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Mol Cell Biol. 1996 Sep; 16(9): 4726–4734.
PMCID: PMC231473

Downstream 28S gene sequences on the RNA template affect the choice of primer and the accuracy of initiation by the R2 reverse transcriptase.


R2 non-long terminal repeat retrotransposable elements insert at a unique site in the 28S rRNA genes of insects. The protein encoded by the single open reading frame of R2 is capable of conducting the initial steps of its integration in vitro. The protein nicks the noncoding strand of the 28S target DNA (the strand which serves as a template for RNA synthesis) and uses the 3' hydroxyl group exposed by this nick to prime reverse transcription of the R2 RNA template. This target-primed reverse transcription (TPRT) reaction requires that the RNA template contains the 250-nucleotide 3' untranslated region of the R2 element. If this RNA template ends at the precise 3' end of the R2 element, then extra nucleotides, which we refer to as nontemplated nucleotides, are added to the target before cDNA synthesis. The presence of downstream 28S gene sequences on the RNA template reduces the total efficiency but eliminates these nontemplated additions, resulting in nearly 90% of all TPRT products reproducing the 3' junctions seen in vivo. Templates with 5 to 10 nucleotides of the 28S sequence are used most efficiently in this in vitro TPRT reaction. The requirement for downstream 28S rRNA sequences probably explains why the R2 elements of most insects differ from the majority of non-long terminal repeat retrotransposons in that they do not contain an A-rich repeat at their 3' junction with the target DNA. The presence of downstream sequences on these in vitro R2 templates also revealed that the R2 reverse transcriptase can prime cDNA synthesis by using the 3' end of another RNA molecule. This RNA-primed cDNA synthesis is not based on sequence complementarity between the RNA primer and the R2 template. The ability to use the 3' end of a noncomplementary RNA molecule has also been seen with the reverse transcriptase of the mitochondrial Mauriceville plasmid of Neurospora crassa.

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Selected References

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  • Aksoy S, Williams S, Chang S, Richards FF. SLACS retrotransposon from Trypanosoma brucei gambiense is similar to mammalian LINEs. Nucleic Acids Res. 1990 Feb 25;18(4):785–792. [PMC free article] [PubMed]
  • Boeke JD, Corces VG. Transcription and reverse transcription of retrotransposons. Annu Rev Microbiol. 1989;43:403–434. [PubMed]
  • Bucheton A. I transposable elements and I-R hybrid dysgenesis in Drosophila. Trends Genet. 1990 Jan;6(1):16–21. [PubMed]
  • Burke WD, Calalang CC, Eickbush TH. The site-specific ribosomal insertion element type II of Bombyx mori (R2Bm) contains the coding sequence for a reverse transcriptase-like enzyme. Mol Cell Biol. 1987 Jun;7(6):2221–2230. [PMC free article] [PubMed]
  • Burke WD, Eickbush DG, Xiong Y, Jakubczak J, Eickbush TH. Sequence relationship of retrotransposable elements R1 and R2 within and between divergent insect species. Mol Biol Evol. 1993 Jan;10(1):163–185. [PubMed]
  • Burke WD, Müller F, Eickbush TH. R4, a non-LTR retrotransposon specific to the large subunit rRNA genes of nematodes. Nucleic Acids Res. 1995 Nov 25;23(22):4628–4634. [PMC free article] [PubMed]
  • Chiang CC, Kennell JC, Wanner LA, Lambowitz AM. A mitochondrial retroplasmid integrates into mitochondrial DNA by a novel mechanism involving the synthesis of a hybrid cDNA and homologous recombination. Mol Cell Biol. 1994 Oct;14(10):6419–6432. [PMC free article] [PubMed]
  • Curcio MJ, Belfort M. Retrohoming: cDNA-mediated mobility of group II introns requires a catalytic RNA. Cell. 1996 Jan 12;84(1):9–12. [PubMed]
  • Eickbush DG, Eickbush TH. Vertical transmission of the retrotransposable elements R1 and R2 during the evolution of the Drosophila melanogaster species subgroup. Genetics. 1995 Feb;139(2):671–684. [PMC free article] [PubMed]
  • Eickbush TH. Transposing without ends: the non-LTR retrotransposable elements. New Biol. 1992 May;4(5):430–440. [PubMed]
  • Evans JP, Palmiter RD. Retrotransposition of a mouse L1 element. Proc Natl Acad Sci U S A. 1991 Oct 1;88(19):8792–8795. [PMC free article] [PubMed]
  • Gabriel A, Boeke JD. Reverse transcriptase encoded by a retrotransposon from the trypanosomatid Crithidia fasciculata. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9794–9798. [PMC free article] [PubMed]
  • Gabriel A, Yen TJ, Schwartz DC, Smith CL, Boeke JD, Sollner-Webb B, Cleveland DW. A rapidly rearranging retrotransposon within the miniexon gene locus of Crithidia fasciculata. Mol Cell Biol. 1990 Feb;10(2):615–624. [PMC free article] [PubMed]
  • Garrett JE, Knutzon DS, Carroll D. Composite transposable elements in the Xenopus laevis genome. Mol Cell Biol. 1989 Jul;9(7):3018–3027. [PMC free article] [PubMed]
  • Hancock JM, Tautz D, Dover GA. Evolution of the secondary structures and compensatory mutations of the ribosomal RNAs of Drosophila melanogaster. Mol Biol Evol. 1988 Jul;5(4):393–414. [PubMed]
  • Inouye M, Inouye S. msDNA and bacterial reverse transcriptase. Annu Rev Microbiol. 1991;45:163–186. [PubMed]
  • Ivanov VA, Melnikov AA, Siunov AV, Fodor II, Ilyin YV. Authentic reverse transcriptase is coded by jockey, a mobile Drosophila element related to mammalian LINEs. EMBO J. 1991 Sep;10(9):2489–2495. [PMC free article] [PubMed]
  • Jakubczak JL, Burke WD, Eickbush TH. Retrotransposable elements R1 and R2 interrupt the rRNA genes of most insects. Proc Natl Acad Sci U S A. 1991 Apr 15;88(8):3295–3299. [PMC free article] [PubMed]
  • Jensen S, Heidmann T. An indicator gene for detection of germline retrotransposition in transgenic Drosophila demonstrates RNA-mediated transposition of the LINE I element. EMBO J. 1991 Jul;10(7):1927–1937. [PMC free article] [PubMed]
  • Kennell JC, Moran JV, Perlman PS, Butow RA, Lambowitz AM. Reverse transcriptase activity associated with maturase-encoding group II introns in yeast mitochondria. Cell. 1993 Apr 9;73(1):133–146. [PubMed]
  • Loh EY, Elliott JF, Cwirla S, Lanier LL, Davis MM. Polymerase chain reaction with single-sided specificity: analysis of T cell receptor delta chain. Science. 1989 Jan 13;243(4888):217–220. [PubMed]
  • Luan DD, Eickbush TH. RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol Cell Biol. 1995 Jul;15(7):3882–3891. [PMC free article] [PubMed]
  • Luan DD, Korman MH, Jakubczak JL, Eickbush TH. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell. 1993 Feb 26;72(4):595–605. [PubMed]
  • Mathias SL, Scott AF, Kazazian HH, Jr, Boeke JD, Gabriel A. Reverse transcriptase encoded by a human transposable element. Science. 1991 Dec 20;254(5039):1808–1810. [PubMed]
  • Michel F, Ferat JL. Structure and activities of group II introns. Annu Rev Biochem. 1995;64:435–461. [PubMed]
  • Pélisson A, Finnegan DJ, Bucheton A. Evidence for retrotransposition of the I factor, a LINE element of Drosophila melanogaster. Proc Natl Acad Sci U S A. 1991 Jun 1;88(11):4907–4910. [PMC free article] [PubMed]
  • 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. [PMC free article] [PubMed]
  • Teng SC, Wang SX, Gabriel A. A new non-LTR retrotransposon provides evidence for multiple distinct site-specific elements in Crithidia fasciculata miniexon arrays. Nucleic Acids Res. 1995 Aug 11;23(15):2929–2936. [PMC free article] [PubMed]
  • Villanueva MS, Williams SP, Beard CB, Richards FF, Aksoy S. A new member of a family of site-specific retrotransposons is present in the spliced leader RNA genes of Trypanosoma cruzi. Mol Cell Biol. 1991 Dec;11(12):6139–6148. [PMC free article] [PubMed]
  • Wang H, Kennell JC, Kuiper MT, Sabourin JR, Saldanha R, Lambowitz AM. The Mauriceville plasmid of Neurospora crassa: characterization of a novel reverse transcriptase that begins cDNA synthesis at the 3' end of template RNA. Mol Cell Biol. 1992 Nov;12(11):5131–5144. [PMC free article] [PubMed]
  • Wang H, Lambowitz AM. The Mauriceville plasmid reverse transcriptase can initiate cDNA synthesis de novo and may be related to reverse transcriptase and DNA polymerase progenitor. Cell. 1993 Dec 17;75(6):1071–1081. [PubMed]
  • Weiner AM, Deininger PL, Efstratiadis A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem. 1986;55:631–661. [PubMed]
  • Whitcomb JM, Hughes SH. Retroviral reverse transcription and integration: progress and problems. Annu Rev Cell Biol. 1992;8:275–306. [PubMed]
  • Xiong YE, Eickbush TH. Functional expression of a sequence-specific endonuclease encoded by the retrotransposon R2Bm. Cell. 1988 Oct 21;55(2):235–246. [PubMed]
  • Xiong Y, Eickbush TH. Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns. Mol Biol Evol. 1988 Nov;5(6):675–690. [PubMed]
  • Xiong Y, Eickbush TH. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 1990 Oct;9(10):3353–3362. [PMC free article] [PubMed]
  • Zimmerly S, Guo H, Eskes R, Yang J, Perlman PS, Lambowitz AM. A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell. 1995 Nov 17;83(4):529–538. [PubMed]
  • Borst P, Bitter W, McCulloch R, Van Leeuwen F, Rudenko G. Antigenic variation in malaria. Cell. 1995 Jul 14;82(1):1–4. [PubMed]

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