Ribonuclease PH plays a major role in the exonucleolytic maturation of CCA-containing tRNA precursors in Bacillus subtilis

Nucleic Acids Research

Volumn 33, Issue 11, 2005, Pages 3636-3643

  Wen, Tingyi ^b,c   Oussenko, Irina A ^a   Pellegrini, Olivier ^b,c   Bechhofer, David H ^a   Condon, Ciarán ^b  

^a INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

^b NEW YORK UNIVERSITY   (United States)

^c UNIVERSITÉ PARIS DESCARTES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; EXONUCLEASE; NUCLEOTIDE; RIBONUCLEASE; RIBONUCLEASE PH; TRANSFER RNA; UNCLASSIFIED DRUG; EXORIBONUCLEASE; RNA PRECURSOR;

3' UNTRANSLATED REGION; ARTICLE; BACILLUS SUBTILIS; BACTERIAL STRAIN; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME ASSAY; ENZYME INHIBITION; ESCHERICHIA COLI; GENETIC CODE; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; NORTHERN BLOTTING; PRIORITY JOURNAL; PROTEIN MOTIF; WILD TYPE; CHEMISTRY; ENZYMOLOGY; KINETICS; METABOLISM; NUCLEOTIDE SEQUENCE; PHYSIOLOGY;

BACILLUS SUBTILIS; ESCHERICHIA COLI; POSIBACTERIA;

BACILLUS SUBTILIS; BASE SEQUENCE; EXORIBONUCLEASES; KINETICS; RNA PRECURSORS; RNA, TRANSFER;

EID: 21244498581     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki675     Document Type: Article

References (34)

1. Frank,D.N., Adamidi,C., Ehringer,M.A., Pitulle,C. and Pace,N.R. (2000) Phylogenetic-comparative analysis of the eukaryal ribonuclease P RNA. RNA, 6, 1895-1904.
2. Li,Z. and Deutscher,M.P. (1996) Maturation pathways for E.coli tRNA precursors: A random multienzyme process in vivo. Cell, 86 503-512.
3. Li,Z. and Deutscher,M.P. (2002) RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors. RNA, 8 97-109.
4. Ow,M.C. and Kushner,S.R. (2002) Initiation of tRNA maturation by RNase E is essential for cell viability in E.coli. Genes Dev., 16, 1102-1115.
5. Li,Z., Pandit,S. and Deutscher,M.P. (1998) 3′ Exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli. Proc. Natl Acad. Sci. USA, 95, 2856-2861.
6. Li de la Sierra-Gallay,I., Pellegrini,O. and Condon,C. (2005) Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z. Nature, 433, 657-661.
7. Condon,C. and Putzer,H. (2002) The phylogenetic distribution of bacterial ribonucleases. Nucleic Acids Res., 30, 5339-5346.
8. Garber,R.L. and Gage,L.P. (1979) Transcription of a cloned Bombyx mori tRNA2Ala gene: Nucleotide sequence of the tRNA precursor and its processing in vitro. Cell, 18, 817-828.
9. Hagenbuchle,O., Larson,D., Hall,G.I. and Sprague,K.U. (1979) The primary transcription product of a silkworm alanine tRNA gene: Identification of in vitro sites of initiation, termination and processing. Cell 18, 1217-1229.
10. Castano,J.G., Tobian,J.A. and Zasloff,M. (1985) Purification and characterization of an endonuclease from Xenopus laevis ovaries which accurately processes the 3′ terminus of human pre-tRNA-Met(i) (3′ pre-tRNase). J. Biol. Chem., 260, 9002-9008.
11. Stange,N. and Beier,H. (1987) A cell-free plant extract for accurate pre-tRNA processing, splicing and modification. EMBO J., 6, 2811-2818.
12. Oommen,A., Li,X.Q. and Gegenheimer,P. (1992) Cleavage specificity of chloroplast and nuclear tRNA 3′-processing nucleases. Mol. Cell. Biol., 12, 865-875.
13. Han,S.J. and Kang,H.S. (1997) Purification and characterization of the precursor tRNA 3′-end processing nuclease from Aspergillus nidulans. Biochem. Biophys. Res. Commun., 233, 354-358.
14. Nashimoto,M. (1997) Distribution of both lengths and 5′ terminal nucleotides of mammalian pre-tRNA 3′ trailers reflects properties of 3′ processing endoribonuclease. Nucleic Acids Res., 25, 1148-1154.
15. Mayer,M., Schiffer,S. and Marchfelder,A. (2000) tRNA 3′ processing in plants: Nuclear and mitochondrial activities differ. Biochemistry, 39, 2096-2105.
16. Mohan,A., Whyte,S., Wang,X., Nashimoto,M. and Levinger,L. (1999) The 3′ end CCA of mature tRNA is an antideterminant for eukaryotic 3′-tRNase. RNA, 5, 245-256.
17. Minagawa,A., Takaku,H., Takagi,M. and Nashimoto,M. (2004) A novel endonucleolytic mechanism to generate the CCA 3′ termini of tRNA molecules in Thermotoga maritima. J. Biol. Chem., 279, 15688-15697.
18. Asha,P.K., Blouin,R.T., Zaniewski,R. and Deutscher,M.P. (1983) Ribonuclease BN: Identification and partial characterization of a new tRNA processing enzyme. Proc. Natl Acad. Sci. USA, 80, 3301-3304.
19. Ezraty,B., Dahlgren,B. and Deutscher,M.P. (2005) The RNase Z homologue encoded by Escherichia coli elaC gene is RNase BN. J. Biol. Chem., 280, 16542-16545.
20. Pellegrini,O., Nezzar,J., Marchfelder,A., Putzer,H. and Condon,C. (2003) Endonucleolytic processing of CCA-less tRNA precursors by RNaseZ in Bacillus subtilis. EMBO J., 22, 4534-4543.
21. Wang,W. and Bechhofer,D.H. (1996) Properties of a Bacillus subtilis polynucleotide phosphorylase deletion strain. J. Bacteriol., 178, 2375-2382.
22. Oussenko,I.A., Abe,T., Ujiie,H., Muto,A. and Bechhofer,D.H. (2005) Participation of 3′-to-5′ exoribonucleases in the turnover of Bacillus subtilis mRNA. J. Bacteriol., 187, 2758-2767.
23. Oussenko,I.A. and Bechhofer,D.H. (2000) The yvaJ gene of Bacillus subtilis encodes a 3′-to-5′ exoribonuclease and is not essential in a strain lacking polynucleotide phosphorylase. J. Bacteriol., 182, 2639-2642.
24. Oussenko,I.A., Sanchez,R. and Bechhofer,D.H. (2002) Bacillus subtilis YhaM, a member of a new family of 3′-to-5′ exonucleases in Gram-positive bacteria. J. Bacteriol., 184, 6250-6259.
25. Craven,M.G., Henner,D.J., Alessi,D., Schauer,A.T., Ost,K.A., Deutscher,M.P. and Friedman,D.I. (1992) Identification of the rph (RNase PH) gene of Bacillus subtilis: Evidence for suppression of cold-sensitive mutations in Escherichia coli. J. Bacteriol., 174, 4727-4735.
26. Luttinger,A., Hahn,J. and Dubnau,D. (1996) Polynucleotide phosphorylase is necessary for competence development in Bacillus subtilis. Mol. Microbiol., 19, 343-356.
27. Mitra,S., Hue,K. and Bechhofer,D.H. (1996) In vitro processing activity of Bacillus subtilis polynucleotide phosphorylase. Mol. Microbiol., 19, 329-342.
28. Even,S., Pellegrini,O., Zig,L., Labas,V., Vinh,J., Brechemmier-Baey,D. and Putzer,H. (2005) Ribonucleases J1 and J2: Two novel endoribonucleases in B.subtilis with functional homology to E.coli RNase E. Nucleic Acids Res., 33, 2141-2152.
29. Dominsky,Z., Yang,X.-C., Kaygun,H., Dadlez,M. and Marzluff,W. (2003) A 3′ exonuclease that specifically interacts with the 3′ end of histone mRNA. Mol. Cell., 12, 295-305.
30. Kennedy,S., Wang,D. and Ruvkun,G. (2004) A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature, 427, 645-649.
31. Kelly,K.O. and Deutscher,M.P. (1992) Characterization of Escherichia coli RNase PH. J. Biol. Chem., 267, 17153-17158.
32. Li,Z. and Deutscher,M.P. (1994) The role of individual exoribonucleases in processing at the 3′ end of Escherichia coli tRNA precursors. J. Biol. Chem., 269, 6064-6071.
33. Cudny,H. and Deutscher,M.P. (1988) 3′ processing of tRNA precursors in ribonuclease-deficient Escherichia coli. Development and characterization of an in vitro processing system and evidence for a phosphate requirement. J. Biol. Chem., 263, 1518-1523.
34. Harlow,L.S., Kadziola,A., Jensen,K.F. and Larsen,S. (2004) Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding. Protein Sci., 13, 668-677.