Determinants in the rpsT mRNAs recognized by the 5′-sensor domain of RNase E

Molecular Microbiology

Volumn 89, Issue 2, 2013, Pages 388-402

  Mackie, George A ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; MESSENGER RNA; OLIGONUCLEOTIDE; PROTEIN RPST; RIBONUCLEASE E; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; ENZYME MODIFICATION; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; GENE TARGETING; IN VITRO STUDY; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CLEAVAGE; PROTEIN DOMAIN; PROTEIN PHOSPHORYLATION; RNA CLEAVAGE; RNA STABILITY; SIGNAL TRANSDUCTION;

BACTERIAL PROTEINS; CATALYTIC DOMAIN; ENDORIBONUCLEASES; OLIGONUCLEOTIDES; RIBOSOMAL PROTEINS; RNA, BACTERIAL; RNA, MESSENGER; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS);

EID: 84880133416     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/mmi.12283     Document Type: Article

References (39)

1. Anupama, K., Leela, J.K., and Gowrishankar, J. (2011) Two pathways for RNase E action in Escherichia coli in vivo and bypass of its essentiality in mutants defective for Rho-dependent transcription termination. Mol Microbiol 82: 1330-1348.
2. Baker, K.E., and Mackie, G.A. (2003) Ectopic RNase E sites promote bypass of 5′-end-dependent mRNA decay in Escherichia coli. Mol Microbiol 47: 75-88.
3. Bandyra, K.J., Said, N., Pfeiffer, V., Górna, M.W., Vogel, J., and Luisi, B.F. (2012) The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Mol Cell 47: 943-953.
4. Callaghan, A.J., Marcaida, M.J., Stead, J.A., McDowall, K.J., Scott, W.G., and Luisi, B.F. (2005) Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature 437: 1187-1191.
5. Carpousis, A.J., Luisi, B.F., and McDowall, K.J. (2009) Endonucleolytic initiation of mRNA decay in Escherichia coli. Prog Mol Biol Transl Sci 85: 91-135.
6. Celesnik, H., Deana, A., and Belasco, J.G. (2007) Initiation of RNA decay in Escherichia coli by pyrophosphate removal. Mol Cell 27: 79-90.
7. Condon, C., and Putzer, H. (2002) The phylogenetic distribution of bacterial ribonucleases. Nucleic Acids Res 30: 5339-5346.
8. Danchin, A. (2009) A phylogenetic view of bacterial ribonucleases. Prog Mol Biol Transl Sci 85: 1-41.
9. Deana, A., Celesnik, H., and Belasco, J.G. (2008) The bacterial enzyme RppH triggers messenger RNA degradation by pyrophosphate removal. Nature 451: 355-359.
10. Garrey, S.M., and Mackie, G.A. (2011) Roles of the 5′-phosphate sensor domain in RNase E. Mol Microbiol 80: 1613-1624.
11. Garrey, S.M., Blech, M., Riffell, J.L., Hankins, J.S., Stickney, L.M., Diver, M., etal. (2009) Substrate binding and active site residues in RNases E and G. Role of the 5′-sensor. J Biol Chem 284: 31843-31850.
12. Hammarlöf, D.S., and Hughes, D. (2008) Mutants of the RNA-processing enzyme RNase E reverse the extreme slow-growth phenotype caused by a mutant translation factor EF-Tu. Mol Microbiol 70: 1194-1209.
13. Jiang, X., and Belasco, J.G. (2004) Catalytic activation of multimeric RNase E and RNase G by 5′-phosphorylated RNA. Proc Natl Acad Sci USA 101: 9211-9216.
14. Jiang, X., Diwa, A., and Belasco, J.G. (2000) Regions of RNase E important for 5′-end-dependent RNA cleavage and autoregulated synthesis. J Bacteriol 182: 2468-2475.
15. Jourdan, S.S., and McDowall, K.J. (2008) Sensing of 5′-monophosphate by Escherichia coli RNase G can significantly enhance association with RNA and stimulate the decay of functional mRNA transcripts in vivo. Mol Microbiol 67: 102-115.
16. Joyce, S.A., and Dreyfus, M. (1998) In the absence of translation, RNase E can bypass 5′ mRNA stabilizers in Escherichia coli. J Mol Biol 282: 241-254.
17. Kaberdin, V.R., Walsh, A.P., Jakobsen, T., McDowall, K.J., and von Gabain, A. (2000) Enhanced cleavage of RNA mediated by an interaction between substrates and the arginine-rich domain of E. coli ribonuclease E. J Mol Biol 301: 257-264.
18. Kido, M., Yamanaka, K., Mitani, T., Niki, H., Ogura, T., and Hiraga, S. (1996) RNase E polypeptides lacking a C-terminal half suppress a mukB mutation in Escherichia coli. J Bacteriol 178: 3917-3925.
19. Kime, L., Jourdan, S.S., and McDowall, K.J. (2008) Identifying and characterizing substrates of the RNase E/G family of enzymes. Methods Enzymol 447: 215-241.
20. Koslover, D.J., Callaghan, A.J., Marcaida, M.J., Garman, E.F., Martick, M., Scott, W.G., and Luisi, B.F. (2008) The crystal structure of the Escherichia coli RNase E apoprotein and a mechanism for RNA degradation. Structure 16: 1238-1244.
21. Lapham, J., Yu, Y.T., Shu, M.D., Steitz, J.A., and Crothers, D.M. (1997) The position of site-directed cleavage of RNA using RNase H and 2′-O-methyl oligonucleotides is dependent on the enzyme source. RNA 3: 950-951.
22. Lehnik-Habrink, M., Lewis, R.J., Mäder, U., and Stülke, J. (2012) RNA degradation in Bacillus subtilis: an interplay of essential endo- and exoribonucleases. Mol Microbiol 84: 1005-1017.
23. Leroy, A., Vanzo, N.F., Sousa, S., Dreyfus, M., and Carpousis, A.J. (2002) Function in Escherichia coli of the non-catalytic part of RNase E: role in the degradation of ribosome-free mRNA. Mol Microbiol 45: 1231-1243.
24. Li, Z., Pandit, S., and Deutscher, M.P. (1999) RNase G (CafA protein) and RNase E are both required for the 5′ maturation of 16S ribosomal RNA. EMBO J 18: 2878-2885.
25. Lopez, P.J., Marchand, I., Joyce, S.A., and Dreyfus, M. (1999) The C-terminal half of RNase E, which organizes the Escherichia coli degradosome, participates in mRNA degradation but not rRNA processing in vivo. Mol Microbiol 33: 188-199.
26. Mackie, G.A. (1986) Structure of the DNA distal to the gene for ribosomal protein S20 of Escherichia coli: presence of a strong terminator and an IS1 element. Nucleic Acids Res 14: 6965-6981.
27. Mackie, G.A. (1992) Secondary structure of the mRNA for ribosomal protein S20. Implications for cleavage by RNase E. J Biol Chem 267: 1054-1061.
28. Mackie, G.A. (1998) Ribonuclease E is a 5′-end-dependent endonuclease. Nature 395: 720-723.
29. Mackie, G.A. (2000) Stabilization of circular rpsT mRNA demonstrates the 5-end-dependence of RNase E action in vivo. J Biol Chem 275: 25069-25072.
30. Mackie, G.A. (2013) RNase E: at the interface of bacterial RNA processing and decay. Nat Rev Microbiol 11: 45-57.
31. Mackie, G.A., and Genereux, J.L. (1993) The role of RNA structure in determining RNase E-dependent cleavage sites in the mRNA for ribosomal protein S20 in vitro. J Mol Biol 234: 998-1012.
32. Massé, E., Escorcia, F.E., and Gottesman, S. (2003) Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev 17: 2374-2383.
33. Morita, T., Maki, K., and Aiba, H. (2005) RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev 19: 2176-2186.
34. Ow, M.C., Liu, Q., and Kushner, S.R. (2000) Analysis of mRNA decay and rRNA processing in Escherichia coli in the absence of RNase E-based degradosome assembly. Mol Microbiol 38: 854-865.
35. Prévost, K., Desnoyers, G., Jacques, J.F., Lavoie, F., and Massé, E. (2011) Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage. Genes Dev 25: 385-396.
36. Richards, J., Luciano, D.J., and Belasco, J.G. (2012) Influence of translation on RppH-dependent mRNA degradation in Escherichia coli. Mol Microbiol 86: 1063-1072.
37. Spickler, C., Stronge, V., and Mackie, G.A. (2001) Preferential cleavage of degradative intermediates of rpsT mRNA by the Escherichia coli degradosome. J Bacteriol 183: 1106-1109.
38. Tock, M.R., Walsh, A.P., Carroll, G., and McDowall, K.J. (2000) The CafA protein required for the 5′-maturation of 16S rRNA is a 5′-end-dependent ribonuclease that has context-dependent broad sequence specificity. J Biol Chem 275: 8726-8732.
39. Vogel, J., and Luisi, B.F. (2011) Hfq and its constellation of RNA. Nat Rev Microbiol 9: 578-589.