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. 2002 Oct;8(10):1348–1360. doi: 10.1017/s1355838202027048

An active precursor in assembly of yeast nuclear ribonuclease P.

Chatchawan Srisawat 1, Felicia Houser-Scott 1, Edouard Bertrand 1, Shaohua Xiao 1, Robert H Singer 1, David R Engelke 1
PMCID: PMC1370342  PMID: 12403471

Abstract

The RNA-protein subunit assembly of nuclear RNase P was investigated by specific isolation and characterization of the precursor and mature forms of RNase P using an RNA affinity ligand. Pre-RNase P was as active in pre-tRNA cleavage as mature RNase P, although it contained only seven of the nine proteins found in mature RNase P. Pop3p and Rpr2p were not required for maturation of the RPR1 RNA subunit and virtually absent from pre-RNase P, implying that they are dispensable for pre-tRNA substrate recognition and cleavage. The RNase P subunit assembly is likely to occur in the nucleolus, where both precursor and mature forms of RNase P RNA are primarily localized. The results provide insight into assembly of nuclear RNase P, and suggest pre-tRNA substrate recognition is largely determined by the RNA subunit.

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Selected References

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  1. Alifano P., Rivellini F., Piscitelli C., Arraiano C. M., Bruni C. B., Carlomagno M. S. Ribonuclease E provides substrates for ribonuclease P-dependent processing of a polycistronic mRNA. Genes Dev. 1994 Dec 15;8(24):3021–3031. doi: 10.1101/gad.8.24.3021. [DOI] [PubMed] [Google Scholar]
  2. Bertrand E., Houser-Scott F., Kendall A., Singer R. H., Engelke D. R. Nucleolar localization of early tRNA processing. Genes Dev. 1998 Aug 15;12(16):2463–2468. doi: 10.1101/gad.12.16.2463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Brusca E. M., True H. L., Celander D. W. Novel RNA-binding properties of Pop3p support a role for eukaryotic RNase P protein subunits in substrate recognition. J Biol Chem. 2001 Aug 29;276(45):42543–42548. doi: 10.1074/jbc.M107293200. [DOI] [PubMed] [Google Scholar]
  4. Chamberlain J. R., Lee Y., Lane W. S., Engelke D. R. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev. 1998 Jun 1;12(11):1678–1690. doi: 10.1101/gad.12.11.1678. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chamberlain J. R., Pagán-Ramos, Kindelberger D. W., Engelke D. R. An RNase P RNA subunit mutation affects ribosomal RNA processing. Nucleic Acids Res. 1996 Aug 15;24(16):3158–3166. doi: 10.1093/nar/24.16.3158. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chu S., Zengel J. M., Lindahl L. A novel protein shared by RNase MRP and RNase P. RNA. 1997 Apr;3(4):382–391. [PMC free article] [PubMed] [Google Scholar]
  7. Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 1988 Nov 25;16(22):10881–10890. doi: 10.1093/nar/16.22.10881. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. De Rijk P., De Wachter R. RnaViz, a program for the visualisation of RNA secondary structure. Nucleic Acids Res. 1997 Nov 15;25(22):4679–4684. doi: 10.1093/nar/25.22.4679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dichtl B., Tollervey D. Pop3p is essential for the activity of the RNase MRP and RNase P ribonucleoproteins in vivo. EMBO J. 1997 Jan 15;16(2):417–429. doi: 10.1093/emboj/16.2.417. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Eder P. S., Kekuda R., Stolc V., Altman S. Characterization of two scleroderma autoimmune antigens that copurify with human ribonuclease P. Proc Natl Acad Sci U S A. 1997 Feb 18;94(4):1101–1106. doi: 10.1073/pnas.94.4.1101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Frank D. N., Adamidi C., Ehringer M. A., Pitulle C., Pace N. R. Phylogenetic-comparative analysis of the eukaryal ribonuclease P RNA. RNA. 2000 Dec;6(12):1895–1904. doi: 10.1017/s1355838200001461. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Frank D. N., Pace N. R. Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu Rev Biochem. 1998;67:153–180. doi: 10.1146/annurev.biochem.67.1.153. [DOI] [PubMed] [Google Scholar]
  13. Goldstein A. L., McCusker J. H. Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast. 1999 Oct;15(14):1541–1553. doi: 10.1002/(SICI)1097-0061(199910)15:14<1541::AID-YEA476>3.0.CO;2-K. [DOI] [PubMed] [Google Scholar]
  14. Guerrier-Takada C., Altman S. Catalytic activity of an RNA molecule prepared by transcription in vitro. Science. 1984 Jan 20;223(4633):285–286. doi: 10.1126/science.6199841. [DOI] [PubMed] [Google Scholar]
  15. Guerrier-Takada C., Altman S. M1 RNA with large terminal deletions retains its catalytic activity. Cell. 1986 Apr 25;45(2):177–183. doi: 10.1016/0092-8674(86)90381-8. [DOI] [PubMed] [Google Scholar]
  16. Hollingsworth M. J., Martin N. C. Alteration of a mitochondrial tRNA precursor 5' leader abolishes its cleavage by yeast mitochondrial RNase P. Nucleic Acids Res. 1987 Nov 11;15(21):8845–8860. doi: 10.1093/nar/15.21.8845. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Houser-Scott F., Ziehler W. A., Engelke D. R. Saccharomyces cerevisiae nuclear ribonuclease P: structure and function. Methods Enzymol. 2001;342:101–117. doi: 10.1016/s0076-6879(01)42539-0. [DOI] [PubMed] [Google Scholar]
  18. Houser-Scott Felicia, Xiao Shaohua, Millikin Christopher E., Zengel Janice M., Lindahl Lasse, Engelke David R. Interactions among the protein and RNA subunits of Saccharomyces cerevisiae nuclear RNase P. Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2684–2689. doi: 10.1073/pnas.052586299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Jacobson M. R., Cao L. G., Taneja K., Singer R. H., Wang Y. L., Pederson T. Nuclear domains of the RNA subunit of RNase P. J Cell Sci. 1997 Apr;110(Pt 7):829–837. doi: 10.1242/jcs.110.7.829. [DOI] [PubMed] [Google Scholar]
  20. Jarrous N., Altman S. Human ribonuclease P. Methods Enzymol. 2001;342:93–100. doi: 10.1016/s0076-6879(01)42538-9. [DOI] [PubMed] [Google Scholar]
  21. Jarrous N., Eder P. S., Guerrier-Takada C., Hoog C., Altman S. Autoantigenic properties of some protein subunits of catalytically active complexes of human ribonuclease P. RNA. 1998 Apr;4(4):407–417. [PMC free article] [PubMed] [Google Scholar]
  22. Jarrous N., Eder P. S., Guerrier-Takada C., Hoog C., Altman S. Autoantigenic properties of some protein subunits of catalytically active complexes of human ribonuclease P. RNA. 1998 Apr;4(4):407–417. [PMC free article] [PubMed] [Google Scholar]
  23. Jarrous N., Reiner R., Wesolowski D., Mann H., Guerrier-Takada C., Altman S. Function and subnuclear distribution of Rpp21, a protein subunit of the human ribonucleoprotein ribonuclease P. RNA. 2001 Aug;7(8):1153–1164. doi: 10.1017/s1355838201010469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Jarrous N., Wolenski J. S., Wesolowski D., Lee C., Altman S. Localization in the nucleolus and coiled bodies of protein subunits of the ribonucleoprotein ribonuclease P. J Cell Biol. 1999 Aug 9;146(3):559–572. doi: 10.1083/jcb.146.3.559. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Jiang T., Altman S. Protein-protein interactions with subunits of human nuclear RNase P. Proc Natl Acad Sci U S A. 2001 Jan 16;98(3):920–925. doi: 10.1073/pnas.021561498. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Komine Y., Kitabatake M., Yokogawa T., Nishikawa K., Inokuchi H. A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli. Proc Natl Acad Sci U S A. 1994 Sep 27;91(20):9223–9227. doi: 10.1073/pnas.91.20.9223. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lee J. Y., Engelke D. R. Partial characterization of an RNA component that copurifies with Saccharomyces cerevisiae RNase P. Mol Cell Biol. 1989 Jun;9(6):2536–2543. doi: 10.1128/mcb.9.6.2536. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Lee J. Y., Evans C. F., Engelke D. R. Expression of RNase P RNA in Saccharomyces cerevisiae is controlled by an unusual RNA polymerase III promoter. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):6986–6990. doi: 10.1073/pnas.88.16.6986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Lee J. Y., Rohlman C. E., Molony L. A., Engelke D. R. Characterization of RPR1, an essential gene encoding the RNA component of Saccharomyces cerevisiae nuclear RNase P. Mol Cell Biol. 1991 Feb;11(2):721–730. doi: 10.1128/mcb.11.2.721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Lindahl L., Fretz S., Epps N., Zengel J. M. Functional equivalence of hairpins in the RNA subunits of RNase MRP and RNase P in Saccharomyces cerevisiae. RNA. 2000 May;6(5):653–658. doi: 10.1017/s1355838200992574. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Ling M. M., Robinson B. H. Approaches to DNA mutagenesis: an overview. Anal Biochem. 1997 Dec 15;254(2):157–178. doi: 10.1006/abio.1997.2428. [DOI] [PubMed] [Google Scholar]
  32. Longtine M. S., McKenzie A., 3rd, Demarini D. J., Shah N. G., Wach A., Brachat A., Philippsen P., Pringle J. R. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast. 1998 Jul;14(10):953–961. doi: 10.1002/(SICI)1097-0061(199807)14:10<953::AID-YEA293>3.0.CO;2-U. [DOI] [PubMed] [Google Scholar]
  33. Lygerou Z., Mitchell P., Petfalski E., Séraphin B., Tollervey D. The POP1 gene encodes a protein component common to the RNase MRP and RNase P ribonucleoproteins. Genes Dev. 1994 Jun 15;8(12):1423–1433. doi: 10.1101/gad.8.12.1423. [DOI] [PubMed] [Google Scholar]
  34. Lygerou Z., Pluk H., van Venrooij W. J., Séraphin B. hPop1: an autoantigenic protein subunit shared by the human RNase P and RNase MRP ribonucleoproteins. EMBO J. 1996 Nov 1;15(21):5936–5948. [PMC free article] [PubMed] [Google Scholar]
  35. Mathews D. H., Sabina J., Zuker M., Turner D. H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol. 1999 May 21;288(5):911–940. doi: 10.1006/jmbi.1999.2700. [DOI] [PubMed] [Google Scholar]
  36. Pagán-Ramos E., Lee Y., Engelke D. R. A conserved RNA motif involved in divalent cation utilization by nuclear RNase P. RNA. 1996 Nov;2(11):1100–1109. [PMC free article] [PubMed] [Google Scholar]
  37. Pagán-Ramos E., Lee Y., Engelke D. R. Mutational analysis of Saccharomyces cerevisiae nuclear RNase P: randomization of universally conserved positions in the RNA subunit. RNA. 1996 May;2(5):441–451. [PMC free article] [PubMed] [Google Scholar]
  38. 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 U S A. 1999 Jul 6;96(14):7803–7808. doi: 10.1073/pnas.96.14.7803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Pluk H., van Eenennaam H., Rutjes S. A., Pruijn G. J., van Venrooij W. J. RNA-protein interactions in the human RNase MRP ribonucleoprotein complex. RNA. 1999 Apr;5(4):512–524. doi: 10.1017/s1355838299982079. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Schmitt M. E., Clayton D. A. Characterization of a unique protein component of yeast RNase MRP: an RNA-binding protein with a zinc-cluster domain. Genes Dev. 1994 Nov 1;8(21):2617–2628. doi: 10.1101/gad.8.21.2617. [DOI] [PubMed] [Google Scholar]
  41. Srisawat C., Engelke D. R. Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins. RNA. 2001 Apr;7(4):632–641. doi: 10.1017/s135583820100245x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Srisawat Chatchawan, Engelke David R. RNA affinity tags for purification of RNAs and ribonucleoprotein complexes. Methods. 2002 Feb;26(2):156–161. doi: 10.1016/S1046-2023(02)00018-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Stolc V., Altman S. Rpp1, an essential protein subunit of nuclear RNase P required for processing of precursor tRNA and 35S precursor rRNA in Saccharomyces cerevisiae. Genes Dev. 1997 Nov 1;11(21):2926–2937. doi: 10.1101/gad.11.21.2926. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Stolc V., Katz A., Altman S. Rpp2, an essential protein subunit of nuclear RNase P, is required for processing of precursor tRNAs and 35S precursor rRNA in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1998 Jun 9;95(12):6716–6721. doi: 10.1073/pnas.95.12.6716. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. doi: 10.1093/nar/22.22.4673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Tranguch A. J., Engelke D. R. Comparative structural analysis of nuclear RNase P RNAs from yeast. J Biol Chem. 1993 Jul 5;268(19):14045–14055. [PubMed] [Google Scholar]
  47. Tranguch A. J., Kindelberger D. W., Rohlman C. E., Lee J. Y., Engelke D. R. Structure-sensitive RNA footprinting of yeast nuclear ribonuclease P. Biochemistry. 1994 Feb 22;33(7):1778–1787. doi: 10.1021/bi00173a022. [DOI] [PubMed] [Google Scholar]
  48. Xiao Shaohua, Scott Felicia, Fierke Carol A., Engelke David R. Eukaryotic ribonuclease P: a plurality of ribonucleoprotein enzymes. Annu Rev Biochem. 2001 Nov 9;71:165–189. doi: 10.1146/annurev.biochem.71.110601.135352. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Ziehler W. A., Morris J., Scott F. H., Millikin C., Engelke D. R. An essential protein-binding domain of nuclear RNase P RNA. RNA. 2001 Apr;7(4):565–575. doi: 10.1017/s1355838201001996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. van Eenennaam H., Jarrous N., van Venrooij W. J., Pruijn G. J. Architecture and function of the human endonucleases RNase P and RNase MRP. IUBMB Life. 2000 Apr;49(4):265–272. doi: 10.1080/15216540050033113. [DOI] [PubMed] [Google Scholar]
  51. van Eenennaam H., Lugtenberg D., Vogelzangs J. H., van Venrooij W. J., Pruijn G. J. hPop5, a protein subunit of the human RNase MRP and RNase P endoribonucleases. J Biol Chem. 2001 Jun 18;276(34):31635–31641. doi: 10.1074/jbc.M103399200. [DOI] [PubMed] [Google Scholar]
  52. van Eenennaam H., Pruijn G. J., van Venrooij W. J. hPop4: a new protein subunit of the human RNase MRP and RNase P ribonucleoprotein complexes. Nucleic Acids Res. 1999 Jun 15;27(12):2465–2472. doi: 10.1093/nar/27.12.2465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. van Eenennaam H., van der Heijden A., Janssen R. J., van Venrooij W. J., Pruijn G. J. Basic domains target protein subunits of the RNase MRP complex to the nucleolus independently of complex association. Mol Biol Cell. 2001 Nov;12(11):3680–3689. doi: 10.1091/mbc.12.11.3680. [DOI] [PMC free article] [PubMed] [Google Scholar]

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