GEO DataSets

(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) Several of the metabolic enzymes in methanotrophic bacteria rely on metals for both their expression and their catalysis. The MxaFI methanol dehydrogenase enzyme complex uses calcium as a cofactor to oxidize methanol, while the alternative methanol dehydrogenase XoxF uses lanthanide metals such as lanthanum and cerium for the same function. Lanthanide metals, abundant in the earth’s crust and widely used in electronic devices, strongly repress the transcription of mxaF yet activate the transcription of xoxF. more...

Organism:

Methylotuvimicrobium buryatense

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26131

8 Samples

Download data: TXT

(Submitter supplied) Methanol is considered as an interesting carbon source in biobased microbial production processes. As Corynebacterium glutamicum is an important host in industrial biotechnology, in particular for amino acid production, we performed studies on the response of this organism to methanol. C. glutamicum wild type was able to convert 13C-labeled methanol to 13CO2. Analysis of global gene expression in the presence of methanol revealed several genes of ethanol catabolism to be up-regulated, indicating that some of the corresponding enzymes are involved in methanol oxidation. more...

Organism:

Corynebacterium glutamicum ATCC 13032

Type:

Expression profiling by array

Platform:

GPL15451

5 Samples

Download data: GPR

(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) 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) 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) 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) In this study we investigated the steady-state growth of Methylotuvimicrobium alcaliphilum 20ZR in media containing calcium (Ca) or lanthanum (La, a REE element). RNA-seq profiling of Methylomicrobium alcaliphilum strain 20ZR in bioreactor on methane. Sample cultures, La-optimum, La-CH4 limited, Ca-optimum and Ca-CH4 limited, were collected and immediately transferred into tubes containing 5 ml of the stop solution (5% water-equilibrated phenol in ethanol). more...

Organism:

Methylotuvimicrobium alcaliphilum 20Z

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34098

8 Samples

Download data: TSV

(Submitter supplied) A total gene expression approach was applied to study the methylotrophic nature of B. methanolicus by comparing the gene expression in bacteria grown methylotropic compared to non-methylotrophic. Genes of interest with different gene expression were quantified in the same RNA samples by real-time PCR, confirming the results found in the microarray experiment. Genes of special interest that are expressed higher when grown methylotrophic, were the RuMP pathway genes located on the pBM19.

Organism:

Bacillus methanolicus

Type:

Expression profiling by array

Platform:

GPL15155

6 Samples

Download data: TXT

(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 goal was to use microarray to compare changes in the global transcription profiles between an engineered bacterial strain and one of its descendants subject to 600 generations of experimental evolution in batch culture. This comparison allowed us to identify a beneficial mutation that substantially increased expression of a novel cobalt transporter cassette in this descendant.

Organism:

Methylorubrum extorquens AM1

Type:

Expression profiling by array

Platform:

GPL6262

1 Sample

Download data: TXT

(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) Methanol (MeOH) is considered to be a poison in humans because of the alcohol dehydrogenase (ADH)-mediated conversion of MeOH into toxic formaldehyde (FA). Our recent genome-wide analysis of the mouse brain demonstrated that an increase in endogenous MeOH after ADH inhibition led to a significant increase in the plasma MeOH concentration and the modification of mRNA synthesis. These findings suggest endogenous MeOH involvement in homeostasis regulation by controlling mRNA levels. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

36 Samples

Download data

(Submitter supplied) Methanol (MeOH) is considered to be a poison in humans because of the alcohol dehydrogenase (ADH)-mediated conversion of MeOH into toxic formaldehyde (FA). Our recent genome-wide analysis of the mouse brain demonstrated that an increase in endogenous MeOH after ADH inhibition led to a significant increase in the plasma MeOH concentration and the modification of mRNA synthesis. These findings suggest endogenous MeOH involvement in homeostasis regulation by controlling mRNA levels. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) Methanol (MeOH) is considered to be a poison in humans because of the alcohol dehydrogenase (ADH)-mediated conversion of MeOH into toxic formaldehyde (FA). Our recent genome-wide analysis of the mouse brain demonstrated that an increase in endogenous MeOH after ADH inhibition led to a significant increase in the plasma MeOH concentration and the modification of mRNA synthesis. These findings suggest endogenous MeOH involvement in homeostasis regulation by controlling mRNA levels. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) We recently showed that methanol emitted by wounded plants might function as a signaling molecule for plant-to-plant and plant-to-animal communications. In mammals, methanol is considered a poison because the enzyme alcohol dehydrogenase (ADH) converts methanol into toxic formaldehyde. However, the detection of methanol in the blood and exhaled air of healthy volunteers suggests that methanol may be a chemical with specific functions rather than a metabolic waste product. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

8 Samples

Download data: TXT