Biology subjects

Labesse, G.

Publications and source records attributed to Labesse, G..

11 recordsLinked to original sources

bioRxiv2026

RyR2-Dependent Calcium Leak Drives the Acute Cardiovascular Manifestations of Ciguatera Poisoning: implications for an emerging climate-sensitive cardiotoxic disease

Background: Ciguatera is the most prevalent non-bacterial seafood poisoning worldwide. It results from the consumption of fish contaminated with ciguatoxins (CTXs). Cardiovascular manifestations are frequently reported in affected patients; however, the molecular mechanisms underlying CTX-induced cardiac dysfunction remain poorly understood. Methods: We investigated the effects of purified CTX-1B and CTX-3C on human induced pluripotent stem-cell-derived ventricular cardiomyocytes. Electrophysiology, intracellular calcium cycling and contractility, and cellular structure were assessed. The RyR2 channel activity was studied in planar lipid bilayers, and molecular docking was used to identify a potential CTX-1B interaction site. Consequences on cardiac function were assessed in rats using echocardiography and EKG. Findings: We found that ciguatoxin exposure rapidly increased diastolic intracellular calcium, with severe impacts on the cardiac excitation-contraction coupling, and caused sarcomeric disorganization in human cardiomyocytes. Single-channel recordings indicated that CTX-1B prolonged RyR2 openings at resting cytosolic calcium and altered ATP-dependent gating. These findings are consistent with a state-dependent remodeling of RyR2 gating rather than uniform potentiation. Docking placed CTX-1B within the RyR2 transmembrane region, near ATP-associated regulatory elements. In rats, CTX-1B caused premature atrial contractions, ventricular ectopy, and acute cardiac dysfunction, with impaired relaxation. Interpretation: These findings identify RyR2-dependent calcium leak as a plausible contributor to ciguatoxin cardiotoxicity and extend the established model based on sodium-channel activation and altered sarcolemmal ion handling. Combined disruption of membrane excitability and intracellular calcium release could explain the rapid electrical and mechanical abnormalities associated with ciguatera. As intensive international shipping traffic and the global dispersal of harmful microalgae via ballast water expand exposure risk alongside the international seafood trade, ciguatera should be considered an emerging global cardiovascular hazard.

physiology↗

bioRxiv2026

Deciphering the nucleotide driven kinetic and oligomeric dynamics in IMPDH regulation

Inosine monophosphate dehydrogenase (IMPDH) controls guanine nucleotide biosynthesis. Here, using biochemical and integrative structural biology approaches, we characterize the class II bacterial IMPDH from Burkholderia thailandensis. We demonstrate that MgGTP acts as a direct allosteric inhibitor independently of MgATP, promoting tetramer-to-octamer assembly via the Bateman domain. When both nucleotides are present, the enzyme exhibits a biphasic response: low MgGTP concentrations enhance activity, whereas higher concentrations restore inhibition. Structural analyses reveal distinct octameric conformations and capture a pre-catalytic Michaelis complex with substrates and effectors bound. These findings uncover a regulatory mechanism where the Bateman domain integrates opposing nucleotide signals to dynamically control guanine nucleotide biosynthesis, highlighting IMPDH as a potential antimicrobial target in pathogenic Burkholderia species.

biochemistry↗

bioRxiv2026

In Silico Structure-Based Interactomic Analysis of the Scaffolding Protein DCAF7

WD40 domains share a widespread {beta}-propeller fold, and often act as versatile scaffold proteins. Despite their central role in organizing dynamic cellular complexes, the molecular and structural mechanisms of many WD40 proteins remain poorly understood. Among them, DCAF7, an ubiquitously expressed and essential gene in human, also encodes a highly conserved WD40 protein in eukaryotic organisms. It is known to interact with multiple and functionnally diverse partners to coordinates cellular activity of several protein kinases as well as transcriptional regulators, thereby modulating key cellular processes such as cell growth, differentiation, and transcriptional regulation. However, the precise mode of action of DCAF7 is unknown and its important divergence in sequence from better characterize WD40 prevent information transfer by similarity. Structural interactomic can reveal how protein-protein interactions (PPIs) occur within an organism and are essential for understanding biological functions and developing new therapeutic strategies. Using SLiMAn2, AlphaFold2/3 and PSSMsearch, we identified a conserved -helical short linear motif (SLiM) in several well known DCAF7 partners that binds to the top surface of its {beta}-propeller. This motif was subsequently used to generate a regular expression, to identify potential new direct binders across the DCAF7 meta-interactome and the human proteome. Domain-domain interactions were also predicted for some other partners. Finally, modeling of oligomeric complexes with such new hits reveals the structural basis of DCAF7 scaffolding, with links to neurodevelopmental disorders such as autism.

bioinformatics↗

bioRxiv2025

Structural and molecular basis of resistance to aminoglycoside antibiotics by APH(3')-IIb from Pseudomonas aeruginosa

Pseudomonas aeruginosa is one of the six bacteria of greatest concern identified by the WHO for its resistance to antibiotics. In the case of aminoglycosides, used in combination with other antibiotics in the treatment of severe infections, resistance is mainly due to modification of the antibiotic by bacterial enzymes. In this study, we have functionally and structurally characterized one such enzyme from P. aeruginosa, aminoglycoside 3-O-phosphotransferase IIb, APH(3)-IIb. The results will provide a better understanding of this resistance mechanism and enable us to envisage solutions for blocking it and restoring the efficacy of aminoglycosides.

biochemistry↗

bioRxiv2024

Understanding evolutionary and functional relationships of RNA polymerases in plant and fungal viruses through structural modeling and divergence date estimations

RNA-dependent RNA polymerases (RdRps) are crucial for RNA virus replication and serve as key marker genes for defining deep taxonomic ranks and for understanding viral evolutionary history. Despite their conserved functions and motifs, the high genetic diversity of RdRps complicates precise sequence comparisons across viral families, hindering accurate taxonomic classification of new species. Three-dimensional (3D) RdRp structures can help overcome these challenges through structure-guided alignments. However, such data are rare for myco- and phytoviruses, limiting investigation of their ecological and evolutionary links. In this study, we focused on the highly divergent order Sobelivirales, which includes sobemoviruses infecting plants -- a taxon known for its ancient origin -- and barnaviruses infecting fungi, which remain relatively unknown. Using deep-learning structural modeling, we generated reliable 3D models for 44 sobemoviral and sobelivirad species. Structure-guided alignments, together with new barnaviral and relevant outgroup sequences, enabled robust phylogenetic reconstruction, allowing us to propose revisions of existing viral families and suggest new evolutionary scenarios. Divergence dates were estimated for the first time at this taxonomical rank using the Prisoner of War model, which revealed a divergence of plant and fungal sobelivirads 27.0 {+/-} 10 million years ago -- much more recent than the separation of their respective hosts. This result suggests that cross-kingdom host shifts have contributed more likely to the evolutionary history of Sobelivirales than strict virus-host codivergence. Based on an extended dataset of 127 species, structure and sequence conservation analyses identified molecular signatures of sobeliviral families. These conserved and extented RdRp motifs will facilitate future taxonomic assignments and the development of diagnostic tools. Our interdisciplinary approach, integrating structure modeling and divergence dating, offers new insights into the evolutionary divergence of plant and fungal viruses, with potential applications to other viral orders and families. Author summaryRNA-dependent RNA polymerases (RdRps) are essential for RNA virus replication and serve as important markers for classifying viruses and understanding their evolution. However, with metagenomic studies that rapidly expand the known diversity of RNA viruses, it is increasingly difficult to compare highly divergent RdRps and accurately classify new species. When available, 3D structures of RdRps can help overcome this challenge through structure-guided alignments. Here, we focused on the highly divergent order Sobelivirales, which groups phytoviruses and mycoviruses. Deep-learning models were used to generate reliable 3D structures for 44 representative viral species. Structure-guided alignments combined with the identification of new barnaviruses and outgroups allowed us to build a more accurate viral phylogeny. Based on this finding, we proposed updates to existing viral families and genera within the order Sobelivirales. We estimated divergence dates using a model that previously uncovered the ancient origins of sobemovirus. Notably, we provided the first estimate of when these plant and fungal viruses diverged [~]27.0 {+/-} 10 million years ago, suggesting cross-kingdom host shifts rather than strict virus-host codivergence. We also identified molecular signatures that are useful for future virus classification and diagnosis, with potential applications to other viral groups.

evolutionary biology↗

bioRxiv2023

Cyclin A/cdk activity and FAM122A-dependent inhibition of PP2A-B55 are essential to trigger mitosis.

Entry into mitosis has been classically attributed to the activation of cyclin B/cdk1 amplification loop by a partial pool of this kinase that becomes active at the end of G2. However, how this pool is activated is still unknown. Here we discovered a new role of the recently identified PP2A-B55 inhibitor FAM122A in triggering mitotic entry. Accordingly, the depletion of the orthologue of FAM122A in C. elegans, prevents entry into mitosis in germline stem cells. Moreover, our data in Xenopus egg extract strongly supports that FAM122A-dependent inhibition of PP2A-B55 could be the initial event promoting mitotic entry. The inhibition of this phosphatase allows the subsequent phosphorylation of first mitotic substrates by cyclin A/cdk resulting in cyclin B/cdk1 and Greatwall (Gwl) activation. However, interestingly, from Gwl activation, Arpp19/ENSA become phosphorylated and compete with FAM122A promoting its dissociation from PP2A-B55 and taking over its inhibition until the end of mitosis.

cell biology↗

bioRxiv2022

SLiMAn: an integrative web server for exploring short linear motif-mediated interactions in interactomes.

Cells express thousands of macromolecules, and their functioning relies on multiple networks of intermolecular interactions. These interactions can be experimentally determine at different spatial and temporal resolutions. But, physical interfaces are not often delineated directly especially in high-throughput experiments. However, numerous three-dimensional structures of complexes have been already solved and sequence conservation allows comparative modeling of additional complexes. A large fraction of protein-protein interactions involves domain and so-called SLiMs (for Short Linear Motifs). Often, SLiMs lie in disordered regions or loops. Their small size and loosely folded nature prevent straightforward detection. SLiMAn (Short Linear Motif Analysis), a new web server is provided to help thorough analysis of interactomics data. Starting from a list of putative interactants such as the output of an interactomics study, SLiMs (from ELM) and SLiM-recognition domains (from Pfam) are extracted and potential pairing are displayed. Additionally, filters are available to dig into the predicted results such as the motif E-value, IUpred2 scoring functions for disorder or BioGRID interaction matches. When structural templates are available, a given SLiM and its recognition domain can be modeled using SCWRL. We illustrate, here, the use of SLiMAn on three distinct examples including one real-case study. We oversee wide-range applications for SLiMAn in the context of massive analysis of protein-protein interactions at proteome-wide scale. This new web server is made freely available at http://sliman.cbs.cnrs.fr.

bioinformatics↗

bioRxiv2021

Structural Evolution of the Ancient Enzyme, Dissimilatory Sulfite Reductase

Dissimilatory sulfite reductase is an ancient enzyme that has linked the global sulfur and carbon biogeochemical cycles since at least 3.47 Gya. While much has been learned about the phylogenetic distribution and diversity of DsrAB across environmental gradients, far less is known about the structural changes that occurred to maintain DsrAB function as the enzyme accompanied diversification of sulfate/sulfite reducing organisms (SRO) into new environments. Analyses of available crystal structures of DsrAB from Archaeoglobus fulgidus and Desulfovibrio vulgaris, representing early and late evolving lineages, respectively, show that certain features of DsrAB are structurally conserved, including active siro-heme binding motifs. Whether such structural features are conserved among DsrAB recovered from varied environments, including hot spring environments that host representatives of the earliest evolving SRO lineage (e.g., MV2-Eury), is not known. To begin to overcome these gaps in our understanding of the evolution of DsrAB, structural models from MV2.Eury were generated and evolutionary sequence co-variance analyses were conducted on a curated DsrAB database. Phylogenetically diverse DsrAB harbor many conserved functional residues including those that ligate active siro-heme(s). However, evolutionary co-variance analysis of monomeric DsrAB subunits revealed several False Positive Evolutionary Couplings (FPEC) that correspond to residues that have co-evolved despite being too spatially distant in the monomeric structure to allow for direct contact. One set of FPECs corresponds to residues that form a structural path between the two active siro-heme moieties across the interface between heterodimers, suggesting the potential for allostery or electron transfer within the enzyme complex. Other FPECs correspond to structural loops and gaps that may have been selected to stabilize enzyme function in different environments. These structural bioinformatics results suggest that DsrAB has maintained allosteric communication pathways between subunits as SRO diversified into new environments. The observations outlined here provide a framework for future biochemical and structural analyses of DsrAB to examine potential allosteric control of this enzyme.

biophysics↗

bioRxiv2020

The study of the determinants controlling Arpp19 phosphatase-inhibitory activity reveals a new Arpp19/PP2A-B55 feedback loop

Arpp19 is a potent inhibitor of PP2A-B55 that regulates this phosphatase to ensure the stable phosphorylation of mitotic/meiotic substrates. At G2-M, Arpp19 is phosphorylated by Greatwall on S67. This phosphorylated Arpp19 form displays a high affinity to PP2A-B55 and a slow dephosphorylation rate, acting as an "unfair" competitor of PP2A-B55 substrates. The molecular determinants conferring slow dephosphorylation kinetics to S67 are unknown. PKA also phosphorylates Arpp19. This phosphorylation performed on S109 is essential to maintain prophase I-arrest in Xenopus oocytes although the underlying signaling mechanism is elusive. Here, we characterized the molecular determinants conferring slow dephosphorylation to S67 and controlling PP2A-B55 inhibitory activity of Arpp19. Moreover, we showed that phospho-S109 restricts S67 phosphorylation by increasing its catalysis by PP2A-B55. Finally, we discovered a double feed-back loop between these two phospho-sites which is essential to coordinate the temporal pattern of Arpp19-dependent PP2A-B55 inhibition and Cyclin B/Cdk1 activation during cell division.

developmental biology↗

bioRxiv2020

Exploring the conformational space of a receptor for drugdesign: an ER α case study

MotivationProtein flexibility is challenging for both experimentalists and modellers, especially in the field of drug design. Estrogen Receptor alpha (ER) is an extensively studied Nuclear Receptor (NR) and a well-known therapeutic target with an important role in development and physiology. It is also a frequent off-target in standard toxicity tests for endocrine disruption. Here, we aim to evaluate the degree to which the conformational space and macromolecular flexibility of this well-characterized drug target can be described. Our approach exploits hundreds of crystallographic structures by means of molecular dynamics simulations and of virtual screening. ResultsThe analysis of hundreds of crystal structures confirms the presence of two main conformational states, known as agonist and antagonist, that mainly differ by the orientation of the C-terminal helix H12 which serves to close the binding pocket. ER also shows some loop flexibility, as well as variable side-chain orientations in its active site. We scrutinized the extent to which standard molecular dynamics simulations or crystallographic refinement as ensemble recapitulate most of the variability features seen by the array of available crystal structure. In parallel, we investigated on the kind and extent of flexibility that is required to achieve convincing docking for all high-affinity ER ligands present in BindingDB. Using either only one conformation with a few side-chains set flexible, or static structure ensembles in parallel during docking led to good quality and similar pose predictions. These results suggest that the several hundreds of crystal structures already known can properly describe the whole conformational universe of ERs ligand binding domain. This opens the road for better drug design and affinity computation. Contactlabesse@cbs.cnrs.fr

bioinformatics↗

bioRxiv2019

Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity

MotivationNowadays, virtual screening (VS) plays a major role in the process of drug development. Nonetheless, an accurate estimation of binding affinities, which is crucial at all stages, is not trivial and may require target-specific fine-tuning. Furthermore, drug design also requires improved predictions for putative secondary targets among which is Estrogen Receptor alpha (ER).\n\nResultsVS based on combinations of Structure-Based VS (SBVS) and Ligand-Based VS (LBVS) is gaining momentum to help characterizing secondary targets of xenobiotics (including drugs and pollutants). In this study, we propose an integrated approach using ligand docking based on multiple structural en-sembles to reflect the conformational flexibility of the receptor. Then, we investigate the impact of the two different types of features (structure-based docking descriptors and ligand-based molecular descriptors) for affinity predictions based on a random forest algorithm. We find that ligand-based features have limited predictive power (rP =0.69, R2=0.47), compared to structure-based features (rP =0.78, R2=0.60) while their combination maintains the overall accuracy (rP =0.77, R2=0.56). Extending the training dataset to include xenobiotics, leads to a novel high-throughput affinity prediction method for ER ligands (rP =0.85, R2=0.71). Methods robustness is tested on several ligand databases and performances are compared with existing rescoring procedures. The presented prediction tool is provided to the community as a dedicated satellite of the @TOME server.\n\nAvailabilityhttp://atome4.cbs.cnrs.fr/ATOME_V3/SERVER/EDMon_v3.html\n\nContactschneider@cbs.cnrs.fr, labesse@cbs.cnrs.fr

bioinformatics↗