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Volume 2011 (2011), Article ID 891531, 12 pages
Assembly of the Complex between Archaeal RNase P Proteins RPP30 and Pop5
1Department of Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210-1214, USA
2Ohio State Biochemistry Program, Ohio State University, Columbus, OH 43210-1214, USA
Received 2 March 2011; Revised 10 August 2011; Accepted 17 August 2011
Academic Editor: Herman van Tilbeurgh
Copyright © 2011 Brandon L. Crowe et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- S. Altman, “A view of RNase P,” Molecular BioSystems, vol. 3, no. 9, pp. 604–607, 2007.
- D. Evans, S. M. Marquez, and N. R. Pace, “RNase P: interface of the RNA and protein worlds,” Trends in Biochemical Sciences, vol. 31, no. 6, pp. 333–341, 2006.
- L. B. Lai, A. Vioque, L. A. Kirsebom, and V. Gopalan, “Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects,” FEBS Letters, vol. 584, no. 2, pp. 287–296, 2010.
- C. Guerrier-Takada, K. Gardiner, and T. Marsh, “The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme,” Cell, vol. 35, no. 3, pp. 849–857, 1983.
- J. A. Pannucci, E. S. Haas, T. A. Hall, J. K. Harris, and J. W. Brown, “RNase P RNAs from some Archaea are catalytically active,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 14, pp. 7803–7808, 1999.
- E. Kikovska, S. G. Svärd, and L. A. Kirsebom, “Eukaryotic RNase P RNA mediates cleavage in the absence of protein,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 7, pp. 2062–2067, 2007.
- P. Schedl and P. Primakoff, “Mutants of Escherichia coli thermosensitive for the synthesis of transfer RNA,” Proceedings of the National Academy of Sciences of the United States of America, vol. 70, no. 7, pp. 2091–2095, 1973.
- S. Niranjanakumari, T. Stams, S. M. Crary, D. W. Christianson, and C. A. Fierke, “Protein component of the ribozyme ribonuclease P alters substrate recognition by directly contacting precursor tRNA,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 26, pp. 15212–15217, 1998.
- J. C. Kurz, S. Niranjanakumari, and C. A. Fierke, “Protein component of Bacillus subtilis RNase P specifically enhances the affinity for precursor-tRNA(Asp),” Biochemistry, vol. 37, no. 8, pp. 2393–2400, 1998.
- J. C. Kurz and C. A. Fierke, “The affinity of magnesium binding sites in the Bacillus subtilis RNase P·Pre-tRNA complex is enhanced by the protein subunit,” Biochemistry, vol. 41, no. 30, pp. 9545–9558, 2002.
- L. Sun and M. E. Harris, “Evidence that binding of C5 protein to P RNA enhances ribozyme catalysis by influencing active site metal ion affinity,” RNA, vol. 13, no. 9, pp. 1505–1515, 2007.
- M. A. Rosenblad, M. D. López, P. Piccinelli, and T. Samuelsson, “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 Research, vol. 34, no. 18, pp. 5145–5156, 2006.
- N. Jarrous and V. Gopalan, “Archaeal/eukaryal RNase P: subunits, functions and RNA diversification,” Nucleic Acids Research, vol. 38, no. 22, pp. 7885–7894, 2010.
- S. Kawano, T. Nakashima, Y. Kakuta, I. Tanaka, and M. Kimura, “Crystal structure of protein Ph1481p in complex with protein Ph1877p of archaeal RNase P from Pyrococcus horikoshii OT3: implication of dimer formation of the holoenzyme,” Journal of Molecular Biology, vol. 357, no. 2, pp. 583–591, 2006.
- J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994.
- J. L. Risler, M. O. Delorme, H. Delacroix, and A. Henaut, “Amino acid substitutions in structurally related proteins. A pattern recognition approach. Determination of a new and efficient scoring matrix,” Journal of Molecular Biology, vol. 204, no. 4, pp. 1019–1029, 1988.
- P. Gouet, E. Courcelle, D. I. Stuart, and F. Métoz, “ESPript: analysis of multiple sequence alignments in PostScript,” Bioinformatics, vol. 15, no. 4, pp. 305–308, 1999.
- J. García De La Torre, M. L. Huertas, and B. Carrasco, “Calculation of hydrodynamic properties of globular proteins from their atomic-level structure,” Biophysical Journal, vol. 78, no. 2, pp. 719–730, 2000.
- Y. Shen, F. Delaglio, G. Cornilescu, and A. Bax, “TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts,” Journal of Biomolecular NMR, vol. 44, no. 4, pp. 213–223, 2009.
- D. S. Garrett, Y. J. Seok, A. Peterkofsky, G. M. Clore, and A. M. Gronenborn, “Identification by NMR of the binding surface for the histidine- containing phosphocarrier protein HPr on the N-terminal domain of enzyme I of the Escherichia coli phosphotransferase system,” Biochemistry, vol. 36, no. 15, pp. 4393–4398, 1997.
- T. A. Hall and J. W. Brown, “Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear RNase P proteins,” RNA, vol. 8, no. 3, pp. 296–306, 2002.
- I. M. Cho, L. B. Lai, D. Susanti, B. Mukhopadhyay, and V. Gopalan, “Ribosomal protein L7Ae is a subunit of archaeal RNase P,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 33, pp. 14573–14578, 2010.
- Y. Kouzuma, M. Mizoguchi, H. Takagi et al., “Reconstitution of archaeal ribonuclease P from RNA and four protein components,” Biochemical and Biophysical Research Communications, vol. 306, no. 3, pp. 666–673, 2003.
- W. P. Boomershine, C. A. McElroy, H. Y. Tsai, R. C. Wilson, V. Gopalan, and M. P. Foster, “Structure of Mth11/Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 26, pp. 15398–15403, 2003.
- W. Y. Chen, D. K. Pulukkunat, I. M. Cho, H. Y. Tsai, and V. Gopalan, “Dissecting functional cooperation among protein subunits in archaeal RNase P, a catalytic ribonucleoprotein complex,” Nucleic Acids Research, vol. 38, no. 22, pp. 8316–8327, 2010.
- H. Y. Tsai, D. K. Pulukkunat, W. K. Woznick, and V. Gopalan, “Functional reconstitution and characterization of Pyrococcus furiosus RNase P,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 44, pp. 16147–16152, 2006.
- N. J. Reiter, A. Osterman, A. Torres-Larios, K. K. Swinger, T. Pan, and A. Mondragón, “Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA,” Nature, vol. 468, no. 7325, pp. 784–791, 2010.
- T. A. Hall and J. W. Brown, “Interactions between RNase P protein subunits in Archaea,” Archaea, vol. 1, no. 4, pp. 247–254, 2004.
- M. Kifusa, H. Fukuhara, T. Hayashi, and M. Kimura, “Protein-protein interactions in the subunits of ribonuclease P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3,” Bioscience, Biotechnology and Biochemistry, vol. 69, no. 6, pp. 1209–1212, 2005.
- F. Houser-Scott, S. Xiao, C. E. Millikin, J. M. Zengel, L. Lindahl, and D. R. Engelke, “Interactions among the protein and RNA subunits of Saccharomyces cerevisiae nuclear RNase P,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 5, pp. 2684–2689, 2002.
- A. V. Kazantsev, A. A. Krivenko, D. J. Harrington et al., “High-resolution structure of RNase P protein from Thermotoga maritima,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 13, pp. 7497–7502, 2003.
- D. J. Sidote, J. Heideker, and D. W. Hoffman, “Crystal structure of archaeal ribonuclease P protein aRpp29 from Archaeoglobus fulgidus,” Biochemistry, vol. 43, no. 44, pp. 14128–14138, 2004.
- T. Numata, I. Ishimatsu, Y. Kakuta, I. Tanaka, and M. Kimura, “Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29,” RNA, vol. 10, no. 9, pp. 1423–1432, 2004.
- Y. Xu, C. D. Amero, D. K. Pulukkunat, V. Gopalan, and M. P. Foster, “Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions,” Journal of Molecular Biology, vol. 393, no. 5, pp. 1043–1055, 2009.
- R. C. Wilson, C. J. Bohlen, M. P. Foster, and C. E. Bell, “Structure of Pfu Pop5, an archael RNase P protein,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 4, pp. 873–878, 2006.
- T. Honda, Y. Kakuta, K. Kimura, J. Saho, and M. Kimura, “Structure of an archaeal homolog of the human protein complex Rpp21-Rpp29 that is a key core component for the assembly of active ribonuclease P,” Journal of Molecular Biology, vol. 384, no. 3, pp. 652–662, 2008.
- H. Takagi, M. Watanabe, Y. Kakuta et al., “Crystal structure of the ribonuclease P protein Ph1877p from hyperthermophilic archaeon Pyrococcus horikoshii OT3,” Biochemical and Biophysical Research Communications, vol. 319, no. 3, pp. 787–794, 2004.
- Y. Kakuta, I. Ishimatsu, T. Numata et al., “Crystal structure of a ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3: an archaeal homologue of human nuclear ribonuclease P protein Rpp21,” Biochemistry, vol. 44, no. 36, pp. 12086–12093, 2005.
- C. D. Amero, W. P. Boomershine, Y. Xu, and M. Foster, “Solution structure of Pyrococcus furiosus RPP21, a component of the archaeal RNase P holoenzyme, and interactions with its RPP29 protein partner,” Biochemistry, vol. 47, no. 45, pp. 11704–11710, 2008.
- L. Li and K. Ye, “Crystal structure of an H/ACA box ribonucleoprotein particle,” Nature, vol. 443, no. 7109, pp. 302–307, 2006.
- H. Fukuhara, M. Kifusa, M. Watanabe et al., “A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3,” Biochemical and Biophysical Research Communications, vol. 343, no. 3, pp. 956–964, 2006.
- D. S. Wishart and D. A. Case, “Use of chemical shifts in macromolecular structure determination,” Nuclear Magnetic Resonance of Biological Macromolecules A, vol. 338, pp. 3–34, 2001.
- T. Wiseman, S. Williston, J. F. Brandts, and L. N. Lin, “Rapid measurement of binding constants and heats of binding using a new titration calorimeter,” Analytical Biochemistry, vol. 179, no. 1, pp. 131–137, 1989.
- K. L. D. Hands-Taylor, L. Martino, R. Tata et al., “Heterodimerization of the human RNase P/MRP subunits Rpp20 and Rpp25 is a prerequisite for interaction with the P3 arm of RNase MRP RNA,” Nucleic Acids Research, vol. 38, no. 12, Article ID gkq141, pp. 4052–4066, 2010.
- A. Perederina, O. Esakova, C. Quan, E. Khanova, and A. S. Krasilnikov, “Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain,” EMBO Journal, vol. 29, no. 4, pp. 761–769, 2010.
- T. Jiang and S. Altman, “Protein-protein interactions with subunits of human nuclear RNase P,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 3, pp. 920–925, 2001.
- J. R. Chamberlain, Y. Lee, W. S. Lane, and D. R. Engelke, “Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP,” Genes and Development, vol. 12, no. 11, pp. 1678–1690, 1998.
- K. Salinas, S. Wierzbicki, L. Zhou, and M. E. Schmitt, “Characterization and purification of Saccharomyces cerevisiae RNase MRP reveals a new unique protein component,” Journal of Biological Chemistry, vol. 280, no. 12, pp. 11352–11360, 2005.
- X. W. Fang, X. J. Yang, K. Littrell et al., “The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits,” RNA, vol. 7, no. 2, pp. 233–241, 2001.
- A. Barrera, X. Fang, J. Jacob, E. Casey, P. Thiyagarajan, and T. Pan, “Dimeric and monomeric Bacillus subtilis RNase P holoenzyme in the absence and presence of Pre-tRNA substrates,” Biochemistry, vol. 41, no. 43, pp. 12986–12994, 2002.
- H. Dong, L. A. Kirsebom, and L. Nilsson, “Growth rate regulation of 4.5 S RNA and M1 RNA the catalytic subunit of Escherichia coli RNase P,” Journal of Molecular Biology, vol. 261, no. 3, pp. 303–308, 1996.
- Z. Li and M. P. Deutscher, “RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors,” RNA, vol. 8, no. 1, pp. 97–109, 2002.
- M. C. Ow and S. R. Kushner, “Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli,” Genes and Development, vol. 16, no. 9, pp. 1102–1115, 2002.
- J. Sambrook, E. F. Fritsch, and T. Maniatis, Molecular Cloning: a Laboratory Manual, Cold Spring Harbor Lab, Plainview, NY, USA, 1989.
- M. Rance, J. P. Loria, and A. G. Palmer, “Sensitivity improvement of transverse relaxation-optimized spectroscopy,” Journal of Magnetic Resonance, vol. 136, no. 1, pp. 92–101, 1999.
- M. Sattler, J. Schleucher, and C. Griesinger, “Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients,” Progress in Nuclear Magnetic Resonance Spectroscopy, vol. 34, no. 2, pp. 93–158, 1999.
- F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer, and A. Bax, “NMRPipe: a multidimensional spectral processing system based on UNIX pipes,” Journal of Biomolecular NMR, vol. 6, no. 3, pp. 277–293, 1995.
- B. A. Johnson, “Using NMRView to visualize and analyze the NMR spectra of macromolecules,” Methods in Molecular Biology, vol. 278, pp. 313–352, 2004.
- A. Bahrami, A. H. Assadi, J. L. Markley, and H. R. Eghbalnia, “Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy,” PLoS Computational Biology, vol. 5, no. 3, Article ID e1000307, 2009.
- E. Gasteiger, C. Hoogland, A. Gattiker, et al., “Protein identification and analysis tools on the ExPASy server,” in The Proteomics Protocols Handbook, J. M. Walker, Ed., pp. 571–607, Humana Press, Totowa, NJ, USA, 2005.
- K. Arnold, L. Bordoli, J. Kopp, and T. Schwede, “The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling,” Bioinformatics, vol. 22, no. 2, pp. 195–201, 2006.