tolerance mechanism

Mechanism of DNA Damage Tolerance

Introduction

  • Author: Xin Bi, University of Rochester

  • Supported by National Science Foundation

  • Open-access publication under CC BY-NC 4.0 license

Abstract

  • DNA damage compromises genome integrity and can lead to cell death.

  • Cells utilize various mechanisms to respond to DNA damage:

    • Damage repair

    • Damage tolerance (DT)

    • Damage checkpoints

  • DT pathway enables bypass of single-stranded DNA (ssDNA) lesions during replication, preventing replication stalling.

  • Two main branches of DT:

    • Translesion Synthesis (TLS):

      • Involves replacement of a replicative DNA polymerase with a specialized TLS polymerase.

      • Intrinsically error-prone.

    • Template Switching (TS):

      • Error-free mechanism involving switching from a damaged template to an undamaged sister strand.

  • Current understanding of these pathways is limited, with ongoing research into their components and regulation.

DNA Damage Tolerance Mechanisms

  • Genomic DNA faces damage from both internal and external sources leading to various lesions.

  • DNA repair mechanisms include:

    • Homologous Recombination (HR) and Non-Homologous End Joining (NHEJ) for double-strand breaks (DSBs).

    • Nucleotide Excision Repair (NER), Base Excision Repair (BER), and DNA Mismatch Repair (MMR) for single-strand lesions.

  • DNA Damage Tolerance (DDT) allows replication to bypass DNA damage while postponing repair.

DDT Process Overview

  • Stalling caused by DNA damage creates a ssDNA gap, which is filled by:

    • TLS: uses specialized polymerases like Pol ζ or η, but is error-prone.

    • TS: uses a newly synthesized undamaged sister strand, promoting error-free repair.

Key Components in DDT

  • PCNA (Proliferating Cell Nuclear Antigen) plays a critical role in DDT regulation through post-translational modifications:

    • Mono-ubiquitination promotes TLS by recruiting TLS polymerases.

    • Poly-ubiquitination activates the Rad5-dependent error-free TS pathway.

  • Other important factors involved in DDT:

    • MRX complex: aids in DSB processing and interacts with DDT pathways.

    • Ino80 complex: supports fork recovery and facilitates Rad18 recruitment.

    • 9-1-1 complex: acts as a damage sensor and facilitates TLS.

    • Srs2 helicase: inhibits unwanted recombination during DNA replication.

Error-Free Template Switching

  • TS involves:

    • Formation of a presynaptic filament with Rad51.

    • Strand invasion by complementary sister strands.

    • Gap filling by replicative polymerase, leading to Sister Chromatid Junction (SCJ) formation.

  • SCJ is resolved to yield two duplex DNA strands after repair synthesis, thus completing the bypass process.

Salvage Homologous Recombination Pathway

  • Salvage HR is an alternative pathway that can promote error-free lesion bypass without PCNA ubiquitination.

  • It activates under different cell cycle phases, usually late S or G2/M phase.

  • Involves similar components as the Rad5 pathway.

Regulatory Mechanisms for DDT Pathway Choice

  • Choice between TLS, Rad5-dependent TS, and salvage HR impacts genome stability significantly.

  • Consultation with components like Srs2, Elg1, and Hmo1 can influence DDT pathway preference:

    • Srs2 prevents overreliance on hyper-recombination pathways.

    • The activity of Hmo1 is involved in maintaining error-free repair processes.

Conclusion

  • Advances have been made in understanding DDT and its components, yet numerous questions remain about regulatory mechanisms and pathway selection.

  • Future research will focus on elucidating the interplay between DDT machinery, pathways, and chromatin structure.