Nucleotide excision by E. coli DNA polymerase I in proofreading and non-proofreading modes

Biochim Biophys Acta. 1988 Dec 20;951(2-3):255-60. doi: 10.1016/0167-4781(88)90094-2.

Abstract

Escherichia coli DNA polymerase I exists in at least two distinct kinetic forms. When it binds to a template, the proofreading activity is usually switched off. As the enzyme progresses along the template, it becomes more and more competent for excision. This phenomenon introduces a link between fidelity and processivity. Processivity is best studied when the chain-length distributions of synthesized polymers are stationary. Even then, however, one cannot avoid multiple initiations on a given template by the same molecule of the enzyme. When synthesis is initiated with primers of lengths 15 or 20, a strange phenomenon is observed. It seems that the polymerase starts by hydrolyzing the primer down to a length of 7-10 nucleotides and only then starts to add nucleotides. It does so in a low-accuracy mode, suggesting that, while the exonuclease is clearly active, it does not contribute to proofreading. The warm-up of the proofreading function is therefore reinterpreted as a switch between two modes of behaviour: a mode 1 of low accuracy in which the 3'----5' exonuclease, while active, is uncoupled from the polymerase and does not contribute to proofreading, and a mode 2 of high accuracy in which the exonuclease is kinetically linked to the polymerase activity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Polymerase I / metabolism*
  • DNA, Bacterial / metabolism*
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics
  • Exodeoxyribonuclease V
  • Exodeoxyribonucleases / metabolism
  • Kinetics
  • Nucleotides / metabolism*
  • Oligodeoxyribonucleotides / metabolism
  • Poly A / metabolism
  • Templates, Genetic

Substances

  • DNA, Bacterial
  • Nucleotides
  • Oligodeoxyribonucleotides
  • oligo (dT)
  • Poly A
  • poly(dA)
  • DNA Polymerase I
  • Exodeoxyribonucleases
  • Exodeoxyribonuclease V