Ribonucleases P/MRP and the expanding ribonucleoprotein world

IUBMB Life

Volumn 64, Issue 6, 2012, Pages 521-528

  Hernandez Cid, Aaron ^a   Aguirre Sampieri, Sergio ^a   Diaz Vilchis, Adelaida ^a   Torres Larios, Alfredo ^a  

^a UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

Author keywords

ncRNA; ribozyme; RNase MRP; RNase P; RNP world; rRNA processing; tRNA processing

Indexed keywords

RIBONUCLEASE; RIBONUCLEASE MRP; RIBONUCLEASE P; RIBONUCLEOPROTEIN; UNCLASSIFIED DRUG;

CELL ORGANELLE; CRYSTAL STRUCTURE; GENOME; HUMAN; MITOCHONDRION; NONHUMAN; PROTEIN FUNCTION; PROTEIN STRUCTURE; REVIEW;

ANIMALS; CATALYTIC DOMAIN; ENDORIBONUCLEASES; EVOLUTION, MOLECULAR; HUMANS; NUCLEIC ACID CONFORMATION; RIBONUCLEASE P; RIBONUCLEOPROTEINS; RNA;

EUKARYOTA;

EID: 84861326296     PISSN: 15216543     EISSN: 15216551     Source Type: Journal    
DOI: 10.1002/iub.1052     Document Type: Review

References (105)

1. Storz, G., (2002) An expanding universe of noncoding RNAs. Science 296, 1260-1263.
2. Forster, A. C., and, Altman, S., (1990) Similar cage-shaped structures for the RNA components of all ribonuclease P and ribonuclease MRP enzymes. Cell 62, 407-409.
3. Li, Y., and, Altman, S., (2004) In search of RNase P RNA from microbial genomes. RNA 10, 1533-1540.
4. Piccinelli, P., Rosenblad, M. A., and, Samuelsson, T., (2005) Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes. Nucleic Acids Res. 33, 4485-4495.
5. Lai, L. B., Chan, P. P., Cozen, A. E., Bernick, D. L., Brown, J. W., et al. (2010) Discovery of a minimal form of RNase P in Pyrobaculum. Proc. Natl Acad. Sci. USA 107, 22493-22498.
6. Marszalkowski, M., Willkomm, D. K., and, Hartmann, R. K., (2008) 5'-end maturation of tRNA in Aquifex aeolicus. Biol. Chem. 389, 395-403.
7. Lombo, T. B., and, Kaberdin, V. R., (2008) RNA processing in Aquifex aeolicus involves RNase E/G and an RNase P-like activity. Biochem. Biophys. Res. Commun. 366, 457-463.
8. Kazantsev, A. V., and, Pace, N. R., (2006) Bacterial RNase P: a new view of an ancient enzyme. Nat. Rev. Microbiol. 4, 729-740.
9. Kirsebom, L. A., (2007) RNase P RNA mediated cleavage: substrate recognition and catalysis. Biochimie 89, 1183-1194.
10. Liu, F., and, Altman, S., (2010) Ribonuclease P. Springer, New York.
11. McClain, W. H., Lai, L. B., and, Gopalan, V., (2010) Trials, travails and triumphs: an account of RNA catalysis in RNase P. J. Mol. Biol. 397, 627-646.
12. Jarrous, N., and, Gopalan, V., (2010) Archaeal/eukaryal RNase P: subunits, functions and RNA diversification. Nucleic Acids Res. 38, 7885-7894.
13. Esakova, O., and, Krasilnikov, A. S., (2010) Of proteins and RNA: the RNase P/MRP family. RNA 16, 1725-1747.
14. Cech, T. R., (2009) Crawling out of the RNA world. Cell 136, 599-602.
15. Wahl, M. C., Will, C. L., and, Luhrmann, R., (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136, 701-718.
16. Schimmel P., (2011) The RNP bridge between two worlds. Nat. Rev. Mol. Cell Biol. 12, 135.
17. Kole, R., Baer, M. F., Stark, B. C., and, Altman, S., (1980) E. coli RNAase P has a required RNA component. Cell 19, 881-887.
18. Cherayil, B., Krupp, G., Schuchert, P., Char, S., and, Soll, D., (1987) The RNA components of Schizosaccharomyces pombe RNase P are essential for cell viability. Gene 60, 157-161.
19. Gossringer, M., Kretschmer-Kazemi Far, R., and, Hartmann, R. K., (2006) Analysis of RNase P protein (rnpA) expression in Bacillus subtilis utilizing strains with suppressible rnpA expression. J. Bacteriol. 188, 6816-6823.
20. Robertson, H. D., Altman, S., and, Smith, J. D., (1972) Purification and properties of a specific Escherichia coli ribonuclease which cleaves a tyrosine transfer ribonucleic acid presursor. J. Biol. Chem. 247, 5243-5251.
21. Peck-Miller, K. A., and, Altman, S., (1991) Kinetics of the processing of the precursor to 4.5 S RNA, a naturally occurring substrate for RNase P from Escherichia coli. J. Mol. Biol. 221, 1-5.
22. Bothwell, A. L., Stark, B. C., and, Altman, S., (1976) Ribonuclease P substrate specificity: cleavage of a bacteriophage phi80-induced RNA. Proc. Natl Acad. Sci. USA 73, 1912-1916.
23. Hartmann, R. K., Heinrich, J., Schlegl, J., and, Schuster, H., (1995) Precursor of C4 antisense RNA of bacteriophages P1 and P7 is a substrate for RNase P of Escherichia coli. Proc. Natl Acad. Sci. USA 92, 5822-5826.
24. Forti, F., Sabbattini, P., Sironi, G., Zangrossi, S., Deho, G., et al. (1995) Immunity determinant of phage-plasmid P4 is a short processed RNA. J. Mol. Biol. 249, 869-878.
25. Alifano, P., Rivellini, F., Piscitelli, C., Arraiano, C. M., Bruni, C. B., et al. (1994) Ribonuclease E provides substrates for ribonuclease P-dependent processing of a polycistronic mRNA. Genes Dev. 8, 3021-3031.
26. Li, Y., and, Altman, S., (2003) A specific endoribonuclease, RNase P, affects gene expression of polycistronic operon mRNAs. Proc. Natl Acad. Sci. USA 100, 13213-13218.
27. Li, Y., and, Altman, S., (2004) Polarity effects in the lactose operon of Escherichia coli. J. Mol. Biol. 339, 31-39.
28. Altman, S., Wesolowski, D., Guerrier-Takada, C., and, Li, Y., (2005) RNase P cleaves transient structures in some riboswitches. Proc. Natl Acad. Sci. USA 102, 11284-11289.
29. Seif, E., and, Altman, S., (2008) RNase P cleaves the adenine riboswitch and stabilizes pbuE mRNA in Bacillus subtilis. RNA 14, 1237-1243.
30. Guerrier-Takada, C., van Belkum, A., Pleij, C. W., and, Altman, S., (1988) Novel reactions of RNAase P with a tRNA-like structure in turnip yellow mosaic virus RNA. Cell 53, 267-272.
31. Komine, Y., Kitabatake, M., Yokogawa, T., Nishikawa, K., and, Inokuchi, H., (1994) A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli. Proc. Natl Acad. Sci. USA 91, 9223-9227.
32. Jung, Y. H., Park, I., and, Lee, Y., (1992) Alteration of RNA I metabolism in a temperature-sensitive Escherichia coli rnpA mutant strain. Biochem. Biophys. Res. Commun. 186, 1463-1470.
33. Jung, Y. H., and, Lee, Y., (1995) RNases in ColE1 DNA metabolism. Mol. Biol. Rep. 22, 195-200.
34. Potuschak, T., Rossmanith, W., and, Karwan, R., (1993) RNase MRP and RNase P share a common substrate. Nucleic Acids Res. 21, 3239-3243.
35. Ko, J.-H., and, Altman, S., (2007) OLE RNA, an RNA motif that is highly conserved in several extremophilic bacteria, is a substrate for and can be regulated by RNase P RNA. Proc. Natl Acad. Sci. USA 104, 7815-7820.
36. Lawrence, N., Wesolowski, D., Gold, H., Bartkiewicz, M., Guerrier-Takada, C., et al. (1987) Characteristics of ribonuclease P from various organisms. Cold Spring Harb. Symp. Quant. Biol. 52, 233-238.
37. Darr, S. C., Pace, B., and, Pace, N. R., (1990) Characterization of ribonuclease P from the archaebacterium Sulfolobus solfataricus. J. Biol. Chem. 265, 12927-12932.
38. Andrews, A. J., Hall, T. A., and, Brown, J. W., (2001) Characterization of RNase P holoenzymes from Methanococcus jannaschii and Methanothermobacter thermoautotrophicus. Biol. Chem. 382, 1171-1177.
39. Engelke, D. R., Gegenheimer, P., and, Abelson, J., (1985) Nucleolytic processing of a tRNAArg-tRNAAsp dimeric precursor by a homologous component from Saccharomyces cerevisiae. J. Biol. Chem. 260, 1271-1279.
40. Krupp, G., Cherayil, B., Frendewey, D., Nishikawa, S., and, Soll, D., (1986) Two RNA species co-purify with RNase P from the fission yeast Schizosaccharomyces pombe. EMBO J. 5, 1697-1703.
41. Wilusz, J. E., Freier, S. M., and, Spector, D.L., (2008) 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 135, 919-932.
42. Sunwoo, H., Dinger, M. E., Wilusz, J. E., Amaral, P. P., Mattick, J. S., et al. (2009) MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res. 19, 347-359.
43. Yang, L., and, Altman, S., (2007) A noncoding RNA in Saccharomyces cerevisiae is an RNase P substrate. RNA 13, 682-690.
44. Gimple, O., and, Schön, A., (2001) In vitro and in vivo processing of cyanelle tmRNA by RNase P. Biol. Chem. 382, 1421-1429.
45. Mattijssen, S., Hinson, E. R., Onnekink, C., Hermanns, P., Zabel, B., et al. (2011) Viperin mRNA is a novel target for the human RNase MRP/RNase P endoribonuclease. Cell Mol. Life Sci. 68, 2469-2480.
46. Chamberlain, J. R., Pagan, R., Kindelberger, D. W., and, Engelke, D. R., (1996) An RNase P RNA subunit mutation affects ribosomal RNA processing. Nucleic Acids Res. 24, 3158-3166.
47. Coughlin, D. J., Pleiss, J. A., Walker, S. C., Whitworth, G. B., and, Engelke, D. R., (2008) Genome-wide search for yeast RNase P substrates reveals role in maturation of intron-encoded box C/D small nucleolar RNAs. Proc. Natl Acad. Sci. USA 105, 12218-12223.
48. Marvin, M. C., Clauder-Munster, S., Walker, S. C., Sarkeshik, A., Yates, J. R., 3rd, et al. (2011) Accumulation of noncoding RNA due to an RNase P defect in Saccharomyces cerevisiae. RNA 17, 1441-1450.
49. Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N., and, Altman, S., (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35, 849-857.
50. Pannucci, J. A., Haas, E. S., Hall, T. A., Harris, J. K., and, Brown, J. W., (1999) RNase P RNAs from some Archaea are catalytically active. Proc. Natl Acad. Sci. USA 96, 7803-7808.
51. Kikovska, E., Svard, S. G., and, Kirsebom, L. A., (2007) Eukaryotic RNase P RNA mediates cleavage in the absence of protein. Proc. Natl. Acad. Sci. USA 104, 2062-2067.
52. Ridanpaa, M., van Eenennaam, H., Pelin, K., Chadwick, R., Johnson, C., et al. (2001) Mutations in the RNA component of RNase MRP cause a pleiotropic human disease, cartilage-hair hypoplasia. Cell 104, 195-203.
53. Rosenbluh, J., Nijhawan, D., Chen, Z., Wong, K. K., Masutomi, K., et al. (2011) RMRP is a non-coding RNA essential for early murine development. PLoS One 6, e26270.
54. Schmitt, M. E., and, Clayton, D. A., (1993) Nuclear RNase MRP is required for correct processing of pre-5.8S rRNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 13, 7935-7941.
55. Lygerou, Z., Allmang, C., Tollervey, D., and, Séraphin, B., (1996) Accurate processing of a eukaryotic precursor ribosomal RNA by ribonuclease MRP in vitro. Science 272, 268-270.
56. Gill, T., Cai, T., Aulds, J., Wierzbicki, S., and, Schmitt, M. E., (2004) RNase MRP cleaves the CLB2 mRNA to promote cell cycle progression: novel method of mRNA degradation. Mol. Cell. Biol. 24, 945-953.
57. Stohl, L. L., and, Clayton, D. A., (1992) Saccharomyces cerevisiae contains an RNase MRP that cleaves at a conserved mitochondrial RNA sequence implicated in replication priming. Mol. Cell. Biol. 12, 2561-2569.
58. Maida, Y., Yasukawa, M., Furuuchi, M., Lassmann, T., Possemato, R., et al. (2009) An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA. Nature 461, 230-235.
59. Chang, D. D., and, Clayton, D. A., (1987) A mammalian mitochondrial RNA processing activity contains nucleus-encoded RNA. Science 235, 1178-1184.
60. Topper, J. N., and, Clayton, D. A., (1990) Secondary structure of the RNA component of a nuclear/mitochondrial ribonucleoprotein. J. Biol. Chem. 265, 13254-13262.
61. Kiss, T., Marshallsay, C., and, Filipowicz, W., (1992) 7-2/MRP RNAs in plant and mammalian cells: association with higher order structures in the nucleolus. EMBO J. 11, 3737-3746.
62. Jaag, H. M., Lu, Q., Schmitt, M. E., and, Nagy, P. D., (2011) Role of RNase MRP in viral RNA degradation and RNA recombination. J. Virol. 85, 243-253.
63. Chen, X. S., Penny, D., and, Collins, L. J., (2011) Characterization of RNase MRP RNA and novel snoRNAs from Giardia intestinalis and Trichomonas vaginalis. BMC Genomics 12, 550.
64. Torres-Larios, A., Swinger, K. K., Pan, T., and, Mondragon, A., (2006) Structure of ribonuclease P-a universal ribozyme. Curr. Opin. Struct. Biol. 16, 327-335.
65. Hipp, K., Galani, K., Batisse, C., Prinz, S., and, Bottcher, B., (2012) Modular architecture of eukaryotic RNase P and RNase MRP revealed by electron microscopy. Nucleic Acids Res 40, 3275-3288.
66. Kazantsev, A. V., Krivenko, A. A., Harrington, D. J., Holbrook, S. R., Adams, P. D., et al. (2005) Crystal structure of a bacterial ribonuclease P RNA. Proc. Natl Acad. Sci. USA 102, 13392-13397.
67. Loria, A., and, Pan, T., (1996) Domain structure of the ribozyme from eubacterial ribonuclease P. RNA 2, 551-563.
68. Noller, H. F., Hoffarth, V., and, Zimniak, L., (1992) Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256, 1416-1419.
69. Zhu, Y., Stribinskis, V., Ramos, K. S., and, Li, Y., (2006) Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA. RNA 12, 699-706.
70. Pan, T., (1995) Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry 34, 902-909.
71. Lecompte, O., Ripp, R., Thierry, J. C., Moras, D., and, Poch, O., (2002) Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res. 30, 5382-5390.
72. Keenan, R. J., Freymann, D. M., Stroud, R. M., and, Walter, P., (2001) The signal recognition particle. Annu. Rev. Biochem. 70, 755-775.
73. Crick, F. H., (1968) The origin of the genetic code. J. Mol. Biol. 38, 367-379.
74. Orgel, L. E., (1968) Evolution of the genetic apparatus. J. Mol. Biol. 38, 381-393.
75. Cech, T. R., (2009) Evolution of biological catalysis: ribozyme to RNP enzyme. Cold Spring Harb. Symp. Quant. Biol. 74, 11-16.
76. Woodhams, M. D., Stadler, P. F., Penny, D., and, Collins, L. J., (2007) RNase MRP and the RNA processing cascade in the eukaryotic ancestor. BMC Evol. Biol. 7 (Suppl 1), S13.
77. Krasilnikov, A. S., Yang, X., Pan, T., and, Mondragon, A., (2003) Crystal structure of the specificity domain of ribonuclease P. Nature 421, 760-764.
78. Krasilnikov, A. S., Xiao, Y., Pan, T., and, Mondragon, A., (2004) Basis for structural diversity in homologous RNAs. Science 306, 104-107.
79. Torres-Larios, A., Swinger, K. K., Krasilnikov, A. S., Pan, T., and, Mondragon, A., (2005) Crystal structure of the RNA component of bacterial ribonuclease P. Nature 437, 584-587.
80. Ataide, S. F., Schmitz, N., Shen, K., Ke, A., Shan, S. O., et al. (2011) The crystal structure of the signal recognition particle in complex with its receptor. Science 331, 881-886.
81. Ban, N., Nissen, P., Hansen, J., Moore P. B., and, Steitz, T.A., (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289, 905-920.
82. Ben-Shem, A., Garreau de Loubresse, N., Melnikov, S., Jenner, L., Yusupova, G., et al. (2011) The structure of the eukaryotic ribosome at 3.0 A resolution. Science 334, 1524-1529.
83. Pomeranz Krummel, D. A., Oubridge, C., Leung, A. K., Li, J., and, Nagai, K., (2009) Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution. Nature 458, 475-480.
84. Reiter, N. J., Osterman, A., Torres-Larios, A., Swinger, K. K., Pan, T., et al. (2010) Structure of a bacterial ribonuclease P holoenzyme in complex with. Nature 2010 468 784-789.
85. Hogg, J. R., and, Collins K., (2008) Structured non-coding RNAs and the
86. Randau, L., Schroder, I., and, Soll, D., (2008) Life without RNase P.
87. Juhas, M., Eberl, L., and, Glass, J. I., (2011) Essence of life:
88. Siegel, R. W., Banta, A. B., Haas, E. S., Brown, J. W., and, Pace, N. R., (1996) Mycoplasma fermentans simplifies our view of the catalytic core of
89. Peters, I. R., Helps, C. R., McAuliffe, L., Neimark, H., Lappin, M. R., et al. (2008) RNase P RNA gene (rnpB) phylogeny of Hemoplasmasand other
90. Holzmann, J., Frank, P., Loffler, E., Bennett, K. L., Gerner, C., et al. (2008) RNase P without RNA: identification and functional reconstitution of the
91. Szklarczyk, R., and, Huynen, M. A., (2010) Mosaic origin of the
92. Rossmanith, W., Tullo, A., Potuschak, T., Karwan, R., and, Sbisa, E., (1995) Human mitochondrial tRNA processing. J. Biol. Chem. 270, 12885-12891.
93. Gobert, A., Gutmann, B., Taschner, A., Gossringer, M., Holzmann, J., et al. (2010) A single Arabidopsis organellar protein has RNase P activity. Nat.
94. Lee, Y. C., Lee, B. J., Hwang, D. S., and, Kang, H. S., (1996) Purification and characterization of mitochondrial ribonuclease P from
95. Lai, L. B., Bernal-Bayard, P., Mohannath, G., Lai, S. M., Gopalan, V., et al. (2011) A functional RNase P protein subunit of bacterial origin in some
96. Hollingsworth, M. J., and, Martin, N. C., (1986) RNase P activity in the mitochondria of Saccharomyces cerevisiae depends on both mitochondrion and
97. Wang, G., Chen, H. W., Oktay, Y., Zhang, J., Allen, E. L., et al. (2010)
98. Stengel, K. F., Holdermann, I., Cain, P., Robinson, C., Wild, K., et al. (2008) Structural basis for specific substrate recognition by the chloroplast
99. Mercer, T. R., Neph, S., Dinger, M. E., Crawford, J., Smith, M. A., et
100. Dang, Y. L., and, Martin, N. C., (1993) Yeast mitochondrial RNase P. Sequence of the RPM2 gene and demonstration that its product is a protein
101. Rubio, M. A., Rinehart, J. J., Krett, B., Duvezin-Caubet, S., Reichert, A. S., et al. (2008) Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import. Proc. Natl Acad. Sci. USA
102. Schneider, A., (2011) Mitochondrial tRNA import and its consequences for
103. Schneider, A., (2001) Unique aspects of mitochondrial biogenesis in
104. Rossmanith, W., (2011) Of P and Z: mitochondrial tRNA processing enzymes.
105. Lu, Q., Wierzbicki, S., Krasilnikov, A. S., and, Schmitt, M. E., (2010) Comparison of mitochondrial and nucleolar RNase MRP reveals identical RNA components with distinct enzymatic activities and protein components. RNA 16, 529-537.