Table 2 Functional roles of proteins examined in this study
ProteinEnzymatic activity: pathway involvement in mitosis
Elg1pa,bSubunit of replication factor C complex: involved in stability of replication fork, HR, and telomere maintenance
Rrm3pbDNA helicase: relieves replication fork pauses at G4 motifs, tRNA genes, and other fork-stalling sequences
Sgs1pbDNA helicase: involved in unwinding of HR intermediates and intermediates formed during DNA replication, unwinds G4 structures; in complex with Dna2p, Top3p, and Rmi1p promotes 5′-3′ resection
Srs2pbDNA helicase: negative regulator of HR at replication fork, promotes resolution of HJs by Mus80p/Mms4p, unwinds triplet repeat hairpins
Tof1pbSubunit of replication-fork-pausing complex: stabilizes replication fork and facilitates progression of fork to prevent genomic alterations; S-phase checkpoint function
Top1pbTopoisomerase I: involved in DNA replication, recombination, and transcription
Exo1pc5′–3′ exonuclease, flap-endonuclease: involved in processing of broken ends, DNA mismatch repair, error-free postreplication pathway, and telomere maintenance
Mre11pcNuclease subunit of Mre11p/Rad50p/Xrs2p complex: processing of DNA ends resulting from DSB, roles in HR and NHEJ, telomere maintenance, and checkpoint functions.
Mus81pcInteracts with Mms4p to form structure-specific endonuclease: promotes reciprocal crossovers in HR pathway
Rad1pcSingle-stranded endonuclease: NER and SSA pathway of HR
Rad50pcPart of complex with Mre11p/Xrs2p: processing of DNA ends resulting from DSB, roles in HR and NHEJ, telomere maintenance, and checkpoint functions.
Rad51pcStrand-exchange protein: most HR pathways except SSA
Rad52pcStimulates Rad51p and anneals single-stranded DNA: all HR pathways
Rad59pcParalog of Rad52p: stimulates SSA
Sae2pcEndo- and exonuclease: roles in resection needed at telomeres and at broken DNA ends for DSB repair by HR; removal of MRX complex from DNA ends
Sml1pcInhibitor of ribonucleotide reductase: DSB repair
Lig4pdSpecialized DNA ligase: NHEJ pathway
Mms2peUbiquitin-conjugating enzyme: involved in error-free postreplication repair
Rad18peE3 ubiquitin ligase: postreplication repair
Rev3pfCatalytic subunit of DNA polymerase ζ: error-prone bypass of lesions during DNA replication
Msh2pgMismatch-binding protein: DNA mismatch repair, processing of DNA branches in SSA pathway
Msh6pgMismatch-binding protein acting with Msh2p: Repair of base–base mismatches
Rif1phRap1p-binding protein: mutant results in increased telomere silencing and elongated telomeres
Sir2phHistone deacetylase: regulates silencing at HML, HMR, telomeres, and rDNA; regulates life span, negative regulator of DNA initiation
Sir3phSilencing protein interacting with Rap1p and Sir2p: regulates silencing at HML, HMR, and telomeres, but not in rDNA
Tel1phProtein kinase: telomere length regulation and DNA damage checkpoint
  • DSB, double-strand break; HJ, Holliday junction; HR, homologous recombination; MRX, Mre11p/Rad50p/Xrs2p; NER, nucleotide excision repair; NHEJ, nonhomologous end-joining; SSA, single-strand annealing.

  • a The functions for these proteins were determined using data in the Saccharomyces Genome Database (

  • b These proteins are involved in stabilization of the replication fork and mutants lacking these proteins have elevated rates of genome instability.

  • c The proteins directly or indirectly affect the repair of double-strand DNA breaks by homologous recombination.

  • d This enzyme is required for “classic” nonhomologous end-joining.

  • e These proteins are utilized in error-free postreplication repair.

  • f Rev3p is required in the error-prone pathway of postreplication repair.

  • g Both Msh2p and Msh6p are required for the repair of base–base mismatches.

  • h These proteins affect telomere length and/or telomere silencing.