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 Journal

Volumn 277, Issue 1, 2010, Pages 244-254

  Molina Sánchez, María D ^a   Martínez Abarca, Francisco ^a   Toro, Nicolás ^a  

^a CSIC   (Spain)

Author keywords

Catalytic RNAs; Maturase; Retroelements; Reverse transcriptase; Splicing

Indexed keywords

AMINO ACID; DEOXYRIBONUCLEASE; INTRON CODED PROTEIN II; RNA BINDING PROTEIN; RNA DIRECTED DNA POLYMERASE; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; DNA BINDING; ENZYME ACTIVITY; GENE DELETION; GENE INSERTION; GENE MUTATION; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; RETROPOSON; RNA SPLICING; SEQUENCE ANALYSIS; SINORHIZOBIUM MELILOTI; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; DNA PRIMERS; ENDORIBONUCLEASES; GENES, BACTERIAL; INTRONS; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEOTIDYLTRANSFERASES; RNA SPLICING; RNA, BACTERIAL; RNA, CATALYTIC; SEQUENCE HOMOLOGY, AMINO ACID; SINORHIZOBIUM MELILOTI;

BACTERIA (MICROORGANISMS); SINORHIZOBIUM MELILOTI;

EID: 73649087319     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2009.07478.x     Document Type: Article

References (35)

1. Michel F Ferat JL (1995) Structure and activities of group II introns. Annu Rev Biochem 64, 435 461.
2. Michel F, Umesono K Ozeki H (1989) Comparative and functional anatomy of group II catalytic introns - a review. Gene 82, 5 30.
3. Carignani G, Groudinsky O, Frezza D, Schiavon E, Bergantino E Slonimski PP (1983) An mRNA maturase is encoded by the first intron of the mitochondrial gene for the subunit I of cytochrome oxidase in S. cerevisiae. Cell 35, 733 742.
4. Moran JV, Mecklenburg KL, Sass P, Belcher SM, Mahnke D, Lewin A Perlman PS (1994) Splicing defective mutants of the COXI gene of yeast mitochondrial DNA: initial definition of the maturase domain of the group II intron aI2. Nucleic Acids Res 22, 2057 2064.
5. Saldanha R, Chen B, Wank H, Matsuura M, Edwards J Lambowitz AM (1999) RNA and protein catalysis in group II intron splicing and mobility reactions using purified components. Biochemistry 38, 9069 9083.
6. Matsuura M, Noah JW Lambowitz AM (2001) Mechanism of maturase-promoted group II intron splicing. EMBO J 20, 7259 7270.
7. Lambowitz AM, Caprara MG, Zimmerly S Perlman PS (1999) Group I and group II ribozymes as RNPs: clues to the past and guides to the future. In The RNA World, 2nd edn (Gesteland RF, Cech RF Atkins JF eds pp 451 485. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
8. Belfort M, Derbyshire V, Parker MM, Cousineau B Lambowitz AM (2002) Mobile introns: pathways and proteins. In Mobile DNA II (Craig NL, Craigie R, Gellert M Lambowitz AM eds pp 761 783. ASM Press Publishers, Washington, DC.
9. Lambowitz AM Zimmerly S (2004) Mobile group II introns. Annu Rev Genet 38, 1 35.
10. 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.
11. San FilippoJ 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.
12. Cui X, Matsuura M, Wang Q, Ma H Lambowitz AM (2004) A group II intron-encoded maturase functions preferentially in cis and requires both the reverse transcriptase and X domains to promote RNA splicing. J Mol Biol 340, 211 231.
13. Blocker FJH, Mohr G, Conlan LH, Qi L, Belfort M Lambowitz A (2005) Domain structure and three-dimensional model of a group II intron-encoded reverse transcriptase. RNA 11, 14 28. (Pubitemid 40041569)
14. Gorbalenya AE (1994) Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family. Protein Sci 3, 1117 1120.
15. Shub DA, Goodrich-Blair H Eddy SR (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.
16. Zimmerly S, Guo H, Eskes R, Yang J, Perlman PS Lambowitz AM (1995) A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell 83, 529 538.
17. Guo H, Zimmerly S, Perlman PS Lambowitz AM (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.
18. Matsuura M, Saldanha R, Ma H, Wank H, Yang J, Mohr G, Cavanagh S, Dunny GM, Belfort M Lambowitz AM (1997) A bacterial group II intron encoding reverse transcriptase, maturase, and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron. Genes Dev 11, 2910 2924.
19. Singh NN Lambowitz AM (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.
20. Toor N, Hausner G Zimmerly S (2001) Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA 7, 1142 1152.
21. Zimmerly S, Hausner G Wu X (2001) Phylogenetic relationships among group II intron ORFs. Nucleic Acids Res 29, 1238 1250.
22. Toro N, Molina-Sánchez MD Fernández-López M (2002) Identification and characterization of bacterial class E group II introns. Gene 299, 245 250.
23. Ferat JL, Le Gouar M Michel F (2003) A group II intron has invaded the genus Azotobacter and inserted within the termination codon of the essential groEL gene. Mol Microbiol 49, 1407 1423.
24. Toro N (2003) Bacteria and archaea group II introns: additional mobile genetic elements in the environment. Environ Microbiol 5, 143 151.
25. Toro N, Jiménez-Zurdo JI García-Rodríguez FM (2007) Bacterial group II introns: not just splicing. FEMS Microbiol Rev 31, 342 358.
26. Simon DM, Claske NA, McNeil BA, Johnson I, Pantuso D, Dai L, Chai D Zimmerly S (2008) Group II introns in Eubacteria and Archaea: ORF-less introns and new varieties. RNA 14, 1704 1713.
27. 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.
28. Dai L Zimmerly S (2002) Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior. Nucleic Acids Res 30, 1091 1102.
29. Muñoz-Adelantado E, San Filippo J, Martínez-Abarca F, García-Rodríguez FM, Lambowitz AM Toro N (2003) Mobility of the Sinorhizobium meliloti group II intron RmInt1 occurs by reverse splicing into DNA, but requires and unknown reverse transcriptase priming mechanism. J Mol Biol 327, 931 943.
30. 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.
31. Jiménez-Zurdo JI, García-Rodríguez FM, Barrientos-Durán A Toro N (2003) DNA target site 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.
32. Costa M, Michel F Toro N (2006) Potential for alternative intron-exon pairings in group II intron RmInt1 from Sinorhizobium meliloti and its relatives. RNA 12, 338 341.
33. 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.
34. Crooks GE, Hon G, Chandonia JM Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14, 1188 1190.
35. Schneider TD Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18, 6097 6100.