Monday, February 9, 2009

Polymerase Dynamics at the Eukaryotic DNA Replication Fork

Renowned French scientist and 1965 Nobel laureate Jacques Monod once said "What's true for E. coli is true for an elephant".
The mechanistic basis for DNA replication is partially an example of this. The extensive studies made on E. coli revealed how DNA is copied, the series of proteins involved, and how it solves the apparent 'problem' of the DNA being in an antiparallel disposition, considering that the polymerase has a polarity (the 'trombone' model. See attached video.). The mechanism (which entails recognition of the origin of replication, assembly of the replication complex, loading of the clamp, etc.) was later shown to be essentially the same in eukaryotes, although almost always involving larger complexes and more proteins (See O’ Donnell’s review for details 1).
Despite the mechanistic similarities between the DNA replication process between prokaryotes and eukaryotes, a particular difference (among many others) involves the polymerases participating in primer synthesis and elongation of the leading and lagging strand.
In E. coli, the primer is synthesized by the product of dnaG, primase, and both the leading and lagging strand are synthesized by polIII core, in the context of a holoenzyme composed of a series of subunits.
In eukaryotes, the primer on the origins (which are multiple in these organisms, in contrast to E. coli, where there is a single origin of replication) is synthesized by DNA Pol α/primase and the leading and lagging strands have been suggested to be synthesized by different polymerases; DNA polymerase{delta} would synthesize the lagging strand and DNA polymerase {epsilon} the leading.

This review discusses evidence that support this model of different polymerases acting on the leading and lagging strands and the dynamics that take place on the replication fork in eukaryotes.

Here's the abstract and references.

Polymerase Dynamics at the Eukaryotic DNA Replication Fork
Peter M. J. Burgers

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110

This review discusses recent insights in the roles of DNA polymerases (Pol) {delta} and {epsilon} in eukaryotic DNA replication. A growing body of evidence specifies Pol {epsilon} as the leading strand DNA polymerase and Pol {delta} as the lagging strand polymerase during undisturbed DNA replication. New evidence supporting this model comes from the use of polymerase mutants that show an asymmetric mutator phenotype for certain mispairs, allowing an unambiguous strand assignment for these enzymes. On the lagging strand, Pol {delta} corrects errors made by Pol {alpha} during Okazaki fragment initiation. During Okazaki fragment maturation, the extent of strand displacement synthesis by Pol {delta} determines whether maturation proceeds by the short or long flap processing pathway. In the more common short flap pathway, Pol {delta} coordinates with the flap endonuclease FEN1 to degrade initiator RNA, whereas in the long flap pathway, RNA removal is initiated by the Dna2 nuclease/helicase.

J. Biol. Chem., Vol. 284, Issue 7, 4041-4045, February 13, 2009

If you are interested in DNA replication, I recommend the chapter on Watson's 'Molecular Biology of the Gene' textbook. I think that chapter gives a nice intro on the concepts you need.

1 Johnson A, O'Donnell M. Cellular DNA replicases: components and dynamics at the replication fork. Annu Rev Biochem. 2005;74:283-315.