Comparative genomics of the eukaryotes.

A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.

[1]  AC Tose.  Cell , 1993, Cell.

[2]  Paul Tempst,et al.  SNAP receptors implicated in vesicle targeting and fusion , 1993, Nature.

[3]  R. Delotto,et al.  Ventralizing signal determined by protease activation in Drosophila embryogenesis , 1994, Nature.

[4]  N. Dyson,et al.  DNA-binding and trans-activation properties of Drosophila E2F and DP proteins. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[5]  H. Horvitz,et al.  C. elegans cell survival gene ced-9 encodes a functional homolog of the mammalian proto-oncogene bcl-2 , 1994, Cell.

[6]  Eric Wieschaus,et al.  A putative cell signal encoded by the folded gastrulation gene coordinates cell shape changes during Drosophila gastrulation , 1994, Cell.

[7]  T. Südhof,et al.  Neuroligin 1: A splice site-specific ligand for β-neurexins , 1995, Cell.

[8]  T. Coleman,et al.  Myt1: A Membrane-Associated Inhibitory Kinase That Phosphorylates Cdc2 on Both Threonine-14 and Tyrosine-15 , 1995, Science.

[9]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[10]  M. Sheetz,et al.  Kinectin, an essential anchor for kinesin-driven vesicle motility. , 1995, Science.

[11]  Lawrence A. Donehower,et al.  Rescue of embryonic lethality in Mdm2-deficient mice by absence of p53 , 1995, Nature.

[12]  R. Ulevitch,et al.  Purification and molecular cloning of an inducible gram-negative bacteria-binding protein from the silkworm, Bombyx mori. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[13]  B. Barrell,et al.  Life with 6000 Genes , 1996, Science.

[14]  K. Anderson,et al.  A conserved signaling pathway: the Drosophila toll-dorsal pathway. , 1996, Annual review of cell and developmental biology.

[15]  P Bork,et al.  Structure and distribution of modules in extracellular proteins , 1996, Quarterly Reviews of Biophysics.

[16]  M. Lagueux,et al.  Croquemort, a novel Drosophila hemocyte/macrophage receptor that recognizes apoptotic cells. , 1996, Immunity.

[17]  M. Vidal,et al.  RBF, a novel RB-related gene that regulates E2F activity and interacts with cyclin E in Drosophila. , 1996, Genes & development.

[18]  Xiaodong Wang,et al.  Induction of Apoptotic Program in Cell-Free Extracts: Requirement for dATP and Cytochrome c , 1996, Cell.

[19]  A. Pearson.  Scavenger receptors in innate immunity. , 1996, Current opinion in immunology.

[20]  F. Hauser,et al.  Molecular Cloning, Genomic Organization, and Developmental Regulation of a Novel Receptor from Drosophila melanogaster Structurally Related to Members of the Thyroid-stimulating Hormone, Follicle-stimulating Hormone, Luteinizing Hormone/Choriogonadotropin Receptor Family from Mammals* , 1997, The Journal of Biological Chemistry.

[21]  R. Nusse,et al.  Wnt signaling: a common theme in animal development. , 1997, Genes & development.

[22]  C. Janeway,et al.  Innate Immunity: The Virtues of a Nonclonal System of Recognition , 1997, Cell.

[23]  J. Spring,et al.  Vertebrate evolution by interspecific hybridisation – are we polyploid? , 1997, FEBS letters.

[24]  N. Perrimon,et al.  Paradigms to study signal transduction pathways in Drosophila. , 1997, Current topics in developmental biology.

[25]  Andrew P. McMahon,et al.  The world according to bedgebog , 1997 .

[26]  J. Gusella,et al.  Rescue of a Drosophila NF1 mutant phenotype by protein kinase A. , 1997, Science.

[27]  S. Artavanis-Tsakonas,et al.  Comparative aspects of Notch signaling in lower and higher eukaryotes. , 1997, Perspectives on developmental neurobiology.

[28]  S. Srinivasula,et al.  Cytochrome c and dATP-Dependent Formation of Apaf-1/Caspase-9 Complex Initiates an Apoptotic Protease Cascade , 1997, Cell.

[29]  D. Tautz,et al.  A screen for fast evolving genes from Drosophila. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[30]  H. Steiner,et al.  A peptidoglycan recognition protein in innate immunity conserved from insects to humans. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[31]  G. Ruvkun,et al.  The taxonomy of developmental control in Caenorhabditis elegans. , 1998, Science.

[32]  Nancy M Bonini,et al.  Expanded Polyglutamine Protein Forms Nuclear Inclusions and Causes Neural Degeneration in Drosophila , 1998, Cell.

[33]  H. Horvitz,et al.  lin-35 and lin-53, Two Genes that Antagonize a C. elegans Ras Pathway, Encode Proteins Similar to Rb and Its Binding Protein RbAp48 , 1998, Cell.

[34]  Iris Salecker,et al.  Polyglutamine-Expanded Human Huntingtin Transgenes Induce Degeneration of Drosophila Photoreceptor Neurons , 1998, Neuron.

[35]  S. Kornbluth,et al.  Scythe: a novel reaper‐binding apoptotic regulator , 1998, The EMBO journal.

[36]  Temple F. Smith,et al.  Comparison of the complete protein sets of worm and yeast: orthology and divergence. , 1998, Science.

[37]  Cori Bargmann.  Neurobiology of the Caenorhabditis elegans genome. , 1998, Science.

[38]  Yue Xiong,et al.  ARF Promotes MDM2 Degradation and Stabilizes p53: ARF-INK4a Locus Deletion Impairs Both the Rb and p53 Tumor Suppression Pathways , 1998, Cell.

[39]  S. Benzer,et al.  Extended life-span and stress resistance in the Drosophila mutant methuselah. , 1998, Science.

[40]  S. Dutcher,et al.  The UNI3 gene is required for assembly of basal bodies of Chlamydomonas and encodes delta-tubulin, a new member of the tubulin superfamily. , 1998, Molecular biology of the cell.

[41]  T. Hunter,et al.  The Croonian Lecture 1997. The phosphorylation of proteins on tyrosine: its role in cell growth and disease. , 1998, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[42]  J. Marsh,et al.  The gastrulation defective gene of Drosophila melanogaster is a member of the serine protease superfamily. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[43]  T. Sawado,et al.  dE2F2, a novel E2F-family transcription factor in Drosophila melanogaster. , 1998, Biochemical and biophysical research communications.

[44]  Andrey Rzhetsky,et al.  A Spatial Map of Olfactory Receptor Expression in the Drosophila Antenna , 1999, Cell.

[45]  T. Stearns,et al.  δ-Tubulin and ɛ-tubulin: two new human centrosomal tubulins reveal new aspects of centrosome structure and function , 1999, Nature Cell Biology.

[46]  P. Hiesinger,et al.  Three‐dimensional reconstruction of the antennal lobe in Drosophila melanogaster , 1999, The Journal of comparative neurology.

[47]  N. Perrimon,et al.  Stress signaling in Drosophila , 1999, Oncogene.

[48]  L K Miller,et al.  An exegesis of IAPs: salvation and surprises from BIR motifs. , 1999, Trends in cell biology.

[49]  Robert D. Finn,et al.  Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins , 1999, Nucleic Acids Res..

[50]  C. Peschle,et al.  Caspase activation without death , 1999, Cell Death and Differentiation.

[51]  J. Vonesch,et al.  Serotonin synchronises convergent extension of ectoderm with morphogenetic gastrulation movements in Drosophila , 1999, Mechanisms of Development.

[52]  John R. Carlson,et al.  A Novel Family of Divergent Seven-Transmembrane Proteins Candidate Odorant Receptors in Drosophila , 1999, Neuron.

[53]  Thomas Kreis,et al.  Guidebook to cytoskeletal and motor proteins , 1999 .

[54]  T. Maniatis,et al.  A Striking Organization of a Large Family of Human Neural Cadherin-like Cell Adhesion Genes , 1999, Cell.

[55]  N. Imamoto,et al.  Acinus is a caspase-3-activated protein required for apoptotic chromatin condensation , 1999, Nature.

[56]  T. Yagi,et al.  Proteins of the CNR Family Are Multiple Receptors for Reelin , 1999, Cell.

[57]  Terri K. Attwood,et al.  PRINTS prepares for the new millennium , 1999, Nucleic Acids Res..

[58]  C. Hashimoto,et al.  Signal transduction by a protease cascade. , 1999, Trends in cell biology.

[59]  S H Kaufmann,et al.  Mammalian caspases: structure, activation, substrates, and functions during apoptosis. , 1999, Annual review of biochemistry.

[60]  R. Hynes.  Cell adhesion: old and new questions. , 1999, Trends in cell biology.

[61]  J. Abrams.  An emerging blueprint for apoptosis in Drosophila. , 1999, Trends in cell biology.

[62]  Amos Bairoch,et al.  The PROSITE database, its status in 1999 , 1999, Nucleic Acids Res..

[63]  G. Rubin,et al.  Synaptic function modulated by changes in the ratio of synaptotagmin I and IV , 1999, Nature.

[64]  Timothy J. Mitchison,et al.  Kin I Kinesins Are Microtubule-Destabilizing Enzymes , 1999, Cell.

[65]  J Capdevila,et al.  Extracellular modulation of the Hedgehog, Wnt and TGF-beta signalling pathways during embryonic development. , 1999, Current opinion in genetics & development.

[66]  Max F. Perutz,et al.  Glutamine repeats and neurodegenerative diseases: molecular aspects. , 1999, Trends in biochemical sciences.

[67]  T. Südhof,et al.  Membrane fusion and exocytosis. , 1999, Annual review of biochemistry.

[68]  Ruedi Aebersold,et al.  Molecular characterization of mitochondrial apoptosis-inducing factor , 1999, Nature.

[69]  S. Korsmeyer,et al.  BCL-2 family members and the mitochondria in apoptosis. , 1999, Genes & development.

[70]  S. Aparício,et al.  Vertebrate evolution: recent perspectives from fish. , 2000, Trends in genetics : TIG.

[71]  Stephen M. Mount,et al.  The genome sequence of Drosophila melanogaster. , 2000, Science.

[72]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[73]  K. Anderson,et al.  Toll signaling pathways in the innate immune response. , 2000, Current opinion in immunology.

[74]  Shmuel Pietrokovski,et al.  Increased coverage of protein families with the Blocks Database servers , 2000, Nucleic Acids Res..

[75]  G. Rubin,et al.  gigas , a Drosophila Homolog of Tuberous Sclerosis Gene Product-2, Regulates the Cell Cycle , 1999, Cell.