Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III

Abstract During DNA replication in E. coli, a switch between DnaG primase and DNA polymerase III holoenzyme (pol III) activities has to occur every time when the synthesis of a new Okazaki fragment starts. As both primase and the χ subunit of pol III interact with the highly conserved C-terminus of single-stranded DNA-binding protein (SSB), it had been proposed that the binding of both proteins to SSB is mutually exclusive. Using a replication system containing the origin of replication of the single-stranded DNA phage G4 (G4ori) saturated with SSB, we tested whether DnaG and pol III can bind concurrently to the primed template. We found that the addition of pol III does not lead to a displacement of primase, but to the formation of higher complexes. Even pol III-mediated primer elongation by one or several DNA nucleotides does not result in the dissociation of DnaG. About 10 nucleotides have to be added in order to displace one of the two primase molecules bound to SSB-saturated G4ori. The concurrent binding of primase and pol III is highly plausible, since even the SSB tetramer situated directly next to the 3′-terminus of the primer provides four C-termini for protein-protein interactions.

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The Mechanism of Replication of Single-Stranded DNA. VI. Requirements for Ribonucleoside Triphosphates and DNA Polymerase III

Canadian Journal of Biochemistry ◽

10.1139/o73-214 ◽

1973 ◽

Vol 51 (12) ◽

pp. 1588-1597 ◽

Cited By ~ 7

Author(s):

David T. Denhardt ◽

Makoto Iwaya ◽

Grant McFadden ◽

Gerald Schochetman

Keyword(s):

Dna Polymerase ◽

Dna Polymerases ◽

Temperature Sensitive ◽

Restrictive Temperature ◽

Dna Polymerase Iii ◽

Single Stranded Dna ◽

E Coli ◽

Polymerase Iii

Evidence is presented that in Escherichia coli made permeable to nucleotides by exposure to toluene, the synthesis of a DNA chain complementary to the infecting single-stranded DNA of bacteriophage [Formula: see text] requires ATP as well as the four deoxyribonucleoside triphosphates. This synthesis results in the formation of the parental double-stranded replicative-form (RF) molecule. The ATP is not required simply to prevent degradation of the ribonucleoside or deoxyribonucleoside triphosphates; it can be partially substituted for by other ribonucleoside triphosphates.No single one of the known E. coli DNA polymerases appears to be uniquely responsible in vivo for the formation of the parental RF. Since [Formula: see text] replicates well in strains lacking all, or almost all, of the in-vitro activities of DNA polymerases I and II, neither of these two enzymes would seem essential; and in a temperature-sensitive E. coli mutant (dnaEts) deficient in DNA polmerase-I activity and possessing a temperature-sensitive DNA polymerase III, the viral single-stranded DNA is efficiently incorporated into an RF molecule at the restrictive temperature. In contrast, both RF replication and progeny single-stranded DNA synthesis are dependent upon DNA polymerase III activity.

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Long-Range PCR Amplification of DNA by DNA Polymerase III Holoenzyme from Thermus thermophilus

Enzyme Research ◽

10.1155/2015/837842 ◽

2015 ◽

Vol 2015 ◽

pp. 1-16 ◽

Cited By ~ 4

Author(s):

Wendy Ribble ◽

Shawn D. Kane ◽

James M. Bullard

Keyword(s):

Dna Synthesis ◽

Dna Polymerase ◽

Thermus Thermophilus ◽

Buffer System ◽

Dna Polymerase Iii ◽

Clamp Loader ◽

Native Form ◽

Polymerase Iii ◽

Essential Components ◽

Pol Iii

DNA replication in bacteria is accomplished by a multicomponent replicase, the DNA polymerase III holoenzyme (pol III HE). The three essential components of the pol III HE are the α polymerase, the β sliding clamp processivity factor, and the DnaX clamp-loader complex. We report here the assembly of the functional holoenzyme from Thermus thermophilus (Tth), an extreme thermophile. The minimal holoenzyme capable of DNA synthesis consists of α, β and DnaX (τ and γ), δ and δ′ components of the clamp-loader complex. The proteins were each cloned and expressed in a native form. Each component of the system was purified extensively. The minimum holoenzyme from these five purified subunits reassembled is sufficient for rapid and processive DNA synthesis. In an isolated form the α polymerase was found to be unstable at temperatures above 65°C. We were able to increase the thermostability of the pol III HE to 98°C by addition and optimization of various buffers and cosolvents. In the optimized buffer system we show that a replicative polymerase apparatus, Tth pol III HE, is capable of rapid amplification of regions of DNA up to 15,000 base pairs in PCR reactions.

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Mutator and Antimutator Effects of the Bacteriophage P1 hot Gene Product

Journal of Bacteriology ◽

10.1128/jb.00630-06 ◽

2006 ◽

Vol 188 (16) ◽

pp. 5831-5838 ◽

Cited By ~ 8

Author(s):

Anna K. Chikova ◽

Roel M. Schaaper

Keyword(s):

Dna Polymerase ◽

Dna Polymerase Iii ◽

Terminal Part ◽

Bacteriophage P1 ◽

E Coli ◽

Polymerase Iii ◽

Mutator Activity ◽

Stabilizing Effect ◽

Mutator Effect ◽

The One

ABSTRACT The Hot (homolog of theta) protein of bacteriophage P1 can substitute for the Escherichia coli DNA polymerase III θ subunit, as evidenced by its stabilizing effect on certain dnaQ mutants that carry an unstable polymerase III ε proofreading subunit (antimutator effect). Here, we show that Hot can also cause an increase in the mutability of various E. coli strains (mutator effect). The hot mutator effect differs from the one caused by the lack of θ. Experiments using chimeric θ/Hot proteins containing various domains of Hot and θ along with a series of point mutants show that both N- and C-terminal parts of each protein are important for stabilizing the ε subunit. In contrast, the N-terminal part of Hot appears uniquely responsible for its mutator activity.

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