The genomic underpinnings of apoptosis in Strongylocentrotus purpuratus

Developmental Biology - Tập 300 Số 1 - Trang 321-334 - 2006
A Robertson1, Jenifer C. Croce2, Seth Carbonneau1, Ekaterina Voronina3, Esther Miranda2, David R. McClay2, James A. Coffman1
1Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
2Duke University, Developmental, Molecular, and Cellular Biology Group, Durham, NC 27708, USA
3Brown University, Department of Molecular Biology, Cellular Biology, and Biochemistry, Providence, RI 02912, USA

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Aravind, 2001, Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons, Science, 291, 1279, 10.1126/science.291.5507.1279

Armstrong, 2006, Mitochondrial membrane permeabilization: the sine qua non for cell death, BioEssays, 28, 253, 10.1002/bies.20370

Barker, 2004, p75NTR is positively promiscuous: novel partners and new insights, Neuron, 42, 529, 10.1016/j.neuron.2004.04.001

Bayascas, 2002, Isolation of AmphiCASP-3/7, an ancestral caspase from amphioxus (Branchiostoma floridae). Evolutionary considerations for vertebrate caspases, Cell Death Differ., 9, 1078, 10.1038/sj.cdd.4401075

Bhardwaj, 2003, Receptor-mediated choreography of life and death, J. Clin. Immunol., 23, 317, 10.1023/A:1025319031417

Bridgham, 2003, All in the family: evolutionary and functional relationships among death receptors, Cell Death Differ., 10, 19, 10.1038/sj.cdd.4401174

Bradham, 2006, The sea urchin kinome: a first look, Dev. Biol., 300, 180, 10.1016/j.ydbio.2006.08.074

Casaccia-Bonnefil, 1999, p75 neurotrophin receptor as a modulator of survival and death decisions, Microsc. Res. Tech., 45, 217, 10.1002/(SICI)1097-0029(19990515/01)45:4/5<217::AID-JEMT5>3.0.CO;2-5

Daniel, 2003, Guardians of cell death: the Bcl-2 family proteins, Essays Biochem., 39, 73, 10.1042/bse0390073

Davies, 2003, Regulation of neuronal survival and death by extracellular signals during development, EMBO J., 22, 2537, 10.1093/emboj/cdg254

Dickey-Sims, 2005, Runx-dependent expression of PKC is critical for cell survival in the sea urchin embryo, BMC Biol., 3, 18, 10.1186/1741-7007-3-18

Du, 2000, Smac, a mitochondrial protein that promotes cytochrome c-dependent caspase activation by eliminating IAP inhibition, Cell, 102, 33, 10.1016/S0092-8674(00)00008-8

Ellis, 1986, Genetic control of programmed cell death in the nematode C. elegans, Cell, 44, 817, 10.1016/0092-8674(86)90004-8

Fainzilber, 1996, CRNF, a molluscan neurotrophic factor that interacts with the p75 neurotrophin receptor, Science, 274, 1540, 10.1126/science.274.5292.1540

Fernandez-Guerra, 2006, The genomic repertoire for cell cycle control and DNA metabolism in S. purpuratus, Dev. Biol., 300, 238, 10.1016/j.ydbio.2006.09.012

Fesik, 2000, Insights into programmed cell death through structural biology, Cell, 103, 273, 10.1016/S0092-8674(00)00119-7

Gross, 1999, BCL-2 family members and the mitochondria in apoptosis, Genes Dev., 13, 1899, 10.1101/gad.13.15.1899

Gupta, 2005, Life and death of lymphocytes: a role in immunosenescence, Immun. Ageing, 2, 12, 10.1186/1742-4933-2-12

Headon, 2001, Gene defect in ectodermal dysplasia implicates a death domain adapter in development, Nature, 414, 913, 10.1038/414913a

Hehlgans, 2005, The intriguing biology of the tumour necrosis factor/tumour necrosis factor receptor superfamily: players, rules and the games, Immunology, 115, 1, 10.1111/j.1365-2567.2005.02143.x

Hengartner, 2000, The biochemistry of apoptosis, Nature, 407, 770, 10.1038/35037710

Hibino, 2006, The immune gene repertoire encoded in the purple sea urchin genome, Dev. Biol., 300, 349, 10.1016/j.ydbio.2006.08.065

Horng, 2001, Drosophila MyD88 is an adapter in the Toll signaling pathway, Proc. Natl. Acad. Sci. U. S. A., 98, 12654, 10.1073/pnas.231471798

Hsu, 1995, The TNF receptor 1-associated protein TRADD signals cell death and NF-kappa B activation, Cell, 81, 495, 10.1016/0092-8674(95)90070-5

Hu, 2000, dFADD, a novel death domain-containing adapter protein for the Drosophila caspase DREDD, J. Biol. Chem., 275, 30761, 10.1074/jbc.C000341200

Inohara, 1997, CLARP, a death effector domain-containing protein interacts with caspase-8 and regulates apoptosis, Proc. Natl. Acad. Sci. U. S. A., 94, 10717, 10.1073/pnas.94.20.10717

Inoue, 2000, Tumor necrosis factor receptor-associated factor (TRAF) family: adapter proteins that mediate cytokine signaling, Exp. Cell Res., 254, 14, 10.1006/excr.1999.4733

Jin, 2005, Overview of cell death signaling pathways, Cancer Biol. Ther., 4, 139, 10.4161/cbt.4.2.1508

Kerr, 1972, Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics, Br. J. Cancer, 26, 239, 10.1038/bjc.1972.33

Khosravi-Far, 2004, Death receptor signals to mitochondria, Cancer Biol. Ther., 3, 1051, 10.4161/cbt.3.11.1173

Koonin, 2000, The NACHT family—A new group of predicted NTPases implicated in apoptosis and MHC transcription activation, Trends Biochem. Sci., 25, 223, 10.1016/S0968-0004(00)01577-2

Koonin, 2002, Origin and evolution of eukaryotic apoptosis: the bacterial connection, Cell Death Differ., 9, 394, 10.1038/sj.cdd.4400991

Kornbluth, 2005, Apoptosis in Drosophila: neither fish nor fowl (nor man, nor worm), J. Cell Sci., 118, 1779, 10.1242/jcs.02377

Kumar, 2004, MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment, Brief. Bioinform., 5, 150, 10.1093/bib/5.2.150

Lesser, 2003, Exposure to ultraviolet radiation causes apoptosis in developing sea urchin embryos, J. Exp. Biol., 206, 4097, 10.1242/jeb.00621

Li, 1997, Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade, Cell, 91, 479, 10.1016/S0092-8674(00)80434-1

Li, 2001, Endonuclease G is an apoptotic DNase when released from mitochondria, Nature, 412, 95, 10.1038/35083620

Liu, 1996, Induction of apoptotic program in cell-free extracts: requirement for dATP and cytochrome c, Cell, 86, 147, 10.1016/S0092-8674(00)80085-9

Miller, 1999, An exegesis of IAPs: salvation and surprises from BIR motifs, Trends Cell Biol., 9, 323, 10.1016/S0962-8924(99)01609-8

Nichols, 1998, The p75 neurotrophin receptor: effects on neuron survival in vitro and interaction with death domain-containing adaptor proteins, Apoptosis, 3, 289, 10.1023/A:1009617426753

Pancer, 2006, The evolution of adaptive immunity, Annu. Rev. Immunol., 24, 497, 10.1146/annurev.immunol.24.021605.090542

Riedl, 2004, Molecular mechanisms of caspase regulation during apoptosis, Nat. Rev., Mol. Cell Biol., 5, 897, 10.1038/nrm1496

Roccheri, 1997, Apoptosis in sea urchin embryos, Biochem. Biophys. Res. Commun., 240, 359, 10.1006/bbrc.1997.7540

Roccheri, 2002, Physiological and induced apoptosis in sea urchin larvae undergoing metamorphosis, Int. J. Dev. Biol., 46, 801

Samanta, M.P., Tongprasit, W., Istrail, S., Cameron, R.A., Tu, Q., Davidson, E.H., and Stolc, V., 2006. A high-resolution transcriptome map of the sea urchin embryo. (Submitted for publication).

Shearwin-Whyatt, 2000, Subcellular localization and CARD-dependent oligomerization of the death adaptor RAIDD, Cell Death Differ., 7, 155, 10.1038/sj.cdd.4400632

Shen, 2001, Physical and functional interactions between Drosophila TRAF2 and Pelle kinase contribute to dorsal activation, Proc. Natl. Acad. Sci. U. S. A., 98, 8596, 10.1073/pnas.141235698

Smith, 1997, Sequence profiles of immunoglobulin and immunoglobulin-like domains, J. Mol. Biol., 274, 530, 10.1006/jmbi.1997.1432

Sullivan, 2006, StellaBase: the Nematostella vectensis Genomics Database, Nucleic Acids Res., 34, D495, 10.1093/nar/gkj020

Susin, 1999, Molecular characterization of mitochondrial apoptosis-inducing factor, Nature, 397, 441, 10.1038/17135

Swofford, D.L., 1998. PAUP* Phylogenetic Analysis Using Parsimony, Version 4 work. Sunderland, MA: Sinauer.

The Sea Urchin Genome Sequencing Consortium, submitted for publication. The genome of the sea urchin Strongylocentrotus purpuratus. Science.

Tibbetts, 2003, The death effector domain protein family: regulators of cellular homeostasis, Nat. Immunol., 4, 404, 10.1038/ni0503-404

Twomey, 2005, Pathways of apoptosis and importance in development, J. Cell. Mol. Med., 9, 345, 10.1111/j.1582-4934.2005.tb00360.x

Uren, 1998, Conservation of baculovirus inhibitor of apoptosis repeat proteins (BIRPs) in viruses, nematodes, vertebrates and yeasts, Trends Biochem. Sci., 23, 159, 10.1016/S0968-0004(98)01198-0

van der Biezen, 1998, The NB-ARC domain: a novel signalling motif shared by plant resistance gene products and regulators of cell death in animals, Curr. Biol., 8, R226, 10.1016/S0960-9822(98)70145-9

Vega, 2004, Stress-induced apoptosis in sea urchin embryogenesis, Mar. Environ. Res., 58, 799, 10.1016/j.marenvres.2004.03.096

Verhagen, 2001, Inhibitor of apoptosis proteins and their relatives: IAPs and other BIRPs, Genome Biol., 2, 10.1186/gb-2001-2-7-reviews3009

Verhagen, 2000, Identification of DIABLO, a mammalian protein that promotes apoptosis by binding to and antagonizing IAP proteins, Cell, 102, 43, 10.1016/S0092-8674(00)00009-X

Voronina, 2001, Apoptosis in sea urchin oocytes, eggs, and early embryos, Mol. Reprod. Dev., 60, 553, 10.1002/mrd.1120

Wang, 2001, The expanding role of mitochondria in apoptosis, Genes Dev., 15, 2922

Wang, 2001, Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction, Genetics, 158, 1311, 10.1093/genetics/158.3.1311

Wang, 2002, Mechanisms of AIF-mediated apoptotic DNA degradation in Caenorhabditis elegans, Science, 298, 1587, 10.1126/science.1076194

Weill, 2005, The caspase family in urochordates: distinct evolutionary fates in ascidians and larvaceans, Biol. Cell, 97, 857, 10.1042/BC20050018

Yoo, 2005, BIR containing proteins (BIRPs): more than just cell death inhibitors, Integr. Biosci., 9, 181, 10.1080/17386357.2005.9647269

Zapata, 2000, The Drosophila tumor necrosis factor receptor-associated factor-1 (DTRAF1) interacts with Pelle and regulates NFkappaB activity, J. Biol. Chem., 275, 12102, 10.1074/jbc.275.16.12102

Zou, 1997, Apaf-1, a human protein homologous to C. elegans CED-4, participates in cytochrome c-dependent activation of caspase-3, Cell, 90, 405, 10.1016/S0092-8674(00)80501-2

Zuzarte-Luis, 2002, Programmed cell death in the developing limb, Int. J. Dev. Biol., 46, 871