WP1.1 The Escherichia coli response to oxygen: from molecular interactions to regulatory modules

Project Leaders: Robert Poole and Jeffrey Green

Post-doctoral staff: Matt Rolfe and Alison Graham

Goal and project description

(Source: original project application)

The data that will be used to create the initial, simple model outlined in WP2.1 have been gathered using a number of different bacterial strains grown at different growth rates, in different media, under different conditions of aeration, and with little attention to dynamics. The diversity of previous approaches clearly limits the potential usefulness of the data and so, to develop a predictive model of the E. coli response to oxygen, new internally consistent quantitative data sets describing the dynamics of the response are needed. Therefore, we will obtain time-resolved transcriptomic, proteomic, metabolomic and biochemical data sets describing the response of E. coli to its oxygen/redox environment. The data sets will then be extended by investigating the consequences of mutations in key genes (e.g. fnr, arcA, cyoA-E, cydAB) in the bacterial response to oxygen. The analysis of mutants will reveal any system redundancies by providing an indication of flexibility in the use of alternative pathways for maintain function.

Experiments carried out in WP1.1

FNR activity at different oxygen levels
Transcriptional profiling of anaerobic/aerobic transitions

SOPs used in WP1.1

Creation of chromosomal β-galactosidase fusions
β-galactosidase assay
Dry cell weight measurement
Measurement of terminal oxidases
RNA isolation
Transcriptional profiling