Biology subjects

Briolat, V.

Publications and source records attributed to Briolat, V..

3 recordsLinked to original sources

bioRxiv2025

The two groups of zebrafish type I interferons target different tissues, paralleling the mammalian type I: type III IFN functional division

Interferons (IFNs) are ancient cytokines that arose in jawed vertebrates [~]400-500 million years ago. IFN systems are present with conserved antiviral functions across vertebrate lineages, including zebrafish (Danio rerio). In mammals, antiviral IFNs are divided between type I interferons (IFN-I), which drive systemic responses, and type III interferons (IFN-III), which protect barrier mucosal epithelia, owing to the specific distribution of their respective receptors. Although zebrafish lack IFN-III, they have IFN-Is which subdivide into 2 groups with distinct receptors, providing a unique opportunity to study how antiviral immunity has evolved in the absence of IFN-III. Whilst previous work has suggested complementary, non-redundant roles for IFNs from these groups, the tissue specificity has not yet been resolved. As larvae, zebrafish only express one group 1 (IFN{varphi}1) and one group 2 IFN (IFN{varphi}3). Using viral infection assays and reporter transgenics, we found that IFNs from group 1 (IFN{varphi}1) and group 2 (IFN{varphi}3) are produced by distinct subsets of cells, with no detectable co-expression. To assess tissue and cell-type-specific responses to these two IFNs, we used ISG reporter fish imaging and whole-larva single cell RNA sequencing after injection of recombinant IFN{varphi}1 and IFN{varphi}3. Despite a similar core ISG response, distinct downstream ISG programs across multiple tissues and organ systems were found. In particular, barrier epithelial cells, such as enterocytes, responded more strongly to IFN{varphi}1, while myeloid cells responded more strongly to IFN{varphi}3. Our results indicate that zebrafish IFN-I families have functionally diversified their antiviral immune responses by tissue context, driven by cellular partitioning of both IFN-I production and response. These results mirror the division of labour between mammalian IFN-I and IFN-III, emphasising the evolutionary importance of tissue division of immune responses, as well as deepening our understanding of the zebrafish as a model for host-pathogen interactions.

immunology↗

bioRxiv2023

Escherichia coli aggregates mediated by native or synthetic adhesins exhibit both core and adhesin-specific transcriptional responses

Bacteria can rapidly tune their physiology and metabolism to adapt to environmental fluctuations. In particular, they can adapt their lifestyle to the close proximity of other bacteria or presence of different surfaces. However, whether these interactions trigger transcriptomic responses is poorly understood. We used a specific set up of E. coli strains expressing native or synthetic adhesins mediating bacterial aggregation to study the transcriptomic changes of aggregated compared to non-aggregated bacteria. Our results show that following aggregation, bacteria exhibit a core response independent of the adhesin type, with differential expression of 56.9% of the coding genome, including genes involved in stress response and anaerobic lifestyle. Moreover, when aggregates were formed via a naturally expressed E. coli adhesin (Antigen 43), the transcriptomic response of the bacteria was more exaggerated compared to aggregates formed via a synthetic adhesin. This suggests that the response to aggregation induced by native E. coli adhesins could have been finely tuned during bacterial evolution. Our study therefore provides insights on the effect of self-interaction in bacteria and allows a better understanding of why bacterial aggregates exhibit increased stress tolerance. ImportanceFormation of bacterial aggregates has an important role in both clinical and ecological contexts. Although these structures have been previously shown to be more resistant to stressful conditions, the genetic basis of this stress tolerance associated with the aggregate lifestyle is poorly understood. Surface sensing mediated by different adhesins can result in varying changes on bacterial physiology. However, whether adhesin-adhesin interactions as well as the type of adhesin mediating aggregation affects bacterial cell physiology is unknown. By sequencing the transcriptomes of aggregated and non-aggregated cells expressing native or synthetic adhesins, we characterized the effects of aggregation and adhesin type on E. coli physiology.

microbiology↗

bioRxiv2019

Interferon-stimulated genes in zebrafish and human define an ancient arsenal of antiviral immunity

The evolution of the interferon (IFN) system, the major innate antiviral mechanism of vertebrates, remains poorly understood. According to the detection of type I IFN genes in cartilaginous fish genomes, the system appeared 500My ago. However, the IFN system integrates many other components, most of which are encoded by IFN-stimulated genes (ISGs). To shed light on its evolution, we have used deep RNA sequencing to generate a comprehensive list of ISGs of zebrafish, taking advantage of the high quality genome annotation in this species. We analyzed larvae after inoculation of recombinant zebrafish type I IFN, or infection with chikungunya virus, a potent IFN inducer. We identified more than 400 zebrafish ISGs, defined as being either directly induced by IFN or induced by the virus in an IFN receptor-dependent manner. Their human orthologues were highly enriched in ISGs, particularly for highly-inducible genes. We identified 72 orthology groups containing ISGs in both zebrafish and human, revealing a core ancestral ISG repertoire, which includes most of the known signaling components of the IFN system. Many downstream effectors were also already present 450 My ago in the common ancestor of tetrapods and bony fish, and diversified as multi-gene families independently in the two lineages. A large proportion of the ISG repertoire is lineage-specific; around 40% of protein-coding zebrafish ISGs had no human orthologue. We identified 14 fish-specific gene families containing multiple ISGs, including finTRIMs. This work illuminates the evolution of the IFN system and provides a rich resource to explore new antiviral mechanisms.\n\nKey pointsO_LIWe established an exhaustive list of larval zebrafish ISGs.\nC_LIO_LIOrthologous ISGs in fish and human identify a large ancestral ISG repertoire.\nC_LI

immunology↗