Biology subjects

Poppeliers, J.

Publications and source records attributed to Poppeliers, J..

4 recordsLinked to original sources

bioRxiv2026

Genomic Potential vs. Pathogenic Reality: Functional Virulence Variation in Pseudomonas aeruginosa

Despite the rapid expansion of bacterial genome sequencing, predicting pathogen virulence from genomic information remains a major challenge. To study this association, we integrate comparative genomics, functional phenotyping, host-pathogen interaction assays, and infection outcomes across a diverse collection of 28 Pseudomonas aeruginosa isolates, representing clinically relevant diversity in serotype, type IV pilus group, and flagellar type. While virulence-associated systems were broadly retained across the strain collection, isolates displayed substantial variation in phenotypic behavior and pathogenicity. Genotypic classifications based on pilus, flagellar, siderophore, or secretion system characteristics were poor predictors of virulence-associated phenotypes. Pathogenicity in a Galleria mellonella model varied markedly among strains and was most strongly associated with surface-associated motility, whereas other virulence traits and quorum-sensing genotypes showed limited predictive value. In a three-dimensional lung epithelial cell model, inflammatory responses were negatively correlated with activity of the type III secretion system effector ExoS, suggesting a role in modulation of host immune signaling. Together, these findings demonstrate that virulence emerges from functional deployment of conserved virulence repertoires, rather than their mere presence. By linking genomic diversity to phenotypic expression, pathogenicity, and host responses within a single strain collection, this study highlights fundamental limitations of gene-content-based virulence prediction and underscores the importance of integrating genomic and functional data to better understand P. aeruginosa virulence.

microbiology↗

bioRxiv2026

High-resolution transcriptome analysis reveals a multilayered and dynamic transcriptional architecture in the archaeal virus SSV1

Fuselloviridae infecting thermoacidophilic Sulfolobales are among the best-studied archaeal viruses, with the Saccharolobus Spindle Shaped Virus 1 (SSV1)-Saccharolobus solfataricus interaction serving as a model system. After infection, SSV1 establishes a chronic infection with new virions continuously budding from the infected cell. UV irradiation triggers virus replication, increased virion production and a tightly orchestrated temporal transcription cycle. However, gene regulatory mechanisms post-UV-induction remain elusive. In this study, we investigated the SSV1 transcriptomic landscape post-UV-induction using high-resolution, long-read ONT-cappable-RNA-sequencing. Through end-to-end sequencing of primary transcripts, we generated a comprehensive transcript map of SSV1, identifying 21 transcription start sites (TSSs), including 12 newly described sites, and 19 termination sites (TTSs), of which 9 are novel. This enabled refinement of transcription units and operon structures across the genome. Five new antisense RNAs were discovered, including one encoded antisense to the open reading frame of a putative viral toxin gene a291, which we hypothesize to be a cis-encoded regulatory RNA. In addition, spontaneous recombination between two direct repeats in the SSV1 structural genes vp1 and vp3 was confirmed. To our knowledge, this is the first implementation of cappable-seq for an archaeal virus, and the first base-resolution analysis of the SSV1 transcriptome. It reveals a previously unappreciated level of transcriptional complexity, illustrating how high-resolution transcriptomics can deepen understanding of viral transcriptome architecture and regulatory networks. ImportanceArchaeal viruses remain among the least understood viruses in the virosphere, despite their ecological and evolutionary significance. Saccharolobus Spindle Shaped Virus 1 (SSV1) is a key model for the study of virus-host interactions in archaea. Yet, its gene regulatory mechanisms have remained poorly resolved. Here, we provide the first base-pair resolution transcriptome of an archaeal virus, revealing a complex and multi-layered transcriptional architecture. We uncover alternative transcription start and termination sites, as well as antisense transcription, pointing to regulatory mechanisms beyond a simple temporal gene expression program. These findings suggest that archaeal viruses use sophisticated transcriptional and post-transcriptional mechanisms similar to those in bacterial and eukaryotic viruses. By establishing a high-resolution map of the SSV1 transcriptome, this work advances our understanding of archaeal virus biology.

microbiology↗

bioRxiv2024

The branched receptor binding complex of Ackermannviridae phages promotes adaptative host recognition

Bacteriophages may express multiple receptor binding proteins, enabling the recognition of distinct and diverse bacterial receptors for infection of a broad range of strains. Ackermannviridae phages recognize diverse O-antigens or K-antigens as receptors by expressing multiple tail spike proteins (TSPs). These TSPs interact and form a branched protein complex protruding from the baseplate attached to the distal tail. Here, we aimed to mimic the evolution of the TSP complex by studying the acquisition of new TSPs without disrupting the functionality of the complex. Using kuttervirus phage S117 as a backbone, we demonstrated the acquisition of entire tsp genes from Kuttervirus and Agtrevirus phages within the Ackermannviridae family. A fifth TSP was designed to interact with the complex and provide new host recognition to expand the branched TSP complex. Interestingly, the acquisition of tsp5 resulted in new variants of the branched TSP complex due to the exchange or deletion of tsp genes. Overall, our study provides novel insight into the development of the branched TSP complex, enabling Ackermannviridae phages to adapt to new hosts.

microbiology↗

bioRxiv2022

Transcriptomics-driven characterisation of novel T7-like temperate Pseudomonas phage LUZ100

The Autographiviridae is a diverse yet distinct family of bacterial viruses marked by a strictly lytic lifestyle and a generally conserved genome organization. We here characterise Pseudomonas aeruginosa phage LUZ100, a distant relative of type phage T7. LUZ100 is a podovirus with a limited host range and identified LPS as the likely phage receptor. Interestingly, infection dynamics of LUZ100 indicated moderate adsorption rates and low virulence, hinting towards temperate behavior. This hypothesis was supported by genomic analysis, which showed that LUZ100 shares the conventional T7-like genome organization, yet encodes key genes associated with a temperate lifestyle. To unravel the peculiar characteristics of LUZ100, ONT-cappable-seq transcriptomics analysis was performed. This data generated a birds-eye view of the LUZ100 transcriptome and enabled the discovery of key regulatory elements, antisense RNA, and transcriptional unit structures. The transcriptional map of LUZ100 also allowed us to identify new RNAP-promoter pairs that can form the basis for biotechnological parts and tools for new synthetic transcription regulation circuitry. The ONT-cappable-seq data revealed that the LUZ100 integrase and a MarR-like regulator (proposed to be involved in the lytic/lysogeny decision), are actively co-transcribed in an operon. In addition, the presence of a phage-specific promoter transcribing the phage-encoded RNA polymerase, raises questions on the regulation of this polymerase, and suggests it is interwoven with the MarR-based regulation. This transcriptomics-driven characterisation of LUZ100 supports the increasing evidence that T7-like phages should not straightforwardly be marked as having a strictly lytic lifecycle. ImportanceBacteriophage T7, considered the model phage of the Autographiviridae family, is marked by a strictly lytic lifecycle and conserved genome organisation. Recently, novel phages of this clade are emerging and showing characteristics associated to a lysogenic lifecycle. Screening for temperate behaviour is of outmost importance in fields like phage therapy, where strictly lytic phages are generally required for therapeutic applications. In this study, weve used an omics-driven approach to characterise the T7-like Pseudomonas aeruginosa phage LUZ100. These results led to the identification of actively transcribed lysogeny-associated genes in the phage genome, pointing out that temperate T7-like phages are emerging more frequent than initially thought. In short, the combination of genomics and transcriptomics allowed us to obtain a better understanding of the biology of non-model Autographiviridae phages, which can be used to optimize the implementation of phages and their regulatory elements in phage therapy and biotechnological applications, respectively.

microbiology↗