Skip to main content
PMC home page
Genetics logoLink to Genetics
. 1998 Mar;148(3):1117–1125. doi: 10.1093/genetics/148.3.1117

Dictyostelium discoideum nuclear plasmid Ddp5 is a chimera related to the Ddp1 and Ddp2 plasmid families.

W K Rieben Jr 1, C M Gonzales 1, S T Gonzales 1, K J Pilkington 1, H Kiyosawa 1, J E Hughes 1, D L Welker 1
PMCID: PMC1460040  PMID: 9539429

Abstract

The 14,955-bp Dictyostelium discoideum nuclear plasmid Ddp5 contains six transcribed open reading frames. One of these is related to the rep gene of the Ddp2 plasmid, and the other five are related to genes present on the Ddp1 plasmid. The absence of a homolog of the Ddp1 G1 gene, coupled with the presence of the Ddp2 rep gene homolog and of a 1.6-kb inverted repeat analogous to the inverted repeats on members of the Ddp2 plasmid family, suggests that Ddp5 uses Ddp2-like replication and copy number control mechanisms and that it should be assigned to the Ddp2 plasmid family. Ddp5 carries genes homologous to the D1/D3 and D2 genes of the Ddp1 plasmid as well as the Ddp1 G2/G3/D4, G5/D6, and G6/G4/D5 genes. The products of the Ddp5 G2-like, G5-like, and G6-like genes are likely to be transcription factors regulating the expression of themselves and of the other Ddp5 genes. The D1-like and D2-like genes may confer a selective advantage to plasmid-bearing cells, because they can be deleted from plasmid-based shuttle vectors with no apparent effect on vector maintenance. Updated sequence information for the Ddp1 G5/D6, D1/D3, and D2 genes as well as the Dmp1 and Dmp2 G5-like genes is presented. The locations of introns in the G5-like and D1-like genes of Ddp5 and in the homologous genes of the Ddp1, Dmp1, and Dmp2 plasmids were identified. These introns all have GU at the 5' intron border and AG at the 3' intron border, are short (59 to 71 nucleotides), and are AT-rich. A conserved HHCC domain was identified in the G5 proteins; this is a putative zinc binding domain and may be involved in protein-DNA interaction.

Full Text

The Full Text of this article is available as a PDF (258.8 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ashktorab H., Welker D. L. Establishment of the nuclear location of Dictyostelium discoideum plasmids. Gene. 1988 May 15;65(1):41–49. doi: 10.1016/0378-1119(88)90415-5. [DOI] [PubMed] [Google Scholar]
  2. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Burke C. J., Sanyal G., Bruner M. W., Ryan J. A., LaFemina R. L., Robbins H. L., Zeft A. S., Middaugh C. R., Cordingley M. G. Structural implications of spectroscopic characterization of a putative zinc finger peptide from HIV-1 integrase. J Biol Chem. 1992 May 15;267(14):9639–9644. [PubMed] [Google Scholar]
  4. Bushman F. D., Engelman A., Palmer I., Wingfield P., Craigie R. Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding. Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3428–3432. doi: 10.1073/pnas.90.8.3428. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chang A. C., Slade M. B., Williams K. L. Identification of the origin of replication of the eukaryote Dictyostelium discoideum nuclear plasmid Ddp2. Plasmid. 1990 Nov;24(3):208–217. doi: 10.1016/0147-619x(90)90004-v. [DOI] [PubMed] [Google Scholar]
  6. Farrar N. A., Kiyosawa H., Hughes J. E., Welker D. L., Williams K. L. Nucleotide sequence of Ddp1, a high copy number nuclear plasmid of Dictyostelium discoideum. Plasmid. 1994 Mar;31(2):184–195. doi: 10.1006/plas.1994.1019. [DOI] [PubMed] [Google Scholar]
  7. Franke J., Podgorski G. J., Kessin R. H. The expression of two transcripts of the phosphodiesterase gene during the development of Dictyostelium discoideum. Dev Biol. 1987 Dec;124(2):504–511. doi: 10.1016/0012-1606(87)90503-3. [DOI] [PubMed] [Google Scholar]
  8. Gurniak C. B., Bang A. G., Noegel A. A. Transcript and sequence analysis of a 5.1 kb contiguous fragment of Dictyostelium discoideum plasmid Ddp1 that contains the origin of replication and codes for several transcripts. Curr Genet. 1990 Apr;17(4):321–325. doi: 10.1007/BF00314879. [DOI] [PubMed] [Google Scholar]
  9. Hughes J. E., Ashtorab H., Welker D. L. Nuclear plasmids in the Dictyostelium slime molds. Dev Genet. 1988;9(4-5):495–504. doi: 10.1002/dvg.1020090426. [DOI] [PubMed] [Google Scholar]
  10. Hughes J. E., Kiyosawa H., Welker D. L. Plasmid maintenance functions encoded on Dictyostelium discoideum nuclear plasmid Ddp1. Mol Cell Biol. 1994 Sep;14(9):6117–6124. doi: 10.1128/mcb.14.9.6117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hughes J. E., Podgorski G. J., Welker D. L. Selection of Dictyostelium discoideum transformants and analysis of vector maintenance using live bacteria resistant to G418. Plasmid. 1992 Jul;28(1):46–60. doi: 10.1016/0147-619x(92)90035-9. [DOI] [PubMed] [Google Scholar]
  12. Hughes J. E., Welker D. L. Copy number control and compatibility of nuclear plasmids in Dictyostelium discoideum. Plasmid. 1989 Nov;22(3):215–223. doi: 10.1016/0147-619x(89)90004-8. [DOI] [PubMed] [Google Scholar]
  13. Hänfler J., Teepe H., Weigel C., Kruft V., Lurz R., Wöstemeyer J. Circular extrachromosomal DNA codes for a surface protein in the (+) mating type of the zygomycete Absidia glauca. Curr Genet. 1992 Oct;22(4):319–325. doi: 10.1007/BF00317929. [DOI] [PubMed] [Google Scholar]
  14. Kiyosawa H., Hughes J. E., Podgorski G. J., Welker D. L. Small circular plasmids of the eukaryote Dictyostelium purpureum define two novel plasmid families. Plasmid. 1993 Sep;30(2):106–118. doi: 10.1006/plas.1993.1038. [DOI] [PubMed] [Google Scholar]
  15. Kiyosawa H., Hughes J. E., Welker D. L. Compatible Dictyostelium mucoroides nuclear plasmids Dmp1 and Dmp2 both belong to the Ddp1 plasmid family. Plasmid. 1994 Mar;31(2):121–130. doi: 10.1006/plas.1994.1013. [DOI] [PubMed] [Google Scholar]
  16. Kiyosawa H., Hughes J. E., Welker D. L. The replication origin position and its relationship to a negative trans-acting transcription regulator encoded by Dictyostelium discoideum nuclear plasmid Ddp1. Curr Genet. 1995 Apr;27(5):479–485. doi: 10.1007/BF00311219. [DOI] [PubMed] [Google Scholar]
  17. Leiting B., Lindner I. J., Noegel A. A. The extrachromosomal replication of Dictyostelium plasmid Ddp2 requires a cis-acting element and a plasmid-encoded trans-acting factor. Mol Cell Biol. 1990 Jul;10(7):3727–3736. doi: 10.1128/mcb.10.7.3727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. 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]
  19. Service R. F. Amino acid alchemy transmutes sheets to coils. Science. 1997 Jul 11;277(5323):179–179. doi: 10.1126/science.277.5323.179. [DOI] [PubMed] [Google Scholar]
  20. Slade M. B., Chang A. C., Williams K. L. The sequence and organization of Ddp2, a high-copy-number nuclear plasmid of Dictyostelium discoideum. Plasmid. 1990 Nov;24(3):195–207. doi: 10.1016/0147-619x(90)90003-u. [DOI] [PubMed] [Google Scholar]
  21. Vincent K. A., Ellison V., Chow S. A., Brown P. O. Characterization of human immunodeficiency virus type 1 integrase expressed in Escherichia coli and analysis of variants with amino-terminal mutations. J Virol. 1993 Jan;67(1):425–437. doi: 10.1128/jvi.67.1.425-437.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Yin Y., Welker D. L. Dictyostelium giganteum plasmid Dgp1 is a member of the Ddp2 plasmid family. Plasmid. 1992 Jul;28(1):37–45. doi: 10.1016/0147-619x(92)90034-8. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES