GEO DataSets

(Submitter supplied) We report the transcriptomic profiles of 2 different Pseudomonas putida derivatives when they are grown in MME medium supplemented with either ammonium or nitrate as the sole nitrogen source. Expression of both heterologous and native genes are examined.

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25301

14 Samples

Download data: CSV

(Submitter supplied) mRNA was sampled during exponential growth (OD600 = 2, Control), then an inhibitory dose of 5 mM catechol was added to the culture and samples were taken again after 1h (Stress)

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by array

Platform:

GPL31933

6 Samples

Download data: CSV, TXT

(Submitter supplied) Aromatic diketones are a major product of formic acid lignin depolymerization. Novosphingobium aromaticivorans can degrade these diketones, but the enzymes used in this process were unknown. We used RNA-Seq to identify aromatic dimer dehydrogenases as potential candidates for the initial reduction of the aromatic G-diketone, then verified this using in vitro enzyme assays.

Organism:

Novosphingobium aromaticivorans DSM 12444

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30162

20 Samples

Download data: XLSX

(Submitter supplied) Pseudomonas putida KT2440 has received increasing attention as an important biocatalyst for the conversion of diverse carbon sources to multiple products, including the olefinic diacid, cis,cis-muconic acid (muconate). P. putida has been previously engineered to produce muconate from glucose; however, periplasmic oxidation of glucose causes substantial 2-ketogluconate accumulation, reducing product yield and selectivity. more...

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28478

9 Samples

Download data: CSV

(Submitter supplied) Pseudomonas putida is characterized by a versatile metabolism and stress tolerance traits that allow the bacterium to cope with different environmental conditions. In this work, the mechanisms that allow P. putida KT2440 to grow in the presence of four sole carbon sources (glucose, citrate, ferulic acid, serine) were investigated by RNA sequencing (RNA-seq) and genome-scale metabolic modeling. Transcriptomic data identified uptake systems for the four carbon sources, and candidates were subjected to preliminary experimental characterization by mutant strain growth to test their involvement in substrate assimilation. more...

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17091

12 Samples

Download data: TXT

(Submitter supplied) Convergent microbial biocatalysis has emerged as a promising approach for the conversion of lignin side-streams into value-added chemicals in recent decades. However, the current knowledge of metabolic pathways directing the bioconversion of lignin-related aromatics is still limited to a few microbial species and unavailable for some of these compounds. Thus, the aim of this study was to identify the genes involved in the bioconversion of aromatic compounds in Xanthomonas citri subsp. more...

Organism:

Xanthomonas citri subsp. citri 306

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34065

38 Samples

Download data: XLSX

(Submitter supplied) Widely reported discrepancies between metabolic flux and transcripts or enzyme levels in bacterial metabolism imply complex regulation mechanisms need to be considered, especially in new bacterial platforms for bioremediation and bioproduction. Comamonas testosteroni strains, which metabolize various natural and xenobiotic aromatic compounds, represent such platforms whose metabolic regulations are still unknown. more...

Organism:

Comamonas testosteroni

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31156

12 Samples

Download data: TSV