An important role for RNase R in mRNA decay

Molecular Cell

Volumn 17, Issue 2, 2005, Pages 313-318

  Cheng, Zhuan Fen ^a   Deutscher, Murray P ^a  

^a UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EXORIBONUCLEASE; MESSENGER RNA; POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE; RIBONUCLEASE; RIBONUCLEASE R; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; NONHUMAN; PROTEIN FUNCTION; RNA DEGRADATION; RNA SEQUENCE; RNA STRUCTURE;

BASE SEQUENCE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EXORIBONUCLEASES; GENE EXPRESSION REGULATION, BACTERIAL; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; POLYADENYLATION; RNA STABILITY; RNA, MESSENGER;

ESCHERICHIA COLI; EUKARYOTA; PROKARYOTA;

EID: 12344330602     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2004.11.048     Document Type: Article

References (29)

1. Blum E., Carpousis A.J., Higgins C.F. Polyadenylation promotes degradation of 3′-structured RNA by the Escherichia coli mRNA degradosome in vitro. J. Biol. Chem. 274:1999;4009-4016
2. Chaney S.G., Boyer P.D. Incorporation of water oxygens into intracellular nucleotides and RNA. II. Predominantly hydrolytic RNA turnover in Escherichia coli. J. Mol. Biol. 64:1972;581-591
3. Cheng Z.-F., Deutscher M.P. Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II. J. Biol. Chem. 277:2002;21624-21629
4. Cheng Z.-F., Deutscher M.P. Quality control of ribosomal RNA mediated by polynucleotide phosphorylase and RNase R. Proc. Natl. Acad. Sci. USA. 100:2003;6388-6393
5. Cheng Z.-F., Zuo Y., Li Z., Rudd K.E., Deutscher M.P. The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. J. Biol. Chem. 273:1998;14077-14080
6. Coburn G.A., Mackie G.A. Reconstitution of the degradation of the mRNA for ribosomal protein S20 with purified enzymes. J. Mol. Biol. 279:1998;1061-1074
7. Coburn G.A., Mackie G.A. Degradation of mRNA in Escherichia coli. an old problem with some new twists Prog. Nucleic Acid Res. Mol. Biol. 62:1999;55-108
8. Coburn G.A., Miao X., Briant D.J., Mackie G.A. Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3′ exonuclease and a DEAD-box RNA helicase. Genes Dev. 13:1999;2594-2603
9. Deutscher M.P., Reuven N.B. Enzymatic basis for hydrolytic versus phosphorolytic mRNA degradation in Escherichia coli and Bacillus subtilis. Proc. Natl. Acad. Sci. USA. 88:1991;3277-3280
10. Donovan W.P., Kushner S.R. Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12. Proc. Natl. Acad. Sci. USA. 83:1986;120-124
11. Gilson E., Clément J.M., Perrin D., Hofnung M. Palindromic units. a case of highly repetitive DNA sequences in bacteria Trends Genet. 3:1987;226-230
12. Higgins C.F., McLaren R.S., Newbury S.F. Repetitive extragenic palindromic sequences, mRNA stability and gene expression. evolution by gene conversion? Gene. 72:1988;3-14
13. Khemici V., Carpousis A.J. The RNA degradosome and poly(A) polymerase of Escherichia coli are required in vivo for the degradation of small mRNA decay intermediates containing REP-stabilizers. Mol. Microbiol. 51:2004;777-790
14. Koo J.T., Choe J., Moseley S.L. HrpA, a DEAH-box RNA helicase, is involved in mRNA processing of a fimbrial operon in Escherichia coli. Mol. Microbiol. 52:2004;1813-1826
15. Kushner S.R. mRNA decay in Escherichia coli comes of age. J. Bacteriol. 184:2002;4658-4665
16. Li Z., Pandit S., Deutscher M.P. Polyadenylation of stable RNA precursors. Proc. Natl. Acad. Sci. USA. 95:1998;12158-12162
17. Li Z., Reimers S., Pandit S., Deutscher M.P. RNA quality control. degradation of defective transfer RNA EMBO J. 21:2002;1132-1138
18. Linn, S., and Deutscher, M.P. (1993). Appendix C, the nucleases of Escherichia coli. In Nucleases, Second Edition (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press) pp. 455-468.
19. Liou G.G., Chang H.Y., Lin C.S., Lin-Chao S. DEAD box RhlB RNA helicase physically associates with exoribonuclease PNPase to degrade double-stranded RNA independent of the degradosome-assembling region of RNase E. J. Biol. Chem. 277:2002;41157-41162
20. Maloy S.R., Nunn W.D. Selection for loss of tetracycline resistance by Escherichia coli. J. Bacteriol. 145:1981;1110-1112
21. Marujo P.E., Hajnsdorf E., Le Derout J., Andrade R., Arraiano C.M., Regnier P. RNase II removes the oligo(A) tails that destabilize the rpsO mRNA of Escherichia coli. RNA. 6:2000;1185-1193
22. McLaren R.S., Newbury S.F., Dance G.S., Causton H.C., Higgins C.F. mRNA degradation by processive 3′-5′ exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo. J. Mol. Biol. 221:1991;81-95
23. Miller, J.H. (1992). Section 25: formula and recipes. In A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press), pp. 25.5.
24. Mohanty B.K., Kushner S.R. Genomic analysis in Escherichia coli demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay. Mol. Microbiol. 50:2003;645-658
25. Rudd K.E. Linkage map of Escherichia coli K12, edition 10. the physical map Microbiol. Mol. Biol. Rev. 62:1998;985-1019
26. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989). Chapter 7, extraction, purification, and analysis of mRNA from eukaryotic cells. In Molecular Cloning: A Laboratory Manual (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press), pp. 7.28-7.29.
27. Spickler C., Mackie G.A. Action of RNase II and polynucleotide phosphorylase against RNAs containing stem-loops of defined structure. J. Bacteriol. 182:2000;2422-2427
28. Steege D.A. Emerging features of mRNA decay in bacteria. RNA. 6:2000;1079-1090
29. Zuo Y., Deutscher M.P. Exoribonuclease superfamilies. structural analysis and phylogenetic distribution Nucleic Acids Res. 29:2001;1017-1026