The hok mRNA family

RNA Biol. 2012 Dec;9(12):1399-404. doi: 10.4161/rna.22746. Epub 2012 Dec 1.


The hok/sok toxin-antitoxin system of Escherichia coli plasmid R1 increases plasmid maintenance by killing plasmid-free daughter cells. The hok/sok locus specifies two RNAs: hok mRNA, which encodes a toxic transmembrane protein, and sok antisense RNA, which binds a complementary region in the hok mRNA and induces transcript degradation. During cell growth, the cis-encoded sok RNA inhibits expression of the Hok toxin. In plasmid-free segregants, the rapid decay of sok RNA relative to hok mRNA permits Hok translation, leading to cell death. This post-segregational killing mechanism relies upon the ability of the hok mRNA to adopt alternative structural configurations, which affect ease of translation and the susceptibility of the molecule to degradation. The full-length hok transcript 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 the sok RNA binding site. During transcription, premature ribosome and sok binding are prevented through the formation of transient metastable hairpins in the 5' end of the nascent transcript. Several hok mRNA paralogs have been identified in the genome of E. 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 the hok mRNA. All three experimentally validated hok mRNA structures are mapped onto this alignment, which has been submitted to the Rfam database for RNA families.

Keywords: RNA structures regulating gene expression; co-transcriptional RNA folding; hok/sok; mutually exclusive RNA structures; post-segregational killing; toxin-antitoxin system; transient RNA structures.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Toxins / genetics
  • Bacterial Toxins / metabolism*
  • Base Sequence
  • Binding Sites
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Gene Expression Regulation, Bacterial
  • Genome, Bacterial*
  • Nucleic Acid Conformation
  • Plasmids / genetics
  • Plasmids / metabolism
  • Protein Biosynthesis
  • RNA Stability
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Ribosomes / genetics
  • Ribosomes / metabolism
  • Sequence Alignment
  • Sequence Homology, Nucleic Acid
  • Transcription, Genetic


  • Bacterial Toxins
  • Escherichia coli Proteins
  • Hok protein, E coli
  • RNA, Bacterial
  • RNA, Messenger
  • Sok antisense RNA, E coli