Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1987 Dec 23;15(24):10179–10198. doi: 10.1093/nar/15.24.10179

The structure and transcription of an element interspersed between tandem arrays of mini-exon donor RNA genes in Trypanosoma brucei.

M Carrington 1, I Roditi 1, R O Williams 1
PMCID: PMC339938  PMID: 2827116

Abstract

Messenger RNAs in Trypanosoma brucei brucei have the same 35 bases at the 5' end. These 35 bases are not encoded contiguously in the genome, but are donated from a 140 base RNA (the mini-exon donor RNA). The mini-exon donor RNA (medRNA) is encoded by 1.35 kbp genes that occur in tandem repeats. A DNA element that is associated with mini-exon donor RNA medRNA genes has been identified and characterised by restriction enzyme mapping and partial sequencing. This element (the medRNA gene associated element: MAE) varies in length between 5.5 and 7 kbp. There are between 20 and 40 copies of the element per haploid genome. In clones of genomic DNA MAEs occurred between two medRNA gene arrays and on both sides of a medRNA gene array. The MAEs were always in the same orientation with respect to the medRNA genes. It is proposed that in the genome MAEs are interspersed between tandem arrays of medRNA genes. The transcription of the element has been investigated. Low levels of a 70-80 base transcript derived from a small part of MAE were detected in steady state RNA. Nuclear run off transcript studies indicated that MAEs were transcribed at high levels and that they possibly contain at least one start and stop of transcription.

Full text

PDF
10192

Images in this article

10188Image
on p.10188
10189Image
on p.10189
10190Image
on p.10190
10191Image
on p.10191
10193Image
on p.10193
10194Image
on p.10194
10196Image
on p.10196

Selected References

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

  1. Biggin M., Farrell P. J., Barrell B. G. Transcription and DNA sequence of the BamHI L fragment of B95-8 Epstein-Barr virus. EMBO J. 1984 May;3(5):1083–1090. doi: 10.1002/j.1460-2075.1984.tb01933.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Borst P. Discontinuous transcription and antigenic variation in trypanosomes. Annu Rev Biochem. 1986;55:701–732. doi: 10.1146/annurev.bi.55.070186.003413. [DOI] [PubMed] [Google Scholar]
  3. Brun R., Schönenberger Cultivation and in vitro cloning or procyclic culture forms of Trypanosoma brucei in a semi-defined medium. Short communication. Acta Trop. 1979 Sep;36(3):289–292. [PubMed] [Google Scholar]
  4. Campbell D. A., Thornton D. A., Boothroyd J. C. Apparent discontinuous transcription of Trypanosoma brucei variant surface antigen genes. 1984 Sep 27-Oct 3Nature. 311(5984):350–355. doi: 10.1038/311350a0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Carrington D. M., Auffret A., Hanke D. E. Polypeptide ligation occurs during post-translational modification of concanavalin A. Nature. 1985 Jan 3;313(5997):64–67. doi: 10.1038/313064a0. [DOI] [PubMed] [Google Scholar]
  6. De Lange T., Berkvens T. M., Veerman H. J., Frasch A. C., Barry J. D., Borst P. Comparison of the genes coding for the common 5' terminal sequence of messenger RNAs in three trypanosome species. Nucleic Acids Res. 1984 Jun 11;12(11):4431–4443. doi: 10.1093/nar/12.11.4431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. De Lange T., Liu A. Y., Van der Ploeg L. H., Borst P., Tromp M. C., Van Boom J. H. Tandem repetition of the 5' mini-exon of variant surface glycoprotein genes: a multiple promoter for VSG gene transcription? Cell. 1983 Oct;34(3):891–900. doi: 10.1016/0092-8674(83)90546-9. [DOI] [PubMed] [Google Scholar]
  8. De Lange T., Michels P. A., Veerman H. J., Cornelissen A. W., Borst P. Many trypanosome messenger RNAs share a common 5' terminal sequence. Nucleic Acids Res. 1984 May 11;12(9):3777–3790. doi: 10.1093/nar/12.9.3777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dorfman D. M., Donelson J. E. Characterization of the 1.35 kilobase DNA repeat unit containing the conserved 35 nucleotides at the 5'-termini of variable surface glycoprotein mRNAs in Trypanosoma brucei. Nucleic Acids Res. 1984 Jun 25;12(12):4907–4920. doi: 10.1093/nar/12.12.4907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Felgner P., Brinkmann U., Zillmann U., Mehlitz D., Abu-Ishira S. Epidemiological studies on the animal reservoir of gambiense sleeping sickness. Part II. Parasitological and immunodiagnostic examination of the human population. Tropenmed Parasitol. 1981 Sep;32(3):134–140. [PubMed] [Google Scholar]
  11. Frischauf A. M., Lehrach H., Poustka A., Murray N. Lambda replacement vectors carrying polylinker sequences. J Mol Biol. 1983 Nov 15;170(4):827–842. doi: 10.1016/s0022-2836(83)80190-9. [DOI] [PubMed] [Google Scholar]
  12. Geigy R., Kauffmann M. Sleeping sickness survey in the Serengeti area (Tanzania) 1971. I. Examination of large mammals for trypanosomes. Acta Trop. 1973;30(1):12–23. [PubMed] [Google Scholar]
  13. Grunstein M., Hogness D. S. Colony hybridization: a method for the isolation of cloned DNAs that contain a specific gene. Proc Natl Acad Sci U S A. 1975 Oct;72(10):3961–3965. doi: 10.1073/pnas.72.10.3961. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Grunstein M., Wallis J. Colony hybridization. Methods Enzymol. 1979;68:379–389. doi: 10.1016/0076-6879(79)68027-8. [DOI] [PubMed] [Google Scholar]
  15. Hasan G., Turner M. J., Cordingley J. S. Ribosomal RNA genes of Trypanosoma brucei. Cloning of a rRNA gene containing a mobile element. Nucleic Acids Res. 1982 Nov 11;10(21):6747–6761. doi: 10.1093/nar/10.21.6747. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kooter J. M., van der Spek H. J., Wagter R., d'Oliveira C. E., van der Hoeven F., Johnson P. J., Borst P. The anatomy and transcription of a telomeric expression site for variant-specific surface antigens in T. brucei. Cell. 1987 Oct 23;51(2):261–272. doi: 10.1016/0092-8674(87)90153-x. [DOI] [PubMed] [Google Scholar]
  17. Laird P. W., Kooter J. M., Loosbroek N., Borst P. Mature mRNAs of Trypanosoma brucei possess a 5' cap acquired by discontinuous RNA synthesis. Nucleic Acids Res. 1985 Jun 25;13(12):4253–4266. doi: 10.1093/nar/13.12.4253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Laird P. W., Zomerdijk J. C., de Korte D., Borst P. In vivo labelling of intermediates in the discontinuous synthesis of mRNAs in Trypanosoma brucei. EMBO J. 1987 Apr;6(4):1055–1062. doi: 10.1002/j.1460-2075.1987.tb04858.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lenardo M. J., Dorfman D. M., Donelson J. E. The spliced leader sequence of Trypanosoma brucei has a potential role as a cap donor structure. Mol Cell Biol. 1985 Sep;5(9):2487–2490. doi: 10.1128/mcb.5.9.2487. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. McMaster G. K., Carmichael G. G. Analysis of single- and double-stranded nucleic acids on polyacrylamide and agarose gels by using glyoxal and acridine orange. Proc Natl Acad Sci U S A. 1977 Nov;74(11):4835–4838. doi: 10.1073/pnas.74.11.4835. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Melton D. A., Krieg P. A., Rebagliati M. R., Maniatis T., Zinn K., Green M. R. Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res. 1984 Sep 25;12(18):7035–7056. doi: 10.1093/nar/12.18.7035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Milhausen M., Nelson R. G., Sather S., Selkirk M., Agabian N. Identification of a small RNA containing the trypanosome spliced leader: a donor of shared 5' sequences of trypanosomatid mRNAs? Cell. 1984 Oct;38(3):721–729. doi: 10.1016/0092-8674(84)90267-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Miller E. N., Turner M. J. Analysis of antigenic types appearing in first relapse populations of clones of Trypanosoma brucei. Parasitology. 1981 Feb;82(1):63–80. doi: 10.1017/s0031182000041871. [DOI] [PubMed] [Google Scholar]
  24. Miller S. I., Landfear S. M., Wirth D. F. Cloning and characterization of a Leishmania gene encoding a RNA spliced leader sequence. Nucleic Acids Res. 1986 Sep 25;14(18):7341–7360. doi: 10.1093/nar/14.18.7341. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Murphy W. J., Watkins K. P., Agabian N. Identification of a novel Y branch structure as an intermediate in trypanosome mRNA processing: evidence for trans splicing. Cell. 1986 Nov 21;47(4):517–525. doi: 10.1016/0092-8674(86)90616-1. [DOI] [PubMed] [Google Scholar]
  26. Nelson R. G., Parsons M., Barr P. J., Stuart K., Selkirk M., Agabian N. Sequences homologous to the variant antigen mRNA spliced leader are located in tandem repeats and variable orphons in trypanosoma brucei. Cell. 1983 Oct;34(3):901–909. doi: 10.1016/0092-8674(83)90547-0. [DOI] [PubMed] [Google Scholar]
  27. Nielsen D. A., Shapiro D. J. Preparation of capped RNA transcripts using T7 RNA polymerase. Nucleic Acids Res. 1986 Jul 25;14(14):5936–5936. doi: 10.1093/nar/14.14.5936. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Parsons M., Nelson R. G., Agabian N. The trypanosome spliced leader small RNA gene family: stage-specific modification of one of several similar dispersed genes. Nucleic Acids Res. 1986 Feb 25;14(4):1703–1718. doi: 10.1093/nar/14.4.1703. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Rackwitz H. R., Zehetner G., Frischauf A. M., Lehrach H. Rapid restriction mapping of DNA cloned in lambda phage vectors. Gene. 1984 Oct;30(1-3):195–200. doi: 10.1016/0378-1119(84)90120-3. [DOI] [PubMed] [Google Scholar]
  30. 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]
  31. Shea C., Lee M. G., Van der Ploeg L. H. VSG gene 118 is transcribed from a cotransposed pol I-like promoter. Cell. 1987 Aug 14;50(4):603–612. doi: 10.1016/0092-8674(87)90033-x. [DOI] [PubMed] [Google Scholar]
  32. Strauss E. C., Kobori J. A., Siu G., Hood L. E. Specific-primer-directed DNA sequencing. Anal Biochem. 1986 Apr;154(1):353–360. doi: 10.1016/0003-2697(86)90536-1. [DOI] [PubMed] [Google Scholar]
  33. Sutton R. E., Boothroyd J. C. Evidence for trans splicing in trypanosomes. Cell. 1986 Nov 21;47(4):527–535. doi: 10.1016/0092-8674(86)90617-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Van der Ploeg L. H., Liu A. Y., Michels P. A., De Lange T., Borst P., Majumder H. K., Weber H., Veeneman G. H., Van Boom J. RNA splicing is required to make the messenger RNA for a variant surface antigen in trypanosomes. Nucleic Acids Res. 1982 Jun 25;10(12):3591–3604. doi: 10.1093/nar/10.12.3591. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  36. Ward E. S., Ellar D. J. Bacillus thuringiensis var. israelensis delta-endotoxin. Nucleotide sequence and characterization of the transcripts in Bacillus thuringiensis and Escherichia coli. J Mol Biol. 1986 Sep 5;191(1):1–11. doi: 10.1016/0022-2836(86)90417-1. [DOI] [PubMed] [Google Scholar]
  37. Young J. R., Donelson J. E., Majiwa P. A., Shapiro S. Z., Williams R. O. analysis of genomic rearrangements associated with two variable antigen genes of Trypanosoma brucei. Nucleic Acids Res. 1982 Feb 11;10(3):803–819. doi: 10.1093/nar/10.3.803. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES