Skip to main content
Journal of Clinical Microbiology logoLink to Journal of Clinical Microbiology
. 1991 Jun;29(6):1194–1201. doi: 10.1128/jcm.29.6.1194-1201.1991

Repeated DNA in Pneumocystis carinii.

S L Stringer 1, S T Hong 1, D Giuntoli 1, J R Stringer 1
PMCID: PMC269968  PMID: 1677941

Abstract

A 16-kb DNA fragment designated Rp3-1 and cloned from the genome of rat-derived Pneumocystis carinii was found to contain sequences that were repeated approximately 70 times per genome. The repeated sequences in Rp3-1 spanned at least 10.4 kb. Sequences in Rp3-1 were present on each of the 16 P. carinii chromosomes resolved by field inversion gel electrophoresis. Most of the P. carinii genomic sequences homologous to those in the Rp3-1 clone appeared to be as long as those in the Rp3-1 clone but were highly polymorphic with respect to restriction enzyme cleavage sites. The Rp3-1 DNA fragment appears to be a member of a family of large, degenerate, dispersed repeats.

Full text

PDF
1194

Images in this article

Selected References

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

  1. Bedbrook J. R., Jones J., O'Dell M., Thompson R. D., Flavell R. B. A molecular description of telometic heterochromatin in secale species. Cell. 1980 Feb;19(2):545–560. doi: 10.1016/0092-8674(80)90529-2. [DOI] [PubMed] [Google Scholar]
  2. Blackburn E. H. The molecular structure of centromeres and telomeres. Annu Rev Biochem. 1984;53:163–194. doi: 10.1146/annurev.bi.53.070184.001115. [DOI] [PubMed] [Google Scholar]
  3. Boeke J. D., Garfinkel D. J., Styles C. A., Fink G. R. Ty elements transpose through an RNA intermediate. Cell. 1985 Mar;40(3):491–500. doi: 10.1016/0092-8674(85)90197-7. [DOI] [PubMed] [Google Scholar]
  4. Cameron J. R., Loh E. Y., Davis R. W. Evidence for transposition of dispersed repetitive DNA families in yeast. Cell. 1979 Apr;16(4):739–751. doi: 10.1016/0092-8674(79)90090-4. [DOI] [PubMed] [Google Scholar]
  5. Carle G. F., Frank M., Olson M. V. Electrophoretic separations of large DNA molecules by periodic inversion of the electric field. Science. 1986 Apr 4;232(4746):65–68. doi: 10.1126/science.3952500. [DOI] [PubMed] [Google Scholar]
  6. Cushion M. T., Ruffolo J. J., Walzer P. D. Analysis of the developmental stages of Pneumocystis carinii, in vitro. Lab Invest. 1988 Mar;58(3):324–331. [PubMed] [Google Scholar]
  7. Dunn B., Szauter P., Pardue M. L., Szostak J. W. Transfer of yeast telomeres to linear plasmids by recombination. Cell. 1984 Nov;39(1):191–201. doi: 10.1016/0092-8674(84)90205-8. [DOI] [PubMed] [Google Scholar]
  8. Edman J. C., Kovacs J. A., Masur H., Santi D. V., Elwood H. J., Sogin M. L. Ribosomal RNA sequence shows Pneumocystis carinii to be a member of the fungi. Nature. 1988 Aug 11;334(6182):519–522. doi: 10.1038/334519a0. [DOI] [PubMed] [Google Scholar]
  9. Edman U., Edman J. C., Lundgren B., Santi D. V. Isolation and expression of the Pneumocystis carinii thymidylate synthase gene. Proc Natl Acad Sci U S A. 1989 Sep;86(17):6503–6507. doi: 10.1073/pnas.86.17.6503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hong S. T., Steele P. E., Cushion M. T., Walzer P. D., Stringer S. L., Stringer J. R. Pneumocystis carinii karyotypes. J Clin Microbiol. 1990 Aug;28(8):1785–1795. doi: 10.1128/jcm.28.8.1785-1795.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Johnson E. M. A family of inverted repeat sequences and specific single-strand gaps at the termini of the Physarum rDNA palindrome. Cell. 1980 Dec;22(3):875–886. doi: 10.1016/0092-8674(80)90564-4. [DOI] [PubMed] [Google Scholar]
  12. Kovacs J. A., Hiemenz J. W., Macher A. M., Stover D., Murray H. W., Shelhamer J., Lane H. C., Urmacher C., Honig C., Longo D. L. Pneumocystis carinii pneumonia: a comparison between patients with the acquired immunodeficiency syndrome and patients with other immunodeficiencies. Ann Intern Med. 1984 May;100(5):663–671. doi: 10.7326/0003-4819-100-5-663. [DOI] [PubMed] [Google Scholar]
  13. Linke M. J., Cushion M. T., Walzer P. D. Properties of the major antigens of rat and human Pneumocystis carinii. Infect Immun. 1989 May;57(5):1547–1555. doi: 10.1128/iai.57.5.1547-1555.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Meade J. C., Shaw J., Lemaster S., Gallagher G., Stringer J. R. Structure and expression of a tandem gene pair in Leishmania donovani that encodes a protein structurally homologous to eucaryotic cation-transporting ATPases. Mol Cell Biol. 1987 Nov;7(11):3937–3946. doi: 10.1128/mcb.7.11.3937. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Mills J. Pneumocystis carinii and Toxoplasma gondii infections in patients with AIDS. Rev Infect Dis. 1986 Nov-Dec;8(6):1001–1011. doi: 10.1093/clinids/8.6.1001. [DOI] [PubMed] [Google Scholar]
  16. Mount S. M., Rubin G. M. Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins. Mol Cell Biol. 1985 Jul;5(7):1630–1638. doi: 10.1128/mcb.5.7.1630. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. O'Hare K., Rubin G. M. Structures of P transposable elements and their sites of insertion and excision in the Drosophila melanogaster genome. Cell. 1983 Aug;34(1):25–35. doi: 10.1016/0092-8674(83)90133-2. [DOI] [PubMed] [Google Scholar]
  18. Pardue M. L. Localization of repeated DNA sequences in Xenopus chromosomes. Cold Spring Harb Symp Quant Biol. 1974;38:475–482. doi: 10.1101/sqb.1974.038.01.051. [DOI] [PubMed] [Google Scholar]
  19. Priimägi A. F., Mizrokhi L. J., Ilyin Y. V. The Drosophila mobile element jockey belongs to LINEs and contains coding sequences homologous to some retroviral proteins. Gene. 1988 Oct 30;70(2):253–262. doi: 10.1016/0378-1119(88)90197-7. [DOI] [PubMed] [Google Scholar]
  20. Roth G. E., Moritz K. B. Restriction enzyme analysis of the germ line limited DNA of Ascaris suum. Chromosoma. 1981;83(2):169–190. doi: 10.1007/BF00286787. [DOI] [PubMed] [Google Scholar]
  21. Rubin G. M. Isolation of a telomeric DNA sequence from Drosophila melanogaster. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 2):1041–1046. doi: 10.1101/sqb.1978.042.01.104. [DOI] [PubMed] [Google Scholar]
  22. Sakaguchi K. Invertrons, a class of structurally and functionally related genetic elements that includes linear DNA plasmids, transposable elements, and genomes of adeno-type viruses. Microbiol Rev. 1990 Mar;54(1):66–74. doi: 10.1128/mr.54.1.66-74.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Scherer S., Stevens D. A. A Candida albicans dispersed, repeated gene family and its epidemiologic applications. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1452–1456. doi: 10.1073/pnas.85.5.1452. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Schwarz-Sommer Z., Leclercq L., Göbel E., Saedler H. Cin4, an insert altering the structure of the A1 gene in Zea mays, exhibits properties of nonviral retrotransposons. EMBO J. 1987 Dec 20;6(13):3873–3880. doi: 10.1002/j.1460-2075.1987.tb02727.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Singer M. F. SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell. 1982 Mar;28(3):433–434. doi: 10.1016/0092-8674(82)90194-5. [DOI] [PubMed] [Google Scholar]
  26. Stringer J. R., Kuhn R. M., Newman J. L., Meade J. C. Unequal homologous recombination between tandemly arranged sequences stably incorporated into cultured rat cells. Mol Cell Biol. 1985 Oct;5(10):2613–2622. doi: 10.1128/mcb.5.10.2613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Stringer S. L., Stringer J. R., Blase M. A., Walzer P. D., Cushion M. T. Pneumocystis carinii: sequence from ribosomal RNA implies a close relationship with fungi. Exp Parasitol. 1989 May;68(4):450–461. doi: 10.1016/0014-4894(89)90130-6. [DOI] [PubMed] [Google Scholar]
  28. Szostak J. W., Blackburn E. H. Cloning yeast telomeres on linear plasmid vectors. Cell. 1982 May;29(1):245–255. doi: 10.1016/0092-8674(82)90109-x. [DOI] [PubMed] [Google Scholar]
  29. Walzer P. D., Linke M. J. A comparison of the antigenic characteristics of rat and human Pneumocystis carinii by immunoblotting. J Immunol. 1987 Apr 1;138(7):2257–2265. [PubMed] [Google Scholar]
  30. Watanabe J., Hori H., Tanabe K., Nakamura Y. Phylogenetic association of Pneumocystis carinii with the 'Rhizopoda/Myxomycota/Zygomycota group' indicated by comparison of 5S ribosomal RNA sequences. Mol Biochem Parasitol. 1989 Jan 15;32(2-3):163–167. doi: 10.1016/0166-6851(89)90067-4. [DOI] [PubMed] [Google Scholar]
  31. Weiner A. M., Deininger P. L., Efstratiadis A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem. 1986;55:631–661. doi: 10.1146/annurev.bi.55.070186.003215. [DOI] [PubMed] [Google Scholar]
  32. Young B. S., Pession A., Traverse K. L., French C., Pardue M. L. Telomere regions in Drosophila share complex DNA sequences with pericentric heterochromatin. Cell. 1983 Aug;34(1):85–94. doi: 10.1016/0092-8674(83)90138-1. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Clinical Microbiology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES