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TALKING POINT the Domains of Death: Evolution of the Apoptosis

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TALKING POINT the Domains of Death: Evolution of the Apoptosis TIBS 24 – FEBRUARY 1999 TALKING POINT domains implicated in programmed cell death. The PSI-BLAST method signifi- cantly increases the database-search sen- The domains of death: evolution of sitivity by incorporating information em- bedded in a multiple sequence alignment the apoptosis machinery into a position-dependent weight matrix (profile), which is employed as the query for iterating the search. This allows the detection even of very subtle sequence L. Aravind, Vishva M. Dixit and Eugene V. Koonin similarities at a statistically significant level5,6; all previously undetected relation- Recent progress in research into programmed cell death has resulted in ships between protein domains reported the identification of the principal protein domains involved in this process. here are statistically supported (having The evolution of many of these domains can be traced back in evolution random expectation values of 0.01 or to unicellular eukaryotes or even bacteria, where the domains appear to lower). Such an exhaustive search was be involved in other regulatory functions. Cell-death systems in animals particularly important for the detection of and plants share several conserved domains, in particular the family of possible progenitors of some of the apop- apoptotic ATPases; this allows us to suggest a plausible, even if still tosis domains in phylogenetically distant incomplete, scenario for the evolution of apoptosis. species, such as yeast or even bacteria. The functional classification of the ‘do- mains of death’ and their phylogenetic PROGRAMMED CELL DEATH, also distribution are shown in Table 1. known as apoptosis, is a major process in animal and plant development1,2. There is Table 1. Phylogenetic distribution of the principal domains involved in programmed cell death a basic similarity between the cell-death events that occur in development and Domain Vertebrates Dm Ce Plants Yeast Bacteria those that occur in response to Ligands, intracellular domains and membrane proteins pathogens and other stress signals; tumor TNF family + ? –? ? – – suppression is a form of this process2,3. TNFR, extracellular The extraordinary research activity of domain + ? –? + – – LRR + + + + –/+a –/+a the past few years has resulted in the BCL-2/BAX + ? + ? – – characterization of the principal molec- Adaptor (protein–protein interaction) domains ular components of the apoptotic ma- DD + ? + ? – – 4 chinery . Like proteins that participate in DED + ? –? ? – – other signaling networks, many of the CARD + + + ? – – proteins involved in apoptosis contain TIRb +++c +– +d BIRb +++?+– multiple domains, and complex patterns MATHb +++++– of interactions between these domains CART + + + ? – – define specific pathways. Here, we pre- Effector and regulatory enzymes sent an inventory of the most important Caspaseb +++?–+e apoptosis domains and report a number Ap-ATPase + ? + + – +f of previously undetected structural and DAP kinase + ? + ? – – IRAK/Pelle kinase + + + + – – evolutionary connections. Using the RIP kinase + ? –? ? – – rapidly accumulating genome sequences, Cell-cycle control, transcription factors and other nuclear functions we trace the phylogenetic distribution of CDK/cyclin + + + + + – each domain and propose a scenario for CKI (KIP/WAF family) + + + + – – the evolution of the apoptosis machinery. RB + + + + – – P53 + ? –? ? – – MYC + + –? –? – – The domains of death and their phylogenetic NF-κB + + (+)b,g ? (+)b,g – distribution E2Fs/Dp1s + + + ? – – Using the gapped BLAST program as CES-2 + + + ? – – well as the iterative program PSI-BLAST5, CAD/ICAD + + –? ? – – we performed a detailed analysis of the aOnly intracellular forms detected. bSignificantly expanded in this study; multiple alignments are sequences of the principal proteins and available as Supplementary Information. cA diverged form in a single protein. dDiverged forms found in Streptomyces, Bacillus subtilis, Synechocystis sp. and Rhizobium. eA single, diverged form detected in Streptomyces. fDetected only in the Actinomycetes and B. subtilis. gThese proteins (C. elegans olf-1 and L. Aravind is at the NCBI, National Library of yeast SPT23) share a conserved immunoglobulin-like DNA-binding domain with NF-κB but cannot be Medicine, NIH, Bethesda, MD 20894, USA, considered its true orthologs. A plus indicates that the domain is present in the phylogenetic lineage; a and at theDept of Biology, Texas A&M minus indicates those lineages whose complete genome sequences are available. A question mark University, College Station, TX 77843, USA; indicates that as yet the domain is not detectable in the lineage but that there are no complete genome V. M. Dixit is at the Dept of Molecular sequences. For the nearly completed C. elegans genome, –? is indicated for the domains missing in the Oncology, Genentech Inc., 1 DNA Way, South current sequence set. Abbreviations used: Ap-ATPase, apoptotic ATPase; Ce, Caenorhabditis elegans; San Francisco, CA 94080-4918, USA; and CDK, cyclin-dependent kinase; CKI, CDK inhibitor; DAP kinase, death-associated protein kinase; DD, E. V. Koonin is at the NCBI, National Library death domain; DED, death-effector domain; Dm, Drosophila melanogaster; IAP, inhibitor of apoptosis; LRR, leucine-rich repeat; TIR, Toll–interleukin-receptor domain; TNF, tumor necrosis factor; TNFR, TNF of Medicine, NIH, Bethesda, MD 20894, USA. receptor. Email: [email protected] Published by Elsevier Science Ltd. PII: S0968-0004(98)01341-3 47 TALKING POINT TIBS 24 – FEBRUARY 1999 Ligands and receptors. The first stage of through the caspases9; the second contains a DD, IRAK/PELLE kinases and apoptosis signaling occurs through the includes a protein kinase cascade (see MyD88 (Ref. 11; see below). interaction between extracellular li- below) and some proteins of the TNFR- The DD–DED–CARD network and other adaptor gands, such as tumor necrosis factor associated factor (TRAF) family that domains. Important components of all (TNF) and their cognate receptors, such activate NF-kB (Ref. 10). cell-death pathways are small protein– as members of the TNF receptor (TNFR) Recently, decoy versions of members protein-interaction domains that are family7. Orthologous relationships be- of the TNFR family of receptors, which present in apoptotic proteins, including tween ligands and receptors are de- have missing or truncated intracellular receptors, adaptors and effectors, in a tectable only among vertebrates. domains, have been discovered; this has variety of combinations (Fig. 1a). These However, characteristic cysteine-rich revealed a new level of control to the domains glue the components of the repeats that are conserved in the extra- apoptotic signaling pathways7. These death machinery together, primarily cellular portions of the receptors are proteins bind the intracellular ligands but through homophilic interactions, and also present in the plant receptor ki- do not transmit the signal and, accord- transmit signals from receptors to nases of the Crinkly family8. These ingly, interrupt the cell-death pathways. downstream effectors, such as the cas- receptors trigger at least two distinct The interleukin 1 (IL-1) signaling pases. The best known of these adap- signaling pathways through their pathway, although not involved in apop- tors is the DD12,13. Two other adaptor intracellular domains. The first pathway tosis, includes components that are domains, namely the death-effector do- involves the death domain (DD) cas- structurally similar to apoptotic pro- main (DED)14 and the caspase activation cade (see below) that communicates teins, namely the IL-1 receptor that and recruitment domain (CARD)15, TLR3 (a) TNFR FAS IL-3R ATRK1 IL-1R Ig Receptors DR2 Ig Ig Cell membrane D D T T D YddK_Bs SC7H1.23_Scoe TRAF1 T T Cr Cr Cr M Adaptors TRADD RAIDD FADD MYD88 DG17 SSI D C D De D D T Cr M SH2 IRAK RIP RICK FEN1 DAP kinase Kin Kin Kin Kin ATP D Kinases D D C Kin JAK JAK1 JAK2 Caspase-8 CED-3Y48E1B.13_Ce F22D3.6_Ce Caspases De De Casp C Casp Casp Ig Casp IAP-1 IAP-CHV SPBIRDP NAIP ARC Caspase inhibitors BBBC BB BBB ATP C k NF- B, p100 NFAT SPT23 Ces-2 N-5 D Nuclear factors Igl NfIg D Igl NfIg NfIg Dbd SH2 NILF-3 STAT Domain key Ankyrin LRR WD40 Fibronectin III DD CARD DED Predicted ATPases TIR Kinase D C De ATP ATP T Kin DNA-binding Immunoglobulin Math Caspase Bir domain fold Ring DNA-binding Ig bZIP SH2 CART TNFR M Casp Dbd Ig NfIg SH2 Cr 48 TIBS 24 – FEBRUARY 1999 TALKING POINT The DD–DED–CARD triad of (b) Animal domains is found only in ani- CED-4 C Ap-ATPase mals; furthermore, DED seems to be limited to vertebrates APAF-1 C Ap-ATPase and arthropods (Table 1). By contrast, as emphasized by our analysis here, TIR and Plant N protein MATH are ancient conserved tobacco T Ap-ATPase domains. Multiple copies of TIR are present in animal Arabidopsis apoptotic receptors and adap- N-protein T Ap-ATPase homolog tors, as well as in plant proteins involved in disease 17 Prokaryotic resistance (Fig. 1a,b) . Using iterative PSI-BLAST searches, Sc6A9.38 T Ap-ATPase we detected previously unno- ticed, divergent versions of AfsR H Ap-ATPase TIR in a Caenorhabditis elegans protein and in proteins from four taxonomically diverse TB-ATPase AC Ap-ATPase H bacteria (see Table 1, Fig. 1a and Box 1). The MATH domain was identified originally in the H Ap-ATPase PHAR009 adaptor proteins of the TRAF family and in membrane pro- 18 GutR H Ap-ATPase teases of the meprin family . We detected multiple copies of MATH in a variety of animal and plant proteins; interest- Domain key ingly, a MATH domain is pres- Adenylyl a-Helical ent in a distinct set of ubiqui- cyclase TIR CARD HTH RCC1 Modified TPR WD40 LRR domain tin hydrolases, and this domain architecture is vertically con- AC T C H served in eukaryotes from yeast to vertebrates (see Fig. 1a and Box 1). TRAF, an apop- Figure 1 tosis adaptor that consists of (a) Distinct domain architectures of receptors, adaptors and effectors involved in programmed cell RING, CART and MATH domains death and their homologs (see facing page). For the caspases, four different architectures are shown.
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