Srs2 and Sgs1 DNA helicases associate with Mre11 in different subcomplexes following checkpoint activation and CDK1-mediated Srs2 phosphorylation

Abstract

Mutations in the genes encoding the BLM and WRN RecQ DNA helicases and the MRE11-RAD50-NBS1 complex lead to genome instability and cancer predisposition syndromes. The Saccharomyces cerevisiae Sgs1 RecQ helicase and the Mre11 protein, together with the Srs2 DNA helicase, prevent chromosome rearrangements and are implicated in the DNA damage checkpoint response and in DNA recombination. By searching for Srs2 physical interactors, we have identified Sgs1 and Mre11. We show that Srs2, Sgs1, and Mre11 form a large complex, likely together with yet unidentified proteins. This complex reorganizes into Srs2-Mre11 and Sgs1-Mre11 subcomplexes following DNA damage-induced activation of the Mec1 and Tel1 checkpoint kinases. The defects in subcomplex formation observed in mec1 and tel1 cells can be recapitulated in srs2-7AV mutants that are hypersensitive to intra-S DNA damage and are altered in the DNA damage-induced and Cdk1-dependent phosphorylation of Srs2. Altogether our observations indicate that Mec1- and Tel1-dependent checkpoint pathways modulate the functional interactions between Srs2, Sgs1, and Mre11 and that the Srs2 DNA helicase represents an important target of the Cdk1-mediated cellular response induced by DNA damage.

FIG. 1.

SRS2, SGS1, and MRE11 physically and genetically interact. (A) The protein regions corresponding to the three Srs2 baits used for the two-hybrid screening are shown: FL (full-length); N (N terminus); and C (C terminus). Consensus sites for Cdk1 kinase and the seven helicase domains (I and Ia to VI) are indicated by solid circles and striped boxes, respectively. (B) The protein fragments of Sgs1 and Mre11, identified by the two-hybrid analysis, are indicated by lines flanking the numbers of corresponding clones, under the schematic representation of the two proteins. Double arrowed lines indicate the Sgs1 and Mre11 protein regions involved in the interaction with Srs2. Previously mapped Sgs1 and Mre11 domains, involved in protein-protein interactions, are also shown. (C) An example of the two-hybrid interaction in haploid strains between Srs2 baits and Mre11-4 and Sgs1-60 clones is shown. The three bait strains, transformed with the corresponding prey plasmids or with pJG4-5 vector (CY5107, CY5109, CY5111, CY5448, CY5445, CY5442, CY5439, CY5436, and CY5435), were spotted on proper media with and without leucine (L), glucose (Glu), galactose (Gal), raffinose (Raf), and 5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside (X-Gal). (D) Srs2, Sgs1, and Mre11 proteins were immunoprecipitated from whole-cell extracts (WCE) prepared from CY3262 and CY5680 or CY2715 and CY5683, respectively, as controls and then analyzed by Western blotting using specific antibodies. WCE lanes are a 1:10 dilution of the immunoprecipitated extracts. (E) The cellular growth of wild-type (W303), srs2Δ (CY2643), sgs1Δ (CY2570), mre11Δ (CY2730), mre11Δ srs2Δ (CY5492), mre11Δ sgs1Δ (CY5670), and srs2Δ sgs1Δ (CY3137) stains was evaluated by plating serial dilutions on YPD plates.

FIG. 2.

Cofractionation analysis of Srs2, Sgs1, and Mre11 proteins using gel filtration chromatography. Crude protein extracts were prepared from strain CY3262 grown in unperturbed conditions (A) or in the presence of MMS (B) and fractionated by gel filtration. The collected fractions were analyzed by Western blotting using specific antibodies against Srs2, Sgs1, Mre11, Rad53, and B subunit as described in Materials and Methods. Specific bands, corresponding to the proteins of interest, are indicated by arrows. TCA extracts from untreated and MMS-treated cells were loaded on the first lane of each gel as controls (TCA). Bold lines and letters from A to D indicate the fractionation peaks for each protein and the cofractionation peaks, respectively. The elution peaks of molecular size standards are indicated by arrows: BD, blue dextran (2,000 kDa); TG, thyroglobulin (670 kDa); AF, apoferritin (440 kDa); AD, alcohol dehydrogenase (150 kDa); BSA, bovine serum albumin (66 kDa).

FIG. 3.

Gel-filtration analysis of srs2Δ, sgs1Δ or mre11Δ strains. Crude protein extracts, obtained from srs2Δ (CY5680), sgs1Δ (CY3137), and mre11Δ (CY5683) strains grown in unperturbed conditions (A) or in the presence of MMS (B), were fractionated by gel filtration and analyzed by Western blotting using antibodies against Srs2, Sgs1, and Mre11. Gel filtration analysis performed on the wild-type strain, taken from Fig. 2, is also shown.

FIG. 4.

Checkpoint kinases Mec1 and Tel1 control the reorganization of DNA damage-specific complexes containing Srs2, Sgs1, and Mre11. Crude protein extracts, prepared from mec1 (CY5849) and tel1 (CY5964) strains grown in unperturbed conditions (A) or in the presence of MMS (B), were fractionated by gel filtration and analyzed by Western blotting using antibodies against Srs2, Sgs1, and Mre11. Gel filtration analysis performed on the wild-type strain, taken from Fig. 2, is also shown.

FIG. 5.

The srs2-7AV mutant is MMS sensitive and defective in DNA damage-induced phosphorylation. (A) TCA protein extracts, obtained from log-phase (L) and MMS-treated (M) cultures, were prepared from the wild type and srs2-7AV mutants and analyzed by Western blotting using specific antibodies against Srs2 and Rad53. (B) Serial dilutions of srs2Δ (CY5680), mec1 (CY5849), tel1 (CY5964), and srs2-7AV (CY6005) mutant strains and the CY3262 strain (wild type), previously grown at equal cell concentrations, were spotted on YPD plates without (UNT) or with MMS at the indicated final concentration. Cellular growth was evaluated after incubation at 28°C for 2 to 3 days.

FIG. 6.

srs2-7AV and srs2-hd mutants are defective in DNA damage-induced subcomplexes formation. Crude protein extracts prepared from srs2-7AV (CY6005) and srs2-hd (CY6002) strains grown in unperturbed conditions (A) or in the presence of MMS (B) were fractionated by gel filtration and analyzed by Western blotting using antibodies against Srs2, Sgs1, and Mre11. Gel filtration analysis performed on the wild-type strain, taken from Fig. 2, is also shown.

FIG. 7.

Model for the redistribution of Srs2, Sgs1, and Mre11 in DNA damage-specific complexes. Srs2, Sgs1, and Mre11 are involved in the formation of complex A under unperturbed conditions. A fraction of Srs2 is also found in cell cycle-dependent complex C*. In response to DNA damage and checkpoint activation, Sgs1 and Mre11 form complex B, while Srs2 and Mre11 form complex D. The phosphorylated Srs2 isoform localizes mainly at complex C. Cdk1-induced Srs2 phosphorylation and Tel1 activity allow the assembly of complexes B and D.