title: Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics.
abstract: Escherichia coliis 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.
authors.affiliation: Institute for System Dynamics, University of Stuttgart, Keplerstraße 7, 70174 Stuttgart, Germany. vonwulffen@isys.uni-stuttgart.de.
authors.forename: Joachim
authors.initials: J
authors.lastname: von Wulffen
authors.affiliation: Institute for System Dynamics, University of Stuttgart, Keplerstraße 7, 70174 Stuttgart, Germany. ulmer.bio@gmail.com.
authors.forename: Andreas
authors.initials: A
authors.lastname: Ulmer
authors.affiliation: Insitute of Medical Genetics and Applied Genomics, University of Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany. guenter.jaeger@cegat.de.
authors.forename: Günter
authors.initials: G
authors.lastname: Jäger
authors.affiliation: Institute for System Dynamics, University of Stuttgart, Keplerstraße 7, 70174 Stuttgart, Germany. oliver.sawodny@isys.uni-stuttgart.de.
authors.forename: Oliver
authors.initials: O
authors.lastname: Sawodny
authors.affiliation: Institute for System Dynamics, University of Stuttgart, Keplerstraße 7, 70174 Stuttgart, Germany. ronny.feuer@isys.uni-stuttgart.de.
authors.forename: Ronny
authors.initials: R
authors.lastname: Feuer
keywords: Escherichia coli; RNA sequencing; oxygen; transcriptional elongation rates; transition