Biology:Activation-induced cytidine deaminase

Short description: Enzyme that creates mutations in DNA

Generic protein structure example

Activation-induced cytidine deaminase, also known as AICDA, AID and single-stranded DNA cytosine deaminase, is a 24 kDa enzyme which in humans is encoded by the AICDA gene. It creates mutations in DNA by deamination of cytosine base, which turns it into uracil (which is recognized as a thymine). In other words, it changes a C:G base pair into a U:G mismatch. The cell's DNA replication machinery recognizes the U as a T, and hence C:G is converted to a T:A base pair. During germinal center development of B lymphocytes, error-prone DNA repair following AID action also generates other types of mutations, such as C:G to A:T. AID is a member of the APOBEC family.

In B cells in the lymph nodes, AID causes mutations that produce antibody diversity, but that same mutation process leads to B cell lymphoma.

Function

This gene encodes a DNA-editing deaminase that is a member of the cytidine deaminase family. The protein is involved in somatic hypermutation, gene conversion, and class-switch recombination of immunoglobulin genes in B cells of the immune system.

AID is currently thought to be the master regulator of secondary antibody diversification. It is involved in the initiation of three separate immunoglobulin (Ig) diversification processes:

1. Somatic hypermutation (SHM), in which the antibody genes are minimally mutated to generate a library of antibody variants, some of which with higher affinity for a particular antigen than any of its close variants
2. Class switch recombination (CSR), in which B cells change their expression from IgM to IgG or other immune types
3. Gene conversion (GC) a process that causes mutations in antibody genes of chickens, pigs and some other vertebrates.

AID has been shown in vitro to be active on single-strand DNA, and has been shown to require active transcription in order to exert its deaminating activity. The involvement of Cis-regulatory factors is suspected as AID activity is several orders of magnitude higher in the immunoglobulin "variable" region than other regions of the genome that are known to be subject to AID activity. This is also true of artificial reporter constructs and transgenes that have been integrated into the genome. A recent publication suggests that high AID activity at a few non-immunoglobulin targets is achieved when transcription on opposite DNA strands converges due to super-enhancer activity.

Recently, AICDA has been implicated in active DNA demethylation. AICDA can deaminate 5-methylcytosine, which can then be replaced with cytosine by base excision repair.

Mechanism

AID is believed to initiate SHM in a multi-step mechanism. AID deaminates cytosine in the target DNA. Cytosines located within hotspot motifs are preferentially deaminated (WRCY motifs W=adenine or thymine, R=purine, C=cytosine, Y=pyrimidine, or the inverse RGYW G=guanine). The resultant U:G (U= uracil) mismatch is then subject to one of a number of fates.

1. The U:G mismatch is replicated across creating two daughter species, one that remains unmutated and one that undergoes a C => T transition mutation. (U is analogous to T in DNA and is treated as such when replicated).
2. The uracil may be excised by uracil-DNA glycosylase (UNG), resulting in an abasic site. This abasic site (or AP, apurinic/apyrimidinic) may be copied by a translesion synthesis DNA polymerase such as DNA polymerase eta, resulting in random incorporation of any of the four nucleotides, i.e. A, G, C, or T. Also, this abasic site may be cleaved by apurinic endonuclease (APE), creating a break in the deoxyribose phosphate backbone. This break can then lead to normal DNA repair, or, if two such breaks occur, one on either strand a staggered double-strand break can be formed (DSB). It is thought that the formation of these DSBs in either the switch regions or the Ig variable region can lead to CSR or GC, respectively.
3. The U:G mismatch may also be recognized by the DNA mismatch repair (MMR) machinery, to be specific by the MutSα(alpha) complex. MutSα is a heterodimer consisting of MSH2 and MSH6. This heterodimer is able to recognize mostly single-base distortions in the DNA backbone, consistent with U:G DNA mismatches. The recognition of U:G mistmatches by the MMR proteins is thought to lead to processing of the DNA through exonucleolytic activity to expose a single-strand region of DNA, followed by error prone DNA polymerase activity to fill in the gap. These error-prone polymerases are thought to introduce additional mutations randomly across the DNA gap. This allows the generation of mutations at AT base pairs.

The level of AID activity in B cells is tightly controlled by modulating AID expression. AID is induced by transcription factors TCF3 (E47), HoxC4, Irf8 and Pax5, and inhibited by PRDM1 (Blimp1) and Id2. At the post-transcriptional level of regulation, AID expression is silenced by mir-155, a small non-coding microRNA controlled by IL-10 cytokine B cell signalling.

Clinical significance

Defects in this gene are associated with Hyper-IgM syndrome type 2. In certain haematological malignancies such as follicular lymphoma persistent AID expression has been linked to lymphomagenesis.

Further reading

• "Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business". Trends Genet. 19 (4): 207–16. 2003. doi:10.1016/S0168-9525(03)00054-4. PMID 12683974. 
• "First AID (activation-induced cytidine deaminase) is needed to produce high affinity isotype-switched antibodies". J. Biol. Chem. 281 (25): 16833–6. 2006. doi:10.1074/jbc.R600006200. PMID 16624806. 
• "Isolation, tissue distribution, and chromosomal localization of the human activation-induced cytidine deaminase (AID) gene". Genomics 68 (1): 85–8. 2001. doi:10.1006/geno.2000.6268. PMID 10950930. 
• "Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hyper-IgM syndrome (HIGM2)". Cell 102 (5): 565–75. 2000. doi:10.1016/S0092-8674(00)00079-9. PMID 11007475. 
• "DNA cloning using in vitro site-specific recombination". Genome Res. 10 (11): 1788–95. 2001. doi:10.1101/gr.143000. PMID 11076863. 
• "Mutations in activation-induced cytidine deaminase in patients with hyper IgM syndrome". Clin. Immunol. 97 (3): 203–10. 2001. doi:10.1006/clim.2000.4956. PMID 11112359. 
• "Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing". EMBO Reports 1 (3): 287–92. 2001. doi:10.1093/embo-reports/kvd058. PMID 11256614. 
• "Association between a new polymorphism in the activation-induced cytidine deaminase gene and atopic asthma and the regulation of total serum IgE levels". The Journal of Allergy and Clinical Immunology 108 (3): 382–6. 2001. doi:10.1067/mai.2001.117456. PMID 11544457. 
• "Activation-induced cytidine deaminase turns on somatic hypermutation in hybridomas". Nature 415 (6873): 802–6. 2002. doi:10.1038/nature714. PMID 11823785. 
• "AID-GFP chimeric protein increases hypermutation of Ig genes with no evidence of nuclear localization". Proceedings of the National Academy of Sciences of the United States of America 99 (10): 7003–8. 2002. doi:10.1073/pnas.092160999. PMID 12011459. Bibcode: 2002PNAS...99.7003R. 
• "AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification". Nature 418 (6893): 99–103. 2002. doi:10.1038/nature00862. PMID 12097915. Bibcode: 2002Natur.418...99P. 
• "Internal IgH class switch region deletions are position-independent and enhanced by AID expression". Proceedings of the National Academy of Sciences of the United States of America 99 (15): 9984–9. 2002. doi:10.1073/pnas.152333499. PMID 12114543. Bibcode: 2002PNAS...99.9984D. 
• "Somatic hypermutation of the AID transgene in B and non-B cells". Proceedings of the National Academy of Sciences of the United States of America 99 (19): 12304–8. 2002. doi:10.1073/pnas.192442899. PMID 12202747. Bibcode: 2002PNAS...9912304M. 
• "Expression of activation-induced cytidine deaminase in human B-cell non-Hodgkin lymphomas". Blood 101 (9): 3574–80. 2003. doi:10.1182/blood-2002-08-2424. PMID 12511417. 
• "Chronic lymphocytic leukemia B cells expressing AID display dissociation between class switch recombination and somatic hypermutation". Blood 101 (10): 4029–32. 2003. doi:10.1182/blood-2002-10-3175. PMID 12521993. 
• "Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase". Proceedings of the National Academy of Sciences of the United States of America 100 (7): 4102–7. 2003. doi:10.1073/pnas.0730835100. PMID 12651944. Bibcode: 2003PNAS..100.4102B. 
• "Type two hyper-IgM syndrome caused by mutation in activation-induced cytidine deaminase". J. Med. Dent. Sci. 50 (1): 41–6. 2003. PMID 12715918. 
• "Human activation-induced cytidine deaminase causes transcription-dependent, strand-biased C to U deaminations". Nucleic Acids Res. 31 (12): 2990–4. 2003. doi:10.1093/nar/gkg464. PMID 12799424. 

External links

• AICDA+protein at the US National Library of Medicine Medical Subject Headings (MeSH)
• Human AICDA genome location and AICDA gene details page in the UCSC Genome Browser.