Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics

Abstract

Escherichia coli is able to shift between anaerobic and aerobic metabolism by adapting its gene expression, e.g., of metabolic genes, to the new environment. The dynamics of gene expression that result from environmental shifts are limited, amongst others, by the time needed for regulation and transcription elongation. In this study, we examined gene expression dynamics after an anaerobic-to-aerobic shift on a short time scale (0.5, 1, 2, 5, and 10 min) by RNA sequencing with emphasis on delay times and transcriptional elongation rates (TER). Transient expression patterns and timing of differential expression, characterized by delay and elongation, were identified as key features of the dataset. Gene ontology enrichment analysis revealed early upregulation of respiratory and iron-related gene sets. We inferred specific TERs of 89 operons with a mean TER of 42.0 nt/s and mean delay time of 22.4 s. TERs correlate with sequence features, such as codon bias, whereas delay times correlate with the involvement of regulators. The presented data illustrate that at very short times after a shift in oxygenation, extensional changes of the transcriptome, such as temporary responses, can be observed. Besides regulation, TERs contribute to the dynamics of gene expression.

Attractor Concepts to Evaluate the Transcriptome-wide Dynamics Guiding Anaerobic to Aerobic State Transition in Escherichia coli

“…were performed by Feuer and colleagues 26 . Briefly, E. coli K-12 strain W3110 cells were grown anaerobically in a 3-liter continuously stirred tank bioreactor at pH7 and 37°C, and stirred at 500 rpm with a Rushton turbine.…”

16S rRNA:rDNA ratios and cell activity staining reveal consistent patterns of soil microbial activity

“…In the corn soil experiment, the drying and re-wetting treatments lasts three and six days, respectively, while the phytohormone treatments lasted only 24 hours, and in the bean soil experiment, treatments were continuously applied for the approximately five weeks of the experiment. Given that differential transcription of RNA can occur within 30 seconds after an environmental stimulus (33) but cell doubling takes considerably longer (~10 minutes for only the very fastest-growing strains under optimal laboratory conditions (34), and many hours for others especially in natural environmental conditions (35 and references therein)), the 16S ratio method may be more sensitive in short time-frames than the CTC staining method. This may explain why the relatively short (24-hour) phytohormone treatments in corn soil resulted in relatively large decreases in percent activity using 16S ratios (average difference of 17.8% activity compared to ‘post-water’), but much smaller (albeit significant) increases in percent activity using CTC staining (average difference of 5.1% activity compared to ‘post-water’) (Fig.…”

Engineering Robust Production Microbes for Large-Scale Cultivation

“…In these early studies, Gluconobacter oxydans was cycled between zones with low and high oxygen availability to study the effect on gluconic acid production. More recent studies used similar approaches to study the effect of oxygen availability on intracellular processes in E. coli and C. glutamicum [18,[33][34][35][36]. In these studies, transcriptional changes between aerobic and anaerobic environments explained observed alterations in stoichiometry and kinetics, as well as production of ethanol and organic acids, indicating that E. coli responds rapidly to dissolved oxygen gradients [33].…”