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  • Review Article
  • Published:

The 3′–5′ exonucleases

Nature Reviews Molecular Cell Biology volume 3, pages 364–376 (2002)Cite this article

Key Points

  • This review summarizes the 3′–5′ exonucleases and their possible roles in DNA-synthetic events.

  • DNA polymerases are required to maintain the integrity of the genome during processes such as DNA replication, DNA repair, translesion DNA synthesis, DNA recombination, cell-cycle control and DNA-damage-checkpoint function.

  • An associated 3′–5′ exonuclease activity allows a polymerase to remove misincorporated nucleotides, and ensures the high-fidelity DNA synthesis that is required for faithful replication.

  • Proofreading 3′–5′ exonucleases can be divided into intrinsic, polymerase-associated enzymes, or independent autonomous enzymes. Polymerase-associated enzymes include Escherichia coli pol I, bacteriophage polymerases, and eukaryotic pols δ, ɛ and γ. Autonomous exonucleases include the mammalian TREX1 and TREX2 enzymes.

  • As well as the proofreading 3′–5′ exonucleases, several new exonucleases have recently been discovered. These include the Werner syndrome (WRN) protein; p53; MRE11 (which is involved in double-strand break repair); two checkpoint proteins, RAD1 and RAD9; APE1 (involved in base-excision repair); and the VDJP protein, which acts in V(D)J recombination.

Abstract

Over the past few years, several new 3′–5′ exonucleases have been identified. In vitro studies of these enzymes have uncovered much about their potential functions in vivo, and certain organisms with a defect in 3′–5′ exonucleases have an increased susceptibility to cancer, especially under conditions of stress. Here, we look at not only the newly discovered enzymes, but also at the roles of other 3′–5′ exonucleases in the quality control of DNA synthesis, where they act as proofreading exonucleases for DNA polymerases during DNA replication, repair and recombination.

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Figure 1: Structure of a DNA polymerase polypeptide that contains a 3′–5′ proofreading exonuclease.
Figure 2: Functional domains of selected 3′–5′ exonucleases.
Figure 3: Intra- and intermolecular proofreading.
Figure 4: Architecture of the replicative DNA polymerase III holoenzyme from E. coli.

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Acknowledgements

We thank V. Kalinin, V. Krutyakov, G. Villani, C. Bieri and U. Sheveleva for their critical reading of the manuscript; Ursi Hübscher, R. Hobi, P. Schrafll and N. Pirogova for their assistance with graphics; T. Steitz for permission to reproduce Figure 1; and K. Ramadan for his assistance on the manuscript. The work carried out in the authors' laboratories was supported by the Swiss National Science Foundation, the European Union TMR grant, the Kanton of Zürich and the Russian Foundation for Basic Research. We apologize to those researchers whose work could not be cited directly because of the strict limit on the number of references.

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Authors and Affiliations

  1. Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich–Irchel, Winterthurerstrasse 190, Zürich, CH-8057, Switzerland

    Igor V. Shevelev & Ulrich Hübscher

  2. Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Leningrad district, Gatchina, 188300, Russia

    Igor V. Shevelev

Authors
  1. Igor V. Shevelev
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  2. Ulrich Hübscher
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Correspondence to Ulrich Hübscher.

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Related links

DATABASES

Interpro

3′–5′ proofreading exonuclease domain

LocusLink

pol α

pol β

pol δ

pol ɛ

pol γ

RAD1

RAD9

<i>Saccharomyces</i> Genome Database

Cdc6

Cdc7

Dbf4

Swiss-Prot

APE1

dnaE

dnaQ

DNA ligase I

FEN-1

holE

E. coli pol I

Exo I

Exo IX

Exo X

HUS1

Ku70

Ku80

large subunit of RF-C

Mre11

NBS1

p53

PCNA

RAD1

RAD9

rad17

Rad50

rec1

RNaseT

RP-A

topoisomerase I

TREX1

TREX2

WRN

Xrs2

Glossary

TRANSLESION DNA SYNTHESIS

DNA synthesis on a DNA molecule that contains altered or missing bases.

MISMATCH REPAIR

This repair process recognizes incorrectly paired bases after DNA replication has occurred. The mismatch repair complex can distinguish between the old and newly synthesized DNA strands.

PRIMASE

A special type of RNA polymerase that can synthesize an RNA primer of ten nucleotides, which is subsequently elongated by a DNA polymerase (such as DNA polymerase α in eukaryotes).

OKAZAKI FRAGMENTS

Short pieces of DNA that are synthesized on the lagging strand at the replication fork.

PROCESSIVE DNA SYNTHESIS

A processive DNA polymerase can synthesize from a few to several thousand nucleotides per binding event to DNA.

DISTRIBUTIVE DNA SYNTHESIS

A distributive DNA polymerase can synthesize only one nucleotide per binding event to DNA.

DNA POLYMERASE (POL) HOLOENZYME

A replicative DNA polymerase complex that consists of a DNA polymerase and several auxiliary proteins (for example, pol δ, proliferating cell nuclear antigen and replication factor-C).

ERROR CATASTROPHE

When mutations accumulate during the lifespan of a cell or organism, there is a point at which the mutations have accumulated to such an extent that the entire system breaks down.

SPONTANEOUS MUTATION FREQUENCY

Mutations that occur in a genome without an obvious influence from the environment (for example, oxidative damage).

ARANUCLEOTIDES

A class of chemical compounds that are analogous to dNTPs, but with an arabinose sugar instead of a deoxyribose (for example, cytosine arabinoside triphosphate). These compounds are widely used in anticancer and antiviral therapies.

ERROR-PRONE CONDITIONS

Conditions in a cell that tend to lead to errors in DNA replication (for example, an imbalance of substrate dNTPs).

ERROR-FREE CONDITIONS

Conditions in a cell that permit DNA replication to occur with a low frequency of errors.

BASE-EXCISION REPAIR

An essential repair mechanism that removes damaged bases from the DNA. The remaining abasic site is recognized by an apurinic/apyrimidinic endonuclease. The gap is then filled by DNA polymerase and sealed by DNA ligase.

KU70/80

An enzyme that is an essential part of the complex that is responsible for non-homologous end joining.

V(D)J RECOMBINATION

The site-specific recombination of immunoglobulin coding regions from multiple copies in the germ line to just one variable (V), one diversity (D) and one joining (J) region in the process of forming a functional immunoglobulin gene in B cells.

CAMPTOTHECIN

A specific inhibitor of DNA topoisomerase I, an enzyme that is responsible for the topology of DNA during replication. DNA topoisomerase I cuts DNA at one strand and subsequently reseals the nick. Camptothecin inhibits DNA topoisomerase I by freezing the enzyme at the nick, and this results in a replication defect.

SECONDARY STRUCTURE

The double helix can form secondary structures when, for instance, palindromic sequences occur. Such structures include stem–loops or 'cloverleafs'.

NON-HOMOLOGOUS END JOINING

A recombination event that allows DNA to be rejoined after double-strand breaks have occurred. This rejoining process does not require homologous DNA sequences.

HETEROLOGOUS DNA

A DNA molecule that has no homology to an existing one.

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Shevelev, I., Hübscher, U. The 3′–5′ exonucleases. Nat Rev Mol Cell Biol 3, 364–376 (2002). https://doi.org/10.1038/nrm804

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