Small RNA-mediated regulation at the level of transcript stability

RNA Biology

Volumn 7, Issue 2, 2010, Pages 140-144

  Caron, Marie Pier ^a,b   Lafontaine, Daniel A ^b   Massé, Eric ^a  

^a UNIVERSITY OF SHERBROOKE   (Canada)

^b UNIVERSITÉ DE SHERBROOKE   (Canada)

Author keywords

MicC; mRNA degradation; RNA degradosome; RNAse E; RyhB; SgrS; Small RNA

Indexed keywords

MESSENGER RNA; TRANSFER RNA; BACTERIAL RNA; MICRORNA; SMALL INTERFERING RNA;

GENE CONTROL; GENE EXPRESSION; NONHUMAN; REVIEW; RNA DEGRADATION; RNA STABILITY; RNA TRANSLATION; BACTERIA; GENE EXPRESSION REGULATION; GENETICS; METABOLISM;

BACTERIA (MICROORGANISMS); EUKARYOTA;

BACTERIA; GENE EXPRESSION REGULATION, BACTERIAL; MICRORNAS; RNA STABILITY; RNA, BACTERIAL; RNA, SMALL INTERFERING;

EID: 77953753696     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.7.2.11056     Document Type: Review

References (62)

1. Brenner S, Jacob F, Meselson M. An unstable intermediate carrying information from genes to ribosomes for protein synthesis. Nature 1961; 575-6.
2. Gros F, Hiatt H, Gilbert W, Kurland CG, Risebrough RW, Watson JD. Unstable ribonucleic acid revealed by pulse labelling of Escherichia coli. Nature 1961; 190:581-5.
3. Coleman J, Green PJ, Inouye M. The use of RNAs complementary to specific mRNAs to regulate the expression of individual bacterial genes. Cell 1984; 37:429-36.
4. Mizuno T, Chou MY, Inouye M. A unique mechanism regulating gene expression: Translational inhibition by a complementary RNA transcript (micRNA). Proc Natl Acad Sci USA 1984; 81:1966-70.
5. Coburn GA, Miao X, Briant DJ, Mackie GA. Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3′ exonuclease and a DEAD-box RNA helicase. Genes Dev 1999; 13:2594-603.
6. Kushner SR. mRNA decay in Escherichia coli comes of age. J Bacteriol 2002; 184:4658-65.
7. Nicholson AW. Function, mechanism and regulation of bacterial ribonucleases. FEMS Microbiol Rev 1999; 23:371-90.
8. Carpousis AJ, Van Houwe G, Ehretsmann C, Krisch HM. Copurification of E. coli RNAase E and PNPase: Evidence for a specific association between two enzymes important in RNA processing and degradation. Cell 1994; 76:889-900.
9. Vanzo NF, Li YS, Py B, Blum E, Higgins CF, Raynal LC, et al. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes Dev 1998; 12:2770-81.
10. Carpousis AJ. The RNA degradosome of Escherichia coli: An mRNA-degrading machine assembled on RNase E. Annu Rev Microbiol 2007; 61:71-87.
11. Mackie GA, Genereaux JL. The role of RNA structure in determining RNase E-dependent cleavage sites in the mRNA for ribosomal protein S20 in vitro. J Mol Biol 1993; 234:998-1012.
12. McDowall KJ, Lin-Chao S, Cohen SN. A + U content rather than a particular nucleotide order determines the specificity of RNase E cleavage. J Biol Chem 1994; 269:10790-6.
13. Ehretsmann CP, Carpousis AJ, Krisch HM. Specificity of Escherichia coli endoribonuclease RNase E: In vivo and in vitro analysis of mutants in a bacteriophage T4 mRNA processing site. Genes Dev 1992; 6:149-59.
14. Lin-Chao S, Wong TT, McDowall KJ, Cohen SN. Effects of nucleotide sequence on the specificity of rne-dependent and RNase E-mediated cleavages of RNA I encoded by the pBR322 plasmid. J Biol Chem 1994; 269:10797-803.
15. McDowall KJ, Kaberdin VR, Wu SW, Cohen SN, Lin-Chao S. Site-specific RNase E cleavage of oligonucleotides and inhibition by stem-loops. Nature 1995; 374:287-90.
16. Mackie GA. Ribonuclease E is a 5′-end-dependent endonuclease. Nature 1998; 395:720-3.
17. Mackie GA. Stabilization of circular rpsT mRNA demonstrates the 5′-end dependence of RNase E action in vivo. J Biol Chem 2000; 275:25069-72.
18. Celesnik H, Deana A, Belasco JG. Initiation of RNA decay in Escherichia coli by 5′ pyrophosphate removal. Mol Cell 2007; 27:79-90.
19. Deana A, Celesnik H, Belasco JG. The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal. Nature 2008; 451:355-8.
20. Prud'homme-Genereux A, Beran RK, Iost I, Ramey CS, Mackie GA, Simons RW. Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: Evidence for a 'cold shock degradosome'. Mol Microbiol 2004; 54:1409-21.
21. Miczak A, Kaberdin VR, Wei CL, Lin-Chao S. Proteins associated with RNase E in a multicomponent ribonucleolytic complex. Proc Natl Acad Sci USA 1996; 93:3865-9.
22. Morita T, Maki K, Aiba H. RNase E-based ribonucleoprotein complexes: Mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev 2005; 19:2176-86.
23. Moller T, Franch T, Hojrup P, Keene DR, Bachinger HP, Brennan RG, Valentin-Hansen P. Hfq: A bacterial sm-like protein that mediates RNA-RNA interaction. Mol Cell 2002; 9:23-30.
24. Zhang A, Wassarman KM, Ortega J, Steven AC, Storz G. The sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol Cell 2002; 9:11-22.
25. Brescia CC, Mikulecky PJ, Feig AL, Sledjeski DD. Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure. RNA 2003; 9:33-43.
26. Kajitani M, Kato A, Wada A, Inokuchi Y, Ishihama A. Regulation of the Escherichia coli hfq gene encoding the host factor for phage Q beta. J Bacteriol 1994; 176:531-4.
27. Schumacher MA, Pearson RF, Moller T, Valentin-Hansen P, Brennan RG. Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: A bacterial sm-like protein. EMBO J 2002; 21:3546-56.
28. Sun X, Zhulin I, Wartell RM. Predicted structure and phyletic distribution of the RNA-binding protein Hfq. Nucleic Acids Res 2002; 30:3662-71.
29. Arluison V, Derreumaux P, Allemand F, Folichon M, Hajnsdorf E, Regnier P. Structural modelling of the sm-like protein Hfq from Escherichia coli. J Mol Biol 2002; 320:705-12.
30. Zhang A, Wassarman KM, Rosenow C, Tjaden BC, Storz G, Gottesman S. Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 2003; 50:1111-24.
31. Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, et al. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet 2008; 4:1000163.
32. Robertson GT, Roop RM Jr. The brucella abortus host factor I (HF-I) protein contributes to stress resistance during stationary phase and is a major determinant of virulence in mice. Mol Microbiol 1999; 34:690-700.
33. Ding Y, Davis BM, Waldor MK. Hfq is essential for Vibrio cholerae virulence and downregulates sigma expression. Mol Microbiol 2004; 53:345-54. (Pubitemid 38901403)
34. Christiansen JK, Larsen MH, Ingmer H, Sogaard-Andersen L, Kallipolitis BH. The RNA-binding protein Hfq of Listeria monocytogenes: Role in stress tolerance and virulence. J Bacteriol 2004; 186:3355-62.
35. Sonnleitner E, Hagens S, Rosenau F, Wilhelm S, Habel A, Jager KE, Blasi U. Reduced virulence of a Hfq mutant of Pseudomonas aeruginosa O1. Microb Pathog 2003; 35:217-28.
36. Sittka A, Pfeiffer V, Tedin K, Vogel J. The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium. Mol Microbiol 2007; 63:193-217. (Pubitemid 44968119)
37. Updegrove T, Wilf N, Sun X, Wartell RM. Effect of Hfq on RprA-rpoS mRNA pairing: Hfq-RNA binding and the influence of the 5′ rpoS mRNA leader region. Biochemistry 2008; 47:11184-95.
38. Masse E, Gottesman S. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci USA 2002; 99:4620-5. (Pubitemid 34286034)
39. Masse E, Escorcia FE, Gottesman S. Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev 2003; 17:2374-83.
40. Jacques JF, Jang S, Prevost K, Desnoyers G, Desmarais M, Imlay J, Masse E. RyhB small RNA modulates the free intracellular iron pool and is essential for normal growth during iron limitation in Escherichia coli. Mol Microbiol 2006; 62:1181-90. (Pubitemid 44655327)
41. Masse E, Vanderpool CK, Gottesman S. Effect of RyhB small RNA on global iron use in Escherichia coli. J Bacteriol 2005; 187:6962-71.
42. Kawamoto H, Morita T, Shimizu A, Inada T, Aiba H. 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 2005; 19:328-38. (Pubitemid 40189296)
43. Morita T, Mochizuki Y, Aiba H. Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction. Proc Natl Acad Sci USA 2006; 103:4858-63.
44. Dubrac S, Touati D. Fur positive regulation of iron superoxide dismutase in Escherichia coli: Functional analysis of the sodB promoter. J Bacteriol 2000; 182:3802-8.
45. Desnoyers G, Morissette A, Prevost K, Masse E. Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA. EMBO J 2009; 28:1551-61.
46. Prevost K, Salvail H, Desnoyers G, Jacques JF, Phaneuf E, Masse E. The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis. Mol Microbiol 2007; 64:1260-73. (Pubitemid 46849016)
47. Vecerek B, Moll I, Blasi U. Control of fur synthesis by the non-coding RNA RyhB and iron-responsive decoding. EMBO J 2007.
48. Geissmann TA, Touati D. Hfq, a new chaperoning role: Binding to messenger RNA determines access for small RNA regulator. EMBO J 2004; 23:396-405. (Pubitemid 38294504)
49. Mitarai N, Benjamin JA, Krishna S, Semsey S, Csiszovszki Z, Masse E, Sneppen K. Dynamic features of gene expression control by small regulatory RNAs. Proc Natl Acad Sci USA 2009; 106:10655-9.
50. Sledjeski DD, Whitman C, Zhang A. Hfq is necessary for regulation by the untranslated RNA DsrA. J Bacteriol 2001; 183:1997-2005. (Pubitemid 32225995)
51. Moll I, Afonyushkin T, Vytvytska O, Kaberdin VR, Blasi U. Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs. RNA 2003; 9:1308-14. (Pubitemid 37310861)
52. Afonyushkin T, Vecerek B, Moll I, Blasi U, Kaberdin VR. Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB. Nucleic Acids Res 2005; 33:1678-89. (Pubitemid 41418396)
53. Vanderpool CK, Gottesman S. Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system. Mol Microbiol 2004; 54:1076-89. (Pubitemid 39491039)
54. Liou GG, Chang HY, Lin CS, 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 2002; 277:41157-62.
55. Wadler CS, Vanderpool CK. A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide. Proc Natl Acad Sci USA 2007; 104:20454-9.
56. Papenfort K, Pfeiffer V, Mika F, Lucchini S, Hinton JC, Vogel J. Sigma(E)-dependent small RNAs of S almonella respond to membrane stress by accelerating global omp mRNA decay. Mol Microbiol 2006; 62:1674-88. (Pubitemid 44813812)
57. Rasmussen AA, Eriksen M, Gilany K, Udesen C, Franch T, Petersen C, Valentin-Hansen P. Regulation of ompA mRNA stability: The role of a small regulatory RNA in growth phase-dependent control. Mol Microbiol 2005; 58:1421-9. (Pubitemid 41705419)
58. Udekwu KI, Darfeuille F, Vogel J, Reimegard J, Holmqvist E, Wagner EG. Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA. Genes Dev 2005; 19:2355-66.
59. Guillier M, Gottesman S. The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator. Nucleic Acids Res 2008; 36:6781-94.
60. Pfeiffer V, Papenfort K, Lucchini S, Hinton JC, Vogel J. Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol 2009; 16:840-6.
61. Figueroa-Bossi N, Valentini M, Malleret L, Bossi L. Caught at its own game: Regulatory small RNA inactivated by an inducible transcript mimicking its target. Genes Dev 2009; 23:2004-15.
62. Overgaard M, Johansen J, Moller-Jensen J, Valentin-Hansen P. Switching off small RNA regulation with trap-mRNA. Mol Microbiol 2009; 73:790-800.