Zymomonas mobilis oxidative stress transcriptomics
Ontology highlight
ABSTRACT:
ORGANISM(S): Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
PROVIDER: GSE304360 | GEO | 2025/11/20
REPOSITORIES: GEO
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| GSE304360_20250627_Kiley_Oxidizing_Stress_RNAseq_FKPM_normalized_counts.txt.gz | Txt | |||
| GSE304360_20250627_Kiley_Oxidizing_Stress_RNAseq_HTSeq_raw_counts.txt.gz | Txt |
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Project description:Deletion of the IscR homolog ZMO_0422 was performed in Zymomonas mobilis to investigate the role of Fe-S cluster biogenesis in Zymomonas. Here we perform genome-wide transcirptomics study to examine transcript chagnes in delta-ZMO_0422 compared to WT Zymomonas mobilis under both aerobic and anaerobic growth conditions.
2025-11-20 | GSE304389 | 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: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. A four-chip study using total RNA recovered from the shaking cultures of wt and RDM-4 strains grown at 30ºC, a non-aerobic culture of wt strain grown at 30ºC, and a non-aerobic culture of RDM-4 strain grown at 38ºC. Each chip measures the expression level of 1,998 genes from Z. mobilis.
2010-10-01 | E-GEOD-22355 | biostudies-arrayexpress
Project description:Lee2010 - Genome-scale metabolic network of
Zymomonas mobilis (iZmobMBEL601)
This model is described in the article:
The genome-scale metabolic
network analysis of Zymomonas mobilis ZM4 explains
physiological features and suggests ethanol and succinic acid
production strategies.
Lee KY, Park JM, Kim TY, Yun H, Lee
SY.
Microb. Cell Fact. 2010; 9: 94
Abstract:
BACKGROUND: Zymomonas mobilis ZM4 is a Gram-negative
bacterium that can efficiently produce ethanol from various
carbon substrates, including glucose, fructose, and sucrose,
via the Entner-Doudoroff pathway. However, systems metabolic
engineering is required to further enhance its metabolic
performance for industrial application. As an important step
towards this goal, the genome-scale metabolic model of Z.
mobilis is required to systematically analyze in silico the
metabolic characteristics of this bacterium under a wide range
of genotypic and environmental conditions. RESULTS: The
genome-scale metabolic model of Z. mobilis ZM4, ZmoMBEL601, was
reconstructed based on its annotated genes, literature,
physiological and biochemical databases. The metabolic model
comprises 579 metabolites and 601 metabolic reactions (571
biochemical conversion and 30 transport reactions), built upon
extensive search of existing knowledge. Physiological features
of Z. mobilis were then examined using constraints-based flux
analysis in detail as follows. First, the physiological changes
of Z. mobilis as it shifts from anaerobic to aerobic
environments (i.e. aerobic shift) were investigated. Then the
intensities of flux-sum, which is the cluster of either all
ingoing or outgoing fluxes through a metabolite, and the
maximum in silico yields of ethanol for Z. mobilis and
Escherichia coli were compared and analyzed. Furthermore, the
substrate utilization range of Z. mobilis was expanded to
include pentose sugar metabolism by introducing metabolic
pathways to allow Z. mobilis to utilize pentose sugars.
Finally, double gene knock-out simulations were performed to
design a strategy for efficiently producing succinic acid as
another example of application of the genome-scale metabolic
model of Z. mobilis. CONCLUSION: The genome-scale metabolic
model reconstructed in this study was able to successfully
represent the metabolic characteristics of Z. mobilis under
various conditions as validated by experiments and literature
information. This reconstructed metabolic model will allow
better understanding of Z. mobilis metabolism and consequently
designing metabolic engineering strategies for various
biotechnological applications.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180031.
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To the extent possible under law, all copyright and related or
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2015-07-30 | MODEL1507180031 | BioModels
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: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.
2014-05-20 | GSE57773 | GEO
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:Investigation of the expression profiling of the ethanologenic Zymomonas mobilis in response to ethanol stress. A six chip study using total RNA recovered from three separate wild-type cultures of Zymomonas mobilis ATCC31821 and three separate cultures of a triple treated with 5% ethanol. Each chip measures the expression level of 1800 genes from Zymomonas mobilis ATCC31821 and the associated plasmids, with three-fold technical redundancy.
2013-12-31 | E-GEOD-39558 | biostudies-arrayexpress
Project description:Investigation of the expression profiling of the ethanologenic Zymomonas mobilis in response to furfural stress. A six chip study using total RNA recovered from three separate wild-type cultures of Zymomonas mobilis ATCC31821 and three separate cultures of a triple treated with 1.0 g/l furfural. Each chip measures the expression level of 1800 genes from Zymomonas mobilis ATCC31821 and the associated plasmids, with three-fold technical redundancy.
2012-05-08 | E-GEOD-37848 | biostudies-arrayexpress
Project description:Zymomonas mobilis is an aerotolerant anaerobe and prolific ethanologen with attractive characteristics for industrial biofuel production. 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. We found that exposure to oxygen profoundly influenced metabolism, inducing both transient metabolic bottlenecks and long-term metabolic remodeling. In particular, oxygen induced a severe but temporary metabolic bottleneck in the methyl erythritol 4-phosphate pathway for isoprenoid biosynthesis, likely caused by oxidative damage to the iron-sulfur co-factors of the final two enzymes of the pathway. This bottleneck was resolved with minimal changes in expression level of enzymes in the pathway but pronounced upregulation of enzymes related to iron-sulfur cluster maintenance and biogenesis (i.e. flavodoxin reductase and the suf operon). We also detected prominent changes in glucose utilization under aerobic conditions. Specifically, we observed increased gluconate production following exposure to oxygen, accounting for 18% of glucose uptake after 24 hours of aerobic growth. Our results suggest that under aerobic conditions, electrons from the oxidation of glucose to gluconate are delivered to the electron transport chain to minimize oxidative damage by reducing reactive oxygen species such as H2O2. This model is supported by the simultaneous upregulation of three membrane-bound dehydrogenases, cytochrome c peroxidase, and a cytochrome bd terminal oxidase.
2019-01-18 | PXD011545 | Pride