Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1271442 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33806438_1.fastq.gz | Fastqsanger.gz | |||
| SRR33806438_2.fastq.gz | Fastqsanger.gz | |||
| SRR33806439_1.fastq.gz | Fastqsanger.gz | |||
| SRR33806439_2.fastq.gz | Fastqsanger.gz | |||
| SRR33806440_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Many species of pathogenic bacteria harbor critical plasmid-encoded virulence factors, and yet the regulation of plasmid replication is often poorly understood despite playing key role in plasmid-encoded gene expression. Human pathogenic Yersinia, including the plague agent Yersinia. pestis and its close relative Y. pseudotuberculosis, require the type III secretion system (T3SS) virulence factor to subvert host defense mechanisms and colonize host tissues. The Yersinia T3SS is encoded on the IncFII plasmid for Yersinia virulence (pYV). Several layers of gene regulation enables a large increase in expression of Yersinia T3SS genes at mammalian body temperature. Surprisingly, T3SS expression is also controlled at the level of gene dosage. The number of pYV molecules relative to the number of chromosomes per cell, referred to as plasmid copy number, increases with temperature. The ability to increase and maintain elevated pYV plasmid copy number, and therefore T3SS gene dosage, at 37˚C is important for Yersinia virulence. In addition, pYV is highly stable in Yersinia at all temperatures, despite being dispensable for growth outside the host. Yet how Yersinia reinforces elevated plasmid replication and plasmid stability remains unclear. In this study, we show that the chromosomal gene pcnB encoding the polyadenylase PAP I is required for regulation of pYV plasmid copy number (PCN), maintenance of pYV in the bacterial population outside the host, robust T3SS activity, and Yersinia virulence in a mouse infection model. Likewise, pcnB/PAP I is also required for robust expression of the Shigella flexneri virulence plasmid-encoded T3SS that, similar to Yersinia, is encoded on a virulence plasmid whose replication is regulated by sRNA. Furthermore, Yersinia and Shigella pcnB/PAP I is required for maintaining normal PCN of model antimicrobial resistance (AMR) plasmids whose replication is regulated by sRNA, thereby increasing antibiotic resistance by ten-fold. These data suggest that pcnB/PAP I contributes to the spread and stabilization of sRNA-regulated virulence and AMR plasmids in bacterial pathogens, and is essential in maintaining the gene dosage required to mediate plasmid-encoded traits. Importantly pcnB/PAP I has been bioinformatically identified in many species of bacteria despite being studied in only a few species to date. Our work highlights the potential importance of pcnB/PAP I in antibiotic resistance, and shows for the first time that pcnB/PAP I reinforces PCN andpromotes virulence plasmid stability in natural pathogenic hosts with a direct impact on bacterial virulence.
2025-03-20 | GSE292107 | GEO
Project description:Plasmids are widely used across molecular biology and are becoming increasingly valuable products, but robust plasmid replication is held back by stability issues in the host. This study investigated how Escherichia coli responds to plasmid stress at the transcriptional level by modulating plasmid copy number, plasmid size, selection marker and carbon source. This GEO contains controls from this study alone.
2025-06-04 | GSE298911 | 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.
2012-12-25 | GSE39636 | GEO
Project description:Genetically programmed deaths play important roles in the biology of unicellular prokaryotic cells. Some gene complexes force their maintenance on the host bacterial cells by killing cells that have lost them. This form of programmed death called post-segregational killing or genetic addiction is brought about by several Type II restriction-modification gene complexes, through restriction attack on the undermethylated chromosome, and underlie their behavior as selfish mobile elements. To learn the genetic steps to death, we examined how carriage and loss of PaeR7I restriction-modification gene complex affect host Escherichia coli cells through transcriptome and experimental analyses. The PaeR7I complex was on a temperature-sensitive plasmid so that the killing was induced by a temperature shift. We used microarrays to detail the global program of gene expression underlying cell death process mediated by PaeR7I restriction-modification system in E. coli. Experiment Overall Design: Post-segregational cell killing was induced by blocking replication of a temperature sensitive plasmid carrying PaeR7I RM gene complex by shifting up the cultivation temperature. At 30℃, the permissive temperature for the plasmid replication, growth as monitored by OD660, of MG1655/pTN9 (r+m+) was indistinguishable from those of MG1655/pTN11 (r-m+) and MG1655/pHSG415 (vector). Cell death was observed at least 4 h after the temperature shift only in MG1655/pTN9 (r+m+) as in the previous works; the increase in viable cell counts stopped and resulted in decrease of cell viability. To analyze global gene expression when cells went to death, we performed transcriptome analysis 0 h, 1h, 1 h 50 min, and 3h after the temperature shift. We used Affimetrix E. coli antisense genome array. Experiments were performed independently twice.
2009-07-04 | E-GEOD-7326 | biostudies-arrayexpress
Project description:Natural plasmids are common in prokaryotes, but few have been documented in eukaryotes. The natural 2µ plasmid present in the yeast Saccharomyces cerevisiae is one of these best-characterized exceptions. This highly stable genetic element has coexisted with its host for millions of years, faithfully segregating at each cell division through a mechanism that remains unclear. Using proximity ligation methods (such as Hi-C, Micro-C) to map the contacts between 2µ plasmid and yeast chromosomes under dozens of different biological conditions, we found that the plasmid is tethered preferentially to regions with low transcriptional activity, often corresponding to long, inactive genes. These contacts do not depend on common chromosome-structuring factors, such as members of the structural maintenance of chromosome complexes (SMC) but depend on a nucleosome-encoded signal associated with RNA Pol II depletion. They appear stable throughout the cell cycle and can be established within minutes. This chromosome hitchhiking strategy may extend beyond the 2µ plasmid/S. cerevisiae pair, as suggested by the binding pattern of the natural eukaryotic plasmid Ddp5 along silent chromosome regions of the amoeba Dictyostelium discoideum.
2025-01-13 | GSE246636 | GEO
Project description:A major limitation to improving small-molecule pharmaceutical production in streptomycetes is the inability of high-copy-number plasmids to tolerate large biosynthetic gene cluster inserts. A recent finding has overcome this barrier. In 2003, Hu et al. discovered a stable, high-copy-number, 81-kb plasmid that significantly elevated production of the polyketide precursor to the antibiotic erythromycin in a heterologous Streptomyces host (J. Ind. Microbiol. Biotechnol. 30:516-522, 2003). Here, we have identified mechanisms by which this SCP2*-derived plasmid achieves increased levels of metabolite production and examined how the 45-bp deletion mutation in the plasmid replication origin increased plasmid copy number. A plasmid intramycelial transfer gene, spd, and a partition gene, parAB, enhance metabolite production by increasing the stable inheritance of large plasmids containing biosynthetic genes. Additionally, high product titers required both activator (actII-ORF4) and biosynthetic genes (eryA) at high copy numbers. DNA gel shift experiments revealed that the 45-bp deletion abolished replication protein (RepI) binding to a plasmid site which, in part, supports an iteron model for plasmid replication and copy number control. Using the new information, we constructed a large high-copy-number plasmid capable of overproducing the polyketide 6-deoxyerythronolide B. However, this plasmid was unstable over multiple culture generations, suggesting that other SCP2* genes may be required for long-term, stable plasmid inheritance.
2007-06-12 | E-SMDB-4078 | 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. 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:overexpressing DnaN did not affect the genomic DNA pattern in a strain that replicated form the plasmid origin of replication oriN and is deleted for the endogenous origin of replication oriC
2009-09-01 | GSE17809 | GEO
Project description:Chlamydia trachomatis causes chronic inflammatory diseases of the eye and genital tract of global medical importance. The chlamydial plasmid plays an important role in the pathophysiology of these diseases as plasmid-deficient organisms are highly attenuated. The plasmid encodes both noncoding RNAs and eight conserved ORFs of undefined function. To understand plasmid gene function we generated plasmid shuttle vectors with deletions in each of the eight ORFs. The individual deletion mutants were used to transform chlamydiae and the transformants were characterized in terms of plasmid biology and transcriptional profiling. We show that pgp1-2, -6 and -8 are essential for plasmid maintenance while the other ORFs can be deleted and the plasmid stably maintained. We further show that a pgp4 knockout mutant exhibits an in vitro phenotype similar to its isogenic plasmid-less strain in terms of abnormal inclusion morphology and lack of glycogen accumulation. Microarray and qRT-PCR analysis revealed that pgp4 is involved in transcriptional regulation of multiple chromosomal genes; including the glycogen synthase gene glgA. Based on our results, we propose that Pgp1 is a plasmid replicative helicase, Pgp2 is a plasmid replication protein, Pgp4 is a transcriptional regulator of virulence associated chromosomal genes, and Pgp6-8 are plasmid partitioning proteins. These findings have important implications for understanding the plasmid’s role in chlamydial pathogenesis and the development of novel antigenically multivalent live-attenuated chlamydial vaccines.
2013-02-28 | GSE40979 | GEO
Project description:Plasmids are one of the important mobile genetic elements in bacterial evolution. In this study, to evaluate the generality of the impact of plasmid carriage on host cell between different plasmids, we compared the response of Pseudomonas putida KT2440 to harboring three natural plasmids; RP4 (IncP-1, multidrug resistance, 60,099-bp), pCAR1 (IncP-7, carbazole-degradative, 200,231-bp) and NAH7 (IncP-9, naphthalene-degradative, 82,232-bp). We prepared two sets of plasmid-harboring strains from independent conjugation events to elucidate the reproducibility of the impact of the plasmid carriage. As results, the fitness was reduced by the carriage of RP4 and pCAR1 in liquid medium, while it was unaffected or even improved for NAH7-harboring strains. RP4-harboring KT2440 formed smaller colonies than the plasmid-free strain on solid medium (1.6% agar). The host cells were elongated by the carriage of the all plasmids, respectively. Copy number determination by quantitative PCR showed that the amount of each plasmid DNA in the host cell did not differed drastically. Whole genome resequencing showed that 13 SNPs (RP4), 24 SNPs (pCAR1) and 5 SNPs (NAH7) were the total differences between the two substrains for each plasmid-harboring strains. Transcriptome analyses showed that the impact of plasmid carriage was constantly larger in RP4-harboring strain than the other two plasmid-harboring strains. Genes involved in metal acquisition and metabolism were commonly affected by the carriage of the three plasmid. Indeed, plasmid-harboring strains showed greater growth inhibition than plasmid-free strains under iron-limiting condition. This feature could become future target to control plasmid spreading.
2018-02-17 | GSE110733 | GEO