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Revista Latinoamericana de Microbiología

2006, Number 2

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Microbiología 2006; 48 (2)

The big world of the small RNAs

Miranda RJ

Language: Spanish
References: 45
Page: 73-78
PDF size: 94.63 Kb.


ABSTRACT

In the last ten years a great number of RNAs have been discovered that function by regulating gene expression and do not code for a protein. This RNAs are named ncRNAs or sRNAs (non coding RNAs or small RNAs). More than 70 sRNAs have been documented in Escherichia coli and function by inhibiting/promoting translation or degradation, some have intrinsic catalytic properties and others modify the activity of a protein. The mechanisms of action of some of them will be reviewed as well as the efforts to find new sRNAs by systematic oriented searches.


REFERENCES

  1. Altuvia, S., D. Weinstein-Fischer, A. Zhang, L. Postow & G.Storz. 1997. A small stable RNA induced by oxidative stress: Role as a pleiotropic regulator and antimutator. Cell 90:43-53.

  2. Argaman, L., R. Hershberg, J.Vogel, G. Bejerano, E.G.H. Wagner, H. Margalit & S. Altuvia. 2001. Novel small RNA-encoding genes in the intergenic region of Escherichia coli. Curr. Biol. 11:941-950.

  3. Batey, RT, S.D. Gilbert, & R.K. Montange. 2004. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432: 411-415.

  4. Chen S, E.A. Lesnik, T.A. Hall, R. Sampath, R.H. Griffey, D.J. Ecker & L.B. Blyn. 2002. A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems 65:157-177.

  5. Chen S., A. Zhang, L.B. Blyn & G. Storz. 2004. MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. J. Bacteriol. 186:6689-6697.

  6. Cromie, M.J., Y. Shi, T. Latifi & E.A. Groisman. An RNA sensor for intracellular Mg2+. 2006. Cell 125:71-84.

  7. Fuchs R.T., F.J. Grundy & T.N. Henkin. 2006. The SMK box is a new SAM-binding RNA for translational regulation of SAM synthetase. Nat. Struct. Mol. Biol. 13:226-233.

  8. Geissman T.A. & D. Touati. 2004. Hfq, a new chaperoning role: Binding to messenger RNA determines access for small RNA regulator. EMBO J. 23:396-405.

  9. Gelfand, M.S., A.A. Mironov, J. Jomantas, Y.I. Kozlov & D.A. Perumov. 1999. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. Trends Genet. 15:439-442.

  10. Gopalan V., A. Vioque & S. Altman. 2002. RNase P: variations and uses. J. Biol. Chem. 277:6759-6762.

  11. Grundy F.J. & T.M. Henkin. 1998. The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. Mol. Microbiol. 30:737-749.

  12. Herskovits A.A., E.S. Bochkareva & E. Bibi. 2000. New prospects in studying the bacterial signal recognition particle pathway. Mol. Microbiol. 38:927-939.

  13. Johansson, J., P. Mandin, A. Renzoni, C. Chiaruttini, M. Springer & P. Cossart. 2002. An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes. Cell 110:551-556.

  14. Kawano M., A.A. Reynolds, J. Miranda-Rios & G. Storz. 2005. Detection of 5’- and 3’ UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res. 33: 1040-1050.

  15. Kubodera T., M. Watanabe, K. Yoshiuchi, N. Yamashita, A. Nishimura, S. Nakai, K. Gomi & H. Hanamoto. 2003. Thiamine- regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5'-UTR. FEBS Lett. 555:516-520.

  16. Majdalani N., C. Cunning, D. Sledejski, T. Elliot & S. Gottesman. 1998. 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. 95:12462- 12467.

  17. Majdalani N., S. Chen, J. Murrow, K. St. John & S. Gottesman. 2001. Regulation of RpoS by a novel small RNA: the characterization of RprA. Mol. Microbiol. 39:1382-1394.

  18. Majdalani N., D. Hernandez & S. Gottesman. 2002. Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Mol. Microbiol. 46:813-826.

  19. Mandal, M., M. Lee, J.E. Barrick, Z. Weinberg, G.M. Emilsson, W.L. Ruzzo & R.R. Breaker. 2004. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306:275-279.

  20. Masse E. & S. Gottesman. 2002. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc. Natl. Acad. Sci. 99:4620-4625.

  21. Mikulecki P.J., M.K. Kaw, C.C. Brescia, J.C. Takach, D.D. Sledjeski & A.L. Feig. 2004. Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs. Nat. Struct. Mol. Biol. 11:1206-1214.

  22. Miranda-Rios J., C. Morera, H. Taboada, A. Davalos, S. Encarnacion, J. Mora & M. Soberon. 1997. Expression of thiamin biosynthetic genes (thiCOGE) and production of symbiotic terminal oxidase cbb3 in Rhizobium etli. J Bacteriol. 179:6887- 6893.

  23. Miranda-Rios, J., M. Navarro & M. Soberon. 2001. A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. Proc. Natl. Acad. Sci. 98:9736-9741.

  24. Mizuno T., M.-Y. Chou & M. Inouye. 1984. A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA). Proc. Natl. Acad. Sci. 81:1966-1970.

  25. Nahvi, A., N. Sudarsan, M.S. Ebert, X. Zou, K.L. Brown & R.R. Breaker. 2002. Genetic control by a metabolite binding mRNA. Chem. Biol. 9:1043-1049.

  26. Opdyke J.A., J.-G. Kang & G. Storz. 2004. GadY, a small- RNA regulator of acid response genes in Escherichia coli. J. Bacteriol. 186:6698-6705.

  27. Rivas E., R.J. Klein, T.A. Jones & S.R. Eddy. 2001. Computational identification of non-coding RNAs in E. coli by comparative genomics. Curr. Biol. 11:1369-1373.

  28. Romeo T. 1998. Global regulation by the small RNA-binding proteion CsrA and the non-coding RNA molecule CsrB. Mol. Microbiol. 29:1321-1330.

  29. Sauter C., J. Basquin & D. Suck. 2003. Sm-like proteins in eubacteria: the crystal structure of the Hfq protein from Escherichia coli. Nucleic Acids Res. 31:4091-4098.

  30. Schumacher M.A., R.F. Pearson, T. Moller, P. Valentin-Hansen & R.G. Brennan. 2002. Structures of a pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Smlike protein. EMBO J. 21:3546-3556.

  31. Sledejski D.D., A. Gupta & S. Gottesman. 1996. The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli. EMBO J. 15:3993-4000.

  32. Stormo, G.D. & Y. Ji. 2001. Do mRNAs act as direct sensors of small molecules to control their expression? Proc. Natl. Acad. Sci. 98:9465-9467.

  33. Sudarsan, N., J.E. Barrick & R.R. Breaker. 2003.Metabolitebinding RNA domains are present in the genes of eukaryotes. RNA 9:644-647.

  34. Sudarsan, N., J.K. Wickiser, S. Nakamura, M.S. Ebert, & R.R. Breaker. 2003. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev. 17:2688-2697.

  35. Tjaden B., R.M. Saxena, S. Stolyar, D.R. Haynor, E. Kolker & C. Rosenow. 2002. Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays. Nucleic Acids Res. 30:3732-3738.-

  36. Vogel J., V. Bartels, T.H. Tang, G. Churakov, J.G. Slagter-Jager, A. Huttenhofer & E.G.H. Wagner. 2003. RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res. 31:6435- 6443.

  37. Wassarman K.M. & G. Storz. 2000. 6S RNA regulates E. coli RNA polymerase activity. Cell 101:613-623.

  38. Wassarman K.M., F. Repoila, C. Rosenow, G. Storz & S. Gottesman. 2001. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev. 15:1637-1651.

  39. Weilbacher, T., K. Suzuki, A.K. Dubey, X. Wang, S. Gudapatay, I. Morozov I, C.S. Baker, D. Georgellis, P. Babitzke & T. Romeo. 2002. A novel sRNA component of the carbon storage regulatory system of Escherichia coli. Mol. Microbiol. 48:657-670.

  40. Wilderman P.J., N.A. Sowa, P.C. Fitzgerald, S. Gottesman, U.A. Ochsner & M.L. Vasil. 2004. Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis. Proc. Natl. Acad. Sci. 101:9792-9797.

  41. Winkler, W., A. Nahvi, & R.R. Breaker. 2002. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419:952-956.

  42. Winkler, W., A. Nahvi, A. Roth, J.A. Collins y R.R. Breaker. 2004. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428:281-286.

  43. Winkler, W.C. & R.R. Breaker. 2005. Regulation of bacterial gene expression by riboswitches. Annu. Rev. Microbiol. 59:487-517.

  44. Zhang A, S. Altuvia, A. Tiwari, L. Argaman, R. Hengge-Aronis & G. Storz. 1998. The oxyS regulatory RNA represses rpoS translation by binding Hfq (HF-1) protein. EMBO J. 17:6061-6068.

  45. Zhang, A., K.M. Wassarman, C. Rosenow, B.C. Tjaden, G. Storz & S. Gottesman. 2003. Global analysis of small RNA and mRNA targets of Hfq. Mol. Microbiol. 50:1111-1124.




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