GEO DataSets

(Submitter supplied) In order for bacteria to thrive, they must be well-adapted to their environmental niche, which may involve specialized metabolism, timely adaptation to shifting environments, and/or the ability to mitigate numerous stressors. These attributes are highly dependent on cellular machinery that can sense both the external and intracellular environment. Methylorubrum extorquens is an extensively studied facultative methylotroph, an organism that can use single-carbon compounds as their sole source of carbon and energy. more...

Organism:

Methylorubrum extorquens PA1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29261

6 Samples

Download data: XLSX

(Submitter supplied) The potency and indiscriminate nature of formaldehyde reactivity upon biological molecules make it a universal stressor. However, some organisms such as Methylorubrum extorquens possess means to rapidly and effectively mitigate formaldehyde-induced damage. EfgA is a recently identified formaldehyde sensor predicted to halt translation in response to elevated formaldehyde as a means to protect cells. more...

Organism:

Methylorubrum extorquens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25388 GPL29545

81 Samples

Download data: TXT

(Submitter supplied) In order to provide information about the gene expression response that occurs when cells experience a change in carbon source, succinate limited chemostat cultures of Methylobacterium extorquens AM1 were grown to and maintained at an OD of ~0.63, transferred to flasks and methanol was added. Cells were harvested for RNA extraction at time: 0 min, 10 min, 30 min, 1 hr, 2 hr, 4 hr and 6 hr post transition. more...

Organism:

Methylorubrum extorquens AM1

Type:

Expression profiling by array

Platform:

GPL6262

24 Samples

Download data: TXT, XLS

(Submitter supplied) Methylorubrum extorquens AM1 is engineered to produce itaconic acid by heterologous expression of cis-aconitic acid decarboxylase. Mutation was also performed on phaR in Methylorubrum extorquens AM1, which regulate poly-beta-hydroxybutyrate accumulation, in attempt to increase carbon flux toward itaconic acid production. However, in our case, itaconic acid production by phaR mutant strain was not higher than that of the wildtype. more...

Organism:

Methylorubrum extorquens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25388

9 Samples

Download data: TXT

(Submitter supplied) We report gene expression profiles for cultures grown in minimal salts medium with 125 mM methanol with and without addition of 2 uM lanthanum chloride

Organism:

Methylorubrum extorquens AM1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26093

5 Samples

Download data: TXT

(Submitter supplied) We report a genetic variant of Methylorubrum extorquens AM1 that hyperaccumulates the heavy lanthanide gadolinium. Using RNA-seq transcriptomics we identified wide-spread metabolic and physiological changes in this strain and experimentally validate several of them, including increased gadolinium transport and storage in an intracellular compartment we name the lanthasome.

Organism:

Methylorubrum extorquens AM1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31182

8 Samples

Download data: TXT

(Submitter supplied) We integrated genomic and transcriptomic analysis of a newly isolated obligate Methylomonas sp. DH-1 grown on methane and methanol. Comparative transcriptomic analysis between methane and methanol as a sole carbon source revealed different transcriptional responses of Methylomonas sp. DH-1, especially in C1 assimilation, the secondary metabolites pathways and the oxidative stress related genes

Organism:

Methylomonas sp. DH-1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23786

6 Samples

Download data: TXT

(Submitter supplied) We report RNA-seq datasets profiling the transcriptional response to a sudden change in growth substrate, from succinate to ethylamine. This detailed combined dataset provides a dynamic assessment of the transcriptional response to a metabolic perturbation. These datasets are the first reported RNA-seq datasets for gene expression in Methylobacterium extorquens AM1

Organism:

Methylorubrum extorquens AM1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19397

12 Samples

Download data: TXT

(Submitter supplied) In order to provide global information on gene expression during growth on C2 compounds, microarray analysis of M. extorquens AM1 cells was carried out, comparing ethylamine-grown cells to succinate-grown cells. This comparison has confirmed previous observations on the inducible nature of some of the enzymes involved in C2 metabolism, such as methylamine (and ethylamine) utilization system (mau), putative enzymes for converting acetaldehyde into acetate and acetyl-CoA, and enzymes of the ethylmalonyl-CoA pathway that has been proposed to operate for assimilation of acetyl-CoA into cell biomass.

Organism:

Methylorubrum extorquens AM1; Methylorubrum extorquens

Type:

Expression profiling by array

Platforms:

GPL6262 GPL10058

4 Samples

Download data: TXT

(Submitter supplied) The meristem-associated endosymbiont M. extorquens DSM13060 significantly increases needle and root growth of Scots pine (Pinus sylvestris L.) seedlings without producing plant hormones, but by aggregating around host nuclei. Here we studied gene expression of the pine host induced by M. extorquens DSM13060 infection. We selected the time point of 90 days post-inoculation for our analysis based, because at this point, Methylorubrum extorquens DSM13060 has systemically colonized the pine seedlings, being found throughout tissues of roots and shoots.

Organism:

Pinus sylvestris; Pinus pinaster

Type:

Expression profiling by array

Platform:

GPL29939

6 Samples

Download data: GPR, TXT, XLS, XLSX