Identification of the Dimer Exchange Interface of the Bacterial DNA Damage Response Protein UmuD

Biochemistry. 2017 Sep 12;56(36):4773-4785. doi: 10.1021/acs.biochem.7b00560. Epub 2017 Aug 29.

Abstract

The Escherichia coli SOS response, an induced DNA damage response pathway, confers survival on bacterial cells by providing accurate repair mechanisms as well as the potentially mutagenic pathway translesion synthesis (TLS). The umuD gene products are upregulated after DNA damage and play roles in both nonmutagenic and mutagenic aspects of the SOS response. Full-length UmuD is expressed as a homodimer of 139-amino-acid subunits, which eventually cleaves its N-terminal 24 amino acids to form UmuD'. The cleavage product UmuD' and UmuC form the Y-family polymerase DNA Pol V (UmuD'2C) capable of performing TLS. UmuD and UmuD' exist as homodimers, but their subunits can readily exchange to form UmuDD' heterodimers preferentially. Heterodimer formation is an essential step in the degradation pathway of UmuD'. The recognition sequence for ClpXP protease is located within the first 24 amino acids of full-length UmuD, and the partner of full-length UmuD, whether UmuD or UmuD', is degraded by ClpXP. To better understand the mechanism by which UmuD subunits exchange, we measured the kinetics of exchange of a number of fluorescently labeled single-cysteine UmuD variants as detected by Förster resonance energy transfer. Labeling sites near the dimer interface correlate with increased rates of exchange, indicating that weakening the dimer interface facilitates exchange, whereas labeling sites on the exterior decrease the rate of exchange. In most but not all cases, homodimer and heterodimer exchange exhibit similar rates, indicating that somewhat different molecular surfaces mediate homodimer exchange and heterodimer formation.

MeSH terms

  • DNA Damage / physiology*
  • Escherichia coli / genetics
  • Escherichia coli / metabolism*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Gene Expression Regulation, Bacterial / physiology
  • Genetic Variation
  • Kinetics
  • Models, Molecular
  • Plasmids
  • Protein Conformation
  • Protein Subunits
  • SOS Response, Genetics / physiology*
  • Serine Endopeptidases / genetics
  • Serine Endopeptidases / metabolism*

Substances

  • Escherichia coli Proteins
  • Protein Subunits
  • Serine Endopeptidases
  • UmuD protease, E coli