Question 1

What happens when a replicative polymerase encounters DNA damage during replication?

Accepted Answer

When a replicative polymerase stalls on a damaged base, specialized enzymes modify the sliding clamp by adding ubiquitin or SUMO proteins. This modification triggers release of the replicative polymerase and recruits a translesion DNA polymerase to the damaged site. The TLS polymerase then inserts a nucleotide across the lesion, allowing replication to continue.

Question 2

How do translesion DNA polymerases differ structurally from regular replicative polymerases?

Accepted Answer

Y family translesion polymerases lack the 3' to 5' exonuclease proofreading domain found in replicative polymerases. They possess a larger, more open active site that accommodates bulky, chemically modified bases, including covalently linked bases in thymine-thymine dimers. These structural features enable TLS polymerases to bypass DNA lesions that would stall regular polymerases.

Question 3

What is damage tolerance and how does it differ from DNA repair?

Accepted Answer

Damage tolerance allows cells to continue DNA replication past lesions without restoring the original DNA sequence. Unlike repair mechanisms, the damaged base or lesion remains in the DNA after translesion synthesis. This process buys time for the cell to repair damage through other pathways while maintaining replication continuity.

Question 4

Why must translesion polymerases extend the DNA strand beyond the lesion before switching back to replicative polymerase?

Accepted Answer

If the replicative polymerase resumes immediately after nucleotide insertion, its 3' to 5' exonuclease proofreading activity will recognize and remove the inserted base. By extending several nucleotides beyond the lesion, the TLS polymerase positions the inserted base away from the active site, protecting it from removal when the replicative polymerase takes over.

Question 5

How does the type of DNA lesion affect translesion polymerase accuracy?

Accepted Answer

Different lesions present different coding challenges. For abasic sites, which lack coding information, polymerases must insert nucleotides without template guidance. The archaeal polymerase Dpo4 preferentially adds adenine opposite abasic sites, while other polymerases may handle similar lesions differently. Some TLS polymerases insert correct nucleotides by chance, while others are error-prone and generate mutations.

Question 6

What role do ubiquitin and SUMO modifications play in translesion DNA synthesis?

Accepted Answer

Ubiquitin and SUMO proteins are covalently added to the sliding clamp when replicative polymerase stalls on damaged DNA. These chemical modifications signal the release of the stalled polymerase and recruit translesion DNA polymerase to the lesion site. Once the TLS polymerase extends the strand beyond the damage, the modification is removed from the clamp, allowing replicative polymerase to resume.

Question 7

How does translesion DNA synthesis relate to restarting stalled replication forks?

Accepted Answer

Translesion DNA synthesis allows cells to bypass lesions and continue replication when forks stall at damaged bases. By inserting nucleotides across lesions and extending the strand, TLS polymerases enable replication to proceed past obstacles that would otherwise halt fork progression. This mechanism works alongside other cellular responses to restarting stalled replication forks.

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