The RmInt1 group II intron has two different retrohoming pathways for mobility using predominantly the nascent lagging strand at DNA replication forks for priming

Nucleic Acids Research

Volumn 32, Issue 9, 2004, Pages 2880-2888

  Martínez Abarca, Francisco ^a   Barrientos Durán, Antonio ^a   Fernández López, Manuel ^a   Toro, Nicolás ^a  

^a CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DEOXYRIBONUCLEASE; PRIMER DNA; RIBONUCLEOPROTEIN; RNA; SINGLE STRANDED DNA; BACTERIAL RNA;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; DNA CLEAVAGE; DNA REPLICATION; DNA SPLICING; DNA STRAND; DNA SYNTHESIS; ENZYME SUBSTRATE; GENE TARGETING; GENETIC CODE; INTRON; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; REVERSE TRANSCRIPTION; SIGNAL TRANSDUCTION; SINORHIZOBIUM MELILOTI; BIOLOGICAL MODEL; DNA TEMPLATE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; RETROPOSON;

BACTERIA (MICROORGANISMS); SINORHIZOBIUM; SINORHIZOBIUM MELILOTI;

DNA REPLICATION; INTRONS; MODELS, GENETIC; MUTAGENESIS, INSERTIONAL; RETROELEMENTS; RNA, BACTERIAL; SINORHIZOBIUM MELILOTI; TEMPLATES, GENETIC; TRANSCRIPTION, GENETIC;

EID: 3042725448     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh616     Document Type: Article

References (48)

1. Michel,F., Umesoko,K. and Ozeki,H. (1989) Comparative and functional anatomy of group II catalytic introns: a review. Gene, 82, 5-30.
2. Ferat,J.L. and Michel,F. (1993) Group II self-splicing introns in bacteria. Nature, 364, 358-361.
3. 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-Tc1/IS3 retroposon superfamily. Mol. Microbiol., 28, 1295-1306.
4. Martínez-Abarca,F. and Toro,N. (2000) Group II introns in the bacterial world. Mol. Microbiol., 38, 917-926.
5. Zimmerly,S., Hausner,G. and Wu,X.C. (2001) Phylogenetic relationships among group II intron ORFs. Nucleic Acids Res., 29, 1238-1250.
6. Dai,L. and Zimmerly,S. (2002) Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behaviour. Nucleic Acids Res., 30, 1091-1102.
7. Dai,L. and Zimmerly,S. (2003) ORF-less and reverse-transcriptase-encoding group II introns in archaebacteria, with a pattern of homing into related group II intron ORFs. RNA, 9, 14-19.
8. Toro,N. (2003) Bacteria and Archaea Group II introns: additional mobile genetic elements in the environment. Environ. Microbiol., 5, 143-151.
9. Michel,F. and Ferat,J.L. (1995) Structure and activities of group II introns. Annu. Rev. Biochem., 64, 435-461.
10. 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. 451-485.
11. 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, 2nd Edn. ASM Press, Washington, DC, pp. 761-783.
12. 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.
13. Martínez-Abarca,F. and Toro,N. (2000) RecA-independent ectopic transposition in vivo of a bacterial group II intron. Nucleic Acids Res., 28, 4397-4402.
14. 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.
15. Muñoz,E., Villadas,P.J. and Toro,N. (2001) Ectopic transposition of a group II intron in natural bacterial populations. Mol. Microbiol., 41, 645-652.
16. 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, 1259-1271.
17. Ichiyanagi,K., Beauregard,A. and Belfort,M. (2003) A bacterial group II intron favors retrotransposition into plasmid targets. Proc. Natl Acad. Sci. USA, 100, 15742-15747.
18. Zimmerly,S., Guo,H., Eskes,R., Yang,J., Perlman,P.S. and Lambowitz,A.M. (1995) A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell, 83, 529-538.
19. Eickbush,T. (1999) Mobile introns: retrohoming by complete reverse splicing. Curr. Biol., 9, 11-14.
20. Toor,N., Hausner,G. and Zimmerly,S. (2001) Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA, 7, 1142-1152.
21. Toro,N., Molina-Sánchez,M.D. and Fernández-López,M. (2002) Identification and characterization of bacterial class E group II introns. Gene, 299, 245-250.
22. Ferat,J.L., Le Gouar,M. and Michel,F. (2003) A group II intron has invaded the genus Azotobacter and is inserted within the termination codon of the essential groEL gene. Mol. Microbiol., 49, 1407-1423.
23. 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.
24. Shub,D.A., Goodrich-Blair,H. and Eddy,S.R. (1994) Amino acid sequence motif of group I endonucleases is conserved in open reading frames of group II introns. Trends Biochem. Sci., 19, 402-404.
25. 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.
26. Eskes,R., Yang,J., Lambowitz,A.M. and Perlman,P.S. (1997) Mobility of yeast mitochondrial group II introns: engineering a new site specificity and retrohoming via full reverse splicing. Cell, 88, 865-874.
27. Cousineau,B., Smith,D., Lawrence-Cavanagh,S., Mueller,J.E., Yang,J., Mills,D., Manias,D., Dunny,G., Lambowitz,A.M. and Belfort,M. (1998) Retrohoming of a bacterial group II intron: mobility via complete reverse splicing, independent of homologous recombination. Cell, 94, 451-462.
28. Eskes,R., Liu,L., Ma,H., Chao,M.Y., Dickson,L., Lambowitz,A.M. and Perlman,P.S. (2000) Multiple homing pathways used by yeast mitochondrial group II introns. Mol. Cell. Biol., 20, 8432-8446.
29. 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.
30. San Filippo,J. and Lambowitz,A.M. (2002) Characterization of the C-terminal DNA-binding/DNA endonuclease region of a group II intron-encoded reverse transcriptase. J. Mol. Biol., 324, 933-951.
31. 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.
32. Jiménez-Zurdo,J.I., García-Rodríguez,F.M., Barrientos-Durán,A. and Toro,N. (2003) DNA-target requirements for homing in vivo of a bacterial group II intron encoding a protein lacking the DNA endonuclease domain. J. Mol. Biol., 326, 413-423.
33. 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, 931-943.
34. Zhong,J. and Lambowitz,A.M. (2003) Group II intron mobility using nascent strands at DNA replication forks to prime reverse transcription. EMBO J., 22, 4555-4565.
35. Villadas,P.J., Velázquez,E., Martínez-Molina,E. and Toro,N. (1995) Identification of nodule dominant Rhizobium meliloti strains carrying pRmeGR4b-type plasmid within indigenous soil populations by PCR using primers derived from specific DNA sequences. FEMS Microbiol. Ecol., 17, 161-168.
36. Robertsen,B.K., Aiman,P., Darvill,A.G., McNeil,M. and Albershein,P. (1981) The structure of acidic extracellular polysaccharides secreted by Rhizobium leguminosarum and Rhizobium trifolii. Plant Physiol., 67, 389-400.
37. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1989) Molecular Cloning: A Laboratory, Manual, 2nd Edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
38. Blatny,J.M., Brautaset,T., Winther-Larsen,H.C., Haugan,K. and Valla,S. (1997) Construction and use of a versatile set of broad-host-range cloning and expression vectors based on the RK2 replicon. Appl. Environ. Microbiol., 63, 370-379.
39. Marsh,J.L., Erfle,M. and Wykes,E.J. (1984) The pIC plasmid and phage vectors with versatile cloning sites for recombinant selection by insertional inactivation. Gene, 32, 481-484.
40. Macián,F., Pérez-Roger,I. and Armengol,M.E. (1994) An improved vector system for constructing transcriptional lacZ fusions: analysis of regulation of the dnaA, dnaN, recF asnd gyrB genes of Escherichia coli. Gene, 145, 17-24.
41. Clackson,T., Güssow,D. and Jones,P.T. (1993) General applications of PCR to gene cloning and manipulation. In Mcpherson,M.J., Quirce,P. and Taylor,G.R. (eds), PCR A Practical Approach. Oxford University Press, Oxford, pp. 202-204.
42. Belfort,M., Chandry,P.S. and Pedersen-Lane,J. (1987) Genetic delineation of functional components of the group I intron in the phage T4 td gene. Cold Spring Harbor Symp. Quant. Biol., 52, 181-192.
43. Ditta,G., Stanfield,S., Corbin,D. and Helinski,D.R. (1980) Broad host range DNA cloning system for Gram-negative bacteria. Construction of gene bank of Rhizobium meliloti. Proc. Natl Acad. Sci. USA, 77, 7347-7351.
44. Toro,N., Martínez-Abarca,F., Fernández-Lopez,M. and Muñoz-Adelantado,E. (2003) Diversity of group II introns in the genome of Sinorhizobium meliloti strain 1021: splicing and mobility of RmInt1. Mol. Genet. Genomics, 268, 628-636.
45. Knonieczny,I. (2003) Strategies for helicase recruitment and loading in bacteria. EMBO Rep., 4, 37-41.
46. Kovach,M.E., Phillips,R.W., Elzer,P.H., Roop.,R.M.II. and Peterson,K.M. (1994) pBBR1MCS: a broad-host-range cloning vector. Biotechniques, 16, 800-802.
47. Antoine,R. and Locht,C. (1992) Isolation and molecular characterization of a novel broad-host-range plasmid from Bordetella bronchiseptica with sequence similarities to plasmids from gram-positive organisms. Mol. Microbiol., 6, 1785-1799.
48. 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.