Localization of a bacterial group II intron-encoded protein in eukaryotic nuclear splicing-related cell compartments

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Nisa Martínez, Rafael ^a   Laporte, Philippe ^b   Jiménez Zurdo, José Ignacio ^a   Frugier, Florian ^b   Crespi, Martin ^b   Toro, Nicolás ^b  

^a CSIC   (Spain)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; BACTERIAL PROTEINS; CELL NUCLEUS; GENE EXPRESSION REGULATION, BACTERIAL; GREEN FLUORESCENT PROTEINS; INTRONS; MUTATION; PROTOPLASTS; REAL-TIME POLYMERASE CHAIN REACTION; RECOMBINANT FUSION PROTEINS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA SPLICING; RNA, BACTERIAL; RNA, MESSENGER; SINORHIZOBIUM MELILOTI; SPLICEOSOMES; SUBCELLULAR FRACTIONS;

EID: 84894185067     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0084056     Document Type: Article

References (40)

1. Michel F, Jacquier A, Dujon B (1982) Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie 64: 867-861.
2. Michel F, Ferat JL (1995) Structure and activities of group II introns. Annu Rev Biochem 64: 435-461.
3. Toro N, Jiménez-Zurdo JI, García-Rodríguez FM (2007) Bacterial group II introns: not just splicing. FEMS Microbiol Rev 31: 342-358. (Pubitemid 46525312)
4. Lambowitz AM, Zimmerly S (2011) Group II introns: mobile ribozymes that invade DNA. Cold Spring Harbor Perspect Biol 1: 3(8): a003616. doi:10.1101/cshperspect.a003616.
5. Grabowski PJ, Seiler SA, Sharp PA (1985) A multicomponent complex is involved in the splicing of messenger RNA precursors. Cell 42: 345-353. (Pubitemid 16237584)
6. Cech TK (1986) The generality of self-splicing RNA: relationship to nuclear mRNA splicing. Cell 44: 207-210.
7. Patel AA, Steitz JA (2003) Splicing double: Insights from the second spliceosome. Nat Rev Mol Cell Biol 4: 960-970. (Pubitemid 37493644)
8. Toor N, Keating KS, Taylor SD, Pyle AM (2008) Crystal structure of a self-spliced group II intron. Science 320: 77-82. (Pubitemid 351490756)
9. Keating KS, Toor N, Perlman PS, Pyle AM (2010) A structural analysis of the group II intron active site and implications for the spliceosome. RNA 16: 1-9.
10. Michel F, Umesono K., Ozeki H (1989) Comparative and functional anatomy of group II catalytic introns, a review. Gene 82: 5-30. (Pubitemid 19248654)
11. Mohr G, Perlman PS, Lambowitz AM (1993) Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acids Res 21: 4991-4997. (Pubitemid 23342504)
12. San Filippo J, Lambowitz AM (2002) Characterization of the C-terminal DNA-binding/DNA endonuclease region of a group II intron-encoded protein. J Mol Biol 324: 933-951. (Pubitemid 41782984)
13. Rogozin IB, Carmel L, Csuros M, Koonin EV (2012) Origin and evolution of spliceosomal introns. Biol Direct 7: 11. doi: 10.1186/1745-6150-7-11.
14. Boeke JD (2003) The unusual phylogenetic distribution of retrotransposons: a hypothesis. Genome Res 13: 1975-1983.
15. Lynch M, Kewalramani A (2003). Messenger RNA surveillance and the evolutionary proliferation of introns. Mol Bio Evol 20: 563-571. (Pubitemid 36437906)
16. Martin W, Koonin EV (2006). Introns and the origin of nucleus-cytosol compartmentalization. Nature 440: 41-45. (Pubitemid 43336261)
17. Koonin EV (2006). The origin of introns and the role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? Biol Direct 1: 22. doi:10.1186/1745-6150-1-22.
18. Koonin EV (2011) The origins of eukaryotes: Endosymbiosis, the strange story of introns, and the ultimate importance of unique events in evolution, In Pearson Education, Inc. (ed), The logic of chance: the nature and origin of biological evolution, 1st ed, FT Press Science, Upper Saddle River, NJ. 171-224.
19. Chalamcharla VR, Curcio MJ, Belfort M (2010) Nuclear expression of a group II intron is consistent with spliceosomal intron ancestry. Genes Dev 24: 827-836.
20. Mastroianni M, Watanabe K, White TB, Zhuang F, Vernon J et al. (2008) Group II intron-based gene targeting reactions in eukaryotes. PLoS ONE (Suppl 9): e3121. doi:10.1371/journal.pone.0003121.
21. Cui X (2005) Ph.D. thesis. The University of Texas at Austin. TX. RNA/protein interactions during group II intron splicing and toward group II intron targeting in mammalian cells. http://hdl.handle.net/2152/1529.
22. Martínez-Abarca F, García-Rodríguez FM, 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. (Pubitemid 30175516)
23. Villadas PJ, Velázquez E, Martínez-Molina E, 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.
24. Robertsen BK, Aiman P, Darvill AG, McNeil M, Albersheim P (1981) The structure of acidic extracellular polysaccharides secreted by Rhizobium leguminosarum and Rhizobium trifolii. Plant Physiol 67: 389-400.
25. Karimi M, Inzé D, Depicker A (2002) GATEWAY vectors for Agrobacterium-mediated plant transformation. Trends Plant Sci 7: 193-195. (Pubitemid 36725938)
26. Nisa-Martinez R, Jiménez-Zurdo JI, Martínez-Abarca F, Muñoz-Adelantado E, Toro N (2007) Dispersion of the RmIntI group II intron in the Sinorhizobium meliloti genome upon acquisition by conjugative transfer. Nucleic Acids Res 35: 214-222. (Pubitemid 46189846)
27. Martínez-Abarca F, Barrientos-Durán A, Fernández- López M, Toro N (2004). 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 Res 32: 2880-2888. (Pubitemid 38898626)
28. Muñoz-Adelantado E, San Filippo J, Martínez-Abarca F, García-Rodríguez FM, Lambowitz AM et al. (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. (Pubitemid 36363703)
29. Jiménez-Zurdo JI, García-Rodríguez FM, Barrientos-Durán A, Toro N (2003) DNA-target 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. (Pubitemid 36279336)
30. Molina-Sánchez MD, Barrientos-Durán A, Toro N (2011) Relevance of the branch point adenosine, coordination loop, and 39 exon binding site for in vivo excision of the Sinorhizobium meliloti group II intron RmInt1. J Biol Chem 286: 21154-21163.
31. Molina-Sánchez MD, Martínez-Abarca F, Toro N (2010) Structural features in the C-terminal region of the Sinorhizobium meliloti RmInt1 group II intron-encoded protein contribute to its maturase and intron DNA-insertion function. FEBS J 277: 244-254.
32. Molina-Sánchez MD, Martínez-Abarca F, Toro N (2006) Excision of the Sinorhizobium meliloti group II intron RmInt1 as circles in vivo. J Biol Chem 281: 28737-28744. (Pubitemid 44507016)
33. Droillard MJ, Boudsocq M, Barbier-Bygoo H, Lauriére C (2002) Different protein kinase families are activated by osmotic stresses in Arabidopsis thaliana cell suspensions. FEBS Lett 527: 43-50. (Pubitemid 35253836)
34. Lorković ZJ, Hilscher J, Barta A (2004) Use of fluorescent protein tags to study nuclear organization of the spliceosomal machinery in transiently transformed living plant cells. Mol Biol Cell 15: 3233-3243. (Pubitemid 38850119)
35. Abràmoff MD, Magalhäes PJ, Ram SJ (2004) Image processing with imageJ. J Biophot Int 7: 36-43.
36. Zhao J, Lambowitz AM (2005) A bacterial group II intron-encoded reverse transcriptase localizes to cellular poles. Proc Natl Acad Sci USA 102: 16233-16140.
37. Nakai K, Kanehisa M (1992) A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14: 897-911. (Pubitemid 23053027)
38. Spector DL, Lamond AI (2011) Nuclear speckles. Cold Spring Harb Perspect Biol 1: 3(2), pii: a000646. doi: 10.1101/cshperspect.a000646.
39. Mohr G, Lambowitz AM (2003) Putative proteins related to group II intron reverse transcriptase/maturases are encoded by nuclear genes in higher plants. Nucleic Acids Res 31: 647-652. (Pubitemid 36175955)
40. Guo W, Mower JP (2013) Evolution of plant mitochondrial intron-encoded maturases: frequent lineage-specific loss and recurrent intracellular transfer to the nucleus, J Mol Evol 77: 43-54.