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Paracoccus denitrificans strain:NBRC 102528

ABSTRACT: Paracoccus denitrificans NBRC 102528 genome sequencing project

PROVIDER: PRJDB6188 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	BJUR01.dat.gz	Other
	BJUR01.fasta.gz	Fasta.gz
	BJUR01.master.dat	Other

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Transcriptome analysis of Paracoccus denitrificans during Cu-limitation

Project description:Transcriptional profiling of Paracoccus denitrificans PD1222 wild type grown to mid-exponential phase in minimal media with either 13 uM (Cu-H) or 0.5 uM (Cu-L) Cu regimes. The goal was to define the effects of Cu-limitation on denitrification genes Two growth conditions, three biological replicates of each condition. Each sample hybridised in a two-channel hybridization against Paracoccus denitrificans genomic DNA as the comparator/reference, which also acted as a control for spot quality. Cu-concentration 13 uM (Cu-H) versus 0.5 uM Cu (Cu-L) in anaerobic growth conditions.

2013-11-18 | E-GEOD-48577 | biostudies-arrayexpress

Transcriptome analysis of Paracoccus denitrificans during Cu-limitation

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Transcriptome analysis of Paracoccus denitrificans during aerobic and anaerobic respiration (denitrification)

Project description:Transcriptional profiling of Paracoccus denitrificans PD1222 wild type incubated in continuous culture (continuous culture (CSTR)) in minimal media with aerobic or anaerobic conditions. The goal was to define the core respiratory genes.

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RNA-seq data of Paracoccus denitrificans grown under different N2O levels

Project description:We report here the RNA seq results of sRNA enriched Paracoccus denitrificans grown under three different N2O levels (high N2O reffered to as CuL/ low N2O reffered to as CuH/ Low N2O aerobic reffered to as CuH O2)

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Transcriptome sequencing of Paracoccus denitrificans ATCC19367 with florfenicol exporsure

Project description:We report the application of transcriptome sequencing technology in florfenicol interfering with denitrification by Paracoccus denitrificans. More than 30 billion bases of sequences were obtained by sequencing analysis. We found 433 differentially expressed genes, of which 292 genes were down-regulated and 141 genes were up-regulated, respectively. Importantly, most of the denitrification genes were suppressed, which further led to the enrichment of key metabolic pathways. The weakening of protein synthesis was consistent with the bacteriostatic mechanism of florfenicol. In particular, we found 42 putative differentially expressed sRNAs. After homologous alignment, target gene prediction and functional analysis, it was proved that the sRNAs differential expression profile is likely to be a key transcription factor affected by antibiotics in denitrification. This study provides new ideas for further control of environmental antibiotic pollution.

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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.

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