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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

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

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

Ileum/colon treated with succinate

Project description:Ileum/colon treated with succinate

| PRJNA608465 | ENA

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

Transcription profiling of Rhizobium leguminosarum biovar viciae strain 3841grown on AMS minimal medium with either succinate ammonia or glucose ammonia as carbon and nitrogen sources

Project description:Rhizobium leguminosarum bivar viciae strain 3841 was grown on AMS minimal medium with either succinate ammonia or glucose ammonia as carbon and nitrogen sources. Gene expression was compared between the two crabon sources. Total RNA was amplified using Genispheres SenseAmp kit.

2008-12-18 | E-MEXP-1962 | biostudies-arrayexpress

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