Eric Peyretaillade

Adherent Invasive Escherichia coli (AIEC) colonize the ileal mucosa of Crohn’s disease patients. Among bacterial virulence factors potentially implicated, type 6 secretion systems (T6SS) are molecular machineries sending effectors in prokaryotic or eukaryotic target cells. Two T6SS have been reported in AIEC LF82 reference strain. Here, we show that T6SS genes are more prevalent in Crohn’s disease patients’ microbiota compared to healthy controls, and that T6SS are more frequent in AIEC pathovar compared to E. coli in general and associated with FimH pathoadaptive polymorphism. The use of an in vitro gastrointestinal system coupled with T6SS promoter reporter assay highlighted expression of LF82 T6SS under gastrointestinal conditions, with a major role for bile salts. In mice infected with AIEC LF82 versus T6SS-deleted mutants, T6SS showed a functional impact in modulating the composition of mucosa-associated gut microbiota. Thus, AIEC may use their T6SS to compete with endogenous microbiota to colonize host mucosa.

Since the advent of sequencing techniques and due to their continuous evolution, it has become easier and less expensive to obtain the complete genome sequence of any organism. Nevertheless, to elucidate all biological processes governing organism development, quality annotation is essential. In genome annotation, predicting gene structure is one of the most important and captivating challenges for computational biology. This aspect of annotation requires continual optimization, particularly for genomes as unusual as those of microsporidia. Indeed, this group of fungal‐related parasites exhibits specific features (highly reduced gene sizes, sequences with high rate of evolution) linked to their evolution as intracellular parasites, requiring the implementation of specific annotation approaches to consider all these features. This review aimed to outline these characteristics and to assess the increasingly efficient approaches and tools that have enhanced the accuracy of gene prediction for microsporidia, both in terms of sensitivity and specificity. Subsequently, a final part will be dedicated to postgenomic approaches aimed at reinforcing the annotation data generated by prediction software. These approaches include the characterization of other understudied genes, such as those encoding regulatory noncoding RNAs or very small proteins, which also play crucial roles in the life cycle of these microorganisms.

With nearly 1700 species, Microsporidia represent a group of obligate intracellular eukaryotes with veterinary, economic and medical impacts. To help understand the biological functions of these microorganisms, complete genome sequencing is routinely used. Nevertheless, the proper prediction of their gene catalogue is challenging due to their taxon-specific evolutionary features. As innovative genome annotation strategies are needed to obtain a representative snapshot of the overall lifestyle of these parasites, the MicroAnnot tool, a dedicated workflow for microsporidian sequence annotation using data from curated databases of accurately annotated microsporidian genes, has been developed. Furthermore, specific modules have been implemented to perform small gene (<300 bp) and transposable element identification. Finally, functional annotation was performed using the signature-based InterProScan software. MicroAnnot’s accuracy has been verified by the re-annotation of four microsporidian genomes for which structural annotation had previously been validated. With its comparative approach and transcriptional signal identification method, MicroAnnot provides an accurate prediction of translation initiation sites, an efficient identification of transposable elements, as well as high specificity and sensitivity for microsporidian genes, including those under 300 bp.

With nearly 1,700 species, Microsporidia represent a group of obligate intracellular eukaryotes with veterinary, economic and medical impacts. To help in understanding the biological functions of these microorganisms, complete genome sequencing is used routinely. Nevertheless, the proper prediction of their gene catalogue is challenging due to taxon-specific evolutionary features. As innovative genome annotation strategies are needed to obtain a representative snapshot of the overall lifestyle of these parasites, the MicroAnnot tool, a dedicated workflow for microsporidian sequence annotation using data from curated databases of accurately annotated microsporidian genes, has been developed. Furthermore, specific modules have been implemented to perform small genes (< 300bp) and transposable element identification. Finally, functional annotation was performed using the signature-based InterProScan software. MicroAnnot’s accuracy has been verified by the re-annotation of four microsporidian genomes for which structural annotation had previously been validated. With its comparative approach and transcriptional signal identification method, MicroAnnot provides accurate prediction of translation initiation sites, efficient identification of transposable elements, as well as high specificity and sensitivity for microsporidian genes including those under 300 bp. Thanks to its web interface (https://microannot.org), MicroAnnot is available to the community to ensure high quality annotation of microsporidian genomes.

Anncaliia algerae belongs to microsporidia, a group of obligate intracellular parasites related to fungi. These parasites are largely spread in water and food-webs and can infect a wide variety of hosts ranging from invertebrates to vertebrates including humans. In humans, microsporidian infections are mainly opportunistic as immunocompetent hosts can clear parasites naturally. Recent studies however have reported persistent microsporidian infections and have highlighted them as a risk factor in colon cancer. This may be a direct result of cell infection or may be an indirect effect of the infectious microenvironment and the host's response. In both cases, this raises the question of the effects of microsporidian infection at the host and host-cell levels.

Antigen 43 (Ag43) expression induces aggregation and biofilm formation that has consequences for bacterial colonisation and infection. Ag43 is secreted through the Type 5 subtype “a” secretion system (T5aSS) and is a prototypical member of the family of self-associating autotransporters (SAATs). As a T5aSS protein, Ag43 has a modular architecture comprised of (i) a signal peptide, (ii) a passenger domain that can be subdivided into three subdomains (SL, EJ, and BL), (iii) an autochaperone (AC) domain, and (iv) an outer membrane translocator. The cell-surface SL subdomain is directly involved in the “Velcro-handshake” mechanism resulting in bacterial autoaggregation. Ag43 is considered to have a ubiquitous distribution in E. coli genomes and many strains harbour multiple agn43 genes. However, recent phylogenetic analyses indicated the existence of four distinct Ag43 classes exhibiting different propensities for autoaggregation and interactions. Given the knowledge of the diversity and distribution of Ag43 in E. coli genomes is incomplete, we have performed a thorough in silico investigation across bacterial genomes. Our comprehensive analyses indicate that Ag43 passenger domains cluster in six phylogenetic classes associated with different SL subdomains. The diversity of Ag43 passenger domains is a result of the association of the SL subtypes with two different EJ-BL-AC modules. We reveal that agn43 is almost exclusively present among bacterial species of the Enterobacteriaceae family and essentially in the Escherichia genus (99.6%) but that it is not ubiquitous in E. coli. The gene is typically present as a single copy but up to five copies of agn43 with different combinations of classes can be observed. The presence of agn43 as well as its different classes appeared to differ between Escherichia phylogroups. Strikingly, agn43 is present in 90% of E. coli from E phylogroup. Our results shed light on Ag43 diversity and provide a rational framework for investigating its role in E. coli ecophysiology and physiopathology.

We present the draft genome sequence of Tubulinosema ratisbonensis , a microsporidium species infecting Drosophila melanogaster . A total of 3,013 protein-encoding genes and an array of transposable elements were identified. This work represents a necessary step to develop a novel model of host-parasite relationships using the highly tractable genetic model D. melanogaster .

Microsporidia are ubiquitous intracellular pathogens whose opportunistic nature led to their increased recognition with the rise of the AIDS pandemic. As the RNA world was largely unexplored in this parasitic lineage, we developed a dedicated in silico methodology to carry out exhaustive identification of ncRNAs across the Encephalitozoon and Nosema genera. Thus, the previously missing U1 small nuclear RNA (snRNA) and small nucleolar RNAs (snoRNAs) targeting only the LSU rRNA were highlighted and were further validated using 5' and 3'RACE-PCR experiments. Overall, the 15 ncRNAs that were found shared between Encephalitozoon and Nosema spp. may represent the minimal core set required for parasitic life. Interestingly, the systematic presence of a CCC- or GGG-like motif in 5' of all ncRNA and mRNA gene transcripts regardless of the RNA polymerase involved suggests that the RNA polymerase machineries in microsporidia species could use common factors. Our data provide additional insights in accordance with the simplification processes observed in these reduce genomes and underline the usefulness of sequencing closely related species to help identify highly divergent ncRNAs in these parasites.