Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes

Abstract

Synthetic lethal genetic interaction networks define genes that work together to control essential functions and have been studied extensively in Saccharomyces cerevisiae using the synthetic genetic array (SGA) analysis technique (ScSGA). The extent to which synthetic lethal or other genetic interaction networks are conserved between species remains uncertain. To address this question, we compared literature-curated and experimentally derived genetic interaction networks for two distantly related yeasts, Schizosaccharomyces pombe and S. cerevisiae. We find that 23% of interactions in a novel, high-quality S. pombe literature-curated network are conserved in the existing S. cerevisiae network. Next, we developed a method, called S. pombe SGA analysis (SpSGA), enabling rapid, high-throughput isolation of genetic interactions in this species. Direct comparison by SpSGA and ScSGA of approximately 220 genes involved in DNA replication, the DNA damage response, chromatin remodeling, intracellular transport, and other processes revealed that approximately 29% of genetic interactions are common to both species, with the remainder exhibiting unique, species-specific patterns of genetic connectivity. We define a conserved yeast network (CYN) composed of 106 genes and 144 interactions and suggest that this network may help understand the shared biology of diverse eukaryotic species.

Fig. 1.

(A) Outline of the SpSGA method. Cells of opposite mating type (h+, h−) are mated on minimal SPA media and allowed to sporulate for 3 days at 26 °C. Then, to enrich for spores, mating plates are transferred to 42° for 3 days—a treatment that kills unmated haploid cells. Following spore enrichment, cells are transferred to rich medium to allow for germination, then transferred again to double-drug medium to select for recombinant double-mutant progeny. S. pombe haploids do not mate on rich medium; therefore, selection for a specific haploid mating type is not required. (B) A portion of the final 1536-formatted miniarray screening plate (YES+Nat+G418) showing a comparison of two queries, a representative control, ura4::kanMX4 (ura4Δ), and a representative query gene, swi3::kanMX4 (swi3Δ). Novel genetic interactions are identified between swi3Δ and mrc1Δ, rad17Δ, ddb1Δ, and fbh1Δ and confirmed by tetrad dissection. Arrows indicate the position of the double deletion mutant, which in one of every four cases is inviable or slow growing.

Fig. 2.

Overlap of the SpSGA HC and ScSGA HC networks. Genes were assigned to single “biological role” categories manually, as described in SI Methods. Eighty-seven SpSGA unique interactions (edges) are in blue, 143 ScSGA unique interactions are in brown, and 54 overlapping interactions are in red. The number of ScSGA unique interactions is larger than the number of SpSGA unique interactions because the ScSGA HC dataset is larger than the corresponding SpSGA HC dataset (see Table 2). A black arrow indicates the position of SPAC3H1.05/STE24, a gene discussed in the text.

Fig. 3.

The conserved yeast network (CYN). SL/SS interactions common to both S. pombe or S. cerevisiae were identified by overlapping literature-curated and experimentally derived datasets, as described (see SI Methods and Table S2). Genes were assigned to a single biological role category as described in SI Methods. The blue arrow indicates the position of mak10/MAK10, and the black arrow indicates the position of rad2/RAD27, both of which are discussed in the text.