title: Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds.
abstract: Volatile organic compounds (VOCs) are commonly used as solvents in various industrial settings. Many of them present a challenge to receiving environments, due to their toxicity and low bioavailability for degradation. Microorganisms are capable of sensing and responding to their surroundings and this makes them ideal detectors for toxic compounds. This study investigates the global transcriptomic responses of Escherichia coli K-12 to selected VOCs at sub-toxic levels. Cells grown in the presence of VOCs were harvested during exponential growth, followed by whole transcriptome shotgun sequencing (RNAseq). The analysis of the data revealed both shared and unique genetic responses compared to cells without exposure to VOCs. Results suggest that various functional gene categories, for example, those relating to Fe/S cluster biogenesis, oxidative stress responses and transport proteins, are responsive to selected VOCs in E. coli. The differential expression (DE) of genes was validated using GFP-promoter fusion assays. A variety of genes were differentially expressed even at non-inhibitory concentrations and when the cells are at their balanced-growth. Some of these genes belong to generic stress response and others could be specific to VOCs. Such candidate genes and their regulatory elements could be used as the basis for designing biosensors for selected VOCs.
authors.affiliation: Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551.
authors.forename: Pui Yi
authors.initials: PY
authors.lastname: Yung
authors.affiliation: Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551.
authors.forename: Letizia Lo
authors.initials: LL
authors.lastname: Grasso
authors.affiliation: Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551.
authors.forename: Abeed Fatima
authors.initials: AF
authors.lastname: Mohidin
authors.affiliation: Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551.
authors.forename: Enzo
authors.initials: E
authors.lastname: Acerbi
authors.affiliation: Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551.
authors.forename: Jamie
authors.initials: J
authors.lastname: Hinks
authors.affiliation: Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551.
authors.forename: Thomas
authors.initials: T
authors.lastname: Seviour
authors.affiliation: Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551.|School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459.|School of Biotechnology, Dublin City University, Collins Avenue, Dublin 9, Ireland.
authors.forename: Enrico
authors.initials: E
authors.lastname: Marsili
authors.affiliation: Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551.|Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, N2-01C-45, Singapore 639798.
authors.forename: Federico M
authors.initials: FM
authors.lastname: Lauro
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology; D048168:Escherichia coli K12 / Q000187:drug effects* / Q000235:genetics*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D063990:Gene Ontology; D058977:Molecular Sequence Annotation; D013312:Stress, Physiological / Q000235:genetics; D059467:Transcriptome; D055549:Volatile Organic Compounds / Q000494:pharmacology*
chemical_list: D055549:Volatile Organic Compounds
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