Relaxed Transcription in Arabidopsis Mitochondria Is Counterbalanced by RNA Stability Control Mediated by Polyadenylation and Polynucleotide Phosphorylase

REFERENCES

• Bollenbach, T. J., G. Schuster, and D. B. Stern. 2004. Cooperation of endo- and exoribonucleases in chloroplast mRNA turnover. Prog. Nucleic Acid Res. Mol. Biol. 78:305–337.
   PubMedGoogle Scholar
• Burger, G., M. W. Gray, and B. F. Lang. 2003. Mitochondrial genomes: anything goes. Trends Genet. 19:709–716.
   PubMed Web of Science ®Google Scholar
• Dreyfus, M., and P. Regnier. 2002. The poly(A) tail of mRNAs: bodyguard in eukaryotes, scavenger in bacteria. Cell 111:611–613.
   PubMed Web of Science ®Google Scholar
• Finnegan, P. M., and G. G. Brown. 1990. Transcriptional and post-transcriptional regulation of RNA levels in maize mitochondria. Plant Cell 2:71–83.
   PubMedGoogle Scholar
• Gagliardi, D., and C. J. Leaver. 1999. Polyadenylation accelerates the degradation of the mitochondrial mRNA associated with cytoplasmic male sterility in sunflower. EMBO J. 18:3757–3766.
   PubMedGoogle Scholar
• Giege, P., and A. Brennicke. 1999. RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc. Natl. Acad. Sci. USA 96:15324–15329.
   PubMed Web of Science ®Google Scholar
• Giege, P., M. Hoffmann, S. Binder, and A. Brennicke. 2000. RNA degradation buffers asymmetries of transcription in Arabidopsis mitochondria. EMBO Rep. 1:164–170.
   PubMedGoogle Scholar
• Hegeman, C. E., C. P. Halter, T. G. Owens, and M. R. Hanson. 2005. Expression of complementary RNA from chloroplast transgenes affects editing efficiency of transgene and endogenous chloroplast transcripts. Nucleic Acids Res. 33:1454–1464.
   PubMedGoogle Scholar
• Johnson, J. M., S. Edwards, D. Shoemaker, and E. E. Schadt. 2005. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 21:93–102.
   PubMed Web of Science ®Google Scholar
• Klein, M., U. Eckert-Ossenkopp, I. Schmiedeberg, P. Brandt, M. Unseld, A. Brennicke, and W. Schuster. 1994. Physical mapping of the mitochondrial genome of Arabidopsis thaliana by cosmid and YAC clones. Plant J. 6:447–455.
   PubMedGoogle Scholar
• Kuhn, K., A. Weihe, and T. Borner. 2005. Multiple promoters are a common feature of mitochondrial genes in Arabidopsis. Nucleic Acids Res. 33:337–346.
   PubMed Web of Science ®Google Scholar
• LaCava, J., J. Houseley, C. Saveanu, E. Petfalski, E. Thompson, A. Jacquier, and D. Tollervey. 2005. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121:713–724.
   PubMed Web of Science ®Google Scholar
• Leino, M., M. Landgren, and K. Glimelius. 2005. Alloplasmic effects on mitochondrial transcriptional activity and RNA turnover result in accumulated transcripts of Arabidopsis orfs in cytoplasmic male-sterile Brassica napus. Plant J. 42:469–480.
   PubMedGoogle Scholar
• Lupold, D. S., A. G. Caoile, and D. B. Stern. 1999. The maize mitochondrial cox2 gene has five promoters in two genomic regions, including a complex promoter consisting of seven overlapping units. J. Biol. Chem. 274:3897–3903.
   PubMed Web of Science ®Google Scholar
• Marker, C., A. Zemann, T. Terhorst, M. Kiefmann, J. P. Kastenmayer, P. Green, J. P. Bachellerie, J. Brosius, and A. Huttenhofer. 2002. Experimental RNomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana. Curr. Biol. 12:2002–2013.
   PubMed Web of Science ®Google Scholar
• Perrin, R., H. Lange, J. M. Grienenberger, and D. Gagliardi. 2004. AtmtPNPase is required for multiple aspects of the 18S rRNA metabolism in Arabidopsis thaliana mitochondria. Nucleic Acids Res. 32:5174–5182.
   PubMedGoogle Scholar
• Perrin, R., E. H. Meyer, M. Zaepfel, Y. J. Kim, R. Mache, J. M. Grienenberger, J. M. Gualberto, and D. Gagliardi. 2004. Two exoribonucleases act sequentially to process mature 3′-ends of atp9 mRNAs in Arabidopsis mitochondria. J. Biol. Chem. 279:25440–25446.
   PubMed Web of Science ®Google Scholar
• Selinger, D. W., K. J. Cheung, R. Mei, E. M. Johansson, C. S. Richmond, F. R. Blattner, D. J. Lockhart, and G. M. Church. 2000. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat. Biotechnol. 18:1262–1268.
   PubMed Web of Science ®Google Scholar
• Stolc, V., M. P. Samanta, W. Tongprasit, H. Sethi, S. Liang, D. C. Nelson, A. Hegeman, C. Nelson, D. Rancour, S. Bednarek, E. L. Ulrich, Q. Zhao, R. L. Wrobel, C. S. Newman, B. G. Fox, G. N. Phillips, Jr., J. L. Markley, and M. R. Sussman. 2005. Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc. Natl. Acad. Sci. USA 102:4453–4458.
   PubMedGoogle Scholar
• Sun, C. W., and J. Callis. 1993. Recent stable insertion of mitochondrial DNA into an Arabidopsis polyubiquitin gene by nonhomologous recombination. Plant Cell 5:97–107.
   PubMedGoogle Scholar
• Touzet, P., and F. Budar. 2004. Unveiling the molecular arms race between two conflicting genomes in cytoplasmic male sterility? Trends Plant Sci. 9:568–570.
   PubMedGoogle Scholar
• Wyers, F., M. Rougemaille, G. Badis, J. C. Rousselle, M. E. Dufour, J. Boulay, B. Regnault, F. Devaux, A. Namane, B. Seraphin, D. Libri, and A. Jacquier. 2005. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121:725–737.
   PubMed Web of Science ®Google Scholar
• Yamada, K., J. Lim, J. M. Dale, H. Chen, P. Shinn, C. J. Palm, A. M. Southwick, H. C. Wu, C. Kim, M. Nguyen, P. Pham, R. Cheuk, G. Karlin-Newmann, S. X. Liu, B. Lam, H. Sakano, T. Wu, G. Yu, M. Miranda, H. L. Quach, M. Tripp, C. H. Chang, J. M. Lee, M. Toriumi, M. M. Chan, C. C. Tang, C. S. Onodera, J. M. Deng, K. Akiyama, Y. Ansari, T. Arakawa, J. Banh, F. Banno, L. Bowser, S. Brooks, P. Carninci, Q. Chao, N. Choy, A. Enju, A. D. Goldsmith, M. Gurjal, N. F. Hansen, Y. Hayashizaki, C. Johnson-Hopson, V. W. Hsuan, K. Iida, M. Karnes, S. Khan, E. Koesema, J. Ishida, P. X. Jiang, T. Jones, J. Kawai, A. Kamiya, C. Meyers, M. Nakajima, M. Narusaka, M. Seki, T. Sakurai, M. Satou, R. Tamse, M. Vaysberg, E. K. Wallender, C. Wong, Y. Yamamura, S. Yuan, K. Shinozaki, R. W. Davis, A. Theologis, and J. R. Ecker. 2003. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302:842–846.
   PubMed Web of Science ®Google Scholar
• Zubko, M. K. 2004. Mitochondrial tuning fork in nuclear homeotic functions. Trends Plant Sci. 9:61–64.
   PubMedGoogle Scholar