Next Article in Journal
The Role of the Transcriptional Response to DNA Replication Stress
Previous Article in Journal
Epigenetics in Stroke Recovery
Article Menu

Export Article

Open AccessArticle
Genes 2017, 8(3), 90; doi:10.3390/genes8030090

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
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)
View Full-Text   |   Download PDF [1374 KB, uploaded 28 February 2017]   |  

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. View Full-Text
Keywords: transcriptional elongation rates; RNA sequencing; transition; oxygen; Escherichia coli transcriptional elongation rates; RNA sequencing; transition; oxygen; Escherichia coli
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

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.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Genes EISSN 2073-4425 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top