PMC

Protein sequences of characterized type I toxins. Transmembrane domains were predicted using the TMPred program (http://www.ch.embnet.org/software/TMPRED_form.html) and are shaded in gray for each protein.

Predicted structures of antitoxin sRNAs. The structures of the plasmid R1 Sok RNA and the E. coli RdlD, SibC, IstR-1, OhsC, and SymR sRNAs were predicted by the program M-fold (http://frontend.bioinfo.rpi.edu/applications/mfold/cgi-bin/rna-form1.cgi). The region of the Sok RNA involved in the initial base-pairing interaction with the hok mRNA and the regions of complementarity between IstR-1 and OhsC and their targets are highlighted in green. The U-turn motif found in SibC is highlighted in blue, and a motif shared by IstR-1, OhsC, and SymR is indicated in red.

Models for three types of regulation of type I toxin-antitoxin loci. SD, Shine-Dalgarno sequences. Red denotes SDs that are blocked, green denotes SDs that are accessible, and black denotes SDs that are accessible upon ribosome binding to an upstream SD. The full-length hok and tisB mRNAs need to be processed (indicated by the broken circle) at the 3′ and 5′ ends, respectively, before they can be translated. This processing brings about a change in secondary structure required to make the critical SD accessible. In addition to blocking ribosome binding, the sRNAs promote cleavage (indicated by the scissors) of the mRNA, thus irreversibly inactivating the target.