The residue immediately upstream of the RNase P cleavage site is a positive determinant

Biochimie

Volumn 84, Issue 8, 2002, Pages 693-703

  Brännvall, Mathias ^a   Fredrik Pettersson, B M ^a   Kirsebom, Leif A ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Divalent metal ions; Ribozyme; RNase P; TRNA precursors; TRNA processing

Indexed keywords

BACTERIAL RNA; HISTIDINE TRANSFER RNA; METAL ION; NUCLEOTIDE; RIBONUCLEASE P; TRANSFER RNA; ADENOSINE TRIPHOSPHATE; GUANINE; MAGNESIUM; PHOSPHORUS; RIBONUCLEASE; RIBOZYME; RNA PRECURSOR; SERINE TRANSFER RNA; STRONTIUM; URACIL;

ARTICLE; CATALYSIS; ENZYME ACTIVE SITE; ESCHERICHIA COLI; GENE EXPRESSION; GENE LOCATION; GENETIC TRANSCRIPTION; KINETICS; NONHUMAN; PRECURSOR; PROMOTER REGION; PROTEIN LOCALIZATION; RESIDUE ANALYSIS; RNA CLEAVAGE; RNA STRUCTURE; BINDING SITE; BIOLOGICAL MODEL; CHEMISTRY; CONFORMATION; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

ADENOSINE TRIPHOSPHATE; BASE SEQUENCE; BINDING SITES; ENDORIBONUCLEASES; ESCHERICHIA COLI; GUANINE; KINETICS; MAGNESIUM; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHOSPHORUS ISOTOPES; RNA PRECURSORS; RNA, CATALYTIC; RNA, TRANSFER, HIS; RNA, TRANSFER, SER; STRONTIUM; SUBSTRATE SPECIFICITY; URACIL;

EID: 0036702994     PISSN: 03009084     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0300-9084(02)01462-1     Document Type: Article

References (69)

1. M.P. Deutscher, tRNA processing nucleases, in: D. Söll, U.L. RajB-handary (Eds.), tRNA: Structure, Biosynthesis and Function, ASM Press, Washington, D.C., 1995, pp. 51-65.
2. C. Guerrier-Takada, K. Gardiner, T. Marsh, N. Pace, S. Altman, The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme, Cell (1983) 849-857.
3. S. Altman, L.A. Kirsebom, P. Ribonuclease, in: R.F. Gesteland, T.R. Cech, J.F. Atkins (Eds.), The RNA World, second ed, Cold Spring Harbor Laboratories Press, Cold Spring Harbor, NY, 1999, pp. 351-380.
4. L.A. Kirsebom, RNase P - a "Scarlet Pimpernel", Mol. Microbiol. 17 (1995) 411-420.
5. L.A. Kirsebom, S.G. Svärd, Base pairing between Escherichia coli RNase P RNA and its substrate, EMBO J. 13 (1994) 4870-4876.
6. S.G. Svärd, U. Kagardt, L.A. Kirsebom, Phylogenetic comparative mutational analysis of the base-pairing between RNase P RNA and its substrate, RNA 2 (1996) 463-472.
7. A. Tallsjö, J. Kufel, L.A. Kirsebom, Interaction between Escherichia coli RNase P RNA and the discriminator base results in slow product release, RNA 2 (1996) 299-307.
8. J. Kufel, L.A. Kirsebom, Different cleavage sites are aligned differently in the active site of M1 RNA, the catalytic subunit of Escherichia coli RNase P, Proc. Natl. Acad. Sci. USA 93 (1996) 6085-6090.
9. M. Brännvall, J.G. Mattsson, S.G. Svärd, L.A. Kirsebom, RNase P RNA structure and cleavage reflect the primary structure of tRNA genes, J. Mol. Biol. 283 (1998) 771-783.
10. T. Meinnel, S. Blanquet, Maturation of pre-tRNAfMet by Escherichia coli RNase P is specified by a guanosine of the 5′-flanking sequence, J. Biol. Chem. 270 (1995) 15908-15914.
11. fMet in cleavage site selection by Escherichia coli RNase P in vitro, Biochemistry 37 (1998) 6041-6049.
12. A. Loria, T. Pan, Recognition of the 5′ leader and the acceptor stem of a pre-tRNA substrate by the ribozyme from Bacillus subtilis RNase P, Biochemistry 37 (1998) 10126-10133.
13. Asp, Biochemistry 37 (1998) 9409-9416.
14. D.M. Crothers, T. Seno, D.G. Söll, Is there a discriminator site in transfer RNA? Proc. Natl. Acad. Sci. USA 69 (1972) 3063-3067.
15. M. Brännvall, L.A. Kirsebom, Manganese ions induce miscleavage in the Escherichia coli RNase P RNA-catalyzed reaction, J. Mol. Biol. 292 (1999) 53-63.
16. J. Kufel, L.A. Kirsebom, The P15-loop of Escherichia coli RNase P RNA is an autonomous divalent metal ion binding domain, RNA 4 (1998) 777-788.
17. J.F. Milligan, D.R. Groebe, G.W. Whiterell, O.C. Uhlenbeck, Oligoribonucleotide synthesis using T7 RNA polymerase and DNA templates, Nucl. Acids Res. 15 (1987) 8783-8798.
18. J. Kufel, L.A. Kirsebom, Residues in Escherichia coli RNase P RNA important for cleavage site selection and divalent metal ion binding, J. Mol. Biol. 263 (1996) 685-698.
19. C. Guerrier-Takada, A. van Belkum, C.W.A. Pleij, S. Altman, Novel reactions of RNase P with a tRNA-like structure in turnip yellow mosaic virus, Cell 53 (1988) 267-272.
20. L.A. Kirsebom, S.G. Svärd, The kinetics and specificity of cleavage by RNase P is mainly dependent on the structure of the amino acid acceptor stem, Nucl. Acids Res. 20 (1992) 425-432.
21. M. Brännvall, L.A. Kirsebom, Metal ion cooperativity in ribozyme cleavage of RNA, Proc. Natl. Acad. Sci. USA 98 (2001) 12943-12947.
22. J.A. Wells, Additivity of mutational effects in proteins, Biochemistry 29 (1990) 8509-8517.
23. J-P. Perreault, S. Altman, Important 2′-hydroxyl groups in model substrates for M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli, J. Mol. Biol 226 (1992) 399-409.
24. J-P. Perreault, S. Altman, Pathway of activation by magnesium ions of substrates for the catalytic subunit of RNase P from Escherichia coli, J. Mol. Biol. 230 (1993) 750-756.
25. His precursors by the catalytic RNA component of RNase P, J. Biol. Chem. 263 (1988) 652-657.
26. U. Burkard, I. Willis, D. Söll, Processing of histidine transfer RNA precursors, J. Biol. Chem. 263 (1988) 2447-2451.
27. P.S. Holm, G. Krupp, The acceptor stem in pre-tRNAs determines the cleavage specificity of RNase P, Nucl. Acids Res. 20 (1992) 421-423.
28. R.M.W. Mans, C. Guerrier-Takada, S. Altman, C.W.A. Pleij, Interaction of RNase P from Escherichia coli with pseudoknotted structures in viral RNAs, Nucl. Acids Res. 18 (1990) 3479-3487.
29. R. Biswas, D.W. Ledman, R.O. Fox, S. Altman, V. Gopalan, Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using disulfide-linked EDTA-Fe, J. Mol. Biol. 296 (2000) 19-31.
30. T. Zuleeg, R.K. Hartmann, R. Kreutzer, S. Limmer, NMR spectroscopic evidence for Mn(2+)Mg(2+) binding to a precursor-tRNA microhelix near the potential RNase P cleavage site, J. Mol. Biol 305 (2001) 181-189.
31. R.K. Gaur, G. Krupp, Modification interferenced approach to detect ribose moieties important for the optimal activity of a ribozyme, Nucl. Acids Res. 21 (1993) 21-26.
32. T. Pan, A. Loria, K. Zhong, Probing of tertiary interactions in RNA: 2′-hydroxyl-base contacts between the RNase P RNA and pre-tRNA, Proc. Natl. Acad. Sci. USA 92 (1995) 12510-12514.
33. A.C. Forster, S. Altman, External guide sequences for an RNA enzyme, Science 249 (1990) 783-786.
34. D. Smith, N.R. Pace, Multiple magnesium ions in the ribonuclease P reaction mechanism, Biochemistry 32 (1993) 5273-5281.
35. S. Kazakov, S. Altman, Site-specific cleavage by metal ion cofactors and inhibitors of M1 RNA, the catalytic subunit of RNase P from Escherichia coli, Proc. Natl. Acad. Sci. USA 88 (1991) 9193-9197.
36. B.-K. Oh, D.N. Frank, N.R. Pace, Participation of the 3′-CCA of tRNA in the binding of catalytic Mg2+ ions by ribonuclease P, Biochemistry 37 (1998) 7277-7283.
37. U. Mueller, H. Schubel, M. Sprinzl, U. Heinemann, Crystal structure of acceptor stem of tRNA(Ala) from Escherichia coli shows unique G·U wobble base pair at 1.16 Å resolution, RNA 5 (1999) 670-677.
38. J.D. Smith, L. Barnett, S. Brenner, R.L. Russell, More mutant tyrosine transfer nucleic acids, J. Mol. Biol. 54 (1970) 1-14.
39. S. Niranjanakumari, T. Stams, S.M. Crary, D.W. Christianson C. Fierke, Protein component of the ribozyme ribonuclease P alters substrate recognition by directly contacting precursor tRNA, Proc. Natl. Acad. Sci. USA 95 (1998) 15212-15217.
40. E.L. Christian, M.E. Harris, The track of the pre-tRNA 5′ leader in the ribonuclease P ribozyme - substrate complex, Biochemistry 38 (1999) 12629-12638.
41. Asp, Biochemistry 37 (1998) 9409-9416.
42. G. Krupp, D. Kahle, T. Vogt, Sequence changes in both flanking sequences of a pre-tRNA influence the cleavage specificity of RNase P, J. Mol. Biol. 217 (1991) 637-648.
43. T. Zuleeg, A. Hansen, T. Pfeiffer, H. Schübel, R. Kreutzer, R.K. Hartmann, S. Limmer, Correlation between processing efficiency for ribonuclease P minimal substrates and conformation of the nucleotide -1 at the cleavage position, Biochemistry 40 (2001) 3363-3369.
44. L.A. Kirsebom, S.G. Svärd, RNase P processing of tRNA precursors, in: G. Krupp, R.K. Gaur (Eds.), Ribozyme Biochemistry and Biotechnology, Eaton Publishing, Natick, MA, 2000, pp. 111-131.
45. C.M. Fraser, et al., Genomic sequence of a Lyme disease spirochete, Borrelia burgdorferi, Nature 390 (1997) 580-586.
46. F. Kunst, et al., The complete genome sequence of the gram-positive bacterium Bacillus subtilis, Nature 390 (1997) 249-256.
47. F.R. Blattner, et al., The complete genome sequence of Escherichia coli K-12, Science 277 (1997) 1453-1474.
48. C.M. Fraser, et al., The minimal gene complement of Mycoplasma genitalium, Science 270 (1995) 397-403.
49. S.T. Cole, et al., Massive gene decay in the leprosy bacillus, Nature 409 (2001) 1007-1011.
50. R. Himmelreich, et al., Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae, Nucl. Acids Res. 24 (1996) 4420-4449.
51. S.T. Cole, et al., Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence, Nature 393 (1998) 537-544.
52. C.K. Stover, et al., Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen, Nature 406 (2000) 959-964.
53. S.G. Andersson, et al., The genome sequence of Rickettsia prowazekii and the origin of mitochondria, Nature 396 (1998) 133-140.
54. J.F. Heidelberg, et al., DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae, Nature 406 (2000) 477-483.
55. R.D. Fleischmann, et al., Whole-genome random sequencing and assembly of Haemophilus influenzae, Science 269 (1995) 496-512.
56. H. Tettelin, et al., Complete genome sequence of Neisseria meningitides serogroup B strain MC58, Science 287 (2000) 1809-1815.
57. M. Kuroda, et al., Whole genome sequencing of meticillin-resistant Staphylococcus aureus, The Lancet 357 (2001) 1225-1240.
58. M. McClelland, et al., Complete genome sequence of Salmonella enterica serovar Typhimurium LT2, Nature 413 (2001) 852-856.
59. K.E. Nelson, et al., Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima, Nature 399 (1999) 323-329.
60. C.M. Fraser, et al., Complete genome sequence Treponema pallidum, the syphilis spirochete, Science 281 (1998) 375-388.
61. J. Parkhill, et al., Genome sequence of Yersinia pestis, the causative agent of plague, Nature 413 (2001) 523-527.
62. "These sequence data were produced by the S. coelicolor sequencing group at the Sanger Institute and can be obtained from ftp://ftp.sanger.ac.uk/pub/S coelicolor".
63. P. Glaser, et al., Comparative genomics of Listeria species, Science 294 (2001) 849-852.
64. H.P. Klenk, et al., The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus, Nature 390 (1997) 364-370.
65. C.J. Bult, et al., Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii, Science 273 (1996) 1058-1073.
66. Q. She, et al., The complete genome of the crenarchaeon Sulfolobus solfataricus P2, Proc. Natl. Acad. Sci. USA 98 (2001) 7835-7840.
67. J. Parkhill, et al., The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences, Nature 403 (2000) 665-668.
68. T. Shimizu, et al., Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater, Proc. Natl. Acad. Sci. USA 99 (2002) 996-1001.
69. E.S. Haas, J.W. Brown, Evolutionary variation in bacterial RNase P RNAs, Nucl. Acids Res. 26 (1998) 4093-4099.