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    interacting partners in various species are important

    steps towards understanding the control of this crucial

    process. The contribution of Dcp1 and Hedls to Dcp2

    activation can now be explored at the molecular level.

    Further cellular, structural and enzymatic analyses will

    undoubtedly reveal new interacting partners of the

    decapping complex and enable the mechanism that leads

    to the irrevocable decision to activate decapping to

    be deciphered.

    AcknowledgementsWe thank Andrzej Dziembowski for his help with the PyMOL software

    and members of the Seraphin laboratory for their support. This work was

    supported by La Ligue contre le Cancer (Equipe Labellisee 2005), the

    CNRS and the Ministry of Research (ACI BCMS).

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    2 Coller, J. and Parker, R. (2004) Eukaryotic mRNA decapping. Annu.

    Rev. Biochem. 73, 861890

    3 Cougot, N. et al. (2004) Cap-tabolism. Trends Biochem. Sci. 29,

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    4 Stoecklin, G. et al. (2006) ARE-mRNA degradation requires the 50

    30

    decay pathway. EMBO Rep. 7, 7277

    5 Yamashita, A. et al. (2005) Concerted action of poly(A) nucleases and

    decapping enzyme in mammalian mRNA turnover. Nat. Struct. Mol.

    Biol. 12, 10541063

    6 Lejeune, F. et al. (2003) Nonsense-mediated mRNA decay in

    mammalian cells involves decapping, deadenylating, and exonucleo-

    lytic activities. Mol. Cell 12, 675687

    7 Conti, E. and Izaurralde, E. (2005) Nonsense-mediated mRNA decay:

    molecular insights and mechanistic variations across species. Curr.

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    8 van Dijk, E. et al. (2002) Human Dcp2: a catalytically active mRNA

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    9 Wang, Z. et al. (2002) The hDcp2 protein is a mammalian mRNA

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    complex associated with hUpf proteins in nonsense-mediated decay.

    Mol. Cell. Biol. 22, 81148121

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    cytoplasmic foci. RNA 8, 14891501

    12 Eystathioy, T. etal. (2003) The GW182 protein colocalizes with mRNA

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    13 Sheth, U. and Parker, R. (2003) Decapping and decay of messengerRNA occur in cytoplasmic processing bodies. Science 300, 805808

    14 Cougot, N. et al. (2004) Cytoplasmic foci are sites of mRNA decay in

    human cells. J. Cell Biol. 165, 3140

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    Dcp2p from Schizosaccharomyces pombe. Nat. Struct. Mol. Biol. 13,

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    16 Fenger-Grn, M.et al. (2005) Multiple processing body factors and the

    ARE binding protein TTP activate mRNA decapping. Mol. Cell 20,

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    17 Steiger, M. et al. (2003) Analysis of recombinant yeast decapping

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    18 Beelman, C.A. et al. (1996) An essential component of the decapping

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    20 She, M. et al. (2004) Crystal structure of Dcp1p and its functional

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    0968-0004/$ - see front matter Q 2006 Elsevier Ltd. All rights reserved.

    doi:10.1016/j.tibs.2006.03.001

    Apoptosomes: protease activation platformsto die from

    Colin Adrain, Gabriela Brumatti and Seamus J. Martin

    Molecular Cell Biology Laboratory, Department of Genetics, The Smurfit Institute, Trinity College, Dublin 2, Ireland

    Apoptosis is orchestrated by members of the caspase

    family of cysteine proteases that exist as latent pro-

    enzymes in healthy cells. Caspase-activating platforms,

    called apoptosomes, initiate caspase activation in

    metazoans as diverse as nematodes and mammals.

    Several recent studies have generated new insights into

    the composition and assembly mechanisms of worm, fly

    and human apoptosomes.

    Apoptosomes promote caspase activation

    During apoptosis, cells actively participate in their own

    elimination by activating proteolytic enzymes, called

    caspases (for cysteine aspartic acid-specific proteases)

    [1]. Initiator caspases become activated at the onset of

    apoptosis and unleash a barrage of proteolytic activity

    within the cell by activating downstream (effector)

    caspases through direct proteolysis. Effector caspases

    dismantle cellular structures and shut down vital bio-

    chemical processes, resulting in controlled cell death and

    phagocyte-mediated removal of cell corpses [2,3]. AnCorresponding author: Martin, S.J. ([email protected]).

    Available online 3 April 2006

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    important route to caspase activation involves the

    assembly of caspase-activating complexes, called apopto-

    somes, in response to diverse forms of cellular stress [4].

    Three recent studies provide fresh insights into the

    composition of worm, fly and mammalian apoptosomes

    and highlight interesting differences between their

    symmetry and assembly mechanisms [57].

    Worm apoptosomes contain CED-4 tetramers

    A single caspase, CED (cell death abnormal)-3, is both

    necessary and sufficient for all developmental pro-

    grammed cell deaths that take place in the nematode

    C. elegans. Genetic and molecular studies have established

    that CED-3 is activated in response to developmental cues

    and that this requires its adapterprotein, CED-4. Normally,

    CED-4 is restrained from activating CED-3 through

    interaction with mitochondrion-tethered CED-9 [8,9].

    CED-9 can be neutralized by EGL-1 (egg-laying defective-

    1), which displaces it from CED-4 to trigger assembly of the

    CED-4CED-3 apoptosome [9]. Until now, the structure of

    the worm apoptosome was obscure.

    Shi and colleagues [5] have recently reconstituted the

    C. elegans cell-death pathway in vitro using purified

    proteins and have found that CED-4, in its inactive state,

    is an asymmetric dimer in complex with a single molecule

    of CED-9 (Figure 1a). Similar observations have also been

    made by Colman and colleagues [10], although these

    authors conclude that the inactive CED-4CED-9 complex

    possesses 2:2 stoichiometry. Assembly of the worm

    apoptosome seems to require CED-4 to further oligomerize

    into a tetrameric particle that functions as an activation

    platform for CED-3 [5]. This is achieved through

    TiBS

    CED-9 CED-4

    CED-3

    DARK

    DRONC

    DIAP1

    Inactive Active

    (a) Worm

    (b) Fly

    (c) Mammalian

    Apaf-1

    Caspase-9

    DRONC

    Caspase-9

    CED-3

    Cyt cdATP

    dATP

    ATP

    CED-4

    DARK

    Apaf-1

    EGL-1CED-13

    ReaperHid

    GrimSickle

    BH3-onlyproteins

    Figure 1. Assembly of worm, fly and human apoptosomes. (a) In the nematode worm, CED-4 (grey octagon) and CED-3 (red circle) can be induced to form apoptosomes

    throughdisplacement of the cell-death-inhibitory protein,CED-9(purple), fromCED-4 dimers.CED-9 canbe displaced by either of theBH3-onlyproteins EGL-1 or CED-13,and

    thispermitsthe further dimerizationof CED-4dimersto formtetramers thatcan activatethe CED-3 caspase. (b) In the fly, the CED-4-related protein,DARK (grey octagon),can

    oligomerize into an octameric structure that contains the CED-3-related protease DRONC (red circle). Fly apoptosomes are thought to be prevented from assemblingthrough

    inhibition of DRONC by DIAP1. DIAP1 can be neutralized by the small proteins Reaper, Hid, Grim or Sickle (which are induced in response to specific stimuli) and this permits

    assembly of the octameric fly apoptosome. (c) In mammals, the CED-4-related protein Apaf-1 can be induced to oligomerize into heptameric apoptosomes that contain

    caspase-9. Thisis controlled by a family of proteins(the BH3-onlymembers of theBcl-2 family) thatbecomeactivated in responseto death triggersand liberateCyt cfromthe

    mitochondrial intermembrane space. Cyt cacts as a co-factor for apoptosome assembly and, in association with dATP, triggers oligomerization of Apaf-1 and its association

    with caspase-9.

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    displacing CED-9 from the CED-4 dimer by the Bcl-2

    homology 3 (BH3)-only protein, EGL-1 (or the related

    CED-13), which induces a major conformational change in

    CED-9 and disrupts the binding interface between the

    latter and CED-4 [5]. The number of molecules of CED-3

    that become associated with the tetrameric CED-4

    apoptosome remains unclear, but this could be as many

    as eight if each CED-4 molecule recruits a CED-3

    homodimer into the complex (Figure 1a). Further studiesare needed to answer this question and also to provide a

    high-resolution view of the fully armed CED-4CED-

    3 apoptosome.

    Fly apoptosomes contain octamers of DARK

    In Drosophila, the CED-4 relative DARK (Drosophila

    Apaf-1-related killer) is essential for programmed cell

    death in many situations and this protein selectively

    interacts with the fly caspase DRONC (Drosophila Nedd2-

    like caspase) [11,12]. Although similar in domain organ-

    ization to CED-4, DARK is a substantially larger protein

    owing to the presence of multiple WD40 repeats at its C

    terminus; this region within DARK might have an auto-

    inhibitory function. Curiously, DRONC activation by

    DARK does not seem to be regulated by either of the two

    known fly relatives of CED-9. Indeed, it is not clear what

    role, if any, CED-9-related proteins have in the regulation

    of programmed cell death in the fly because data have yet

    to emerge to suggest that they function as important

    arbiters of cell fate in this organism. Instead, the fly death

    machinery is repressed mainly by the caspase-inhibitory

    protein Drosophila inhibitor-of-apoptosis protein 1

    (DIAP1) [13]. Inactivation of the gene encoding DIAP1

    results in widespread cell death, leading to lethality early

    in development. Thus, DIAP1 might constitutively associ-

    ate with fly caspases such as DRONC and prevent

    spontaneous activation of these proteases (Figure 1b).

    Akey and colleag ues have recent ly res olve d the

    structure of oligomerized DARK at 18.8 A using electron

    cryo-microscopy [6]. The active DARK apoptosome is an

    impressive wheel-like octamer that forms in the presence

    (a) Fly

    Top view Bottom view Domain model

    (b) Human

    Top view Bottom view Domain model

    CARD NBD HD1 WHD HD2 8 6

    CARD Cyt cNBD HD1 WHD HD2 7 6

    Figure 2. Structure of the fly and human apoptosomes. (a) Surface views (left and middle) and domain model (right) of the fly apoptosome. The fly apoptosome comprises

    eight molecules of DARK (depicted) and an, as yet, unknown number of molecules of the fly caspase DRONC (not shown). Assembly of the fly apoptosome from DARK

    monomers can be initiated through neutralization of the fly caspase-inhibitory protein, DIAP1, by Reaper, Hid or Grim. Assembled apoptosomes are likely to recruit several

    molecules of the DRONC protease (via the CARD domains of DARK that are located towards the centre of the apoptosome), which probably results in DRONC activation

    through an allosteric mechanism. (b) Surface views (left and middle) and domain model (right) of the human apoptosome. Assembly of Apaf-1 apoptosomes is initiated by

    theescapeof Cyt cfromthe mitochondrial intermembrane spaceinto the cytosol.This event is regulated by members of the Bcl-2familythat caneither promoteCyt crelease

    (BH3-only proteinsand the Baxsubfamily)or antagonizeit (Bcl-2, Bcl-xL andrelatedproteins).Cyt cpromotesApaf-1oligomerizationby interacting withthe C-terminal WD40

    repeats within Apaf-1, which fold into two b-propellers that are located towards the periphery of the structure. Assembled Apaf-1 apoptosomes recruit several molecules of

    caspase-9 (not shown) and promote auto-activation of this protease through an allosteric mechanism. Domains within DARK and Apaf-1 are colour-coded as indicated.

    Abbreviations: b, b propellers; CARD, caspase-recruitment domain; HD, helix domain; NBD, nucleotide-binding domain; WHD, winged-helix domain. Part (a) reproduced,

    with permission, from Ref. [6]; Part (b) reproduced, with permission, from Ref. [7].

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    of dATP (2 0-deoxyadenosine 50-triphosphate), but not ATP

    (Figures 1b and 2a). Interestingly, DARK apoptosomes

    were also found to further dimerize into double-wheeled

    structures, but the significance of this remains unclear at

    present. The number of DRONC molecules that become

    recruited to DARK apoptosomes is also not known because

    these were assembled in the absence of caspase, but it is

    likely that it is a similar number to that of DARK

    subunits. The natural trigger for oligomerization ofDARK is not yet clear and it remains possible that binding

    partners that repress spontaneous DARK oligomerization

    in vivo exist. It is also possible that DARK could exist in a

    pre-oligomerized state and that activation of the fly

    apoptosome is regulated at the level of DRONC recruit-

    ment into the complex. Activation of the fly apoptosome is

    controlled by three proteins Reaper, Hid and Grim the

    expression of which can be induced by various death

    stimuli [13,14]. Any one of these three proteins can

    neutralize DIAP1 and can either permit recruitment of

    DRONC into the apoptosome or unmask the activity of

    pre-recruited DRONC. The structure of the fully

    assembled fly apoptosome loaded with the DRONCprotease awaits determination.

    Human apoptosomes contain Apaf-1 heptamers

    In vertebrates, the CED-4-relative Apaf-1 constitutes the

    scaffold upon which the apoptosome is assembled [15].

    Like DARK, the C-terminal region of Apaf-1 contains

    multiple WD40 repeats, which are absent in CED-4, and

    these are involved in regulating the assembly of the Apaf-

    1 apoptosome. Although 12 human caspases have been

    identified, only one of these caspase-9 can associate

    with Apaf-1 to form apoptosomes [15,16]. Surprisingly,

    assembly of the human apoptosome is controlled by

    the electron-transport protein cytochrome c (Cyt c),

    which is released from mitochondria during apoptosis

    and triggers oligomerization of Apaf-1 into a wheel-like

    heptameric complex (Figures 1c and 2b). Although human

    relatives of CED-9 including Bcl-2 and Bcl-xL do

    regulate the assembly of Apaf-1 apoptosomes, this is

    achieved indirectly by regulating the release of Cyt c from

    the mitochondrial intermembrane space and not through

    direct interaction with Apaf-1 [17].

    A recent paper from Akey and colleagues has provided

    new views of the Apaf-1 apoptosome at 12.8 A resolution

    [7]. The human and fly apoptosomes are similar in overall

    structure, but a major difference is the number of subunits

    they contain (Figure 2). The central hub of the Apaf-1

    apoptosome is formed by lateral interactions between thenucleotide-binding and oligomerization domains. The hub

    is capped with a crown of caspase-recruitment domains

    (CARDs), which are the regions within Apaf-1 that are

    responsible for capturing caspase-9 molecules through a

    similar motif located at the N terminus of caspase-9.

    The spokes of the apoptosome are formed by the

    C-terminal WD-40 repeats, which fold into two b

    propellers to form a cleft that is likely to be important in

    regulating the propensity of Apaf-1 to oligomerize. To

    date, the precise location and number of Cyt c molecules

    within the human apoptosome has been obscure, although

    it has been proposed that Cyt c binding to the cleft within

    the Apaf-1 b propellers could trigger a conformational

    change that permits apoptosome oligomerization [18,19].

    Confirming this, Akey and colleagues docked a single

    molecule of Cyt c within this cleft, suggesting that Cyt c

    binds to Apaf-1 with a 1:1 stoichiometry [7]. However, it

    should be noted that the assignments of the b-propellers

    and Cyt c are based on docking experiments rather than

    genuine atomic structures. The current study by Akey and

    colleagues provides a strikingly detailed view of theassembled apoptosome, albeit lacking Caspase-9 [7], but,

    from previous studies, it is likely that the caspase forms a

    dome on top of the central hub [19] (Figure 2). However,

    the precise arrangement and number of caspase-9

    molecules within the Apaf-1 apoptosome remains to be

    determined. Consequently, it is also unclear how recruit-

    ment of caspase-9 to the apoptosome results in activation

    of this protease, although an allosteric mechanism

    is probable.

    Structural clues about apoptosome latency

    Alth ough assembl y of the worm, fly and human

    apoptosomes is regulated in different ways, they sharea common requirement for binding of ATP or dATP and

    an ability to form wheel-like oligomeric structures.

    Although there is no evidence at present that either

    CED-4 or DARK can hydrolyse the bound nucleotide, a

    recent study from Wang and colleagues indicates that

    dATP hydrolysis is essential for proper assembly of the

    Apaf-1 apoptosome [20]. In the absence of Cyt c, Apaf-1

    is monomeric, contains a single dATP molecule and

    cannot interact with Caspase-9. The new data suggest

    that Cyt c triggers a conformational change within Apaf-

    1 that is driven by hydrolysis of the bound dATP to

    dADP, followed by exchange for dATP and oligomeriza-

    tion of Apaf-1 into the heptameric complex that can then

    recruit and activate caspase-9 [7,20].

    Concluding remarks

    Recent studies have provided substantial insights into the

    structure of worm, fly and human apoptosomes but it

    should be noted that, in all cases, these apoptosomes have

    been built using recombinant proteins in the absence of

    their caspase partners. The isolation and characterization

    of native apoptosomes from apoptotic cells is likely to be a

    formidable challenge. In addition, several important

    questions remain unresolved. Although, it is clear that

    CED-3 is an integral part of the worm apoptosome, few

    substrates for this protease have yet to be identified. A

    similar lack of knowledge pertains to how DRONCcoordinates death in the fly, although, in this instance,

    at least two other proteases are activated downstream. It

    is also perplexing that, although CED-9 relatives have

    been found in the fly, they do not seem to have either a

    direct or indirect role in regulating assembly of the fly

    apoptosome. Neither does there seem to be a role for Cyt c

    in regulating fly apoptosomes, despite the structural

    similarity between Apaf-1 and DARK. In mammals, the

    Apaf-1caspase-9 apoptosome is now well characterized,

    but several studies have provided tantalizing evidence

    that another apoptosome that activates caspase-2 could

    also exist [2123].

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    To die will be an awfully big adventure (J.M. Barrie)

    how true this has turned out to be, at least at the

    cellular level.

    AcknowledgementsWe apologize to authors whose papers could not be cited owing to space

    constraints. We are grateful to Science Foundation Ireland for ongoing

    support of work in our laboratory and to Christopher W. Akey for kindly

    providing the structures presented in Figure 2.

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    doi:10.1016/j.tibs.2006.03.004

    Assembling the bacterial segrosome

    Finbarr Hayes1 and Daniela Barilla` 2

    1Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street,

    Manchester, M1 7ND, UK2Department of Biology (Area 10), University of York, PO Box 373, York, YO10 5YW, UK

    Genome segregation in prokaryotes is a highly orderedprocess that integrates with DNA replication, cytokin-

    esis and other fundamental facets of the bacterial cell

    cycle. The segrosome is the nucleoprotein complex that

    mediates DNA segregation in bacteria, its assembly and

    organization is best understood for plasmid partition.

    The recent elucidation of structures of the ParB plasmid

    segregation protein bound to centromeric DNA, and of

    the tertiary structures of other segregation proteins, are

    key milestones in the path to deciphering the molecularbasis of bacterial DNA segregation.

    DNA segregation in prokaryotes

    DNA segregation is a fundamental process that cells

    perform with high precision to ensure stable genome

    transmission during cytokinesis. Whereas chromosome

    segregation in eukaryotes is comparatively well described

    [1], the understanding of the molecular mechanisms that

    direct genome partition in prokaryotes is more rudimen-

    tary. Plasmids are tractable model systems with which to

    decipher the DNA-segregation process in bacteria:

    Corresponding authors: Hayes, F. ([email protected]), Barilla, D.

    ([email protected] ).

    Available online 11 April 2006

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