The Tolerome: A Database of Transcriptome-Level Contributions to Diverse Escherichia coli Resistance and Tolerance Phenotypes

Tolerance and resistance are complex biological phenotypes that are desirable bioengineering goals for those seeking to design industrial strains or prevent the spread of antibiotic resistance. Over decades of research, a wealth of information has been generated to attempt to decode a molecular basis for tolerance, but to fully achieve the goal of engineering tolerance, researchers must be able to easily learn from a variety of data sources. To this end, we here describe a resource designed to enable scrutiny of diverse tolerance phenotypes. We have curated hundreds of gene expression studies exploring the response of Escherichia coli to chemical and environmental perturbations, from antibiotics to biofuels and solvents and more. Overall, our efforts give rise to a database encompassing more than 56 000 gene expression changes across 89 different stress conditions. This resource is designed for compatibility with the Resistome database, which includes more than 5000 strains with mutations conferring resistance or sensitivity but no transcriptomic data. Thus, the work here results in the first combined resource specialized to tolerance and resistance in E. coli that supports investigations across genomic, transcriptomic, and phenotypic levels. We leverage the database to identify promising bioengineering targets by searching globally across multiple stress conditions as well as by narrowing the focus to fewer conditions of interest, such as biofuel stress and antibiotic stress. We discuss some of the most frequently differentially expressed or coexpressed genes, and predict which transcription factors and sigma factors most likely contribute to gene expression profiles in a wide array of conditions. We also compare profiles from sensitive and resistant strains, gaining knowledge of how responses differ per overrepresented gene ontology terms. Finally, we search for genes that are frequently differentially expressed but not mutated, with the expectation that these may present interesting targets for future engineering efforts. The curated data presented here is publicly available, and should be advantageous to those studying a variety of bacterial tolerance phenotypes.