Publications

2024

• Interplay of actin nematodynamics and anisotropic tension controls endothelial mechanics
  
  • Dessalles Claire
  • Cuny Nicolas
  • Boutillon Arthur
  • Salipante Paul F
  • Babataheri Avin
  • Barakat Abdul I
  • Salbreux Guillaume
  , 2024. Blood vessels expand and contract actively, while continuously experiencing dynamic external stresses from the blood flow. The mechanical response of the vessel wall is that of a composite material: its mechanical properties depend on a diverse set of cellular mechanical components, which change dynamically as cells respond to external stress. Mapping the relationship between these underlying cellular processes and emergent tissue mechanics is an on-going challenge, in particular in endothelial cells. Here we use a microstretcher mimicking the native environment of blood vessels to assess both the mechanics and cellular dynamics of an endothelial tube in response to a physiological increase in luminal pressure. The characterization of the instantaneous monolayer elasticity reveals a strain-stiffening, actin-dependent and substrate-responsive behavior. In response to a maintained pressure increase, the tissue displays a fluid-like expansion, accompanied by the reorientation of cell shape and of actin fibers. This actindriven reorientation depends on focal adhesions and adherens junctions, two key mechanosensors. We introduce a mechanical model coupling actin fiber nematodynamics with active and elastic tension generation by actin fibers in the endothelium, which recapitulates the response to pressure of endothelial tubes. (10.1101/2024.03.10.584287)
  DOI : 10.1101/2024.03.10.584287
• Factors Affecting the Population of Excited Charge Transfer States in Adenine/Guanine Dinucleotides: A Joint Computational and Transient Absorption Study
  
  • Petropoulos Vasilis
  • Martinez-Fernandez Lara
  • Uboldi Lorenzo
  • Maiuri Margherita
  • Cerullo Giulio
  • Balanikas Evangelos
  • Markovitsi Dimitra
  Biomolecules, MDPI, 2024, 14 (12), pp.1548. There is compelling evidence that the absorption of low-energy UV radiation directly by DNA in solution generates guanine radicals with quantum yields that are strongly dependent on the secondary structure. Key players in this unexpected phenomenon are the photo-induced charge transfer (CT) states, in which an electric charge has been transferred from one nucleobase to another. The present work examines the factors affecting the population of these states during electronic relaxation. It focuses on two dinucleotides with opposite orientation: 5′-dApdG-3′ (AG) and 5′-dGpdA-3′ (GA). Quantum chemistry calculations determine their ground state geometry and the associated Franck–Condon states, map their relaxation pathways leading to excited state minima, and compute their absorption spectra. It has been shown that the most stable conformer is anti-syn for AG and anti-anti for GA. The ground state geometry governs both the excited states populated upon UV photon absorption and the type of excited state minima reached during their relaxation. Their fingerprints are detected in the transient absorption spectra recorded with excitation at 266 nm and a time resolution of 30 fs. Our measurements reveal that in the large majority of dinucleotides, chromophore coupling is already operative in the ground state and that the charge transfer process occurs within ~120 fs. The competition among various relaxation pathways affects the quantum yields of the CT state formation in each dinucleotide, which are estimated to be 0.18 and 0.32 for AG and GA, respectively. (10.3390/biom14121548)
  DOI : 10.3390/biom14121548
• Archaerhodopsin 3 is an ideal template for the engineering of highly fluorescent optogenetic reporters
  
  • Herasymenko Krystyna
  • Walisinghe Danushka
  • Konno Masae
  • Barneschi Leonardo
  • de Waele Isabelle
  • Sliwa Michel
  • Inoue Keiichi
  • Olivucci Massimo
  • Haacke Stefan
  Chemical Science, The Royal Society of Chemistry, 2024, 16 (2), pp.761-774. Archaerhodopsin-3 (AR-3) variants stand out among other rhodopsins in that they display a weak, but voltage-sensitive, near-infrared fluorescence emission. This has led to their application in optogenetics both in cell cultures and small animals. However, in the context of improving the fluorescence characteristics of the next generation of AR-3 reporters, an understanding of their ultrafast light-response in light-adapted conditions, is mandatory. To this end, we present a combined experimental and computational investigation of the excited state dynamics and quantum yields of AR-3 and its DETC and Arch-5 variants. The latter always display a mixture of all-trans/15-anti and 13-cis/15-syn isomers, which leads to a bi-exponential excited state decay. The isomerisation quantum yield is reduced more than 20 times as compared to WT AR-3 and proves that the steady-state fluorescence is induced by a single absorption photon event. In wild-type AR-3, we show that a 300 fs, barrier-less and vibrationally coherent isomerization is driven by an unusual covalent electronic character of its all-trans retinal chromophore leading to a metastable twisted diradical (TIDIR), in clear contrast to the standard charge-transfer scenario established for other microbial rhodopsins. We discuss how the presence of TIDIR makes AR-3 an ideal candidate for the design of variants with a one-photon induced fluorescence possibly reaching the emission quantum yield of the top natural emitter neorhodopsin (NeoR). (10.1039/d4sc05120c)
  DOI : 10.1039/d4sc05120c
• Etude de la perméabilisation de la membrane plasmique par spectroscopie térahertz : thérapie photodynamique et protéolyse de la trypsine
  
  • Lordon de Bonniol Du Tremont Blandine
  , 2024. Le térahertz désigne la zone de fréquence entre 0.1 et 10 THz, entre les domaines de l’infrarouge et des ondes radios. Les ondes térahertz présentent une forte sensibilité à l’eau et à ses changements de configurations, induits notamment par la présence de solutés. Bénéficiant des récents développements technologiques, la région térahertz du spectre électromagnétique offre un potentiel important dans le domaine de la biologie, et dans notre cas, du domaine biomédical.Les méthodes permettant de suivre en temps réel les échanges moléculaires à travers la membrane des cellules vivantes sont encore rares.Notre groupe a développé un montage de routine combinant les ondes térahertz avec une configuration en réflexion totale atténuée (ATR). Ce dispositif permet d'obtenir des informations en temps réel et de quantifier les échanges entre les membranes cellulaires induits par la perméabilisation de la membrane plasmique des cellules épithéliales.Il y a trois axes principaux à ce travail de thèse. Le premier concerne la caractérisation et le développement technologique du dispositif térahertz. Cela a permis d’améliorer la répétabilité et la stabilité des mesures. Le second axe est l’étude de la perméabilisation induite par la thérapie photodynamique, un traitement contre certains types de cancers. Cette étude s’est faite en collaboration avec une équipe de biologistes et de chimistes du laboratoire Softmat à Toulouse. Une comparaison constante de l'évaluation de l'intégrité de la membrane plasmique avec le dispositif térahertz et avec les techniques biologiques standard est effectuée. Le dispositif térahertz, combiné à ces méthodes biologiques, a montré une augmentation de l’efficacité de la thérapie photodynamique lorsque les photosensibilisateurs sont encapsulés par des nanovecteurs micellaires. D’autres types de nanovecteurs ont ensuite été étudiés. Les résultats biologiques et térahertz montrent que selon le type de nanovecteur, les dynamiques de perméabilisation de la membrane plasmique sont différentes. Enfin, le troisième axe est l’étude de la perméabilisation induite par la protéolyse de la trypsine, enzyme utilisée en culture cellulaire pour détacher des cellules de leur substrat. L’étude de ce processus par le dispositif térahertz, combinée à un modèle multicouche, à de l'imagerie confocale et de la fluorescence, a montré que cette procédure quotidienne en culture cellulaire induit des échanges de petites molécules à travers la membrane plasmique.
• Study of the Physiological Response of NucS to Genotoxic Stress in Actinobacteria
  
  • Bayard Anaïs
  , 2024. DNA replication accuracy ensures proper genetic transmission. Damage from external factors or internal events threatens genomic integrity. Actinobacteria, lacking canonical MMR proteins, possess NucS (EndoMS), an ATP-independent enzyme involved in a non-canonical mismatch repair pathway. While NucS's activity on mismatches is documented, its in vivo role and implications in DNA Damage Repair systems require further understanding.This study aims to characterise NucS's role in Double-Strand Break Repair (DSBR). Our findings show that mScarlet1-NucSD144A forms polar foci in response to DNA damage, especially DSBs and complex recruitment in apoptosis-like cells.Corynebacterium glutamicum, CglΔnucS bacteria exhibits higher homologous recombination (HR) activation and increased DSBs compared to CglWT, indicating NucS's role in DSBR efficiency and regulation. CglΔnucS bacteria have a growth advantage under genotoxic stress, likely due to altered DSBR mechanisms. Bioinformatic analyses predict NucS interactions with key enzymes of RH and other DNA repair pathways and metabolism and energy regulation.NucS may bind and stabilise free DNA ends generated by DSBs, balancing HR and participating in DSB repair through microhomology-mediated end joining (MMEJ). Future studies should explore post-translational modifications and metabolic conditions regulating NucS reponse and its in vitro activity on DSBs and HR intermediates.
• Design, Synthesis, and In Vitro Antimalarial Evaluation of New 1,3,5-Tris[(4-(Substituted-Aminomethyl)Phenoxy)Methyl]Benzenes
  
  • Albenque-Rubio Sandra
  • Guillon Jean
  • Agnamey Patrice
  • Damiani Céline
  • Savrimoutou Solène
  • Mustière Romain
  • Pinaud Noël
  • Moreau Stéphane
  • Mergny Jean-Louis
  • Ronga Luisa
  • Kanavos Ioannis
  • Marchivie Mathieu
  • Moukha Serge
  • Dozolme Pascale
  • Sonnet Pascal
  • Cohen Anita
  Drugs and Drug Candidates, MDPI, 2024, 3 (3), pp.615-637. By taking into account our previously described series of 1,3,5-tris[(4-(substituted-aminomethyl)phenyl)methyl]benzene compounds, we have now designed, prepared, and evaluated in vitro against Plasmodium falciparum a novel series of structural analogues of these molecules, i.e., the 1,3,5-tris[(4-(substituted-aminomethyl)phenoxy)methyl]benzene derivatives. The pharmacological data showed antimalarial activity with IC50 values in the sub and μM range. The in vitro cytotoxicity of these new nitrogen polyphenoxymethylbenzene compounds was also evaluated on human HepG2 cells. The 1,3,5-tris[(4-(substituted-aminomethyl)phenoxy)methyl]benzene derivative 1m was found as one of the most potent and promising antimalarial candidates with favorable cytotoxic to antiprotozoal properties in the P. falciparum strains W2 and 3D7. In conclusion, this 1,3,5-tris[(4-(pyridin-3-ylmethylaminomethyl)phenoxyl)methyl]benzene 1m (IC50 = 0.07 μM on W2, 0.06 μM on 3D7, and 62.11 μM on HepG2) was identified as the most promising antimalarial derivative with selectivity indexes (SI) of 887.29 on the W2 P. falciparum chloroquine-resistant strain, and of 1035.17 on the chloroquine-sensitive and mefloquine decreased sensitivity strain 3D7. It has been previously described that the telomeres of P. falciparum could represent potential targets for these types of polyaromatic compounds; therefore, the capacity of our novel derivatives to stabilize the parasitic telomeric G-quadruplexes was assessed using a FRET melting assay. However, with regard to the stabilization of the protozoal G-quadruplex, we observed that the best substituted derivatives 1, which exhibited some interesting stabilization profiles, were not the most active antimalarial compounds against the two Plasmodium strains. Thus, there were no correlations between their antimalarial activities and selectivities of their respective binding to G-quadruplexes. (10.3390/ddc3030035)
  DOI : 10.3390/ddc3030035
• The Balance Between Shear Flow and Extracellular Matrix in Ovarian Cancer‐on‐Chip
  
  • Chen Changchong
  • Boché Alphonse
  • Wang Zixu
  • Lopez Elliot
  • Peng Juan
  • Carreiras Franck
  • Schanne-Klein Marie‐claire
  • Chen Yong
  • Lambert Ambroise
  • Aimé Carole
  Advanced Healthcare Materials, Wiley, 2024, 13 (23), pp.2400938. Ovarian cancer is the most lethal gynecologic cancer in developed countries. In the tumor microenvironment, the extracellular matrix (ECM) and flow shear stress are key players in directing ovarian cancer cells invasion. Artificial ECM models based only on ECM proteins are used to build an ovarian tumor‐on‐chip to decipher the crosstalk between ECM and shear stress on the migratory behavior and cellular heterogeneity of ovarian tumor cells. This work shows that in the shear stress regime of the peritoneal cavity, the ECM plays a major role in driving individual or collective ovarian tumor cells migration. In the presence of basement membrane proteins, migration is more collective than on type I collagen regardless of shear stress. With increasing shear stress, individual cell migration is enhanced; while, no significant impact on collective migration is measured. This highlights the central position that ECM and flow shear stress should hold in in vitro ovarian cancer models to deepen understanding of cellular responses and improve development of ovarian cancer therapeutic platforms. In this frame, adding flow provides significant improvement in biological relevance over the authors’ previous work. Further steps for enhanced clinical relevance require not only multiple cell lines but also patient‐derived cells and sera. (10.1002/adhm.202400938)
  DOI : 10.1002/adhm.202400938
• Reversible photoregulation of G-quadruplex DNA structures by non-covalent azobenzene derivatives
  
  • Perrin Auriane
  • Nay Bastien
  • Hache François
  • Changenet-Barret, Pascale
  , 2024. G-quadruplexes (G4) are non-canonical DNA structures involved in important cell regulatory functions associated with their folding mechanism. The design of small ligands capable of modulating their formation/stabilization is therefore of growing interest for the development of new anti-cancer therapies. In particular, the reversible control of G4s using bistable photoswitches offers promising perspectives for applications in photopharmacology and DNA nanotechnology, but remains largely unexploited [1]. It has long been demonstrated that the folding/unfolding of human telomeric (HT) G4 sequences can be induced by azobenzene-derived photoswitches [2]. However, the dynamics and mechanisms underlying these processes have never been investigated. Here we present a comprehensive study of complexes made of non-covalent azobenzenes bearing quaternary ammonium substituents (AZO) with different G4 sequences, by using a combination of stationary and time-resolved optical and chiroptical spectroscopic methods. This study revealed a non-cooperative binding mode of AZO with HT G4 sequences of the type 5'-GGG(TTAGGG)3-3' and the thrombin-binding aptamer G4 sequence, 5'-GGTTGGTGTGGTTGG-3' (TBA), in the absence of physiological cations. The binding of AZO to DNA induces the formation of parallel G4 topologies that can be reversibly unfolded under UV/visible excitation without noticeable fatigue. Femtosecond transient absorption measurements show that the isomerization of AZO is slowed by a factor of 4 in the presence of G4 (62ps vs. 16ps), while millisecond time-resolved circular dichroism provides evidence that G4 unfolding takes place within a few tens of milliseconds [3].
• Quantitative Assessment of Collagen Remodeling during a Murine Pregnancy
  
  • Ramella-Roman Jessica C
  • Mahendroo Mala
  • Raoux Clothilde
  • Latour Gaël
  • Schanne-Klein Marie-Claire
  ACS photonics, American Chemical Society, 2024, 11 (9), pp.3536-3544. <div><p>Uterine cervical remodeling is a fundamental feature of pregnancy, facilitating the delivery of the fetus through the cervical canal. Yet, we still know very little about this process due to the lack of methodologies that can quantitatively and unequivocally pinpoint the changes the cervix undergoes during pregnancy. We utilize polarization-resolved second harmonic generation to visualize the alterations the cervix extracellular matrix, specifically collagen, undergoes during pregnancy with exquisite resolution. This technique provides images of the collagen orientation at the pixel level (0.4 μm) over the entire murine cervical section. They show tight and ordered packing of collagen fibers around the os at the early stage of pregnancy and their disruption at the later stages. Furthermore, we utilize a straightforward statistical analysis to demonstrate the loss of order in the tissue, consistent with the loss of mechanical properties associated with this process. This work provides a deeper understanding of the parturition process and could support research into the cause of pathological or premature birth.</p></div> (10.1021/acsphotonics.4c00337)
  DOI : 10.1021/acsphotonics.4c00337
• Confinement energy landscape classification reveals membrane receptor nano-organization mechanisms
  
  • Yu Chao
  • Richly Maximilian
  • Hoang Thi Thuy
  • El Beheiry Mohammed
  • Türkcan Silvan
  • Masson Jean-Baptiste
  • Alexandrou Antigoni
  • Bouzigues Cedric I
  Biophysical Journal, Biophysical Society, 2024, 123 (13), pp.1882-1895. The cell membrane organization has an essential functional role through the control of membrane receptor confinement in micro- or nanodomains. Several mechanisms have been proposed to account for these properties, although some features have remained controversial, notably the nature, size, and stability of cholesterol- and sphingolipid-rich domains or lipid rafts. Here, we probed the effective energy landscape acting on single-nanoparticle-labeled membrane receptors confined in raft nanodomains— epidermal growth factor receptor (EGFR), Clostridium perfringens ε-toxin receptor (CPεTR), and Clostridium septicum α-toxin receptor (CSαTR)—and compared it with hop-diffusing transferrin receptors. By establishing a new analysis pipeline combining Bayesian inference, decision trees, and clustering approaches, we systematically classified single-protein trajectories according to the type of effective confining energy landscape. This revealed the existence of only two distinct organization modalities: confinement in a quadratic energy landscape for EGFR, CPεTR, and CSαTR (A), and free diffusion in confinement domains resulting from the steric hindrance due to F-actin barriers for transferrin receptor (B). The further characterization of effective confinement energy landscapes by Bayesian inference revealed the role of interactions with the domain environment in cholesterol- and sphingolipid-rich domains with (EGFR) or without (CPεTR and CSαTR) interactions with F-actin to regulate the confinement energy depth. These two distinct mechanisms result in the same organization type (A). We revealed that the apparent domain sizes for these receptor trajectories resulted from Brownian exploration of the energy landscape in a steady-state-like regime at a common effective temperature, independently of the underlying molecular mechanisms. These results highlight that confinement domains may be adequately described as interaction hotspots rather than rafts with abrupt domain boundaries. Altogether, these results support a new model for functional receptor confinement in membrane nanodomains and pave the way to the constitution of an atlas of membrane protein organization. (10.1016/j.bpj.2024.06.001)
  DOI : 10.1016/j.bpj.2024.06.001
• Angle-Resolved Linear Dichroism to Probe the Organization of Highly Ordered Collagen Biomaterials
  
  • Krins Natacha
  • Wien Frank
  • Schmeltz Margaux
  • Pérez Javier
  • Dems Dounia
  • Debons Nicolas
  • Laberty-Robert Christel
  • Schanne-Klein Marie-Claire
  • Aimé Carole
  Biomacromolecules, American Chemical Society, 2024, 25 (9), pp.6181-6187. Controlling the assembly of high-order structures is central to soft-matter and biomaterial engineering. Angle-resolved linear dichroism can probe the ordering of chiral collagen molecules in the dense state. Collagen triple helices were aligned by solvent evaporation. Their ordering gives a strong linear dichroism (LD) that changes sign and intensity with varying sample orientations with respect to the beam linear polarization. Being complementary to circular dichroism, which probes the structure of chiral (bio)molecules, LD can shift from the molecular to the supramolecular scale and from the investigation of the conformation to interactions. Supported by multiphoton microscopy and X-ray scattering, we show that LD provides a straightforward route to probe collagen alignment, determine the packing density, and monitor denaturation. This approach could be adapted to any assembly of chiral (bio)macromolecules, with key advantages in detecting large-scale assemblies with high specificity to aligned and chiral molecules and improved sensitivity compared to conventional techniques. (10.1021/acs.biomac.4c00860)
  DOI : 10.1021/acs.biomac.4c00860
• Impact of trypsin on cell cytoplasm during detachment of cells studied by terahertz sensing
  
  • Lordon Blandine
  • Campion Tiffany
  • Gibot Laure
  • Gallot Guilhem
  Biophysical Journal, Biophysical Society, 2024, 123 (16), pp.2476-2483. Trypsin is a very common enzyme used in cell culture to harvest cells by cleaving the proteins responsible for cell adhesion. However, trypsin also induces undesirable effects on cells, such as altering membrane proteins and the cytoskeleton, changing the composition of the cytoplasm and the cell volume, and even leading to cell death when used improperly. Using attenuated total reflection in the terahertz domain, confocal microscopy, and the propidium iodide test, we quantified in real time the change in cytoplasmic content induced by trypsin proteolysis on Madin-Darby canine kidney epithelial cells. We have observed a cytoplasmic modification from the very first seconds of trypsinization, following the change of cell volume due to mechanical re-equilibrium of the membrane. We found that the cytoplasmic alteration is associated with a transfer of small solutes: electrolytes and metabolites. We also found a very good nonlinear correlation between the side effects monitored by terahertz sensing and the cell height, regardless of the dependence of the cell height on trypsin concentration and exposure time. (10.1016/j.bpj.2024.06.011)
  DOI : 10.1016/j.bpj.2024.06.011
• La réparation archéenne de l’ADN
  
  • L’hermitte-Stead Caroline
  • Bayard Anaïs
  • Aleksandrov Alexey
  • Lestini Roxane
  • Myllykallio Hannu
  , 2024, pp.27-47. Dans toute cellule, l’ADN est en permanence endommagé par des mutagènes endogènes et exogènes. C’est pourquoi des mécanismes de réparation complexes impliquant un grand nombre de protéines ont évolués afin de permettre la réparation de l’ADN essentielle au maintien de l’intégrité du génome et de la survie cellulaire. Ce chapitre présente les principales voies de réparation retrouvées chez les archées. (10.51926/ISTE.9169.ch2)
  DOI : 10.51926/ISTE.9169.ch2
• A Cost‐Effective Hemin‐Based Artificial Enzyme Allows for Practical Applications
  
  • Qiu Dehui
  • He Fangni
  • Liu Yuan
  • Zhou Zhaoxi
  • Yang Yuqin
  • Long Zhongwen
  • Chen Qianqian
  • Chen Desheng
  • Wei Shijiong
  • Mao Xuanxiang
  • Zhang Xiaobo
  • Mergny Jean‐louis
  • Monchaud David
  • Ju Huangxian
  • Zhou Jun
  Advanced Science, Wiley Open Access, 2024, 11 (32), pp.2402237. Abstract Nanomaterials excel in mimicking the structure and function of natural enzymes while being far more interesting in terms of structural stability, functional versatility, recyclability, and large‐scale preparation. Herein, the story assembles hemin, histidine analogs, and G‐quadruplex DNA in a catalytically competent supramolecular assembly referred to as assembly‐activated hemin enzyme (AA‐heminzyme). The catalytic properties of AA‐heminzyme are investigated both in silico (by molecular docking and quantum chemical calculations) and in vitro (notably through a systematic comparison with its natural counterpart horseradish peroxidase, HRP). It is found that this artificial system is not only as efficient as HRP to oxidize various substrates (with a turnover number k cat of 115 s −1) but also more practically convenient (displaying better thermal stability, recoverability, and editability) and more economically viable, with a catalytic cost amounting to &lt;10% of that of HRP. The strategic interest of AA‐heminzyme is further demonstrated for both industrial wastewater remediation and biomarker detection (notably glutathione, for which the cost is decreased by 98% as compared to commercial kits). (10.1002/advs.202402237)
  DOI : 10.1002/advs.202402237
• G-quadruplex forming motifs in the promoter region of the B-MYB proto-oncogene
  
  • Miranda André
  • Cucchiarini Anne
  • Esnault Cyril
  • Andrau Jean-Christophe
  • Oliveira Paula
  • Mergny Jean‐louis
  • Cruz Carla
  International Journal of Biological Macromolecules, Elsevier, 2024, 270, pp.132244. To combat cancer, a comprehensive understanding of the molecular mechanisms and behaviors involved in carcinogenesis is crucial, as tumorigenesis is a complex process influenced by various genetic events and disease hallmarks. The B-MYB gene encodes a transcription factor involved in cell cycle regulation, survival, and differentiation in normal cells. B-MYB can be transformed into an oncogene through mutations, and abnormal expression of B-MYB has been identified in various cancers, including lung cancer, and is associated with poor prognosis. Targeting this oncogene is a promising approach for anti-cancer drug design. B-MYB has been deemed undruggable in previous reports, necessitating the search for novel therapeutic options. In this study, we found that the B-MYB gene promoter contains several G/C rich motifs compatible with G-quadruplex (G4) formation. We investigated and validated the existence of G4 structures in the promoter region of B-MYB, first in vitro using a combination of bioinformatics, biophysical, and biochemical methods, then in cell with the recently developed G4access method. (10.1016/j.ijbiomac.2024.132244)
  DOI : 10.1016/j.ijbiomac.2024.132244
• The contribution of multiphoton microscopy to our knowledge of parchments
  
  • Robinet Laurianne
  • Galante Giulia
  • Heu-Thao Sylvie
  • Schanne-Klein Marie-Claire
  • Latour Gael
  , 2024.
• G-quadruplex ligands as potent lysosome regulators
  
  • Ferret Lucille
  • Alvarez-Valadez Karla
  • Rivière Jennifer
  • Muller Alexandra
  • Bohálová Natalia
  • Yu Luo
  • Guittat Lionel
  • Brázda Vaclav
  • Kroemer Guido
  • Mergny Jean-Louis
  • Djavaheri-Mergny Mojgan
  , 2023, pp.1901-1915. Guanine-quadruplex structures (G4) are unusual nucleic acid conformations formed by guanine-rich DNA and RNA sequences and known to control gene expression mechanisms, from transcription to protein synthesis. So far, a number of molecules that recognize G4 have been developed for potential therapeutic applications in human pathologies, including cancer and infectious diseases. These molecules are called G4 ligands. When the biological effects of G4 ligands are studied, the analysis is often limited to nucleic acid targets. However, recent evidence indicates that G4 ligands may target other cellular components and compartments such as lysosomes and mitochondria. Here, we summarize our current knowledge of the regulation of lysosome by G4 ligands, underlying their potential functional impact on lysosome biology and autophagic flux, as well as on the transcriptional regulation of lysosomal genes. We outline the consequences of these effects on cell fate decisions and we systematically analyzed G4-prone sequences within the promoter of 435 lysosome-related genes. Finally, we propose some hypotheses about the mechanisms involved in the regulation of lysosomes by G4 ligands. (10.1080/15548627.2023.2170071)
  DOI : 10.1080/15548627.2023.2170071
• Non-random spatial organization of telomeres varies during the cell cycle and requires LAP2 and BAF
  
  • Keller Debora
  • Stinus Sonia
  • Umlauf David
  • Gourbeyre Edith
  • Biot Eric
  • Olivier Nicolas
  • Mahou Pierre
  • Beaurepaire Emmanuel
  • Andrey Philippe
  • Crabbe Laure
  iScience, Elsevier, 2024, 27 (4), pp.109343. Spatial genome organization within the nucleus influences major biological processes and is impacted by the configuration of linear chromosomes. Here, we applied 3D spatial statistics and modeling on high-resolution telomere and centromere 3D-structured illumination microscopy images in cancer cells. We found a multi-scale organization of telomeres that dynamically evolved from a mixed clustered-and-regular distribution in early G1 to a purely regular distribution as cells progressed through the cell cycle. In parallel, our analysis revealed two pools of peripheral and internal telomeres, the proportions of which were inverted during the cell cycle. We then conducted a targeted screen using MadID to identify the molecular pathways driving or maintaining telomere anchoring to the nuclear envelope observed in early G1. Lamina-associated polypeptide (LAP) proteins were found transiently localized to telomeres in anaphase, a stage where LAP2α initiates the reformation of the nuclear envelope, and impacted telomere redistribution in the next interphase together with their partner barrier-to-autointegration factor (BAF). (10.1016/j.isci.2024.109343)
  DOI : 10.1016/j.isci.2024.109343
• Catalytic mechanism of fatty acid photodecarboxylase: on the detection and stability of the initial carbonyloxy radical intermediate
  
  • Aleksandrov Alexey
  • Bonvalet Adeline
  • Müller Pavel
  • Sorigué Damien
  • Beisson Fred
  • Antonucci Laura
  • Solinas Xavier
  • Joffre Manuel
  • Vos Marten
  Angewandte Chemie International Edition, Wiley-VCH Verlag, 2024, 63 (19), pp.e202401376. In fatty acid photodecarboxylase (FAP), light‐induced formation of the primary radical product RCOO$^●$ from fatty acid RCOO– occurs in 300 ps, upon which CO2 is released quasi‐immediately. Based on the hypothesis that aliphatic RCOO$^●$ (spectroscopically uncharacterized because unstable) absorbs in the red similarly to aromatic carbonyloxy radicals such as 2,6‑dichlorobenzoyloxy radical (DCB$^●$), much longer‐lived linear RCOO$^●$ has been suggested recently. We performed quantum chemical reaction pathway and spectral calculations. These calculations are in line with the experimental DCB$^●$decarboxylation dynamics and spectral properties and show that in contrast to DCB$^●$, aliphatic RCOO$^●$ radicals a) decarboxylate with a very low energetic barrier and on the timescale of a few ps and b) exhibit little red absorption. A time‐resolved infrared spectroscopy experiment confirms very rapid, &lt;&lt;300 ps RCOO$^●$ decarboxylation in FAP. We argue that this property is required for the observed high quantum yield of hydrocarbons formation by FAP. (10.1002/anie.202401376)
  DOI : 10.1002/anie.202401376
• Correction of non-random mutational biases along a linear bacterial chromosome by the mismatch repair endonuclease NucS
  
  • Dagva Oyut
  • Thibessard Annabelle
  • Lorenzi Jean-Noël
  • Labat Victor
  • Piotrowski Emilie
  • Rouhier Nicolas
  • Myllykallio Hannu
  • Leblond Pierre
  • Bertrand Claire
  Nucleic Acids Research, Oxford University Press, 2024, 52 (9), pp.5033-5047. The linear chromosome of Streptomyces exhibits a highly compartmentalized structure with a conserved central region flanked by variable arms. As double strand break (DSB) repair mechanisms play a crucial role in shaping the genome plasticity of Streptomyces, we investigated the role of EndoMS/NucS, a recently characterized endonuclease involved in a non-canonical mismatch repair (MMR) mechanism in archaea and actinobacteria, that singularly corrects mismatches by creating a DSB. We showed that Streptomyces mutants lacking NucS display a marked colonial phenotype and a drastic increase in spontaneous mutation rate. In vitro biochemical assays revealed that NucS cooperates with the replication clamp to efficiently cleave G/T, G/G and T/T mismatched DNA by producing DSBs. These findings are consistent with the transition-shifted mutational spectrum observed in the mutant strains and reveal that NucS-dependent MMR specific task is to eliminate G/T mismatches generated by the DNA polymerase during replication. Interestingly, our data unveil a crescent-shaped distribution of the transition frequency from the replication origin towards the chromosomal ends, shedding light on a possible link between NucS-mediated DSBs and Streptomyces genome evolution. (10.1093/nar/gkae132)
  DOI : 10.1093/nar/gkae132
• Modeling and Predicting Second-Harmonic Generation from Protein Molecular Structure
  
  • Asadipour Bahar
  • Beaurepaire Emmanuel
  • Zhang Xingjian
  • Chessel Anatole
  • Mahou Pierre
  • Supatto Willy
  • Schanne-Klein Marie-Claire
  • Stringari Chiara
  Physical Review X, American Physical Society, 2024, 14 (1), pp.011038. (10.1103/PhysRevX.14.011038)
  DOI : 10.1103/PhysRevX.14.011038
• G-quadruplex ligands in cancer therapy: Progress, challenges, and clinical perspectives
  
  • Figueiredo Joana
  • Mergny Jean-Louis
  • Cruz Carla
  Life Sciences, Elsevier, 2024, 340, pp.122481. Guanine-rich sequences can form G-quadruplexes (G4) in living cells, making these structures promising anti- cancer targets. Compounds able to recognize these structures have been investigated as potential anticancer drugs; however, no G4 binder has yet been approved in the clinic. Here, we describe G4 ligands structure-activity relationships, in vivo effects as well as clinical trials. Addressing G4 ligand characteristics, targeting challenges, and structure-activity relationships, this review provides insights into the development of potent and selective G4-targeting molecules for therapeutic applications. (10.1016/j.lfs.2024.122481)
  DOI : 10.1016/j.lfs.2024.122481
• Chirped pulse upconversion for femtosecond mid-infrared spectroscopy at 100 kHz
  
  • Jonušas Mindaugas
  • Bournet Quentin
  • Bonvalet Adeline
  • Natile Michele
  • Guichard Florent
  • Zaouter Yoann
  • Georges Patrick
  • Druon Frédéric
  • Hanna Marc
  • Joffre Manuel
  Optics Express, Optical Society of America - OSA Publishing, 2024, 32 (5), pp.8020. We demonstrate that chirped pulse up-conversion (CPU), a method routinely used with systems based on 1-kHz Titanium:Sapphire lasers, can be extended to a repetition rate of 100 kHz with an Ytterbium diode-pumped femtosecond amplifier. Individual mid-infrared spectra can thus be measured directly in the near infrared using a fast CMOS linescan camera. After an appropriate Fourier processing, a spectral resolution of 1.1 cm-1 is reported, currently limited by our spectrometer. Additionally, we demonstrate the application of CPU to a pump-probe measurement of the vibrational relaxation in carboxy-hemoglobin, and we show that the combination of fast scanning and fast acquisition enables a straightforward removal of pump scattering interference. (10.1364/oe.515291)
  DOI : 10.1364/oe.515291
• Spatial modeling of telomere intra-nuclear distribution reveals non-random organization that varies during cell cycle and depends on LAP2 and BAF
  
  • Keller Debora
  • Stinus Sonia
  • Umlauf David
  • Gourbeyre Edith
  • Biot Eric
  • Olivier Nicolas
  • Mahou Pierre
  • Beaurepaire Emmanuel
  • Andrey Philippe
  • Crabbe Laure
  , 2022. Abstract Genome organization within the 3D nuclear volume influences major biological processes but is completely lost during mitosis, which represents a major challenge to maintain cellular identity and cell fate. To restore a functional G1 nucleus for the next cell cycle, it is imperative to reestablish genome organization during post-mitotic nuclear assembly. Importantly, the configuration of linear chromosomes has been shown to directly impact spatial genome architecture. Both centromeres and telomeres are known to associate with nuclear structures, such as the nuclear envelope, and support chromatin distribution. Here, using high-resolution 3D imaging combined with 3D spatial statistics and modeling, we showed that telomeres generally followed a regular distribution compared to what is expected under a random organization. While the preferential localization of telomeres at nuclear periphery was restricted to early G1, we found a strong clustering of centromeres in addition to their predominant peripheral localization at all cell cycle stages. We then conducted a targeted screen using MadID to identify the molecular pathways driving or maintaining telomere anchoring to the nuclear envelope. Among these factors, we could show that LAP2α transiently localizes to telomeres in anaphase, at a stage where LAP2α initiates the reformation of the nuclear envelope. Moreover, co-depletion of LAP proteins and their partner BAF impacted telomere redistribution in the next interphase. There results suggest that in addition to their crucial role in genome protection, telomeres also participate in reshaping functional G1 nuclei after mitosis. (10.1101/2022.12.22.521599)
  DOI : 10.1101/2022.12.22.521599
• Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
  
  • Bhatt Uditi
  • Cucchiarini Anne
  • Luo Yu
  • Evans Cameron
  • Mergny Jean-Louis
  • Iyer K. Swaminathan
  • Smith Nicole
  Genome Research, Cold Spring Harbor Laboratory Press, 2024, pp.gr.278236.123. Secondary structure is a principal determinant of lncRNA function, predominantly regarding scaffold formation and interfaces with target molecules. Noncanonical secondary structures that form in nucleic acids have known roles in regulating gene expression and include G-quadruplexes (G4s), intercalated-motifs (iMs), and R-loops (RLs). In this paper, we utilized computational tools G4-iM Grinder and QmRLFS-finder to predict the formation of each of these structures throughout the lncRNA transcriptome in comparison to protein-coding transcripts. The importance of the predicted structures in lncRNA in biological contexts was assessed by combining our results with publicly available lncRNA tissue expression data followed by pathway analysis. The formation of predicted G4 (pG4) and iM (piM) structures in select lncRNA sequences was determined in vitro using biophysical experiments under near-physiological conditions. We found that the majority of the tested pG4s form highly stable G4 structures and identify many previously unreported G4s in biologically important lncRNAs. In contrast, none of the piM sequences were able to form iM structures, consistent with the idea that RNA is unable to form iMs. These C-rich sequences instead formed Z-RNA structures, which have not been previously observed in regions containing cytosine repeats and represent an interesting and under-explored target for protein-RNA interactions. Our results highlight the prevalence and potential structure-associated functions of noncanonical secondary structures in lncRNA and observe G4 and Z-RNA structure formation in many lncRNA sequences for the first time, furthering understanding of the structure-function relationship in lncRNAs. (10.1101/gr.278236.123)
  DOI : 10.1101/gr.278236.123