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A single Arabidopsis organellar protein has RNase P activity

Nature Structural & Molecular Biology volume 17, pages 740–744 (2010)Cite this article

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Abstract

The ubiquitous endonuclease RNase P is responsible for the 5′ maturation of tRNA precursors. Until the discovery of human mitochondrial RNase P, these enzymes had typically been found to be ribonucleoproteins, the catalytic activity of which is associated with the RNA component. Here we show that, in Arabidopsis thaliana mitochondria and plastids, a single protein called 'proteinaceous RNase P' (PRORP1) can perform the endonucleolytic maturation of tRNA precursors that defines RNase P activity. In addition, PRORP1 is able to cleave tRNA-like structures involved in the maturation of plant mitochondrial mRNAs. Finally, we show that Arabidopsis PRORP1 can replace the bacterial ribonucleoprotein RNase P in Escherichia coli cells. PRORP2 and PRORP3, two paralogs of PRORP1, are both localized in the nucleus.

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Figure 1: PRORP proteins define a novel family of putative nucleases present in a wide array of eukaryote lineages.
Figure 2: PRORP1 is mitochondrial and chloroplastic, whereas PRORP2 and PRORP3 are nuclear.
Figure 3: PRORP1 is essential.
Figure 4: PRORP1 has RNase P activity.
Figure 5: Arabidopsis PRORP1 can functionally replace E. coli RNase P in vivo.

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References

  1. Evans, D., Marquez, S.M. & Pace, N.R. RNase P: interface of the RNA and protein worlds. Trends Biochem. Sci. 31, 333–341 (2006).

    Article  CAS  PubMed  Google Scholar 

  2. Hartmann, R.K., Gößringer, M., Spath, B., Fischer, S. & Marchfelder, A. The making of tRNAs and more—RNase P and tRNase Z. Prog. Mol. Biol. Transl. Sci. 85, 319–368 (2009).

    Article  CAS  PubMed  Google Scholar 

  3. Walker, S.C. & Engelke, D.R. Ribonuclease P: the evolution of an ancient RNA enzyme. Crit. Rev. Biochem. Mol. Biol. 41, 77–102 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Lai, L.B., Vioque, A., Kirsebom, L.A. & Gopalan, V. Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects. FEBS Lett. 584, 287–296 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N. & Altman, S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35, 849–857 (1983).

    Article  CAS  PubMed  Google Scholar 

  6. Pannucci, J.A., Haas, E.S., Hall, T.A., Harris, J.K. & Brown, J.W. RNase P RNAs from some Archaea are catalytically active. Proc. Natl. Acad. Sci. USA 96, 7803–7808 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Kikovska, E., Svard, S.G. & Kirsebom, L.A. Eukaryotic RNase P RNA mediates cleavage in the absence of protein. Proc. Natl. Acad. Sci. USA 104, 2062–2067 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Wang, M.J., Davis, N.W. & Gegenheimer, P. Novel mechanisms for maturation of chloroplast transfer RNA precursors. EMBO J. 7, 1567–1574 (1988).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Marchfelder, A. Plant mitochondrial RNase P. Mol. Biol. Rep. 22, 151–156 (1995).

    Article  CAS  PubMed  Google Scholar 

  10. Schön, A. Ribonuclease P from plant nuclei and photosynthetic organelles. Mol. Biol. Rep. 22, 139–145 (1995).

    Article  PubMed  Google Scholar 

  11. Thomas, B.C., Gao, L., Stomp, D., Li, X. & Gegenheimer, P.A. Spinach chloroplast RNase P: a putative protein enzyme. Nucleic Acids Symp. Ser. 33, 95–98 (1995).

    CAS  Google Scholar 

  12. Thomas, B.C., Li, X. & Gegenheimer, P. Chloroplast ribonuclease P does not utilize the ribozyme-type pre-tRNA cleavage mechanism. RNA 6, 545–553 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Holzmann, J. et al. RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme. Cell 135, 462–474 (2008).

    Article  CAS  PubMed  Google Scholar 

  14. Lurin, C. et al. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell 16, 2089–2103 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Hartmann, E. & Hartmann, R.K. The enigma of ribonuclease P evolution. Trends Genet. 19, 561–569 (2003).

    Article  CAS  PubMed  Google Scholar 

  16. Piccinelli, P., Rosenblad, M.A. & Samuelsson, T. Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes. Nucleic Acids Res. 33, 4485–4495 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Rosenblad, M.A., Lopez, M.D., Piccinelli, P. & Samuelsson, T. Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes. Nucleic Acids Res. 34, 5145–5156 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Guerrier-Takada, C. & Altman, S. Catalytic activity of an RNA molecule prepared by transcription in vitro. Science 223, 285–286 (1984).

    Article  CAS  PubMed  Google Scholar 

  19. Rossmanith, W. & Holzmann, J. Processing mitochondrial (t)RNAs: new enzyme, old job. Cell Cycle 8, 1650–1653 (2009).

    Article  CAS  PubMed  Google Scholar 

  20. Barkan, A. Proteins encoded by a complex chloroplast transcription unit are each translated from both monocistronic and polycistronic mRNAs. EMBO J. 7, 2637–2644 (1988).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Giegé, P., Hoffmann, M., Binder, S. & Brennicke, A. RNA degradation buffers asymmetries of transcription in Arabidopsis mitochondria. EMBO Rep. 1, 164–170 (2000).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Hanic-Joyce, P.J., Spencer, D.F. & Gray, M.W. In vitro processing of transcripts containing novel tRNA-like sequences ('t-elements') encoded by wheat mitochondrial DNA. Plant Mol. Biol. 15, 551–559 (1990).

    Article  CAS  PubMed  Google Scholar 

  23. Bellaoui, M., Pelletier, G. & Budar, F. The steady-state level of mRNA from the Ogura cytoplasmic male sterility locus in Brassica cybrids is determined post-transcriptionally by its 3′ region. EMBO J. 16, 5057–5068 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Forner, J., Weber, B., Thuss, S., Wildum, S. & Binder, S. Mapping of mitochondrial mRNA termini in Arabidopsis thaliana: t-elements contribute to 5′ and 3′ end formation. Nucleic Acids Res. 35, 3676–3692 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Wegscheid, B. & Hartmann, R.K. The precursor tRNA 3′-CCA interaction with Escherichia coli RNase P RNA is essential for catalysis by RNase P in vivo. RNA 12, 2135–2148 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Srisawat, C. et al. An active precursor in assembly of yeast nuclear ribonuclease P. RNA 8, 1348–1360 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Kiss, T., Marshallsay, C. & Filipowicz, W. 7–2/MRP RNAs in plant and mammalian cells: association with higher order structures in the nucleolus. EMBO J. 11, 3737–3746 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Schmitz-Linneweber, C. & Small, I. Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci. 13, 663–670 (2008).

    Article  CAS  PubMed  Google Scholar 

  29. Beick, S., Schmitz-Linneweber, C., Williams-Carrier, R., Jensen, B. & Barkan, A. The pentatricopeptide repeat protein PPR5 stabilizes a specific tRNA precursor in maize chloroplasts. Mol. Cell. Biol. 28, 5337–5347 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Dupureur, C.M. Roles of metal ions in nucleases. Curr. Opin. Chem. Biol. 12, 250–255 (2008).

    Article  CAS  PubMed  Google Scholar 

  31. Steitz, T.A. & Steitz, J.A. A general two-metal-ion mechanism for catalytic RNA. Proc. Natl. Acad. Sci. USA 90, 6498–6502 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Helm, M. et al. Search for characteristic structural features of mammalian mitochondrial tRNAs. RNA 6, 1356–1379 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Florentz, C., Sohm, B., Tryoen-Toth, P., Putz, J. & Sissler, M. Human mitochondrial tRNAs in health and disease. Cell. Mol. Life Sci. 60, 1356–1375 (2003).

    Article  CAS  PubMed  Google Scholar 

  34. Vogel, J. & Hess, W.R. Complete 5′ and 3′ end maturation of group II intron-containing tRNA precursors. RNA 7, 285–292 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Kirsebom, L.A. RNase P RNA mediated cleavage: substrate recognition and catalysis. Biochimie 89, 1183–1194 (2007).

    Article  CAS  PubMed  Google Scholar 

  36. Holzmann, J. & Rossmanith, W. tRNA recognition, processing, and disease: hypotheses around an unorthodox type of RNase P in human mitochondria. Mitochondrion 9, 284–288 (2009).

    Article  CAS  PubMed  Google Scholar 

  37. Dereeper, A. et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 36, W465–W469 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Edgar, R.C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113 (2004).

    Article  PubMed  PubMed Central  Google Scholar 

  39. Gascuel, O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14, 685–695 (1997).

    Article  CAS  PubMed  Google Scholar 

  40. Chevenet, F., Brun, C., Banuls, A.L., Jacq, B. & Christen, R. TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics 7, 439 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  41. Gleave, A.P. A versatile binary vector system with a T-DNA organisational structure conducive to efficient integration of cloned DNA into the plant genome. Plant Mol. Biol. 20, 1203–1207 (1992).

    Article  CAS  PubMed  Google Scholar 

  42. Abel, S. & Theologis, A. Transient transformation of Arabidopsis leaf protoplasts: a versatile experimental system to study gene expression. Plant J. 5, 421–427 (1994).

    Article  CAS  PubMed  Google Scholar 

  43. Giegé, P., Sweetlove, L. & Leaver, C. Identification of mitochondrial protein complexes in Arabidopsis using two-dimensional Blue-Native polyacrylamide gel electrophoresis. Plant Mol. Biol. Rep. 21, 133–144 (2003).

    Article  Google Scholar 

  44. Uyttewaal, M. et al. PPR336 is associated with polysomes in plant mitochondria. J. Mol. Biol. 375, 626–636 (2008).

    Article  CAS  PubMed  Google Scholar 

  45. Rayapuram, N., Hagenmuller, J., Grienenberger, J.M., Bonnard, G. & Giegé, P. The three mitochondrial encoded CcmF proteins form a complex that interacts with CCMH and c-type apocytochromes in Arabidopsis. J. Biol. Chem. 283, 25200–25208 (2008).

    Article  CAS  PubMed  Google Scholar 

  46. Lamattina, L., Gonzalez, D., Gualberto, J. & Grienenberger, J.M. Higher plant mitochondria encode an homologue of the nuclear-encoded 30-kDa subunit of bovine mitochondrial complex I. Eur. J. Biochem. 217, 831–838 (1993).

    Article  CAS  PubMed  Google Scholar 

  47. Meyer, E.H. et al. AtCCMH, an essential component of the c-type cytochrome maturation pathway in Arabidopsis mitochondria, interacts with apocytochrome c. Proc. Natl. Acad. Sci. USA 102, 16113–16118 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Rossmanith, W., Tullo, A., Potuschak, T., Karwan, R. & Sbisa, E. Human mitochondrial tRNA processing. J. Biol. Chem. 270, 12885–12891 (1995).

    Article  CAS  PubMed  Google Scholar 

  49. Cruz-Reyes, J., Piller, K.J., Rusche, L.N., Mukherjee, M. & Sollner-Webb, B. Unexpected electrophoretic migration of RNA with different 3′ termini causes a RNA sizing ambiguity that can be resolved using nuclease P1-generated sequencing ladders. Biochemistry 37, 6059–6064 (1998).

    Article  CAS  PubMed  Google Scholar 

  50. Stragier, P., Bonamy, C. & Karmazyn-Campelli, C. Processing of a sporulation σ factor in Bacillus subtilis: how morphological structure could control gene expression. Cell 52, 697–704 (1988).

    Article  CAS  PubMed  Google Scholar 

  51. Gößringer, M. & Hartmann, R.K. Function of heterologous and truncated RNase P proteins in Bacillus subtilis. Mol. Microbiol. 66, 801–813 (2007).

    Article  Google Scholar 

  52. Gößringer, M., Kretschmer-Kazemi Far, R. & Hartmann, R.K. Analysis of RNase P protein (rnpA) expression in Bacillus subtilis utilizing strains with suppressible rnpA expression. J. Bacteriol. 188, 6816–6823 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank T. Potuschak for critical reading of the manuscript. This work was supported by the Centre National de la Recherche Scientifique, by research grant 07-JCJC-0123 from the Agence Nationale de la Recherche (ANR) to P.G., by grants P17453 and I299 from the Austrian Science Fund (FWF) to W.R. and by grant HA-1672/7-5/14-3 from the Deutsche Forschungsgemeinschaft (DFG) to R.K.H.

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Author notes

  1. Bernard Gutmann, Andreas Taschner and Markus Gößringer: These authors contributed equally to this work.

  2. Walter Rossmanith and Philippe Giegé: These authors contributed equally to this work.

Authors and Affiliations

  1. Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Strasbourg, France

    Anthony Gobert, Bernard Gutmann & Philippe Giegé

  2. Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna, Austria

    Andreas Taschner, Johann Holzmann & Walter Rossmanith

  3. Institute for Pharmaceutical Chemistry, Philipps-Universität Marburg, Marburg, Germany

    Markus Gößringer & Roland K Hartmann

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Contributions

A.G., R.K.H., J.H., W.R. and P.G. conceived and designed the experiments; A.G., B.G., A.T., M.G. and P.G. performed the experiments; A.G., B.G., A.T., M.G., R.K.H., W.R. and P.G. analyzed the data; A.G., R.K.H., W.R. and P.G. wrote the paper.

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Correspondence to Walter Rossmanith or Philippe Giegé.

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Gobert, A., Gutmann, B., Taschner, A. et al. A single Arabidopsis organellar protein has RNase P activity. Nat Struct Mol Biol 17, 740–744 (2010). https://doi.org/10.1038/nsmb.1812

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