Polymerase Processivity: Measurement and Mechanisms

Abstract

The processivity of DNA synthesis by a DNA polymerase is defined as the number of nucleotides that a polymerase can incorporate into DNA during a single template‐binding event, before dissociating from a DNA template. The overall efficiency of DNA synthesis increases when the processivity of a polymerase increases.

Keywords: DNA polymerase; DNA replication; processivity; polymerase accessory proteins

Figure 1.

Structure of the Escherichia coli β sliding clamp. The β clamp encircles the DNA molecule (with its axis orientated perpendicular to the plane of the diagram, not shown), associates with the polIII core and holds it firmly in place so that primer extension can proceed. This ribbon diagram of the polypeptide backbone of a dimer of β subunits was generated from the coordinates from crystallographic data. Reproduced with permission from Kong et al..

Figure 2.

The steps that occur when γ complex loads β onto DNA. Biochemical evidence suggests that β most likely exists as a dimer in solution. The γ complex assembles the dimeric β clamp onto DNA in a reaction that requires the hydrolysis of ATP. In the presence of ATP, the γ complex binds β and may open one or both dimer interfaces to assemble β onto the DNA. Then the γ complex dissociates so that the β–DNA complex is free to interact with the core polymerase.

Figure 3.

Stimulation of the activities of the Escherichia coli α–ε DNA polymerase III core subunits and of DNA polymerase II by accessory factors. SSB is E. coli single‐stranded binding protein. Reproduced with permission from Bonner et al. .

close

References

Bambara RA, Fay PJ and Mallaber LM (1995) Methods of analyzing processivity. Methods in Enzymology 262: 270–280.

Bloom LB, Turner J, Kelman Z, Beechem JM, O'Donnell M and Goodman MF (1996) Dynamics of loading the β sliding clamp of DNA polymerase III onto DNA. Journal of Biological Chemistry 271: 30699–30708.

Bonner CA, Stukenberg PT, Rajogopalan M et al. (1992) Processive DNA synthesis by DNA polymerase II mediated by DNA polymerase III accessory proteins. Journal of Biological Chemistry 267: 11431–11438.

Doubié S, Tabor S, Long AM, Richardson CC and Ellenberger T (1998) Crystal structure of bacteriophage T7 DNA replication complex at 2.2Å resolution. Nature 391: 251–258.

Kelman Z and O'Donnell M (1995) DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine. Annual Review of Biochemistry 64: 171–200.

Kong X‐P, Onrust R, O'Donnell M and Kuriyan J (1992) Three‐dimensional structure of the β subunit of E.coli DNA polymerase III holoenzyme: A sliding DNA clamp. Cell 69: 425–437.

Krishna TSR, Kong X‐P, Gary S, Burgers PM and Kuriyan J (1994) Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell 79: 1233–1243.

Reddy MK, Weitzel SE and von Hippel PH (1992) Processive proofreading is intrinsic to T4 DNA polymerase. Journal of Biological Chemistry 267: 14157–14166.

Singhal RK and Wilson SH (1993) Short gap‐filling synthesis by DNA polymerase β is processive. Journal of Biological Chemistry 268: 15906–15911.

Tabor S, Huber HE and Richardson CC (1987) Escherichia coli thioredoxin confers processivity on the DNA polymerase activity of the gene 5 protein of bacteriophage T7. Journal of Biological Chemistry 262: 16212–16223.

Further Reading

Herendeen DR and Kelly TJ (1996) DNA polymerase III: running rings around the fork. Cell 84: 5–8.

Kelman Z and O'Donnell M (1995) DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine. Annual Review of Biochemistry 64: 171–200.

Kelman Z, Hurwitz J and O'Donnell M (1998) Processivity of DNA polymerases: two mechanisms, one goal. Structure 6: 121–125.

Kornberg A and Baker TA (1992) DNA Replication. New York: WH Freeman.

McHenry CS (1991) DNA polymerase III holoenzyme: Components, structure, and mechanism of a true replicative complex. Journal of Biological Chemistry 266: 19127–19130.

Stillman B (1994) Smart machines at the replication fork. Cell 78: 725–728.

Von Hippel PH, Fairfield FR and Dolejsi MK (1994) On the processivity of polymerases. Annals of the New York Academy of Sciences 726: 118–131.

Wyman C and Botcham M (1995) DNA replication. A familiar ring to DNA polymerase processivity. Current Biology 5: 334–337.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Bloom, Linda B, and Goodman, Myron F(Apr 2001) Polymerase Processivity: Measurement and Mechanisms. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0001052]