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

microbial archaea diversity

Project description:microbial archaea diversity Metagenome

| PRJNA786714 | ENA

Marine biofilm-forming bacteria proteome

Project description:2D-gel and nanoLC-MS/MS experiment

2012-10-03 | PRD000333 | Pride

Study of diversity of mineral-forming bacteria in sabkha mats and sediments of mangrove forest in Qatar.

Project description:The involvement of microorganisms in carbonate minerals and modern dolomite formation in evaporitic environments occupied with microbial mats (i.e., sabkha) and in mangrove forests is evidenced, while its potential diversity requires further elucidation. Microorganisms can create supersaturated microenvironments facilitating the formation of various carbonate minerals through specific metabolic pathways. This is particularly important in arid environments, where deposition and sedimentary structures can occur. This study investigated the biodiversity of halophilic, heterotrophic, and aerobic mineral-forming bacteria in mangrove forests and living and decaying mats of Qatari sabkha. The diversity study was performed at the protein level using MALDI-TOF mass spectrometry protein profiles combined with principal component analysis (PCA), which revealed a high diversity of isolated strains at the taxonomy and protein profile levels. The diversity of the minerals formed in pure cultures was evidenced by SEM/EDS and XRD analysis. Different types of carbonate minerals (calcium carbonate, magnesium carbonates, and high-magnesium calcites) were formed in pure cultures of the studied strains, which might explain their occurrence in the bulk composition of the sediments from where the strains were isolated. These results illuminate the diversity of biological mineral-formation processes in the extreme environments of Qatari sabkhas and mangroves, explaining the high diversity of minerals in these environments.

| S-EPMC10470404 | biostudies-literature

Virulence Plasmids of Spore-Forming Bacteria.

Project description:Plasmid-encoded virulence factors are important in the pathogenesis of diseases caused by spore-forming bacteria. Unlike many other bacteria, the most common virulence factors encoded by plasmids in Clostridium and Bacillus species are protein toxins. Clostridium perfringens causes several histotoxic and enterotoxin diseases in both humans and animals and produces a broad range of toxins, including many pore-forming toxins such as C. perfringens enterotoxin, epsilon-toxin, beta-toxin, and NetB. Genetic studies have led to the determination of the role of these toxins in disease pathogenesis. The genes for these toxins are generally carried on large conjugative plasmids that have common core replication, maintenance, and conjugation regions. There is considerable functional information available about the unique tcp conjugation locus carried by these plasmids, but less is known about plasmid maintenance. The latter is intriguing because many C. perfringens isolates stably maintain up to four different, but closely related, toxin plasmids. Toxin genes may also be plasmid-encoded in the neurotoxic clostridia. The tetanus toxin gene is located on a plasmid in Clostridium tetani, but the botulinum toxin genes may be chromosomal, plasmid-determined, or located on bacteriophages in Clostridium botulinum. In Bacillus anthracis it is well established that virulence is plasmid determined, with anthrax toxin genes located on pXO1 and capsule genes on a separate plasmid, pXO2. Orthologs of these plasmids are also found in other members of the Bacillus cereus group such as B. cereus and Bacillus thuringiensis. In B. thuringiensis these plasmids may carry genes encoding one or more insecticidal toxins.

| S-EPMC9851182 | biostudies-literature

Early biofilm forming bacteria

Project description:Early biofilm forming bacteria Metagenome

| PRJNA705154 | ENA