Chapter six - AID and Somatic Hypermutation
Introduction
Diversity in antibodies is produced during two stages in B cell development. In pre-B cells, rearrangement of variable (V), diversity (D), and joining (J) gene segments occurs to produce the primary repertoire of immunoglobulin (Ig) receptors. In mature B cells, Ig receptors undergo affinity maturation (AM) and class switch recombination (CSR) to produce the secondary, or memory, repertoire of antibodies. The latter event occurs after antigen binds to the receptor, which initiates a dynamic cascade of cell signaling events to cause cellular activation (Gauld et al., 2002, Kurosaki, 2002, Niiro & Clark, 2002). The result of this activation is the differentiation of B cells into plasma or memory cells, which now express a large repertoire of antibodies to clear a plethora of different foreign antigens.
Diversity in the secondary repertoire is created by modifying rearranged V(D)J sequences and switching heavy chain constant genes (CH). Alteration of the V gene sequence is achieved by either direct mutagenesis or DNA strand breaks during gene conversion (GC), where strand breaks are repaired using different pseudo-V gene segments in a templated recombination mechanism. In either case, cells containing mutations that increase antibody affinity will be selected to divide and further mutate, while mutations that decrease affinity will be lost through apoptosis. Alteration of the CH gene occurs by DNA strand breaks in the switch (S) regions flanking the different CH gene exons. Breaks in two different S regions are then repaired by nonhomologous end joining to remove the intervening introns and exons. This recombination event allows of production of a defined VDJ exon with different CH gene isotypes to regulate antibody function.
A single enzyme is responsible for initiating diversity in V(D)J and CH genes: activation-induced deaminase (AID), which is a cytosine deaminase that enzymatically converts cytosine to uracil. Uracil is mutagenic when paired with guanosine in DNA, since dU mimics dT during replication, and the U:G mismatch triggers error-prone DNA repair in B cells. Thus, AID introduces somatic hypermutation (SHM) by converting dC to dU. In this chapter, the initiating events caused by AID are referred to as SHM, regardless of whether dU is found in the V or S regions. If dU occurs in V(D)J genes, SHM can produce AM or GC. If dU occurs in S regions, SHM can produce CSR. Furthermore, the proteins that process dU, such as UNG, MSH2, MSH6, and DNA polymerases, have the same activity whether dU is located in the V(D)J or S regions. Therefore, SHM, caused by AID-generated dU, underpins the three mechanisms of AM, GC, and CSR.
One key aspect of AID biology is the balance between mutagenic diversity and genomic integrity. When AID functions at non-Ig loci, both mutation and translocations can promote carcinogenesis (Ramiro et al., 2007). Thus, it is imperative to the organism that AID activity will be tightly controlled to inhibit possible oncogenic transformation, while still allowing the production of a wide diversity of antibodies. In this chapter, we highlight the intricate aspects of AID biology and regulation.
Section snippets
AID, The Master Catalyst
The mechanisms of AM, GC, and CSR were significantly advanced by the ground-breaking discovery of AID (Muramatsu et al., 1999) and its subsequent genetic analysis in humans, mice, and chickens (Arakawa et al., 2002, Rada et al., 2002b, Revy et al., 2000). Broader analysis of AID indicates that an intricate network of regulatory mechanisms controls its expression at the levels of gene transcription, mRNA stability, protein localization, protein phosphorylation, and cell signaling.
Global targeting to the Ig loci
The Ig loci are mutated in well-defined regions encoding rearranged V genes on the heavy and light chain loci, and S regions on the heavy chain locus. Sequence analysis has shown that mutation occurs in a 2-kb region around V(D)J genes (Lebecque and Gearhart, 1990) and in a 4–7-kb region around S regions (Xue et al., 2006). Thus, it can be assumed that AID functions on 10− 5 to 10− 6 of the genome at a given time, suggesting that precise levels of regulation target AID to such a small percentage
Deoxyuracil in DNA
Since the first identification of AID, extensive work has been performed in an attempt to elucidate the mechanism of how it promotes genomic mutation. Initial identification of the sequence similarity between AID and APOBEC1 suggested that AID may function as an RNA deaminase (Muramatsu et al., 1999). Honjo et al. (2005) proposed an RNA editing model in which AID binds to an unidentified mRNA partner in the cytoplasm and deaminates C to U. The edited mRNA would then produce a protein, perhaps
Conclusion
Even with the shear girth of information on AID biology, it is still unclear how the cell fully coordinates deamination events with mutagenic repair. As mentioned earlier, the mechanisms of AM, GC, and CSR start with a single protein, yet require extensive cellular coordination to produce the initiating deamination. It has been established that AID is tightly regulated at the levels of transcription, translation, phosphorylation, ubiquitination, cellular localization, protein stability, and
Acknowledgments
This work was supported entirely by the Intramural Research Program of the NIH, National Institute on Aging. We gratefully thank Sebastian Fugmann and Huseyin Saribasak for their insightful comments.
References (203)
- et al.
Nucleotide excision repair in an immunoglobulin variable gene is less efficient than in a housekeeping gene
Mol. Immunol.
(2007) - et al.
Requirement of non-canonical activity of uracil DNA glycosylase for class switch recombination
J. Biol. Chem.
(2007) - et al.
Elements regulating somatic hypermutation of an immunoglobulin kappa gene: Critical role for the intron enhancer/matrix attachment region
Cell
(1994) - et al.
Biochemical analysis of hypermutational targeting by wild type and mutant activation-induced cytidine deaminase
J. Biol. Chem.
(2004) - et al.
Activation-induced cytosine deaminase (AID) is actively exported out of the nucleus but retained by the induction of DNA breaks
J. Biol. Chem.
(2004) - et al.
Interaction between antibody-diversification enzyme AID and spliceosome-associated factor CTNNBL1
Mol. Cell
(2008) - et al.
MicroRNA-155 suppresses activation-induced cytidine deaminase-mediated Myc-Igh translocation
Immunity
(2008) - et al.
Mismatch repair deficiency interferes with the accumulation of mutations in chronically stimulated B cells and not with the hypermutation process
Immunity
(1998) - et al.
Somatic hypermutation in the heavy chain locus correlates with transcription
Immunity
(1998) - et al.
Involvement of the E2A basic helix-loop-helix protein in immunoglobulin heavy chain class switching
Mol. Immunol.
(1996)
RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators
Mol. Cell
Activation-induced deaminase-mediated class switch recombination is blocked by anti-IgM signaling in a phosphatidylinositol 3-kinase-dependent fashion
Mol. Immunol.
Repetitive sequences in class-switch recombination regions of immunoglobulin heavy chain genes
Cell
Immunoglobulin class-switch recombination in mice devoid of any S mu tandem repeat
Blood
A portable hot spot recognition loop transfers sequence preferences from APOBEC family members to activation-induced cytidine deaminase
J. Biol. Chem.
PMS2-deficiency diminishes hypermutation of a lambda1 transgene in young but not older mice
Mol. Immunol.
The mismatch repair protein Msh6 influences the in vivo AID targeting to the Ig locus
Immunity
Chromatin structural analyses of the mouse Igkappa gene locus reveal new hypersensitive sites specifying a transcriptional silencer and enhancer
J. Biol. Chem.
Normal hypermutation in antibody genes from congenic mice defective for DNA polymerase iota
DNA Repair (Amst.)
Reevaluation of the role of DNA polymerase theta in somatic hypermutation of immunoglobulin genes
DNA Repair (Amst).
Absence of DNA polymerase theta results in decreased somatic hypermutation frequency and altered mutation patterns in Ig genes
DNA Repair (Amst.)
Proteasomal degradation restricts the nuclear lifespan of AID
J. Exp. Med.
Requirement of the activation-induced deaminase (AID) gene for immunoglobulin gene conversion
Science
A role for PCNA ubiquitination in immunoglobulin hypermutation
PLoS Biol.
Increased transcription levels induce higher mutation rates in a hypermutating cell line
J. Immunol.
Involvement of Rad18 in somatic hypermutation
Proc. Natl. Acad. Sci. USA
Altered somatic hypermutation and reduced class-switch recombination in exonuclease 1-mutant mice
Nat. Immunol.
The AID antibody diversification enzyme is regulated by protein kinase A phosphorylation
Nature
Uracil DNA glycosylase activity is dispensable for immunoglobulin class switch
Science
Further evidence for involvement of a noncanonical function of uracil DNA glycosylase in class switch recombination
Proc. Natl. Acad. Sci. USA
Cutting edge: DNA polymerases mu and lambda are dispensable for Ig gene hypermutation
J. Immunol.
A cis-acting diversification activator both necessary and sufficient for AID-mediated hypermutation
PLoS Genet.
Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase
Proc. Natl. Acad. Sci. USA
The chicken immunoglobulin lambda light chain gene is transcriptionally controlled by a modularly organized enhancer and an octamer-dependent silencer
Nucleic Acids Res.
Transcriptional pausing and stalling causes multiple clustered mutations by human activation-induced deaminase
FASEB J.
Role of activation-induced deaminase protein kinase A phosphorylation sites in Ig gene conversion and somatic hypermutation
J. Immunol.
Transcription-targeted DNA deamination by the AID antibody diversification enzyme
Nature
Replication protein A interacts with AID to promote deamination of somatic hypermutation targets
Nature
Integrity of the AID serine-38 phosphorylation site is critical for class switch recombination and somatic hypermutation in mice
Proc. Natl. Acad. Sci. USA
Analysis of intergenic transcription and histone modification across the human immunoglobulin heavy-chain locus
Proc. Natl. Acad. Sci. USA
Regulation of AID expression in the immune response
J. Exp. Med.
The mouse IgH 3′-enhancer
Eur. J. Immunol.
DNA sequences mediating class switching in alpha-immunoglobulins
Science
miR-181b negatively regulates activation-induced cytidine deaminase in B cells
J. Exp. Med.
Induction of activation-induced cytidine deaminase gene expression by IL-4 and CD40 ligation is dependent on STAT6 and NFkappaB
Int. Immunol.
Contribution of DNA polymerase eta to immunoglobulin gene hypermutation in the mouse
J. Exp. Med.
DNA polymerase eta is the sole contributor of A/T modifications during immunoglobulin gene hypermutation in the mouse
J. Exp. Med.
Altering the pathway of immunoglobulin hypermutation by inhibiting uracil-DNA glycosylase
Nature
Immunoglobulin gene conversion in chicken DT40 cells largely proceeds through an abasic site intermediate generated by excision of the uracil produced by AID-mediated deoxycytidine deamination
Eur. J. Immunol.
Dependence of antibody gene diversification on uracil excision
J. Exp. Med.
Cited by (162)
DNA flexibility can shape the preferential hypermutation of antibody genes
2024, Trends in ImmunologySomatic mutation patterns at Ig and Non-Ig Loci
2024, DNA RepairThe landscape of somatic mutations in lymphoblastoid cell lines
2023, Cell GenomicsA novel activation-induced cytidine deaminase mutation in an adult with hyper-immunoglobulin M syndrome
2021, Annals of Allergy, Asthma and ImmunologyPanorama of stepwise involvement of the IgH 3′ regulatory region in murine B cells
2021, Advances in Immunology