Transcriptome of Pseudomonas putida KT2440 harboring plasmid RP4 during conjugative transfer
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ABSTRACT: We analyzed gene expression during conjugative transfer of plasmid RP4. Pairs of rifampicin-susceptible (RifS) and -resistance (RifR) strains of Pseudomonas putida KT2440 were conjugated for 10 minute on filter membrane in the presence of rifampicin to discriminate the expression changes in the donor and recipient cells.
Project description:The goals of this study are to use SWATH-MS to detect bacterial proteomic profiles of E. coli K-12 LE392 with conjugative RP4 plasmid, P. putida KT2440, and their protein response under the exposure of six kinds of non-antibiotic pharmaceuticals, i.e., ibuprofen (ibu), naproxen (nap), gemfibrozil (gem), iopromide (iop), diclofenac (dic), propanolol (pro). Each treatment condition was conducted in triplicate. By comparing the proteomic profiles of experimental groups and control group, the effects of these non-antibiotic pharmaceuticals on translational levels can be revealed.
Project description:The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid in response to 0, 0.02, 20 and 2000 μg/L triclosan for 2 h, in duplicate, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
Project description:The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis. This dataset is related to PXD007089.
Project description:The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis. This dataset is related to PXD007090.
Project description:The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid in response to 0 and 1 μg/L AgNPs or silver ion for 2 h, in duplicate, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
Project description:The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the proteome, acetylome, and succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis.
Project description:The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the proteome, acetylome, and succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis.
Project description:We used Progenika oligonucleotide arrays to monitor the gene expression after cold shock from 30°C to 10°C. The 10°C samples of the P. putida wild type were compared to those of the respective P. putida KT2440 Tn5 mutants affected in either cbrA (PP4695), cbrB (PP4696), pcnB (PP4697), vacB (PP4880) or bipA (PP5044).