Biology subjects

Stephanie, M.

Publications and source records attributed to Stephanie, M..

3 recordsLinked to original sources

bioRxiv2026

A hierarchical regulatory cascade defines the temporal window of natural transformation in Staphylococcus aureus

Natural transformation (NT), a major mechanism of horizontal gene transfer, promotes bacterial genome plasticity and contributes to the dissemination of antibiotic resistance. NT requires the development of competence, a transient and tightly regulated physiological state that is induced by environmental cues. Although competence has recently been demonstrated in the human pathogen Staphylococcus aureus, the regulatory architecture and temporal coordination governing its development remain poorly understood. Using a highly sensitive luciferase-based transcriptional reporter, we demonstrate that NT gene expression in S. aureus is transient, thereby defining a temporal window during which DNA uptake and recombination can occur. We further identify two classes of NT genes with distinct regulatory requirements and activation kinetics: Class I genes require both SigH and ComK1 and are activated approximately 2.5 hours later than Class II genes, which are regulated exclusively by ComK1. Mechanistically, we demonstrate that ComK1 activates sigH transcription, establishing a hierarchical regulatory cascade that explains its essential role in Class I gene expression. Finally, time-resolved transcriptomic analyses identify the global regulator CodY as an early regulator of competence that differentially controls comK1 and sigH transcription, thereby linking metabolic adaptation to competence development. Together, our findings define the regulatory architecture that governs competence development in S. aureus and reveal how a hierarchical cascade integrates environmental and metabolic cues to restrict horizontal gene transfer to a precise developmental window. This work provides a mechanistic framework for understanding how bacteria coordinate physiological adaptation with genome diversification through NT. Author summaryBacteria constantly evolve by acquiring new genetic information from their environment. One important mechanism driving this process is natural transformation, which allows bacterial cells to take up and integrate exogenous DNA into their genomes. However, this process is not continuously active: bacteria must first enter a specialized physiological state called competence. How pathogens control the development of competence remain poorly understood. In this study, we investigate how the human pathogen Staphylococcus aureus regulates natural transformation. Using a highly sensitive reporter system that allows us to monitor gene expression over time, we show that competence is activated only during a limited period, creating a defined window during which bacteria can acquire new DNA sequences. We uncover a hierarchical regulatory cascade involving the transcription factors ComK1 and SigH that controls the sequential activation of natural transformation genes. We further identify the metabolic regulator CodY as an upstream regulator that connects bacterial physiological state with the initiation of competence. Our findings reveal that natural transformation is not a random or continuous process, but a precisely timed developmental program controlled by multiple regulatory layers. By defining how S. aureus coordinates environmental sensing, metabolism, and horizontal gene transfer, this work provides new insight into how bacterial pathogens generate genetic diversity and adapt to changing environments, including conditions that may promote the emergence of antibiotic resistance.

microbiology↗

bioRxiv2024

m6A-mediated epi-transcriptomic dysregulation underlies synaptic dysfunction in fragile X syndrome

Fragile X syndrome (FXS), the leading genetic cause of intellectual disability, arises from FMR1 gene silencing and loss of the FMRP protein. N6-methyladenosine (m6A) is a prevalent mRNA modification essential for post-transcriptional regulation. FMRP is known to bind to and regulate the stability of m6A-containing transcripts. However, how loss of FMRP impacts on transcriptome-wide m6A modifications in FXS patients remains unknown. To answer this question, we generated cortical neurons differentiated from induced pluripotent stem cells (iPSC) derived from healthy subjects and FXS patients. In electrophysiology recordings, we validated that synaptic and neuronal network defects in iPSC-derived FXS neurons corresponded to the clinical EEG data of the patients from which the corresponding iPSC line was derived. In analysis of transcriptome-wide methylation, we show that FMRP deficiency led to increased translation of m6A writers, resulting in hypermethylation that primarily affecting synapse-associated transcripts and increased mRNA decay. Conversely, in the presence of an m6A writer inhibitor, synaptic defects in FXS neurons were rescued. Taken together, our findings uncover that an FMRP-dependent epi-transcriptomic mechanism contributes to FXS pathogenesis by disrupting m6A modifications in FXS, suggesting a promising avenue for m6A- targeted therapies.

neuroscience↗

bioRxiv2021

Differential regulation of degradation and immune pathways underlies adaptation of the symbiotic nematode Laxus oneistus to oxic-anoxic interfaces

Eukaryotes may experience oxygen deprivation under both physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all eukaryotes studied so far conserve energy by suppressing their metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is underexplored. One such animal is the marine nematode Laxus oneistus. It thrives, invariably coated by its sulfur-oxidizing symbiont Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, transcriptomics and proteomics showed that, whether in anoxia or not, L. oneistus mostly expressed genes involved in ubiquitination, energy generation, oxidative stress response, immune response, development, and translation. Importantly, ubiquitination genes were also upregulated when the nematode was subjected to anoxic sulfidic conditions, together with genes involved in autophagy, detoxification and ribosome biogenesis. We hypothesize that these degradation pathways were induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients. Remarkably, when L. oneistus was subjected to anoxic sulfidic conditions, lectin and mucin genes were also upregulated, potentially to promote the attachment of its thiotrophic symbiont. Furthermore, the nematode appeared to survive oxygen deprivation by using an alternative electron carrier (rhodoquinone) and acceptor (fumarate), to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., amino acid biosynthesis, development, feeding, mating) were upregulated, together with the worms Toll- like innate immunity pathway and several immune effectors (e.g., Bacterial Permeability Increasing proteins, fungicides). In conclusion, we hypothesize that, in anoxic sulfidic sand, L. oneistus upregulates degradation processes, rewires oxidative phosphorylation and by reinforces its coat of bacterial sulfur-oxidizers. In upper sand layers, instead, it appears to produce broad-range antimicrobials and to exploit oxygen for biosynthesis and development.

genomics↗