Controlled degradation by ClpXP protease tunes the levels of the excision repair protein UvrA to the extent of DNA damage

Mol Microbiol. 2009 Feb;71(4):912-24. doi: 10.1111/j.1365-2958.2008.06574.x. Epub 2008 Dec 18.

Abstract

UV irradiation damages DNA and activates expression of genes encoding proteins helpful for survival under DNA stress. These proteins are often deleterious in the absence of DNA damage. Here, we investigate mechanisms used to regulate the levels of DNA-repair proteins during recovery by studying control of the nucleotide excision repair (NER) protein UvrA. We show that UvrA is induced after UV irradiation and reaches maximum levels between approximately 20 and 120 min post UV. During post-UV recovery, UvrA levels decrease principally as a result of ClpXP-dependent protein degradation. The rate of UvrA degradation depends on the amount of unrepaired pyrimidine dimers present; this degradation rate is initially slow shortly after UV, but increases as damage is repaired. This increase in UvrA degradation as repair progresses is also influenced by protein-protein interactions. Genetic and in vitro experiments support the conclusion that UvrA-UvrB interactions antagonize degradation. In contrast, Mfd appears to act as an enhancer of UvrA turnover. Thus, our results reveal that a complex network of interactions contribute to tuning the level of UvrA in the cell in response to the extent of DNA damage and nicely mirror findings with excision repair proteins from eukaryotes, which are controlled by proteolysis in a similar manner.

Publication types

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

MeSH terms

  • Adenosine Triphosphatases / genetics
  • Adenosine Triphosphatases / metabolism*
  • Bacterial Proteins / metabolism
  • DNA Damage*
  • DNA Repair*
  • DNA, Bacterial / metabolism
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • Endopeptidase Clp / genetics
  • Endopeptidase Clp / metabolism*
  • Escherichia coli / genetics
  • Escherichia coli / metabolism*
  • Escherichia coli / radiation effects
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Sequence Deletion
  • Transcription Factors / metabolism
  • Ultraviolet Rays

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Transcription Factors
  • transcription repair coupling factor protein, Bacteria
  • ClpXP protease, E coli
  • Endopeptidase Clp
  • UvrA protein, E coli
  • Adenosine Triphosphatases