title: Dissecting the fidelity of bacteriophage RB69 DNA polymerase: site-specific modulation of fidelity by polymerase accessory proteins.
abstract: Bacteriophage RB69 encodes a replicative B-family DNA polymerase (RB69 gp43) with an associated proofreading 3' exonuclease. Crystal structures have been determined for this enzyme with and without DNA substrates. We previously described the mutation rates and kinds of mutations produced in vivo by the wild-type (Pol(+) Exo(+)) enzyme, an exonuclease-deficient mutator variant (Pol(+) Exo(-)), mutator variants with substitutions at Tyr(567) in the polymerase active site (Pol(M) Exo(+)), and the double mutator Pol(M) Exo(-). Comparing the mutational spectra of the Pol(+) Exo(-) and Pol(+) Exo(+) enzymes revealed the patterns and efficiencies of proofreading, while Tyr(567) was identified as an important determinant of base-selection fidelity. Here, we sought to determine how well the fidelities of the same enzymes are reflected in vitro. Compared to their behavior in vivo, the three mutator polymerases exhibited modestly higher mutation rates in vitro and their mutational predilections were also somewhat different. Although the RB69 gp43 accessory proteins exerted little or no effect on total mutation rates in vitro, they strongly affected mutation rates at many specific sites, increasing some rates and decreasing others.
authors.affiliation: Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Bebenek
authors.forename: Geraldine T
authors.initials: GT
authors.lastname: Carver
authors.forename: Holly Kloos
authors.initials: HK
authors.lastname: Dressman
authors.forename: Farid A
authors.initials: FA
authors.lastname: Kadyrov
authors.forename: Joseph K
authors.initials: JK
authors.lastname: Haseman
authors.forename: Vasiliy
authors.initials: V
authors.lastname: Petrov
authors.forename: William H
authors.initials: WH
authors.lastname: Konigsberg
authors.forename: Jim D
authors.initials: JD
authors.lastname: Karam
authors.forename: John W
authors.initials: JW
authors.lastname: Drake
mesh_terms: D017104:Bacteriophage M13 / Q000235:genetics; D001483:Base Sequence; D004247:DNA / Q000378:metabolism*; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism*; D066298:In Vitro Techniques; D008969:Molecular Sequence Data; D009154:Mutation; D014764:Viral Proteins / Q000378:metabolism*
chemical_list: D014764:Viral Proteins; D004247:DNA; D004259:DNA-Directed DNA Polymerase; C463461:bacteriophage RB69 DNA polymerase