Functional dissection of sRNA translational regulators by nonhomologous random recombination and in vivo selection

Chemistry and Biology

Volumn 12, Issue 7, 2005, Pages 757-767

  Liu, Jane M ^a   Bittker, Joshua A ^a   Lonshteyn, Maria ^a   Liu, David R ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DSRA RNA; SIGMA FACTOR; UNTRANSLATED RNA;

ARTICLE; BINDING SITE; CHEMISTRY; ESCHERICHIA COLI; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN PROCESSING;

BASE SEQUENCE; BINDING SITES; ESCHERICHIA COLI; MOLECULAR SEQUENCE DATA; PROTEIN MODIFICATION, TRANSLATIONAL; RECOMBINATION, GENETIC; RNA, UNTRANSLATED; SIGMA FACTOR; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI;

EID: 22544467019     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2005.05.014     Document Type: Article

References (39)

1. L. Argaman, R. Hershberg, J. Vogel, G. Bejerano, E.G. Wagner, H. Margalit, and S. Altuvia Novel small RNA-encoding genes in the intergenic regions of Escherichia coli Curr. Biol. 11 2001 941 950
2. M. Lagos-Quintana, R. Rauhut, W. Lendeckel, and T. Tuschl Identification of novel genes coding for small expressed RNAs Science 294 2001 853 858
3. N.C. Lau, L.P. Lim, E.G. Weinstein, and D.P. Bartel An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans Science 294 2001 858 862
4. R.C. Lee, and V. Ambros An extensive class of small RNAs in Caenorhabditis elegans Science 294 2001 862 864
5. K.M. Wassarman, F. Repoila, C. Rosenow, G. Storz, and S. Gottesman Identification of novel small RNAs using comparative genomics and microarrays Genes Dev. 15 2001 1637 1651
6. S. Gottesman Stealth regulation: biological circuits with small RNA switches Genes Dev. 16 2002 2829 2842
7. K.M. Wassarman Small RNAs in bacteria: diverse regulators of gene expression in response to environmental changes Cell 109 2002 141 144
8. R. Hershberg, S. Altuvia, and H. Margalit A survey of small RNA-encoding genes in Escherichia coli Nucleic Acids Res. 31 2003 1813 1820
9. E. Masse, N. Majdalani, and S. Gottesman Regulatory roles for small RNAs in bacteria Curr. Opin. Microbiol. 6 2003 120 124
10. J. Vogel, V. Bartels, T.H. Tang, G. Churakov, J.G. Slagter-Jager, A. Huttenhofer, and E.G.H. Wagner RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria Nucleic Acids Res. 31 2003 6435 6443
11. A. Zhang, K.M. Wassarman, C. Rosenow, B.C. Tjaden, G. Storz, and S. Gottesman Global analysis of small RNA and mRNA targets of Hfq Mol. Microbiol. 50 2003 1111 1124
12. S. Altuvia Regulatory small RNAs: the key to coordinating global regulatory circuits J. Bacteriol. 186 2004 6679 6680
13. S. Gottesman The small RNA regulators of Escherichia coli: Roles and mechanisms Annu. Rev. Microbiol. 58 2004 303 328
14. G. Storz, J.A. Opdyke, and A. Zhang Controlling mRNA stability and translation with small, noncoding RNAs Curr. Opin. Microbiol. 7 2004 140 144
15. M. Kawano, A.A. Reynolds, J. Miranda-Rios, and G. Storz Detection of 5′- and 3′-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli Nucleic Acids Res. 33 2005 1040 1050
16. R. Hengge-Aronis Signal transduction and regulatory mechanisms involved in control of the sigma(S) (RpoS) subunit of RNA polymerase Microbiol. Mol. Biol. Rev. 66 2002 373 395
17. F. Repoila, N. Majdalani, and S. Gottesman Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm Mol. Microbiol. 48 2003 855 861
18. D. Sledjeski, and S. Gottesman A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli Proc. Natl. Acad. Sci. USA 92 1995 2003 2007
19. D.D. Sledjeski, A. Gupta, and S. Gottesman The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli EMBO J. 15 1996 3993 4000
20. N. Majdalani, C. Cunning, D. Sledjeski, T. Elliott, and S. Gottesman DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription Proc. Natl. Acad. Sci. USA 95 1998 12462 12467
21. R.A. Lease, and M. Belfort A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures Proc. Natl. Acad. Sci. USA 97 2000 9919 9924
22. R.A. Lease, M.E. Cusick, and M. Belfort Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci Proc. Natl. Acad. Sci. USA 95 1998 12456 12461
23. R.A. Lease, and S.A. Woodson Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA J. Mol. Biol. 344 2004 1211 1223
24. S. Altuvia, D. Weinstein-Fischer, A. Zhang, L. Postow, and G. Storz A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator Cell 90 1997 43 53
25. A. Zhang, S. Altuvia, A. Tiwari, L. Argaman, R. Hengge-Aronis, and G. Storz The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein EMBO J. 17 1998 6061 6068
26. M. Zuker Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res. 31 2003 3406 3415
27. S. Altuvia, A. Zhang, L. Argaman, A. Tiwari, and G. Storz The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding EMBO J. 17 1998 6069 6075
28. D.D. Sledjeski, C. Whitman, and A. Zhang Hfq is necessary for regulation by the untranslated RNA DsrA J. Bacteriol. 183 2001 1997 2005
29. P.J. Mikulecky, M.K. Kaw, C.C. Brescia, J.C. Takach, D.D. Sledjeski, and A.L. Feig Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS, and poly(A) RNAs Nat. Struct. Mol. Biol. 11 2004 1206 1214
30. A. Zhang, K.M. Wassarman, J. Ortega, A.C. Steven, and G. Storz The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs Mol. Cell 9 2002 11 22
31. T. Moller, T. Franch, P. Hojrup, D.R. Keene, H.P. Bachinger, R.G. Brennan, and P. Valentin-Hansen Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction Mol. Cell 9 2002 23 30
32. R.A. Lease, and S.A. Woodson Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA J. Mol. Biol. 344 2004 1211 1223
33. J.A. Bittker, B.V. Le, and D.R. Liu Nucleic acid evolution and minimization by nonhomologous random recombination Nat. Biotechnol. 20 2002 1024 1029
34. J.A. Bittker, B.V. Le, J.M. Liu, and D.R. Liu Directed evolution of protein enzymes using nonhomologous random recombination Proc. Natl. Acad. Sci. USA 101 2004 7011 7016
35. L. Brown, and T. Elliott Mutations that increase expression of the rpoS gene and decrease its dependence on hfq function in Salmonella typhimurium J. Bacteriol. 179 1997 656 662
36. S.C. Kampranis, A.J. Howells, and A. Maxwell The interaction of DNA gyrase with the bacterial toxin CcdB: evidence for the existence of two gyrase-CcdB complexes J. Mol. Biol. 293 1999 733 744
37. L.M. Guzman, D. Belin, M.J. Carson, and J. Beckwith Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter J. Bacteriol. 177 1995 4121 4130
38. P.M. Pryciak, and L.H. Hartwell AKR1 encodes a candidate effector of the G beta gamma complex in the Saccharomyces cerevisiae pheromone response pathway and contributes to control of both cell shape and signal transduction Mol. Cell. Biol. 16 1996 2614 2626
39. E. Masse, F.E. Escorcia, and S. Gottesman Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli Genes Dev. 17 2003 2374 2383