RNA editing in hornwort chloroplasts makes more than half the genes functional

Nucleic Acids Research

Volumn 31, Issue 9, 2003, Pages 2417-2423

  Kugita, Masanori ^a   Yamamoto, Yuhei ^a   Fujikawa, Takeshi ^a   Matsumoto, Tohoru ^a   Yoshinaga, Koichi ^a  

^a SHIZUOKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; RIBOSOME RNA; TRANSFER RNA; URACIL; CHLOROPLAST RNA; COMPLEMENTARY DNA; PLANT RNA; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE;

ANTICODON; ARABIDOPSIS; ARTICLE; CHLOROPLAST; CHLOROPLAST GENETICS; CONTROLLED STUDY; GENE CONVERSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC CODE; INTRON; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; RNA EDITING; RNA PROCESSING; RNA SEQUENCE; RNA TRANSCRIPTION; AMINO ACID SUBSTITUTION; BINDING SITE; CHEMISTRY; CODON; DNA SEQUENCE; GENE; GENETIC TRANSCRIPTION; GENETICS; MOLECULAR GENETICS; PHYSIOLOGY; PLANT;

ANTHOCEROS; ANTHOCEROS FORMOSAE; ARABIDOPSIS; BRYOPHYTES; PTERIDOPHYTA;

AMINO ACID SUBSTITUTION; BASE SEQUENCE; BINDING SITES; CODON; DNA, COMPLEMENTARY; GENES, PLANT; INTRONS; MOLECULAR SEQUENCE DATA; NADH DEHYDROGENASE; PLANTS; PROTON-TRANSLOCATING ATPASES; RNA EDITING; RNA, CHLOROPLAST; RNA, PLANT; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION, GENETIC;

EID: 0037736768     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg327     Document Type: Article

References (45)

1. Covello,P.S. and Gray,M.W. (1989) RNA editing in plant mitochondria. Nature, 341, 662-666.
2. Gualberto,J.M., Lamattina,L., Bonnard,G., Weil,J.H. and Grienenberger,J.M. (1989) RNA editing in wheat mitochondria results in the conservation of protein sequences. Nature, 341, 660-662.
3. Hiesel,R., Wissinger,B., Schuster,W. and Brennicke,A. (1989) RNA editing in plant mitochondria. Science, 246, 1632-1634.
4. Hoch,B., Maier,R.M., Appel,K., Igloi,G.L. and Koessel,H. (1991) Editing of a chloroplast mRNA by creation of an initiation codon. Nature, 353, 178-180.
5. Yu,W. and Schuster,W. (1995) Evidence for a site-specific cytidine deamination reaction involved in C to U RNA editing of plant mitochondria. J. Biol. Chem., 270, 18227-18233.
6. Hirose,T., Fan,H., Suzuki,J.Y., Wakasugi,T., Tsudzuki,T., Koessel,H. and Sugiura,M. (1996) Occurrence of silent RNA editing in chloroplasts: its species specificity and the influence of environmental and developmental conditions. Plant Mol. Biol., 30, 667-672.
7. Giege,P. and Brennicke,A. (1999) RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc. Natl Acad. Sci. USA, 96, 15324-15329.
8. Maier,R.M., Neckermann,K., Igloi,G.L. and Koessel,H. (1995) 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, 614-628.
9. Hirose,T., Kusumegi,T., Tsudzuki,T. and Sugiura,M. (1999) RNA editing sites in tobacco chloroplast transcripts: editing as a possible regulator of chloroplast RNA polymerase activity. Mol. Gen. Genet., 262, 462-467.
10. Wakasugi,T., Hirose,T., Horihata,M., Tsudzuki,T., Koessel,H. and Sugiura,M. (1996) Creation of a novel protein-coding region at the RNA level in black pine chloroplasts: the pattern of RNA editing in the gymnosperm chloroplast is different from that in angiosperms. Proc. Natl Acad. Sci. USA, 93, 8766-8770.
11. Yoshinaga,K. (1997) RNA editing in land plants. In Iwatsuki,K. and Raven,P.H. (eds), Evolution and Diversification of Land Plants. Springer, Tokyo, pp. 45-60.
12. Yoshinaga,K., Iinuma,H., Masuzawa,T. and Ueda,K. (1996) Extensive RNA editing of U to C in addition to C to U substitution in the rbcL transcripts of hornwort chloroplasts and the origin of RNA editing in green plants. Nucleic Acids Res., 24, 1008-1014.
13. Yoshinaga,K., Kakehi,T., Shima,Y., Iinuma,H., Masuzawa,T. and Ueno,M. (1997) Extensive RNA editing and possible double-stranded structures determining editing sites in the atpB transcripts of hornwort chloroplasts. Nucleic Acids Res., 25, 4830-4834.
14. Chaudhuri,S., Carrer,H. and Maliga,P. (1995) Site-specific factor involved in the editing of the psbL mRNA in tobacco plastids. EMBO J., 14, 2951-2957.
15. Bock,R. and Koop,H.U. (1997) Extraplastidic site-specific factors mediate RNA editing in chloroplasts. EMBO J., 16, 3282-3288.
16. Hirose,T. and Sugiura,M. (2001) Involvement of a site-specific transacting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system. EMBO J., 20, 1144-1152.
17. Bock,R., Hermann,M. and Koessel,H. (1996) In vivo dissection of cis-acting determinants for plastid RNA editing. EMBO J., 15, 5052-5059.
18. Bock,R., Hermann,M. and Fuchs,M. (1997) Identification of critical nucleotide positions for plastid RNA editing site recognition. RNA, 3, 1194-1200.
19. Chaudhuri,S. and Maliga,P. (1996) Sequences directing C to U editing of the plastid psbL mRNA are located within a 22 nucleotide segment spanning the editing site. EMBO J., 15, 5958-5964.
20. Chaudhuri,S. and Maliga,P. (1997) New insights into plastid RNA editing. Trends Plant Sci., 2, 5-6.
21. Hermann,M. and Bock,R. (1999) Transfer of plastid RNA-editing activity to novel sites suggests a critical role for spacing in editing-site recognition. Proc. Natl Acad. Sci. USA, 96, 4856-4861.
22. Miyamoto,T., Obokata,J. and Sugiura,M. (2002) Recognition of RNA editing sites is directed by unique proteins in chloroplasts: biochemical identification of cis-acting elements and trans-acting factors involved in RNA editing in tobacco and pea chloroplasts. Mol. Cell. Biol., 22, 6726-6734.
23. Bock,R. (2000) Sense from nonsense: how the genetic information of chloroplasts is altered by RNA editing. Biochimie, 82, 549-557.
24. Bock,R. and Maliga,P. (1995) In vivo testing of a tobacco plastid DNA segment for guide RNA function in psbL editing. Mol. Gen. Genet., 247, 439-443.
25. Gawel,N.J. and Jarret,R.L. (1991) A modified CTAB DNA extraction procedure for Musa and Ipomoea. Plant Mol. Biol. Rep., 9, 262-266.
26. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1989) Molecular Cloning: A Laboratory Manual (Second edition). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
27. Kugita,M., Kaneko,A., Yamamoto,Y., Takeya,Y., Matsumoto,T. and Yoshinaga,K. (2003) The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants. Nucleic Acids Res., 31, 716-721.
28. Schuster,W., Hiesel,R., Wissinger,B. and Brennicke,A. (1990) RNA editing in the cytochrome b locus of the higher plant Oenothera berteriana includes a U-to-C transition. Mol. Cell. Biol., 10, 2428-2431.
29. Gualberto,J.M., Weil,J.H. and Grienenberger,J.M. (1990) Editing of the wheat coxIII transcript: evidence for twelve C to U and one U to C conversions and for sequence similarities around editing sites. Nucleic Acids Res., 18, 3771-3776.
30. Kudla,J. and Bock,R. (1999) RNA editing in an untranslated region of the Ginkgo chloroplast genome. Gene, 234, 81-86.
31. Schuster,W., Unseld,M., Wissinger,B. and Brennicke,A. (1990) Ribosomal protein S14 transcripts are edited in Oenothera mitochondria. Nucleic Acids Res., 18, 229-233.
32. Stern,D.B. and Gruissem,W. (1987) Control of plastid gene expression: 3′ inverted repeats act as mRNA processing and stabilizing elements, but do not terminate transcription. Cell, 51, 1145-1157.
33. Michel,F. and Ferat,J.L. (1995) Structure and activities of group II introns. Annu. Rev. Biochem., 64, 435-461.
34. Sutton,C.A., Conklin,P.L., Pruitt,K.D. and Hanson,M.R. (1991) Editing of pre-mRNAs can occur before cis- and trans-splicing in Petunia mitochondria. Mol. Cell. Biol., 11, 4274-4277.
35. Ruf,S., Zeltz,P. and Koessel,H. (1994) Complete RNA editing of unspliced and dicistronic transcripts of the intron-containing reading frame IRF170 from maize chloroplasts. Proc. Natl Acad Sci. USA, 91, 2295-2299.
36. Marechal-Drouard,L., Ramamonjisoa,D., Cosset,A., Weil,J.H. and Dietrich,A. (1993) Editing corrects mispairing in the acceptor stem of bean and potato mitochondrial phenylalanine transfer RNAs. Nucleic Acids Res., 21, 4909-4914.
37. Binder,S., Marchfelder,A. and Brennicke,A. (1994) RNA editing of tRNA(Phe) and tRNA(Cys) in mitochondria of Oenothera berteriana is initiated in precursor molecules. Mol. Gen. Genet., 244, 67-74.
38. Marechal-Drouard,L., Kumar,R., Remacle,C. and Small,I. (1996) RNA editing of larch mitochondrial tRNA(His) precursors is a prerequisite for processing. Nucleic Acids Res., 24, 3229-3234.
39. Fey,J., Tomita,K., Bergdoll,M. and Marechal-Drouard,L. (2000) Evolutionary and functional aspects of C-to-U editing at position 28 of tRNA(Cys)(GCA) in plant mitochondria. RNA, 6, 470-474.
40. Alfonzo,J.D., Blanc,V., Estevez,A.M., Rubio,M.A. and Simpson,L. (1999) C to U editing of the anticodon of imported mitochondrial tRNA(Trp) allows decoding of the UGA stop codon in Leishmania tarentolae. EMBO J., 18, 7056-7062.
41. Qin,P.Z. and Pyle,A.M. (1998) The architectural organization and mechanistic function of group II intron structural elements. Curr. Opin. Struct. Biol., 8, 301-308.
42. Boudvillain,M. and Pyle,A.M. (1998) Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis. EMBO J., 17, 7091-7104.
43. Carrillo,C., Chapdelaine,Y. and Bonen,L. (2001) Variation in sequence and RNA editing within core domains of mitochondrial group II introns among plants. Mol. Gen. Genet., 264, 595-603.
44. Steinhauser,S., Beckert,S., Capesius,I., Malek,O. and Knoop,V. (1999) Plant mitochondrial RNA editing. J. Mol. Evol., 48, 303-312.
45. Kyte,J. and Doolittle,R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 157, 105-132.