Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps

Systematic analysis of synthetic lethality (SL) constitutes a critical tool for systems biology to decipher molecular pathways. The most accepted mechanistic explanation of SL is that the two genes function in parallel, mutually compensatory pathways, known as between-pathway SL. However, recent genome-wide analyses in yeast identified a significant number of within-pathway negative genetic interactions. The molecular mechanisms leading to within-pathway SL are not fully understood. Here, we propose a novel mechanism leading to within-pathway SL involving two genes functioning in a single non-essential pathway. This type of SL termed within-reversible-pathway SL involves reversible pathway steps, catalyzed by different enzymes in the forward and backward directions, and kinetic trapping of a potentially toxic intermediate. Experimental data with recombinational DNA repair genes validate the concept. Mathematical modeling recapitulates the possibility of kinetic trapping and revealed the potential contributions of synthetic, dosage-lethal interactions in such a genetic system as well as the possibility of within-pathway positive masking interactions. Analysis of yeast gene interaction and pathway data suggests broad applicability of this novel concept. These observations extend the canonical interpretation of synthetic-lethal or synthetic-sick interactions with direct implications to reconstruct molecular pathways and improve therapeutic approaches to diseases such as cancer. Author Summary: Organizing gene functions into molecular pathways is a major challenge in biology. The observation that two viable gene mutations become lethal when combined as a double mutant has been developed into a major genetic tool called synthetic lethality. The classic interpretation of synthetic lethality stipulates that the two mutations identify genes that work in parallel, mutually compensatory pathways that together perform an essential function. However, a significant number of negative interactions are caused by defects affecting a single molecular pathway. Here, we recapitulate by mathematical modeling recent experimental data that demonstrate synthetic lethality between mutations in genes acting in a single, non-essential molecular pathway. We propose a novel mechanism involving reversible pathways steps and trapping of an intermediate. The modeling also predicts that overexpression of certain genes functioning in reversible pathways will lead to synthetic lethality with gene defects in the same pathway. Our results significantly broaden the interpretation of synthetic lethal and synthetic dosage effects, which fundamentally impacts the assignment of genes to pathways. The concept of synthetic lethality has been applied to cancer therapy, and our modeling results suggest new approaches to how to target a single pathway to induce synthetic lethality in cancer cells.