Figure 1. Effects of chromosomally encoded ncRNAs on their mRNA or protein targets
As well as examples provided in the text, additional ones are ncRNAs with a mode of action that is known or speculated. Notations are: ncRNA/target; +, RNA duplex degradation; −, no degradation of the RNA duplex; (d), degradation not demonstrated; (h), involvement of Hfq not demonstrated; (p), pairing not demonstrated; (dh), neither Hfq involvement nor degradation demonstrated; (he), Hfq involvement not demonstrated and effect predicted. An, Anamoeba sp.; Bb, Borrelia burgdorferi; Bs, B. subtilis; Ca, Clostridium acetobutylicum; Col, ncRNA from the plasmid ColE1, target from E. coli host (tryptophanase, TnaA); Ct, Chlamydia trachomatis; Ec, E. coli; Ent, enterobacteriaceae; Lm, L. monocytogenes; Pa, Ps. aeruginosa; Sa, S. aureus; St, Salmonella Typhimurium; Sy, Synechocystis Sp.; Ub, ubiquitous in all bacteria; Vc, V. cholerae. MICs/OMPs*, ncRNAs acting on envelope integrity; these are: MicF, MicC, MicA, MicX, RybB, RydC, RseX, OmrA, OmrB, InvR and IpeX (note that IpeX does not require Hfq to act on ompC mRNA), (see Table* on the right side of the panel; references available in Guillier et al., 2006; Vogel and Papenfort, 2006; Bossi and Figueroa-Bossi, 2007; Davis and Waldor, 2007). References are: DsrA- and RprA/rpoS (Majdalani et al., 1998, 2001); GlmY- and GlmZ/glmS (Kalamorz et al., 2007; Urban et al., 2007); GcvB/gltI/argT/ilvJ/dppA/oppA (Sharma et al., 2007); OxyS/rpoS (Zhang et al., 1998); OxyS/fhlA (Altuvia et al., 1998); DsrA/hns* (Lease and Belfort, 2000), *DsrA is supposed to pair with both the TIR and the 3′ end of hns mRNA; DicF/ftsZ (Faubladier et al., 1990); p3RNA/glnA (Fierro-Monti et al., 1992); Spot42/galK (Møller et al., 2002a, 2002a); GadY/gadX (Opdyke et al., 2004); RldD/ldrD (Kawano et al., 2002); Rli ncRNAs (Mandin et al., 2007); IthA/hctA (Grieshaber et al., 2006); RnpB/RnpA, tmRNA/SmpB and 4.5S/Ffh (Pichon and Felden, 2007); for other ncRNAs, references are mentioned in the text.
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