Group II intron mobility using nascent strands at DNA replication forks to prime reverse transcription

EMBO Journal

Volumn 22, Issue 17, 2003, Pages 4555-4565

  Zhong, Jin ^a   Lambowitz, Alan M ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

DNA replication; Retrotransposon; Reverse transcriptase; Ribozyme

Indexed keywords

DEOXYRIBONUCLEASE; RIBOZYME;

3' UNTRANSLATED REGION; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; DNA CLEAVAGE; DNA REPLICATION; DNA STRAND; INTRON; LACTOCOCCUS LACTIS; NONHUMAN; PRIORITY JOURNAL; RETROPOSON; REVERSE TRANSCRIPTION;

BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; DNA REPLICATION; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; GENES, BACTERIAL; INTRONS; LACTOCOCCUS LACTIS; MODELS, BIOLOGICAL; MUTATION; RNA SPLICING; RNA, BACTERIAL; TRANSCRIPTION, GENETIC;

LACTOCOCCUS; LACTOCOCCUS LACTIS; POSIBACTERIA; PROKARYOTA; STREPTOCOCCUS;

EID: 0042236980     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/cdg433     Document Type: Article

References (32)

1. Aizawa, Y., Xiang, Q., Lambowitz, A.M. and Pyle, A.M. (2003) The pathway for DNA recognition and RNA integration by a group II intron retrotransposon. Mol. Cell, 11, 795-805.
2. Bazaral, M. and Helinski, D.R. (1970) Replication of a bacterial plasmid and an episome in Escherichia coli. Biochemistry, 9, 399-406.
3. Belfort, M., Derbyshire, V., Parker, M.M., Cousineau, B. and Lambowitz, A.M. (2002) Mobile introns: pathways and proteins. In Craig, N.L., Craigie, R., Gellert, M. and Lambowitz, A.M. (eds), Mobile DNA II. ASM Press Publishers, Washington, DC, pp. 761-783.
4. Dai, L. and Zimmerly, S. (2002) Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior. Nucleic Acids Res., 30, 1091-1102.
5. Dickson, L., Huang, H.R., Liu, L., Matsuura, M., Lambowitz, A.M. and Perlman, P.S. (2001) Retrotransposition of a yeast group II intron occurs by reverse splicing directly into ectopic DNA sites. Proc. Natl Acad. Sci. USA, 98, 13207-13212.
6. D'Souza, L.M. and Zhong, J. (2002) Mutations in the Lactococcus lactis Ll.LtrB group II intron that retain mobility in vivo. BMC Mol. Biol., 3, 17.
7. Gorbalenya, A.E. (1994) Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family. Protein Sci., 3, 1117-1120.
8. Guo, H., Zimmerly, S., Perlman, P.S. and Lambowitz, A.M. (1997) Group II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in double-stranded DNA. EMBO J., 16, 6835-6848.
9. Guo, H., Karberg, M., Long, M., Jones, J.P., III, Sullenger, B. and Lambowitz, A.M. (2000) Group II introns designed to insert into therapeutically relevant DNA target sites in human cells. Science, 289, 452-457.
10. Hamilton, C.M., Aldea, M., Washburn, B.K., Babitzke, P. and Kushner, S.R. (1989) New method for generating deletions and gene replacements in Escherichia coli. J. Bacteriol., 171, 4617-4622.
11. Ichiyanagi, K., Beauregard, A., Lawrence, S., Smith, D., Cousineau, B. and Belfort, M. (2002) Retrotransposition of the Ll.LtrB group II intron proceeds predominantly via reverse splicing into DNA targets. Mol. Microbiol., 46, 1259-1272.
12. Jiménez-Zurdo, J.I., García-Rodríguez, F.M., Barrientos-Durán, A. and Toro, N. (2003) DNA target site requirement for homing in vivo of a bacterial group II intron encoding a protein lacking the DNA endonuclease domain. J. Mol. Biol., 326, 413-423.
13. Karberg, M., Guo, H., Zhong, J., Coon, R., Perutka, J. and Lambowitz, A.M. (2001) Group II introns as controllable gene targeting vectors for genetic manipulation of bacteria. Nat. Biotechnol., 19, 1162-1167.
14. Lambowitz, A.M., Caprara, M.G., Zimmerly, S. and Perlman, P.S. (1999) Group I and group II ribozymes as RNPs: clues to the past and guides to the future. In Gesteland, R.F., Cech, T.R. and Atkins, J.F. (eds), The RNA World, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 451-484.
15. Martínez-Abarca, F. and Toro, N. (2000a) RecA-independent ectopic transposition in vivo of a bacterial group II intron. Nucleic Acids Res., 28, 4397-4402.
16. Martínez-Abarca, F. and Toro, N. (2000b) Group II introns in the bacterial world. Mol. Microbiol., 38, 917-926.
17. Martínez-Abarca, F., Zekri, S. and Toro, N. (1998) Characterization and splicing in vivo of a Sinorhizobium meliloti group II intron associated with particular insertion sequences of the IS630-Tcl/IS3 retroposon superfamily. Mol. Microbiol., 28, 1295-1306.
18. Martínez-Abarca, F., García-Rodríguez, F.M. and Toro, N. (2000) Homing of a bacterial group II intron with an intron-encoded protein lacking a recognizable endonuclease domain. Mol. Microbiol., 35, 1405-1412.
19. Michel, F. and Ferat, J.L. (1995) Structure and activities of group II introns. Annu. Rev. Biochem., 64, 435-461.
20. Mohr, G., Smith, D., Belfort, M. and Lambowitz, A.M. (2000) Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences. Genes Dev., 14, 559-573.
21. Muñoz-Adelantado, E., San Filippo, J., Martínez-Abarca, F., García-Rodríguez, F.M., Lambowitz, A.M. and Toro, N. (2003) Mobility of the Sinorhizobium meliloti group II intron RmInt1 occurs by reverse splicing into DNA, but requires an unknown reverse transcriptase priming mechanism. J. Mol. Biol., 327, 932-943.
22. Pham, P., Bertram, J.G., O'Donnell, M., Woodgate, R. and Goodman, M.F. (2001) A model for SOS-lesion-targeted mutations in Escherichia coli. Nature, 409, 366-370.
23. Rownd, R. (1969) Replication of a bacterial episome under relaxed control. J. Mol. Biol., 44, 387-402.
24. Saldanha, R., Chen, B., Wank, H., Matsuura, M., Edwards, J. and Lambowitz, A.M. (1999) RNA and protein catalysis in group II intron splicing and mobility reactions using purified components. Biochemistry, 38, 9069-9083.
25. San Filippo, J. and Lambowitz, A.M. (2002) Characterization of the C-terminal DNA-binding/DNA endonuclease region of a group II intron-encoded protein. J. Mol. Biol., 324, 933-951.
26. Shub, D.A., Goodrich-Blair, H. and Eddy, S.R. (1994) Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns. Trends Biochem. Sci., 19, 402-404.
27. Singh, N.N. and Lambowitz, A. (2001) Interaction of a group II intron ribonucleoprotein endonuclease with its DNA target site investigated by DNA footprinting and modification interference. J. Mol. Biol., 309, 361-386.
28. Wang, G.H. and Seeger, C. (1992) The reverse transcriptase of hepatitis B virus acts as a protein primer for viral DNA synthesis. Cell, 71, 663-670.
29. Wang, H. and Lambowitz, A.M. (1993) The Mauriceville plasmid reverse transcriptase can initiate cDNA synthesis de novo and may be related to reverse transcriptase and DNA polymerase progenitor. Cell, 75, 1071-1081.
30. Yang, J., Mohr, G., Perlman, P.S. and Lambowitz, A.M. (1998) Group II intron mobility in yeast mitochondria: target DNA-primed reverse transcription activity of aI1 and reverse splicing into DNA transposition sites in vitro. J. Mol. Biol., 282, 505-523.
31. Yeo, C.C., Tham, J.M., Yap, M.W. and Poh, C.L. (1997) Group II intron from Pseudomonas alcaligenes NCIB 9867 (P25X): entrapment in plasmid RP4 and sequence analysis. Microbiology, 143, 2833-2840.
32. Zhong, J., Karberg, M. and Lambowitz, A.M. (2003) Targeted and random bacterial gene disruption using a group II intron (targetron) vector containing a retrotransposition-activated selectable marker. Nucleic Acids Res., 31, 1656-1664.