Degradation of plastid unspliced transcripts and lariat group II introns

Biochimie

Volumn 90, Issue 3, 2008, Pages 474-483

  del Campo, Eva M ^a   Casano, Leonardo M ^a  

^a UNIVERSITY OF ALCALÁ   (Spain)

Author keywords

Group II intron; RNA degradation; RNA turnover; Splicing

Indexed keywords

PROTEIN ATPF; PROTEIN NDHA; PROTEIN PETB; RIBONUCLEASE III; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

ARTICLE; CHLOROPLAST; CONTROLLED STUDY; GENE STRUCTURE; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASTID; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA DEGRADATION; RNA SEQUENCE; RNA SPLICING;

BASE SEQUENCE; CHLOROPLASTS; INTRONS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PLANT PROTEINS; PLASTIDS; RNA PRECURSORS; RNA SPLICING; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

PROKARYOTA;

EID: 38949108938     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2007.10.006     Document Type: Article

References (30)

1. Pyle A.M., Fedorova O., and Waldsich C. Folding of group II introns: a model system for large, multidomain RNAs?. Trends Biochem. Sci. 32 (2007) 138-145
2. Chu V.T., Liu Q., Podar M., Perlman P.S., and Pyle A.M. More than one way to splice an RNA: branching without a bulge and splicing without branching in group II introns. RNA 4 (1998) 1186-1202
3. Vogel J., and Borner T. Lariat formation and a hydrolytic pathway in plant chloroplast group II intron splicing. EMBO J. 21 (2002) 3794-3803
4. Liere K., and Link G. RNA-binding activity of the matK protein encoded by the chloroplast trnK intron from mustard (Sinapis alba L.). Nucleic Acids Res. 23 (1995) 917-921
5. Sheveleva E.V., and Hallick R.B. Recent horizontal intron transfer to a chloroplast genome. Nucleic Acids Res. 32 (2004) 803-810
6. Ostersetzer O., Cooke A.M., Watkins K.P., and Barkan A. CRS1, a chloroplast group II intron splicing factor, promotes intron folding through specific interactions with two intron domains. Plant Cell 17 (2005) 241-255
7. Alvarez, and Wise J.A. Activation of a cryptic 5′ splice site by U1 snRNA. RNA 7 (2001) 342-350
8. Del Campo E.M., Sabater B., and Martin M. Transcripts of the ndhH-D operon of barley plastids: possible role of unedited site III in splicing of the ndhA intron. Nucleic Acids Res. 28 (2000) 1092-1098
9. Schmitz-Linneweber C., Tillich M., Herrmann R.G., and Maier R.M. Heterologous, splicing-dependent RNA editing in chloroplasts: allotetraploidy provides trans-factors. EMBO J. 20 (2001) 4874-4883
10. Del Campo E.M., Sabater B., and Martín M. Characterization of the 5′- and 3′-ends of mRNAs of ndhH, ndhA and ndhI genes of the plastid ndhH-D operon. Biochimie 88 (2006) 347-357
11. Bollenbach T.J., Schuster G., and Stern D.B. Cooperation of endo- and exoribonucleases in chloroplast mRNA turnover. Prog. Nucleic Acid Res. Mol. Biol. 78 (2004) 305-337
12. Jones J.D., Dunsmuir P., and Bedbrook J. High level expression of introduced chimaeric genes in regenerated transformed plants. EMBO J. 4 (1985) 2411-2418
13. Maier R.M., Neckermann K., Igloi G.L., and Kossel H. Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol. 251 (1995) 614-628
14. Schmitz-Linneweber C., Maier R.M., Alcaraz J.P., Cottet A., Herrmann R.G., and Mache R. The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Plant Mol. Biol. 45 (2001) 307-315
15. Mathews D.H., Sabina J., Zuker M., and Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288 (1999) 911-940
16. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (2003) 3406-3415
17. Kudla J., Hayes R., and Gruissem W. Polyadenylation accelerates degradation of chloroplast mRNA. EMBO J. 15 (1996) 7137-7146
18. Kim J.K., and Hollingsworth M.J. Splicing of group II introns in spinach chloroplasts (in vivo): analysis of lariat formation. Curr. Genet. 23 (1993) 175-180
19. Ooi S.L., Samarsky D.A., Fournier M.J., and Boeke J.D. Intronic snoRNA biosynthesis in Saccharomyces cerevisiae depends on the lariat-debranching enzyme: intron length effects and activity of a precursor snoRNA. RNA 4 (1998) 1096-1110
20. Barkan A., Walker M., Nolasco M., and Johnson D. A nuclear mutation in maize blocks the processing and translation of several chloroplast mRNAs and provides evidence for the differential translation of alternative mRNA forms. EMBO J. 13 (1994) 3170-3181
21. Rock C.D., Barkan A., and Taylor W.C. The maize plastid psbB-psbF-petB-petD gene cluster: spliced and unspliced petB and petD RNAs encode alternative products. Curr. Genet. 12 (1987) 69-77
22. Barkan A. Tissue-dependent plastid RNA splicing in maize: transcripts from four plastid genes are predominantly unspliced in leaf meristems and roots. Plant Cell 1 (1989) 437-445
23. Bousquet-Antonelli C., Presutti C., and Tollervey D. Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102 (2000) 765-775
24. Clement J.Q., Maiti S., and Wilkinson M.F. Localization and stability of introns spliced from the Pem homeobox gene. J. Biol. Chem. 276 (2001) 16919-16930
25. Robertson H.D., Dickson E., and Jelinek W. Determination of nucleotide sequences from double-stranded regions of HeLa cell nuclear RNA. J. Mol. Biol. 115 (1977) 571-589
26. Danin-Kreiselman M., Lee C.Y., and Chanfreau G. RNAse III-mediated degradation of unspliced pre-mRNAs and lariat introns. Mol. Cell 11 (2003) 1279-1289
27. Susi P., Hohkuri M., Wahlroos T., and Kilby N.J. Characteristics of RNA silencing in plants: similarities and differences across kingdoms. Plant Mol. Biol. 54 (2004) 157-174
28. Collins R.E., and Cheng X. Structural domains in RNAi. FEBS Lett. 579 (2005) 5841-5849
29. Logsdon Jr. J.M., Stoltzfus A., and Doolittle W.F. Molecular evolution: recent cases of spliceosomal intron gain?. Curr. Biol. 8 (1998) R560-R563
30. Watkins K.P., Kroeger T.S., Cooke A.M., Williams-Carrier R.E., Friso G., Belcher S.E., Klaas J., van Wijk K.J., and Barkan A. A ribonuclease III domain protein functions in group II intron splicing in maize chloroplasts. Plant Cell 19 (2007) 2606-2623