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. 1985 Aug 26;13(16):5789–5804. doi: 10.1093/nar/13.16.5789

Apparent generation of a segmented mRNA from two separate tandem gene families in Trypanosoma cruzi.

A Gonzalez, T J Lerner, M Huecas, B Sosa-Pineda, N Nogueira, P M Lizardi
PMCID: PMC321912  PMID: 2412209

Abstract

Using a cDNA for an abundant Trypanosoma cruzi mRNA as probe, we have cloned and sequenced a gene which is organized in at least 20 nearly perfect tandem repeats of 940 base pairs. The 5' end of the mRNA has been sequenced by primer extension and found to contain a 35 nucleotide mini-exon (or spliced-leader) sequence that is ubiquitous in trypanosome mRNAs. This sequence, however, is not present in the tandem genomic repeats which encode the exon containing the major portion of the mRNA. Previous studies have shown that the 35-nucleotide sequence is encoded by a separate tandem gene family. One model to explain the formation of a segmented mRNA invokes priming of transcription by a small RNA which contains the leader sequence at its 5' end. However, northern blot analysis of total trypanosome RNA reveals a ladder of molecules larger than the mature mRNA, which appear to be faithful multimeric copies of the tandem gene. The discrete sizes of these RNAs correspond to those expected for partially processed precursors. These observations lend credence to the possibility of an alternative model where segmented mRNAs are generated by inter-molecular splicing.

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Selected References

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

  1. Biggin M. D., Gibson T. J., Hong G. F. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. doi: 10.1073/pnas.80.13.3963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Boothroyd J. C., Cross G. A. Transcripts coding for variant surface glycoproteins of Trypanosoma brucei have a short, identical exon at their 5' end. Gene. 1982 Dec;20(2):281–289. doi: 10.1016/0378-1119(82)90046-4. [DOI] [PubMed] [Google Scholar]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. Ghosh P. K., Reddy V. B., Piatak M., Lebowitz P., Weissman S. M. Determination of RNA sequences by primer directed synthesis and sequencing of their cDNA transcripts. Methods Enzymol. 1980;65(1):580–595. doi: 10.1016/s0076-6879(80)65061-7. [DOI] [PubMed] [Google Scholar]
  9. Gonzalez A., Prediger E., Huecas M. E., Nogueira N., Lizardi P. M. Minichromosomal repetitive DNA in Trypanosoma cruzi: its use in a high-sensitivity parasite detection assay. Proc Natl Acad Sci U S A. 1984 Jun;81(11):3356–3360. doi: 10.1073/pnas.81.11.3356. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Huang P. L., Roberts B. E., Pratt D. M., David J. R., Miller J. S. Structure and arrangement of the beta-tubulin genes of Leishmania tropica. Mol Cell Biol. 1984 Jul;4(7):1372–1383. doi: 10.1128/mcb.4.7.1372. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kooter J. M., De Lange T., Borst P. Discontinuous synthesis of mRNA in trypanosomes. EMBO J. 1984 Oct;3(10):2387–2392. doi: 10.1002/j.1460-2075.1984.tb02144.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Krieg P. A., Melton D. A. Functional messenger RNAs are produced by SP6 in vitro transcription of cloned cDNAs. Nucleic Acids Res. 1984 Sep 25;12(18):7057–7070. doi: 10.1093/nar/12.18.7057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Krug R. M., Broni B. A., Bouloy M. Are the 5' ends of influenza viral mRNAs synthesized in vivo donated by host mRNAs? Cell. 1979 Oct;18(2):329–334. doi: 10.1016/0092-8674(79)90052-7. [DOI] [PubMed] [Google Scholar]
  14. Krämer A., Keller W., Appel B., Lührmann R. The 5' terminus of the RNA moiety of U1 small nuclear ribonucleoprotein particles is required for the splicing of messenger RNA precursors. Cell. 1984 Aug;38(1):299–307. doi: 10.1016/0092-8674(84)90551-8. [DOI] [PubMed] [Google Scholar]
  15. Lai M. M., Baric R. S., Brayton P. R., Stohlman S. A. Characterization of leader RNA sequences on the virion and mRNAs of mouse hepatitis virus, a cytoplasmic RNA virus. Proc Natl Acad Sci U S A. 1984 Jun;81(12):3626–3630. doi: 10.1073/pnas.81.12.3626. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Landfear S. M., McMahon-Pratt D., Wirth D. F. Tandem arrangement of tubulin genes in the protozoan parasite Leishmania enriettii. Mol Cell Biol. 1983 Jun;3(6):1070–1076. doi: 10.1128/mcb.3.6.1070. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Lazzarini R. A., Keene J. D., Schubert M. The origins of defective interfering particles of the negative-strand RNA viruses. Cell. 1981 Oct;26(2 Pt 2):145–154. doi: 10.1016/0092-8674(81)90298-1. [DOI] [PubMed] [Google Scholar]
  18. Lerner M. R., Boyle J. A., Mount S. M., Wolin S. L., Steitz J. A. Are snRNPs involved in splicing? Nature. 1980 Jan 10;283(5743):220–224. doi: 10.1038/283220a0. [DOI] [PubMed] [Google Scholar]
  19. Lipps H. J., Nordheim A., Lafer E. M., Ammermann D., Stollar B. D., Rich A. Antibodies against Z DNA react with the macronucleus but not the micronucleus of the hypotrichous ciliate stylonychia mytilus. Cell. 1983 Feb;32(2):435–441. doi: 10.1016/0092-8674(83)90463-4. [DOI] [PubMed] [Google Scholar]
  20. Lizardi P. M. Genetic polymorphism of silk fibroin studied by two-dimensional translation pause fingerprints. Cell. 1979 Oct;18(2):581–589. doi: 10.1016/0092-8674(79)90074-6. [DOI] [PubMed] [Google Scholar]
  21. Lizardi P. M. Methods for the preparation of messenger RNA. Methods Enzymol. 1983;96:24–38. doi: 10.1016/s0076-6879(83)96006-8. [DOI] [PubMed] [Google Scholar]
  22. Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
  23. 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]
  24. Mount S. M., Pettersson I., Hinterberger M., Karmas A., Steitz J. A. The U1 small nuclear RNA-protein complex selectively binds a 5' splice site in vitro. Cell. 1983 Jun;33(2):509–518. doi: 10.1016/0092-8674(83)90432-4. [DOI] [PubMed] [Google Scholar]
  25. Murphy W. J., Brentano S. T., Rice-Ficht A. C., Dorfman D. M., Donelson J. E. DNA rearrangements of the variable surface antigen genes of the trypanosomes. J Protozool. 1984 Feb;31(1):65–73. doi: 10.1111/j.1550-7408.1984.tb04291.x. [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. Nelson R. G., Parsons M., Selkirk M., Newport G., Barr P. J., Agabian N. Sequences homologous to variant antigen mRNA spliced leader in Trypanosomatidae which do not undergo antigenic variation. Nature. 1984 Apr 12;308(5960):665–667. doi: 10.1038/308665a0. [DOI] [PubMed] [Google Scholar]
  28. Nogueira N., Bianco C., Cohn Z. Studies on the selective lysis and purification of Trypanosoma cruzi. J Exp Med. 1975 Jul 1;142(1):224–229. doi: 10.1084/jem.142.1.224. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Nordheim A., Pardue M. L., Lafer E. M., Möller A., Stollar B. D., Rich A. Antibodies to left-handed Z-DNA bind to interband regions of Drosophila polytene chromosomes. Nature. 1981 Dec 3;294(5840):417–422. doi: 10.1038/294417a0. [DOI] [PubMed] [Google Scholar]
  30. Padgett R. A., Mount S. M., Steitz J. A., Sharp P. A. Splicing of messenger RNA precursors is inhibited by antisera to small nuclear ribonucleoprotein. Cell. 1983 Nov;35(1):101–107. doi: 10.1016/0092-8674(83)90212-x. [DOI] [PubMed] [Google Scholar]
  31. Parsons M., Nelson R. G., Watkins K. P., Agabian N. Trypanosome mRNAs share a common 5' spliced leader sequence. Cell. 1984 Aug;38(1):309–316. doi: 10.1016/0092-8674(84)90552-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Plotch S. J., Bouloy M., Ulmanen I., Krug R. M. A unique cap(m7GpppXm)-dependent influenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription. Cell. 1981 Mar;23(3):847–858. doi: 10.1016/0092-8674(81)90449-9. [DOI] [PubMed] [Google Scholar]
  33. Sakonju S., Bogenhagen D. F., Brown D. D. A control region in the center of the 5S RNA gene directs specific initiation of transcription: I. The 5' border of the region. Cell. 1980 Jan;19(1):13–25. doi: 10.1016/0092-8674(80)90384-0. [DOI] [PubMed] [Google Scholar]
  34. Seebeck T., Whittaker P. A., Imboden M. A., Hardman N., Braun R. Tubulin genes of Trypanosoma brucei: a tightly clustered family of alternating genes. Proc Natl Acad Sci U S A. 1983 Aug;80(15):4634–4638. doi: 10.1073/pnas.80.15.4634. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Spaan W., Delius H., Skinner M., Armstrong J., Rottier P., Smeekens S., van der Zeijst B. A., Siddell S. G. Coronavirus mRNA synthesis involves fusion of non-contiguous sequences. EMBO J. 1983;2(10):1839–1844. doi: 10.1002/j.1460-2075.1983.tb01667.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Sun Y. L., Xu Y. Z., Chambon P. A simple and efficient method for the separation and detection of small DNA fragments by electrophoresis in formamide containing agarose gels and Southern blotting to DBM-paper. Nucleic Acids Res. 1982 Oct 11;10(19):5753–5763. doi: 10.1093/nar/10.19.5753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Thomas P. S. Hybridization of denatured RNA and small DNA fragments transferred to nitrocellulose. Proc Natl Acad Sci U S A. 1980 Sep;77(9):5201–5205. doi: 10.1073/pnas.77.9.5201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Thomashow L. S., Milhausen M., Rutter W. J., Agabian N. Tubulin genes are tandemly linked and clustered in the genome of trypanosoma brucei. Cell. 1983 Jan;32(1):35–43. doi: 10.1016/0092-8674(83)90494-4. [DOI] [PubMed] [Google Scholar]
  39. Tullis R. H., Rubin H. Calcium protects DNase I from proteinase K: a new method for the removal of contaminating RNase from DNase I. Anal Biochem. 1980 Sep 1;107(1):260–264. doi: 10.1016/0003-2697(80)90519-9. [DOI] [PubMed] [Google Scholar]
  40. Van der Ploeg L. H., Cornelissen A. W., Michels P. A., Borst P. Chromosome rearrangements in Trypanosoma brucei. Cell. 1984 Nov;39(1):213–221. doi: 10.1016/0092-8674(84)90207-1. [DOI] [PubMed] [Google Scholar]
  41. 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]
  42. 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]
  43. Wang A. H., Quigley G. J., Kolpak F. J., Crawford J. L., van Boom J. H., van der Marel G., Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 1979 Dec 13;282(5740):680–686. doi: 10.1038/282680a0. [DOI] [PubMed] [Google Scholar]
  44. Yang V. W., Lerner M. R., Steitz J. A., Flint S. J. A small nuclear ribonucleoprotein is required for splicing of adenoviral early RNA sequences. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1371–1375. doi: 10.1073/pnas.78.3.1371. [DOI] [PMC free article] [PubMed] [Google Scholar]

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