Assay of Editing of Exogenous RNAs in Chloroplast Extracts of Arabidopsis, Maize, Pea, and Tobacco

Methods in Enzymology

Volumn 424, Issue , 2007, Pages 459-482

  Hayes, Michael L ^a   Hanson, Maureen R ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTIDINE; NUCLEOTIDE; OLIGONUCLEOTIDE; URIDINE; PLANT RNA; PRIMER DNA;

ACCURACY; ARABIDOPSIS; CHLOROPLAST; CONSENSUS SEQUENCE; ISOTOPE LABELING; MAIZE; NONHUMAN; PEA; POISONED PRIMER EXTENSION ASSAY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; QUANTITATIVE ASSAY; REVIEW; RNA EDITING; TOBACCO; ARTICLE; BINDING COMPETITION; BIOCHEMISTRY; CHEMISTRY; GENETIC PROCEDURES; GENETICS; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLASTID;

ARABIDOPSIS; NICOTIANA TABACUM; PISUM SATIVUM; TRACHEOPHYTA; ZEA MAYS;

ARABIDOPSIS; BASE SEQUENCE; BINDING, COMPETITIVE; BIOCHEMISTRY; CHLOROPLASTS; DNA PRIMERS; GENETIC TECHNIQUES; MOLECULAR SEQUENCE DATA; PEAS; PLASTIDS; RNA EDITING; RNA, PLANT; TOBACCO; ZEA MAYS;

EID: 34548589169     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(07)24021-2     Document Type: Chapter

References (27)

1. Bock R., Kossel H., and Maliga P. Introduction of a heterologous editing site into the tobacco plastid genome: The lack of RNA editing leads to a mutant phenotype. EMBO J. 13 (1994) 4623-4628
2. Bock R., Hermann M., and Kossel H. In vivo dissection of cis-acting determinants for plastid RNA editing. EMBO J. 15 (1996) 5052-5059
3. Bock R., Hermann M., and Fuchs M. Identification of critical nucleotide positions for plastid RNA editing site recognition. RNA 3 (1997) 1194-1200
4. Chaudhuri S., and Maliga P. 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 (1996) 5958-5964
5. Chaudhuri S., Carrer H., and Maliga P. Site-specific factor involved in the editing of the psbL mRNA in tobacco plastids. EMBO J. 14 (1995) 2951-2957
6. Hayes M.L., and Hanson M.R. Identification of a sequence motif critical for editing of a tobacco chloroplast transcript. RNA 13 (2007) 281-288
7. Hayes M.L., Reed M.L., Hegeman C.E., and Hanson M.R. Sequence elements critical for efficient RNA editing of a tobacco chloroplast transcript in vivo and in vitro. Nucleic Acids Res. 34 (2006) 3742-3754
8. Hegeman C.E., Halter C.P., Owens T.G., and Hanson M.R. Expression of complementary RNA from chloroplast transgenes affects editing efficiency of transgene and endogenous chloroplast transcripts. Nucleic Acids Res. 33 (2005) 1454-1464
9. Hegeman C.E., Hayes M.L., and Hanson M.R. Substrate and cofactor requirements for RNA editing of chloroplast transcripts in Arabidopsis in vitro. Plant J. 42 (2005) 124-132
10. Hirose T., and Sugiura M. Involvement of a site-specific trans-acting 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 (2001) 1144-1152
11. Kotera E., Tasaka M., and Shikanai T. A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature 433 (2005) 326-330
12. Kunst L. Preparation of physiologically active chloroplasts from Arabidopsis. Methods Mol. Biol. 82 (1998) 43-48
13. Miyamoto T., Obokata J., and Sugiura M. 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 (2002) 6726-6734
14. Miyamoto T., Obokata J., and Sugiura M. A site-specific factor interacts directly with its cognate RNA editing site in chloroplast transcripts. Proc. Natl. Acad. Sci. USA 101 (2004) 48-52
15. Nakajima Y., and Mulligan R.M. Nucleotide specificity of the RNA editing reaction in pea chloroplasts. J. Plant Physiol. 162 (2005) 1347-1354
16. Okuda K., Nakamura T., Sugita M., Shimizu T., and Shikanai T. A pentatricopeptide repeat protein is a site-recognition factor in chloroplast RNA editing. J. Biol. Chem. 281 (2006) 37661-37667
17. Peeters N.M., and Hanson M.R. Transcript abundance supercedes editing efficiency as a factor in developmental variation of chloroplast gene expression. RNA 8 (2002) 497-511
18. Peltier J.B., Ytterberg J., Liberles D.A., Roepstorff P., and van Wijk K.J. Identification of a 350-kDa ClpP protease complex with 10 different Clp isoforms in chloroplasts of Arabidopsis thaliana. J. Biol. Chem. 276 (2001) 16318-16327
19. Reed M.L., and Hanson M.R. A heterologous maize rpoB editing site is recognized by transgenic tobacco chloroplasts. Mol. Cell. Biol. 17 (1997) 6948-6952
20. Reed M.L., Peeters N.M., and Hanson M.R. A single alteration 20 nt 5′ to an editing target inhibits chloroplast RNA editing in vivo. Nucleic Acids Res. 29 (2001) 1507-1513
21. Roberson L.M., and Rosenthal J.J. An accurate fluorescent assay for quantifying the extent of RNA editing. RNA 12 (2006) 1907-1912
22. Sasaki T., Yukawa Y., Wakasugi T., Yamada K., and Sugiura M. A simple in vitro RNA editing assay for chloroplast transcripts using fluorescent dideoxynucleotides: Distinct types of sequence elements required for editing of ndh transcripts. Plant J. 47 (2006) 802-810
23. Sasaki Y., Kozaki A., Ohmori A., Iguchi H., and Nagano Y. Chloroplast RNA editing required for functional acetyl-CoA carboxylase in plants. J. Biol. Chem. 276 (2001) 3937-3940
24. Schmitz-Linneweber C., Kushnir S., Babiychuk E., Poltnigg P., Herrmann R.G., and Maier R.M. Pigment deficiency in nightshade/tobacco cybrids is caused by the failure to edit the plastid ATPase alpha-subunit mRNA. Plant Cell 17 (2005) 1815-1828
25. Somerville C.R., Sommerville S.C., and Ogren W.L. Isolation of photosynthetically active protoplasts and chloroplasts from Arabidopsis thaliana. Plant Sci. Lett. 21 (1981) 89-96
26. Takenaka M., and Brennicke A. In vitro RNA editing in pea mitochondria requires NTP or dNTP, suggesting involvement of an RNA helicase. J. Biol. Chem. 278 (2003) 47526-47533
27. Zito F., Kuras R., Choquet Y., Kossel H., and Wollman F.A. Mutations of cytochrome b6 in Chlamydomonas reinhardtii disclose the functional significance for a proline to leucine conversion by petB editing in maize and tobacco. Plant Mol. Biol. 33 (1997) 79-86