GEO DataSets

(Submitter supplied) Zymomonas mobilis ZM4 produces near theoretical yields of ethanol with high specific productivity and recombinant strains are able to ferment both C-5 and C-6 sugars. However, the genetic and physiological basis of the ZM4 response to various industrially-relevant stresses is poorly understood. In this study, the dynamics of ZM4 oxygen stress responses were elucidated by characterizing the transcriptomic and metabolomic profiles of aerobic and anaerobic fermentations using whole-genome microarray analysis and gas chromatography-mass spectrometry. more...

Organism:

Zymomonas mobilis

Type:

Expression profiling by array

Platform:

GPL6431

24 Samples

Download data: TXT

(Submitter supplied) This study is aimed for the identification of novel small RNAs under different ethanol producing conditions. We have applied transcriptome analysis to facilitate identification and validation of 15 novel sRNAs in Zymomonas mobilis. We furthermore characterize their expression in the context of high and low levels of intracellular ethanol. Here, we report that 3 of the sRNAs (Zms2, Zms4 and Zms6) are differentially expressed under aerobic and anaerobic conditions, when low and high ethanol productions are observed respectively. more...

Organism:

Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18707

2 Samples

Download data: TXT

(Submitter supplied) Background Zymomonas mobilis ZM4 is a capable ethanologenic bacterium with high ethanol productivity and ethanol tolerance. Previous studies indicated that several stress-related proteins and changes in the ZM4 membrane lipid composition may contribute to ethanol tolerance. However, the molecular mechanisms of its ethanol stress response have not been elucidated fully. Methodology/Principal Findings In this study, ethanol stress responses were investigated using systems biology approaches. more...

Organism:

Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

Type:

Expression profiling by array

Platform:

GPL10278

16 Samples

Download data: TXT

(Submitter supplied) Zymomonas mobilis is an excellent ethanologenic bacterium. Biomass pretreatment and saccharification provides access to simple sugars, but also produces inhibitors such as acetate and furfural. Our previous work has identified and confirmed the genetic change of a 1.5-kb deletion in the sodium acetate tolerant Z. mobilis mutant (AcR) leading to constitutively elevated expression of a sodium proton antiporter encoding gene nhaA, which contributes to the sodium acetate tolerance of AcR mutant. more...

Organism:

Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

Type:

Expression profiling by array

Platform:

GPL11220

16 Samples

Download data: TXT

(Submitter supplied) In this study, we reported the updated chromosome and plasmid sequence of ZM4, and its two engineered xylose-utilizing strains derivatives (strains 2032 and 8b). The majority of plasmid genes have either homologs from other organisms or some conserved domains. Our bioinformatics analysis suggested that several plasmid genes may be essential genes of ZM4. To further validate the function of these plasmid genes, an RNA-Seq pipeline was developed for Z. more...

Organism:

Zymomonas mobilis subsp. mobilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24485

17 Samples

Download data: TXT

(Submitter supplied) High glucose concentrations were desirable for ethanol fermentation of Zymomonas mobilis, but it can lead to decrease in ethanol production and productivity. Sorbitol as a compatible solute can be absorbed or synthesized to counteract the detrimental osmotic stress caused from external high glucose concentrations by Z. mobilis. Currently, molecular mechanisms of tolerance to high glucose concentrations and sorbitol promoting ethanol fermentation are still unclear for Z. more...

Organism:

Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

Type:

Expression profiling by array

Platform:

GPL17542

12 Samples

Download data: PAIR

(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) In our previous study, we successfully constructed an engineered Zymomonas mobilis ZM532 strain tolerant these double inhibitors by genome shuffling, but the molecular mechanisms of tolerance to these inhibitors are still unknown. The goal of this study investigated the responses of ZM532 and wild-type ZM4 to acetic acid and furfural using Transcriptome

Organism:

Zymomonas mobilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29852

12 Samples

Download data: TXT

(Submitter supplied) High-resolution “tiling” expression data for Zymomonas mobilis ZM4 growing in rich and minimal media, heat-shocked, or at high ethanol

Organism:

Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

Type:

Expression profiling by genome tiling array

Platform:

GPL17859

5 Samples

Download data: FTR, TXT

(Submitter supplied) We report the genome changes associated with a Zymomonas mobilis sodium acetate-tolerant mutant (AcR). We used comparative genomics, transcriptomics, and genetics to show nhaA over-expression conferred sodium acetate (NaAc) tolerance in Z. mobilis. We observed a synergistic effect for sodium and acetate ions that enhanced toxicity against the wild-type strain (ZM4), which was not observed for similar concentrations of potassium and ammonium acetate under controlled laboratory conditions. more...

Organism:

Zymomonas mobilis

Type:

Expression profiling by array

Platform:

GPL9192

20 Samples

Download data: CALLS, PAIR

(Submitter supplied) Nimblegen proprietary.

Organism:

Zymomonas mobilis

1 Series

1 Related Platform

20 Samples

Download data: CSV, NDF

(Submitter supplied) Looking at the expression levels of all the genes of Zymomonas mobilis ZM4; and in particular we would like to predict the strengths of the genes located on the native plasmids.

Organism:

Zymomonas mobilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33295

3 Samples

Download data: TXT

(Submitter supplied) we performed time series microarray analyses to investigate transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration. Published on J. Bacteriol., 190 (1), 286-299, 2008. Major changes in gene expression profiles occurred in the initial 15 min after the shift from anaerobic-light to aerobic-dark conditions, with changes continuing to occur up to 4 hours postshift. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Dataset:

GDS3296

Platform:

GPL162

24 Samples

Download data: CEL

Analysis of the facultative photosynthetic anaerobe Rhodobacter sphaeroides at various time points during the transition from anaerobic-light to aerobic-dark growth conditions. Results provide insight into molecular mechanisms underlying the transition from one homeostatic state to another.

Organism:

Rhodobacter sphaeroides 2.4.1

Type:

Expression profiling by array, count, 2 growth protocol, 6 time sets

Platform:

GPL162

Series:

GSE12269

24 Samples

Download data: CEL

(Submitter supplied) Investigation of the expression profiling of the ethanologenic Zymomonas mobilis in response to ethanol stress.

Organism:

Zymomonas mobilis; Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

Type:

Expression profiling by array

Platform:

GPL15541

6 Samples

Download data: PAIR

(Submitter supplied) As part of a comprehensive post-genomic investigation of the model archaeon Halobacterium sp. NRC-1, we used whole genome DNA microarrays to compare transcriptional profiles of cells grown anaerobically via arginine fermentation versus cells either respiring aerobically in the presence of oxygen or anaerobically using trimethylamine N-oxide (TMAO) as a terminal electron acceptor.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL15637

5 Samples

Download data: TXT

(Submitter supplied) Zymomonas mobilis is an aerotolerant anaerobe and prolific ethanologen with attractive characteristics for industrial bioproduct generation. However, there is currently insufficient knowledge of the impact that environmental factors have on flux through industrially relevant biosynthetic pathways. Here, we examine the effect of oxygen exposure on metabolism and gene expression in Z. mobilis by combining targeted metabolomics, mRNA sequencing, and shotgun proteomics. more...

Organism:

Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26046

38 Samples

Download data: TXT

(Submitter supplied) Saccharomyces cerevisiae CEN.PK113-1A was grown in glucose-limited chemostat culture with 0%, 0.5%, 1.0%, 2.8% or 20.9% O2 in the inlet gas (D= 0.10 /h, pH5, 30C).

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2529

22 Samples

Download data: CEL

(Submitter supplied) Transcriptional profiling of P. gingivalis cells comparing control cells grown in anaerobic conditions with cells grown in the presence of 6% of oxygen

Organism:

Porphyromonas gingivalis

Type:

Expression profiling by array

Platform:

GPL9149

5 Samples

Download data: GPR

(Submitter supplied) In this study we focus on two Saccharomyces cerevisiae strains with varying production of heterologous α-amylase and we compare the metabolic fluxes and transcriptional regulation at aerobic and anaerobic conditions, in particular with the objective to identify the final electron acceptor for protein folding. We found that anaerobic conditions showed high amount of amylase productions when comparing to aerobic conditions and the genome-scale transcriptional analysis suggested that genes related to the endoplasmic reticulum (ER), lipid synthesis and stress responses were generally up-regulated at anaerobic conditions. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL2529

18 Samples

Download data: CEL