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| Status |
Public on Jul 25, 2012 |
| Title |
The IHF regulon of exponentially growing Pseudomonas putida cells |
| Platform organism |
Pseudomonas putida KT2440 |
| Sample organism |
Pseudomonas putida |
| Experiment type |
Expression profiling by array
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| Summary |
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 (13) C-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.
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| Overall design |
We compared the transcriptional profiles of P. putida mt-2 and the ihfA mutant. Samples were hybridized on a P. putida genome-wide oligonucleotide-based DNA microarray (Progenika Biopharma SA). RNA samples of seven independent biological samples were mixed in three pools. A dye-swap was performed.
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| Contributor(s) |
Silva-Rocha R, ChavarrÃa M, Kleijn RJ, Sauer U, de Lorenzo V |
| Citation(s) |
22510163 |
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| Submission date |
Aug 06, 2010 |
| Last update date |
Sep 21, 2012 |
| Contact name |
Victor de Lorenzo |
| Organization name |
CNB-CSIC
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| Department |
Systems Biology
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| Street address |
Darwin 3
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| City |
Campus de Cantoblanco |
| State/province |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
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| Platforms (1) |
| GPL10767 |
Progenika Biopharma Pseudomonas putida MPA-02-0001 |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA131011 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE23499_RAW.tar |
3.7 Mb |
(http)(custom) |
TAR (of GPR) |
| Processed data included within Sample table |
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