We have described a comprehensive and quantitative analysis of genetic interactions among 26 non-essential genes involved in resistance to MMS-induced DNA damage. A conceptually simple multiplicative model was used to define genetic interactions between these genes. The validity of this model is supported here by the fact that the fitness defects of gene pairs without functional links usually combine multiplicatively, and that deviation from this model is predictive of shared function. This model has not been applied in previous large-scale genetic interaction studies8,10–12,14,15,18
. As a result, some gene pairs might have been previously misinterpreted as being in common or compensatory pathways if the multiplicative neutral model adopted here is correct.
In the absence of MMS, our methods classified 12% of gene pairs as aggravating interactions and 6% as alleviating interactions (). Genome-wide screens have estimated the frequency of aggravating genetic interactions (synthetic lethality and synthetic sickness) to be ~0.5% among non-essential genes15
. The ~24-fold enrichment in aggravating interaction frequency that we observed in the absence of MMS illustrates the utility of chemogenomic fitness screens in identifying functionally related subsets of genes and in quantitatively measuring their genetic interactions. Notably, we further enriched the number of alleviating and aggravating interactions to 21% and 14%, respectively, by growing deletion strains in the presence of MMS. The enrichment of functional links among alleviating gene pairs further underscores the value of systematic screens that can capture such interactions13,18
The adaptive value of the sexual mode of reproduction has been much debated. The deterministic theory argues that, if aggravating epistasis is prevalent, then sexual reproduction is selective because it enables deleterious mutations to be purged from genomes3
. Previous studies aimed at measuring the relative frequencies of alleviating and aggravating interactions have yielded conflicting results4–6
. Here, all single-gene deletions produced a quantifiable phenotype relative to wild type (); thus, every gene pair in our data set was interrogated for both alleviating and aggravating interactions. The observation that aggravating interactions occurred more frequently than alleviating interactions (; both with and without MMS) is consistent with the deterministic theory. An important caveat, however, is that the genes that we studied were not chosen randomly.
The relative MMS sensitivities of single and double mutants were used to distinguish distinct subtypes of alleviating genetic interactions. We found that coequal interactions (where Sxy
) occur between gene pairs that typically have the highest genetic congruence scores ( and ) and coequality is generally indicative of protein complexes that function as cohesive units25,26,28,32,33
. Systematically discovered alleviating interactions (where Sx
) accurately predicted the order of previously characterized biochemical processes. In addition, we found that shu1
Δ and csm2
Δ could partially suppress the MMS sensitivity of rad54
() and, similar to deletions in homologous recombination genes44
, rescue the synthetic lethality of an hpr5Δrad54Δ
double-deletion mutant (Supplementary Fig. 3
). These data extend previous findings linking the Shu complex to homologous recombination26
and place this complex upstream of Rad54 in homologous recombination–mediated repair of both MMS-induced and spontaneous DNA damage.
Genetic congruence between MPH1
led to the hypothesis and observation that the fitness of mph1Δmus81Δ
double-deletion strains in MMS can be improved by deleting genes important for homologous recombination and is consistent with the idea that the Mph1 helicase is involved in resolving homologous recombination-dependent toxic DNA intermediates (). Even though the Mph1 protein shows similar substrate specificity to Sgs1 in vitro40
, whether it has the same substrate specificity as Sgs1 in vivo
remains to be determined. Two of our results argue against this possibility: first, we did not observe any interaction between these two genes, as might be expected if they resolve the same intermediate; and second, although the rad59
Δ deletion suppressed the sensitivity of mph1Δmus81Δ
, it did not rescue the synthetic lethality of sgs1Δmus81Δ
. This observation suggests that Mph1 may distinguish itself from Sgs1 by acting on substrates generated by a RAD59
Of the roughly 6,000 genes in the yeast genome, fewer than 1,200 are essential for viability under optimal growth conditions (rich medium at 30 °C)22,46
. Consistent with studies involving random mutations4,5
and computational studies of yeast metabolism19
, most of our gene pairs followed a multiplicative relationship (). This level of robustness will undoubtedly hinder efforts to understand the functional organization of the cell on a systems level. Our results emphasize the utility of systematic and quantitative double-deletion studies, but they also show that additional perturbations, either genetic or chemical, will be necessary to reveal the full architecture of cellular pathways.