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sRNAs and their targets sRNA RyhB* RyhB Target fur sodB RyhB sdhC RyhB sdhD RyhB bfr RyhB ftnA RyhB fumA RyhB acnA RyhB MicA shiA ompA RseX RseX MicC ompA ompC ompC RybB RybB RybB ompC ompW rpoE IpeX ompC IpeX ompF MicF ompF OmrA* fepA Reference (Vecerek et al., 2007) (Masse and Gottesman, 2002; Urban and Vogel, 2007) (Masse and Gottesman, 2002) (Masse and Gottesman, 2002) (Masse and Gottesman, 2002) (Masse and Gottesman, 2002) (Masse and Gottesman, 2002) (Masse and Gottesman, 2002) (Prevost et al., 2007) (Rasmussen et al., 2005; Udekwu et al., 2005; Urban and Vogel, 2007) (Douchin et al., 2006) (Douchin et al., 2006) (Chen et al., 2004; Urban and Vogel, 2007) (Johansen et al., 2006) (Johansen et al., 2006) (Thompson et al., 2007) (Castillo-Keller et al., 2006) (Castillo-Keller et al., 2006) (Aiba et al., 1987; Andersen and Delihas, 1990; Mizuno et al., 1984; Ramani et al., 1994; Urban and Vogel, 2007) (Guillier and Gottesman, 2006) OmrA fecA OmrA cirA OmrA ompT OmrB* fecA OmrB cirA OmrB ompT OmrB OmrA OxyS gntP gntP fhlA OxyS rpoS OxyS OxyS OxyS RprA yobF wrbA ybaY rpoS DsrA rpoS DsrA hns Sok mok-hok GcvB oppA (Guillier and Gottesman, 2006) (Guillier and Gottesman, 2006) (Guillier and Gottesman, 2006) (Guillier and Gottesman, 2006) (Guillier and Gottesman, 2006) (Guillier and Gottesman, 2006) (Tjaden et al., 2006) (Tjaden et al., 2006) (Altuvia et al., 1998; Argaman and Altuvia, 2000) (Altuvia et al., 1997; Zhang et al., 1997; Zhang et al., 1998) (Tjaden et al., 2006) (Tjaden et al., 2006) (Tjaden et al., 2006) (Majdalani et al., 2001; Majdalani et al., 2002) (Lease et al., 1998; Majdalani et al., 1998; Majdalani et al., 2002; Sledjeski et al., 1996) (Lease et al., 1998; Sledjeski and Gottesman, 1995; Urban and Vogel, 2007) (Franch et al., 1997; Franch et al., 1999; Gerdes et al., 1992; Gerdes et al., 1990; Pedersen and Gerdes, 1999; Thisted and Gerdes, 1992; Thisted et al., 1994) (Tjaden et al., 2006; Urbanowski et al., 2000) GcvB dppA Istr1 SgrS tisAB ptsG Spot42 galK RdlD SymR DicF ldrD symE ftsZ GadY gadX RydC yejABEF (Tjaden et al., 2006; Urban and Vogel, 2007; Urbanowski et al., 2000) (Vogel et al., 2004) (Kawamoto et al., 2006; Kawamoto et al., 2005; Kimata et al., 2001; Morita et al., 2005; Urban and Vogel, 2007; Vanderpool and Gottesman, 2004) (Moller et al., 2002; Urban and Vogel, 2007) (Kawano et al., 2002) (Kawano et al., 2007) (Tetart et al., 1992; Tetart and Bouche, 1992) Positive! (Opdyke et al., 2004) (Antal et al., 2005) *Additional targets based on microarray data were suggested for RyhB (Masse et al., 2005) and for OmrA and OmrB (Guillier and Gottesman, 2006). References Aiba, H., Matsuyama, S., Mizuno, T., and Mizushima, S. (1987) Function of micF as an antisense RNA in osmoregulatory expression of the ompF gene in Escherichia coli. J Bacteriol 169: 3007-3012 Altuvia, S., Weinstein-Fischer, D., Zhang, A., Postow, L., and Storz, G. (1997) A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator. Cell 90: 43-53 Altuvia, S., Zhang, A., Argaman, L., Tiwari, A., and Storz, G. (1998) The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding. Embo J 17: 6069-6075 Andersen, J., and Delihas, N. (1990) micF RNA binds to the 5' end of ompF mRNA and to a protein from Escherichia coli. Biochemistry 29: 9249-9256 Antal, M., Bordeau, V., Douchin, V., and Felden, B. (2005) A small bacterial RNA regulates a putative ABC transporter. J Biol Chem 280: 7901-7908 Argaman, L., and Altuvia, S. (2000) fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex. J Mol Biol 300: 1101-1112 Castillo-Keller, M., Vuong, P., and Misra, R. (2006) Novel mechanism of Escherichia coli porin regulation. J Bacteriol 188: 576-586 Chen, S., Zhang, A., Blyn, L. B., and Storz, G. (2004) MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. J Bacteriol 186: 6689-6697 Douchin, V., Bohn, C., and Bouloc, P. (2006) Down-regulation of porins by a small RNA bypasses the essentiality of the regulated intramembrane proteolysis protease RseP in Escherichia coli. J Biol Chem 281: 12253-12259 Dubey, A. K., Baker, C. S., Romeo, T., and Babitzke, P. (2005) RNA sequence and secondary structure participate in high-affinity CsrA-RNA interaction. Rna 11: 15791587 Franch, T., Gultyaev, A. P., and Gerdes, K. (1997) Programmed cell death by hok/sok of plasmid R1: processing at the hok mRNA 3'-end triggers structural rearrangements that allow translation and antisense RNA binding. J Mol Biol 273: 38-51 Franch, T., Thisted, T., and Gerdes, K. (1999) Ribonuclease III processing of coaxially stacked RNA helices. J Biol Chem 274: 26572-26578 Gerdes, K., Nielsen, A., Thorsted, P., and Wagner, E. G. (1992) Mechanism of killer gene activation. Antisense RNA-dependent RNase III cleavage ensures rapid turn-over of the stable hok, srnB and pndA effector messenger RNAs. J Mol Biol 226: 637-649 Gerdes, K., Thisted, T., and Martinussen, J. (1990) Mechanism of post-segregational killing by the hok/sok system of plasmid R1: sok antisense RNA regulates formation of a hok mRNA species correlated with killing of plasmid-free cells. Mol Microbiol 4: 18071818 Guillier, M., and Gottesman, S. (2006) Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs. Mol Microbiol 59: 231-247 Johansen, J., Rasmussen, A. A., Overgaard, M., and Valentin-Hansen, P. (2006) Conserved small non-coding RNAs that belong to the sigmaE regulon: role in downregulation of outer membrane proteins. J Mol Biol 364: 1-8 Kawamoto, H., Koide, Y., Morita, T., and 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 Kawamoto, H., Morita, T., Shimizu, A., Inada, T., and 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 Kawano, M., Aravind, L., and Storz, G. (2007) An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin. Mol Microbiol 64: 738-754 Kawano, M., Oshima, T., Kasai, H., and Mori, H. (2002) Molecular characterization of long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-aminoacid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli. Mol Microbiol 45: 333-349 Kimata, K., Tanaka, Y., Inada, T., and 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 Lease, R. A., Cusick, M. E., and Belfort, M. (1998) Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci. Proc Natl Acad Sci U S A 95: 12456-12461 Liu, M. Y., Gui, G., Wei, B., Preston, J. F., 3rd, Oakford, L., Yuksel, U., Giedroc, D. P., and Romeo, T. (1997) The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli. J Biol Chem 272: 17502-17510 Majdalani, N., Chen, S., Murrow, J., St John, K., and Gottesman, S. (2001) Regulation of RpoS by a novel small RNA: the characterization of RprA. Mol Microbiol 39: 1382-1394 Majdalani, N., Cunning, C., Sledjeski, D., Elliott, T., and Gottesman, S. (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 U S A 95: 12462-12467 Majdalani, N., Hernandez, D., and Gottesman, S. (2002) Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Mol Microbiol 46: 813826 Masse, E., and Gottesman, S. (2002) A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci U S A 99: 4620-4625 Mizuno, T., Chou, M. Y., and Inouye, M. (1984) A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA). Proc Natl Acad Sci U S A 81: 1966-1970 Moller, T., Franch, T., Udesen, C., Gerdes, K., and Valentin-Hansen, P. (2002) Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon. Genes Dev 16: 1696-1706 Morita, T., Maki, K., and Aiba, H. (2005) RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev 19: 2176-2186 Opdyke, J. A., Kang, J. G., and Storz, G. (2004) GadY, a small-RNA regulator of acid response genes in Escherichia coli. J Bacteriol 186: 6698-6705 Pedersen, K., and Gerdes, K. (1999) Multiple hok genes on the chromosome of Escherichia coli. Mol Microbiol 32: 1090-1102 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 Ramani, N., Hedeshian, M., and Freundlich, M. (1994) micF antisense RNA has a major role in osmoregulation of OmpF in Escherichia coli. J Bacteriol 176: 5005-5010 Rasmussen, A. A., Eriksen, M., Gilany, K., Udesen, C., Franch, T., Petersen, C., and 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 Sledjeski, D., and Gottesman, S. (1995) A small RNA acts as an antisilencer of the HNS-silenced rcsA gene of Escherichia coli. Proc Natl Acad Sci U S A 92: 2003-2007 Sledjeski, D. D., Gupta, A., and Gottesman, S. (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 Tetart, F., Albigot, R., Conter, A., Mulder, E., and Bouche, J. P. (1992) Involvement of FtsZ in coupling of nucleoid separation with septation. Mol Microbiol 6: 621-627 Tetart, F., and Bouche, J. P. (1992) Regulation of the expression of the cell-cycle gene ftsZ by DicF antisense RNA. Division does not require a fixed number of FtsZ molecules. Mol Microbiol 6: 615-620 Thisted, T., and Gerdes, K. (1992) Mechanism of post-segregational killing by the hok/sok system of plasmid R1. Sok antisense RNA regulates hok gene expression indirectly through the overlapping mok gene. J Mol Biol 223: 41-54 Thisted, T., Sorensen, N. S., Wagner, E. G., and Gerdes, K. (1994) Mechanism of postsegregational killing: Sok antisense RNA interacts with Hok mRNA via its 5'-end singlestranded leader and competes with the 3'-end of Hok mRNA for binding to the mok translational initiation region. Embo J 13: 1960-1968 Thompson, K. M., Rhodius, V. A., and Gottesman, S. (2007) {sigma}E regulates and is regulated by a small RNA in Escherichia coli. J Bacteriol Tjaden, B., Goodwin, S. S., Opdyke, J. A., Guillier, M., Fu, D. X., Gottesman, S., and Storz, G. (2006) Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res 34: 2791-2802 Udekwu, K. I., Darfeuille, F., Vogel, J., Reimegard, J., Holmqvist, E., and Wagner, E. G. (2005) Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA. Genes Dev 19: 2355-2366 Udekwu, K. I., and Wagner, E. G. (2007) Sigma E controls biogenesis of the antisense RNA MicA. Nucleic Acids Res 35: 1279-1288 Urban, J. H., and Vogel, J. (2007) Translational control and target recognition by Escherichia coli small RNAs in vivo. Nucleic Acids Res 35: 1018-1037 Urbanowski, M. L., Stauffer, L. T., and Stauffer, G. V. (2000) The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. Mol Microbiol 37: 856-868 Vanderpool, C. K., and 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 Vecerek, B., Moll, I., and Blasi, U. (2007) Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding. Embo J 26: 965-975 Vogel, J., Argaman, L., Wagner, E. G., and Altuvia, S. (2004) The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide. Curr Biol 14: 2271-2276 Weilbacher, T., Suzuki, K., Dubey, A. K., Wang, X., Gudapaty, S., Morozov, I., Baker, C. S., Georgellis, D., Babitzke, P., and Romeo, T. (2003) A novel sRNA component of the carbon storage regulatory system of Escherichia coli. Mol Microbiol 48: 657-670 Zhang, A., Altuvia, S., and Storz, G. (1997) The novel oxyS RNA regulates expression of the sigma s subunit of Escherichia coli RNA polymerase. Nucleic Acids Symp Ser 27-28 Zhang, A., Altuvia, S., Tiwari, A., Argaman, L., Hengge-Aronis, R., and Storz, G. (1998) The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. Embo J 17: 6061-6068