Requirement for end-joining and checkpoint functions, but not RAD52-mediated recombination, after EcoRI endonuclease cleavage of Saccharomyces cerevisiae DNA

Abstract

RAD52 and RAD9 are required for the repair of double-strand breaks (DSBs) induced by physical and chemical DNA-damaging agents in Saccharomyces cerevisiae. Analysis of EcoRI endonuclease expression in vivo revealed that, in contrast to DSBs containing damaged or modified termini, chromosomal DSBs retaining complementary ends could be repaired in rad52 mutants and in G1-phase Rad+ cells. Continuous EcoRI-induced scission of chromosomal DNA blocked the growth of rad52 mutants, with most cells arrested in G2 phase. Surprisingly, rad52 mutants were not more sensitive to EcoRI-induced cell killing than wild-type strains. In contrast, endonuclease expression was lethal in cells deficient in Ku-mediated end joining. Checkpoint-defective rad9 mutants did not arrest cell cycling and lost viability rapidly when EcoRI was expressed. Synthesis of the endonuclease produced extensive breakage of nuclear DNA and stimulated interchromosomal recombination. These results and those of additional experiments indicate that cohesive ended DSBs in chromosomal DNA can be accurately repaired by RAD52-mediated recombination and by recombination-independent complementary end joining in yeast cells.

FIG. 1

Expression of EcoRI and HO from centromeric plasmids inhibits the growth of rad52 and rad9 strains. Late-log-phase cells were inoculated into Gal + Glu − Ura liquid medium at time zero and counted with a hemacytometer as described in Materials and Methods. Abbreviations: pRS, pRS316; pHO, pGALHO; pERI, YCpGal:RIb.

FIG. 2

rad52 cells synthesizing EcoRI and HO are chronically arrested as large-budded cells. The distribution of unbudded (▩), small-budded (░⃞), and large-budded (▪) cells during growth of T334 (Rad⁺) and T334ΔR52T (rad52) strains in galactose media is shown (see Materials and Methods).

FIG. 3

Endonuclease-induced G₂ arrest is largely dependent on rad9. The accumulation of large-budded cells in Rad⁺ and rad9 strains after induction of EcoRI and HO endonuclease expression is shown.

FIG. 4

Plasmid-based synthesis of EcoRI and HO causes cell killing in rad9 mutants but not in Rad⁺ or rad52 cells. Cells grown in Gal + Glu − Ura medium (maintaining selection for the plasmid) were rescued onto synthetic Glu-Com plates as described in Materials and Methods. Symbols: □, pRS316; ◊, pGALHO; ○, YCpGal:Rlb.

FIG. 5

Growth of rad52 cells containing integrated GAL1::EcoRI is inhibited in 2% galactose medium. Growth of cells containing GAL1::EcoRI integrated at LYS2 or HIS3 in glucose (YPD) or Glu + Gal (YPD+Gal) medium.

FIG. 6

Effects of chromosome-based expression of EcoRI on cell cycling and survival. (A to C) Analysis of cell cycling after induction of endonuclease synthesis in Δlys2::(GAL1::EcoRI) fusion strains. (D to F) Survival of Rad⁺, rad52, and rad9 strains containing the Δlys2::(GAL1::EcoRI) construction after growth in YPD or YPD + Gal medium.

FIG. 7

Expression of EcoRI causes growth inhibition and cell killing in hdf1 mutants. Strains YLKL350, YLKL351, and YLKL389 (Δhis3::GALEcoRI) were used for the assays. (A) Growth of YLKL389 (Δhdf1::HIS3) in YPD and YPD+2%Gal. (B) Survival of Rad⁺, Δrad52, and Δhdf1 strains in YPD+2%Gal.

FIG. 8

Expression of EcoRI in Rad⁺ and rad52 cells produces extensive breakage of chromosomal DNA. (A and B) DNA was purified from cells containing YCpGal:RIb at the indicated times after induction in galactose. (C and D) Analysis of DNA purified from cells containing chromosomal Δhis3::(GAL1::EcoRI) fusions (YLKL350 and YLKL351).

FIG. 9

Alternative pathways of repair for DSBs containing damaged ends (∗) or ends with complementary overhangs. RAD52-mediated homologous recombination is required for repair of DSBs with damaged termini produced by physical and chemical DNA-damaging agents (e.g., ionizing radiation) but is not essential for repair of DSBs containing complementary ends (see the text for details).