Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss

Open Access
Publisher Website
Google Scholar
Abstract
Many genes can be deleted with little phenotypic consequences. By what mechanism and to what extent the presence of duplicate genes in the genome contributes to this robustness against deletions has been the subject of considerable interest. Here, we exploit the availability of high‐density genetic interaction maps to provide direct support for the role of backup compensation, where functionally overlapping duplicates cover for the loss of their paralog. However, we find that the overall contribution of duplicates to robustness against null mutations is low (∼25%). The ability to directly identify buffering paralogs allowed us to further study their properties, and how they differ from non‐buffering duplicates. Using environmental sensitivity profiles as well as quantitative genetic interaction spectra as high‐resolution phenotypes, we establish that even duplicate pairs with compensation capacity exhibit rich and typically non‐overlapping deletion phenotypes, and are thus unable to comprehensively cover against loss of their paralog. Our findings reconcile the fact that duplicates can compensate for each other's loss under a limited number of conditions with the evolutionary instability of genes whose loss is not associated with a phenotypic penalty. ### Synopsis Much of our understanding of biological processes has been derived from the characterization of the functional consequence to an organism of altering one or more of its genes. Efforts to systematically evaluate the phenotypic effects of gene loss, however, have been hampered by the fact that the disruption of most genes has surprisingly modest effects on cell growth and viability. The high proportion of genes with no apparent deletion effect has wide‐ranging practical and theoretical implications and has been the subject of considerable interest ([Wagner, 2000][1], [2005][2]; [Giaever et al , 2002][3]; [Gu et al , 2003][4]; [Papp et al , 2004][5]; [Kafri et al , 2005][6]). One factor that has been implicated as contributing to the high degree of dispensability is the abundance of closely related paralogs present in most genomes ([Winzeler et al , 1999][7]; [Wagner, 2000][1]; [Giaever et al , 2002][3]). Indeed, recent work in S. cerevisiae has shown that the existence of a paralog elsewhere in the genome significantly increases the chance that deletion of a given gene has little effect on growth ([Gu et al , 2003][4]). However, current analyses have been mostly correlative, and direct mechanistic evidence supporting or refuting the role of backup compensation in mutational robustness is still largely missing. Furthermore, backup between duplicates is not easily justified in evolutionary terms, in that a genuine ability to comprehensively cover for the loss of another gene is evolutionarily unstable ([Brookfield, 1992][8]). Here, we exploit the recent availability of high‐density quantitative genetic interaction profiles (EMAPs) to address these issues directly. To test whether SSL paralogs can account for the excess fitness of duplicates, we classified genes into fitness categories according to their deletion growth defect (Materials and methods). The subset of genes covered by our combined data set exhibits an over‐representation of duplicate genes in the weak/no deletion phenotype (WNP) class similar to that reported previously ([Gu et al , 2003][4]) ([Figure 1B][9]). Strikingly, this difference corresponds to the number of WNP duplicates that have an SSL interaction with their corresponding paralog ([Figure 1C][9]). Our data thus provide direct evidence that it is indeed duplicate compensation that accounts for the observed difference in deletion growth defect between duplicates and singletons, at least for the genes covered by our data set. Apart from the mechanism itself, the characteristic features of buffering duplicates have received considerable attention ([Gu et al , 2003][4]; [Kafri et al , 2005][6]; [Wagner, 2005][2]). Our data allowed us to unambiguously distinguish the subset of duplicates whose dispensability can be attributed to the existence of a backup paralog. The ability to identify backup duplicates directly put us in a position to study their features, and how they differ from other duplicates without buffering properties. In particular, we asked to what extent the observed buffering in rich media reflects functional similarity and a genuine ability to cover for the loss of a paralog in a broader range of conditions. To assess the extent to which SSL duplicates can provide genuine backup under compromising conditions, we fist used genetic interaction profiles as a more stringent test for redundancy that assesses the effect of gene loss in the background of additional gene deletions. In contrast to the expectation that truly buffered duplicates should have few if any synthetic interactions, we find that the number is in fact substantial and often exceeds that of random genes and non‐SSL duplicates ([Figure 2B][10]). Similarly, using a recent data set of sensitivity profiles of deletion strains to a range of agents and environments ([Brown et al , 2006][11]), we find that the deletion of SSL duplicates across a range of environments has on average no weaker (and in fact a slightly stronger) effect on cellular growth rate than that of non‐SSL duplicates or random genes. Taken together, these findings suggest that the backup capacity of SSL duplicates is limited and not indicative of a comprehensive ability to cover for the loss of the paralogous partner. We next tested the degree of functional similarity of buffering duplicates using similarity in genetic interaction as well as environmental sensitivity profiles as indicators of shared functionality ([Tong et al , 2004][12]; [Schuldiner et al , 2005][13]; [Brown et al , 2006][11]; [Pan et al , 2006][14]). In spite of their rich media buffering properties, we find that the interaction and...