Ornithine capture by a translating ribosome controls bacterial polyamine synthesis

Nat Microbiol. 2020 Apr;5(4):554-561. doi: 10.1038/s41564-020-0669-1. Epub 2020 Feb 24.


Polyamines are essential metabolites that play an important role in cell growth, stress adaptation and microbial virulence1-3. To survive and multiply within a human host, pathogenic bacteria adjust the expression and activity of polyamine biosynthetic enzymes in response to different environmental stresses and metabolic cues2. Here, we show that ornithine capture by the ribosome and the nascent peptide SpeFL controls polyamine synthesis in γ-proteobacteria by inducing the expression of the ornithine decarboxylase SpeF4, via a mechanism involving ribosome stalling and transcription antitermination. In addition, we present the cryogenic electron microscopy structure of an Escherichia coli ribosome stalled during translation of speFL in the presence of ornithine. The structure shows how the ribosome and the SpeFL sensor domain form a highly selective binding pocket that accommodates a single ornithine molecule but excludes near-cognate ligands. Ornithine pre-associates with the ribosome and is then held in place by the sensor domain, leading to the compaction of the SpeFL effector domain and blocking the action of release factor 1. Thus, our study not only reveals basic strategies by which nascent peptides assist the ribosome in detecting a specific metabolite, but also provides a framework for assessing how ornithine promotes virulence in several human pathogens.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Base Sequence
  • Binding Sites
  • Enterococcus faecalis / genetics
  • Enterococcus faecalis / metabolism
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Escherichia coli / pathogenicity
  • Models, Molecular
  • Ornithine / chemistry*
  • Ornithine / metabolism
  • Ornithine Decarboxylase / chemistry*
  • Ornithine Decarboxylase / genetics
  • Ornithine Decarboxylase / metabolism
  • Peptide Termination Factors / chemistry
  • Peptide Termination Factors / genetics
  • Peptide Termination Factors / metabolism
  • Phylogeny
  • Polyamines / chemistry
  • Polyamines / metabolism
  • Protein Binding
  • Protein Biosynthesis
  • Protein Interaction Domains and Motifs
  • RNA, Transfer / chemistry
  • RNA, Transfer / genetics
  • RNA, Transfer / metabolism
  • Ribosomes / chemistry*
  • Ribosomes / metabolism
  • Salmonella typhimurium / genetics
  • Salmonella typhimurium / metabolism
  • Salmonella typhimurium / pathogenicity
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Thermus thermophilus / genetics
  • Thermus thermophilus / metabolism
  • Virulence


  • Bacterial Proteins
  • Peptide Termination Factors
  • Polyamines
  • RNA, Transfer
  • Ornithine
  • Ornithine Decarboxylase