Institut de Biologie Structurale

Calcium ions (Ca2+) orchestrate cellular physiology as a versatile and ubiquitous second messenger, regulating a wide range of intracellular processes, including muscle contraction, secretion, metabolism, cell proliferation, and cell death. Here, we show that optogenetic cytosolic alkalization induced by the outward proton-pumping microbial rhodopsin Arch3 from Halorubrum sodomense triggers extracellular calcium influx into the cytosol of human cells. This elevation in cytosolic Ca2+ is accompanied by a subsequent increase in mitochondrial matrix Ca2+ concentration and depletion of cellular ATP. Together, these findings demonstrate how changes in cytosolic pH can modulate calcium signaling, mitochondrial physiology, and the induction of cell death. These insights are important for fundamental studies of cell physiology and may contribute to the development of improved anticancer therapeutic strategies.

RumC1 is a structurally unique bacteriocin with broad-spectrum efficacy, including against multidrug-resistant pathogens, yet acting by an undefined mechanism. By integrating genetics, biochemistry, computational modeling and single-cell fluorescence microscopy, we demonstrate that RumC1 is a distinct cell-wall-targeting toxin. First, all RumC1-resistant mutants isolated through a high-rate, genome-wide mutagenic screening exhibited specific impairments in peptidoglycan homeostasis regulation, pinpointing this pathway as critical for RumC1 activity. Second, RumC1 selectively accumulates within neosynthesized peptidoglycan, leading to cell growth arrest and death in a dose-dependent manner. Third, we characterize the RumIc1 immunity protein of the RumC1 biosynthetic cluster as a peptidase acting at the cell surface to protect the cells by trimming the stem peptide crucial for cell-wall assembly. As such, RumIc1 provides cross-protection against vancomycin, while RumC1 is demonstrated to act differently from this glycopeptide antibiotic. Collectively, these findings establish RumC1 as a toxin targeting a key peptidoglycan intermediate of cell wall maturation.

Summary Membrane tubules form at Golgi compartments to facilitate membrane and cargo flow in intracellular trafficking. Here we show that the small GTPase Arf1, an inducer of membrane curvature and key regulator of trafficking, is able to form strongly curved tubules in the presence of lipids and GTPγS in vitro without the need for further coat components. Using cryo-electron microscopy, we determined the structures of tubular Arf1-scaffolds with diameters of 195 and 215 Å at 3.1 and 3.8 Å resolutions, respectively. The nucleotide-bound globular domains of Arf1 form polar helical lattices ( i.e. directional assemblies with distinct start/finish orientations), with conserved interfaces and a consistent back-to-face orientation along the filaments. The rigid coat is tethered to the membrane by a flexible linker and anchored by an amphipathic helix (AH) that is free to diffuse and make space within the leaflet, allowing for accommodation of transmembrane cargo. The diversity of tubular diameters observed would allow various cargo sizes to be accommodated in the lumen, while maintaining the local coat architecture. Apart from serving as tubular transport intermediates, Arf1-scaffolds may also play a role at the neck of COPI vesicle on the route to scission.

Chemoresistance remains a major obstacle to effective cancer treatment, often driven by enhanced DNA repair mechanisms that enable tumor cells to withstand genotoxic therapies. One such pathway involves the atypical DNA damage repair complex ALKBH3–ASCC, activated by the E3 ligase RNF113A in response to alkylation damage. We previously showed that SMYD3-dependent methylation of RNF113A stimulates this pathway, enhancing DNA repair and promoting resistance.Here, we identify KDM7B/PHF8 as the bona fide RNF113A demethylase, establishing one of the first functional examples of a dynamic, reversible non-histone methylation event regulating genome integrity. KDM7B antagonizes SMYD3 activity by maintaining low levels of methylated RNF113A, thereby limiting ASCC activation and sensitizing cancer cells to alkylating agents. To dissect this regulation in depth, we focused on small cell lung cancer (SCLC), a particularly aggressive malignancy characterized by limited therapeutic options and rapid acquisition of resistance. In SCLC, high KDM7B levels correlate with improved patient prognosis, whereas xenografts with reduced expression exhibit diminished responses to alkylating treatment. Moreover, CRISPR-based on/off modulation of KDM7B in genetically engineered SCLC mouse models demonstrates its central role in determining tumor response to chemotherapy.Our findings position the RNF113A–ASCC axis as a central modulator of chemoresistance, regulated through a post-translational methylation switch representing an innovative therapeutic vulnerability that could be exploited to enhance the efficacy of alkylating agents. Targeting this pathway may provide new opportunities to overcome chemoresistance, with KDM7B levels serving as a predictive biomarker to guide treatment in SCLC.

Class A penicillin-binding proteins (aPBPs) are involved in the biosynthesis and remodelling of peptidoglycan (PG). The human bacterial pathogen Streptococcus pneumoniae produces three aPBPs, which are regulated to maintain the bacterium's ovoid shape. Evidence suggests that PBP1a and PBP2a activities are closely coordinated; however, their precise functions remain unclear. Here we characterized the pneumococcal S protein, which contains a LysM-PG-binding domain and a GpsB-interacting domain. Using S protein fusion constructs or mutant bacterial strains, we show that S protein localizes to the division ring and is required to prevent premature cell lysis and minicell formation due to aberrant division site placement. S protein interacts with PBP1a and activates its PG synthesis activity. Co-immunoprecipitation experiments combined with biochemical, genetic, structural prediction and microscopy analyses suggest that S protein is part of a larger multiprotein complex containing aPBPs and PG-modifying enzymes, and coordinated by the scaffolding protein GpsB. Together, these findings suggest that a GpsB-associated complex orchestrates PG biosynthesis and remodelling in S. pneumoniae.

DEAD-box proteins such as Dhh1 play essential roles in RNA metabolism and the formation of biomolecular condensates, with a modular architecture comprising folded domains and disordered regions. To elucidate how this architecture shapes conformational dynamics in solution, we combined solution scattering experiments and multi-scale simulations on core and full-length constructs. Enhanced-sampling simulations captured a dynamic ensemble of core conformations stabilized by transient interdomain contacts that underpin functional regulation. Coarse-grained modelling revealed that disordered tails behave as independent modules exerting minimal influence on core dynamics. This integrated approach reveals a modular organization balancing structural heterogeneity and functional specificity, providing a framework for studying DEAD-box proteins in phase separation.

The complement system plays a paradoxical role in systemic lupus erythematosusphysiopathology, acting both as a protective mechanism and as a driver of tissue injury, depending on disease stage. Neutrophil extracellular traps (NETs) further exacerbate disease activity by promoting complement activation and autoantigen exposure, forming an amplifying inflammatory loop. Lupus nephritis remains challenging to monitor using conventional complement biomarkers such as CH50, C3, and C4; the utility of anti-C1q, anti-ficolin, and anti-C1s antibodies, along with tissue-based markers such as renal C4d and C5b-9 deposits, as markers of disease activity and prognosis, is discussed. Interestingly, noncanonical functions of complement, including intracellular roles in immune cell metabolism regulation, have been recently described. Understanding the crosstalk between complement, NETs, and immune metabolism may provide new targets for therapeutic intervention.

Communication at synapses is facilitated by postsynaptic receptors, which convert a chemical signal into an electrical response. For ligand-gated ion channels, agonist binding triggers rapid transitions through intermediate states leading to a transient open-pore conformation, with these transitions shaping the postsynaptic response. In this work, we determine structures of the muscle-type nicotinic acetylcholine receptor in unliganded, mono-liganded, and di-liganded states. Agonist binding to a single site stabilizes a closed structure where an entire principal agonist-binding subunit transitions to an active-like conformation, whereas the other unoccupied principal subunit remains inactive, albeit poised for activation. Uniting this intermediate structure with single-channel recordings informs a sequential activation mechanism where asynchronous subunit transitions prime the receptor for activation-a finding with implications for an entire superfamily of pentameric ligand-gated ion channels.

Abstract Manganese dioxide is a material that is more and more used in its particular form, for many industrial applications such as chemical catalysis or for batteries. Thus, workers can be exposed to this particulate chemical. It is known that overexposure to manganese leads to a brain disease called manganism. However, manganese is also known to impact the pulmonary function, which is important as pulmonary exposure is of prime importance for workers. We thus investigated the effects of manganese dioxide on macrophages, i.e. the scavenger cells that take particulates in charge in our bodies. To this purpose, we used a combination of proteomic and targeted approaches, in order to obtain a wide view of the cellular responses to manganese dioxide. We also used a repeated exposure mode, in order to better mimic occupational exposure. Our results point out the fact that manganese oxide nanoparticles are rather toxic for macrophages and induce mitochondrial dysfunction, oxidative stress and a pro-inflammatory response. Environmental significance Manganese dioxide is more and more used in batteries, so that workers in batteries factories are exposed to this metallic oxide. As always for particulate materials, macrophages are the first line of defense of the organism. We thus investigated the effects of manganese dioxide on macrophages, using a repeated exposure scheme to mimic occupational exposure, and the effects were documented by a combination of proteomic and targeted approaches. The functional effects include mitochondrial dysfunction, oxidative stress and inflammation.

Abstract Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labeling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a new crystal structure, reproduce these elevated barriers and reveal how the crystal restrains motions.