The Escherichia coli dynamical response to oxygen: from molecular interactions to regulatory modules

SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".

The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.

Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...

"Systems Understanding of Microbial Oxygen responses" (SUMO) investigates how Escherichia coli senses oxygen, or the associated changes in oxidation/reduction balance, via the Fnr and ArcA proteins, how these systems interact with other regulatory systems, and how the redox response of an E. coli population is generated from the responses of single cells. There are five sub-projects to determine system properties and behaviour and three sub-projects to employ different and complementary modelling ...

Changing the oxygen availability leads to an adaptation of Escherichia coli at different biological levels. After pertubation of oxygen in chemostat experiments there are very quick responses. This investigation deals with this dynamical behaviour (transitions) of Escherichia coli within the aerobiosis scale. The change for different biological variables, in different areas of the organism like the electron transport chain, the TCA cycle or globally is investigated by wildtype and mutants experiments ...

This assay involved the determination of transcriptional profiles at 0, 2, 5, 10, 15 and 20 minutes through aerobic to anaerobic gas transitions and anaerobic to aerobic gas transitions. In each case an aerobic or anaerobic steady state was created, RNA sampled (0 min) and then the gas supply changed. RNA samples were then taken from the time at which the gas supply was changed.

For anaerobic conditions 5% CO2, 95% N2 was used.

The full transcriptional dataset is available from ArrayExpress ...

This .csv file contains the filtered datset of the aerobic to anaerobic transition. Values are shown if they show a statistically significant change relative to the 0 minute transcriptional profile (t-test p<0.05 and 2-fold cut-off).

This .csv file contains the filtered datset of the anaerobic to aerobic transition. Values are shown if they show a statistically significant change relative to the 0 minute transcriptional profile (t-test p<0.05 and 2-fold cut-off).

This is a pdf showing a graph of the dissolved oxygen tension of the culture during an aerobic to anaerobic transition.

This is a pdf showing a graph of the dissolved oxygen tension of the culture during an anaerobic to aerobic transition.

This .csv file contains the entire transcriptional dataset of the aerobic to anaerobic transition. The values shown are the gene-expression ratio at 2, 5, 10, 15 and 20 minutes relative to the 0 minute timepoint.

This .csv file contains the entire transcriptional dataset of the anaerobic to aerobic transition. The values shown are the gene-expression ratio at 2, 5, 10, 15 and 20 minutes relative to the 0 minute timepoint.

This protocol describes the transcriptional profiling of E. coli cultures using microarrays. The protocol utilises RNA isolated as described in another SOP (SUMO RNA isolation from E. coli) and with hybridisation to Ocimum Ocichip E. coli K-12 microarrays.

This SOP describes the preparation of E. coli RNA

This document describes the chemostat conditions to run comparable experiments in different bioreactors in different labs.