procaspases require homodimerization for activation.
authors.affiliation: Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland.
authors.forename: Maximilian L
authors.initials: ML
authors.lastname: Würstle
authors.affiliation: Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland. Electronic address: mrehm@rcsi.ie.
authors.forename: Markus
authors.initials: M
authors.lastname: Rehm
mesh_terms: D000494:Allosteric Regulation; D017209:Apoptosis; D053478:Apoptosomes / Q000737:chemistry / Q000502:physiology*; D053477:Apoptotic Protease-Activating Factor 1 / Q000737:chemistry / Q000502:physiology; D053453:Caspase 9 / Q000737:chemistry / Q000502:physiology*; D020134:Catalytic Domain; D003198:Computer Simulation; D004789:Enzyme Activation; D006367:HeLa Cells; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D011485:Protein Binding; D055503:Protein Multimerization; D011498:Protein Precursors / Q000737:chemistry / Q000502:physiology*; D049490:Systems Biology
chemical_list: C506592:APAF1 protein, human; D053478:Apoptosomes; D053477:Apoptotic Protease-Activating Factor 1; D011498:Protein Precursors; C506433:CASP9 protein, human; D053453:Caspase 9
keywords: Apaf-1; Apoptosis; Apoptosome; Caspase; Caspase-3; Caspase-9; Cell Death; Computational Biology; Systems Biology
references.citation: Cell Death Differ. 2013 Nov;20(11):1521-31
references.pmid: 23933815
references.citation: Cell. 1997 Aug 8;90(3):405-13
references.pmid: 9267021
references.citation: J Biol Chem. 2009 Nov 20;284(47):32717-24
references.pmid: 19801675
references.citation: Structure. 2010 May 12;18(5):571-83
references.pmid: 20462491
references.citation: Cell Death Differ. 2012 Jan;19(1):13-20
references.pmid: 22095286
references.citation: J Med Chem. 2006 Jun 29;49(13):3763-5
references.pmid: 16789732
references.citation: Mol Cell. 2008 Apr 25;30(2):239-47
references.pmid: 18439902
references.citation: Exp Cell Res. 2012 Jul 1;318(11):1269-77
references.pmid: 22542855
references.citation: J Biol Chem. 2012 Nov 30;287(49):41546-59
references.pmid: 23038270
references.citation: J Cell Biol. 2004 Sep 13;166(6):839-51
references.pmid: 15364960
references.citation: Cell. 1996 Jul 12;86(1):147-57
references.pmid: 8689682
references.citation: PLoS Biol. 2005 Jun;3(6):e183
references.pmid: 15941357
references.citation: J Biol Chem. 1999 Mar 26;274(13):8359-62
references.pmid: 10085063
references.citation: Genes Dev. 1999 Dec 15;13(24):3179-84
references.pmid: 10617566
references.citation: Mol Cell. 2007 Nov 30;28(4):624-37
references.pmid: 18042457
references.citation: Cell. 1997 Nov 14;91(4):479-89
references.pmid: 9390557
references.citation: EMBO J. 2012 Mar 7;31(5):1279-92
references.pmid: 22246185
references.citation: Mol Cell. 2008 Apr 11;30(1):11-25
references.pmid: 18406323
references.citation: Mol Cell. 2003 Feb;11(2):529-41
references.pmid: 12620239
references.citation: Cell Death Dis. 2014 May 29;5:e1259
references.pmid: 24874731
references.citation: Structure. 2013 Apr 2;21(4):501-15
references.pmid: 23561633
references.citation: Cell Death Dis. 2013 May 16;4:e629
references.pmid: 23681224
references.citation: J Cell Biol. 1999 Jan 25;144(2):281-92
references.pmid: 9922454
references.citation: Structure. 2011 Aug 10;19(8):1074-83
references.pmid: 21827944
references.citation: J Biol Chem. 2009 Aug 14;284(33):21777-21781
references.pmid: 19473994
references.citation: EMBO J. 2006 Sep 20;25(18):4338-49
references.pmid: 16932741
references.citation: J Biol Chem. 2012 May 25;287(22):18573-83
references.pmid: 22493447
references.citation: J Biol Chem. 2008 Aug 8;283(32):22105-12
references.pmid: 18550520
references.citation: J Mol Biol. 2004 Oct 8;343(1):1-28
references.pmid: 15381417
references.citation: J Biol Chem. 2001 May 4;276(18):14545-8
references.pmid: 11278258
references.citation: J Cell Biol. 2003 Sep 15;162(6):1031-43
references.pmid: 12975347
references.citation: Nat Cell Biol. 2000 Mar;2(3):156-62
references.pmid: 10707086
references.citation: Structure. 2011 Aug 10;19(8):1084-96
references.pmid: 21827945
references.citation: Mol Cell. 2006 Apr 21;22(2):259-68
references.pmid: 16630893
references.citation: Cell Death Differ. 2008 Feb;15(2):322-31
references.pmid: 17975551
references.citation: J Biol Chem. 2000 Oct 6;275(40):31199-203
references.pmid: 10940292
references.citation: J Biol Chem. 1999 Aug 6;274(32):22686-92
references.pmid: 10428850
references.citation: Br J Pharmacol. 2007 Dec;152(7):1012-20
references.pmid: 17906689
references.citation: Mol Cell. 1998 Jun;1(7):949-57
references.pmid: 9651578
references.citation: J Cell Biol. 2001 Apr 16;153(2):319-28
references.pmid: 11309413
references.citation: J Biol Chem. 2011 Dec 30;286(52):44457-66
references.pmid: 22065589
references.citation: Mol Cell. 2002 Feb;9(2):423-32
references.pmid: 11864614
references.citation: Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4197-202
references.pmid: 11904389
references.citation: Hepatology. 2000 Oct;32(4 Pt 1):750-60
references.pmid: 11003619
references.citation: Biochim Biophys Acta. 2008 Oct;1783(10):1903-13
references.pmid: 18590777
references.citation: Mol Cell. 2003 Feb;11(2):519-27
references.pmid: 12620238
references.citation: J Biol Chem. 2000 Mar 3;275(9):6067-70
references.pmid: 10692394
references.citation: J Biol Chem. 2004 May 7;279(19):19665-82
references.pmid: 14993223
references.citation: J Biol Chem. 2003 Mar 7;278(10):8091-8
references.pmid: 12506111
references.citation: Exp Cell Res. 2012 Jul 1;318(11):1213-20
references.pmid: 22406265
references.citation: Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):11928-31
references.pmid: 11035811
references.citation: EMBO J. 2001 Mar 1;20(5):998-1009
references.pmid: 11230124
references.citation: Proc Natl Acad Sci U S A. 2001 Dec 4;98(25):14250-5
references.pmid: 11734640
references.citation: EMBO J. 2004 May 19;23(10):2134-45
references.pmid: 15103327
references.citation: Biochem Pharmacol. 1973 Dec 1;22(23):3099-108
references.pmid: 4202581
references.citation: Science. 2003 Jan 10;299(5604):223-6
references.pmid: 12522243
references.citation: Cell. 2011 Mar 18;144(6):926-39
references.pmid: 21414484
references.citation: Front Biosci. 2007 May 01;12:3343-54
references.pmid: 17485304
references.citation: J Cell Sci. 2011 Oct 15;124(Pt 20):3450-63
references.pmid: 21984814
references.citation: EMBO J. 2009 Jul 8;28(13):1916-25
references.pmid: 19494828
references.citation: Mol Cell. 2006 Apr 21;22(2):269-75
references.pmid: 16630894
references.citation: Cell. 2004 Jun 25;117(7):855-8
references.pmid: 15210107
references.citation: Nature. 1999 Jun 10;399(6736):549-57
references.pmid: 10376594
references.citation: PLoS Comput Biol. 2006 Sep 15;2(9):e120
references.pmid: 16978046
references.citation: Cell Death Differ. 2004 Nov;11(11):1179-91
references.pmid: 15257302
references.citation: Cell Death Dis. 2014 May 29;5:e1258
references.pmid: 24874730
references.citation: Nat Rev Mol Cell Biol. 2007 May;8(5):405-13
references.pmid: 17377525