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  • Review Article
  • Published:

DNA polymerases in adaptive immunity

Nature Reviews Immunology volume 8, pages 302–312 (2008)Cite this article

Key Points

  • Multiple molecular events take place during the life of a B cell, first when the B-cell receptor (BCR) is assembled in the bone marrow during the generation of the pre-immune repertoire and later during an immune response in secondary lymphoid organs through the process of affinity maturation (known as somatic hypermutation, SHM) and isotype switching. Specific DNA polymerases are involved at each of these molecular steps.

  • Mammals have 15 DNA polymerases (including terminal deoxynucleotidyl transferase). Four are involved in semi-conservative replication and 11 are involved in different tasks, such as the removal of damaged bases (Polβ), the rejoining of DNA ends during non-homologous end joining (NHEJ) (Polλ and Polμ) and the bypass of DNA lesions that block the replication fork (Y family polymerases and Polζ).

  • The assembly of the immunoglobulin receptor involves the joining of immunoglobulin coding regions that are distantly located in the genome. These coding ends are subject to several enzymatic activities that include nucleotide trimming and template-dependent and -independent DNA synthesis. A large diversity is thus created at the sites of the exon junctions, by varying the length of the complementarity-determining region 3 (CDR3). Polλ and Polμ participate in these processes, being involved during the recombination of the heavy- and light-chain loci, respectively.

  • During SHM, mostly point mutations are introduced in the variable heavy- and light-chain genes of the BCR presented by B cells engaged in an immune response. The mechanism is initiated by the deamination of cytidines into uracils through the action of activation-induced cytidine deaminase (AID). Thereafter, these U-G mismatches are recognized by two different repair pathways, mediated by either uracil glycosylase (UNG) or the mismatch recognition complex, MSH2–MSH6. Two DNA polymerases have been shown unequivocally to be recruited during these error-prone repair processes: Polη, which generates all mutations at A/T bases during the normal physiological SHM process, and Rev1, which contributes some of the G/C mutation transversion mutations.

  • A model for SHM is proposed that attempts to include all the data collected from various mouse and human experimental settings. In this model, the two repair pathways involved in SHM appear to function outside of their normal roles in the base-excision repair or mismatch repair processes, and to compete rather than collaborate once the U-G mismatches have been generated by AID.

Abstract

To cope with an unpredictable variety of potential pathogenic insults, the immune system must generate an enormous diversity of recognition structures, and it does so by making stepwise modifications at key genetic loci in each lymphoid cell. These modifications proceed through the action of lymphoid-specific proteins acting together with the general DNA-repair machinery of the cell. Strikingly, these general mechanisms are usually diverted from their normal functions, being used in rather atypical ways in order to privilege diversity over accuracy. In this Review, we focus on the contribution of a set of DNA polymerases discovered in the past decade to these unique DNA transactions.

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Figure 1: DNA transactions during the formation of the B-cell repertoire.
Figure 2: Junctional diversification during V(D)J recombination at the immunoglobulin locus.
Figure 3: Possible roles of DNA polymerases at V(D)J junctions.
Figure 4: The C over G targeting bias mediated by AID is equalized by the mismatch repair pathway.
Figure 5: Two competitive pathways for hypermutation: the MSH2–MSH6 complex prevents uracil-DNA glycosylase (UNG) from performing error-free repair.

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Acknowledgements

We thank our colleagues at INSERM U783 for contributing to this Review by many discussions and for sharing unpublished data. We apologize to those whose work could not be cited because of space limitations.

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  1. Institut National de la Santé et de la Recherche Médicale (INSERM) U783, Développement du système immunitaire, Faculté de Médecine, Université Paris Descartes, Site Necker–Enfants Malades, 156 rue de Vaugirard, 75730, Paris Cedex 15, France

    Jean-Claude Weill & Claude-Agnès Reynaud

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  1. Jean-Claude Weill
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Glossary

B-cell receptor

(BCR). A term used to refer to the immunoglobulin molecule present at the B-cell surface, irrespective of its heavy chain isotype.

V(D)J recombination

Somatic rearrangement of variable (V), diversity (D) and joining (J) regions of the genes that encode antigen receptors, leading to repertoire diversity of both T-cell and B-cell receptors.

Somatic hypermutation

(SHM). A process by which antigen-activated B cells in germinal centres acquire point mutations targeted to the variable regions of rearranged immunoglobulin gene segments. The B cells are subsequently selected for those expressing the 'best' mutations on the basis of the ability of the surface immunoglobulin to bind antigen. This process occurs in activated B cells in all jawed vertebrates, but it also occurs in immature B cells in sheep to generate the pre-immune repertoire.

Class-switch recombination

(CSR). Also known as class or isotype switching, this term refers to a region-specific recombination process that occurs in antigen-activated B cells. Recombination takes place between 'switch region' DNA sequences located upstream from each immunoglobulin heavy-chain constant region genes and results in a change from the IgM to one of the IgG, IgA or IgE isotypes. This imparts flexibility to the humoral immune response and allows it to exploit the different capacities of the immunoglobulins to activate the appropriate downstream effector mechanisms.

Gene conversion

A non-reciprocal homologous recombination event in which the donor gene(s) remains unmodified and an acceptor gene acquires the recombined segment. In chickens, variable (V) pseudogenes are donors that modify the functional, rearranged V gene in follicles of the bursa of Fabricius to generate a diverse pre-immune repertoire.

Base-excision repair

A DNA-repair pathway that removes single non-canonical bases from the DNA, such as deaminated or oxidized bases, and replaces them with an appropriate base templated on the opposite DNA strand. Repair is initiated by a DNA glycosylase that is specialized for a particular type of damage, and nucleotide replacement is performed by DNA polymerase β.

Non-homologous end joining

(NHEJ). A process that joins broken DNA ends independently of extended base homology. Components of this pathway include the proteins Ku70, Ku80, Artemis, X-ray repair cross-complementing protein 4 (XRCC4), DNA ligase IV, Cernunnos (also known as XLF) and the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs).

Replication fork

The site in double-stranded DNA at which the template strands are separated, allowing a newly formed copy of the DNA to be synthesized, with the fork moving in the direction of leading strand synthesis.

Translesion DNA synthesis

(TLS). A process that allows the bypass of DNA damage that otherwise blocks the progression of the replication fork, through the replacement of the replicative polymerase with specialized polymerases (known as TLS polymerases) that can copy non-instructive DNA lesions. TLS polymerases have low fidelity on undamaged templates. Most TLS polymerases belong to the Y family polymerases.

Recombination-activating genes

(RAG1 and RAG2). RAG1 and RAG2 are involved in creating the synapsis and the double-strand DNA breaks required for the assembly of the dispersed gene segments that encode the complete protein chains of B-cell and T-cell receptors.

Synapsis

Non-covalent juxtaposition of two non-adjacent stretches of DNA.

Recombination signal sequences

(RSSs). Conserved elements that constitute recognition sites for the V(D)J recombinase proteins that are encoded by recombination-activating gene 1 (RAG1) and RAG2. They consist of a palindromic heptamer that is immediately adjacent to the coding gene segments — V (variable), D (diversity) or J (joining) — and is separated by a 12- or 23-base-pair spacer from a conserved nonamer sequence.

Complementarity-determining regions

(CDRs). The three hypervariable antigen-receptor regions (in both chains of the T-cell and B-cell receptors) that interact with the antigen. The third CDR (CDR3) is partly encoded by the germline variable (V), diversity (D) and joining (J) regions of each receptor chain. Extensive diversity is generated in CDR3 during gene rearrangement by nucleotide trimming and/or template-independent nucleotide additions by terminal deoxynucleotidyl transferase.

Deamination

Removal of an amine group from a pyrimidine or purine nucleic-acid base. Deamination of cytosine and adenosine yields uracil and inosine, respectively.

Mismatch repair

A repair pathway that recognizes mismatched bases that arise in DNA because of errors made by replicative DNA polymerases. These are then repaired by an excision system that removes a tract of DNA including the mismatch, and re-copies the original strand. The mismatch repair complex includes a mismatch-binding moiety (such as MSH2–MSH6), and an effector part (such as MLH1–PMS2) that triggers excision of the mismatch-containing DNA sequence.

Abasic site

A common form of DNA damage in which a base is lost from a strand of DNA, spontaneously or by the action of DNA repair enzymes, such as uracil glycosylase, while leaving the phosphodiester bond intact.

Xeroderma pigmentosum

(XP). A rare inherited human disorder, in which patients are sensitive to the DNA-damaging effects of sunlight. XP can be caused by disabling any of eight different genes. Seven of the genes, denoted XPA–XPG, encode components of the nucleotide excision-repair pathway. A variant form of the syndrome, XPV, corresponds to the inactivation of the gene encoding DNA polymerase η.

Transition mutations

Base changes in DNA in which a pyrimidine (C or T) is replaced by another pyrimidine, or a purine (A or G) is replaced by another purine.

Hotspot motif

A short DNA motif (DGYW or WRCH; where D denotes adenosine (A), guanosine (G) or thymidine (T); Y denotes cytidine (C) or T; W denotes A or T; R denotes A or G; and H denotes T, C or A) at which mutations are preferentially targeted during somatic hypermutation.

Transversion mutations

Base changes in DNA in which a pyrimidine (C or T) is replaced by a purine (A or G), or a purine is replaced by a pyrimidine.

Proliferating cell nuclear antigen

(PCNA). PCNA was first identified as a DNA sliding clamp for replicative polymerases, but is now known to coordinate the organization of protein partners that are involved in many processes, including DNA replication, DNA repair and cell-cycle control.

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Weill, JC., Reynaud, CA. DNA polymerases in adaptive immunity. Nat Rev Immunol 8, 302–312 (2008). https://doi.org/10.1038/nri2281

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