Quantitative Genome-Wide Genetic Interaction Screens Reveal Global Epistatic Relationships of Protein Complexes in Escherichia coli

Abstract

Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI) screens can provide insights into the biological role(s) of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.

The Oxidative Stress Network of Mycobacterium tuberculosis Reveals Coordination between Radical Detoxification Systems

“…Surviving mutants were recovered from these animals and the relative representation of each transposon mutant was compared between the WT and ctpC::hyg libraries to generate a map of 181 aggravating or alleviating mutations (Figure 1A–C). This number of interacting genes was consistent with that observed for highly-connected “hub” genes in S. cerevisiae and E. coli genetic interaction maps, and our previous GI studies in Mtb (Babu et al, 2014; Costanzo et al, 2010; Griffin et al, 2011; Joshi et al, 2006). Among the previously recognized ROS detoxification systems, the peroxiredoxin, ahpE , showed the strongest interaction with ctpC (Table S1), whereas weaker and statistically non-significant interactions were found with katG and ahpCD .…”

Assembly pathway of a bacterial complex iron sulfur molybdoenzyme

“…The group of M. Babu has applied this approach to E. coli (138,139), and their findings support our proposed DMSO reductase maturation pathway. Specifically, the work suggests that protein homeostasis groups together the roles of chaperoning, protein folding, and proteases.…”

Coordinate Regulation of the Suf and Isc Fe-S Cluster Biogenesis Pathways by IscR Is Essential for Viability of Escherichia coli

“…Recently, a genome-wide genetic interaction screen revealed possible functional associations between components of the Suf pathway and the RavA-ViaA ATPase complex, in addition to products of the ynjABCDEFI genes that currently lack annotations to specific cellular pathways (41). Further studies are needed to establish what role these additional factors may play in the regulation of Suf and in maintaining Fe-S cluster homeostasis.…”