Abstract
We have determined the complete nucleotide sequence of pDG1, a plasmid found in a wild isolate of Dictyostelium. The 4439-bp long pDG1 contains only one, 2718-bases-long, open reading frame (ORF) and nearly perfect inverted repeats of 551 bp and 552 bp. Northern-blot analysis showed that only one 2.7-kb poly (A)+ RNA transcript was expressed at a maximum level, 2 h (early aggregation stage) after the onset of development. The expression of this transcript was suppressed by the addition of cAMP. In the upstream region of the ORF, there are several putative consensus sequences, e.g. (1) TGACTTAGAA-AAATT which is a putative site for cleavage by topoisomerase I, and (2) TGACGACA which may be a cAMP-responsive element, found in several genes that are regulated by cAMP at the level of transcription. A possible mechanism of the partitioning of pDG1 into daughter cells is discussed.
Full text
PDF













Images in this article
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Ahern K. G., Howard P. K., Firtel R. A. Identification of regions essential for extrachromosomal replication and maintenance of an endogenous plasmid in Dictyostelium. Nucleic Acids Res. 1988 Jul 25;16(14B):6825–6837. doi: 10.1093/nar/16.14.6825. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bonven B. J., Gocke E., Westergaard O. A high affinity topoisomerase I binding sequence is clustered at DNAase I hypersensitive sites in Tetrahymena R-chromatin. Cell. 1985 Jun;41(2):541–551. doi: 10.1016/s0092-8674(85)80027-1. [DOI] [PubMed] [Google Scholar]
- Broach J. R., Hicks J. B. Replication and recombination functions associated with the yeast plasmid, 2 mu circle. Cell. 1980 Sep;21(2):501–508. doi: 10.1016/0092-8674(80)90487-0. [DOI] [PubMed] [Google Scholar]
- Cappello J., Handelsman K., Lodish H. F. Sequence of Dictyostelium DIRS-1: an apparent retrotransposon with inverted terminal repeats and an internal circle junction sequence. Cell. 1985 Nov;43(1):105–115. doi: 10.1016/0092-8674(85)90016-9. [DOI] [PubMed] [Google Scholar]
- Cech T. R., Brehm S. L. Replication of the extrachromosomal ribosomal RNA genes of Tetrahymena thermophilia. Nucleic Acids Res. 1981 Jul 24;9(14):3531–3543. doi: 10.1093/nar/9.14.3531. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chirgwin J. M., Przybyla A. E., MacDonald R. J., Rutter W. J. Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. Biochemistry. 1979 Nov 27;18(24):5294–5299. doi: 10.1021/bi00591a005. [DOI] [PubMed] [Google Scholar]
- Clark-Walker G. D., Azad A. A. Hybridizable sequences between cytoplasmic ribosomal RNAs and 3 micron circular DNAs of Saccharomyces cerevisiae and Torulopsis glabrata. Nucleic Acids Res. 1980 Mar 11;8(5):1009–1022. doi: 10.1093/nar/8.5.1009. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cockburn A. F., Taylor W. C., Firtel R. A. Dictyostelium rDNA consists of non-chromosomal palindromic dimers containing 5S and 36S coding regions. Chromosoma. 1978 Dec 21;70(1):19–29. doi: 10.1007/BF00292212. [DOI] [PubMed] [Google Scholar]
- Cohen S. M., Knecht D., Lodish H. F., Loomis W. F. DNA sequences required for expression of a Dictyostelium actin gene. EMBO J. 1986 Dec 1;5(12):3361–3366. doi: 10.1002/j.1460-2075.1986.tb04651.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Collins J. Instability of palindromic DNA in Escherichia coli. Cold Spring Harb Symp Quant Biol. 1981;45(Pt 1):409–416. doi: 10.1101/sqb.1981.045.01.055. [DOI] [PubMed] [Google Scholar]
- Comb M., Birnberg N. C., Seasholtz A., Herbert E., Goodman H. M. A cyclic AMP- and phorbol ester-inducible DNA element. 1986 Sep 25-Oct 1Nature. 323(6086):353–356. doi: 10.1038/323353a0. [DOI] [PubMed] [Google Scholar]
- Datta S., Firtel R. A. An 80-bp cis-acting regulatory region controls cAMP and development regulation of a prestalk gene in Dictyostelium. Genes Dev. 1988 Mar;2(3):294–304. doi: 10.1101/gad.2.3.294. [DOI] [PubMed] [Google Scholar]
- Doolittle W. F., Sapienza C. Selfish genes, the phenotype paradigm and genome evolution. Nature. 1980 Apr 17;284(5757):601–603. doi: 10.1038/284601a0. [DOI] [PubMed] [Google Scholar]
- Firtel R. A., Bonner J. Characterization of the genome of the cellular slime mold Dictyostelium discoideum. J Mol Biol. 1972 May 28;66(3):339–361. doi: 10.1016/0022-2836(72)90419-6. [DOI] [PubMed] [Google Scholar]
- Firtel R. A., Silan C., Ward T. E., Howard P., Metz B. A., Nellen W., Jacobson A. Extrachromosomal replication of shuttle vectors in Dictyostelium discoideum. Mol Cell Biol. 1985 Nov;5(11):3241–3250. doi: 10.1128/mcb.5.11.3241. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Goodchild J., Michniewicz J., Seto-Young D., Narang S. A novel deletion found during cloning of a synthetic palindromic DNA. Gene. 1985;33(3):367–371. doi: 10.1016/0378-1119(85)90246-x. [DOI] [PubMed] [Google Scholar]
- Hartley J. L., Donelson J. E. Nucleotide sequence of the yeast plasmid. Nature. 1980 Aug 28;286(5776):860–865. doi: 10.1038/286860a0. [DOI] [PubMed] [Google Scholar]
- Hoshikawa Y., Iida Y., Iwabuchi M. Nucleotide sequence of the transcriptional initiation region of Dictyostelium discoideum rRNA gene and comparison of the initiation regions of three lower eukaryotes' genes. Nucleic Acids Res. 1983 Mar 25;11(6):1725–1734. doi: 10.1093/nar/11.6.1725. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Janssens P. M., Van Haastert P. J. Molecular basis of transmembrane signal transduction in Dictyostelium discoideum. Microbiol Rev. 1987 Dec;51(4):396–418. doi: 10.1128/mr.51.4.396-418.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Karrer K. M., Gall J. G. The macronuclear ribosomal DNA of Tetrahymena pyriformis is a palindrome. J Mol Biol. 1976 Jun 25;104(2):421–453. doi: 10.1016/0022-2836(76)90280-1. [DOI] [PubMed] [Google Scholar]
- Kessin R. H. Genetics of early Dictyostelium discoideum development. Microbiol Rev. 1988 Mar;52(1):29–49. doi: 10.1128/mr.52.1.29-49.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kimmel A. R., Firtel R. A. Sequence organization in Dictyostelium: unique structure at the 5'-ends of protein coding genes. Nucleic Acids Res. 1983 Jan 25;11(2):541–552. doi: 10.1093/nar/11.2.541. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kojo H., Greenberg B. D., Sugino A. Yeast 2-micrometer plasmid DNA replication in vitro: origin and direction. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7261–7265. doi: 10.1073/pnas.78.12.7261. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
- Messing J. New M13 vectors for cloning. Methods Enzymol. 1983;101:20–78. doi: 10.1016/0076-6879(83)01005-8. [DOI] [PubMed] [Google Scholar]
- Metz B. A., Ward T. E., Welker D. L., Williams K. L. Identification of an endogenous plasmid in Dictyostelium discoideum. EMBO J. 1983;2(4):515–519. doi: 10.1002/j.1460-2075.1983.tb01456.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Montminy M. R., Sevarino K. A., Wagner J. A., Mandel G., Goodman R. H. Identification of a cyclic-AMP-responsive element within the rat somatostatin gene. Proc Natl Acad Sci U S A. 1986 Sep;83(18):6682–6686. doi: 10.1073/pnas.83.18.6682. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nellen W., Firtel R. A. High-copy-number transformants and co-transformation in Dictyostelium. Gene. 1985;39(2-3):155–163. doi: 10.1016/0378-1119(85)90309-9. [DOI] [PubMed] [Google Scholar]
- Nellen W., Silan C., Saur U., Firtel R. A. Regulatory sequences in the promoter of the Dictyostelium Actin 6 gene. EMBO J. 1986 Dec 1;5(12):3367–3372. doi: 10.1002/j.1460-2075.1986.tb04652.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ness P. J., Koller T., Thoma F. Topoisomerase I cleavage sites identified and mapped in the chromatin of Dictyostelium ribosomal RNA genes. J Mol Biol. 1988 Mar 5;200(1):127–139. doi: 10.1016/0022-2836(88)90338-5. [DOI] [PubMed] [Google Scholar]
- Noegel A., Metz B. A., Williams K. L. Developmentally regulated transcription of Dictyostelium discoideum plasmid Ddp1. EMBO J. 1985 Dec 30;4(13B):3797–3803. doi: 10.1002/j.1460-2075.1985.tb04150.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Noegel A., Welker D. L., Metz B. A., Williams K. L. Presence of nuclear associated plasmids in the lower eukaryote Dictyostelium discoideum. J Mol Biol. 1985 Sep 20;185(2):447–450. doi: 10.1016/0022-2836(85)90416-4. [DOI] [PubMed] [Google Scholar]
- Orii H., Suzuki K., Tanaka Y., Yanagisawa K. A new type of plasmid from a wild isolate of Dictyostelium species: the existence of closely situated long inverted repeats. Nucleic Acids Res. 1987 Feb 11;15(3):1097–1107. doi: 10.1093/nar/15.3.1097. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pabo C. O., Sauer R. T. Protein-DNA recognition. Annu Rev Biochem. 1984;53:293–321. doi: 10.1146/annurev.bi.53.070184.001453. [DOI] [PubMed] [Google Scholar]
- Pears C. J., Williams J. G. Identification of a DNA sequence element required for efficient expression of a developmentally regulated and cAMP-inducible gene of Dictyostelium discoideum. EMBO J. 1987 Jan;6(1):195–200. doi: 10.1002/j.1460-2075.1987.tb04738.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ragheb J. A., Dottin R. P. Structure and sequence of a UDP glucose pyrophosphorylase gene of Dictyostelium discoideum. Nucleic Acids Res. 1987 May 11;15(9):3891–3906. doi: 10.1093/nar/15.9.3891. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Saing K. M., Orii H., Tanaka Y., Yanagisawa K., Miura A., Ikeda H. Formation of deletion in Escherichia coli between direct repeats located in the long inverted repeats of a cellular slime mold plasmid: participation of DNA gyrase. Mol Gen Genet. 1988 Sep;214(1):1–5. doi: 10.1007/BF00340170. [DOI] [PubMed] [Google Scholar]
- Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schaap P., van Driel R. V. Induction of post-aggregative differentiation in Dictyostelium discoideum by cAMP. Evidence of involvement of the cell surface cAMP receptor. Exp Cell Res. 1985 Aug;159(2):388–398. doi: 10.1016/s0014-4827(85)80012-4. [DOI] [PubMed] [Google Scholar]
- Silver B. J., Bokar J. A., Virgin J. B., Vallen E. A., Milsted A., Nilson J. H. Cyclic AMP regulation of the human glycoprotein hormone alpha-subunit gene is mediated by an 18-base-pair element. Proc Natl Acad Sci U S A. 1987 Apr;84(8):2198–2202. doi: 10.1073/pnas.84.8.2198. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Som T., Armstrong K. A., Volkert F. C., Broach J. R. Autoregulation of 2 micron circle gene expression provides a model for maintenance of stable plasmid copy levels. Cell. 1988 Jan 15;52(1):27–37. doi: 10.1016/0092-8674(88)90528-4. [DOI] [PubMed] [Google Scholar]
- Staden R. Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucleic Acids Res. 1982 Aug 11;10(15):4731–4751. doi: 10.1093/nar/10.15.4731. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Staden R. Graphic methods to determine the function of nucleic acid sequences. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):521–538. doi: 10.1093/nar/12.1part2.521. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sussman R., Rayner E. P. Physical characterization of deoxyribonucleic acids in Dictyostelium discoideum. Arch Biochem Biophys. 1971 May;144(1):127–137. doi: 10.1016/0003-9861(71)90462-0. [DOI] [PubMed] [Google Scholar]
- Szostak J. W., Wu R. Insertion of a genetic marker into the ribosomal DNA of yeast. Plasmid. 1979 Oct;2(4):536–554. doi: 10.1016/0147-619x(79)90053-2. [DOI] [PubMed] [Google Scholar]
- Toh-e A., Araki H., Utatsu I., Oshima Y. Plasmids resembling 2-micrometers DNA in the osmotolerant yeasts Saccharomyces bailii and Saccharomyces bisporus. J Gen Microbiol. 1984 Oct;130(10):2527–2534. doi: 10.1099/00221287-130-10-2527. [DOI] [PubMed] [Google Scholar]
- Toh H., Hayashida H., Miyata T. Sequence homology between retroviral reverse transcriptase and putative polymerases of hepatitis B virus and cauliflower mosaic virus. 1983 Oct 27-Nov 2Nature. 305(5937):827–829. doi: 10.1038/305827a0. [DOI] [PubMed] [Google Scholar]
- Volkert F. C., Broach J. R. Site-specific recombination promotes plasmid amplification in yeast. Cell. 1986 Aug 15;46(4):541–550. doi: 10.1016/0092-8674(86)90879-2. [DOI] [PubMed] [Google Scholar]
- Warrick H. M., Spudich J. A. Codon preference in Dictyostelium discoideum. Nucleic Acids Res. 1988 Jul 25;16(14A):6617–6635. doi: 10.1093/nar/16.14.6617. [DOI] [PMC free article] [PubMed] [Google Scholar]