Thehok/sok toxin-antitoxin system ofEscherichia coliplasmid R1 increases plasmid maintenance by killing plasmidfree daughter cells. Thehok/sok locus specifies two RNAs:hokmRNA, which encodes a toxic transmembrane protein, andsokantisense RNA, which binds a complementary region in thehokmRNA and induces transcript degradation. During cell growth, the cis-encodedsokRNA inhibits expression of the Hok toxin. In plasmid-free segregants, the rapid decay ofsokRNA relative tohokmRNA permits Hok translation, leading to cell death. This post-segregational killing mechanism relies upon the ability of thehokmRNA to adopt alternative structural configurations, which affect ease of translation and the susceptibility of the molecule to degradation. The full-lengthhoktranscript is stable, highly structured and immune to ribosome and antisense RNA binding. Gradual 3' end processing produces dramatic structural rearrangements in the mRNA, which render the molecule translationally active and expose thesokRNA binding site. During transcription, premature ribosome andsokbinding are prevented through the formation of transient metastable hairpins in the 5' end of the nascent transcript. SeveralhokmRNA paralogs have been identified in the genome ofE. coli,and Hok protein orthologs found in the genomes of Enterobacteria. Using a combination of automated search and extensive manual editing, we compiled a multiple sequence alignment for thehokmRNA. All three experimentally validatedhokmRNA structures are mapped onto this alignment, which has been submitted to the Rfam database for RNA families.