1887

Chapter 6 : Recent Studies of RNase P

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

Recent Studies of RNase P , Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818333/9781555810733_Chap06-1.gif /docserver/preview/fulltext/10.1128/9781555818333/9781555810733_Chap06-2.gif

Abstract:

This chapter is primarily a progress report on work with the enzyme from . RNase P, the endonuclease responsible for the biosynthesis of the 5' termini of mature tRNA, is a ribonucleoprotein. The chapter primarily focuses on relationships between the structure and function of the subunits of RNase P, as determined from studies with the enzyme from eubacterial sources. Two important goals of current research on RNase P are identification of the active site of the enzyme and elucidation of the details of the chemical reaction governed by it. Several lines of evidence have implicated the region in M1 RNA that contains at least nucleotides 60 to 92, 230 to 260, and 290 to 360 as being essential for catalysis. The evidence comes from analysis of deletion mutants, studies of the binding of both individual tRNA precursors and the protein cofactor to M1 RNA, and studies of the binding of divalent metal ions to M1 RNA. Some point mutations that significantly affect the activity of M1 RNA are also located in these regions. A summary of these results is shown in the chapter. The protein cofactor of RNase P from (C5 protein) is a highly basic molecule of 119 amino acids, with a molecular mass of 13,800 daltons.

Citation: Altman S, Talbot S, Kirsebom L. 1995. Recent Studies of RNase P , p 67-78. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch6
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
Figure 1

Secondary structures of substrates for RNase P. (A) The precursor to (SuUAG) (pTyr) from . (В) The precursor to 4.5S RNA ( ). (С) Model substrate derived from tRNA from ( ) and one composed of two oligoribonucleotides, with the external guide sequence (EGS) indicated ( ).

Citation: Altman S, Talbot S, Kirsebom L. 1995. Recent Studies of RNase P , p 67-78. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch6
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Proposed secondary structure of RNA subunit (Ml RNA) of RNase Ρ from (A, left) and general model, based on phylogenetic comparisons, for all RNA subunits of RNase Ρ (В, right). In (A), nucleotides that can be deleted without major negative effects on catalytic function ( ) are boxed. In (B), absolutely conserved nucleotides in RNAs from RNase Ρ from various bacteria are shown in capital letters; nucleotides that are not invariant, but are conserved in at least 90% of the available sequences, are shown in lower case letters. Nucleotides that are conserved in fewer than 90% of RNAs are shown with filled circles (•). Nucleotides that are not present in all sequences, but are absent from fewer than 10% of the available sequences, are indicated with open circles (°); nucleotides absent from more than 10% of the sequences are not shown. Reprinted in part from reference with permission.

Citation: Altman S, Talbot S, Kirsebom L. 1995. Recent Studies of RNase P , p 67-78. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch6
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Hypothetical cage structure for RNA subunits of RNase P, as illustrated by cage for RNA from RNase Ρ of ( ). The vertical lines below the lowermost sequences indicate nucleotides that can form base pairs with sequences (not shown) in the central portions of the RNA. Nucleotides depicted in lowercase letters are conserved in terms of both nature and position in the RNAs from RNase Ρ from eubacterial sources. The structures shown in Fig. 2 are based on more recent phylogenetic comparisons and differ in a few details in helical regions from that shown in Fig. 3 .

Citation: Altman S, Talbot S, Kirsebom L. 1995. Recent Studies of RNase P , p 67-78. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch6
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

Proposed secondary structure of RNA subunit of RNase Ρ from human tissue. Nucleotides (79–84 and 318–323) in bold letters participate in pseudo-knot formation ( ).

Citation: Altman S, Talbot S, Kirsebom L. 1995. Recent Studies of RNase P , p 67-78. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch6
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
Figure 5

Proposed pathway for the activation of substrates in the reaction catalyzed by RNase Ρ (57). P1 and P2 refer to the products of cleavage of S by RNase P.

Citation: Altman S, Talbot S, Kirsebom L. 1995. Recent Studies of RNase P , p 67-78. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch6
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6
Figure 6

Regions of tRNA precursor important in determination of site and rate of cleavage by RNase P. The ovals surround critical regions of the phosphodiester backbone. Conserved nucleotides in the P loop and the 3′ terminal CCA sequence, as well as the very common G · С pair at the base of the acceptor stem, are shown. The arrow indicates the site of cleavage of RNase P.

Citation: Altman S, Talbot S, Kirsebom L. 1995. Recent Studies of RNase P , p 67-78. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch6
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555818333.chap6
1. Altman, S. 1971. Isolation of tyrosine tRNA precursor molecules. Nature New Biol. 229:1921.
2. Alunan, S., 1979. Biosynthesis of suppressor transfer RNA, p. 173189. In J. E. Celis, and J. D. Smith (ed.), Nonsense Mutations and tRNA Suppressors. Academic Press, New York.
3. Altman, S. 1989. Ribonuclease P: an enzyme with a catalytic RNA subunit. Adv. Enzymol. 62:136.
4. Altman, S.,, and H. D. Robertson. 1973. RNA precursor molecules and ribonucleases in E. coli. Mol. Cell. Biochem. 1:8393.
5. Airman, S.,, and J. D. Smith. 1971. Tyrosine tRNA precursor molecule polynucleotide sequence. Nature New Biol. 233:3539.
5a. Altman, S.,, D. Wesolowski,, and R. Puranam. 1993. Nucleotide sequences of the RNA subunit of RNase P from several mammals. Genomics 18:418422.
6. Baer, M. F.,, R. M. Reilly,, G. M. McCorkle,, T.-Y. Hai,, S. Altman,, and U. L. RajBhandary. 1988. The recognition by RNase P of precursor tRNAs. J. Biol. Chem. 263:23442351.
7. Bartkiewicz, M.,, H. Gold,, and S. Altman. 1989. Identification and characterization of an RNA molecule that copurifies with RNase P activity from HeLa cells. Genes Dev. 3:488499.
8. Beaudry, A. A.,, and G. E. Joyce. 1992. Directed evolution of an RNA enzyme. Science 257:635641.
9. Bothwell, A. L. M.,, R. Garber,, and S. Altman. 1976. Isolation and nucleotide sequence of precursor molecules to E. coli 4.SS RNA. J. Biol. Chem. 251:77097716.
10. Brown, J. W.,, and N. R. Pace. 1992. Ribonuclease P RNA and protein subunits from bacteria. Nucleic Acids Res. 20:14511456.
11. Burdon, R. H. 1971. Ribonucleic acid maturation in animal cells. Prog. Nucleic Acid Res. Mol. Biol. 11:3379.
12. Burgin, A. B.,, and N. R. Pace. 1990. Mapping the active site of ribonuclease P RNA using a substrate containing a photo-affinity agent. EMBO J. 9:41114118.
13. Burkard, U.,, I. Willis,, and D. Soli. 1988. Processing of histidine transfer RNA precursors. J. Biol. Chem. 263:24472451.
14. Carrara, G.,, P. Calandra,, P. Fruscoloni,, M. Doria,, and G. P. Tocchini-Valentini. 1989. Site selection by Xenopus laevis RNase P. Cell 58:3745.
15. Darr, S. C.,, J. W. Brown,, and N. R. Pace. 1992. The varieties of ribonuclease P. Trends Biochem. Sci. 17:178182.
16. Darr, S. C.,, K. Zito,, D. Smith,, and N. R. Pace. 1992. Contributions of phylogenetically variable structural elements to the function of the ribozyme ribonuclease P. Biochemistry 31:328333.
17. Doersen, C.-J.,, C. Guerrier-Takada,, S. Altman,, and G. Attardi. 1985. Characterization of an RNase P activity from HeLa cell mitochondria: comparison with cytosol RNase P activity. J. Biol. Chem. 260:59425949.
18. Eckstein, F. 1985. Nucleoside phosphorothioates. Annu. Rev. Biochem. 54:367402.
19. Forster, A. C.,, and S. Altman. 1990. External guide sequence for an RNA enzyme. Science 249:783786.
20. Forster, A. C.,, and S. Altman. 1990. Similar cage-shaped structures for the RNA components of all ribonuclease P and ribonuclease MRP enzymes. Cell 62:407409.
21. Fujika, M. Q.,, M. Yoshihawa,, and N. Ogasawara. 1990. Structure of the dnaA region of Micrococcus luteus: conservation and variations among eubacteria. Gene 93:7378.
22. Gardiner, D. J.,, T. L. Marsh,, and N. R. Pace. 1985. Ion dependence and mechanism in the Bacillus subtilis RNase P reaction. J. Biol. Chem. 260:54155419.
23. Gold, H. A.,, and S. Altman. 1986. Reconstitution of RNase P activity using inactive subunits from E. coli and HeLa cells. Cell 44:243249.
24. Gold, H. A.,, J. N. Topper,, D. A. Clayton,, and J. Craft. 1989. The RNA-processing enzyme RNase MRP is identical to the Th autoantigen and related to RNase P. Science 245:13771380.
25. Green, C.,, and B. Void. 1988. Structural requirements for processing of synthetic tRNAHis precursors by the catalytic RNA component of RNase P. J. Biol. Chem. 263:652657.
26. Guerrier-Takada, C.,, and S. Altman. 1984. The structure in solution of Ml RNA, the catalytic subunit of ribonuclease P from Escherichia coli. Biochemistry 23:63276334.
27. Guerrier-Takada, C.,, and S. Altman. 1992. Reconstitution of enzymatic activity from fragments of Ml RNA. Proc. Natl. Acad. Sci. USA 89:12661270.
28. Guerrier-Takada, C.,, K. Gardiner,, T. Marsh,, N. R. Pace,, and S. Altman. 1983. The RNA moiety of RNase P is the catalytic subunit of the enzyme. Cell 35:849857.
29. Guerrier-Takada, C.,, K. Haydock,, L. Allen,, and S. Altman. 1986. Metal ion requirements and other aspects of the reaction catalyzed by Ml RNA, the RNA subunit of ribonuclease P from Escherichia coli. Biochemistry 25:15091515.
30. Guerrier-Takada, C.,, N. Lumelsky,, and S. Altman. 1989. Specific interactions in RNA enzyme-substrate complexes. Science 286:15781584.
31. Guerrier-Takada, C.,, W. H. McClain,, and S. Altman. 1984. Cleavage of tRNA precursors by the RNA subunit of E. coli ribonuclease P (Ml RNA) is influenced by 3'-proximal CCA in the substrates. Cell 38:219224.
32. Gupta, R. 1984. Halobacterium volcanii tRNAs. J. Biol. Chem. 259:94619471.
33. Haas, E. S.,, D. P. Morse,, J. W. Brown,, F. J. Schmidt,, and N. R. Pace. 1991. Long-range structure in ribonuclease P RNA. Science 254:853856.
34. Hansen, F. G.,, E. G. Hansen,, and T. Atlung. 1985. Physical mapping and nucleotide sequence of the mpA gene that encodes the protein component of RNase P in Escherichia coli. Gene 38:8593.
35. Hollingsworth, M. J.,, and N. C. Martin. 1986. RNase P activity in the mitochondria of Saccharomyces cerevisiae depends on both mitochondrion- and nucleus-encoded components. Mol. Cell. Biol. 6:10581064.
36. Holm, P. S.,, and G. Krupp. 1992. The acceptor stem in pre-tRNAs determines the cleavage specificity of RNase P. Nucleic Acids Res. 20:421423.
37. Kahle, D.,, U. Wehmeyer,, S. Char,, and G. Krupp. 1990. The methylation of one specific guanosine in a pre-tRNA prevents cleavage by RNase P and by the catalytic Ml RNA. Nucleic Acids Res. 18:837844.
38. Kahle, D.,, U. Wehmeyer,, and G. Krupp. 1990. Substrate recognition by RNase P and by the catalytic Ml RNA: identification of possible contact points in pre-tRNAs. EMBO J. 9:19291937.
39. Kazakov, S.,, and S. Altman. Unpublished data.
40. Kazakov, S.,, and S. Altman. 1991. Site-specific cleavage by metal ion cofactors and inhibitors of Ml RNA, the catalytic subunit of RNase P from E. coli. Proc. Natl. Acad. Sci. USA 88:91939197.
41. Kirsebom, L. Unpublished data.
42. Kirsebom, L. A.,, M. F. Baer,, and S. Altman. 1988. Differential effects of mutations in the protein and RNA moieties of RNase P on the efficiency of suppression by various tRNA suppressors. J. Mol. Biol. 204:879888.
43. Kirsebom, L. A.,, and S. G. Svärd. 1992. The kinetics and specificity of cleavage by RNase P is mainly dependent on the structure of the amino acid acceptor stem. Nucleic Acids Res. 20:425432.
44. Knap, A. K.,, D. Wesolowski,, and S. Altman. 1990. Protection from chemical modification of nucleotides in complexes of Ml RNA, the catalytic subunit of RNase P from E. coli, and tRNA precursors. Biochimie 72:779790.
45. Kole, R.,, M. Baer,, B. Stark,, and S. Altman. 1980. E. coli RNase P has a required RNA component in vivo. Cell 19:881887.
46. Krupp, G.,, D. Kahle,, T. Vogt, and S Char. 1991. Sequence changes in both flanking sequences of a pre-tRNA influence the cleavage specificity of RNase P. J. Mol. Biol. 217:637648.
47. Lee, J.-Y.,, C. E. Rohlman,, L. A. Molony,, and D. R. Engelke. 1991. Characterization of RPR1, an essential gene encoding the RNA component of Saccharomyces cerevisiae nuclear RNase P. Mol. Cell. Biol. 11:721730.
48. Li, Y.,, C. Guerrier-Takada,, and S. Altman. 1992. Targeted cleavage of mRNA in vitro by RNase P from Escherichia coli. Proc. Natl. Acad. Sci. USA 89:31853189.
49. Lumelsky, N.,, and S. Altman. 1988. Selection and characterization of randomly produced mutants in the gene coding for Ml RNA. J. Mol. Biol. 202:443454.
50. Mans, R. M. W.,, C. Guerrier-Takada,, S. Altman,, and C. W. A. Pleij. 1990. Interaction of RNase P from Escherichia coli with pseudoknotted structures in viral RNAs. Nucleic Acids Res. 18:34793487.
51. Martin, N. C. Personal communication.
52. McClain, W. H.,, C. Guerrier-Takada,, and S. Altman. 1987. Model substrates for an RNA enzyme. Science 238:527530.
53. Morales, M. J.,, C. A. Wise,, M. J. Hollingsworth,, and N. C. Martin. 1989. Characterization of yeast mitochondrial RNase P: an intact RNA subunit is not essential for activity in vitro. Nucleic Acids Res. 17:68656881.
54. Pearson, D.,, I. Willis,, H. Hottinger,, J. Bell,, A. Kumar,, U. Leupold,, and D. Soli. 1988. Mutations preventing expression of sup3 tRNASer nonsense suppressors of Schizosaccharomyces pombe. Mol. Cell. Biol. 5:808815.
55. Peck-Miller, K. A.,, and S. Altman. 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. 221:15.
56. Perreault, J.-P.,, and S. Altman. 1992. Imponant 2'-hydroxyl groups in model substrates for Ml RNA, the catalytic RNA subunit of RNase P from Escherichia coli. J. Mol. Biol. 226:399409.
57. Perreault, J.-P.,, and S. Altman. 1992. Important 2'-hydroxyl groups in model substrates for Ml RNA, the catalytic RNA subunit of RNase P from Escherichia coli. J. Mol. Biol. 226:399409.
58. Perreault, J.-P.,, D. Labuda,, N. Usman,, J.-H. Yang,, and R. Cedergren. 1991. Relationship between 2'-hydroxyls and magnesium binding in the hammerhead RNA domain: a model for ribozyme catalysis. Biochemistry 30:40204025.
59. Poritz, M. A.,, K. Stnib,, and P. Walter. 1988. Human SRP and E. coli 4.5S RNA contain a highly homologous structural domain. Cell 55:46.
60. Puranam, R.,, and G. Attardi. Personal communication.
61. Puranam, R.,, D. Wesolowski,, and S. Altman. Unpublished data.
62. Reed, R. E.,, M. F. Baer,, C. Guerrier-Takada,, H. Donis-Keller,, and S. Altman. 1982. Nucleotide sequence of the gene encoding the RNA subunit (Ml RNA) of ribonuclease P from Escherichia coli. Cell 30:627636.
63. Reich, C.,, G. J. Olsen,, B. Pace,, and N. R. Pace. 1988. Role of the protein moiety of RNase P, a ribonucleoprotein enzyme. Science 239:178181.
64. Reilly, R. M.,, and U. L. RajBhandary. 1986. A single mutation in loop IV of Escherichia coli SuIII blocks processing at both 5'- and 3'-ends of the precursor tRNA. J. Biol. Chem. 261:29282935.
65. Robertson, D. L.,, and G. F. Joyce. 1990. Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature (London) 344:467468.
66. Robertson, H. D.,, S. Altman,, and J. D. Smith. 1972. Purification and properties of a specific Escherichia coli ribonuclease which cleaves a tyrosine transfer ribonucleic acid precursor. J. Biol. Chem. 247:52435251.
67. Sakano, H.,, S. Yamada,, T. Ikemura,, Y. Shimura,, and H. Ozeki. 1974. Temperature-sensitive mutants of Escherichia coli for tRNA biosynthesis. Nucleic Acids Res. 1:355371.
68. Schedi, P.,, and P. Primakoff. 1973. Mutants of Escherichia coli thermosensitive for the synthesis of transfer RNA. Proc. Natl. Acad. Sci. USA 70:20912095.
69. Schmidt, O.,, J.-I. Mao,, R. Ogden,, J. Beckmann,, H. Sakano,, J. Abelson,, and D. Soil. 1980. Dimeric tRNA precursors in yeast. Nature (London) 287:750752.
70. Shiraishi, H.,, and Y. Shimura. 1986. Mutations affecting two distinct functions of the RNA component of RNase P. EMBO J. 5:36733679.
71. Shiraishi, H.,, and Y. Shimura. 1988. Functional domains of the RNA component of ribonuclease P revealed by chemical probing of mutant RNAs. EMBO J. 7:38173821.
72.Skovgaard, 0.1990. Nucleotide sequence of Proteus mirabilis DNA fragment homologous to the 60k-rnpA-rpmM-dnaA-dnaN-recF-gyrB region of E. coli. Gene 93:2734.
73. Smith, J. D. 1976. Transcription and processing of transfer RNA precursors. Prog. Nucleic Acid Res. Mol. Biol. 16:2573.
74. Smith, J. D., 1979. Suppressor tRNAs in prokaryotes, p. 109125. In J. E. Celis, and J. D. Smith (ed.), Nonsense Mutations and tRNA Suppressors. Academic Press, New York.
75. Sprinzl, M.,, N. Dank,, S. Nock,, and A. Schön. 1991. Compilation of tRNA and tRNA gene sequences. Nucleic Acids Res. 19:21272171.
76. Stark, B. C.,, R. Kole,, E. J. Bowman,, and S. Altman. 1978. Ribonuclease P: an enzyme with an essential RNA component. Proc. Natl. Acad. Sci. USA 75:37173721.
77. Svàrd, S. G.,, and L. A. Kirsebom. 1992. Several regions of a tRNA precursor determine the Escherichia coli RNase P cleavage site. J. Mol. Biol. 227:10191031.
78. Talbot, S.,, and S. Altman. 1994. Kinetic and thermodynamic analysis of RNA-protein interactions in the RNase P holoenzyme from Escherichia coli. Biochemistry 33:14061411.
79. Thurlow, D. L.,, D. Shilowski,, and T. L. Marsh. 1991. Nucleotides in precursor tRNAs that are required intact for catalysis by RNase P RNAs. Nucleic Acids Res. 19:885891.
80. Vioque, A.,, J. Arnez,, and S. Altman. 1988. Protein-RNA interactions in the RNase P holoenzyme from Escherichia coli. J. Mol. Biol. 202:835848.
81. Wang, J. W.,, N. W. Davis,, and P. Gegenheimer. 1988. Novel mechanisms for maturation of chloroplast transfer RNA precursors. EMBO J. 7:15671574.
82. Waugh, D. S.,, C. J. Green,, and N. R. Pace. 1989. The design and catalytic properties of a simplified ribonuclease P RNA. Science 244:15691571.
83. Westhof, E.,, and S. Altman. 1994. Three-dimensional working model of Ml RNA, the catalytic RNA subunit of ribonuclease P from Escherichia coli. Proc. Natl. Acad. Sci. USA 91:51335137.
84. Wise, C. A.,, and N. C. Martin. 1991. Dramatic size variation of yeast mitochondrial RNAs suggests that RNase P RNAs can be quite small. J. Biol. Chem. 266:1915419157.
85. Yuan, Y.,, E.-S. Hwang,, and S. Altman. 1992. Targeted cleavage of messenger RNA by human RNase P. Proc. Natl. Acad. Sci. USA 89:80068010.
86. Zimmerly, S.,, V. Gamulin,, U. Burkard,, and D. Soil. 1990. The RNA component of RNase P in Schizosaccharomyces species. FEBS Lett. 271:189193.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error