Manured soil
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA718741 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14118100_1.fastq.gz | Fastqsanger.gz | |||
| SRR14118100_2.fastq.gz | Fastqsanger.gz | |||
| SRR14118603_1.fastq.gz | Fastqsanger.gz | |||
| SRR14118603_2.fastq.gz | Fastqsanger.gz | |||
| SRR14118604_1.fastq.gz | Fastqsanger.gz |
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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.
2022-12-23 | GSE219270 | GEO
Project description:Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution. Transfer of conjugative plasmids is a complex process that needs to be synchronized with the physiological state of the bacterial host. While several host transcription factors are known to control the plasmid-borne transfer control genes, RNA-based regulatory circuits for host-plasmid communication remain unknown. Here, we describe a post-transcriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two different seed pairing domains to recognize and activate the mRNAs of both the sigma-factor S and RicI, a cytoplasmic membrane protein. The latter is a hitherto unknown conjugation inhibitor whose transcription requires S. Together, RprA and S constitute a feed-forward loop with AND-gate logic which tightly controls RicI synthesis for selective suppression of plasmid conjugation under membrane stress. This study reports the first sRNA-controlled feed-forward loop based on double target activation and an unexpected function for a core-genome encoded small RNA in controlling extrachromosomal DNA transfer.
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Project description:High-resolution mapping of the pCAR1 plasmid transcriptomes in the original host Pseudomonas resinovorans CA10 and the transconjugant Pseudomonas putida KT2440(pCAR1) While plasmids are replicated autonomously in their hosts, the transcription of plasmid genes can be switched through horizontal transfer by the change in the transcriptional networks. To examine whether and how the plasmid genome is differentially expressed, we analyzed the transcriptomes of the 199,035-bp IncP-7 carbazole catabolic and conjugative plasmid pCAR1 in the original host Pseudomonas resinovorans CA10 and the transconjugant Pseudomonas putida KT2440(pCAR1) during growth on carbazole or succinate using the high-resolution tiling array. The tiling array successfully detected the relatively large catabolic operons, for which transcription was induced during growth on carbazole regardless of the host. Compared between the hosts, nearly identical regions of pCAR1 were transcribed, but two hypothetical operons, i.e., ORF100-108 and ORF145-146, were transcribed at higher levels in KT2440(pCAR1) than in CA10. We verified the differential expression in heterologous hosts using quantitative RT-PCR. The tiling array analysis clearly revealed the transcription start sites, for which the positions and extents agreed with the primer extension experiments. Our data demonstrate that the transcriptome of the transmissible plasmid is altered through horizontal transfer, and we identified probable genes that are involved in plasmid functions in various hosts. This approach can be used to visualize flexible prokaryotic transcriptomes comprehensively. Keywords: high-resolution RNA mapping
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Project description:The type VI secretion system (T6SS) is a highly sophisticated nanomachine widely used by bacteria to achieve competitive advantage and to potentiate horizontal gene transfer. Plasmid conjugation plays crucial roles in bacterial evolution by driving adaptation to environmental stimuli and pathogenicity. The lethal effect mediated by T6SS is detrimental to horizontal gene transfer by conjugation, while bacteria have evolved T6SS repression mechanisms regulated by plasmid to accomplish conjugative transfer. Two TetR family regulators encoded by large conjugative plasmid (LCP) in Acinetobacter baumannii have been proved similar in T6SS restriction, which seems redundant in function. Here, the global regulation roles and multiple DNA binding sites of two plasmid-sourced TetRs were identified. The two TetRs showed distinct preferences in similar roles of T6SS inhibition and binding with DNA probes. Crystal structures of TetRs were solved for illuminating the regulatory mechanism and possible reasons for difference in functions. In addition, plasmid-sourced TetRs also significantly downregulated biofilm formation and bacterial colonization, as well as influenced bacterial virulence in cultured cells and murine pneumonia infection models. Taken together, this work comprehensively elucidates the roles and regulatory mechanisms of TetRs and clarifies their similarity and difference in function, providing insights into plasmid encoded chromosome regulation pathways.
2025-08-16 | GSE277926 | GEO
Project description:The type VI secretion system (T6SS) is a highly sophisticated nanomachine widely used by bacteria to achieve competitive advantage and to potentiate horizontal gene transfer. Plasmid conjugation plays crucial roles in bacterial evolution by driving adaptation to environmental stimuli and pathogenicity. The lethal effect mediated by T6SS is detrimental to horizontal gene transfer by conjugation, while bacteria have evolved T6SS repression mechanisms regulated by plasmid to accomplish conjugative transfer. Two TetR family regulators encoded by large conjugative plasmid (LCP) in Acinetobacter baumannii have been proved similar in T6SS restriction, which seems redundant in function. Here, the global regulation roles and multiple DNA binding sites of two plasmid-sourced TetRs were identified. The two TetRs showed distinct preferences in similar roles of T6SS inhibition and binding with DNA probes. Crystal structures of TetRs were solved for illuminating the regulatory mechanism and possible reasons for difference in functions. In addition, plasmid-sourced TetRs also significantly downregulated biofilm formation and bacterial colonization, as well as influenced bacterial virulence in cultured cells and murine pneumonia infection models. Taken together, this work comprehensively elucidates the roles and regulatory mechanisms of TetRs and clarifies their similarity and difference in function, providing insights into plasmid encoded chromosome regulation pathways.
2025-08-16 | GSE277925 | GEO
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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Project description:The completely sequenced catabolic plasmid pCAR1 of Pseudomonas resinovorans CA10 confers the ability to degrade carbazole upon the recipient strain Pseudomonas putida KT2440. To study the coordinated expression of pCAR1 with its host chromosome, transcriptome of the transconjugant strain KT2440(pCAR1) was analyzed at growth with carbazole as the sole carbon source compared to succinate as an alternative carbon source. Next, horizontal gene transfer of a plasmid potentially alters the transcriptome of its host chromosome. Transcriptome of the transconjugant strain KT2440(pCAR1) was compared to the parental strain KT2440 at the same growth conditions. Furthermore, pCAR1 encodes a possible global regulator designated ORF70, which belongs to the MvaT family of H-NS-like nucleoid-associated proteins in Pseudomonas. To investigate the regulon under the control of ORF70, transcriptome of KT2440(pCAR1deltaORF70) was compared to the parental strain KT2440(pCAR1) at the same growth conditions. Keywords: Comparative transcriptome analysis
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Project description:Plasmids are extrachromosomal genetic elements commonly found in bacteria. Plasmids are known to fuel bacterial evolution through horizontal gene transfer (HGT), but recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond HGT remains poorly explored. In this study, we investigate the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of various multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveil that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded IS1 elements. Specifically, IS1-mediated gene inactivations expedite the adaptation rate of clinical strains in vitro and foster within-patient adaptation in the gut. We decipher the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings propose that plasmid-mediated IS transposition represents a crucial mechanism for swift bacterial adaptation.
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