Biology subjects

Bardy, P.

Publications and source records attributed to Bardy, P..

5 recordsLinked to original sources

bioRxiv2025

A bacterial CARD-NLR immune system controls the release of gene transfer agents

Bacteria have evolved a wide array of immune systems to detect and defend against external threats including mobile genetic elements (MGEs) such as bacteriophages, plasmids, and transposons. MGEs are often selfish, exploiting their bacterial hosts to propagate, however they can also provide adaptive advantages through horizontal gene transfer. Gene transfer agents (GTAs), which are non-infectious domesticated prophages, represent a unique class of beneficial MGEs that facilitate bacterial gene transfer. Despite their domestication, GTAs retain phage-like features, including the requirement for host cell lysis to release particles, that may inadvertently trigger host immunity. How GTAs might avoid, subvert, or possibly adopt host immune systems to complete their life stages is poorly understood. Here, we identify a tripartite system, LypABC, that is essential for GTA-mediated cell lysis in Caulobacter crescentus. LypABC resembles caspase recruitment domain-nucleotide-binding leucine-rich repeat (CARD-NLR) anti-phage defence systems that mediate abortive infection wherein infected cells die to prevent phage proliferation, thereby protecting the overall bacterial population. LypABC-deficient cells produce host DNA-packed GTA particles and eventually die but cannot lyse to release GTA particles. Moreover, overproduction of LypABC is highly toxic to both GTA-producing and non-producing cells, highlighting the need for strict regulation. We find that such regulation is achieved transcriptionally by a repressor, RogB, which binds the promoters of lypABC and of essential GTA activator genes, thus coupling GTA activation and host cell lysis. While traditionally considered antagonistic towards MGEs, our findings here suggest that immunity components are versatile and can be adapted to support MGEs.

microbiology↗

bioRxiv2024

Large scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome

Transducing bacteriophages and gene transfer agents (GTA) are constrained by their capsids structural properties in the length of host DNA they can package. Nanopore sequencing of intact capsid-packaged DNA molecules with full-sized reads can be used to establish the precise lengths and identity of individual packaged DNA molecules and their association with specific bacterial hosts. This approach was validated using a few well-characterised transducing systems, and then applied to study bacterial DNA encapsidation in the faecal microbiomes from three healthy human donors. Bacterial DNA encapsidation appears to be widespread in the microbiome with up to 5.4% of capsid-packaged DNA in the gut virome being of bacterial (non-prophage) origin. Generalised transduction and GTA activity are especially prevalent in the families Oscillospiraceae and Ruminococcaceae, whereas an example of lateral transduction was observed in genus Bacteroides. In addition to that, induction of prophages in a variety of highly prevalent gut bacteria was observed.

microbiology↗

bioRxiv2024

Cell attachment and tail contraction of S. aureus phage phi812

Phages with contractile tails employ elaborate mechanisms to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Here, we used cryo-EM to show that the baseplate of phage 812, a member of the Kayvirus genus, which infects Gram-positive Staphylococcus strains, is formed of a core, wedge modules, and baseplate arms carrying receptor-binding proteins 1 and 2 and tripod complexes. Upon binding to a host cell, the receptor-binding proteins of phage 812 baseplate reorient and undergo conformational changes. The changes to the tripod complexes trigger the release of the central spike and weld proteins, which expose peptidoglycan-degrading domains of the hub proteins. Changes in the positions of baseplate arms are transmitted through wedge modules to tail sheath initiator proteins. The ring of the tail sheath initiator proteins expands and triggers the contraction of the tail sheath, which shortens to 50% and pushes the tail tube 10-30 nm into the bacterial cytoplasm. Homologous molecular mechanisms are probably shared by phages of the Herelleviridae family with contractile tails to infect Gram-positive bacteria.

microbiology↗

bioRxiv2024

Dynamics of bacterial biofilm development imaged using light sheet fluorescence microscopy

Biofilm formation exacerbates bacterial infections and interferes with industrial processes. However, the dynamics of biofilm development is not entirely understood. Here, we present a microfluidic cultivation system that enables continuous imaging of biofilm growth using light sheet fluorescence microscopy (LSFM). We studied the development of biofilms of the human pathogens Staphylococcus aureus and Pseudomonas aeruginosa. Due to the low phototoxicity of LSFM, biofilms can be continuously imaged without adverse effects on their development. Whereas S. aureus forms 50-70-m-thick mushroom-like structures, a P. aeruginosa biofilm is 10-15 m thick with cell clusters 25 m in diameter. A combined biofilm, inoculated with an equal OD600 ratio of S. aureus and P. aeruginosa, resulted in the formation of large mushroom-like clusters of S. aureus cells that were subsequently dispersed by invading P. aeruginosa. A higher inoculation ratio favoring P. aeruginosa resulted in the formation of small and stable S. aureus clusters overgrown with P. aeruginosa cells. Applying conditioned media from S. aureus and P. aeruginosa coculture to a single-species S. aureus biofilm induced its dispersion. Integrating a microfluidic system into LSFM enables the visualization of biofilm formation dynamics and the effects of compounds on biofilm development.

microbiology↗

bioRxiv2024

A stargate mechanism of Microviridae genome delivery unveiled by cryogenic electron tomography

Single-stranded DNA bacteriophages of the Microviridae family are major components of the global virosphere. Microviruses are highly abundant in aquatic ecosystems and are prominent members of the mammalian gut microbiome, where their diversity has been linked to various chronic health disorders. Despite the clear importance of microviruses, little is known about the molecular mechanism of host infection. Here, we have characterized an exceptionally large microvirus, Ebor, and provide crucial insights into long-standing mechanistic questions. Cryogenic electron microscopy of Ebor revealed a capsid with trimeric protrusions that recognise lipopolysaccharides on the host surface. Cryogenic electron tomography of the host cell colonized with virus particles demonstrated that the virus initially attaches to the cell via five such protrusions, located at the corners of a single pentamer. This interaction triggers a stargate mechanism of capsid opening along the 5-fold symmetry axis, enabling delivery of the virus genome. Despite variations in specific virus-host interactions among different Microviridae family viruses, structural data indicate that the stargate mechanism of infection is universally employed by all members of the family. Startlingly, our data reveal a mechanistic link for the opening of relatively small capsids made out of a single jelly-roll fold with the structurally unrelated giant viruses.

microbiology↗