Rolfe, M.D., Ocone, A., Stapleton, M.R. et al. (5 more authors) (2012) Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations. Open Biology, 2 (7). 120091. ISSN 2046-2441
Abstract
Understanding gene regulation requires knowledge of changes in transcription factor (TF) activities. Simultaneous direct measurement of numerous TF activities is currently impossible. Nevertheless, statistical approaches to infer TF activities have yielded non-trivial and verifiable predictions for individual TFs. Here, global statistical modelling identifies changes in TF activities from transcript profiles of Escherichia coli growing in stable (fixed oxygen availabilities) and dynamic (changing oxygen availability) environments. A core oxygen-responsive TF network, supplemented by additional TFs acting under specific conditions, was identified. The activities of the cytoplasmic oxygen-responsive TF, FNR, and the membrane-bound terminal oxidases implied that, even on the scale of the bacterial cell, spatial effects significantly influence oxygen-sensing. Several transcripts exhibited asymmetrical patterns of abundance in aerobic to anaerobic and anaerobic to aerobic transitions. One of these transcripts, ndh, encodes a major component of the aerobic respiratory chain and is regulated by oxygen-responsive TFs ArcA and FNR. Kinetic modelling indicated that ArcA and FNR behaviour could not explain the ndh transcript profile, leading to the identification of another TF, PdhR, as the source of the asymmetry. Thus, this approach illustrates how systematic examination of regulatory responses in stable and dynamic environments yields new mechanistic insights into adaptive processes.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2012 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0/, which permits unrestricted use, provided the original author and source are credited. |
Keywords: | Escherichia coli; mathematical modelling; oxygen-sensing; systems biology; transcript profiling; Aerobiosis; Anaerobiosis; Bacterial Outer Membrane Proteins; Escherichia coli; Escherichia coli Proteins; Iron-Sulfur Proteins; Kinetics; Models, Biological; Oxygen; Repressor Proteins |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield) > Department of Molecular Biology and Biotechnology (Sheffield) |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 19 Dec 2016 10:13 |
Last Modified: | 19 Dec 2016 10:13 |
Published Version: | http://dx.doi.org/10.1098/rsob.120091 |
Status: | Published |
Publisher: | The Royal Society |
Refereed: | Yes |
Identification Number: | 10.1098/rsob.120091 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:108130 |