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| Status |
Public on Oct 01, 2010 |
| Title |
Expression analysis of Sphingomonas paucimobilis sp. EPA505 during biodegradation kinetics of various PAHs and detection of gene in a contaminated soil S3 |
| Platform organism |
Sphingomonas paucimobilis |
| Sample organisms |
Sphingomonas paucimobilis; uncultured organism |
| Experiment type |
Expression profiling by array
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| Summary |
Studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. During the biodegradation kinetics with phenanthrene, fluoranthene or a mix of both pollutants, we identified the targeted set of genes induced by these pollutants, compared to basal expression detected with glucose.
Hybridizing total DNA extracted from S3, we show the efficiency of our probe design to study a complex environment. Despite the relative small size of our probes (23-mers), their sensitivity is reliable as we can detect the presence of genes in this complex mixture.
Obtained results are further described in Sébastien Terrat, Eric Peyretaillade, Olivier Gonçalves, Eric Dugat-Bony, Fabrice Gravelat, and Pierre Peyret. 2010 - Studying the ‘Unkown’ with Metabolic Design, a new probe design software for explorative functional microarrays development. Nucleic Acids Research (submited).
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| Overall design |
A 17 chip study was realized using total RNA recovered from separate cultures of Sphingomonas paucimobilis sp. EPA505 with phenanthrene, fluoranthene or a mix of these both pollutants as sole carbon and energy source. A negative kinetic expermient was realized with glucose as sole carbon and energy source. Each chip measures the expression level of 8 genes from Sphingomonas paucimobilis sp. EPA505 with 23-mer probes (a total of 8,048 probes) using a new design approach. We also assess metabolic capacities of microbial communities in an aromatic hydrocarbons contaminated soil named S3. Each probe was spotted in triplicate, and a total of 8,863 random probes was used to determine the background noise.
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| Contributor(s) |
TERRAT S, PEYRETAILLADE E, GONCALVES O, DUGAT-BONY E, GRAVELAT F, PEYRET P |
| Citation(s) |
20860850 |
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| Submission date |
Apr 20, 2010 |
| Last update date |
Mar 22, 2012 |
| Contact name |
TERRAT Sebastien |
| E-mail(s) |
sebastien.terrat@gmail.com
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| Phone |
33(0)473407604
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| Fax |
33(0)473407670
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| Organization name |
UMR CNRS 6023
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| Department |
Génomique Intégrée des Interactions Microbiennes
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| Lab |
Laboratoire Microorganismes : Génome et Environnement
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| Street address |
24, avenue des Landais, Campus des Cézeaux
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| City |
AUBIERE |
| ZIP/Postal code |
63171 |
| Country |
France |
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| Platforms (1) |
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| Samples (17)
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| Relations |
| BioProject |
PRJNA126403 |
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