Abstract
Mitochondria are genetic compartments with their own enzymatic equipment for maintenance and expression of their genetic information. As in all genetic systems, gene expression has to be regulated, and in mitochondria this also has to be coordinated with the expression of nuclear-encoded mitochondrial proteins. Presently, there is virtually no information available about the mechanistic details and the enzymes involved in these processes. There is still much to be learned about how plant mitochondrial gene expression is managed and to what extent the contribution of transcription initiation and posttranscriptional processes, respectively, contribute to this control. As one prerequisite for better understanding of the mechanisms and regulatory controls, more fundamental data on mitochondrial transcription initiation and posttranscriptional RNA processing are necessary. As part of the essential methodology, we present methods for the analysis of the 5′ and 3′ extremities of mitochondrial transcripts and the identification of transcription initiation sites. An in organello system is described for the functional investigation of ribonucleic acid editing in plant mitochondria.
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References
Hoffmann, M., Kuhn, J., Däschner, K., and Binder, S. (2001) The RNA world of plant mitochondria. Prog. Nucleic Acid Res. Mol. Biol. 70, 119–154.
Binder, S. and Brennicke, A. (2003) Gene expression in plant mitochondria: transcriptional and posttranscriptional control. Phil. Trans. R. Soc. Lond. B. 358, 181–199.
Marchfelder, A. and Binder, S. (2004) Plastid and plant mitochondrial RNA processing and RNA stability, in Molecular Biology and Biotechnology of Plant Organelles (Daniell, H. and Chase, C., eds.), Springer, Dordrecht, The Netherlands, pp. 261–294.
Kühn, K., Weihe, A., and Borner, T. (2005) Multiple promoters are a common feature of mitochondrial genes in Arabidopsis. Nucleic Acids Res. 33, 337–346.
Mulligan, R. M., Maloney, A. P., and Walbot, V. (1988) RNA processing and multiple transcription initiation sites result in transcript size heterogeneity in maize mitochondria. Mol. Gen. Genet. 211, 373–380.
Sugino, A., Snoper, T. J., and Cozzarelli, N. R. (1977) Bacteriophage T4 RNA ligase. Reaction intermediates and interaction of substrates. J. Biol. Chem. 252, 1732–1738.
England, T. E., Gumport, R. I., and Uhlenbeck, O. C. (1977) Dinucleoside pyrophosphate are substrates for T4-induced RNA ligase. Proc. Natl. Acad. Sci. USA 74, 4839–4842.
Fromont-Racine, M., Bertrand, E., Pictet, R., and Grange, T. (1993) A highly sensitive method for mapping the 5′ termini of mRNAs. Nucleic Acids Res. 21, 1683–1684.
Bensing, B. A., Meyer, B. J., and Dunny, G. M. (1996) Sensitive detection of bacterial transcription initiation sites and differentiation from RNA processing sites in the pheromone-induced plasmid transfer system of Enterococcus faecalis. Proc. Natl. Acad. Sci. USA 93, 7794–7799.
Kuhn, J. and Binder, S. (2002) RT-PCR analysis of 5′ to 3′-end-ligated mRNAs identifies the extremities of cox2 transcripts in pea mitochondria. Nucleic Acids Res. 30, 439–446.
Brennicke, A., Marchfelder, A., and Binder, S. (1999) RNA editing. FEMS Microbiol. Rev. 23, 297–316.
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, 15,324–15,329.
Small, I. D. and Peeters, N. (2000) The PPR motif-a TPR-related motif prevalent in plant organellar proteins. Trends Biochem. Sci. 25, 46–47.
Kotera, E., Tasaka, M., and Shikanai, T. (2005) A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature 433, 326–330.
Staudinger, M. and Kempken, F. (2004) In organello editing of mitochondrial atp9, cox2 and nad9 transcripts. Endocytobiosis Cell. Res. 15, 551–556.
Staudinger, M. and Kempken, F. (2003) Electroporation of isolated higher-plant mitochondria: transcripts of an introduced cox2 gene, but not an atp6 gene, are edited in organello. Mol. Genet. Genomics 269, 553–561.
Staudinger, M., Bolle, N., and Kempken, F. (2005) Mitochondrial electroporation and in organello RNA editing of chimeric atp6 transcripts. Mol. Genet. Genomics 273, 130–136.
Binder, S. (1995) Mitochondrial nucleic acid purification and analysis. Methods Mol. Biol. 49, 383–389.
Binder, S. and Grohmann, L. (1995) Isolation of mitochondria. Methods Mol. Biol. 49, 377–381.
Klein, M., Binder, S., and Brennicke, A. (1998) Purification of mitochondria from Arabidopsis. Methods Mol. Biol. 82, 49–53.
Newton, K. J. (1994) Procedures for isolating mitochondria and mitochondrial DNA and RNA, in The Maize Handbook (Freeling, M. and Walbot, V., eds.), Springer, New York, pp. 549–556.
Binder, S. and Brennicke, A. (1993) Transcription initiation sites in mitochondria of Oenothera berteriana. J. Biol. Chem. 268, 7849–7855.
Farr’e, J. C. and Araya, A. (2001) Gene expression in isolated plant mitochondria: high fidelity of transcription, splicing and editing of a transgene product in electroporated organelles. Nucleic Acids Res. 29, 2484–2491.
Kempken, F., Mullen, J. A., Pring, D. R., and Tang, H. V. (1991) RNA editing of sorghum mitochondrial atp6 transcripts changes 15 amino acids and generates a carboxy-terminus identical to yeast. Curr. Genet. 20, 417–422.
Kumar, R. and Levings, C. S., 3rd (1993) RNA editing of a chimeric maize mitochondrial gene transcript is sequence specific. Curr. Genet. 23, 154–159.
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© 2007 Humana Press Inc., Totowa, NJ
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Kempken, F., Bolle, N., Forner, J., Binder, S. (2007). Transcript End Mapping and Analysis of RNA Editing in Plant Mitochondria. In: Leister, D., Herrmann, J.M. (eds) Mitochondria. Methods in Molecular Biology™, vol 372. Humana Press. https://doi.org/10.1007/978-1-59745-365-3_13
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DOI: https://doi.org/10.1007/978-1-59745-365-3_13
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