DNA, the blueprint of life, is constantly exposed to various factors that can alter its structure. One common alteration is the deamination of cytosine, a fundamental chemical change affecting one of DNA’s building blocks. This process involves the spontaneous or induced modification of a specific base within the genetic code. Understanding cytosine deamination is important as it is a frequent form of DNA damage with significant implications for genetic stability.
The Chemical Transformation of Cytosine
Deamination is a chemical reaction involving the removal of an amine group from a molecule. In DNA, cytosine undergoes deamination when its amino group (-NH2) is replaced by a keto group (=O). This transformation converts cytosine (C) into uracil (U), a base normally found in RNA but not in DNA. This change can occur spontaneously due to its hydrolytic instability in an aqueous cellular environment. Additionally, environmental factors or chemicals, such as nitrous acid, can induce this process.
Impact on DNA and Genetic Information
The presence of uracil in a DNA strand creates a mismatched base pair, as uracil is not a standard component of DNA. Cytosine normally pairs with guanine (C-G). When cytosine deaminates to uracil, the original C-G pair becomes a U-G mismatch within the DNA helix. During DNA replication, DNA polymerase often misinterprets uracil. Instead, uracil preferentially pairs with adenine (A).
This mispairing leads to a permanent alteration in the genetic sequence. One of the two new DNA molecules produced after replication will correctly retain the original C-G pair. However, the other new DNA molecule will have a U-A pair. In the next round of replication, this U-A pair will lead to a T-A base pair where there should have been a C-G pair. This specific point mutation, a C-G to T-A transition, represents a common consequence of uncorrected cytosine deamination.
Cellular Repair of Deamination Damage
Cells possess mechanisms to counteract DNA damage, including the repair of deaminated cytosine. The primary pathway responsible for this is Base Excision Repair (BER), a system that removes damaged or incorrect bases from DNA. This repair process is initiated by enzymes called DNA glycosylases, which constantly scan the DNA for anomalies.
Uracil-DNA glycosylase (UDG) is an enzyme within the BER pathway that recognizes and excises uracil from the DNA backbone, creating an abasic site where the sugar-phosphate backbone remains but the base is missing. An enzyme called AP endonuclease then recognizes this site and cleaves the DNA backbone, creating a single-strand break. DNA polymerase fills the gap by inserting the correct nucleotide, using the intact complementary strand as a template. Finally, DNA ligase seals the remaining nick, restoring the integrity of the double helix. This process ensures uracil is efficiently removed from DNA, preventing potentially harmful mutations.
The Problem of Methylated Cytosine
While spontaneous deamination of cytosine to uracil is common, a more problematic outcome arises when methylated cytosine undergoes deamination. Cytosine can be modified with a methyl group at its fifth carbon position, forming 5-methylcytosine (5mC). This methylation is a normal epigenetic modification that plays a role in gene regulation and silencing in many organisms. When 5-methylcytosine undergoes deamination, it loses its amine group and transforms into thymine (T), rather than uracil.
This conversion of 5-methylcytosine to thymine presents a significant challenge for cellular repair systems. Unlike uracil, which is readily recognized as an abnormal base in DNA, thymine is a natural component of DNA. This means that the T-G mismatch created by the deamination of 5-methylcytosine is harder for repair systems to identify than a U-G mismatch. Consequently, these sites, particularly in regions rich in cytosine-guanine dinucleotides (CpG sites), become hotspots for mutations in the genome. If left unrepaired, these T-G mismatches can lead to C-G to T-A transition mutations following DNA replication, contributing to genetic variation and potentially disease.
Programmed Deamination in Biology and Disease
Deamination is not only a random damaging event; it can also be a controlled process carried out by specific enzymes. The APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) family of enzymes provides an example of this programmed deamination. These enzymes are part of the innate immune system, designed to protect the host from viral infections. They function by purposefully deaminating cytosine bases within the DNA or RNA of invading viruses, converting them into uracil and thereby disrupting the viral life cycle.
However, when the activity of these APOBEC enzymes becomes dysregulated, they can mistakenly target the host cell’s own DNA. This misdirection leads to widespread cytosine deamination in host DNA, generating numerous C-to-T transition mutations and sometimes C-to-G transversions. Such excessive mutagenesis can drive the development and progression of various cancers, including bladder, breast, head and neck, and lung cancers. The mutations induced by APOBEC enzymes contribute to the genetic diversity within tumors, influencing cancer evolution and potentially affecting treatment responses.