Both authors contributed equally to the work.
The IHF regulon of exponentially growing Pseudomonas putida cells
Article first published online: 17 APR 2012
© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd
Special Issue: Baeza
Volume 15, Issue 1, pages 49–63, January 2013
How to Cite
Silva-Rocha, R., Chavarría, M., Kleijn, R. J., Sauer, U. and de Lorenzo, V. (2013), The IHF regulon of exponentially growing Pseudomonas putida cells. Environmental Microbiology, 15: 49–63. doi: 10.1111/j.1462-2920.2012.02750.x
- Issue published online: 3 JAN 2013
- Article first published online: 17 APR 2012
- Received 21 January, 2012; revised 19 March, 2012; accepted 20 March, 2012.
Integration host factor (IHF) sites are largely absent from intergenic regions of ORFs encoding central metabolic functions in Pseudomonas putida mt-2. To gain an insight into this unequal distribution of otherwise abundant IHF-binding sequences, the transcriptome of IHF-plus and IHF-minus cells growing exponentially on glucose as sole carbon source was examined. In parallel, the cognate metabolic fluxes of the wild-type P. putida strain and its ihfA derivative were determined by culturing cells to a steady-state physiological regime with 13C-labelled glucose. While expression of many transcripts was altered by the lack of IHF, flux balance analysis revealed that the ihfA mutation did not influence central carbon metabolism. Identification of multiple IHF sites adjacent to genes responsive to the factor allowed a refinement of the consensus and the mapping of the preferred binding positions for activation or repression of associated promoters. That few (if any) of the genes affected by IHF involved core pathways suggested that the central carbon metabolism tolerates the loss of the factor. Instead, IHF controlled various cell surface-related functions and downregulated genes encoding ribosomal proteins, the alpha subunit of RNA polymerase and components of the ATP synthase. These results were confirmed with lacZ fusions to a suite of promoters detected in the transcriptome as affected by IHF. Taken together, the data suggest that IHF plays a role in the physiological shift that sets P. putida for entering stationary phase.