The genetic blueprint for all living organisms is encoded in DNA, a molecule whose structure must be preserved for cells to function correctly. This instruction manual guides cellular activities, and any alterations to its sequence can have profound consequences for the entire organism. The integrity of this genetic information is constantly under threat from numerous sources. Preserving the DNA sequence is an ongoing battle for every cell, ensuring that when a cell divides, each new daughter cell receives a complete and accurate copy of the genetic instructions.
Understanding DNA Damage and Replication Roadblocks
DNA is a dynamic structure constantly exposed to agents that can alter its chemical makeup. These sources of damage are both external, like ultraviolet (UV) radiation from the sun, and internal, from the cell’s own metabolic processes. These agents can create bulky lesions or modify DNA bases, distorting the double helix structure and creating physical impediments on the DNA template.
When a cell prepares to divide, it duplicates its genome using high-precision enzymes called replicative DNA polymerases. These primary polymerases are designed for accuracy but their structure is tuned to operate on an undamaged DNA helix. When this replication machinery encounters a lesion, its progress can be abruptly halted, creating a replication roadblock.
A stalled replication fork can lead to severe problems, including fork collapse, which leaves the genome only partially duplicated. This incomplete replication can trigger cell death or lead to large-scale chromosomal breaks. To prevent these outcomes, cells have developed alternative strategies to handle such roadblocks.
What Are Translesion Polymerases?
When a replication fork stalls at a site of DNA damage, the cell can activate a tolerance mechanism called translesion synthesis (TLS). This process uses specialized enzymes known as translesion polymerases. Unlike high-fidelity replicative polymerases, TLS polymerases are designed to continue DNA synthesis directly across a damaged template. Their main function is to resolve the immediate crisis of a stalled replication fork.
These enzymes are part of the cell’s DNA damage tolerance pathways, which allow replication to proceed despite the presence of lesions. This approach differs from direct DNA repair, where the damage is physically removed before replication continues. With TLS, the bypass happens first, and the actual repair of the lesion can be addressed later.
There are several distinct types of TLS polymerases, often grouped into families. The Y-family is one of the most well-studied and includes enzymes like Polymerase η (Pol eta), Polymerase ι (Pol iota), and Polymerase κ (Pol kappa). Another is Rev1. Each of these enzymes has a preference for bypassing certain types of DNA lesions.
The deployment of these polymerases is a controlled process. They are recruited to the stalled replication fork only when needed, performing their bypass function before being quickly replaced by the standard replicative polymerase. This regulation ensures these lower-fidelity enzymes are used sparingly.
The Unique Mechanism of Damage Bypass
The ability of translesion polymerases to synthesize DNA across distorted templates stems from their unique molecular structure. Unlike replicative polymerases, which have a snug, restrictive active site, TLS polymerases possess a much more open and accessible active site. This flexible architecture can physically accommodate bulky lesions, such as thymine dimers caused by UV light, that would block a high-fidelity polymerase.
This structural difference allows a TLS polymerase to bind to the stalled replication fork and perform the bypass. The process involves two main steps: the insertion of a nucleotide opposite the damaged base and the extension of the strand. Some TLS polymerases can perform both steps, while in other cases, one polymerase acts as an “inserter” and another as an “extender.”
A defining characteristic of this bypass mechanism is its potential for introducing errors. Because the active site is less discerning and the template base is damaged, the TLS polymerase may insert an incorrect nucleotide. However, Polymerase η can accurately insert two adenine bases opposite a UV-induced thymine dimer, making it an error-free bypass for this specific damage.
Another feature of TLS polymerases is their low processivity. This means they synthesize only a very short patch of DNA before detaching from the template. This ensures their activity is brief and localized to the site of damage. Once the lesion has been bypassed, the TLS polymerase dissociates, and a high-fidelity polymerase resumes accurate DNA synthesis.
Consequences of Translesion Synthesis Activity
The activity of translesion polymerases presents a fundamental trade-off for the cell, balancing immediate survival against long-term genetic fidelity. Their primary benefit is the prevention of replication fork collapse. By enabling the replication machinery to bypass lesions, TLS ensures that the entire genome can be duplicated before cell division, preventing chromosome breaks and subsequent cell death. This function is important for cellular survival in the face of persistent DNA damage.
This survival, however, often comes at a cost. The inherently error-prone nature of many TLS polymerases means that while they solve the problem of a stalled fork, they frequently do so by introducing mutations into the DNA sequence. When a TLS polymerase inserts an incorrect nucleotide opposite a damaged base, this error can become permanently fixed in the genome.
In the context of cancer, the role of TLS is complex. The increased mutation rate fueled by TLS can contribute to the accumulation of genetic changes that lead to malignancy. Conversely, cancer cells often co-opt TLS pathways to survive the DNA-damaging effects of chemotherapy and radiation, making them a target for new therapies.
While somatic mutations are often detrimental, the mutations introduced into germline cells (sperm and egg) by TLS can have broader implications. Over evolutionary timescales, the genetic variation generated through such processes can provide the raw material for natural selection. This highlights the dual nature of translesion synthesis: a necessary mechanism for survival that also contributes to long-term evolution.