UmuD(2) inhibits a non-covalent step during DinB-mediated template slippage on homopolymeric nucleotide runs

J Biol Chem. 2010 Jul 23;285(30):23086-95. doi: 10.1074/jbc.M110.115774. Epub 2010 May 13.

Abstract

Escherichia coli DinB (DNA polymerase IV) possesses an enzyme architecture resulting in specialized lesion bypass function and the potential for creating -1 frameshifts in homopolymeric nucleotide runs. We have previously shown that the mutagenic potential of DinB is regulated by the DNA damage response protein UmuD(2). In the current study, we employ a pre-steady-state fluorescence approach to gain a mechanistic understanding of DinB regulation by UmuD(2). Our results suggest that DinB, like its mammalian and archaeal orthologs, uses a template slippage mechanism to create single base deletions on homopolymeric runs. With 2-aminopurine as a fluorescent reporter in the DNA substrate, the template slippage reaction results in a prechemistry fluorescence change that is inhibited by UmuD(2). We propose a model in which DNA templates containing homopolymeric nucleotide runs, when bound to DinB, are in an equilibrium between non-slipped and slipped conformations. UmuD(2), when bound to DinB, displaces the equilibrium in favor of the non-slipped conformation, thereby preventing frameshifting and potentially enhancing DinB activity on non-slipped substrates.

Publication types

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

MeSH terms

  • Base Sequence
  • DNA / chemistry
  • DNA / genetics
  • DNA / metabolism
  • DNA Damage
  • DNA Polymerase beta / genetics
  • DNA Polymerase beta / metabolism*
  • DNA-Directed DNA Polymerase / metabolism*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Fluorescent Dyes / metabolism
  • Mutagenesis
  • Nucleic Acid Conformation
  • Nucleotides / chemistry
  • Nucleotides / genetics
  • Nucleotides / metabolism*
  • Rec A Recombinases / metabolism
  • Serine Endopeptidases / pharmacology*
  • Templates, Genetic

Substances

  • DinB protein, E coli
  • Escherichia coli Proteins
  • Fluorescent Dyes
  • Nucleotides
  • DNA
  • Rec A Recombinases
  • DNA Polymerase beta
  • DNA-Directed DNA Polymerase
  • UmuD protein, E coli
  • Serine Endopeptidases