Mechanism of DNA damage tolerance

Table 1 Components and regulators of DNA damage tolerance¹

Factor/complex	Functions/properties
Rad6/Rad18	E2 ubiquitin conjugase/E3 ubiquitin ligase complex; promotes mono-ubiquitination of PCNA at lysine 164 (PCNA-K164)
Rad5/Mms2/Ubc13	E3 ubiquitin ligase/E2 ubiquitin conjugase complex; promotes poly-ubiquitination of PCNA-K164; has ATPase activity
Pol30	Forms a homotrimer (PCNA); its ubiquitination and sumoylation regulates the choice of DDT mechanism
Ubc9/Siz1	E2 SUMO conjugase/E3 SUMO ligase complex; promotes PCNA sumoylation
DNA polymerase ζ	TLS polymerase; consists of subunits Rev3, Rev7, Pol31 and Pol32 with Rev3 being the catalytic subunit
Rev1	dCMP transferase; required for TLS by Pol ζ
DNA polymerase η (Rad30)	TLS polymerase
DNA polymerase δ (Pol3/Pol31/Pol32)	Lagging strand DNA polymerase; Pol3 is the catalytic subunit; promotes repair synthesis in error-free DDT; Pol32 is not essential for DNA replication but is required for repair synthesis
Rad51	Components of HR responsible for homology search and strand invasion; Rad51 molecules bind ssDNA to form a presynaptic filament important for subsequent strand invasion; both Rad55 and Rad57 are paralogs of Rad51; Rad55/Rad57 stabilizes Rad51 nucleoprotein filament and inhibits Srs2 helicase activity
Rad52
Rad54
Rad55/Rad57
Srs2	3′-5′ helicase and translocase; disrupts Rad51 nucleoprotein filaments; inhibits salvage HR pathway thereby channeling DNA lesions to Rad5 pathway
Sgs1/Top3/Rmi1	Resolves SCJ intermediates generated in error-free DDT
RFA (replication factor A) (Rfa1/Rfa2/Rfa3)	ssDNA binding complex; is involved in DNA replication, repair and recombination; RFA-ssDNA nucleofilament helps recruit Rad18
Exo1	5’-3’ exonuclease; promotes resection of dsDNA break ends; functions in DNA damage repair, recombination, replication, and telomere integrity; is required for SCJ formation in error-free DDT
9-1-1 complex (Ddc1/Mec3/Rad17)	Ring shaped DNA clamp; is involved in DNA check point signaling; facilitates Pol ζ recruitment; is required for SCJ formation in error-free DDT; interacts with Exo1
MRX complex (Mre11-Rad50-Xrs2)	3’-5’ exonuclease and ssDNA endonuclease; is potentially involved in both TLS and TS branches of DDT; interacts with Rad18
Shu complex (Shu1/Shu2/ Csm2/Psy3)	Is involved in error-free DDT; interacts with Rad55/Rad57
Ino80	Chromatin remodeler; associates with replication forks and promotes fork progression; required for Rad18 and Rad51 recruitment to replications forks, PCNA poly-ubiquitination and SCJ formation
Elg1	Unloads PCNA from chromatin during DNA replication; regulates choice of DDT pathway
Hmo1	HMGB homolog; binds ssDNA and DNA with an altered conformation; bends DNA; interacts with Elg1; may help channel DNA lesions to Rad5 pathway; required for SCJ formation in S phase
Fun30	Chromatin remodeler; facilitates long-range resection of dsDNA ends; potentially regulates choice of DDT pathway

¹Listed are DDT factors in S. cerevisiae. ATPase: Adenosine triphosphatase; dCMP: Deoxycytidine monophosphate; DDT: DNA damage tolerance; dsDNA: Double stranded DNA; HMGB: High-mobility group protein B; HR: Homologous recombination; K: Lysine; PCNA: Proliferating cell nuclear antigen; RFA: Replication factor A; S: Synthesis; SCJ: Sister chromatid junction; ssDNA: Single stranded DNA; SUMO: Small ubiquitin-like modifier; TLS: Translesion synthesis; TS: Template switching; Ub: Ubiquitin.