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Pseudonocardia dioxanivorans strain CB1190 during growth on THF or succinate

ABSTRACT: Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth on THF (tetradhydrofuran) or succinate, and re-analysis of GSE33197 published expression data.

ORGANISM(S): Pseudonocardia dioxanivorans CB1190

PROVIDER: GSE48814 | GEO | 2013/07/12

SECONDARY ACCESSION(S): PRJNA211830

REPOSITORIES: GEO

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Pseudonocardia dioxanivorans strain CB1190 during growth on THF or succinate

Project description:Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth on THF (tetradhydrofuran) or succinate, and re-analysis of GSE33197 published expression data. Two new treatments, based on carbon/energy source used for growth: THF and succinate. Three previously published treatments (pyruvate, dioxane, and glycolate) from GEO Series GSE33197 were also reanalyzed. Triplicate microarrays (biological replicates) were prepared for each treatment. Gene expression changes were compared directly between the new treatments (THF vs. succinate) and to previously published data during growth on pyruvate (GEO accession numbers GSM821862-GSM821864) in order to yield THF vs. pyruvate and succinate vs. pyruvate contrasts. Included as part of the re-analysis of GSE33197 were data from dioxane and glycolate treatments (GSM821865-GSM821870). The complete dataset representing: (1) the THF- and succinate-treated CB1190 Samples and (2) the pyruvate-, dioxane- and glycolate-treated CB1190 Samples from Series GSE33197 (re-processed using RMA), is linked below as a supplementary file (GSE48814_complete_data.txt).

2013-07-12 | E-GEOD-48814 | biostudies-arrayexpress

Transcription profiling of Rhizobium leguminosarum bv viciae strain 3841 grown on AMS minimal media with succinate and ammonia compared to succinate GABA

Project description:Rhizobium leguminosarun bv viciae strain 3841 was grown on AMS minimal medium with sucinate and ammonia and compared to a culture grown on succinate GABA

2008-11-10 | E-MEXP-1894 | biostudies-arrayexpress

Engineering of Corynebacterium glutamicum for growth and succinate production from levoglucosan as a pyrolytic sugar substrate

Project description:We deveolped the C. glutamicum strains that is able to utilize levoglucoan as sole carbon and produce succinate. To understand the cellular metabolism in a levoglucosan-utilizing strain, we compared the mRNA profiling of a levoglucosan-utilizing strains grown in either glucose or levoglucosan.

2016-03-17 | GSE68483 | GEO

RNA-seq of Paracoccus denitrificans Pd1222 and a ramB deletion mutant during growth on succinate and acetate

Project description:The alphaproteobacterium Paracoccus denitrificans Pd1222 has two different, yet functionally redundant acetyl-CoA assimilation routes: the Ethylmalonyl-CoA pathway (EMCP) and the glyoxylate cycle (GC). The EMPC and the GC each tightly control the balance between catabolism and anabolism by shifting flux away from the oxidation of acetyl-CoA in the tricarboxylic acid (TCA) cycle towards biomass formation. RamB (encoded by Pden_1365), a member of the ScfR family, is a transcriptional regulator in P. denitrificans Pd1222 that controls expression of GC. To analyze the role of RamB in the coordinated regulation of metabolic plasticity, we analyzed the global transcriptome of P. denitrificans Pd1222, as well as the ramB-deletion strain during mid-exponential growth phase on defined minimal medium with acetate or succinate as carbon sources.

2023-06-06 | E-MTAB-12482 | biostudies-arrayexpress

Pseudonocardia dioxanivorans CB1190

Project description:Pseudonocardia dioxanivorans strain CB1190 during growth on THF or succinate

| PRJNA211830 | ENA

The Pseudomonas fluorescens Crc affects the length of the transition phase during diauxic growth

Project description:Pseudomonads, unlike enteric bacteria, prefer to utilize tricarboxylic acid cycle intermediates over glucose. The crc gene has been implicated to impart repression on glucose and other metabolic enzymes in various Pseudomonas species when grown in a mixture of glucose and various organic acids. The crc gene of P. fluorescens strain MB101 has been identified and a crc deletion derivative was constructed. Unlike a crc mutant of P. aeruginosa described earlier, the P. fluorescens deletion mutant crc did not begin to catabolize glucose until most of the succinate has been utilized in a medium containing both carbon sources. The transition phase during diauxic growth in succinate/glucose media was found to be shorter in a strain lacking crc and considerably longer in a strain overproducing Crc as compared to the wild type. DNA microarray analyses were performed with wild-type and crc mutant strains during the transition phase from succinate to glucose. In the wild-type strain, high expression signals were obtained for genes normally induced in cells that approach or are in stationary phase. By contrast, deletion mutant crc cells showed higher expression signals for genes associated with rapid growth than the wild-type strain. Taken together, this data indicates that Crc influences the length of the lag during the transition phase from succinate to glucose by directly or indirectly affecting the mRNA levels of target genes. Keywords: time course strain comparison

2008-09-11 | GSE5829 | GEO

Succinate dehydrogenase deficiency-driven succinate accumulation induces drug resistance in acute myeloid leukemia via ubiquitin-cullin regulation

Project description:Drug resistance is vital for the poor prognosis of acute myeloid leukemia (AML) patients, but the underlying mechanism remains poorly understood. Given the unique microenvironment of bone marrow, we reasoned that drug resistance of AML might rely on distinct microenvironment-associated metabolic processes. Here, we identified SDH deficiency and over-cumulative succinate as typical features in AML, with a marked function in causing the resistance of AML cells to a wide range of anti-cancer therapies. Mechanistically, succinate promoted the accumulation of oncogenic proteins in a manner that precedes transcriptional activation. This function was mediated by succinate-triggered upregulation of UBC12 phosphorylation, which impaired its E2 function in cullins neddylation. Notably, decreasing succinate levels by fludarabine could effectively restore the drug sensitivity of SDH-deficient AML PDX. Together, we uncover a novel function of succinate in driving drug resistance by regulating p-UBC12/cullin activity, and indicate reshaping succinate metabolism as a promising treatment for SDH-deficient AML.

2024-08-27 | GSE247623 | GEO

Transcription profiling of Rhizobium leguminosarum biovar viciae strain 3841 inoculated onto vetch seeds compared to cells grown in free-living culture on succinate ammonia AMS

Project description:Rhizobium leguminosarum biovar viciae strain 3841 was inoculated onto Viccia cracca seeds and bacteroids were harvested at 28d. Gene expression was then compared to free-living Rhizobium leguminosarum biovar viciae strain 3841 grown on succinate ammonia AMS.

2008-11-30 | E-MEXP-1924 | biostudies-arrayexpress

Succinate diminishes biological activity and mitochondrial function of human adipose-derived stem cells

Project description:Alterations in succinate levels have been associated with various metabolic and inflammatory diseases. However, little is currently known about whether adipose-derived stem cells (ADSCs) undergo changes when exposed to succinate. Here, we investigate the biological properties, mitochondrial function and immunophenotype of ADSCs treated with succinate. We observed that reduced biological activity of ADSCs following by succinate stimulated. Of note, succinate treated-ADSCs exhibit mitochondrial dysfunctions, including increased mitochondrial fragments, decreased mitochondrial mass, increased ROS production, reduced Oxidative phosphorylation (OXPHOS). Furthermore, transcriptome analysis revealed that the downregulation of genes involved in cell proliferation, OXPHOS and metabolism, whereas the signaling pathways related to cancer, apoptosis, inflammation were upregulated upon succinate treatment. The findings indicate that ADSCs exposed to succinate exhibit signs of mitochondrial dysfunction, inflammation, and a significant decrease in biological activity.

2024-08-30 | GSE275624 | GEO

Transcription profiling of Rhizobium leguminosarum biovar viciae strain 3841 inoculated onto pea seeds compared to cells grown in free-living culture on succinate ammonia AMS

Project description:Rhizobium leguminosarum bv viciae strain 3841 was inoculated onto pea (Pisum sativum) seeds and nodules were harvested at 28 d. The gene expression was compared to free-living bacteria grown on succinate ammonia AMS medium.

2008-11-30 | E-MEXP-1925 | biostudies-arrayexpress

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