Skip to main content

Advertisement

SpringerLink
Log in

Revamp a model—status and prospects of the Dictyostelium genome project

  • Review Article
  • Published:
Current Genetics Aims and scope Submit manuscript

Abstract

International efforts are underway that aim at determining the complete genome sequence of the social amoeba Dictyostelium discoideum. As strategy, a whole chromosome shotgun (WCS) approach was chosen and each of the six Dictyostelium chromosomes was assigned to project partners. The project is well advanced, chromosome 2 was recently published, and it is expected that the sequences of chromosomes 1 and 6 and a gene catalogue for the complete genome will be available at the end of this year. The genome sequence, together with powerful molecular genetic tools, will undoubtedly further accelerate Dictyostelium research into a number of fundamental biological processes that are common to a wide range of eukaryotes. Furthermore, it will constitute the basis for genome-wide functional analyses. The integration of results from these studies should ultimately lead to a better understanding of the complex networks that govern cellular behavior and development.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.

Similar content being viewed by others

References

  • Aboobaker AA, Blaxter ML (2000) Medical significance of Caenorhabditis elegans. Ann Med 32:23–30

    CAS  PubMed  Google Scholar 

  • Adams MD, et al (2000) The genome sequence of Drosophila melanogaster. Science 287:2185–2195

    Article  PubMed  Google Scholar 

  • Alizadeh AA, et al (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403:503–511

    PubMed  Google Scholar 

  • Anjard C, the Dictyostelium sequencing consortium, Loomis WF (2002) Evolutionary analyses of ABC transporters of Dictyostelium discoideum. Eukaryot Cell 1:643–652

    Article  CAS  PubMed  Google Scholar 

  • Aparicio S, et al (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301–1310

    Article  CAS  PubMed  Google Scholar 

  • Baldauf SL (1999) A search for the origins of animals and fungi: comparing and combining molecular data. Am Nat 154:S178–S188

    PubMed  Google Scholar 

  • Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972–977

    Article  CAS  PubMed  Google Scholar 

  • Bapteste E, et al (2002) The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci USA 99:1414–1419

    Article  CAS  PubMed  Google Scholar 

  • Blaauw M, Linskens MH, Haastert PJ van (2000) Efficient control of gene expression by a tetracycline-dependent transactivator in single Dictyostelium discoideum cells. Gene 252:71–82

    Article  CAS  PubMed  Google Scholar 

  • Bockaert J, Pin JP (1999) Molecular tinkering of G protein-coupled receptors: an evolutionary success. EMBO J 18:1723–1729

    CAS  PubMed  Google Scholar 

  • Cho RJ, et al (2001) Transcriptional regulation and function during the human cell cycle. Nat Genet 27:48–54

    CAS  PubMed  Google Scholar 

  • Chung CY, Funamoto S, Firtel RA (2001) Signaling pathways controlling cell polarity and chemotaxis. Trends Biochem Sci 26:557–566

    Article  CAS  PubMed  Google Scholar 

  • Cockburn AF, Taylor WC, Firtel RA (1978) Dictyostelium rDNA consists of non-chromosomal palindromic dimers containing 5S and 36S coding regions. Chromosoma 70:19–29

    CAS  PubMed  Google Scholar 

  • Cox EC, Vocke CD, Walter S, Gregg KY, Bain ES (1990) Electrophoretic karyotype for Dictyostelium discoideum. Proc Natl Acad Sci USA 87:8247–8251

    CAS  PubMed  Google Scholar 

  • De Lozanne A, Spudich JA (1987) Disruption of the Dictyostelium myosin heavy chain gene by homologous recombination. Science 236:1086–1091

    PubMed  Google Scholar 

  • Dear PH (1997) HAPPY mapping. In: Dear PH (ed) Genome mapping—a practical approach. IRL Press, London, pp 95–124

  • DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale Science. 278:680–686

  • Döring V, Schleicher M, Noegel AA (1991) Dictyostelium annexin VII (synexin). cDNA sequence and isolation of a gene disruption mutant. J Biol Chem 266:17509–17515

    PubMed  Google Scholar 

  • Eichinger L, Lee SS, Schleicher M (1999) Dictyostelium as model system for studies of the actin cytoskeleton by molecular genetics. Microsc Res Tech 47:124–134

    Article  CAS  PubMed  Google Scholar 

  • Farbrother P, Müller S, Noegel AA, Eichinger L (2002) Comparison of probe preparation methods for DNA microarrays. Biotechniques 33:884–888

    CAS  PubMed  Google Scholar 

  • Fortini ME, Skupski MP, Boguski MS, Hariharan IK (2000) A survey of human disease gene counterparts in the Drosophila genome. J Cell Biol 150:F23–F30

    CAS  PubMed  Google Scholar 

  • Gardner MJ, et al (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419:498–511

    Article  CAS  PubMed  Google Scholar 

  • Gavin AC, et al (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141–147

    CAS  PubMed  Google Scholar 

  • Ge H, Liu Z, Church GM, Vidal M (2001) Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 29:482–486

    CAS  PubMed  Google Scholar 

  • Gerisch G (1987) Cyclic AMP and other signals controlling cell development and differentiation in Dictyostelium. Annu Rev Biochem 56:853–879

    Article  CAS  PubMed  Google Scholar 

  • Gerisch G, Weber I (2000) Cytokinesis without myosin II. Curr Opin Cell Biol 12:126–132

    Article  CAS  PubMed  Google Scholar 

  • Glöckner G (2000) Large scale sequencing and analysis of AT-rich eukaryote genomes. Curr Genomics 1:289–299

    Google Scholar 

  • Glöckner G, et al (2001) The complex repeats of Dictyostelium discoideum. Genome Res 11:585–594

    Article  PubMed  Google Scholar 

  • Glöckner G, et al (2002) Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature 418:79–85

    Article  PubMed  Google Scholar 

  • Goffeau A, et al (1996) Life with 6000 genes. Science 274:546–567

    CAS  PubMed  Google Scholar 

  • Goldberg JM, Bosgraaf L, Van Haastert PJ, Smith JL (2002) Identification of four candidate cGMP targets in Dictyostelium. Proc Natl Acad Sci USA 99:6749–6754

    Article  CAS  PubMed  Google Scholar 

  • Hägele S, Kohler R, Merkert H, Schleicher M, Hacker J, Steinert M (2000) Dictyostelium discoideum: a new host model system for intracellular pathogens of the genus Legionella. Cell Microbiol 2:165–171

    Article  PubMed  Google Scholar 

  • Hammond DL (2001) GABA-B receptors: new tricks by an old dog. Curr Opin Pharmacol 1:26-30

    Article  CAS  PubMed  Google Scholar 

  • Ho Y, et al (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180–183

    CAS  PubMed  Google Scholar 

  • Holland IB, Blight MA (1999) ABC-ATPases, adaptable energy generators fuelling transmembrane movement of a variety of molecules in organisms from bacteria to humans. J Mol Biol 293:381–399

    Article  CAS  PubMed  Google Scholar 

  • Howard PK, Ahern KG, Firtel RA (1988) Establishment of a transient expression system for Dictyostelium discoideum. Nucleic Acids Res 16:2613–2623

    CAS  PubMed  Google Scholar 

  • Iranfar N, Fuller D, Sasik R, Hwa T, Laub M, Loomis WF (2001) Expression patterns of cell-type-specific genes in Dictyostelium. Mol Biol Cell 12:2590–2600

    CAS  PubMed  Google Scholar 

  • Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98:4569–4574

    CAS  PubMed  Google Scholar 

  • Kay RR, Williams JG (1999) The Dictyostelium genome project an invitation to species hopping. Trends Genet 15:294–297

    Article  CAS  PubMed  Google Scholar 

  • Kemmeren P, et al (2002) Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol Cell 9:1133–1143

    CAS  PubMed  Google Scholar 

  • Knecht DA, Loomis WF (1987) Antisense RNA inactivation of myosin heavy chain gene expression in Dictyostelium discoideum. Science 236:1081–1086

    CAS  PubMed  Google Scholar 

  • Konfortov BA, Cohen HM, Bankier AT, Dear PH (2000) A high-resolution HAPPY map of Dictyostelium discoideum chromosome 6. Genome Res 10:1737–1742

    Article  CAS  PubMed  Google Scholar 

  • Kreppel L, Kimmel AR (2002) Genomic database resources for Dictyostelium discoideum. Nucleic Acids Res 30:84–86

    Article  CAS  PubMed  Google Scholar 

  • Krogh A (2000) Using database matches with for HMMGene for automated gene detection in Drosophila. Genome Res 10:523–528

    Article  CAS  PubMed  Google Scholar 

  • Kuma K, Nikoh N, Iwabe N, Miyata T (1995) Phylogenetic position of Dictyostelium inferred from multiple protein data sets. J Mol Evol 41:238–246

    CAS  PubMed  Google Scholar 

  • Kuspa A, Loomis WF (1992) Tagging developmental genes in Dictyostelium by restriction enzyme-mediated integration of plasmid DNA. Proc Natl Acad Sci USA 89:8803–8807

    CAS  PubMed  Google Scholar 

  • Kuspa A, Loomis WF (1996) Ordered yeast artificial chromosome clones representing the Dictyostelium discoideum genome. Proc Natl Acad Sci USA 93:5562–5566

    Article  CAS  PubMed  Google Scholar 

  • Kuspa A, Sucgang R, Shaulsky G (2001) The promise of a protist: the Dictyostelium genome project. Funct Integr Genomics 1:279–293

    Article  CAS  PubMed  Google Scholar 

  • Lander ES, et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921

    CAS  PubMed  Google Scholar 

  • Li G, Alexander H, Schneider N, Alexander S (2000) Molecular basis for resistance to the anticancer drug cisplatin in Dictyostelium. Microbiology 146:2219–2227

    CAS  PubMed  Google Scholar 

  • Liu T, Williams JG, Clarke M (1992) Inducible expression of calmodulin antisense RNA in Dictyostelium cells inhibits the completion of cytokinesis. Mol Biol Cell 3:1403–1413

    CAS  PubMed  Google Scholar 

  • Loomis WF (1996) Genetic networks that regulate development in Dictyostelium cells. Microbiol Rev 60:135–150

    CAS  PubMed  Google Scholar 

  • Loomis WF, Kuspa A (1997) The genome of Dictyostelium discoideum. In: Loomis WF, Kuspa A (eds) Dictyostelium—a model system for cell and developmental biology. Universal Academic Press, New York, pp 15–30

  • Loomis WF, Smith DW (1995) Consensus phylogeny of Dictyostelium. Experientia 51:1110–1115

    CAS  PubMed  Google Scholar 

  • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964

    Google Scholar 

  • Maniak M (2002) Conserved features of endocytosis in Dictyostelium. Int Rev Cytol 221:257–287

    CAS  PubMed  Google Scholar 

  • Maniak M, Rauchenberger R, Albrecht R, Murphy J, Gerisch G (1995) Coronin involved in phagocytosis: dynamics of particle-induced relocalization visualized by a green fluorescent protein tag. Cell 83:915–924

    CAS  PubMed  Google Scholar 

  • Manstein DJ, Titus MA, De Lozanne A, Spudich JA (1989) Gene replacement in Dictyostelium: generation of myosin null mutants. EMBO J 8:923–932

    CAS  PubMed  Google Scholar 

  • Martens H, Novotny J, Oberstrass J, Steck TL, Postlethwait P, Nellen W (2002) RNAi in Dictyostelium: the role of RNA-directed RNA polymerases and double-stranded RNase. Mol Biol Cell 13:445–453

    Article  CAS  PubMed  Google Scholar 

  • Morio T, et al (1998) The Dictyostelium developmental cDNA project: generation and analysis of expressed sequence tags from the first-finger stage of development. DNA Res 5:335–340

    CAS  PubMed  Google Scholar 

  • Mullikin JC, Ning Z (2003) The Phusion assembler. Genome Res 13:81–90

    Article  CAS  PubMed  Google Scholar 

  • Nellen W, Silan C, Firtel RA (1984) DNA-mediated transformation in Dictyostelium discoideum: regulated expression of an actin gene fusion. Mol Cell Biol 4:2890–2898

    CAS  PubMed  Google Scholar 

  • Noegel AA, Schleicher M (2000) The actin cytoskeleton of Dictyostelium: a story told by mutants. J Cell Sci 113:759–766

    CAS  PubMed  Google Scholar 

  • Ogawa S, et al (2000) The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization. Mol Gen Genet 263:514–519

    Article  CAS  PubMed  Google Scholar 

  • Parent CA, Devreotes PN (1999) A cell′s sense of direction. Science 284:765–770

    Article  CAS  PubMed  Google Scholar 

  • Parra G, Blanco E, Guigo R (2000) GeneID in Drosophila. Genome Res 10:511–515

    Article  CAS  PubMed  Google Scholar 

  • Rivero F, Dislich H, Glöckner G, Noegel AA (2001) The Dictyostelium discoideum family of Rho-related proteins. Nucleic Acids Res 29:1068–1079

    Article  CAS  PubMed  Google Scholar 

  • Robinson DN, Spudich JA (2000) Dynacortin, a genetic link between equatorial contractility and global shape control discovered by library complementation of a Dictyostelium discoideum cytokinesis mutant. J Cell Biol 150:823–838

    Article  CAS  PubMed  Google Scholar 

  • Sasik R, Iranfar N, Hwa T, Loomis WF (2002) Extracting transcriptional events from temporal gene expression patterns during Dictyostelium development. Bioinformatics 18:61–66

    Article  CAS  PubMed  Google Scholar 

  • Skriwan C, et al (2002) Various bacterial pathogens and symbionts infect the amoeba Dictyostelium discoideum. Int J Med Microbiol 291:615–624

    PubMed  Google Scholar 

  • Solomon JM, Isberg RR (2000) Growth of Legionella pneumophila in Dictyostelium discoideum: a novel system for genetic analysis of host-pathogen interactions. Trends Microbiol 8:478–480

    Article  CAS  PubMed  Google Scholar 

  • Stechmann A, Cavalier-Smith T (2002) Rooting the eukaryote tree by using a derived gene fusion. Science 297:89–91

    Article  CAS  PubMed  Google Scholar 

  • Sucgang R, et al (2003) Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium. Nucleic Acids Res 31:2361–2368

    Article  CAS  PubMed  Google Scholar 

  • the Arabidopsis genome initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    PubMed  Google Scholar 

  • the C. elegans sequencing consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:2012–2018

    PubMed  Google Scholar 

  • the Gene ontology consortium (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29

    CAS  PubMed  Google Scholar 

  • Thomason P, Traynor D, Kay R (1999) Taking the plunge. Terminal differentiation in Dictyostelium. Trends Genet 15:15–19

    Article  CAS  PubMed  Google Scholar 

  • Uetz P, et al (2000) A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature 403:623–627

    CAS  PubMed  Google Scholar 

  • Urushihara H (1996) Choice of partners: sexual cell interactions in Dictyostelium discoideum. Cell Struct Funct 21:231–236

    CAS  PubMed  Google Scholar 

  • Van Driessche N, et al (2002) A transcriptional profile of multicellular development in Dictyostelium discoideum. Development 129:1543–1552

    PubMed  Google Scholar 

  • Wang N, Wu WI, De Lozanne A (2002) BEACH family of proteins: phylogenetic and functional analysis of six Dictyostelium BEACH proteins. J Cell Biochem 86:561–570

    Article  CAS  PubMed  Google Scholar 

  • Williams RS, Eames M, Ryves WJ, Viggars J, Harwood AJ (1999) Loss of a prolyl oligopeptidase confers resistance to lithium by elevation of inositol (1,4,5) trisphosphate. EMBO J 18:2734–2745

    Article  CAS  PubMed  Google Scholar 

  • Williams RS, Cheng L, Mudge AW, Harwood AJ (2002) A common mechanism of action for three mood-stabilizing drugs. Nature 417:292–295

    Article  CAS  PubMed  Google Scholar 

  • Winckler T, et al (2001) Gene function analysis by amber stop codon suppression: CMBF is a nuclear protein that supports growth and development of Dictyostelium amoebae. J Mol Biol 305:703–714

    Article  CAS  PubMed  Google Scholar 

  • Witke W, Nellen W, Noegel A (1987) Homologous recombination in the Dictyostelium alpha-actinin gene leads to an altered mRNA and lack of the protein. EMBO J 6:4143–4148

    CAS  PubMed  Google Scholar 

  • Wood V, et al (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415:871–880

    CAS  PubMed  Google Scholar 

  • Yale J, Bohnert HJ (2001) Transcript expression in Saccharomyces cerevisiae at high salinity. J Biol Chem 276:15996–16007

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

I wish to thank all members of the Dictyostelium genome sequencing consortium for their contributions to the joint project. I am indebted to Drs. A.A. Noegel and F. Rivero (Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany) for critical reading of the manuscript and to the latter in addition for his contributions to D. discoideum as a model organism and to Fig. 2. I also would like to thank Drs. A.A. Noegel, R. Kay (Medical Research Council, Cambridge, UK) and G. Glöckner (IMB Jena, Jena, Germany) for their input to the Dictyostelium phylogeny. I am very grateful to Drs. M.J. Grimson and R.L. Blanton (Department of Biological Sciences, Texas Technical University, Tex.) for providing Fig. 1 and to Dr. Neil Hall (Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Hinxton, UK) for Fig. 3. The Dictyostelium genome project is funded by the Deutsche Forschungsgemeinschaft, the National Institutes of Health, the Medical Research Council, and the European Union. The support of Köln Fortune is also acknowledged.

Author information

Authors and Affiliations

  1. Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, 50931, Köln, Germany

    Ludwig Eichinger

Authors
  1. Ludwig Eichinger
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ludwig Eichinger.

Additional information

Communicated by S. Hohmann

Rights and permissions

Reprints and permissions

About this article

Cite this article

Eichinger, L. Revamp a model—status and prospects of the Dictyostelium genome project. Curr Genet 44, 59–72 (2003). https://doi.org/10.1007/s00294-003-0416-1

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00294-003-0416-1

Keywords

Search

Navigation