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. 1987 Dec 1;6(12):3819–3826. doi: 10.1002/j.1460-2075.1987.tb02718.x

Multiple copies of a retroposon interrupt spliced leader RNA genes in the African trypanosome, Trypanosoma gambiense.

S Aksoy 1, T M Lalor 1, J Martin 1, L H Van der Ploeg 1, F F Richards 1
PMCID: PMC553854  PMID: 2828038

Abstract

The 140-nucleotide spliced leader (SL) RNA, involved in mRNA maturation in the African trypanosomes and in other kinetoplastida, is encoded by a tandem array of spliced leader genes. We show that the 1.4-kb SL gene repeat unit in Trypanosoma gambiense is organized in tandem arrays confined to two large (minimum size 350-450 kb) restriction fragments. SL genes in both arrays are interrupted by a total of eight conserved insertion elements. Cleavage of genomic DNA at restriction sites present within the insertion element but not in the SL gene repeat, releases variable numbers of SL genes from the tandem array. Since the insertion element contains a terminal poly(A) track of 36 bases and because a 49-bp duplication of target DNA has occurred at the integration site, we conclude that it is a retroposon. This retropson is uniquely associated with the SL gene clusters. These retroposons presumably originated from a single insertion event after which their copy number increased, possibly through unequal sister chromatid exchange.

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Selected References

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

  1. Benton W. D., Davis R. W. Screening lambdagt recombinant clones by hybridization to single plaques in situ. Science. 1977 Apr 8;196(4286):180–182. doi: 10.1126/science.322279. [DOI] [PubMed] [Google Scholar]
  2. Bernards A., Kooter J. M., Michels P. A., Moberts R. M., Borst P. Pulsed field gradient electrophoresis of DNA digested in agarose allows the sizing of the large duplication unit of a surface antigen gene in trypanosomes. Gene. 1986;42(3):313–322. doi: 10.1016/0378-1119(86)90235-0. [DOI] [PubMed] [Google Scholar]
  3. Bernards A., Van der Ploeg L. H., Frasch A. C., Borst P., Boothroyd J. C., Coleman S., Cross G. A. Activation of trypanosome surface glycoprotein genes involves a duplication-transposition leading to an altered 3' end. Cell. 1981 Dec;27(3 Pt 2):497–505. doi: 10.1016/0092-8674(81)90391-3. [DOI] [PubMed] [Google Scholar]
  4. 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]
  5. 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]
  6. 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]
  7. Dale R. M., McClure B. A., Houchins J. P. A rapid single-stranded cloning strategy for producing a sequential series of overlapping clones for use in DNA sequencing: application to sequencing the corn mitochondrial 18 S rDNA. Plasmid. 1985 Jan;13(1):31–40. doi: 10.1016/0147-619x(85)90053-8. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. Hasan G., Turner M. J., Cordingley J. S. Complete nucleotide sequence of an unusual mobile element from trypanosoma brucei. Cell. 1984 May;37(1):333–341. doi: 10.1016/0092-8674(84)90329-5. [DOI] [PubMed] [Google Scholar]
  10. Hu N., Messing J. The making of strand-specific M13 probes. Gene. 1982 Mar;17(3):271–277. doi: 10.1016/0378-1119(82)90143-3. [DOI] [PubMed] [Google Scholar]
  11. Kimmel B. E., ole-MoiYoi O. K., Young J. R. Ingi, a 5.2-kb dispersed sequence element from Trypanosoma brucei that carries half of a smaller mobile element at either end and has homology with mammalian LINEs. Mol Cell Biol. 1987 Apr;7(4):1465–1475. doi: 10.1128/mcb.7.4.1465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. 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]
  13. Lanham S. M. Separation of trypanosomes from the blood of infected rats and mice by anion-exchangers. Nature. 1968 Jun 29;218(5148):1273–1274. doi: 10.1038/2181273a0. [DOI] [PubMed] [Google Scholar]
  14. McDonell M. W., Simon M. N., Studier F. W. Analysis of restriction fragments of T7 DNA and determination of molecular weights by electrophoresis in neutral and alkaline gels. J Mol Biol. 1977 Feb 15;110(1):119–146. doi: 10.1016/s0022-2836(77)80102-2. [DOI] [PubMed] [Google Scholar]
  15. Merritt S. C., Tschudi C., Konigsberg W. H., Richards F. F. Reverse transcription of trypanosome variable antigen mRNAs initiated by a specific oligonucleotide primer. Proc Natl Acad Sci U S A. 1983 Mar;80(6):1536–1540. doi: 10.1073/pnas.80.6.1536. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Meselson M. S., Radding C. M. A general model for genetic recombination. Proc Natl Acad Sci U S A. 1975 Jan;72(1):358–361. doi: 10.1073/pnas.72.1.358. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. 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]
  18. 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]
  19. Murphy N. B., Pays A., Tebabi P., Coquelet H., Guyaux M., Steinert M., Pays E. Trypanosoma brucei repeated element with unusual structural and transcriptional properties. J Mol Biol. 1987 Jun 20;195(4):855–871. doi: 10.1016/0022-2836(87)90490-6. [DOI] [PubMed] [Google Scholar]
  20. 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]
  21. 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]
  22. Parsons M., Nelson R. G., Stuart K., Agabian N. Variant antigen genes of Trypanosoma brucei: genomic alteration of a spliced leader orphon and retention of expression-linked copies during differentiation. Proc Natl Acad Sci U S A. 1984 Feb;81(3):684–688. doi: 10.1073/pnas.81.3.684. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Potter S. S. Rearranged sequences of a human Kpn I element. Proc Natl Acad Sci U S A. 1984 Feb;81(4):1012–1016. doi: 10.1073/pnas.81.4.1012. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Sanger F., Coulson A. R., Barrell B. G., Smith A. J., Roe B. A. Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencing. J Mol Biol. 1980 Oct 25;143(2):161–178. doi: 10.1016/0022-2836(80)90196-5. [DOI] [PubMed] [Google Scholar]
  25. 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]
  26. Schwartz D. C., Cantor C. R. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell. 1984 May;37(1):67–75. doi: 10.1016/0092-8674(84)90301-5. [DOI] [PubMed] [Google Scholar]
  27. Schwartz D. C., Saffran W., Welsh J., Haas R., Goldenberg M., Cantor C. R. New techniques for purifying large DNAs and studying their properties and packaging. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):189–195. doi: 10.1101/sqb.1983.047.01.024. [DOI] [PubMed] [Google Scholar]
  28. Shea C., Glass D. J., Parangi S., Van der Ploeg L. H. Variant surface glycoprotein gene expression site switches in Trypanosoma brucei. J Biol Chem. 1986 May 5;261(13):6056–6063. [PubMed] [Google Scholar]
  29. Smith G. P. Evolution of repeated DNA sequences by unequal crossover. Science. 1976 Feb 13;191(4227):528–535. doi: 10.1126/science.1251186. [DOI] [PubMed] [Google Scholar]
  30. Soares M. B., Schon E., Henderson A., Karathanasis S. K., Cate R., Zeitlin S., Chirgwin J., Efstratiadis A. RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon. Mol Cell Biol. 1985 Aug;5(8):2090–2103. doi: 10.1128/mcb.5.8.2090. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  32. Tschudi C., Young A. S., Ruben L., Patton C. L., Richards F. F. Calmodulin genes in trypanosomes are tandemly repeated and produce multiple mRNAs with a common 5' leader sequence. Proc Natl Acad Sci U S A. 1985 Jun;82(12):3998–4002. doi: 10.1073/pnas.82.12.3998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. 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]
  34. Van der Ploeg L. H. Discontinuous transcription and splicing in trypanosomes. Cell. 1986 Nov 21;47(4):479–480. doi: 10.1016/0092-8674(86)90608-2. [DOI] [PubMed] [Google Scholar]
  35. Van der Ploeg L. H., Schwartz D. C., Cantor C. R., Borst P. Antigenic variation in Trypanosoma brucei analyzed by electrophoretic separation of chromosome-sized DNA molecules. Cell. 1984 May;37(1):77–84. doi: 10.1016/0092-8674(84)90302-7. [DOI] [PubMed] [Google Scholar]
  36. Yamamoto K. R., Alberts B. M., Benzinger R., Lawhorne L., Treiber G. Rapid bacteriophage sedimentation in the presence of polyethylene glycol and its application to large-scale virus purification. Virology. 1970 Mar;40(3):734–744. doi: 10.1016/0042-6822(70)90218-7. [DOI] [PubMed] [Google Scholar]

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