The functional relationships underlying a synthetic genetic network

Abstract

Here, we focus on synthetic lethal genetic interactions, examples of genetic enhancements, where mutations in two different genes result in lethality but only when present together. We recently identified the synthetic lethal network around the PKC1 gene encoding the essential protein kinase C of yeast. We found that this network is heavily enriched for interactions with genes whose products are closely linked to Pkc1 signallng in vivo. Here, we show that: the PKC1 gene elicits a distinct spectrum of genetic interactions to SLT2, encoding a non-essential component of the very same signaling pathway. We also show that the terminal phenotype underlying the synthetic lethal network around PKC1 is not uniform. Synthetic lethal genetic networks thus appear to be very heterogeneous in nature with important implications for what functional relationships can be discovered from them.

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Acknowledgements

This research was supported by grants from the Biotechnology and Biological Sciences Research Council, UK (C20144 and BB/E011632 to Joseph V. Gray). We thank Hong Xu and Huiming Ding for discussions. The authors declare that they have no competing financial interests.

Figures and Tables

Figure 1 The synthetic genetic interaction network around PKC1 identified components of the CWI pathway and is distinct from the network around SLT2, encoding a non-essential component of the pathway. (A) Simplified schematic of the CWI pathway indicating where the products of nine of the 21 genes that are synthetic lethal with PKC1 lie in the pathway. Known or newly confirmed components are in yellow. Transcriptional targets are shown in orange. Protein protein interactions are indicated by blue lines. Filled arrows indicate direct activations: dashed arrows indicate indirect activations. (B) Schematic indicating the extent of overlap between the hypomorphic-null synthetic lethal network around PKC1 and the null-null network around the non-essential SLT2, encoding a key downstream component of the pathway (A). The network around SLT2 is derived predominantly from data from systematic screens.3 Yellow and orange target genes are as for (A) above. Purple target gene products are implicated as acting in the CWI pathway via epistasis analysis alone.10

Figure 2 The synthetic lethal network around PKC1 is underpinned by heterogeneity of terminal phenotype. WT and mutant cultures in early logarithmic phase were grown in the absence or presence of staurosporine (30 µg/mL) in rich medium at 25°C for 4 hours. Percent (%) lysis was determined by propidium iodide staining.14 Untreated cells (wild-type and single mutant) showed little lysis. Treatment of wild-type cells with staurosporine caused significant lysis (37%) although growth of the culture overall was not inhibited (data not shown). The extent of cell lysis varied dramatically between mutants in the presence of staurosporine, even though growth of all mutant cell cultures was inhibited by this concentration of the drug (data not shown). The synthetic lethal network around PKC1 is thus associated with heterogeneity of phenotype: some combinations compromise cell integrity, others do not.

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