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Activation-induced cytidine deaminase

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AICDA
Available structures
PDBOrtholog search: PDBe RCSB
Identifiers
AliasesAICDA, AID, ARP2, CDA2, HEL-S-284, HIGM2, activation-induced cytidine deaminase, activation induced cytidine deaminase
External IDsOMIM: 605257; MGI: 1342279; HomoloGene: 7623; GeneCards: AICDA; OMA:AICDA - orthologs
Orthologs
SpeciesHumanMouse
Entrez

57379

11628

Ensembl

ENSG00000111732

ENSMUSG00000040627

UniProt

Q9GZX7

Q9WVE0

RefSeq (mRNA)

NM_020661
NM_001330343

NM_009645

RefSeq (protein)

NP_001317272
NP_065712

NP_033775

Location (UCSC)Chr 12: 8.6 – 8.61 MbChr 6: 122.53 – 122.54 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

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.[5] It creates mutations in DNA[6][7] 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 can also lead to B cell lymphoma.[8]

Function

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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.[5][9]

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,[10] and has been shown to require active transcription in order to exert its deaminating activity.[11][12][13] 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.[14]

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.[15]

Mechanism

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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.[16]

  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.[17] At the post-transcriptional level of regulation, AID expression is silenced by mir-155, a small non-coding microRNA[18][19] controlled by IL-10 cytokine B cell signalling.[20]

Clinical significance

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Defects in this gene are associated with Hyper-IgM syndrome type 2.[21] In certain haematological malignancies such as follicular lymphoma persistent AID expression has been linked to lymphomagenesis.[22]

References

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  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000111732 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000040627 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ a b "Entrez Gene: AICDA activation-induced cytidine deaminase".
  6. ^ Petersen-Mahrt, Svend K.; Harris, Reuben S.; Neuberger, Michael S. (2002-07-04). "AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification". Nature. 418 (6893): 99–103. Bibcode:2002Natur.418...99P. doi:10.1038/nature00862. ISSN 0028-0836. PMID 12097915. S2CID 4388160.
  7. ^ "Q9GZX7 (AICDA_HUMAN)". Retrieved 26 January 2013.
  8. ^ Lenz G, Staudt LM (2010). "Aggressive Lymphomas". N Engl J Med. 362 (15): 1417–29. doi:10.1056/NEJMra0807082. PMC 7316377. PMID 20393178.
  9. ^ Sheppard EC, Morrish RB, Dillon MJ, Leyland R, Chahwan R (2018). "Epigenomic Modifications Mediating Antibody Maturation". Frontiers in Immunology. 9: 355–372. doi:10.3389/fimmu.2018.00355. PMC 5834911. PMID 29535729.
  10. ^ Bransteitter R, Pham P, Scharff MD, Goodman MF (Apr 1, 2003). "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. Bibcode:2003PNAS..100.4102B. doi:10.1073/pnas.0730835100. PMC 153055. PMID 12651944.
  11. ^ Chaudhuri J, Tian M, Khuong C, Chua K, Pinaud E, Alt FW (Apr 17, 2003). "Transcription-targeted DNA deamination by the AID antibody diversification enzyme". Nature. 422 (6933): 726–30. Bibcode:2003Natur.422..726C. doi:10.1038/nature01574. PMID 12692563. S2CID 771802.
  12. ^ Sohail A, Klapacz J, Samaranayake M, Ullah A, Bhagwat AS (Jun 15, 2003). "Human activation-induced cytidine deaminase causes transcription-dependent, strand-biased C to U deaminations". Nucleic Acids Research. 31 (12): 2990–4. doi:10.1093/nar/gkg464. PMC 162340. PMID 12799424.
  13. ^ Ramiro AR, Stavropoulos P, Jankovic M, Nussenzweig MC (May 2003). "Transcription enhances AID-mediated cytidine deamination by exposing single-stranded DNA on the nontemplate strand". Nature Immunology. 4 (5): 452–6. doi:10.1038/ni920. PMID 12692548. S2CID 11431823.
  14. ^ Meng FL, Du Z, Federation A, Hu J, Wang Q, Kieffer-Kwon KR, Meyers RM, Amor C, Wasserman CR, Neuberg D, Casellas R, Nussenzweig MC, Bradner JE, Liu XS, Alt FW (2014). "Convergent Transcription at Intragenic Super-Enhancers Targets AID-Initiated Genomic Instability". Cell. 159 (7): 1538–48. doi:10.1016/j.cell.2014.11.014. PMC 4322776. PMID 25483776.
  15. ^ Morgan HD, Dean W, Coker HA, Reik W, Petersen-Mahrt SK (2004). "Activation-induced Cytidine Deaminase Deaminates 5-Methylcytosine in DNA and Is Expressed in Pluripotent Tissues". J. Biol. Chem. 279 (50): 52353–52360. doi:10.1074/jbc.M407695200. PMID 15448152.
  16. ^ Sheppard EC, Morrish RB, Dillon MJ, Leyland R, Chahwan R (2018). "Epigenomic Modifications Mediating Antibody Maturation". Frontiers in Immunology. 9: 355–372. doi:10.3389/fimmu.2018.00355. PMC 5834911. PMID 29535729.
  17. ^ Xu Z, Pone EJ, Al-Qahtani A, Park SR, Zan H, Casali P (2007-01-01). "Regulation of aicda expression and AID activity: relevance to somatic hypermutation and class switch DNA recombination". Critical Reviews in Immunology. 27 (4): 367–97. doi:10.1615/critrevimmunol.v27.i4.60. PMC 2994649. PMID 18197815.
  18. ^ Dorsett Y, McBride KM, Jankovic M, Gazumyan A, Thai TH, Robbiani DF, Di Virgilio M, Reina San-Martin B, Heidkamp G, Schwickert TA, Eisenreich T, Rajewsky K, Nussenzweig MC (May 2008). "MicroRNA-155 suppresses activation-induced cytidine deaminase-mediated Myc-Igh translocation". Immunity. 28 (5): 630–8. doi:10.1016/j.immuni.2008.04.002. PMC 2713656. PMID 18455451.
  19. ^ Teng G, Hakimpour P, Landgraf P, Rice A, Tuschl T, Casellas R, Papavasiliou FN (May 2008). "MicroRNA-155 is a negative regulator of activation-induced cytidine deaminase". Immunity. 28 (5): 621–9. doi:10.1016/j.immuni.2008.03.015. PMC 2430982. PMID 18450484.
  20. ^ Fairfax KA, Gantier MP, Mackay F, Williams BR, McCoy CE (Jan 2015). "IL-10 regulates Aicda expression through miR-155". Journal of Leukocyte Biology. 97 (1): 71–8. doi:10.1189/jlb.2A0314-178R. PMID 25381386. S2CID 9138000.
  21. ^ Luo Z, Ronai D, Scharff MD (2004). "The role of activation-induced cytidine deaminase in antibody diversification, immunodeficiency, and B-cell malignancies". J. Allergy Clin. Immunol. 114 (4): 726–35, quiz 736. doi:10.1016/j.jaci.2004.07.049. PMID 15480307.
  22. ^ Scherer, F; Navarrete, MA; Bertinetti-Lapatki, C; Boehm, J; Schmitt-Graeff, A; Veelken, H (January 2016). "Isotype-switched follicular lymphoma displays dissociation between activation-induced cytidine deaminase expression and somatic hypermutation". Leukemia & Lymphoma. 57 (1): 151–60. doi:10.3109/10428194.2015.1037758. PMID 25860234. S2CID 31242381.

Further reading

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