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Y-family DNA polymerases and their role in tolerance of cellular DNA damage

Nature Reviews Molecular Cell Biology volume 13, pages 141–152 (2012)Cite this article

Subjects

Key Points

  • Replication past DNA damage by translesion synthesis (TLS) requires specialized DNA polymerases, most of which belong to the Y-family. They have open structures that can accommodate damaged bases in their active sites and are conserved in all organisms.

  • Y-family members have specialized features enabling them to synthesize DNA past specific lesions. As an example, the main ultraviolet light photoproduct is constrained by DNA polymerase η (Pol η) in a molecular splint, such that base pairing is maintained despite the distortion caused by the lesion.

  • As these polymerases have a low fidelity on undamaged DNA, they are regulated at several different levels. In Escherichia coli, their concentration is under the control of the SOS response — low in undamaged cells but induced by damage.

  • In vertebrate cells, they are concentrated in replication factories in S phase, especially following DNA damage, but are also specifically regulated at stalled forks within these factories. The sliding clamp accessory protein PCNA (proliferating cell nuclear antigen) is a key regulator, and all family members have PCNA-binding motifs.

  • When the replication fork is stalled at damage, PCNA is ubiquitylated. This increases the affinity of the polymerases for PCNA by virtue of the ubiquitin-binding motifs present in all of the Y-family polymerases.

  • Under most circumstances, REV1 has a non-catalytic role and acts as a scaffold by virtue of a carboxy-terminal sequence that binds the other Y-family polymerases. Ubiquitylation of PCNA is required for carrying out TLS across gaps behind the replication forks, whereas REV1 is involved in directing TLS at the stalled forks.

Abstract

The past 15 years have seen an explosion in our understanding of how cells replicate damaged DNA and how this can lead to mutagenesis. The Y-family DNA polymerases lie at the heart of this process, which is commonly known as translesion synthesis. This family of polymerases has unique features that enable them to synthesize DNA past damaged bases. However, as they exhibit low fidelity when copying undamaged DNA, it is essential that they are only called into play when they are absolutely required. Several layers of regulation ensure that this is achieved.

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Figure 1: The basic mechanism of translesion synthesis.
Figure 2: Structures of the Y-family DNA polymerases.
Figure 3: Evolutionarily conserved roles of DNA polymerases in translesion synthesis.
Figure 4: Domains of the Y-family polymerases.
Figure 5: Different levels of regulation of the Y-family polymerases.
Figure 6: Non-canonical roles of Y-family polymerases.

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Acknowledgements

We thank A. Vaisman (US National Institute of Child Health and Human Development (NICHD)/US National Institutes of Health (NIH)) for help in generating figure 2. J.E.S. is funded by the Medical Research Council, Association for International Cancer Research and The Fanconi Anaemia Research Fund; A.R.L. is funded by a Medical Research Council programme grant; and R.W. is funded by the NICHD/NIH Intramural Research Program.

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Authors and Affiliations

  1. Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Hills Road, CB2 0QH, Cambridge, UK

    Julian E. Sale

  2. Genome Damage and Stability Centre, University of Sussex, Falmer, BN1 9RQ, Brighton, UK

    Alan R. Lehmann

  3. Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, 20892-3371, Maryland, USA

    Roger Woodgate

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  1. Julian E. Sale
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SUPPLEMENTARY INFORMATION

S1 (box)

Glossary

Damage tolerance

A general term for mechanisms that allow the replication machinery to complete replication despite the presence of DNA damage and without removing the damage.

Replication fork

The point on a replicating DNA molecule where replication is actually taking place and one parental strand generates two daughter strands in a Y-like structure.

Variant form of xeroderma pigmentosum

(XPV). An autosomal recessive disorder that is characterized by increased sensitivity to sunlight and risk of skin cancer, which is due to mutations in DNA polymerase-ɛ.

dCMP transferase

An enzyme activity that adds dCMP onto the end of a growing DNA chain without the need for a template.

B-family polymerase

On the basis of phylogenetic relationships, DNA polymerases (Pols) can be classified into different families. B-family polymerases include Escherichia coli Pol II and eukaryotic Pol α, Pol δ, Pol ɛ and Pol ζ.

Cyclobutane pyrimidine dimer

(CPD). The most common ultraviolet light photoproduct, in which two adjacent pyrimidines are joined together by a cyclobutane ring between their 5 and 6 positions. T-T dimers are the most abundant CPDs, although C-T, T-C and C-C dimers are also possible. Several isomers of a CPD can exist. The most common isomer is a cis-syn CPD.

Processivity

The ability of a polymerase to extend a growing DNA chain before it dissociates.

Non-DNA carbon chain

This simply refers to the replacement of a stretch of DNA with a saturated aliphatic chain. It is, of course, not something that is found in vivo, but the ability of translesion synthesis polymerases to bypass such a structure illustrates their broad adaptability when dealing with problematic regions of the genome.

Abasic site

A site in DNA where the base has been lost by hydrolysis of the base–sugar (glycosidic) bond.

B-form

The most common form of the DNA double helix in aqueous environments. In this form, the bases are perpendicular to the axis of the helix.

Syn conformation

Nucleotides can exist in two conformations, anti or syn, depending upon rotation of the base around the glycosidic bond. In order for normal base pairing to occur in DNA, the nucleotide is usually in the anti conformation.

DT40 cells

A B cell line derived from an avian leukosis virus-induced bursal lymphoma in a white leghorn chicken.

SOS response

Following DNA damage to Escherichia coli, and a few related species of bacteria, 40–50 genes are induced, including several DNA repair proteins. This is known as the SOS response.

Replication factories

The clustering of replication and repair proteins into discrete subnuclear foci, which are visible under the light microscope, suggests that multiple replication forks can group together in what has been termed a replication factory.

PCNA

(Proliferating cell nuclear antigen). The trimeric sliding clamp that tethers DNA polymerases and other factors to DNA in a sequence-independent manner, such that they can readily translocate up and down the duplex DNA. The prokaryotic version, which is almost structurally identical, is a dimeric complex called the β-clamp.

Ubiquitin

A 76-amino-acid peptide that can be conjugated to proteins either singly (mono-ubiquitylation) or in a variety of chains (poly-ubiquitylation). It tags proteins for degradation but is now known to also control cell physiology principally through modulating protein–protein interactions.

SUMO

(Small ubiquitin-like modifier). A post-translation modification related to ubiquitin. Like ubiquitylation, SUMOylation can alter interactions with other proteins.

E3 ubiquitin ligase

An enzyme that catalyses the transfer of ubiquitin from the E2 ubiquitin-conjugating enzyme to the target protein.

E2 ubiquitin-conjugating enzyme

A class of enzymes responsible, in conjunction with an E3 ubiquitin ligase, for attaching ubiquitin to target proteins. Ubiquitin, after activation, is transferred to an E2 ubiquitin-conjugating enzyme, which then interacts with an E3 ubiquitin ligase to effect ubiquitin transfer to the target protein.

RPA

(Replication protein A). Eukaryotic protein that binds specifically to single-stranded DNA.

Activation-induced deaminase

(AID). An enzyme that hydrolytically deaminates cytosines in nucleic acids, resulting in the substitution of cytosines with uracils.

Uracil DNA glycosylase

(UNG). An enzyme that disrupts the glycosidic bond between uracil in DNA and the deoxyribose sugar, generating free uracil and an abasic site in the DNA.

G quadruplex

A class of DNA secondary structure formed in regions of G-rich DNA of the general sequence G3–5-L1–7-G3–5-L1–7-G3–5-L1–7-G3–5 (where L can be any base). The structures are characterized by stacks of planar arrays of four Hoogsteen-bonded dG bases coordinated by a monovalent metal ion.

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Sale, J., Lehmann, A. & Woodgate, R. Y-family DNA polymerases and their role in tolerance of cellular DNA damage. Nat Rev Mol Cell Biol 13, 141–152 (2012). https://doi.org/10.1038/nrm3289

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