Proteomic profiling of ClpXP substrates after DNA damage reveals extensive instability within SOS regulon

Mol Cell. 2006 Apr 21;22(2):193-204. doi: 10.1016/j.molcel.2006.03.007.


ClpXP, a bacterial AAA+ protease, controls intracellular levels of many stress-response proteins. To investigate substrate profile changes caused by a specific environmental stress, quantitative mass spectrometry (SILAC) was used to analyze proteins trapped by ClpXP(trap) before and after DNA damage. The abundance of half of the trapped proteins changed more than 3-fold after damage. Overrepresented substrates included the DNA-repair proteins RecN and UvrA. Among SOS-response proteins, 25% were ClpXP substrates and, importantly, nearly all of the highly induced regulon members were rapidly degraded. Other proteins, including the stress regulator sigma(S), were underrepresented in ClpXP(trap) after DNA damage; overproduction experiments suggest that simple substrate competition does not account for this reduced recognition. We conclude that damage-response proteins are an unusually rapidly degraded family and that ClpXP has substantial capacity to process the influx of newly synthesized substrates while maintaining the ability to degrade its other substrates in an environmentally responsive manner.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / metabolism
  • Blotting, Western
  • DNA Damage*
  • Enzyme Inhibitors / pharmacology
  • Escherichia coli / genetics
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Gene Deletion
  • Gene Expression Profiling*
  • Half-Life
  • Kinetics
  • Mass Spectrometry
  • Nalidixic Acid / pharmacology
  • Peptide Hydrolases / chemistry*
  • Peptide Hydrolases / metabolism*
  • Proteomics*
  • Regulon*
  • SOS Response, Genetics*
  • Substrate Specificity
  • Transcription, Genetic


  • Enzyme Inhibitors
  • Escherichia coli Proteins
  • Nalidixic Acid
  • Peptide Hydrolases
  • Adenosine Triphosphatases