Biology subjects

Lisa, M.-N.

Publications and source records attributed to Lisa, M.-N..

6 recordsLinked to original sources

bioRxiv2026

STARD3 mediates non-vesicular cholesterol transport in Caenorhabditis elegans

Cholesterol transport plays a pivotal role in regulating development and metabolism in Caenorhabditis elegans, a sterol-auxotrophic organism. Here, we identify the nematode cholesterol-binding protein STARD3 and provide structural and functional evidence for its role in non-vesicular sterol mobilization. Using biophysical and high-resolution structural methods, we show that the START domain (Ce-START) of C. elegans STARD3 binds cholesterol with high affinity and adopts a fold conserved with its human ortholog. Crystal structures of Ce-START in both apo and cholesterol-bound forms reveal key determinants of sterol recognition and conformational changes upon ligand binding. Functional analysis of a C. elegans stard3 knockout strain demonstrates that STARD3 is essential for cholesterol trafficking under sterol-limited conditions and that it genetically interacts with the NPC1/NPC2 pathway to sustain cholesterol mobilization. Collectively, these results establish STARD3 as a crucial cholesterol transporter in C. elegans and underscore the evolutionary conservation of START-domain proteins, reinforcing the utility of C. elegans as a model for studying intracellular cholesterol dynamics.

biophysics↗

bioRxiv2025

WHOOPER Web application for Hands-On identification of proteins co-Occurrence among Phyla, focused on user ERgonomics

SummaryWHOOPER is an intuitive web application designed to facilitate the analysis of protein co-occurrence across taxa. By integrating HHblits and HMMER, it enables efficient detection of remote homologs across extensive proteomic datasets. Its results interface combines an original data representation with advanced dynamic filtering functionalities to enable real-time exploration and exploitation of alignment data. Addressing key limitations of existing tools, WHOOPER streamlines workflows for studying protein prevalence, co-occurrence, and phylogenetic patterns, supporting seamless export for downstream evolutionary and functional genomics research. Availability and implementationThe code for Whopper is available at https://github.com/SmartBioInf/whooper. A public instance allowing the screening of more than 7500 reference proteomes from eukaryotes, bacteria, and archaea is available at: https://whooper.migale.inrae.fr Contactsylvain.marthey@inrae.fr

bioinformatics↗

bioRxiv2024

Tertiary and quaternary structure remodeling by occupancy of the substrate binding pocket in a large glutamate dehydrogenase

Glutamate dehydrogenases (GDHs) catalyze the oxidative deamination of L-glutamate to 2-oxoglutarate using NAD(P)+ as a cofactor. The large type of GDHs (L-GDHs) displays a dynamic homotetrameric architecture that alternates between open and closed states. However, the catalytic mechanism and the functional relevance of the large conformational changes in L-GDHs remain poorly understood. Here, we use cryo-EM to investigate the structure and the conformational landscape of the mycobacterial L-GDH composed of 180 kDa subunits (mL-GDH180) when incubated with L-glutamate and NAD+. Classification of the heterogeneous population of tetramers reveals opening-closing motions and sorting of individual subunits resolves the occupancy of the cofactor and substrate binding pockets. Cryo-EM maps show that ligand binding to the glutamate binding pocket is accompanied by structural changes in a region approximately two nanometers away from the active site, leading to the formation of a previously undetected interaction between the catalytic domains of neighboring subunits in mL-GDH180 closed tetrameric states. Our findings indicate that the occupancy of the substrate binding site of mL-GDH180 is linked to a remodeling of both the tertiary and quaternary structure of the enzyme. STATEMENT FOR A BROADER AUDIENCEThis work reveals how the binding of L-glutamate and NAD+ reshapes the architecture of a large glutamate dehydrogenase, linking active site occupancy to long-range structural remodeling. By capturing previously unseen conformational transitions with cryo-electron microscopy, we provide insights into the molecular logic of enzyme function in mycobacteria. These findings establish a framework to understand how structural plasticity supports metabolic control.

molecular biology↗

bioRxiv2024

The chemoreceptor controlling the Wsp-like transduction pathway in Halomonas titanicae KHS3 binds purine derivatives

The chemosensory pathway HtChe2 from the marine bacterium Halomonas titanicae KHS3 controls the activity of a diguanylate cyclase. Constitutive activation of the pathway results in colony morphology alterations and increased ability to form biofilm. Such characteristics resemble the behaviour of the Wsp pathway of Pseudomonas. In this work we investigate the specificity of Htc10, the only chemoreceptor coded within the HtChe2 gene cluster. Thermal shift analyses performed with the Htc10 ligand-binding domain led to the identification of purine derivatives as ligands. This ligand-binding domain was crystallized in the presence of guanine or hypoxanthine and its structure was solved by X-ray protein crystallography. The sensor domain adopts a double-cache folding, with ligands bound to the membrane-distal pocket. A high-resolution structure of the occupied guanine-binding pocket allowed the identification of the involved residues. These residues were validated by site directed mutagenesis and thermal shift or isothermal calorimetry analyses of the protein variants. The dissociation constants for guanine or hypoxanthine of the intact domain were in the low micromolar range. To our knowledge, this is the first description of binding specificity for a chemoreceptor that controls the activity of an associated diguanylate cyclase, and opens the way for dynamic studies of the signalling behaviour of this kind of sensory complex. A comparison between Htc10 and the functionally equivalent WspA receptor from Pseudomonas revealed no significant sequence similarities. In contrast, highly conserved Htc10-like receptors were found in distant bacteria carrying HtChe2-like clusters.

microbiology↗

bioRxiv2021

Coping with oxidative stress in extreme environments: the distinctive roles played by Acinetobacter sp. Ver3 superoxide dismutases

Acinetobacter sp. Ver3 is a polyextremophilic strain characterized by a high tolerance to radiation and pro-oxidants. The Ver3 genome comprises the sodB and sodC genes encoding an iron (AV3SodB) and a copper/zinc superoxide dismutase (AV3SodC), respectively; however, the specific role(s) of these genes has remained elusive. We show that the expression of sodB remained unaltered in different oxidative stress conditions whereas sodC was up-regulated in the presence of blue light. Besides, we studied the changes in the in vitro activity of each SOD enzyme in response to diverse agents and solved the crystal structure of AV3SodB at 1.34 [A], one of the highest resolutions achieved for a SOD. Cell fractionation studies interestingly revealed that AV3SodB is located in the cytosol whereas AV3SodC is also found in the periplasm. Consistently, a bioinformatic analysis of the genomes of 53 Acinetobacter species pointed out the presence of at least one SOD type in each compartment, suggesting that these enzymes are separately required to cope with oxidative stress. Surprisingly, AV3SodC was found in an active state also in outer membrane vesicles, probably exerting a protective role. Overall, our multidisciplinary approach highlights the relevance of SOD enzymes when Acinetobacter spp. are confronted with oxidizing agents.

microbiology↗

bioRxiv2020

3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme

Glutamate dehydrogenases (GDHs) are widespread metabolic enzymes that play key roles in nitrogen homeostasis. Large glutamate dehydrogenases composed of 180 kDa subunits (L-GDHs180) contain long N- and C-terminal segments flanking the catalytic core. Despite the relevance of L-GDHs180 in bacterial physiology, the lack of structural data for these enzymes has limited the progress of functional studies. Here we show that the mycobacterial L-GDH180 (mL-GDH180) adopts a quaternary structure that is radically different from that of related low molecular weight enzymes. Intersubunit contacts in mL-GDH180 involve a C-terminal domain that we propose as a new fold and a flexible N-terminal segment comprising ACT-like and PAS-type domains that could act as metabolic sensors for allosteric regulation. These findings uncover unique aspects of the structure-function relationship in the subfamily of L-GDHs.

microbiology↗