Biology subjects

Bulgheresi, S.

Publications and source records attributed to Bulgheresi, S..

6 recordsLinked to original sources

bioRxiv2026

Conserved lifestyle-associated chromosome architectures across mammalian symbionts

Bacterial chromosome biology has largely focused on bacteria that are either free-living or facultatively associated with eukaryotes. Therefore, it is not known how obligate animal symbionts organize their chromosomes. Here, we studied the chromosome organization of three species of multicellular Neisseriaceae that colonize the oral cavity of mammals, Alysiella filiformis, Simonsiella muelleri and Conchiformibius steedae. DNA fluorescence in situ hybridization showed that - irrespective of their ploidy - their chromosomes are longitudinally configured with the origin of DNA replication consistently localized at their host-attached poles throughout the cell cycle. Immunolocalization, ChIP-seq and EMSA implicated ParBS complexes in maintaining this stable chromosome orientation. Moreover, chromosome conformation capture across two species and three growth conditions further revealed conserved lifestyle-associated chromosome architectures, including planktonic-specific ParB-associated chromatin loops and condition-specific chromatin frontiers. Together, our findings show that obligate mammalian symbionts maintain stable longitudinal chromosome orientations irrespective of ploidy while remodeling higher-order chromosome architecture according to physiological state. Distinct yet conserved chromosome architectures characterize exponential, stationary and surface-associated growth, indicating that bacterial genome folding reflects lifestyle and environmental context.

microbiology↗

bioRxiv2026

Emergence of histone-based chromatin complexity in Asgard archaea

The emergence of the eukaryotes coincided with the diversification of histone proteins and their post-translational modifications by enzymes that constitute the core of eukaryotic chromatin. Yet the evolutionary origins of this regulatory machinery are unknown. Here, we show that the key molecular components of histone-based chromatin regulation are present in the Asgard archaea, the closest prokaryotic relatives of eukaryotes. Asgard histones are abundant and have extended N-terminal tails rich in lysine residues that can be post-translationally modified, all of which are features shared with eukaryotic histones. In line with these findings, we identify enzymes from Asgard archaea that deposit or remove lysine acetylation on histone tails in vitro. Moreover, Asgard sirtuin deacetylases (SIR2 proteins) restore chromatin silencing in yeast, demonstrating the functional compatibility of Asgard enzymes with eukaryotic histone substrates. Our findings establish that the foundations of histone-based chromatin predate eukaryogenesis and place Asgard archaea as an evolutionary intermediate in the emergence of eukaryotic chromatin.

evolutionary biology↗

bioRxiv2025

Dynamic protrusions mediate unique crawling motility in Asgard Archaea (Promethearchaeota)

Crawling motility is a hallmark of eukaryotic cells and requires a dynamic actin cytoskeleton, regulated adhesion, and spatially organized signalling pathways1-3. Asgard archaea (phylum Promethearchaeota) which are considered the closest known prokaryotic relatives of eukaryotes potentially encode these functions within their large set of eukaryotic signature proteins4-9. The few cultivated members show a complex cell morphology, consisting of a central cell body from which several protrusions extend, filled with an actin-based cytoskeleton10,11. Here, live cell microscopy of two organisms of the Loki- and Hodarchaea lineages10,12 showed that they dynamically and drastically change their cell shape on a minute time scale and grow and retract their extensive protrusions with a speed of 1.5 to 5.3 {micro}m/min, respectively. After adhering to a glass surface, cells employ their protrusions to undergo active crawling motion. In the presence of selected actin inhibitors however, the observed dynamics were arrested, suggesting a central role of actin in these processes. The observed cellular plasticity and motility are unique features among prokaryotes and might have been crucial for the emergence of the first eukaryotic cells that are thought to have formed through the association of a member of the Promethearchaeota and an alphaproteobacterium, the ancestor of mitochondria.

microbiology↗

bioRxiv2023

Stable chromosome configuration and loop-based polarization in animal symbionts

Chromosome partitioning precedes the division of the cytoplasm, and its evolution is linked with the positioning of the division plane. So far, bacterial chromosome biology has heavily focused on transversally dividing, free-living ones. Here, we determined the chromosome organization of three longitudinally dividing Neisseriaceae exclusively inhabiting the oral cavity of mammals. We showed that in all three multicellular bacteria the origin of DNA replication is invariably located at the host-attached (proximal) pole. Next, 3C-seq revealed loop-based folding of the ori region in Alysiella filiformis and Simonsiella muelleri. Moreover, genes involved in cell motility, piliation and signal transduction mechanisms were specifically looped when transcriptionally and translationally active cells adhered to a substrate, but not when cultured in liquid. Overall, we propose that proximal positioning of the ori and loop-based folding of its surrounding DNA may mediate localized translation of proteins involved in host colonization.

genomics↗

bioRxiv2021

Differential regulation of degradation and immune pathways underlies adaptation of the symbiotic nematode Laxus oneistus to oxic-anoxic interfaces

Eukaryotes may experience oxygen deprivation under both physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all eukaryotes studied so far conserve energy by suppressing their metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is underexplored. One such animal is the marine nematode Laxus oneistus. It thrives, invariably coated by its sulfur-oxidizing symbiont Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, transcriptomics and proteomics showed that, whether in anoxia or not, L. oneistus mostly expressed genes involved in ubiquitination, energy generation, oxidative stress response, immune response, development, and translation. Importantly, ubiquitination genes were also upregulated when the nematode was subjected to anoxic sulfidic conditions, together with genes involved in autophagy, detoxification and ribosome biogenesis. We hypothesize that these degradation pathways were induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients. Remarkably, when L. oneistus was subjected to anoxic sulfidic conditions, lectin and mucin genes were also upregulated, potentially to promote the attachment of its thiotrophic symbiont. Furthermore, the nematode appeared to survive oxygen deprivation by using an alternative electron carrier (rhodoquinone) and acceptor (fumarate), to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., amino acid biosynthesis, development, feeding, mating) were upregulated, together with the worms Toll- like innate immunity pathway and several immune effectors (e.g., Bacterial Permeability Increasing proteins, fungicides). In conclusion, we hypothesize that, in anoxic sulfidic sand, L. oneistus upregulates degradation processes, rewires oxidative phosphorylation and by reinforces its coat of bacterial sulfur-oxidizers. In upper sand layers, instead, it appears to produce broad-range antimicrobials and to exploit oxygen for biosynthesis and development.

genomics↗

bioRxiv2020

Anaerobic sulfur oxidation underlies adaptation of a chemosynthetic symbiont to oxic-anoxic interfaces

Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by monocultures of thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. However, nothing is known about how these variations affect their physiology or metabolism. Here, by applying omics, Raman microspectroscopy and stable isotope labelling, we investigated the effect of oxygen on Candidatus Thiosymbion oneisti. Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation were upregulated in oxic conditions, together with genes involved in organic carbon assimilation, polyhydroxyalkanoate (PHA) biosynthesis, nitrogen fixation and urea utilization. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand its deleterious effects, and the symbiont appeared to proliferate less. Based on its physiological response to oxygen, we propose that Ca. T. oneisti may exploit anaerobic sulfur oxidation coupled to denitrification to proliferate in anoxic sand. However, the ectosymbiont would still profit from the oxygen available in superficial sand, as the energy-efficient aerobic respiration would facilitate carbon and nitrogen assimilation by the ectosymbiont. IMPORTANCEChemoautotrophic endosymbionts are famous for exploiting sulfur oxidization to feed marine organisms with fixed carbon. However, the physiology of thiotrophic bacteria thriving on the surface of animals (ectosymbionts) is less understood. One long standing hypothesis posits that attachment to animals that migrate between reduced and oxic environments would boost sulfur oxidation, as the ectosymbionts would alternatively access sulfide and oxygen, the most favorable electron acceptor. Here, we investigated the effect of oxygen on the physiology of Candidatus Thiosymbion oneisti, a Gammaproteobacterium which lives attached to marine nematodes inhabiting shallow water sand. Surprisingly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions. Furthermore, under anoxia, the ectosymbiont appeared to be less stressed and to proliferate more. We propose that animal-mediated access to oxygen, rather than enhancing sulfur oxidation, would facilitate assimilation of carbon and nitrogen by the ectosymbiont.

microbiology↗