Activation-Induced (Cytidine) Deaminase
Encyclopedia
Activation-induced deaminase (AID) is a 24 kDa enzyme
that creates deliberate mutations in DNA
.
AID removes the amino group from a cytidine
base, turning it into a uridine
(which is recognized as a thymidine
). In other words, it changes a CG base pair into a UG base pair, which the cell's DNA repair machinery recognizes as a TG base pair, and finally ends up as a TA base pair.
In B cells in the lymph nodes, AID causes mutations that produce antibody diversity, but that same mutation process leads to B-cell lymphoma.
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: somatic hypermutation
(SHM), in which the antibody genes are shuffled to provide enough diversity to deal with millions of antigens; class switch recombination (CSR), in which B cells change their expression from IgM to IgG or other immune types; and gene conversion
(GC).
AID has been shown in vitro
to be active on single stranded 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 transgene
s that have been integrated into the genome
.
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
that creates deliberate mutations in DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
.
AID removes the amino group from a cytidine
Cytidine
Cytidine is a nucleoside molecule that is formed when cytosine is attached to a ribose ring via a β-N1-glycosidic bond...
base, turning it into a uridine
Uridine
Uridine is a molecule that is formed when uracil is attached to a ribose ring via a β-N1-glycosidic bond.If uracil is attached to a deoxyribose ring, it is known as a deoxyuridine....
(which is recognized as a thymidine
Thymidine
Thymidine is a chemical compound, more precisely a pyrimidine deoxynucleoside. Deoxythymidine is the DNA nucleoside T, which pairs with deoxyadenosine in double-stranded DNA...
). In other words, it changes a CG base pair into a UG base pair, which the cell's DNA repair machinery recognizes as a TG base pair, and finally ends up as a TA base pair.
In B cells in the lymph nodes, AID causes mutations that produce antibody diversity, but that same mutation process leads to B-cell lymphoma.
AID is currently thought to be the master regulator of secondary antibody
Antibody
An antibody, also known as an immunoglobulin, is a large Y-shaped protein used by the immune system to identify and neutralize foreign objects such as bacteria and viruses. The antibody recognizes a unique part of the foreign target, termed an antigen...
diversification. It is involved in the initiation of three separate immunoglobulin (Ig) diversification processes: somatic hypermutation
Somatic hypermutation
Somatic hypermutation is a mechanism inside cells that is part of the way the immune system adapts to the new foreign elements that confront it . SHM diversifies the receptors used by the immune system to recognize foreign elements and allows the immune system to adapt its response to new threats...
(SHM), in which the antibody genes are shuffled to provide enough diversity to deal with millions of antigens; class switch recombination (CSR), in which B cells change their expression from IgM to IgG or other immune types; and gene conversion
Gene conversion
Gene conversion is an event in DNA genetic recombination, which occurs at high frequencies during meiotic division but which also occurs in somatic cells. It is a process by which DNA sequence information is transferred from one DNA helix to another DNA helix, whose sequence is altered.It is one...
(GC).
AID has been shown in vitro
In vitro
In vitro refers to studies in experimental biology that are conducted using components of an organism that have been isolated from their usual biological context in order to permit a more detailed or more convenient analysis than can be done with whole organisms. Colloquially, these experiments...
to be active on single stranded DNA, and has been shown to require active transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
in order to exert its deaminating activity. The involvement of Cis
Cis
Cis may have the following meanings:* "Cis-" as a prefix of Latin origin, meaning "on the same side [as]" or "on this side [of]", with several derived usages:** In chemistry, cis- refers to cis-trans isomerism...
-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 transgene
Transgene
A transgene is a gene or genetic material that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another....
s that have been integrated into the genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
.
Mechanism
AID is believed to initiate SHM in a multi-step mechanism. AID deaminates cytidine in the target DNA. Cytidines located within hotspot motifs are preferentially deaminated (WRCY motifs W=adenosine or thymidine, R=purine, C=cytidine, Y=pyrimidine, or the inverse RGYW G=guanidine). The resultant U:G (U= uridine) mismatch is then subject to one of a number of fates.- 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).
- The uridine may be excised by uracil DNA glycosylase (UDG) resulting in an abasic site. This abasic site (or AP, apurinicPurineA purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. Purines, including substituted purines and their tautomers, are the most widely distributed kind of nitrogen-containing heterocycle in nature....
/apyrimidinicPyrimidinePyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring...
) if replicated across will result in random incorporation of any of the four nucleotideNucleotideNucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s. i.e. A, G, C or T. Alternately this abasic site can be cleaved by apurinic endonucleaseEndonucleaseEndonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain, in contrast to exonucleases, which cleave phosphodiester bonds at the end of a polynucleotide chain. Typically, a restriction site will be a palindromic sequence four to six nucleotides long. Most...
(APE) creating a break in the deoxyriboseDeoxyriboseDeoxyribose, more, precisely 2-deoxyribose, is a monosaccharide with idealized formula H---3-H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of an oxygen atom...
phosphatePhosphateA phosphate, an inorganic chemical, is a salt of phosphoric acid. In organic chemistry, a phosphate, or organophosphate, is an ester of phosphoric acid. Organic phosphates are important in biochemistry and biogeochemistry or ecology. Inorganic phosphates are mined to obtain phosphorus for use in...
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. - The U:G mismatch can be recognized by the DNA mismatch repairDNA mismatch repairDNA mismatch repair is a system for recognizing and repairing erroneous insertion, deletion and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage....
(MMR) machinery, most notably MutSa(alpha). MutSa is a heterodimer consisting of MSH2MSH2MSH2 is a gene commonly associated with Hereditary nonpolyposis colorectal cancer.-Interactions:MSH2 has been shown to interact with Exonuclease 1, MSH3, MSH6, CHEK2, MAX, Ataxia telangiectasia and Rad3 related and BRCA1.-Further reading:...
and MSH6MSH6MSH6 is a gene commonly associated with hereditary nonpolyposis colorectal cancer.-Function:MSH6 contributes to ADP and ATP binding. It also contributes to ATPase activity...
. 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.