Hfq proximity and orientation controls RNA annealing

Nucleic Acids Research

Volumn 40, Issue 17, 2012, Pages 8690-8697

  Panja, Subrata ^a   Woodson, Sarah A ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA; MESSENGER RNA; PROTEIN HFQ; SIGMA FACTOR RPOS; SMALL UNTRANSLATED RNA; TRANSFER RNA; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BASE PAIRING; BINDING SITE; CONTROLLED STUDY; GEL MOBILITY SHIFT ASSAY; GENE EXPRESSION; GENE EXPRESSION REGULATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE;

5' UNTRANSLATED REGIONS; BACTERIAL PROTEINS; BASE PAIRING; BINDING SITES; HOST FACTOR 1 PROTEIN; RNA, MESSENGER; RNA, SMALL UNTRANSLATED; SIGMA FACTOR;

BACTERIA (MICROORGANISMS);

EID: 84866949691     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks618     Document Type: Article

References (38)

1. Storz, G., Vogel, J. and Wassarman, K.M. (2011) Regulation by small RNAs in bacteria: expanding frontiers. Mol. Cell, 43, 880-891.
2. Kaberdin, V.R. and Blasi, U. (2006) Translation initiation and the fate of bacterial mRNAs. FEMS Microbiol. Rev., 30, 967-979. (Pubitemid 44583798)
3. Gottesman, S., McCullen, C.A., Guillier, M., Vanderpool, C.K., Majdalani, N., Benhammou, J., Thompson, K.M., FitzGerald, P.C., Sowa, N.A. and FitzGerald, D.J. (2006) Small RNA regulators and the bacterial response to stress. Cold Spring Harbor Symp. Quant. Biol., 71, 1-11.
4. Beisel, C.L. and Storz, G. (2010) Base pairing small RNAs and their roles in global regulatory networks. FEMS Microbiol. Rev., 34, 866-882.
5. Hao, Y., Zhang, Z.J., Erickson, D.W., Huang, M., Huang, Y., Li, J., Hwa, T. and Shi, H. (2011) Quantifying the sequence-function relation in gene silencing by bacterial small RNAs. Proc. Natl Acad. Sci. USA, 108, 12473-12478.
6. Vogel, J. and Luisi, B.F. (2011) Hfq and its constellation of RNA. Nat. Rev. Microbiol., 9, 578-589.
7. Caron, M.P., Lafontaine, D.A. and Masse, E. (2010) Small RNA-mediated regulation at the level of transcript stability. RNA Biol., 7, 140-144.
8. Aiba, H. (2007) Mechanism of RNA silencing by Hfq-binding small RNAs. Curr. Opin. Microbiol., 10, 134-139. (Pubitemid 46590050)
9. Zhang, A., Wassarman, K.M., Ortega, J., Steven, A.C. and Storz, G. (2002) The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol. Cell, 9, 11-22. (Pubitemid 34127767)
10. Schumacher, M.A., Pearson, R.F., Moller, T., Valentin-Hansen, P. and Brennan, R.G. (2002) Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein. EMBO J., 21, 3546-3556. (Pubitemid 34760584)
11. Mikulecky, P.J., Kaw, M.K., Brescia, C.C., Takach, J.C., Sledjeski, D.D. and Feig, A.L. (2004) Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs. Nat. Struct. Mol. Biol., 11, 1206-1214.
12. Link, T.M., Valentin-Hansen, P. and Brennan, R.G. (2009) Structure of Escherichia coli Hfq bound to polyriboadenylate RNA. Proc. Natl Acad. Sci. USA, 106, 19292-19297.
13. Rajkowitsch, L. and Schroeder, R. (2007) Dissecting RNA chaperone activity. RNA, 13, 2053-2060. (Pubitemid 350127547)
14. Hopkins, J.F., Panja, S. and Woodson, S.A. (2011) Rapid binding and release of Hfq from ternary complexes during RNA annealing. Nucleic Acids Res., 39, 5193-5202.
15. Hwang, W., Arluison, V. and Hohng, S. (2011) Dynamic competition of DsrA and rpoS fragments for the proximal binding site of Hfq as a means for efficient annealing. Nucleic Acids Res., 39, 5131-5139.
16. Adamson, D.N. and Lim, H.N. (2011) Essential requirements for robust signaling in Hfq dependent small RNA networks. PLoS Comput Biol, 7, e1002138.
17. Fender, A., Elf, J., Hampel, K., Zimmermann, B. and Wagner, E.G. (2010) RNAs actively cycle on the Sm-like protein Hfq. Genes Dev., 24, 2621-2626.
18. Lease, R.A. and Woodson, S.A. (2004) Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA. J. Mol. Biol., 344, 1211-1223. (Pubitemid 39550474)
19. Lorenz, C., Gesell, T., Zimmermann, B., Schoeberl, U., Bilusic, I., Rajkowitsch, L., Waldsich, C., von Haeseler, A. and Schroeder, R. (2010) Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts. Nucleic Acids Res., 38, 3794-3808.
20. Soper, T.J. and Woodson, S.A. (2008) The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA. RNA, 14, 1907-1917.
21. Updegrove, T., Wilf, N., Sun, X. and Wartell, R.M. (2008) Effect of Hfq on RprA-rpoS mRNA pairing: Hfq-RNA binding and the influence of the 50 rpoS mRNA leader region. Biochemistry, 47, 11184-11195.
22. Soper, T., Mandin, P., Majdalani, N., Gottesman, S. and Woodson, S.A. (2010) Positive regulation by small RNAs and the role of Hfq. Proc. Natl Acad. Sci. USA, 107, 9602-9607.
23. Brescia, C.C., Mikulecky, P.J., Feig, A.L. and Sledjeski, D.D. (2003) Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure. RNA, 9, 33-43. (Pubitemid 36206300)
24. Geissmann, T.A. and Touati, D. (2004) Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator. EMBO J., 23, 396-405. (Pubitemid 38294504)
25. Ishikawa, H., Otaka, H., Maki, K., Morita, T. and Aiba, H. (2012) The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 30 poly(U) tail. RNA, 18, 1062-1074.
26. Cao, Y., Wu, J., Liu, Q., Zhao, Y., Ying, X., Cha, L., Wang, L. and Li, W. (2010) sRNATarBase: a comprehensive database of bacterial sRNA targets verified by experiments. RNA, 16, 2051-2057.
27. Prevost, K., Salvail, H., Desnoyers, G., Jacques, J.F., Phaneuf, E. and Masse, E. (2007) The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis. Mol. Microbiol., 64, 1260-1273. (Pubitemid 46849016)
28. Beisel, C.L., Updegrove, T.B., Janson, B.J. and Storz, G. (2012) Multiple factors dictate target selection by Hfq-binding small RNAs. EMBO J., 31, 1961-1974.
29. Salim, N.N. and Feig, A.L. (2010) An upstream Hfq binding site in the fhlA mRNA leader region facilitates the OxyS-fhlA interaction. PLoS One, 5, e13028.
30. Hopkins, J.F., Panja, S., McNeil, S.A. and Woodson, S.A. (2009) Effect of salt and RNA structure on annealing and strand displacement by Hfq. Nucleic Acids Res., 37, 6205-6213.
31. Soper, T.J., Doxzen, K. and Woodson, S.A. (2011) Major role for mRNA binding and restructuring in sRNA recruitment by Hfq. RNA, 17, 1544-1550.
32. Arluison, V., Hohng, S., Roy, R., Pellegrini, O., Regnier, P. and Ha, T. (2007) Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA. Nucleic Acids Res., 35, 999-1006. (Pubitemid 46344724)
33. Olejniczak, M. (2011) Despite similar binding to the Hfq protein regulatory RNAs widely differ in their competition performance. Biochemistry, 50, 4427-4440.
34. Panja, S. and Woodson, S.A. (2012) Hexamer to Monomer Equilibrium of E. coli Hfq in Solution and Its Impact on RNA Annealing. J. Mol. Biol., 417, 406-412.
35. Sauer, E. and Weichenrieder, O. (2011) Structural basis for RNA 30-end recognition by Hfq. Proc. Natl Acad. Sci. USA, 108, 13065-13070.
36. Vecerek, B., Rajkowitsch, L., Sonnleitner, E., Schroeder, R. and Blasi, U. (2008) The C-terminal domain of Escherichia coli Hfq is required for regulation. Nucleic Acids Res., 36, 133-143.
37. Lee, T. and Feig, A.L. (2008) The RNA binding protein Hfq interacts specifically with tRNAs. RNA, 14, 514-523. (Pubitemid 351397816)
38. Cunning, C., Brown, L. and Elliott, T. (1998) Promoter substitution and deletion analysis of upstream region required for rpoS translational regulation. J. Bacteriol., 180, 4564-4570. (Pubitemid 28405582)