The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli.

Jean-Philippe Côté,Sebastian S Gehrke,Amrita Bharat,Eric D Brown,Shawn French,Craig R Macnair,Chand S Mangat,Paul Dunman

doi:10.1128/mbio.01714-16

Abstract

ABSTRACTConventional efforts to describe essential genes in bacteria have typically emphasized nutrient-rich growth conditions. Of note, however, are the set of genes that become essential when bacteria are grown under nutrient stress. For example, more than 100 genes become indispensable when the model bacterium Escherichia coli is grown on nutrient-limited media, and many of these nutrient stress genes have also been shown to be important for the growth of various bacterial pathogens in vivo. To better understand the genetic network that underpins nutrient stress in E. coli, we performed a genome-scale cross of strains harboring deletions in some 82 nutrient stress genes with the entire E. coli gene deletion collection (Keio) to create 315,400 double deletion mutants. An analysis of the growth of the resulting strains on rich microbiological media revealed an average of 23 synthetic sick or lethal genetic interactions for each nutrient stress gene, suggesting that the network defining nutrient stress is surprisingly complex. A vast majority of these interactions involved genes of unknown function or genes of unrelated pathways. The most profound synthetic lethal interactions were between nutrient acquisition and biosynthesis. Further, the interaction map reveals remarkable metabolic robustness in E. coli through pathway redundancies. In all, the genetic interaction network provides a powerful tool to mine and identify missing links in nutrient synthesis and to further characterize genes of unknown function in E. coli. Moreover, understanding of bacterial growth under nutrient stress could aid in the development of novel antibiotic discovery platforms.

Highlights

Conventional efforts to describe essential genes in bacteria have typically emphasized nutrient-rich growth conditions
For the pathogen Mycobacterium tuberculosis, the synthesis of certain vitamins is crucial for the establishment of an infection [13, 20], and this has prompted several groups to look for inhibitors of biotin and pantothenate biosynthesis [21]
The approach relies on the high-throughput engineering of double deletion mutants by bacterial conjugation, where a query gene deletion is combined with every single gene deletion mutant in the Keio collection

Summary

Introduction

Conventional efforts to describe essential genes in bacteria have typically emphasized nutrient-rich growth conditions. We studied a group of genes that are essential for the growth of Escherichia coli under nutrient limitation, culture conditions that arguably better represent nutrient availability during an infection than rich microbiological media. It is worth noting that synthetic interactions often involve genes that are not linked on the chromosome and that are not related to each other Overall, these examples highlight instances where gene essentiality is highly dependent on genetic context. The environmental context of nutrient stress may well be a better proxy for the conditions during an infection than rich microbiological media This expands the list of potential targets for antimicrobial therapies and facilitates whole-cell screening and target discovery platforms that make use of suppression by nutrients [22, 23]. Our data highlight a surprising number and density of genetic interactions inherent in nutrient biosynthesis, including important redundancy to buffer perturbations associated with nutrient stress

Methods

Results

Conclusion