Substrate recognition by ribonucleoprotein ribonuclease MRP

RNA

Volumn 17, Issue 2, 2011, Pages 356-364

  Esakova, Olga ^a   Perederina, Anna ^a   Quan, Chao ^a   Berezin, Igor ^a   Krasilnikov, Andrey S ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

In vitro selection; Ribonuclease MRP; Ribonucleoprotein; RNase MRP; Saccharomyces cerevisiae

Indexed keywords

CYTOSINE; RIBONUCLEASE; RIBONUCLEOPROTEIN; RNASE MRP; UNCLASSIFIED DRUG;

ARTICLE; ENZYME ANALYSIS; GENE SEQUENCE; IN VITRO STUDY; NONHUMAN; PRIORITY JOURNAL; RNA STRUCTURE; SACCHAROMYCES CEREVISIAE;

BASE SEQUENCE; BINDING SITES; ENDORIBONUCLEASES; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; RNA; RNA PRECURSORS; RNA, FUNGAL; RNA, TRANSFER; SACCHAROMYCES CEREVISIAE; SUBSTRATE SPECIFICITY;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 78751564349     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2393711     Document Type: Article

References (45)

1. Altman S, Kirsebom L. 1999. Ribonuclease P. In The RNA world, 2nd ed. (ed. RF Gesteland, et al.), pp. 351-380. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
2. Brown TS, Bevilacqua PC. 2005. Method for assigning double-stranded RNA structures. Biotechniques 38: 368-372.
3. Cai T, Aulds J, Gill T, Cerio M, Schmitt ME. 2002. The Saccharomyces cerevisiae RNase mitochondrial RNA processing is critical for cell cycle progression at the end of mitosis. Genetics 161: 1029-1042.
4. Chamberlain JR, Lee Y, Lane WS, Engelke DR. 1998. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev 12: 1678-1690. (Pubitemid 28299518)
5. Chang DD, Clayton DA. 1987a. A novel endoribonuclease cleaves at a priming site of mouse mitochondrial DNA replication. EMBO J 6: 409-417.
6. Chang DD, Clayton DA. 1987b. A mammalian mitochondrial RNA processing activity contains nucleus-encoded RNA. Science 235: 1178-1184.
7. Chu S, Archer RH, Zengel JM, Lindahl L. 1994. The RNA of RNase MRP is required for normal processing of ribosomal RNA. Proc Natl Acad Sci 91: 659-663. (Pubitemid 24041461)
8. Esakova O, Krasilnikov AS. 2010. Of proteins and RNA: The RNase P/MRP family. RNA 16: 1725-1747.
9. Esakova O, Perederina A, Quan C, Schmitt ME, Krasilnikov AS. 2008. Footprinting analysis demonstrates extensive similarity between eukaryotic RNase P and RNase MRP holoenzymes. RNA 14: 1558-1567.
10. Gill T, Cai T, Aulds J, Wierzbicki S, Schmitt ME. 2004. RNase MRP cleaves the CLB2 mRNA to promote cell cycle progression: Novel method of mRNA degradation. Mol Cell Biol 24: 945-953.
11. Gill T, Aulds J, Schmitt ME. 2006. A specialized processing body that is temporally and asymmetrically regulated during the cell cycle in Saccharomyces cerevisiae. J Cell Biol 173: 35-45.
12. Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S. 1983. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35: 849-857.
13. Karwan R, Bennett JL, Clayton DA. 1991. Nuclear RNase MRP processes RNA at multiple discrete sites: interaction with an upstream G box is required for subsequent downstream cleavages. Genes Dev 5: 1264-1276.
14. Kikovska E, Svard SG, Kirsebom LA. 2007. Eukaryotic RNase P RNA mediates cleavage in the absence of protein. Proc Natl Acad Sci 104: 2062-2067.
15. Kirsebom LA. 2007. RNase P RNA-mediated cleavage: Substrate recognition and catalysis. Biochimie 89: 1183-1194.
16. Kiss T, Filipowicz W. 1992. Evidence against a mitochondrial location of the 7-2/MRP RNA in mammalian cells. Cell 70: 11-16.
17. Krasilnikov AS, Yang X, Pan T, Mondragon A. 2003. Crystal structure of the specificity domain of ribonuclease P. Nature 421: 760-764.
18. Krasilnikov AS, Xiao Y, Pan T, Mondragon A. 2004. Basis for structural diversity in homologous RNAs. Science 306: 104-107.
19. Lindahl L, Fretz S, Epps N, Zengel JM. 2000. Functional equivalence of hairpins in the RNA subunits of RNase MRP and RNase P in Saccharomyces cerevisiae. RNA 6: 653-658.
20. Lindahl L, Bommankanti A, Li X, Hayden L, Jones A, Khan M, Oni T, Zengel JM. 2009. RNase MRP is required for entry of 35S precursor rRNA into the canonical processing pathway. RNA 15: 1407-1416.
21. Lopez MD, Rosenblad MA, Samuelsson T. 2009. Conserved and variable domains of RNase MRP RNA. RNA Biol 6: 208-220.
22. Lu Q, Wierzbicki S, Krasilnikov AS, Schmitt ME. 2010. Comparison of mitochondrial and nucleolar RNase MRP reveals identical RNA components with distinct enzymatic activities and protein components. RNA 16: 529-537.
23. Lygerou Z, Mitchell P, Petfalski E, Seraphin B, Tollervey D. 1994. The POP1 gene encodes a protein component common to the RNase MRP and RNase P ribonucleoproteins. Genes Dev 8: 1423-1433.
24. Lygerou Z, Allmang C, Tollervey D, Seraphin B. 1996. Accurate processing of a eukaryotic precursor ribosomal RNA by Ribonuclease MRP in vitro. Science 272: 268-270.
25. Martin AN, Li Y. 2007. RNase MRP RNA and human genetic diseases. Cell Res 17: 219-226.
26. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH. 2004. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci 101: 7287-7292.
27. Milligan JF, Uhlenbeck OC. 1989. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol 180: 51-62.
28. Pan T. 1995. Novel RNA substrates for the ribozyme from Bacillus subtilis Ribonuclease P identified by in vitro selection. Biochemistry 34: 8458-8464.
29. 2+. Biochemistry 31: 3887-3895.
30. Pannucci JA, Haas ES, Hall TA, Harris JK, Brown JW. 1999. RNase P RNAs from some Archaea are catalytically active. Proc Natl Acad Sci 96: 7803-7808.
31. Perederina A, Esakova O, Quan C, Khanova E, Krasilnikov AS. 2010. Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain. EMBO J 29: 761-769.
32. Piccinelli P, Rosenblad MA, Samuelsson T. 2005. Identification and analysis of Ribonuclease P and MRP RNA in a broad range of eukaryotes. Nucleic Acids Res 33: 4485-4495.
33. Reiter NJ, Osterman A, Torres-Larios A, Swinger KK, Pan T, Mondragon A. 2010. Structure of a bacterial ribonuclease P in complex with tRNA. Nature 468: 784-789.
34. Ridanpaa M, Eenennaam H, Pelin K, Chadwick R, Johnson C, Yuan B, vanVenrooij W, Pruijn G, Salmela R, Rockas S, et al. 2001. Mutations in the RNA component of RNase MRP cause a pleiotropic human disease, Cartilage-Hair Hypoplasia. Cell 104: 195-203.
35. Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B. 1999. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17: 1030-1032.
36. Rosenblad MA, Lopez MD, Piccinelli P, Samuelsson T. 2006. 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.
37. Salinas K, Wierzbicki S, Zhou L, Schmitt ME. 2005. Characterization and purification of Saccharomyces cerevisiae RNase MRP reveals a new unique protein component. J Biol Chem 280: 11352-11360. (Pubitemid 40418443)
38. Schmitt ME, Clayton DA. 1992. Yeast site-specific ribonucleoprotein endoribonuclease MRP contains an RNA component homologous to mammalian RNase MRP RNA and essential for cell viability. Genes Dev 6: 1975-1985.
39. Schmitt ME, Clayton DA. 1993. Nuclear RNase MRP is required for correct processing of pre-5.8S rRNA in Saccharomyces cerevisiae. Mol Cell Biol 13: 7935-7941.
40. Schneider MD, Bains AK, Rajendra TK, Dominski Z, Matera AG, Simmons AJ. 2010. Functional characterization of the Drosophila MRP (mitochondrial RNA processing) RNA gene. RNA 16: 2120-2130.
41. Thomas BC, Chamberlain J, Engelke DR, Gegenheimer P. 2000. Evidence for an RNA-based catalytic mechanism in eukaryotic nuclear ribonuclease P. RNA 6: 554-562. (Pubitemid 30212233)
42. Torres-Larios A, Swinger KK, Krasilnikov AS, Pan T, Mondragon A. 2005. Crystal structure of the RNA component of bacterial ribonuclease P. Nature 437: 584-587. (Pubitemid 41613559)
43. Torres-Larios A, Swinger KK, Pan T, Mondragon A. 2006. Structure of ribonuclease P - a universal ribozyme. Curr Opin Struct Biol 16: 327-335.
44. Venema J, Tollervey D. 1996. RRP5 is required for formation of both 18S and 5.8S rRNA in yeast. EMBO J 15: 5701-5714. (Pubitemid 26385629)
45. Welting TJM, Kikkert BJ, van Venrooij WJ, Pruijn GJM. 2006. Differential association of protein subunits with the human RNase MRP and RNase P complexes. RNA 12: 1373-1382.