Biology subjects

Grosjean, N.

Publications and source records attributed to Grosjean, N..

5 recordsLinked to original sources

bioRxiv2026

A pooled screening approach reveals bacterial chemoreceptors for short-chain carboxylic acids

Bacterial chemotaxis is a key process in host colonization and virulence, mediated by large repertoires of chemoreceptors. Despite their physiological and ecological importance, mapping these chemoreceptors to their cognate metabolic ligands remains a major challenge due to the vast number of potential interactions. To address this, we developed a pooled screening assay that enriches functional chemoreceptors from a gene library. Using this approach, we identified a previously uncharacterized group of chemoreceptors in Pseudomonas species with Cache_3-Cache_2 domains that sense short-chain C3 carboxylic acids. Sequence and computational structural analyses revealed that these chemoreceptors exhibit domain features similar to a recently reported C1 formate chemoreceptor despite substantial sequence divergence. Functional assays of representative chemoreceptors confirmed robust chemotactic responses to C3 carboxylic acids, with limited responses to formate. Integrating structural and molecular dynamics analyses suggests that increased binding pocket size and altered flexibility, relative to the formate chemoreceptor, facilitate recognition of larger C3 carboxylic acid ligands. Together, our approach provides a simple and scalable framework for mapping ligand-chemoreceptor interactions and enables systematic characterization across diverse metabolites.

microbiology↗

bioRxiv2026

DAP-seq Reveals Cluster-Situated Regulator Control of Numerous Streptomyces Natural Product Biosynthetic Genes

Natural products (NPs) are a rich source of therapeutic and agricultural compounds. Unfortunately, many promising metabolites are not expressed under standard laboratory conditions. Deepening our understanding of the regulatory networks governing NP biosynthetic genes is essential for unlocking this hidden chemical diversity. Cluster-situated regulators (CSRs) are transcription factors involved in the regulation of NPs, but their full regulatory range has remained elusive due to limited genome-wide data. Using DNA Affinity Purification Sequencing (DAP-seq), we defined the predicted regulons for 84 CSR homologs across 78 Streptomyces strains. CSRs in this cohort exerted influence across multiple cellular processes, with particularly strong impacts on other transcription factors throughout the genome. Approximately 30% of predicted NP biosynthetic gene clusters (BGCs) contained CSR-regulated genes. In strains encoding multiple CSR homologs, we observed substantial overlap in BGC regulation. Together, these results greatly expand the genomic landscape of CSR activity and provide a foundation for improved bioinformatic strategies to predict and interpret regulatory control of NP biosynthesis.

genetics↗

bioRxiv2024

Early changes in the properties of CA3 engram cells explored with a novel viral tool

Forming new memories after a one-time experience requires initial encoding then consolidation over time. During learning, multimodal information converges onto the hippocampus, activating sparse neuronal assemblies which are thought to form a memory representation through concerted activity and synaptic interconnectivity. In this work, we use a novel tool for fast fluorescent labeling of engram neurons (FLEN). FLEN is based on c-Fos activity-dependent transient expression of a destabilized fluorescent marker ZsGreen1 rapidly after one-trial learning. With FLEN, we explore the electrophysiological properties of c-Fos activated CA3 pyramidal neurons a few hours following one-trial learning of an episodic-like memory. In parallel, we employ the Robust Activity Marker (RAM) system, which provides activity-dependent labelling 24 hours following a novel experience. Comparing FLEN+ and RAM+ neurons allows to characterize how the properties of neuronal assemblies evolve during an initial phase of consolidation. Whereas no difference was observed in the excitability of FLEN+ vs. FLEN-neurons, RAM+ neurons were more excitable than RAM-neurons. This suggests that CA3 pyramidal neurons recruited in an engram progressively acquire increased excitability as compared to neurons which were not activated by the one-trial contextual memory task. On the other hand, like RAM+ neurons, FLEN+ CA3 neurons show an increased number of excitatory inputs. Overall, with the FLEN strategy, we can show that both the intrinsic excitability and the synaptic properties of CA3 pyramidal neurons undergo progressive plastic changes over the first day following a one-trial memory task.

neuroscience↗

bioRxiv2024

An atlas of conserved transcription factor binding sites reveals the cell type-resolved gene regulatory landscape of flowering plants

Transcription factors (TFs) are proteins that bind DNA to control where and when genes are expressed. In plants, dozens of TF families interact with distinct sets of binding sites (TFBSs) that reflect each TFs role in organismal function and species-specific adaptations. However, defining these roles and understanding broader patterns of regulatory evolution remains challenging, as predicted TFBSs may lack a clear impact on transcription, and experimentally-derived TF binding maps to date are modest in scale or restricted to model organisms. Here, we present a scalable TFBS assay that we leveraged to create an atlas of nearly 3,000 genome-wide binding site maps for 360 TFs in 10 species spanning 150 million years of flowering plant evolution. We find that TF orthologs from distant species retain nearly identical binding preferences, suggesting that regulatory evolution primarily arises from gain and loss of TFBSs. Within lineages however, conserved TFBSs are over-represented and found in regions harboring signatures of functional regulatory elements. Moreover, genes with conserved TFBSs showed a striking enrichment for cell type-specific expression in single-nuclei RNA atlases, providing a robust marker of each TFs activity and developmental role. Finally, we compare distant lineages, illustrating how ancient regulatory modules were recruited and rewired to enable adaptations underlying the evolutionary success of grasses.

genomics↗

bioRxiv2024

Abrogation of presynaptic facilitation at hippocampal mossy fiber synapses impacts neural ensemble activity and spatial memory

Presynaptic short-term plasticity is thought to play a major role in the process of spike transfer within local circuits. Mossy fiber synapses between the axons of dentate gyrus (DG) granule cells and CA3 pyramidal cells (Mf-CA3 synapses) display a remarkable extent of presynaptic plasticity which endows these synaptic connections with detonator properties. The pattern of action potential firing, in the form of high frequency bursts in the DG, strongly controls the amplitude of synaptic responses and information transfer to CA3. Here we have investigated the role of presynaptic facilitation at Mf-CA3 synapses in the operation of CA3 circuits in vivo and in memory encoding. Syt7, a calcium sensor necessary for presynaptic facilitation, was selectively abrogated, in DG granule cells using Syt7 conditional KO mice (DG Syt7 KO mice). In hippocampal slices, we extend previous analysis to show that short-term presynaptic facilitation is selectively suppressed at Mf-CA3 synapses in the absence of Syt7, without any impact on basal synaptic properties and long-term potentiation. Short-term plasticity was found to be crucial for spike transfer between the DG and CA3 in conditions of naturalistic patterns of presynaptic firing. At the network level, in awake head-fixed mice, the abrogation of short-term plasticity largely reduced the co-activity of CA3 pyramidal cells. Finally, whereas DG Syt7 KO mice are not impaired in behavioral tasks based on pattern separation, they show deficits in spatial memory tasks which rely on the process of pattern completion. These results shed new light on the role of the detonator properties of DG-CA3 synapses, and give important insights into how this key synaptic feature translate at the population and behavioral levels.

neuroscience↗