Publications

2025

• Mechanism of Arp2/3 complex branch disassembly by human Coro7
  
  • Shatery Nejad Nooshin
  • Boczkowska Malgorzata
  • Hilal Rouba
  • Fregoso Fred E
  • Barrie Kyle R
  • Rebowski Grzegorz
  • Saks Andrew J
  • Gautreau Alexis M
  • de la Cruz Enrique M
  • Dominguez Roberto
  Nature Communications, Nature Publishing Group, 2025, 16 (1), pp.9809. Arp2/3 complex nucleates branched actin networks that drive cell motility and intracellular trafficking. Coronins, a family of seven proteins in humans, inhibit Arp2/3 complex in vitro and reduce branch density in cells. Coro7, a distant member of this family, features two β-propeller domains (β1β2) and C-terminal Central-Acidic (CA) domains and remains poorly studied. Here, cryo-EM and biochemical data show that CA binds subunit Arp3 of free Arp2/3 complex with ~1 µM affinity, inhibiting polymerization like Arpin, while displacing Arp3’s autoinhibitory C-terminal tail and promoting the active, short-pitch conformation, like WASP-family nucleation-promoting factors. Full-length Coro7, however, does not inhibit Arp2/3 complex polymerization but effectively induces debranching, whereas the isolated β1β2 or CA domains do not. In cells, Coro7 depletion disrupts ER-Golgi transport, which is rescued by full-length Coro7 but not by truncated variants. These results suggest that Coro7 functions as an Arp2/3 complex branch disassembly factor implicated in actin-dependent ER-Golgi trafficking. (10.1038/s41467-025-64787-z)
  DOI : 10.1038/s41467-025-64787-z
• Total synthesis of photoswitchable latrunculin B enables reversible control of actin polymerization and cell migration
  
  • Gamet Antoine
  • Ciss Ismaila
  • Courtois Arthur
  • Joyeux Benjamin
  • Gautreau Alexis
  • Romero Stéphane
  • Le Clainche Christophe
  • Nay Bastien
  , 2025. The actin cytoskeleton plays a central role in regulating essential cellular properties such as cell shape, contraction, division, or migration. The filament growth, controlled by subtle regulation mechanisms, can also be inhibited by small molecules preventing actin polymerization, like latrunculin B. This compound has been widely used in cell biology to inhibit cytokinesis or cell migration. To further these applications and provide a mean for the spatiotemporal control of cell migration, we pre-pared photoswitchable latrunculin B through total synthesis, allowing the incorporation of a light-responsive azobenzene moiety. One of these modified latrunculins displayed excellent photophysical properties, with good photostationary states (ca. 90/10 in the two reversible states), long half-lives and excellent fatigue resistance during photoswitching, performed at 370 nm and 440 nm. The Z-photoisomer induced a significant inhibition of the growth of single actin filaments in vitro, com-paratively to the E-isomer—a reversible behavior that was rationalized through molecular docking. Most importantly, this inhibition was photoinduced in migrating cells, stopping actin-dependent membrane dynamics in a reversible manner, and was induced locally in a single cell. (10.26434/chemrxiv-2025-1grsk)
  DOI : 10.26434/chemrxiv-2025-1grsk
• Polarizable models for selected Endocrine Disrupting Chemicals and their hosts
  
  • Mazurek Anna
  • Thirion Valentin
  • Szeleszczuk Lukasz
  • Piquemal Jean-Philip
  • Clavaguera Carine
  • Simonson Thomas
  Journal of Computational Biophysics and Chemistry, World Scientific, 2025. Steroid hormones like estradiol and progesterone bind to nuclear hormone receptors and regulate gene transcription. They compete with pollutants and Endocrine Distrupting Chemicals (EDCs) like bisphenol A. When administered as medication, estradiol and progesterone are themselves considered EDCs. To allow modeling studies, parameters for the polarizable AMOEBA force field were derived here for these three molecules, along with the host molecule cyclodextrin and two phosphorylated forms of p-cresol and tyrosine. Indeed, phosphorylation of an Estrogen Receptor tyrosine regulates estradiol action. AMOEBA-optimized molecular structures were in good agreement with quantum mechanics, and interaction energies with water or ammonium well-reproduced. Molecular dynamics simulations of crystal structures showed improved agreement with experiment over an additive force field; the mean relative error for unit cell volumes was reduced by more than two. A short MD simulation of the estradiol-estrogen receptor complex was done as a proof of principle and was structurally stable. Although additional simulations are desirable, the developed parameters should already be useful for studying hormone and EDC interactions with their hosts. (10.1142/S273741652640003X)
  DOI : 10.1142/S273741652640003X
• Improved Physics-Based Single-Position Protein Sequence Redesign with a Residue-Pairwise Generalized Born Model
  
  • Gaillard Thomas
  Journal of Physical Chemistry B, American Chemical Society, 2025, 129 (41), pp.10699-10710. <div><p>Computational protein design (CPD) aims at creating proteins with new properties.</p><p>Applications include the design of new catalytic reactions, new peptide ligands, vaccines, or new materials. A key element of CPD is the energy or scoring function, used to discriminate the sequences and conformations. We use an energy function combining molecular mechanics (MM) with generalized Born (GB) solvation, along with approximations that make the model pairwise decomposable. Our CPD approach is implemented in the Proteus software. The use of a physics-based energy function ensures a certain transferability and explanatory power to the model. An ambitious problem, often used to evaluate CPD approaches, is the redesign of full protein sequences, in which the sequence of all positions is optimized at the same time.</p><p>We obtained good results previously, with protein cores similar to natives and Superfamily recognition of the sequences close to 100%. A possibility to further improve our results consists in reducing the errors due to the pairwise decomposition of the solvation terms. Our group has proposed an approach called "fluctuating dielectric boundary" (FDB) allowing an exact decomposition of the GB term. It was previously applied only to the sidechains. The goal of the present work is to extend the GB FDB approach to the whole protein and to apply it to the single-position redesign of protein sequences. A notable improvement of the quality of designed sequences is obtained. This allows our Proteus program to have one of the most realistic electrostatic model among CPD approaches.</p></div> (10.1021/acs.jpcb.5c03662)
  DOI : 10.1021/acs.jpcb.5c03662
• RNA Processing and Decay Pathways in Archaea: Emerging Insights on the Function and Evolution of the Archaeal Specific Ski2-Like RNA Helicases
  
  • Cirio Charles
  • Ansart Maël
  • Schmitt Emmanuelle
  • Bouvier Marie
  • Clouet-D’orval Béatrice
  , 2025, 38, pp.123-157. In this chapter, we examine the current understanding of gene expression regulation by post-transcriptional RNA processing and decay pathways in Archaea, addressing critical bottlenecks and scientific advances. We highlight the RNA degrading machines and the associated RNA helicases engaged in these processes. Our focus is on how our understanding of these pathways contributes to a more comprehensive understanding of the evolutionary relationship between Archaea and Eukarya. Integrating insights from biochemical and evolutionary research has enabled us to identify Ski2-like RNA helicases as major players in RNA decay pathways in Archaea and Eukarya. In conclusion, we propose that this RNA helicase family has evolved to connect the RNA-degrading enzymes and ribosomes, in order to regulate gene expression across Eukarya and Archaea. Moreover, the presence of the ASH-Ski2 helicase in the Asgard clade, which is more closely related to Eukarya, supports the hypothesis that a common ancestor of the Ski2-like RNA helicase existed prior the emergence of the Eukarya. (10.1007/978-3-032-03300-0_6)
  DOI : 10.1007/978-3-032-03300-0_6
• Acrylamide-induced noradrenergic axon degeneration is promoted via a non-cell autonomous mechanism, involving microglial Tnfaip2/TNF-α and oxidative stress pathways
  
  • Zong Cai
  • Sato Harue
  • Schneider Benoit
  • Shichino Shigeyuki
  • Ueha Satoshi
  • Wu Bin
  • Matsushima Kouji
  • Okayama Toshitsugu
  • Ikeo Kazuho
  • Urushitani Makoto
  • Ito Hidenori
  • Iwama Sho
  • Fergany Alzahraa
  • Ichihara Sahoko
  • Ohsako Seiichiroh
  • Ichihara Gaku
  Journal of Hazardous Materials, Elsevier, 2025, 496, pp.139125. Environmental toxicants such as acrylamide or 1-bromopropane induce cognitive dysfunction in humans. We previously reported specific noradrenergic neuronal degeneration induced by acrylamide or 1-bromopropane in rodents. In this study, we applied in vivo and in vitro models as well as bulk and single-cell transcriptomic analyses to uncover the underlying mechanisms. RNA-seq of brains of acrylamide-exposed mice revealed a transcriptomic profile involving genes related to multiple neurodegenerative diseases and oxidative stress pathways. Single-cell RNA-seq for microglia identified upregulation of immunoregulation-, inflammation-, and oxidative stress- related pathways, and identified the upregulation of Tnfaip2 (a TNF-α effector), in multiple microglial sub-clusters. Further results of our in vitro interaction model showed that compared to direct acrylamide exposure, exposure to conditioned medium (CM) of acrylamide-exposed BV2 microglia significantly decreased 1C11NE axon density, and RNA-seq for 1C11NE identified similar transcriptomic profiles to those of brains of acrylamide-exposed mice. RNA-seq for BV2 microglia showed upregulation of various oxidative stress related genes. Further inhibition experiments demonstrated that TNF-α inhibition or anti-oxidation alleviated acrylamide-induced axonal degeneration in 1C11NE neurons. Finally, in vivo TNF-α knockout alleviated acrylamide-induced neurotoxicity. Our study demonstrated that acrylamide-induced noradrenergic axon degeneration is promoted via a non-cell autonomous mechanism, involving microglial Tnfaip2/TNF-α and oxidative stress pathways. (10.1016/j.jhazmat.2025.139125)
  DOI : 10.1016/j.jhazmat.2025.139125
• Circular RNAs in Archaea
  
  • Becker Hubert
  • Ferreira-Cerca Sébastien
  , 2025, 1485, pp.451-464. Circular RNA molecules were first described more than 40 years ago. However, it is only recently that the broadness of their phylogenetic distribution has been revealed. Since their discoveries, numerous studies have characterized the molecular mechanisms and function underlying these peculiar molecules, mostly in diverse eukaryotic species. In contrast, studies focusing on the biology of circular RNAs in archaea remain relatively scarce. In this chapter, we provide an overview of the discovery of circular RNAs in archaea and summarize our knowledge of their biology, with an emphasis on circular pre-ribosomal RNAs and Box C/D RNAs. (10.1007/978-981-96-9428-0_26)
  DOI : 10.1007/978-981-96-9428-0_26
• An overview of basic pathophysiological interactions between gut bacteria and their host
  
  • Simonson Mathilde
  • Simonson Thomas
  • Nobécourt Estelle
  Frontiers in Nutrition, Frontiers Media S.A., 2025, 12, pp.1565609. Sometimes referred to as a “forgotten organ,” the gut microbiome (GMB) of humans includes hundreds of commensal bacterial species, which carry several million genes and complement our physiology. Commensal bacteria break down indigestible dietary fiber and provide essential metabolites. These often have a dual action: as “stand-alone” chemicals (e.g., combustibles or emulsifiers) and as signaling molecules that influence host gene expression and physiology. A second function of gut bacteria is to help maintain the intestinal barrier, partly by conditioning the host immune system. Alteration and damage to the GMB have been linked to many pathologies. This review provides an introduction to the more basic mechanisms of GMB-host interaction. It focuses on (a) gut bacteria and their metabolites, and (b) the metabolites’ role in host gene regulation and homeostasis. To this end, recent articles were selected, along with some earlier ground-breaking articles. We consider microbiome composition and intestinal homeostasis, microbiome composition and dysbiosis, immune modulation, gut bacteria metabolite chemistry and host gene regulation. (10.3389/fnut.2025.1565609)
  DOI : 10.3389/fnut.2025.1565609
• Synthesis of photoactivatable molecules for the spatiotemporal control of cell motility with light
  
  • Lucas Morane
  • Courtois Arthur
  • Joyeux Benjamin
  • Gautreau Alexis
  • Romero Stéphane
  • Le Clainche Christophe
  • Nay Bastien
  , 2025.
• Translation in Archaea
  
  • Schmitt Emmanuelle
  • Mechulam Yves
  , 2025 (1), pp.193-232. The translation elongation step involves a succession of decoding, peptide bond formation and translocation cycles. The basic mechanism is very similar in bacteria and eukaryotes, which have been extensively studied. The trees obtained are consistent with the phylogenies deduced from the study of ribosomal RNAs, showing a bifurcation of the branches of the Crenarchaeotes and Euryarchaeotes within the archaea domain. Selenium is a trace element that can be incorporated, in a co-translational way, in the form of selenocysteine into some very specific proteins in all three domains of life. One-third of proteins are produced by membrane-associated ribosomes. The synthesis of these proteins is localized by the signal recognition particle complex and its membrane-associated receptor. After translation has been completed, the ribosome must be prepared for a new translation cycle. (10.1002/9781394372560.ch7)
  DOI : 10.1002/9781394372560.ch7
• Ribosome and Transfer RNA Biogenesis
  
  • Basta-Le Berre Tamara
  • Ferreira-Cerca Sébastien
  , 2025 (1). This chapter focuses on the birth and maturation of ribosomal subunits and transfer RNA (tRNA) molecules in archaea. The ribosomal subunits and tRNA biogenesis processes ensure the production of some of the core molecular components of the translation process. Despite being a distinct domain of life, archaea are often characterized by a mixture of bacterial and eukaryotic features. Ribosome and tRNA biogenesis pathways are not an exception to this rule and as such their studies provide valuable insights into the evolution of these molecular processes and ultimately the evolution of life on Earth. When possible, key conceptual similarities and differences between the biogenesis pathways across the different domains of life will be highlighted. The chapter presents some general information about the diversity, distribution and function of tRNA modifications. It describes, as an example, the synthesis and function of two tRNA modifications specific for archaea. (10.1002/9781394372560.ch5)
  DOI : 10.1002/9781394372560.ch5
• RNA anchoring of Upf1 facilitates recruitment of Dcp2 in the NMD decapping complex
  
  • Ruiz-Gutierrez Nadia
  • Dupas Jeanne
  • Auquier Elvire
  • Barbarin-Bocahu Irène
  • Gaudon-Plesse Claudine
  • Saveanu Cosmin
  • Graille Marc
  • Le Hir Hervé
  Nucleic Acids Research, Oxford University Press, 2025, 53 (5), pp.gkaf160. Upf1 RNA helicase is a pivotal factor in the conserved nonsense-mediated mRNA decay (NMD) process. Upf1 is responsible for coordinating the recognition of premature termination codons (PTCs) in a translation-dependent manner and subsequently triggering mRNA degradation. Multiple factors assist Upf1 during these two consecutive steps. In Saccharomyces cerevisiae, Upf2 and Upf3 associated with Upf1 (Upf1-2/3) contribute to PTC recognition but are absent from the Upf1-decapping complex that includes Nmd4, Ebs1, Dcp1, and Dcp2. Despite their importance for NMD, the organization and dynamics of these Upf1-containing complexes remain unclear. Using recombinant proteins, here we show how distinct domains of Upf1 make direct contacts with Dcp1/Dcp2, Nmd4, and Ebs1. These proteins also bind to each other, forming an extended network of interactions within the Upf1-decapping complex. Dcp2 and Upf2 compete for the same binding site on the N-terminal CH domain of Upf1, which explains the presence of two mutually exclusive Upf1-containing complexes in cells. Our data demonstrate that Nmd4-assisted recruitment of Upf1 promotes anchoring of the decapping enzyme to NMD targets. (10.1093/nar/gkaf160)
  DOI : 10.1093/nar/gkaf160
• Transition state-based computational enzyme design
  
  • Gaillard Thomas
  • Simonson Thomas
  , 2025, 2979, pp.165-186. Our approach to computational protein design is physics-based. We develop a software called Proteus, allowing both physics-based energy evaluation and sequence-conformation exploration. Unlike knowledge-based models, a physics-based energy function facilitates the consideration of unusual chemical entities, such as novel ligands or transition states. Additionally, the adaptive landscape flattening method allows direct sampling on free energy difference between two states. We show here how these ingredients combined can benefit enzyme design. As an illustration, we revisit the stereospecificity inversion of tyrosyl-tRNA synthetase. Following a tutorial presentation, we explore various design criteria that can be related to enzyme experimental parameters. Our model is able to retrieve the native sequence when targeting L-tyrosine. Mutations predicted to favor D-tyrosine are proposed. (10.1007/978-1-0716-4828-5_11)
  DOI : 10.1007/978-1-0716-4828-5_11
• Cys-tRNAj as a Second Translation Initiator for Priming Proteins with Cysteine in Bacteria
  
  • Paupelin-Vaucelle Humbeline
  • Boschiero Claire
  • Lazennec-Schurdevin Christine
  • Schmitt Emmanuelle
  • Mechulam Yves
  • Marlière Philippe
  • Pezo Valérie
  ACS Omega, ACS Publications, 2025. We report the construction of an alternative protein priming system to recode genetic translation in Escherichia coli by designing, through trial and error, a chimeric initiator whose sequence identity points partly to elongator tRNA Cys and partly to initiator tRNA f Met . The elaboration of a selection based on the N-terminal cysteine imperative for the function of glucosamine-6phosphate synthase, an essential enzyme in bacterial cell wall synthesis, was a crucial step to achieve the engineering of this Cys-tRNA j . Iterative improvement of successive versions of Cys-tRNA j was corroborated in vitro by using a biochemical luciferase assay and in vivo by selecting for translation priming of E. coli thymidylate synthase. Condensation assays using specific fluorescent reagent FITC-Gly-cyanobenzothiazole provided biochemical evidence of cysteine coding at the protein priming stage. We showed that translation can be initiated, by N-terminal incorporation of cysteine, at a codon other than UGC by expressing a tRNA j with the corresponding anticodon. The optimized tRNA j is now available to recode the priming of an arbitrary subset of proteins in the bacterial proteome with absolute control of their expression and to evolve the use of xenonucleotides and the emergence of a tXNA j in vivo. (10.1021/acsomega.4c08326#)
  DOI : 10.1021/acsomega.4c08326#
• Original Adverse Outcome Pathway linking neuronal exposure to nanoparticles to the onset of Alzheimer’s disease
  
  • Schneider Benoit
  Alzheimer's & Dementia : the Journal of the Alzheimer's Association, Alzheimer's Association / Wiley, 2025, 20 (S1), pp.e087445. (10.1002/alz.087445)
  DOI : 10.1002/alz.087445
• Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity
  
  • Bourgeois Gabrielle
  • Coureux Pierre-Damien
  • Lazennec-Schurdevin Christine
  • Madru Clément
  • Gaillard Thomas
  • Duchateau Magalie
  • Chamot-Rooke Julia
  • Bourcier Sophie
  • Mechulam Yves
  • Schmitt Emmanuelle
  Nature Communications, Nature Publishing Group, 2025, 16 (1), pp.348. The archaeal ribosome is of the eukaryotic type. TACK and Asgard superphyla, the closest relatives of eukaryotes, have ribosomes containing eukaryotic ribosomal proteins not found in other archaea, eS25, eS26 and eS30. Here, we investigate the case of Saccharolobus solfataricus , a TACK crenarchaeon, using mainly leaderless mRNAs. We characterize the small ribosomal subunit of S. solfataricus bound to SD-leadered or leaderless mRNAs. Cryo-EM structures show eS25, eS26 and eS30 bound to the small subunit. We identify two ribosomal proteins, aS33 and aS34, and an additional domain of eS6. Leaderless mRNAs are bound to the small subunit with contribution of their 5’-triphosphate group. Archaeal eS26 binds to the mRNA exit channel wrapped around the 3’ end of rRNA, as in eukaryotes. Its position is not compatible with an SD:antiSD duplex. Our results suggest a positive role of eS26 in leaderless mRNAs translation and possible evolutionary routes from archaeal to eukaryotic translation. (10.1038/s41467-024-55718-5)
  DOI : 10.1038/s41467-024-55718-5
• TRMT112, a master activator of several methyltransferases modifying factors involved in RNA maturation and translation
  
  • Wang Can
  • Tay Laurianne L. E.
  • Hu Wanwan
  • Corre Morgane
  • Graille Marc
  Frontiers in RNA Research, Frontiers Media, 2025, 3, pp.1556979. Most RNAs and many protein factors involved in mRNA maturation and translation are decorated by numerous and diverse chemical modifications, which contribute to the efficiency, fidelity and regulation of these complex and essential cellular processes. Among those modifications, methylation catalyzed mainly by S-adenosyl-L-methionine (SAM) dependent methyltransferases (MTases) is the most common one. TRMT112 is a small protein acting as an allosteric regulator of several MTases. Initial studies focusing on TRMT112 and its associated MTases were performed in Saccharomyces cerevisiae whereas only few were expanded to human cells, leading to the identification and characterization of four TRMT112 partners in yeast (Trm11, Bud23, Mtq2 and Trm9) and five in human cells (TRMT11, BUD23, MTQ2/HemK2 and two Trm9 orthologues ALKBH8 and TRMT9B). Recent studies have identified several novel MTase partners of human TRMT112, namely METTL5, THUMPD2 and THUMPD3. Interestingly, all these TRMT112-MTase complexes modify factors (RNAs and proteins) involved in mRNA maturation and translation processes and growing evidence supports the importance of these MTases in cancer and correct brain development. In this review, we summarize the current knowledge on TRMT112 protein and its various MTase partners in eukaryotes and archaea. (10.3389/frnar.2025.1556979)
  DOI : 10.3389/frnar.2025.1556979
• ADAM Sheddase Activity Promotes the Detachment of Small Extracellular Vesicles From the Plasma Membrane
  
  • Bizingre Chloé
  • Arellano-Anaya Zaira
  • Picard Flavien
  • Pietri Mathéa
  • Baudry Anne
  • Roussel Florence
  • Bianchi Clara
  • Alleaume-Butaux Aurélie
  • Ardila-Osorio Hector
  • Romao Maryse
  • Lavieu Grégory
  • Raposo Graça
  • Schneider Benoit
  Journal of Extracellular Vesicles, Taylor & Francis, 2025, 14 (7), pp.e70114. Small extracellular vesicles (SEVs) are involved in diverse functions in normal and pathological situations, including intercellular communication, immunity, metastasis and neurodegeneration. Cell release of SEVs is assumed to occur passively right after multivesicular bodies of the endocytic pathway fuse with the plasma membrane. We show here that the completion of SEV release depends on membrane‐bound ADAM10 and ADAM17 sheddases that promote the detachment of SEVs from the cell surface by catalysing the cleavage of adhesion proteins of the SEV membrane. The intensity of ADAM10/17‐mediated release of SEVs depends on a balanced control of 3‐phosphoinositide–dependent kinase 1 (PDK1) and ERK1/2 signalling pathways converging on 90‐kDa ribosomal S6 kinase‐2 (RSK2), which, in turn, fine‐tunes ADAM17 bioavailability and ADAM10/17 enzymatic activities at the plasma membrane, according to a mechanism that relies, at least in part, on variation of the rhomboid‐like pseudoprotease iRhom2 cell surface level. By identifying a new proteolytic step involved in the basal release of SEVs, our work may help understand how the deregulation of ADAM10/17‐mediated discharge of SEVs contributes to several pathological states. (10.1002/jev2.70114)
  DOI : 10.1002/jev2.70114