Transcriptome of Pseudomonas putida KT2440 harboring plasmid RP4 during conjugative transfer
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PROVIDER: PRJNA612297 | ENA |
REPOSITORIES: ENA
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Project description: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.
2020-03-13 | GSE146879 | GEO
Project description:Impacts of plasmid carriage on its host cell were comprehensively analyzed using conjugative plasmid pCAR1 in the three different kinds of hosts, Pseudomonas putida KT2440, P. aeruginosa PAO1, and P. fluorescens Pf0-1. Various analyses of the host phenotype showed that pCAR1 carriage reduced host fitness, swimming motility, and resistances to osmotic- or pH-stress, and brought about the alterations of primary metabolic capacities in the TCA cycle or those several steps away from the TCA cycle in the host cells. Growth phase-dependent transcriptome analyses were performed with the classification of the annotated genes based on their identities among the three hosts and their putative functions. pCAR1 carriage affected host transcriptome more greatly at the transition and stationary phases in each host. The transcriptome responses were more similar between KT2440 and PAO1 than between other host combinations, and many genes, such as for ribosomal proteins, F-type ATPase, and RNAP core, in both strains were commonly not suppressed in their stationary phases. These responses may have resulted in the reduction of host fitness, motility, and stress resistances. Host-specific responses to plasmid carriage were transcriptional changes of genes on putative prophage or foreign DNA regions. The extent of the impacts in host phenotypes and transcriptomes was similarly the largest in KT2440 and the lowest in Pf0-1. The host alterations controlled by pCAR1 carriage are important for understanding the fate of the plasmid and its host, plasmid maintenance, expression of plasmid genes, the host cell physiology, and host survivability in the environment. The growth-dependent change of chromosomal RNA maps from exponential to early stationary phases of pCAR1-harboring KT2440 and non-pCAR1 harboring KT2440 were compared. The growth-dependent change of chromosomal RNA maps from exponential to early stationary phases of pCAR1-harboring PAO1 and non-pCAR1 harboring PAO1 were compared. The growth-dependent change of chromosomal RNA maps from exponential to early stationary phases of pCAR1-harboring Pf0-1 and non-pCAR1 harboring Pf0-1 were compared. The growth-dependent change of RNA maps from exponential to early stationary phases of plasmid pCAR1possessed by 3 kinds of hosts were compared.
2012-12-25 | E-GEOD-39636 | biostudies-arrayexpress
Project description:Tn insertion library was used for recipient for conjugative transfer of pESBL, F, and R388 plasmids. For both recipient and the resulting exconjugant libraries, Tn insertion sites were determined by illumina sequencing
2023-02-13 | E-MTAB-11704 | biostudies-arrayexpress
Project description:Conjugative transfer of bacterial plasmid is one of the major mechanisms of horizontal gene transfer, which is mediated by direct contact between donor and recipient cells. Gene expression of a conjugative plasmid is tightly regulated mostly by plasmid-encoded transcriptional regulators, but it remains obscure how differently plasmid genes are expressed in each cell during the conjugation event. Here, we report a comprehensive analysis of gene expression during conjugative transfer of plasmid RP4, which is transferred between isogenic strains of Pseudomonas putida KT2440 at very high frequency. To discriminate the expression changes in the donor and recipient cells, we took advantage of conjugation in the presence of rifampicin (Rif). Within 10 min of mating, we successfully detected transient transcription of plasmid genes in the resultant transconjugant cells. This phenomenon known as zygotic induction is likely attributed to derepression of multiple RP4-encoded repressors. Interestingly, we also observed that the traJIH operon encoding relaxase and its auxiliary proteins were upregulated specifically in the donor cells. Identification of the 5' end of the zygotically induced traJ mRNA confirmed that the transcription start site of traJ was located 24-nt upstream of the nick site in the origin of transfer (oriT) as previously reported. Since the traJ promoter is encoded on the region to be transferred first, the relaxase may be expressed in the donor cell after regeneration of the oriT-flanking region, which in itself is likely to displace the autogenous repressors around oriT. This study provides new insights into the regulation of plasmid transfer processes.
| S-EPMC7314908 | biostudies-literature
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.
2022-02-15 | PXD012642 | Pride
Project description:Integrative and conjugative elements (ICEs), a.k.a., conjugative transposons, are mobile genetic elements involved in many biological processes, including the spread of antibiotic resistance. Unlike conjugative plasmids that are extra-chromosomal and replicate autonomously, ICEs are integrated in the chromosome and replicate passively during chromosomal replication. It is generally thought that ICEs do not replicate autonomously. We found that when induced, Bacillus subtilis ICEBs1 replicates as a plasmid. The ICEBs1 origin of transfer (oriT) served as the origin of replication and the conjugal DNA relaxase served as the replication initiation protein. Autonomous replication of ICEBs1 conferred genetic stability to the excised element, but was not required for mating. The B. subtilis helicase PcrA that mediates unwinding and replication of Gram-positive rolling circle replicating plasmids was required for ICEBs1 replication and mating. Nicking of oriT by the relaxase and unwinding by PcrA likely directs transfer of a single-strand of ICEBs1 into recipient cells. This SuperSeries is composed of the SubSeries listed below.
2009-10-16 | GSE18380 | GEO
Project description:MvaT proteins are recognized as a member of H-NS family proteins in pseudomonads. IncP-7 conjugative plasmid pCAR1, which was originally found in Pseudomonas resinovorans, carries an mvaT homologous gene, pmr. In Pseudomonas putida KT2440 bearing pCAR1, it was previously reported that pmr and chromosomally-encoded homologous genes, turA and turB, are majorly transcribed, and that Pmr interacts with TurA and TurB in vitro (Yun et al. J. Bacteriol. 192:4720-4731, 2010). In the present study, we clarified how the three MvaT proteins regulate the transcriptome of P. putida KT2440(pCAR1). Modified ChIP-chip analyses suggested that the binding sites of Pmr, TurA, and TurB in P. putida KT2440(pCAR1) genome were almost identical; nevertheless, transcriptome analyses using deletion mutants of each MvaT protein gene at the log and early-stationary growth phases clearly suggested that their regulons were different with one another. Especially, significant dissimilarity of regulons was found between Pmr and other two proteins. Transcriptions of the larger number of genes were affected by Pmr deletion at the early-stationary phase than at the log phase, suggesting that Pmr minimizes the pCAR1 effects on host fitness more effectively at the early-stationary phase. On the other hand, similarity found between the regulons of TurA and TurB implied that they may have complementary roles as global transcriptional regulators in response to the plasmid carriage. ChIP-chip: Pseudomonas putida KT2440 harboring plasmid pCAR1 cells were ChIPed with His-tag (C-terminus of each MvaT homologs) and compared with input control. Transcriptome analysis: Chromosomal RNA maps of mvaT deletion mutants were compared with those of wild-type cells.
2015-09-03 | E-GEOD-72637 | biostudies-arrayexpress
Project description:Impacts of plasmid carriage on its host cell were comprehensively analyzed using conjugative plasmid pCAR1 in the three different kinds of hosts, Pseudomonas putida KT2440, P. aeruginosa PAO1, and P. fluorescens Pf0-1. Various analyses of the host phenotype showed that pCAR1 carriage reduced host fitness, swimming motility, and resistances to osmotic- or pH-stress, and brought about the alterations of primary metabolic capacities in the TCA cycle or those several steps away from the TCA cycle in the host cells. Growth phase-dependent transcriptome analyses were performed with the classification of the annotated genes based on their identities among the three hosts and their putative functions. pCAR1 carriage affected host transcriptome more greatly at the transition and stationary phases in each host. The transcriptome responses were more similar between KT2440 and PAO1 than between other host combinations, and many genes, such as for ribosomal proteins, F-type ATPase, and RNAP core, in both strains were commonly not suppressed in their stationary phases. These responses may have resulted in the reduction of host fitness, motility, and stress resistances. Host-specific responses to plasmid carriage were transcriptional changes of genes on putative prophage or foreign DNA regions. The extent of the impacts in host phenotypes and transcriptomes was similarly the largest in KT2440 and the lowest in Pf0-1. The host alterations controlled by pCAR1 carriage are important for understanding the fate of the plasmid and its host, plasmid maintenance, expression of plasmid genes, the host cell physiology, and host survivability in the environment.
2012-12-25 | GSE39636 | GEO
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.
2019-04-01 | GSE112451 | GEO
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.
2020-02-01 | GSE128246 | GEO