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

1
Institute for System Dynamics, University of Stuttgart, Keplerstraße 7, 70174 Stuttgart, Germany
2
Insitute of Medical Genetics and Applied Genomics, University of Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany
*
Author to whom correspondence should be addressed.
Academic Editor: Thierry Wirth
Genes 2017, 8(3), 90; https://doi.org/10.3390/genes8030090
Received: 15 December 2016 / Revised: 10 February 2017 / Accepted: 20 February 2017 / Published: 28 February 2017
(This article belongs to the Section Microbial Genetics and Genomics)
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. View Full-Text
Keywords: transcriptional elongation rates; RNA sequencing; transition; oxygen; Escherichia coli transcriptional elongation rates; RNA sequencing; transition; oxygen; Escherichia coli
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Von Wulffen, J.; Ulmer, A.; Jäger, G.; Sawodny, O.; Feuer, R. Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics. Genes 2017, 8, 90.

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