Ontology highlight
ABSTRACT:
PROVIDER: PRJNA823807 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Vertical and horizontal gene transfer tradeoffs direct plasmid fitness
| PRJNA907834 | ENA
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:Plasmid maintenance costs to bacterial hosts is closely linked to the mechanisms that underlie plasmid fitness and how these costs are resolved. Herein, we performed multiple (63) serial passage to explore the compensatory mechanisms of co-evolution of multidrug-resistant IncHI2 plasmid pJXP9 and S. Typhimurium strain ATCC 14028 with or without antibiotic selection. pJXP9 could be maintained at for hundreds of generations even without drug exposure. Decreased lag times and higher competitive advantages were observed in end-point evolved strains bearing pJXP9 compared to ancestral strains. Genomic and transcriptomic analyses revealed that the fitness costs of pJXP9 in ATCC 14028 were derived from not only specific plasmid genes, particularly the multidrug-resistant region and conjugation transfer region I, but also the conflicts resulting from chromosomal gene interactions. Correspondingly, plasmid-borne deletions of these regions could compensate the fitness cost due to the presence of the plasmid. Furthermore, mutations and mRNA alterations in chromosomal genes involved in physiological functions were also adaptative. These functions included decreased flagellar motility, oxidative stress resistance and fumaric acid synthesis, and increased Cu resistance. Our findings suggest that plasmid maintenance through plasmid-bacteria co-evolution is a trade-off between increasing plasmid vertical transmission and impairing its horizontal transmission and bacterial physiological phenotypes.
2022-03-02 | GSE197475 | GEO
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.
2019-05-01 | GSE126149 | 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 | 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:au11-03_gravite - action of microgravity on root development - Action of microgravity on root development - Arabidopsis were grown on horizontal or vertical clinostat for 4, 8 or 12 days. Seedlings on horizontal clinostat were in simulated microgravity and seedlings on vertical clinostat are considered as a control. Comparison was made between plants grown on simulated microgravitry and vertical position.
2012-08-01 | GSE39631 | GEO
Project description:au11-03_gravite - action of microgravity on root development - Action of microgravity on root development - Arabidopsis were grown on horizontal or vertical clinostat for 4, 8 or 12 days. Seedlings on horizontal clinostat were in simulated microgravity and seedlings on vertical clinostat are considered as a control. Comparison was made between plants grown on simulated microgravitry and vertical position. 6 dye-swap - treated vs untreated comparison
2012-07-31 | E-GEOD-39631 | biostudies-arrayexpress
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
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.
2015-03-24 | GSE67187 | GEO