Expression analysis of a respiration-deficient mutant of Zymomonas mobilis
Ontology highlight
ABSTRACT:
ORGANISM(S): Zymomonas mobilis subsp. mobilis ATCC 29191
SUBMITTER: Takeshi Hayashi
PROVIDER: E-GEOD-22355 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Investigation of whole-genome gene expression level changes in RDM-4 strain of Zymomonas mobilis respiration-deficient mutant compared to the wild-type strain. The mutant strains were isolated from the antibiotics-resistant mutants of Z. mobilis ZM6. The RDM strains exhibited much higher ethanol fermentation abilities than the wild-type strain under aerobic conditions. The strains also gained thermotolerance and exhibited higher ethanol productivities at high temperature (39 ºC) under both non-aerobic and aerobic conditions compared with the wild-type strain. To evaluate the mechanisms of aerobic fermentation and thermotolerance of the RDM strain, we performed the microarray experiments.
2010-10-01 | GSE22355 | GEO
Project description: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. In the absence of oxygen, ZM4 consumed glucose more rapidly, had a higher growth rate, and ethanol was the major end-product. Under aerobic conditions, much less ethanol was observed with other end-products produced, including acetate, lactate, and acetoin. In the early exponential phase, no genes were detected as being significantly differentially expressed between aerobic and anaerobic conditions via microarray analysis. However, microarray analysis of the stationary phase cultures revealed that 166 genes were significantly differentially expressed by more than two-fold. Quantitative-PCR validated the expression values for seventeen genes from different categories of stationary phase microarray data. Transcripts for Entner-Doudoroff pathway genes and gene pdc, encoding a key enzyme leading to the ethanol production, were at least 30-fold more abundant under anaerobic conditions at stationary phase based on quantitative-PCR results. Expression of stress response genes was found to be greater under oxygen stress conditions. GC-MS analysis of stationary phase intracellular metabolites indicated that ZM4 under anaerobic conditions contained lower levels of amino acids, glucose and ED pathway intermediates, whereas metabolites such as ribitol, trehalose, myristic acid, glyceric acid, glucose 6-phosphate, mannose 6-phosphate, and 4-hydroxybutanoic acid were more abundant than under aerobic conditions. Transcriptomic and metabolomic data were consistent with faster glucose consumption and greater ethanol production under anaerobic conditions and suggested gene targets for deletion and improved fermentation. Keywords: Time course/ Stress Response A total of 24 samples were analyzed. These consisted of two times points, (3 hours and 26 hours) under two conditions (anaerobic and aerobic). There were 3 biological replicates and two dye swaps. Each microarray containted one to two probes per predicted coding sequence.
2010-05-18 | E-GEOD-10302 | biostudies-arrayexpress
Project description:Thermotolerance development of robust Saccharomyces cerevisiae is necessary to enhance enzyme activity of cellulase, lower cooling costs, and reduce cell harm from the bad-distributed heat transfer in large-scale fermentation. The process-based studies of adaptive evolution have been well documented, but it remains unknown for the underlying molecular mechanism of the improved thermotolerance and the facilitated ethanol fermentability derived from adaptive evolution. Here, a robust thermotolerant S. cerevisiae Z100 was obtained with significantly improved ethanol fermentability under the stress of high temperature (50 oC) after 91 days’ adaptive evolution. RNA sequencing showed that adaptive evolution and its derived thermotolerance contributed to the unique gene transcriptional landscapes of the evolved strain. An interesting phenomenon was that the gene transcriptional signals of carbon metabolism were strengthened not at 50 oC but at 30 oC in S. cerevisiae Z100, and thus suggested that the improved thermotolerance led to the enhanced ethanol fermentability at 30 oC. The deeply repressed gene transcriptional expression indicated ribosome would be another key thermotolerant mechanism for the evolved strain. This study would provide a robust thermotolerant S. cerevisiae for bioethanol production and an important clue for future synthetic biology to thermotolerance engineering of fermentation strains.
2021-08-20 | GSE182342 | GEO
Project description:we aimed to screen candidate kinase genes under the stress of phenolic aldehydes during ethanol fermentation for Zymomonas mobilis ZM4
2022-03-25 | GSE199182 | GEO
Project description: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. mobilis. To better understand mechanisms with which high concentrations of glucose and sorbitol affect physiology and metabolism of Z. mobilis ATCC31821 (ZM4), the global transcriptional responses of ZM4 to the challenge of high glucose concentration and sorbitol were profiled using whole genome microarray analysis. Swings J, Deley J. Bacterial Rev. 1977, 41(1): 1-46. Loos H, Kramer R, Sahm H and Sprenger GA. J Bacteriol. 1994, 176(24):7688–7693.
2014-10-14 | GSE49620 | GEO
Project description: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. These data suggests that in this organism regulatory RNAs can be associated with metabolic functions involved in ethanol stress responses. Z. mobilis was grown under aerobic and anaerobic conditions which showed low and high ethanol production, respectively. Each samples were sequenced for identification of small RNA candidates and differentially expressed candidates between two conditions.
2014-05-20 | E-GEOD-57773 | biostudies-arrayexpress
Project description:Protein phosphorylation is an important post translational modification that plays a major role in cellular regulatory processes in both eukaryotes and prokaryotes. In recent years, aided by advancements in mass spectrometry techniques, there has been a growing interest in studying protein phosphorylation in prokaryotic model organisms. There are, however, only a limited number of phosphoproteomics reports on non-model organisms. Here, using mass spectrometry, we performed a genome wide investigation of protein phosphorylation in the non-model organism and biofuel producer Zymomonas mobilis under anaerobic, aerobic, and N2-fixing conditions. Our phosphoproteome analysis revealed 125 unique phosphorylated proteins and 172 unique phosphopeptides across these three growth conditions. The phosphoproteins identified belonged to major pathways, including glycolysis, TCA cycle, protein biosynthesis, electron transport, and nitrogen fixation. Quantitative analysis revealed significant and widespread changes in protein phosphorylation across anaerobic, aerobic, and N2-fixing growth conditions. For example, two different serine residues of KDPG aldolase, an Entner-Doudoroff pathway enzyme, were differentially phosphorylated under aerobic and N2-fixing conditions. On the other hand, the final enzyme in the ethanol fermentation pathway, alcohol dehydrogenase, showed phosphorylation on its Ser99 only under N2-fixing condition while its Ser126 was only phosphorylated under anaerobic condition. Moreover, nitrogenases and nitrogen regulatory proteins were differentially phosphorylated at multiple sites under aerobic and N2-fixing conditions. Altogether, this study provides new knowledge regarding potential phosphorylation regulatory sites of specific proteins in pathways relevant to ethanol production and overall physiology and establishes new ground for future engineering of Z. mobilis for advanced biofuel production.
2019-08-08 | PXD014065 | Pride
Project description: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. In this study, we further investigated the responses of AcR and wild-type ZM4 to sodium acetate stress in minimum media using both transcriptomics and a metabolic labeling approach for quantitative proteomics the first time. Proteomic measurements at two time points identified about eight hundreds proteins, or about half of the predicted proteome. Extracellular metabolite analysis indicated AcR overcame the acetate stress quicker than ZM4 with a concomitant earlier ethanol production in AcR mutant, although the final ethanol yields and cell densities were similar between two strains. Transcriptomic samples were analyzed for four time points and revealed that the response of Z. mobilis to sodium acetate stress is dynamic, complex and involved about one-fifth of the total predicted genes from all different functional categories. The modest correlations between proteomic and transcriptomic data may suggest the involvement of posttranscriptional control. In addition, the transcriptomic data of forty-four microarrays from four experiments for ZM4 and AcR under different conditions were combined to identify strain-specific, media-responsive, growth phase-dependent, and treatment-responsive gene expression profiles. Together this study indicates that minimal medium has the most dramatic effect on gene expression compared to rich medium followed by growth phase, inhibitor, and strain background. Genes involved in protein biosynthesis, glycolysis and fermentation as well as ATP synthesis and stress response play key roles in Z. mobilis metabolism with consistently strong expression levels under different conditions.
2014-05-08 | GSE25443 | GEO
Project description: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. In this study, we further investigated the responses of AcR and wild-type ZM4 to sodium acetate stress in minimum media using both transcriptomics and a metabolic labeling approach for quantitative proteomics the first time. Proteomic measurements at two time points identified about eight hundreds proteins, or about half of the predicted proteome. Extracellular metabolite analysis indicated AcR overcame the acetate stress quicker than ZM4 with a concomitant earlier ethanol production in AcR mutant, although the final ethanol yields and cell densities were similar between two strains. Transcriptomic samples were analyzed for four time points and revealed that the response of Z. mobilis to sodium acetate stress is dynamic, complex and involved about one-fifth of the total predicted genes from all different functional categories. The modest correlations between proteomic and transcriptomic data may suggest the involvement of posttranscriptional control. In addition, the transcriptomic data of forty-four microarrays from four experiments for ZM4 and AcR under different conditions were combined to identify strain-specific, media-responsive, growth phase-dependent, and treatment-responsive gene expression profiles. Together this study indicates that minimal medium has the most dramatic effect on gene expression compared to rich medium followed by growth phase, inhibitor, and strain background. Genes involved in protein biosynthesis, glycolysis and fermentation as well as ATP synthesis and stress response play key roles in Z. mobilis metabolism with consistently strong expression levels under different conditions. A sixteen array study using total RNA recovered from wild-type cultures of Zymomonas mobilis subsp mobilis ZM4 and acetate-tolerant mutant AcR at different time points of 130, 148, 166, and 190h post-inoculation with 10g/L sodium acetate (NaAc) treatment were carried out to investigate the expression differences between ZM4 and AcR. Two biological replicates for treatment or control condition.
2014-05-08 | E-GEOD-25443 | biostudies-arrayexpress
Project description: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. In the absence of oxygen, ZM4 consumed glucose more rapidly, had a higher growth rate, and ethanol was the major end-product. Under aerobic conditions, much less ethanol was observed with other end-products produced, including acetate, lactate, and acetoin. In the early exponential phase, no genes were detected as being significantly differentially expressed between aerobic and anaerobic conditions via microarray analysis. However, microarray analysis of the stationary phase cultures revealed that 166 genes were significantly differentially expressed by more than two-fold. Quantitative-PCR validated the expression values for seventeen genes from different categories of stationary phase microarray data. Transcripts for Entner-Doudoroff pathway genes and gene pdc, encoding a key enzyme leading to the ethanol production, were at least 30-fold more abundant under anaerobic conditions at stationary phase based on quantitative-PCR results. Expression of stress response genes was found to be greater under oxygen stress conditions. GC-MS analysis of stationary phase intracellular metabolites indicated that ZM4 under anaerobic conditions contained lower levels of amino acids, glucose and ED pathway intermediates, whereas metabolites such as ribitol, trehalose, myristic acid, glyceric acid, glucose 6-phosphate, mannose 6-phosphate, and 4-hydroxybutanoic acid were more abundant than under aerobic conditions. Transcriptomic and metabolomic data were consistent with faster glucose consumption and greater ethanol production under anaerobic conditions and suggested gene targets for deletion and improved fermentation. Keywords: Time course/ Stress Response
2008-10-10 | GSE10302 | GEO