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.
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
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.
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.
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)
Project description:Quantitative proteomic analysis of Paracoccus denitrificans PD1222 wild type and NtrY defective mutant in denitrifying conditions (anaerobiosis, nitrate as nitrogen source)
Project description:Bacteriophages represent a largely untapped reservoir of regulatory elements that can expand the genetic toolbox for engineering non‑model hosts. Using ONT‑cappable‑sequencing, we mapped full‑length primary transcripts across five Pseudomonas phages and identified 232 transcription start sites (TSSs) and 176 transcription termination sites (TTSs), including 38 intrinsic factor‑independent terminators. Motif discovery revealed 59 s70-like promoters in KIL5, 37 in KIL3b, and unique phage‑encoded RNA polymerase (RNAP) promoter motifs for KNP, ϕ2, and pphageB21, enabling discrimination between host‑ and phage‑dependent transcriptional control. To verify these predictions, a subset of ten promoters and five terminators was quantitatively characterized in vivo in P. fluorescens strain GL-S-306, demonstrating promoter activities spanning a large dynamic range and terminator efficiencies allowing complete transcriptional termination. These data establish the first experimentally validated, phage‑derived library of promoters and terminators for P. fluorescens and P. syringae, providing chassis‑specific regulatory parts that enable more finetuned gene‑expression than current cross‑species SynBio tools. Our results position phage transcriptomics as a scalable strategy for mining regulatory elements tailored to non‑model bacterial hosts and accelerate the development of new synthetic biology platforms.
