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Series GSE71851 Query DataSets for GSE71851
Status Public on Jul 07, 2016
Title High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2 [tiling array]
Organism Pseudomonas putida
Experiment type Expression profiling by genome tiling array
Summary Pseudomonas putida mt-2 metabolizes m-xylene and other aromatic compounds through the enzymes encoded by the xyl operons of the TOL plasmid pWW0 along with other chromosomally-encoded activities. Tiling arrays of densely overlapping oligonucleotides were designed to cover every gene involved in this process, allowing dissection of operon structures and exposing the interplay of plasmid and chromosomal functions. All xyl sequences were transcribed in response to aromatic substrates and the 3'-termini of both upper and lower mRNA operons extended beyond the ir coding regions, i.e., the 3'-end of the lower operon mRNA penetrated into the convergent xylS regulatory gene. Furthermore, xylR mRNA for the master m-xylene responsive regulator of the system was decreased by aromatic substrates, while the cognate upper operon mRNA was evenly stable throughout its full length. RNA-seq confirmed these data at a single-nucleotide level and refined the formerly misannotated xylL sequence. The chromosomal ortho route for degradation of benzoate (the ben, cat clusters and some pca genes) was activated by this aromatic, but not by the TOL substrates, toluene or m-xylene. We advocate this scenario as a testbed of natural 16 retroactivity between a pre-existing metabolic network and a new biochemical pathway implanted through gene transfer.
 
Overall design Custom Agilent tiling microarrays containing relevant regions of pWW0 plasmid were hybridized with two RNA samples each: altered and control (two channel-format). Four biological replicates were hybridized independently for each comparison.
 
Contributor(s) Kim J, Pérez-Pantoja D, Silva-Rocha R, Oliveros JC, de Lorenzo V
Citation(s)
  • Kim J, Pérez-Pantoja D, Silva-Rocha R, Oliveros JC et al. High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2. Environ Microbiol 2016 Oct;18(10):3327-3341. PMID: 26373670
Submission date Aug 07, 2015
Last update date Jul 10, 2016
Contact name Juan Carlos Oliveros
Organization name CNB, CSIC
Street address Darwin 3
City Cantoblanco
State/province Madrid
ZIP/Postal code 28049
Country Spain
 
Platforms (1)
GPL20782 Agilent-027322 Pseudomonas putida tiling array (Feature Number version)
Samples (28)
GSM1846852 p.putida (mt2)-m-xylene_vs_control-R1 (GenePix)
GSM1846853 p.putida (mt2)-m-xylene_vs_control-R2 (GenePix)
GSM1846854 p.putida (mt2)-m-xylene_vs_control-R3 (GenePix)
This SubSeries is part of SuperSeries:
GSE71853 High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2
Relations
BioProject PRJNA292322

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE71851_RAW.tar 110.0 Mb (http)(custom) TAR (of GPR, TXT)
Processed data included within Sample table

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