Biology subjects

COKELAER, T.

Publications and source records attributed to COKELAER, T..

4 recordsLinked to original sources

bioRxiv2026

Initiation codon context governs translation-coupled mRNA decay and coordinated expression in the human parasite Leishmania

In the absence of canonical, promoter-based transcriptional regulation, Leishmania has evolved alternative regulatory mechanisms for adaptive gene expression, including post-transcriptional control via differential mRNA turnover. While this mechanism is recognized as critical in Leishmania, fundamental aspects of transcript stability in these parasites remain to be elucidated, such as the role of translation initiation-mediated mRNA decay. We addressed this important gap by investigating the role of the initiation codon context (Kozak sequence) in gene expression in L. donovani. Mapping Kozak sequences across the trypanosomatid genomes revealed important differences in nucleotide preference across the genus and sub-genus levels, suggesting important cis-regulatory function. Within a single species, only a small subset of possible Kozak sequences is associated with several start codons, further supporting their role in expression control. Transgenic L. donovani lines expressing EGFP under the control of distinct Kozak variants indeed demonstrated that the nucleotide context of the start codon directly modulates both protein expression and mRNA stability, which was associated with increased recruitment of mRNA to heavy polysomes. Parasite exposure to the translation inhibitor cycloheximide restored EGFP expression driven by a weak Kozak sequence, revealing a direct link between mRNA stability and Kozak-mediated translatability. RNA-seq analysis of parasites arrested for transcription or translation elongation revealed transcripts enriched for the GO terms RNA modification and pseudouridine synthesis as key targets for translation-dependent mRNA turnover. The segregation of these transcripts into functional clusters with distinct Kozak profiles further suggests that Kozak sequence composition defines Kozak-governed regulons in Leishmania. Within this regulatory framework, the -3 nucleotide is identified as the key positional determinant driving differential transcript abundance. Our work uncovers a key role for translation initiation-coupled mRNA decay in Leishmania gene expression regulation adding a previously underappreciated layer of post-transcriptional regulation in parasite adaptation.

genomics↗

bioRxiv2026

Genetic introgression and transcriptomic plasticity are associated with enhanced Leishmania infantum pathogenicity causing human cutaneous leishmaniasis in Tunisia

The protozoan parasite Leishmania infantum exhibits significant genetic variability among isolates, influencing disease manifestation and treatment response. Although L. infantum is classically described as the causative agent of Visceral Leishmaniasis (VL) - often associated with immune deficiency, cases of Cutaneous Leishmaniasis (CL) caused by this species in immunocompetent individuals have been reported in different countries. To investigate the molecular basis of this unusual shift in tissue tropism and pathogenicity, we applied comparative genomic and transcriptomic approaches on two canine isolates (CanL) and two human isolates associated with Cutaneous Leishmaniasis (CL) in Tunisia. While the CanL isolates showed close genetic similarity to the L. infantum reference strain (JPCM5), the CL isolates formed a separate, highly divergent cluster based on SNP localization and frequency, differing not only from JPCM5 but also from each other. Utilizing the metagenomics sequence classification tool Kraken, we revealed a complex hybrid nature of the CL isolates, showing introgression from L. donovani and L. tropica, suggesting that hybridization has played a key role in generating novel phenotypic traits. Integration of RNA-seq and DNA-seq data demonstrated that only a minority of gene expression variation within and in-between the CanL or CL groups reflected gene dosage effects due to copy number variation, while the majority of expression differences were independent of gene dosage, implying post-transcriptional regulatory mechanisms contributing to parasite adaptation. In conclusion, our study identifies hybridization, genome instability, and transcriptomic adaptation as interconnected drivers of the L. infantum evolutionary potential. These mechanisms can collectively enhance parasite fitness gain, potentially explaining the emergence of cutaneous disease forms in a species traditionally linked to visceral infection. Author SummaryThis research reveals that hybridization between distinct Leishmania parasite species could be a key mechanism driving the evolution of new disease forms. By demonstrating that cutaneous leishmaniasis (CL) cases are caused by hybrid L. infantum parasites whose genomes show introgression with DNA from L. donovani and L. tropica, this study reveals a molecular mechanism potentially linked to the emergence of tegumentary disease from a species traditionally known to cause visceral infection. These findings contribute to our understanding of Leishmania evolution, the emergence of atypical forms of leishmaniasis linked to hybridization, and the impact of genome instability and transcriptomic adaptation as potent forces for generating phenotypic diversity and enhancing parasite fitness.

genomics↗

bioRxiv2025

Colorectal Cancer-Associated Streptococcus gallolyticus: A Hidden Diversity Exposed

Streptococcus gallolyticus subsp. gallolyticus (SGG) is a bacterial pathogen implicated in bacteremia and endocarditis, and is often associated with colon tumors in elderly individuals. The development of colorectal cancer (CRC) has been linked to intestinal dysbiosis, characterized by increased proportions of SGG and other intestinal microbes. In this study, we present the complete nucleotide sequence of five novel clinical isolates of SGG associated with colorectal cancer, revealing unexpected genetic diversity. Sequencing an additional 30 SGG clinical isolates provided a more comprehensive description of this genetic diversity. We did not identify a pathogenicity island specific to CRC-associated SGG isolates. Most of these human-derived SGG isolates exhibit resistance to multiple antibiotics. Our findings also offer additional insights into multilocus sequence typing (MLST), capsular loci, and pilus organization. Analysis of the repertoire of surface proteins reveals high potential for binding and foraging complex polysaccharides. Finally, comparative genomics with the phylogenetically closest non-pathogenic subspecies S. gallolyticus subps. macedonicus, confirmed that SGG pathogenicity-associated factors mostly rely on a large repertoire of surface proteins involved in host colonization, presence of C5a peptidase to avoid innate immunity, bile salt hydrolase to persist in the gut, and of specific bacteriocin and type VII-dependent effectors to colonize the host colon. Additionally, the presence of extracellular polysaccharides in SGG probably helps the bacterium survive in harsher conditions. ImportanceStreptococcus gallolyticus subsp. gallolyticus (SGG) was the first intestinal bacterium associated with colorectal cancer. It is now widely accepted that colonic microbiota dysbiosis contributes to oncogenesis, with a higher relative abundance of several potentially pro-carcinogenic bacteria. For example, the oncogenic role of Escherichia coli pks+ and enterotoxinogenic Bacteroides fragilis in colorectal cancer have been well established identifying the role of genetic loci encoding toxins. Through the sequencing and analysis of 11 clinical SGG isolates from CRC patients and comparisons with non-CRC isolates, we uncovered a significant diversity among CRC-associated strains. Our findings suggest that SGG association with CRC is complex and is not linked to a specific strain or pathogenicity island, thus highlighting the opportunistic and versatile nature of SGG.

microbiology↗

bioRxiv2023

Bile-induced biofilm formation in Bacteroides thetaiotaomicron requires magnesium efflux by an RND pump

Bacteroides thetaiotaomicron is a prominent member of the human gut microbiota contributing to nutrient exchange, gut function, and maturation of the hosts immune system. This obligate anaerobe symbiont can adopt a biofilm lifestyle and it was recently shown that B. thetaiotaomicron biofilm formation is promoted by the presence of bile, a process also requiring a B. thetaiotaomicron extracellular DNase, which is not, however, regulated by bile. Here we showed that bile induces the expression of several Resistance-Nodulation-Division (RND) efflux pumps and that inhibiting their activity with a global competitive efflux inhibitor impaired bile-dependent biofilm formation. We then showed that, among the bile-induced RND-efflux pumps, only the tripartite BT3337-BT3338-BT3339 pump, re-named BipABC (for Bile Induced Pump A (BT3337), B (BT3338) and C (BT3339), is required for biofilm formation. We demonstrated that BipABC is involved in the efflux of magnesium to the biofilm extracellular matrix, which leads to a decrease of eDNA concentration. The release of magnesium in the biofilm matrix also impacts biofilm structure, potentially by modifying the electrostatic repulsion forces within the matrix, reducing interbacterial distance and allowing bacteria to interact more closely and form denser biofilms. Our study therefore identifies a new molecular determinant of B. thetaiotaomicron biofilm formation in response to bile salts and provides a better understanding on how an intestinal chemical cue regulates biofilm formation in a major gut symbiont. IMPORTANCEBacteroides thetaiotaomicron is a prominent member of the human gut microbiota able to degrade dietary and host polysaccharides, altogether contributing to nutrient exchange, gut function, and maturation of the hosts immune system. This obligate anaerobe symbiont can adopt a biofilm community lifestyle, providing protection against environmental factors that might, in turn, protect the host from dysbiosis and dysbiosis-related diseases. It was recently shown that B. thetaiotaomicron exposure to intestinal bile promotes biofilm formation. Here we reveal that a specific B. thetaiotaomicron membrane efflux pump is induced in response to bile, leading to the release of magnesium ions, potentially reducing electrostatic repulsion forces between components of the biofilm matrix. This leads to a reduction of interbacterial distance and strengthens the biofilm structure. Our study therefore provides a better understanding of how bile promotes biofilm formation in a major gut symbiont, potentially promoting microbiota resilience to stress and dysbiosis events.

microbiology↗