GEO DataSets

(Submitter supplied) RNA-seq analysis revealed that genes involved in urea uptake and metabolism were significantly upregulated in the Clo1313_2031 deletion strain, suggesting that deletion of Clo1313_2031 mimics nitrogen starvation in C. thermocellum. Additionally, genes encoding the RNF-complex were also more highly expressed and in turn may have a potential role in increasing ethanol production.

Organism:

Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20122

8 Samples

Download data: TXT, XLSX

(Submitter supplied) Background: The ability of Clostridium thermocellum ATCC 27405 wild-type strain to hydrolyze cellulose and ferment the degradation products directly to ethanol and other metabolic byproducts makes it an attractive candidate for consolidated bioprocessing of cellulosic biomass to biofuels. In this study, whole-genome microarrays were used to investigate the expression of C. thermocellum mRNA during growth on crystalline cellulose in controlled replicate batch fermentations. more...

Organism:

Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL13640

39 Samples

Download data: TXT

(Submitter supplied) Four C. thermocellum DSM-1313 derived strains were assessed using metabolite and DNA microarray tools in order to better understand carbon and electron flow within this organism. C. thermocellum is able to ferment cellulose into its fermentation end products L-lactate, acetate, formate, hydrogen gas, and ethanol, with the latter being the desired end product to be used as biorenewable fuel. In addition to the parent strain (genotype: hpt spo0A), strains with either or both of the genes encoding lactate dehydrogenase (ldh) and phosphate acetyltransferase (pta) deleted were studied. more...

Organism:

Acetivibrio thermocellus ATCC 27405; Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by array

Platform:

GPL13117

24 Samples

Download data: XYS

(Submitter supplied) Clostridium thermocellum is a candidate for cellulosic ethanol production. It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Understanding how this organism regulates gene expression is of importance for developing a better fundamental understanding of this industrial relevant bacterium. We are primarily interested in gene regulation by three predicted LacI regulators. more...

Organism:

Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20122

36 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of Haloferax mediterranei DglnA and HM26 strains in two different culture media: a) cells were grown exponentially on complex media + 40 mM Gln, b) cells were shifted to nitrogen starvation conditions (72h). In the Nsta(∆glnA)-Cx and Nsta-Cx contrasts, glnA2 was up-regulated, and glnA3 did not show any difference. Therefore, glnA2 and glnA3 were unable to compensate lack of glnA because either they do not properly encode GS or are not expressed under the same conditions.

Organism:

Haloferax mediterranei

Type:

Expression profiling by array

Platform:

GPL18892

8 Samples

Download data: TXT

(Submitter supplied) Clostridium thermocellum is a Gram-positive, anaerobic, thermophilic bacterium that ferments cellulose into ethanol. It is a candidate industrial consolidated bioprocess (CBP) biocatalyst for lignocellulosic bioethanol production. However, C. thermocellum is relatively sensitive to ethanol compared to yeast. Previous studies have investigated the membrane and protein composition of wild-type and ethanol tolerant strains, but relatively little is known about the genome changes associated with the ethanol tolerant C. more...

Organism:

Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL11186

30 Samples

Download data: CALLS, PAIR

(Submitter supplied) Clostridium thermocellum is a promising CBP candidate organism capable of directly converting lignocellulosic biomass to ethanol. Low yields, productivities and growth inhibition prevent industrial deployment of this organism for commodity fuel production. Symptoms of potential redox imbalance such as incomplete substrate utilization, and fermentation products characteristic of overflow metabolism, have been observed during growth. more...

Organism:

Acetivibrio thermocellus ATCC 27405; Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by array

Platform:

GPL20749

32 Samples

Download data: TXT

(Submitter supplied) Earlier studies pointed to the ability of C. thermocellum to exquisitely control gene expression in response to growth rate and the presence of insoluble cellulose or soluble compounds such as cellobiose. This microarray study was carried out in order to examine expression responses of the entire genome. The use of the chemostat technique allowed the effects of different growth rates to be analyzed separately from the effects of different substrates.

Organism:

Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL10557

11 Samples

Download data: PAIR

(Submitter supplied) Background: The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It is capable of both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Intolerance to stresses routinely encountered during industrial fermentations may hinder the commercial development of this organism. Results: In this study, C. more...

Organism:

Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL15992

43 Samples

Download data: TXT

(Submitter supplied) Clostridium (Ruminiclostridium) thermocellum is recognized for its ability to ferment cellulosic biomass directly, but it cannot naturally grow on xylose. Recently, C. thermocellum (KJC335) was engineered to utilize xylose through expressing a heterologous xylose catabolizing pathway. Here, we compared KJC335’s transcriptomic responses to xylose versus cellobiose as the primary carbon source and assessed how the bacteria adapted to utilize xylose. more...

Organism:

Acetivibrio thermocellus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27465

6 Samples

Download data: XLSX

(Submitter supplied) Differential RNA-Seq analyses to investigate the basis for metabolic inhibition of Clostridium thermocellum M1570 by xylose. The M1570 strain was developed in the C. thermocellum DSM 1313 Δhpt background strain. Lactate dehydrogenase (Ldh) and phosphotransacetylase (Pta) genes are deleted (Argyros DA, Tripathi SA, Barrett TF, Rogers SR, Feinberg LF, Olson DG, Foden JM, Miller BB, Lynd LR, Hogsett DA, Caiazza NC: High ethanol titers from cellulose by using metabolically engineered thermophilic, anaerobic microbes. more...

Organism:

Acetivibrio thermocellus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21122

8 Samples

Download data: TXT, XLSX

(Submitter supplied) The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. To gain insights into the C. thermocellum genes, using an updated version of the C. thermocellum ATCC 27405 genome annotation, that are required for specific growth on the cellulosic feedstocks of either pretreated switchgrass or Populus, duplicate fermentations were conducted with a 5 g/L solid substrate loading. more...

Organism:

Acetivibrio thermocellus 27405; Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL17171

8 Samples

Download data: CALLS, PAIR