This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Higgs, D. C.
Right arrow Articles by Stern, D. B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Higgs, D. C.
Right arrow Articles by Stern, D. B.

 Previous Article  |  Next Article 

Molecular and Cellular Biology, December 1999, p. 8479-8491, Vol. 19, No. 12
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

Small cis-Acting Sequences That Specify Secondary Structures in a Chloroplast mRNA Are Essential for RNA Stability and Translation

David C. Higgs,1,dagger Risa S. Shapiro,2 Karen L. Kindle,3,Dagger and David B. Stern1,*

Boyce Thompson Institute for Plant Research,1 and Division of Biological Sciences2 and Plant Science Center,3 Cornell University, Ithaca, New York 14853

Nucleus-encoded proteins interact with cis-acting elements in chloroplast transcripts to promote RNA stability and translation. We have analyzed the structure and function of three such elements within the Chlamydomonas petD 5' untranslated region; petD encodes subunit IV of the cytochrome b6/f complex. These elements were delineated by linker-scanning mutagenesis, and RNA secondary structures were investigated by mapping nuclease-sensitive sites in vitro and by in vivo dimethyl sulfate RNA modification. Element I spans a maximum of 8 nucleotides (nt) at the 5' end of the mRNA; it is essential for RNA stability and plays a role in translation. This element appears to form a small stem-loop that may interact with a previously described nucleus-encoded factor to block 5'right-arrow3' exoribonucleolytic degradation. Elements II and III, located in the center and near the 3' end of the 5' untranslated region, respectively, are essential for translation, but mutations in these elements do not affect mRNA stability. Element II is a maximum of 16 nt in length, does not form an obvious secondary structure, and appears to bind proteins that protect it from dimethyl sulfate modification. Element III spans a maximum of 14 nt and appears to form a stem-loop in vivo, based on dimethyl sulfate modification and the sequences of intragenic suppressors of element III mutations. Furthermore, mutations in element II result in changes in the RNA structure near element III, consistent with a long-range interaction that may promote translation.

* Corresponding author. Mailing address: Boyce Thompson Institute for Plant Research, Cornell University, Tower Rd., Ithaca, NY 14853. Phone: (607) 254-1306. Fax: (607) 255-6695. E-mail: ds28{at}cornell.edu.

dagger Present address: Department of Biological Sciences, University of Wisconsin---Parkside, Kenosha, Wis.

Dagger Present address: Cereon Genomics, Cambridge, Mass.

Molecular and Cellular Biology, December 1999, p. 8479-8491, Vol. 19, No. 12
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


This article has been cited by other articles:

  • Schwarz, C., Elles, I., Kortmann, J., Piotrowski, M., Nickelsen, J. (2007). Synthesis of the D2 Protein of Photosystem II in Chlamydomonas Is Controlled by a High Molecular Mass Complex Containing the RNA Stabilization Factor Nac2 and the Translational Activator RBP40. Plant Cell 19: 3627-3639 [Abstract] [Full Text]  
  • Klinkert, B., Elles, I., Nickelsen, J. (2006). Translation of chloroplast psbD mRNA in Chlamydomonas is controlled by a secondary RNA structure blocking the AUG start codon. Nucleic Acids Res 34: 386-394 [Abstract] [Full Text]  
  • Suay, L., Salvador, M. L., Abesha, E., Klein, U. (2005). Specific roles of 5' RNA secondary structures in stabilizing transcripts in chloroplasts. Nucleic Acids Res 33: 4754-4761 [Abstract] [Full Text]  
  • Murakami, S., Kuehnle, K., Stern, D. B. (2005). A spontaneous tRNA suppressor of a mutation in the Chlamydomonas reinhardtii nuclear MCD1 gene required for stability of the chloroplast petD mRNA. Nucleic Acids Res 33: 3372-3380 [Abstract] [Full Text]  
  • Grossman, A. R. (2005). Paths toward Algal Genomics. Plant Physiol. 137: 410-427 [Full Text]  
  • Rymarquis, L. A., Handley, J. M., Thomas, M., Stern, D. B. (2005). Beyond Complementation. Map-Based Cloning in Chlamydomonas reinhardtii. Plant Physiol. 137: 557-566 [Abstract] [Full Text]  
  • Erickson, B., Stern, D. B., Higgs, D. C. (2005). Microarray Analysis Confirms the Specificity of a Chlamydomonas reinhardtii Chloroplast RNA Stability Mutant. Plant Physiol. 137: 534-544 [Abstract] [Full Text]  
  • Nishimura, Y., Kikis, E. A., Zimmer, S. L., Komine, Y., Stern, D. B. (2004). Antisense Transcript and RNA Processing Alterations Suppress Instability of Polyadenylated mRNA in Chlamydomonas Chloroplasts. Plant Cell 16: 2849-2869 [Abstract] [Full Text]  
  • Grossman, A. R., Harris, E. E., Hauser, C., Lefebvre, P. A., Martinez, D., Rokhsar, D., Shrager, J., Silflow, C. D., Stern, D., Vallon, O., Zhang, Z. (2003). Chlamydomonas reinhardtii at the Crossroads of Genomics. Eukaryot Cell 2: 1137-1150 [Full Text]  
  • Zerges, W., Auchincloss, A. H., Rochaix, J.-D. (2003). Multiple Translational Control Sequences in the 5' Leader of the Chloroplast psbC mRNA Interact With Nuclear Gene Products in Chlamydomonas reinhardtii. Genetics 163: 895-904 [Abstract] [Full Text]  
  • Maul, J. E., Lilly, J. W., Cui, L., dePamphilis, C. W., Miller, W., Harris, E. H., Stern, D. B. (2002). The Chlamydomonas reinhardtii Plastid Chromosome: Islands of Genes in a Sea of Repeats. Plant Cell 14: 2659-2679 [Abstract] [Full Text]  
  • Esposito, D., Hicks, A. J., Stern, D. B. (2001). A Role for Initiation Codon Context in Chloroplast Translation. Plant Cell 13: 2373-2384 [Abstract] [Full Text]  
  • Kuroda, H., Maliga, P. (2001). Complementarity of the 16S rRNA penultimate stem with sequences downstream of the AUG destabilizes the plastid mRNAs. Nucleic Acids Res 29: 970-975 [Abstract] [Full Text]  
  • Singh, M., Boutanaev, A., Zucchi, P., Bogorad, L. (2001). Gene elements that affect the longevity of rbcL sequence-containing transcripts in Chlamydomonas reinhardtii chloroplasts. Proc. Natl. Acad. Sci. USA 10.1073/pnas.041609798v1 [Abstract] [Full Text]  
  • Vaistij, F. E., Boudreau, E., Lemaire, S. D., Goldschmidt-Clermont, M., Rochaix, J.-D. (2000). Characterization of Mbb1, a nucleus-encoded tetratricopeptide-like repeat protein required for expression of the chloroplast psbB/psbT/psbH gene cluster in Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA 97: 14813-14818 [Abstract] [Full Text]  
  • Ossenbühl, F., Nickelsen, J. (2000). cis- and trans-Acting Determinants for Translation of psbD mRNA in Chlamydomonas reinhardtii. Mol. Cell. Biol. 20: 8134-8142 [Abstract] [Full Text]  
  • Shteiman-Kotler, A., Schuster, G. (2000). RNA-binding characteristics of the chloroplast S1-like ribosomal protein CS1. Nucleic Acids Res 28: 3310-3315 [Abstract] [Full Text]  
  • Horlitz, M., Klaff, P. (2000). Gene-specific trans-Regulatory Functions of Magnesium for Chloroplast mRNA Stability in Higher Plants. J. Biol. Chem. 275: 35638-35645 [Abstract] [Full Text]  
  • Hicks, A., Drager, R. G., Higgs, D. C., Stern, D. B. (2002). An mRNA 3' Processing Site Targets Downstream Sequences for Rapid Degradation in Chlamydomonas Chloroplasts. J. Biol. Chem. 277: 3325-3333 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»