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Packaging of DNA:RNA hybrids in extracellular vesicles and their horizontal transfer in cancer

ABSTRACT: Packaging of DNA:RNA hybrids in extracellular vesicles and their horizontal transfer in cancer

PROVIDER: PRJEB30647 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3046940_1.fastq.gz	Fastqsanger.gz
	ERR3046940_2.fastq.gz	Fastqsanger.gz
	ERR3046941_1.fastq.gz	Fastqsanger.gz
	ERR3046941_2.fastq.gz	Fastqsanger.gz
	ERR3046942_1.fastq.gz	Fastqsanger.gz

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Packaging of DNA:RNA hybrids in extracellular vesicles and their horizontal transfer in cancer

Project description:RNAs isolated from ZR751 (acceptors/responders) and BT474 (non-acceptors/non-responders) cells following education with EV-Hybridlow (EV-DNA from normoxic cancer cells) and EV-Hybridhigh (EV-DNA from IH-derived cancer cells) were sequenced.

2020-12-31 | E-MTAB-7586 | biostudies-arrayexpress

Horizontal gene transfer in Vibrio cholerae

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Vertical and horizontal gene transfer tradeoffs direct plasmid fitness

Project description:Plasmid fitness is directed by two orthogonal processes—vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical E. coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.

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Horizontal mitochondrial transfer from microenvironment increases glioblastoma tumorigenicity

Project description:Horizontal mitochondrial transfer from microenvironment increases glioblastoma tumorigenicity

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Prevalence of multi-resistant plasmids in hospital inhalable particulate matter (PM) and its impact on horizontal gene transfer

Project description:Antibiotic resistance is exacerbated by the exchange of antibiotic resistance genes (ARGs) between microbes from diverse habitats. Plasmids are important ARGs mobile elements and are spread by horizontal gene transfer (HGT). In this study, we demonstrated the presence of multi-resistant plasmids from inhalable particulate matter (PM) and its effect on gene horizontal transfer. Three transferable multi-resistant plasmids were identified from PM in a hospital, using conjugative mating assays and nanopore sequencing. pTAir-3 contained 26 horizontal transfer elements and 10 ARGs. Importantly pTAir-5 harbored carbapenem resistance gene (blaOXA) which shows homology to plasmids from human and pig commensal bacteria, thus indicating that PM is a media for antibiotic resistant plasmid spread. In addition, 125 μg/mL PM2.5 and PM10 significantly increased the conjugative transfer rate by 110% and 30%, respectively, and augmented reactive oxygen species (ROS) levels. Underlying mechanisms were revealed by identifying the upregulated expressional levels of genes related to ROS, SOS, cell membranes, pilus generation, and transposition via genome-wide RNA sequencing. The study highlights the airborne spread of multi-resistant plasmids and the impact of inhalable PM on the horizontal transfer of antibiotic resistance.

2022-10-31 | GSE159850 | GEO

Conjugation, genetic reprogamming and horizontal transfer of pathogenicity between Roseobacters

Project description:Horizontal transfer of plasmids is one of the main drivers of bacterial adaptation, resulting e.g. in the spread of antibiotic resistance. We investigated the marine Roseobacter group and studied how conjugation affects the gene expression and biology of the new host. We showed that the two syntenic 126 kb and 191 kb plasmids of Dinoroseobacter shibae can be conjugated into representatives of all major lineages of Rhodobacteraceae. In the model organism Phaeobacter inhibens their acquisition resulted in differential expression of genes related to motility, transport and the synthesis of vitamins. Moreover, the decrease of the potent antibiotic tropodithietic acid reduced the energetic burden of Phaeobacter and resulted in an enhanced growth. While the T4SS systems of both plasmids were silenced in the new host, the ability to kill the dinoflagellate was exclusively transferred via the 191 kb plasmid from D. shibae to P. inhibens. Our findings showed drastic consequences of plasmid conjugation; genetic reprogramming of the novel host resulted in considerable fitness changes leading to the prediction that horizontal gene transfer triggers bacterial speciation.

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An epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element

Project description:Horizontal transfer of the integrative and conjugative element ICEMlSymR7A converts non symbiotic Mesorhizobium spp. into nitrogen-fixing legume symbionts. Here we discover subpopulations of Mesorhizobium japonicum R7A become epigenetically primed for quorum-sensing (QS) and QS-activated horizontal transfer. Isolated populations in this state termed R7A* maintained these phenotypes in laboratory culture but did not transfer the R7A* state to recipients of ICEMlSymR7A following conjugation. We previously demonstrated ICEMlSymR7A transfer and QS are repressed by the antiactivator QseM in R7A populations and that the adjacently-coded DNA-binding protein QseC can represses qseM transcription. Here RNA-sequencing revealed qseM expression was repressed in R7A* cells and that RNA antisense to qseC was abundant in R7A but not R7A*. Deletion of the antisense-qseC promoter converted cells into an R7A*-like state. An adjacently-coded QseC2 protein bound two operator sites and repressed antisense-qseC transcription. Plasmid overexpression of QseC2 stimulated the R7A* state, which persisted following curing of this plasmid. The epigenetic maintenance of the R7A* state required ICEMlSymR7A-encoded copies of both qseC and qseC2. Therefore QseC and QseC2, together with their DNA-binding sites and overlapping promoters, form a stable epigenetic switch that establishes binary control over qseM transcription and primes a subpopulation of R7A cells for QS and horizontal transfer.

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Vertical and horizontal gene transfer tradeoffs direct plasmid fitness

Project description:Vertical and horizontal gene transfer tradeoffs direct plasmid fitness

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Horizontal transfer of mesenchymal stem cell-derived mitochondria and its effect on activated murine B lymphocytes

Project description:Mesenchymal stem cells (MSCs) are cells with high regenerative and immunosuppressive capacity that are known to be very potent donors of functional mitochondria to all surrounding cells, including immune cells. As metabolism shapes immune cell response and phenotype, mitochondrial transfer might be one of the main immunosuppressive mechanisms used by stem cells. However, the precise mechanism underlying horizontal mitochondrial transfer and its effect on some cell populations has yet to be discovered. In our project, we have shown that MSCs transfer mitochondria to B lymphocytes less efficiently in comparison to other immune populations. To describe the effect of mitochondrial transfer on activated B lymphocytes, MSCs were co-cultivated with B lymphocytes which were activated prior to co-cultivation. Then B cell acceptors and non-acceptors of mitochondria were sorted for further RNA isolation and the performance of bulk RNA-seq.

2024-03-02 | E-MTAB-13438 | biostudies-arrayexpress

DNA packaging bias and differential expression of gene transfer agent genes within a population during production and release of the Rhodobacter capsulatus gene transfer agent, RcGTA

Project description:Rhodobacter capsulatus produces a gene transfer agent (GTA) called RcGTA. RcGTA is a phage-like particle that packages R. capsulatus DNA and transfers it to other R. capsulatus cells. Low-resolution techniques suggested RcGTA packages random DNA. Analysis of the RcGTA terminase sequence revealed a distant relationship to the phage T4 terminase protein, which can also perform sequence-independent packaging. We quantified the relative frequency of packaging for each gene in the genome by hybridization of DNA from RcGTA particles to an R. capsulatus microarray. All genes were found within the RcGTA particles, and random packaging was observed at a genome-wide scale. However, the genes encoding the RcGTA particle were under-packaged compared to other regions. Single-cell expression analysis demonstrated that RcGTA gene expression is not uniform within a culture. We propose a mechanism by which high levels of RcGTA gene transcription in the most active RcGTA producing cells hinders access of the packaging machinery to these genes, which causes a reduction in their packaging frequency. This sub-population gene expression phenomenon likely explains the lack of observed cell lysis in RcGTA producing cultures. DNA extracted from within RcGTA particles produced by DE442, an RcGTA overproducer, was hybridized to an Affymetrix genechip custom array in order to quantify the relative frequency with which any given gene was packaged within the particles. These data were MAS5 normalized. An underlying packaging bias was suspected to be transcription related, so these frequencies were compared to expression levels within the population, as determined by hybridization of late-stationary RNA samples of DE442 and of the wildtype (SB1003) to the same custom array. These data were RMA normalized.

2012-05-21 | E-GEOD-33176 | biostudies-arrayexpress

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