Activation-induced cytidine deaminase

Last updated
AICDA
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases AICDA , AID, ARP2, CDA2, HEL-S-284, HIGM2, activation-induced cytidine deaminase, activation induced cytidine deaminase
External IDs OMIM: 605257 MGI: 1342279 HomoloGene: 7623 GeneCards: AICDA
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_020661
NM_001330343

NM_009645

RefSeq (protein)

NP_001317272
NP_065712

NP_033775

Location (UCSC) Chr 12: 8.6 – 8.61 Mb Chr 6: 122.53 – 122.54 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/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, AID also generates other types of mutations, such as C:G to A:T. The mechanism by which these other mutations are created is not well understood. It is a member of the APOBEC family.

Contents

In B cells in the lymph nodes, AID causes mutations that produce antibody diversity, but that same mutation process leads to B cell lymphoma. [8]

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. [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

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

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]

Related Research Articles

Deamination is the removal of an amino group from a molecule. Enzymes that catalyse this reaction are called deaminases.

<span class="mw-page-title-main">CpG site</span> Region of often-methylated DNA with a cytosine followed by a guanine

The CpG sites or CG sites are regions of DNA where a cytosine nucleotide is followed by a guanine nucleotide in the linear sequence of bases along its 5' → 3' direction. CpG sites occur with high frequency in genomic regions called CpG islands.

In immunology, affinity maturation is the process by which TFH cell-activated B cells produce antibodies with increased affinity for antigen during the course of an immune response. With repeated exposures to the same antigen, a host will produce antibodies of successively greater affinities. A secondary response can elicit antibodies with several fold greater affinity than in a primary response. Affinity maturation primarily occurs on membrane immunoglobulin of germinal center B cells and as a direct result of somatic hypermutation (SHM) and selection by TFH cells.

Hypergammaglobulinemia is a medical condition with elevated levels of gamma globulin. It is a type of immunoproliferative disorder.

<span class="mw-page-title-main">Germinal center</span> Lymphatic tissue structure

Germinal centers or germinal centres (GCs) are transiently formed structures within B cell zone (follicles) in secondary lymphoid organs – lymph nodes, ileal Peyer's patches, and the spleen – where mature B cells are activated, proliferate, differentiate, and mutate their antibody genes during a normal immune response; most of the germinal center B cells (BGC) are removed by tingible body macrophages. There are several key differences between naive B cells and GC B cells, including level of proliferative activity, size, metabolic activity and energy production. The B cells develop dynamically after the activation of follicular B cells by T-dependent antigen. The initiation of germinal center formation involves the interaction between B and T cells in the interfollicular area of the lymph node, CD40-CD40L ligation, NF-kB signaling and expression of IRF4 and BCL6.

<span class="mw-page-title-main">APOBEC3G</span> Protein and coding gene in humans

APOBEC3G is a human enzyme encoded by the APOBEC3G gene that belongs to the APOBEC superfamily of proteins. This family of proteins has been suggested to play an important role in innate anti-viral immunity. APOBEC3G belongs to the family of cytidine deaminases that catalyze the deamination of cytidine to uridine in the single stranded DNA substrate. The C-terminal domain of A3G renders catalytic activity, several NMR and crystal structures explain the substrate specificity and catalytic activity.

Michael Samuel Neuberger FRS FMedSci was a British biochemist and immunologist.

<span class="mw-page-title-main">Hyper-IgM syndrome type 2</span> Primary immune deficiency disorder

Hyper IgM Syndrome Type 2 is a rare disease. Unlike other hyper-IgM syndromes, Type 2 patients identified thus far did not present with a history of opportunistic infections. One would expect opportunistic infections in any immunodeficiency syndrome. The responsible genetic lesion is in the AICDA gene found at 12p13.

<span class="mw-page-title-main">Immunoglobulin class switching</span> Biological mechanism

Immunoglobulin class switching, also known as isotype switching, isotypic commutation or class-switch recombination (CSR), is a biological mechanism that changes a B cell's production of immunoglobulin from one type to another, such as from the isotype IgM to the isotype IgG. During this process, the constant-region portion of the antibody heavy chain is changed, but the variable region of the heavy chain stays the same. Since the variable region does not change, class switching does not affect antigen specificity. Instead, the antibody retains affinity for the same antigens, but can interact with different effector molecules.

<span class="mw-page-title-main">PSME4</span> Protein found in humans

Proteasome activator complex subunit 4 is a protein that in humans is encoded by the PSME4 gene.

<span class="mw-page-title-main">APOBEC1</span> Protein-coding gene in the species Homo sapiens

Apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 also known as C->U-editing enzyme APOBEC-1 is a protein that in humans is encoded by the APOBEC1 gene.

<span class="mw-page-title-main">Cytidine deaminase</span> Protein-coding gene in the species Homo sapiens

Cytidine deaminase is an enzyme that in humans is encoded by the CDA gene.

<span class="mw-page-title-main">APOBEC3A</span> Protein-coding gene in the species Homo sapiens

Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A, also known as APOBEC3A, or A3A is a gene of the APOBEC3 family found in humans, non-human primates, and some other mammals. It is a single-domain DNA cytidine deaminase with antiviral effects. While other members of the family such as APOBEC3G are believed to act by editing ssDNA by removing an amino group from cytosine in DNA, introducing a cytosine to uracil change which can ultimately lead to a cytosine to thymine mutation, one study suggests that APOBEC3A can inhibit parvoviruses by another mechanism. The cellular function of APOBEC3A is likely to be the destruction of foreign DNA through extensive deamination of cytosine.Stenglein MD, Burns MB, Li M, Lengyel J, Harris RS. "APOBEC3 proteins mediate the clearance of foreign DNA from human cells". Nature Structural & Molecular Biology. 17 (2): 222–9. doi:10.1038/nsmb.1744. PMC 2921484. PMID 20062055.

<span class="mw-page-title-main">APOBEC</span> Enzyme involved in messenger RNA editing

APOBEC is a family of evolutionarily conserved cytidine deaminases.

<span class="mw-page-title-main">Framework region</span>

In molecular biology, a framework region is a subdivision of the variable region (Fab) of the antibody. The variable region is composed of seven amino acid regions, four of which are framework regions and three of which are hypervariable regions. The framework region makes up about 85% of the variable region. Located on the tips of the Y-shaped molecule, the framework regions are responsible for acting as a scaffold for the complementarity determining regions (CDR), also referred to as hypervariable regions, of the Fab. These CDRs are in direct contact with the antigen and are involved in binding antigen, while the framework regions support the binding of the CDR to the antigen and aid in maintaining the overall structure of the four variable domains on the antibody. To increase its stability, the framework region has less variability in its amino acid sequences compared to the CDR.

Somatic hypermutation is a cellular mechanism by which the immune system adapts to the new foreign elements that confront it, as seen during class switching. A major component of the process of affinity maturation, SHM diversifies B cell receptors used to recognize foreign elements (antigens) and allows the immune system to adapt its response to new threats during the lifetime of an organism. Somatic hypermutation involves a programmed process of mutation affecting the variable regions of immunoglobulin genes. Unlike germline mutation, SHM affects only an organism's individual immune cells, and the mutations are not transmitted to the organism's offspring. Because this mechanism is merely selective and not precisely targeted, somatic hypermutation has been strongly implicated in the development of B-cell lymphomas and many other cancers.

<span class="mw-page-title-main">Kataegis</span>

In molecular biology, kataegis describes a pattern of localized hypermutations identified in some cancer genomes, in which a large number of highly patterned basepair mutations occur in a small region of DNA. The mutational clusters are usually several hundred basepairs long, alternating between a long range of C→T substitutional pattern and a long range of G→A substitutional pattern. This suggests that kataegis is carried out on only one of the two template strands of DNA during replication. Compared to other cancer-related mutations, such as chromothripsis, kataegis is more commonly seen; it is not an accumulative process but likely happens during one cycle of replication.

Antibody structure is made up of two heavy-chains and two light-chains. These chains are held together by disulfide bonds. The arrangement or processes that put together different parts of this antibody molecule play important role in antibody diversity and production of different subclasses or classes of antibodies. The organization and processes take place during the development and differentiation of B cells. That is, the controlled gene expression during transcription and translation coupled with the rearrangements of immunoglobulin gene segments result in the generation of antibody repertoire during development and maturation of B cells.

Mutational signatures are characteristic combinations of mutation types arising from specific mutagenesis processes such as DNA replication infidelity, exogenous and endogenous genotoxin exposures, defective DNA repair pathways, and DNA enzymatic editing.

<span class="mw-page-title-main">Nina Papavasiliou</span> Immunologist

Nina Papavasiliou is an immunologist and Helmholtz Professor in the Division of Immune Diversity at the German Cancer Research Center in Heidelberg, Germany. She is also an adjunct professor at the Rockefeller University, where she was previously associate professor and head of the Laboratory of Lymphocyte Biology. She is best known for her work in the fields of DNA and RNA editing.

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000111732 - Ensembl, May 2017
  2. 1 2 3 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. 1 2 "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