title: Genome-wide Escherichia coli stress response and improved tolerance towards industrially relevant chemicals.
abstract: BACKGROUND
  Economically viable biobased production of bulk chemicals and biofuels typically requires high product titers. During microbial bioconversion this often leads to product toxicity, and tolerance is therefore a critical element in the engineering of production strains.
  
  
  RESULTS
  Here, a systems biology approach was employed to understand the chemical stress response of Escherichia coli, including a genome-wide screen for mutants with increased fitness during chemical stress. Twelve chemicals with significant production potential were selected, consisting of organic solvent-like chemicals (butanol, hydroxy-γ-butyrolactone, 1,4-butanediol, furfural), organic acids (acetate, itaconic acid, levulinic acid, succinic acid), amino acids (serine, threonine) and membrane-intercalating chemicals (decanoic acid, geraniol). The transcriptional response towards these chemicals revealed large overlaps of transcription changes within and between chemical groups, with functions such as energy metabolism, stress response, membrane modification, transporters and iron metabolism being affected. Regulon enrichment analysis identified key regulators likely mediating the transcriptional response, including CRP, RpoS, OmpR, ArcA, Fur and GadX. These regulators, the genes within their regulons and the above mentioned cellular functions therefore constitute potential targets for increasing E. coli chemical tolerance. Fitness determination of genome-wide transposon mutants (Tn-seq) subjected to the same chemical stress identified 294 enriched and 336 depleted mutants and experimental validation revealed up to 60 % increase in mutant growth rates. Mutants enriched in several conditions contained, among others, insertions in genes of the Mar-Sox-Rob regulon as well as transcription and translation related gene functions.
  
  
  CONCLUSIONS
  The combination of the transcriptional response and mutant screening provides general targets that can increase tolerance towards not only single, but multiple chemicals.
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.
authors.forename: Martin Holm
authors.initials: MH
authors.lastname: Rau
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.
authors.forename: Patricia
authors.initials: P
authors.lastname: Calero
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.
authors.forename: Rebecca M
authors.initials: RM
authors.lastname: Lennen
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.
authors.forename: Katherine S
authors.initials: KS
authors.lastname: Long
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark. atn@biosustain.dtu.dk.
authors.forename: Alex T
authors.initials: AT
authors.lastname: Nielsen
mesh_terms: D015107:4-Butyrolactone / Q000494:pharmacology; D056804:Biofuels; D000440:Butanols / Q000494:pharmacology; D002072:Butylene Glycols / Q000494:pharmacology; D004361:Drug Tolerance / Q000235:genetics; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics* / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000235:genetics; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics*; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D009154:Mutation; D009930:Organic Chemicals / Q000494:pharmacology; D018085:Regulon; D012997:Solvents / Q000494:pharmacology; D013312:Stress, Physiological / Q000235:genetics*; D013386:Succinates / Q000494:pharmacology; D049490:Systems Biology / Q000379:methods
chemical_list: D056804:Biofuels; D000440:Butanols; D002072:Butylene Glycols; D029968:Escherichia coli Proteins; D009930:Organic Chemicals; D012997:Solvents; D013386:Succinates; C039681:1,4-butanediol; D015107:4-Butyrolactone; C005229:itaconic acid
keywords: Biochemicals; Chemical stress; E. coli; Systems biology; Tn-seq; Tolerance; Transcription analysis