Two-piece tmRNA in cyanobacteria and its structural analysis

Nucleic Acids Res. 2002 May 1;30(9):2018-24. doi: 10.1093/nar/30.9.2018.


tmRNA acts to rescue stalled bacterial ribosomes while encoding a peptide tag added trans-translationally to the nascent peptide, targeting it for proteolysis. The permuted gene structure found in a group of cyanobacteria is shown to produce a two-piece mature tmRNA, as had been observed previously for the independently permuted gene of alpha-proteobacteria. The pieces have been mapped onto the gene sequence and aligned for the permuted cyanobacterial tmRNA sequences, including four novel sequences. Structural probing and base pair co-variations support a secondary structure model in which two pairings in the tRNA-like domain hold the two pieces together, and the coding piece bearing the tag reading frame additionally contains a single transient pseudoknot and three other stem-loops. This represents a dramatic reduction in pseudoknot number from the five present in one-piece cyanobacterial tmRNA.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • Cyanobacteria / genetics*
  • Genes, Bacterial
  • Models, Genetic
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Phylogeny
  • RNA Precursors / analysis
  • RNA, Bacterial / chemistry*
  • RNA, Bacterial / genetics
  • Sequence Alignment
  • Sequence Analysis, RNA


  • RNA Precursors
  • RNA, Bacterial
  • tmRNA

Associated data

  • GENBANK/AY082654
  • GENBANK/AY082655