Initiation of RNA decay in Escherichia coli by 5' pyrophosphate removal

Mol Cell. 2007 Jul 6;27(1):79-90. doi: 10.1016/j.molcel.2007.05.038.


The common belief that endonucleolytic cleavage is the initial, rate-determining step of mRNA decay in Escherichia coli fails to explain the influence of 5' termini on the half-lives of primary transcripts. We have re-examined the initial events of RNA degradation in that organism by devising an assay to probe the 5' phosphorylation state of RNA and by employing a self-cleaving hammerhead ribozyme to investigate the degradative consequences of an unphosphorylated 5' end. These studies have identified a previously unrecognized prior step in decay that triggers subsequent internal cleavage by the endonuclease RNase E and thereby governs RNA longevity: the rate-determining conversion of a triphosphorylated to a monophosphorylated 5' terminus. Our findings redefine the role of RNase E in RNA degradation and explain how unpaired 5'-terminal nucleotides can facilitate access to internal cleavage sites within primary transcripts. Moreover, these results reveal a striking parallel between the mechanisms of mRNA decay in prokaryotic and eukaryotic organisms.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Base Sequence
  • Diphosphates / isolation & purification
  • Diphosphates / metabolism*
  • Escherichia coli / genetics*
  • Hydroxyl Radical
  • Models, Biological
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Phosphorylation
  • RNA Stability*
  • RNA, Bacterial / biosynthesis
  • RNA, Bacterial / chemistry*
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism*
  • RNA, Messenger / biosynthesis
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism


  • Diphosphates
  • RNA, Bacterial
  • RNA, Messenger
  • Hydroxyl Radical