RNase E action at a distance: Degradation of target mRNAs mediated by an Hfq-binding small RNA in bacteria

Genes and Development

Volumn 25, Issue 4, 2011, Pages 294-298

  Morita, Teppei ^a   Aiba, Hiroji ^a  

^a SUZUKA UNIVERSITY OF MEDICAL SCIENCE   (Japan)

Author keywords

Hfq; mRNA decay; RNA degradosome; RNase E; RyhB; Small RNA; Translation initiation

Indexed keywords

MESSENGER RNA; RIBONUCLEASE E; RIBONUCLEOPROTEIN; RNA; RNA BINDING PROTEIN; RNA BINDING PROTEIN HFQ; RNA RYHB; UNCLASSIFIED DRUG;

BACTERIUM; CHROMOSOME PAIRING; ENZYME ACTIVITY; ENZYME DEGRADATION; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA DEGRADATION;

BACTERIA; ENDORIBONUCLEASES; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; HOST FACTOR 1 PROTEIN; MODELS, BIOLOGICAL; PROTEIN BINDING; RNA INTERFERENCE; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA STABILITY; RNA, BACTERIAL; RNA, MESSENGER; RNA, SMALL INTERFERING;

BACTERIA (MICROORGANISMS);

EID: 79951701614     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.2030311     Document Type: Review

References (32)

1. Aiba H. 2007. Mechanism of RNA silencing by Hfq-binding small RNAs. Curr Opin Microbiol 10: 134-139. (Pubitemid 46590050)
2. Belasco JG. 2010. All things must pass: Contrasts and commonalities in eukaryotic and bacterial mRNA decay. Nat Rev Mol Cell Biol 11: 467-478.
3. Carpousis AJ. 2007. The RNA degradosome of Escherichia coli: An mRNA-degrading machine assembled on RNase E. Annu Rev Microbiol 61: 71-87. (Pubitemid 350058200)
4. Carthew RW, Sontheimer EJ. 2009. Origins and mechanisms of miRNAs and siRNAs. Cell 136: 642-655.
5. Gottesman S. 2004. The small RNA regulators of Escherichia coli: Roles and mechanisms. Annu Rev Microbiol 58: 303-328. (Pubitemid 39551989)
6. Gottesman S. 2005. Micros for microbes: Non-coding regulatory RNAs in bacteria. Trends Genet 21: 399-404. (Pubitemid 40835726)
7. Gottesman S, Storz G. 2010. Bacterial small RNA regulators: Versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 1: 1-16.
8. Ikeda Y, Yagi M, Morita T, Aiba H. 2011. Hfq binding at RhlB recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli. Mol Microbiol 79: 419-432.
9. Kawamoto H, Morita T, Shimizu A, Inada T, Aiba H. 2005. Implication of membrane localization of target mRNA in the action of a small RNA: Mechanism of post-transcriptional regulation of glucose transporter in Escherichia coli. Genes Dev 19: 328-338. (Pubitemid 40189296)
10. Kawamoto H, Koide Y, Morita T, Aiba H. 2006. Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq. Mol Microbiol 61: 1013-1022. (Pubitemid 44134177)
11. Kimata K, Tanaka Y, Inada T, Aiba H. 2001. Expression of the glucose transporter gene, ptsG, is regulated at the mRNA degradation step in response to glycolytic flux in Escherichia coli. EMBO J 20: 3587-3595. (Pubitemid 32634365)
12. Maki K, Uno K, Morita T, Aiba H. 2008. RNA, but not protein partners, is directly responsible for translational silencing by a bacterial Hfq-binding small RNA. Proc Natl Acad Sci 105: 10332-10337.
13. Maki K, Morita T, Otaka H, Aiba H. 2010. A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA. Mol Microbiol 76: 782-792.
14. Massé E, Gottesman S. 2002. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci 99: 4620-4625. (Pubitemid 34286034)
15. Massé E, Escorcia FE, Gottesman S. 2003. Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev 17: 2374-2383. (Pubitemid 37214786)
16. Mizuno T, Chou MY, Inouye M. 1984. A unique mechanism regulating gene expression: Translational inhibition by a complementary RNA transcript (micRNA). Proc Natl Acad Sci 81: 1966-1970. (Pubitemid 14146587)
17. Moller T, Franch T, Hojrup P, Keene DR, Bachinger HP, Brennan RG, Valentin-Hansen P. 2002. Hfq: A bacterial Sm-like protein that mediates RNA-RNA interaction. Mol Cell 9: 23-30. (Pubitemid 34127768)
18. Morita T, El-Kazzaz W, Tanaka Y, Inada T, Aiba H. 2003. Accumulation of glucose 6-phosphate or fructose 6-phosphate is responsible for destabilization of glucose transporter mRNA in Escherichia coli. J Biol Chem 278: 15608-15614. (Pubitemid 36799670)
19. Morita T, Kawamoto H, Mizota T, Inada T, Aiba H. 2004. Enolase in the RNA degradosome plays a crucial role in the rapid decay of glucose transporter mRNA in the response to phosphosugar stress in Escherichia coli. Mol Microbiol 54: 1063-1075. (Pubitemid 39491038)
20. Morita T, Maki K, Aiba H. 2005. RNase E-based ribonucleoprotein complexes: Mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev 19: 2176-2186. (Pubitemid 41330319)
21. Morita T, Mochizuki Y, Aiba H. 2006. Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction. Proc Natl Acad Sci 103: 4858-4863.
22. Pfeiffer V, Papenfort K, Lucchini S, Hinton JC, Vogel J. 2009. Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol 16: 840-846.
23. Prévost K, Desnoyers G, Jacques J-F, Lavoie F, Massé E. 2011. Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage. Genes Dev (this issue). doi: 10.1101/gad.2001711.
24. Ptashne M. 1986. Gene regulation by proteins acting nearby and at a distance. Nature 322: 697-701. (Pubitemid 16074119)
25. Rasmussen AA, Eriksen M, Gilany K, Udesen C, Franch T, Petersen C, Valentin-Hansen P. 2005. Regulation of ompA mRNA stability: The role of a small regulatory RNA in growth phase-dependent control. Mol Microbiol 58: 1421-1429. (Pubitemid 41705419)
26. Storz G, Opdyke JA, Zhang A. 2004. Controlling mRNA stability and translation with small, noncoding RNAs. Curr Opin Microbiol 7: 140-144. (Pubitemid 38447046)
27. Valentin-Hansen P, Eriksen M, Udesen C. 2004. The bacterial Sm-like protein Hfq: A key player in RNA transactions. Mol Microbiol 51: 1525-1533. (Pubitemid 38406529)
28. Vanderpool CK, Gottesman S. 2004. Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system. Mol Microbiol 54: 1076-1089. (Pubitemid 39491039)
29. Waters LS, Storz G. 2009. Regulatory RNAs in bacteria. Cell 136: 615-628.
30. Worrall JA, Gorna M, Crump NT, Phillips LG, Tuck AC, Price AJ, Bavro VN, Luisi BF. 2008. Reconstitution and analysis of the multienzyme Escherichia coli RNA degradosome. J Mol Biol 382: 870-883.
31. Zhang A, Altuvia S, Tiwari A, Argaman L, Hengge-Aronis R, Storz G. 1998. The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. EMBO J 17: 6061-6068. (Pubitemid 28474799)
32. Zhang A, Wassarman KM, Ortega J, Steven AC, Storz G. 2002. The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol Cell 9: 11-22. (Pubitemid 34127767)