GEO DataSets

(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) 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) 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) 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) Background Lignocellulosic biomass is a promising renewable feedstock for biofuel production. Acetate is one of the major inhibitors liberated from hemicelluloses during hydrolysis. An understanding of the toxic effects of acetate on the fermentation microorganism and the efficient utilization of mixed sugars of glucose and xylose in the presence of hydrolysate inhibitors is crucial for economic biofuel production. more...

Organism:

Zymomonas mobilis

Type:

Expression profiling by genome tiling array

Platform:

GPL18675

30 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 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) We collected sample-matched multiomics data including RNA-seq, transcription start site sequencing (TSS-seq), termination sequencing (term-seq), ribosome profiling, and label-free shotgun proteomic mass spectrometry across different growth conditions to improve annotation and assign functional sites in the Zymomonas mobilis subsp. mobilils ZM4 genome. Proteomics and ribosome profiling informed revisions of protein-coding genes, which included 44 start codon changes and 42 added proteins. more...

Organism:

Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL27722 GPL26046

94 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Background: Lignocellulosic biomass is a promising renewable feedstock for the microbial production of fuels. To release the major fermentable sugars such as glucose and xylose, pretreatment, hydrolysis, and subsequent conditioning of biomass feedstock are needed. During this process, many toxic compounds are produced or introduced which subsequently inhibit microbial growth and in many cases the production titer and rate. more...

Organism:

Zymomonas mobilis

Type:

Expression profiling by genome tiling array

Platform:

GPL18675

30 Samples

Download data: TXT

(Submitter supplied) To investigate the molecular mechanism of the increased bioethanol fermentability, we carried out RNA-Seq sequencing assays for the wild and mutant strain Z. mobilis after pretreated with cold plasma. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at one time points.

Organism:

Zymomonas mobilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33295

6 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) 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