Ontology highlight
ABSTRACT:
PROVIDER: PRJNA559221 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Kin competition accelerates experimental range expansion in an arthropod herbivore
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Project description:Range expansion underlies historical introgressive hybridization in the Iberian hare
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Project description:Community-level interactions between plants and soil biota during range expansion
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Project description:Although continual expansion of the brain during primate evolution accounts for our enhanced cognitive capabilities, the drivers of brain evolution have scarcely been explored. Tree shrews are closely related to primates that comparing their brains to primate brains at the single-cell level will provide new insights into the evolution of the primate brain.
2023-07-15 | GSE233757 | GEO
Project description:Evolutionary relationships and range evolution of greenhood orchids
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Project description:Histone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, in recent years histone proteins have been identified in a few bacterial clades, in particular the phylum Bdellovibrionota, and these histones have been proposed to exhibit a range of divergent features compared to histones in archaea and eukaryotes. However, no experimental functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription and three-dimensional genome organization in a member of Bdellovibrionota (a Bacteriovorax strain). We find that Bacteriovorax chromatin is characterized by preferential accessibility around promoter regions, similar to what is observed in eukaryotes with compact genomes such as yeast, and also to some archaea. As in eukaryotes, chromatin accessibility positively correlates with gene expression. Mapping active transcription through single-strand DNA (ssDNA) profiling revealed that Bacteriovorax promoters exhibit very strong polymerase pausing, unlike in yeast, but similar to the state of mammalian and fly promoters. Finally, the Bacteriovorax genome exists in a three-dimensional (3D) conformation analogous to that of other bacteria without histones, organized by the parABS system and along the axis defined by replication origin and termination regions. These results provide a foundation for understanding the chromatin biology of the unique Bdellovibrionota bacteria and the deep evolution of chromatin organization across the tree of life.
2023-12-06 | GSE245010 | GEO
Project description:Small RNAs are the non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across wide range of bacteria, mainly by controlling mRNA stabilization or regulating translation. Identification and functional characterization of sRNAs that has been carried out in various plant growth promoting bacteria have shown to help the bacterial cell cope up with environmental stress. Till now no study has been carried out to uncover these regulatory molecules in diazotrophic alpha-proteobacterium Azospirillum brasilense Sp245. RNA-Seq is a suitable approach for expression-based sRNA identification in bacteria.
2020-11-01 | GSE117764 | GEO
Project description:The rise of antibiotic resistance in many bacterial pathogens has been driven by the spread of a few successful strains, suggesting that some bacteria are genetically pre-disposed to evolving resistance. We tested this hypothesis by challenging a diverse set of 222 strains of Staphylococcus aureus with the antibiotic ciprofloxacin in a large-scale evolution experiment. Surprisingly, we found that a single efflux pump, norA, causes widespread variation in evolvability across the diversity of S. aureus. In most lineages of S. aureus, elevated norA expression potentiated evolution by increasing the fitness benefit provided by resistance mutations in DNA topoisomerase under ciprofloxacin treatment. Amplification of norA provided a further mechanism of rapid evolution, but this was restricted to strains from CC398. Crucially, chemically inhibiting NorA effectively prevented the evolution of resistance across the diversity of S. aureus. Our study shows that the underlying genetic diversity of pathogenic bacteria plays a key role in shaping resistance evolution. Understanding this link makes it possible to predict which strains are likely to evolve resistance and to optimize inhibitor use to prevent this outcome.
2020-07-05 | GSE150762 | GEO
Project description:In addition to their well-known role as stress-associated catecholamine hormones in animals and humans, epinephrine (EPI) and norepinephrine (NE) act as interkingdom signals between eukaryotic hosts and bacteria. However, the molecular basis of their effects on bacteria is not well understood. In initial phenotypic studies utilizing Vibrio campbellii as a model organism, we characterized the bipartite mode of action of catecholamines, which consists of promotion of growth under iron limitation, and enhanced colony expansion. In order to identify the molecular targets of the hormones, we designed and synthesized tailored probes for chemical proteomic studies. As the catechol group in EPI and NE acts as iron chelator and is prone to form a reactive quinone moiety, we devised a photoprobe based on the adrenergic agonist phenylephrine (PE), which solely influenced colony expansion on soft agar. Using this probe, we identified CheW, located at the core of the chemotaxis signaling network, as a major target. In vitro studies confirmed that EPI, NE, PE, as well as labetalol, a clinically applied antagonist, bind to purified CheW with affinity constants in the sub-micromolar range. In line with these findings, exposure of V. campbellii to these adrenergic agonists affects the chemotactic control of the bacterium. This study highlights a previously unknown effect of eukaryotic signaling molecules on bacterial motility.
2022-04-04 | PXD029119 | Pride