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The last 50 bibliographies
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The white gene as a transgenesis marker for the cricket Gryllus bimaculatus
- Journal : G3: Genes, Genomes, Genetics
- 2024
- Abstract The cricket Gryllus bimaculatus is an emerging model insect of the order Orthoptera that is used in a wide variety of biological research themes. This hemimetabolous species appears highly complementary to Drosophila and other well-established holometabolous models. To improve transgenesis applications in G. bimaculatus, we have designed a transformation marker gene inspired from the widespread Drosophila mini-white+. Using CRISPR/Cas9, we first generated a loss-of-function mutant allele of the Gb-white gene (Gb-w), which exhibits a white eye coloration at all developmental stages. We then demonstrate that transgenic insertions of a piggyBac vector containing a 3xP3-Gb-w+ cassette rescue eye pigmentation. As an application, we used this vector to generate G. bimaculatus lines expressing a centromeric histone H3 variant (CenH3.1) fused to EGFP and validated EGFP-CenH3.1 detection at cricket centromeres. Finally, we demonstrate that Minos-based germline transformation and site-specific plasmid insertion with the ΦC31 integrase system function in G. bimaculatus.
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Deciphering Molecular Mechanisms Involved in the Modulation of Human Aquaporins' Water Permeability by Zinc Cations: A Molecular Dynamics Approach.
- Journal : Int J Mol Sci
- 2024
- Aquaporins (AQPs) constitute a wide family of water channels implicated in allkind of physiological processes. Zinc is the second most abundant trace elementin the human body and a few studies have highlighted regulation of AQP0 and AQP4by zinc. In the present work, we addressed the putative regulation of AQPs byzinc cations in silico through molecular dynamics simulations of human AQP0,AQP2, AQP4, and AQP5. Our results align with other scales of study and several invitro techniques, hence strengthening the reliability of this regulation by zinc.We also described two distinct putative molecular mechanisms associated with theincrease or decrease in AQPs' water permeability after zinc binding. Inassociation with other studies, our work will help deciphering the interactionnetworks existing between zinc and channel proteins.
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Retinal atrophy, inflammation, phagocytic and metabolic disruptions develop in the MerTK-cleavage-resistant mouse model.
- Journal : Front Neurosci
- 2024
- In the eye, cells from the retinal pigment epithelium (RPE) facing theneurosensory retina exert several functions that are all crucial for long-termsurvival of photoreceptors (PRs) and vision. Among those, RPE cells phagocytoseunder a circadian rhythm photoreceptor outer segment (POS) tips that areconstantly subjected to light rays and oxidative attacks. The MerTK tyrosinekinase receptor is a key element of this phagocytic machinery required for POSinternalization. Recently, we showed that MerTK is subjected to the cleavage ofits extracellular domain to finely control its function. In addition, monocytesin retinal blood vessels can migrate inside the inner retina and differentiateinto macrophages expressing MerTK, but their role in this context has not beenstudied yet. We thus investigated the ocular phenotype of MerTKcleavage-resistant (MerTK(CR)) mice to understand the relevance of thischaracteristic on retinal homeostasis at the RPE and macrophage levels. MerTK(CR)retinae appear to develop and function normally, as observed in retinal sections,by electroretinogram recordings and optokinetic behavioral tests. Monitoring ofMerTK(CR) and control mice between the ages of 3 and 18 months showed thedevelopment of large degenerative areas in the central retina as early as 4months when followed monthly by optical coherence tomography (OCT) plus fundusphotography (FP)/autofluorescence (AF) detection but not by OCT alone. Thedegenerative areas were associated with AF, which seems to be due to infiltratedmacrophages, as observed by OCT and histology. MerTK(CR) RPE primary culturesphagocytosed less POS in vitro, while in vivo, the circadian rhythm of POSphagocytosis was deregulated. Mitochondrial function and energy production werereduced in freshly dissected RPE/choroid tissues at all ages, thus showing ametabolic impairment not present in macrophages. RPE anomalies were detected byelectron microscopy, including phagosomes retained in the apical area andvacuoles. Altogether, this new mouse model displays a novel phenotype that couldprove useful to understanding the interplay between RPE and PRs in inflammatoryretinal degenerations and highlights new roles for MerTK in the regulation of theenergetic metabolism and the maintenance of the immune privilege in the retina.
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Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition.
- Journal : Nucleic Acids Res
- 2024
- RNA helicases function as versatile enzymes primarily responsible for remodelingRNA secondary structures and organizing ribonucleoprotein complexes. In ourstudy, we conducted a systematic analysis of the helicase-related activities ofEscherichia coli HrpA and presented the structures of both its apo form and itscomplex bound with both conventional and non-canonical DNAs. Our findings revealthat HrpA exhibits NTP hydrolysis activity and binds to ssDNA and ssRNA indistinct sequence-dependent manners. While the helicase core plays an essentialrole in unwinding RNA/RNA and RNA/DNA duplexes, the N-terminal extension in HrpA,consisting of three helices referred to as the APHB domain, is crucial for ssDNAbinding and RNA/DNA duplex unwinding. Importantly, the APHB domain is implicatedin binding to non-canonical DNA structures such as G-quadruplex and i-motif, andthis report presents the first solved i-motif-helicase complex. This research notonly provides comprehensive insights into the multifaceted roles of HrpA as anRNA helicase but also establishes a foundation for further investigations intothe recognition and functional implications of i-motif DNA structures in variousbiological processes.
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The catalytic triad of rice NARROW LEAF1 involves H234.
- Journal : Nat Plants
- 2024
- NARROW LEAF1 (NAL1) exerts a multifaceted influence on leaf morphology and cropyield. Recent crystal study proposed that histidine 233 (H233) is part of thecatalytic triad. Here we report that unlike suggested previously, H234 instead ofH233 is a component of the catalytic triad alongside residues D291 and S385 inNAL1. Remarkably, residue 233 unexpectedly plays a pivotal role in regulatingNAL1's proteolytic activity. These findings establish a strong foundation forutilizing NAL1 in breeding programs aimed at improving crop yield.
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Omecamtiv mecarbil and Mavacamten target the same myosin pocket despite opposite effects in heart contraction.
- Journal : Nat Commun
- 2024
- Inherited cardiomyopathies are common cardiac diseases worldwide, leading in thelate stage to heart failure and death. The most promising treatments againstthese diseases are small molecules directly modulating the force produced byβ-cardiac myosin, the molecular motor driving heart contraction. Omecamtivmecarbil and Mavacamten are two such molecules that completed phase 3 clinicaltrials, and the inhibitor Mavacamten is now approved by the FDA. In contrast toMavacamten, Omecamtiv mecarbil acts as an activator of cardiac contractility.Here, we reveal by X-ray crystallography that both drugs target the same pocketand stabilize a pre-stroke structural state, with only few local differences.All-atom molecular dynamics simulations reveal how these molecules producedistinct effects in motor allostery thus impacting force production in oppositeway. Altogether, our results provide the framework for rational drug developmentfor the purpose of personalized medicine.
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Stimulation of ATP Hydrolysis by ssDNA Provides the Necessary Mechanochemical Energy for G4 Unfolding.
- Journal : J Mol Biol
- 2024
- The G-quadruplex (G4) is a distinct geometric and electrophysical structurecompared to classical double-stranded DNA, and its stability can impede essentialcellular processes such as replication, transcription, and translation. Thisstudy focuses on the BsPif1 helicase, revealing its ability to bind independentlyto both single-stranded DNA (ssDNA) and G4 structures. The unfolding activity ofBsPif1 on G4 relies on the presence of a single tail chain, and the covalentcontinuity between the single tail chain and the G4's main chain is necessary forefficient G4 unwinding. This suggests that ATP hydrolysis-driven ssDNAtranslocation exerts a pull force on G4 unwinding. Molecular dynamics simulationsidentified a specific region within BsPif1 that contains five crucial amino acidsites responsible for G4 binding and unwinding. A "molecular wire stripper" modelis proposed to explain BsPif1's mechanism of G4 unwinding. These findings providea new theoretical foundation for further exploration of the G4 developmentmechanism in Pif1 family helicases.
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Aquaporin Modulation by Cations, a Review.
- Journal : Curr Issues Mol Biol
- 2024
- Aquaporins (AQPs) are transmembrane channels initially discovered for their rolein water flux facilitation through biological membranes. Over the years, a muchmore complex and subtle picture of these channels appeared, highlighting manyother solutes accommodated by AQPs and a dense regulatory network finely tuningcell membranes' water permeability. At the intersection between severaltransduction pathways (e.g., cell volume regulation, calcium signaling, potassiumcycling, etc.), this wide and ancient protein family is considered an importanttherapeutic target for cancer treatment and many other pathophysiologies.However, a precise and isoform-specific modulation of these channels function isstill challenging. Among the modulators of AQPs functions, cations have beenshown to play a significant contribution, starting with mercury beinghistorically associated with the inhibition of AQPs since their discovery. Whilethe comprehension of AQPs modulation by cations has improved, a unifyingmolecular mechanism integrating all current knowledge is still lacking. In aneffort to extract general trends, we reviewed all known modulations of AQPs bycations to capture a first glimpse of this regulatory network. We paid particularattention to the associated molecular mechanisms and pinpointed the residuesinvolved in cation binding and in conformational changes tied up to themodulation of the channel function.
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Plasticity and environment-specific relationships between gene expression and fitness in Saccharomyces cerevisiae.
- Journal : Nat Ecol Evol
- 2024
- The environment influences how an organism's genotype determines its phenotype and how this phenotype affects its fitness. Here, to better understand this dual role of environment in the production and selection of phenotypic variation, we determined genotype-phenotype-fitness relationships for mutant strains of Saccharomyces cerevisiae in four environments. Specifically, we measured how promoter mutations of the metabolic gene TDH3 modified expression level and affected growth for four different carbon sources. In each environment, we observed a clear relationship between TDH3 expression level and fitness, but this relationship differed among environments. Mutations with similar effects on expression in different environments often had different effects on fitness and vice versa. Such environment-specific relationships between phenotype and fitness can shape the evolution of phenotypic plasticity. We also found that mutations disrupting binding sites for transcription factors had more variable effects on expression among environments than those disrupting the TATA box, which is part of the core promoter. However, mutations with the most environmentally variable effects on fitness were located in the TATA box, because of both the lack of plasticity of TATA box mutations and environment-specific fitness functions. This observation suggests that mutations affecting different molecular mechanisms contribute unequally to regulatory sequence evolution in changing environments.
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Condensin loop extrusion properties, roadblocks, and role in homology search in S. cerevisiae
- Journal : BioRxiv
- 2024
- The in vivo mechanism, regulations by cis-acting roadblocks, and biological functions of loop extrusion by eukaryotic SMC complexes are incompletely defined. Here, using Hi-C, we identified two condensin-dependent contact stripes at the Recombination Enhancer (RE) and the rDNA in S. cerevisiae. We show that oriented, unidirectional loop extrusion proceeds from these sites with an estimated processivity ∼170 kb and a density ∼0.04-0.18 that varies across the cell cycle. Centromeres and highly-transcribed RNA PolII-dependent genes are permeable condensin roadblocks. Other positionally labile elements such as replication forks and Smc5/6 complexes bound to substrates generated in the absence of Top2 also hinder loop extrusion by condensin. Cohesin is not an obstacle for condensin. Finally, a DNA double-strand break at MAT blocks condensin, which results in the rapid establishment of a long-range RE-MAT loop that juxtaposes the recombination machinery with its HMLα donor target. Hence, all budding yeast SMCs are involved in recombinational DNA repair. We propose a revised model for donor selection during MAT switching that exploits specific properties of loop extrusion by condensin. It can serve as a paradigm for the establishment of other types of selective interactions along chromosomes.
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ProA and ProB repeat sequences shape genome organization, and enhancers open domains
- Journal : bioRxiv
- 2023
- There is a growing awareness that repeat sequences (RepSeq) - the main constituents of the human genome - are also prime players in its organization. Here we propose that the genome should be envisioned as a supersystem with three main subsystems, each composed of functionally redundant, cooperating elements. We define herein ProA and ProB RepSeqs as sequences that promote either the A/euchromatin or the B/heterochromatin compartment. ProA and ProB RepSeqs shape A/B partitioning, such that the relative proportions of ProA and ProB RepSeqs determine the propensity of a chromosome segment to adopt either an A or a B configuration. In human, core ProA RepSeqs are essentially made of Alu elements, whereas core ProB RepSeqs consist of young L1 and some Endogenous Retroviruses (ERVs) as well as a panel of AT-rich microsatellites and pericentromeric and telomeric satellites. Additionally, RepSeqs with more indefinite character and, importantly, their derivatives known as “transcriptional enhancers”, can shift between ProA and ProB functions and thus act to open or close specific chromatin domains depending on the cellular context. In this framework, genes and their promoters appear as a special class of RepSeqs that, in their active, transcribed state, reinforce the openness of their surroundings. Molecular mechanisms involve cooperativity between ProB elements, presumably underpinned by the condensate-like properties of heterochromatin, which ProA elements oppose in several ways. We provide strong arguments that altered CpG methylation patterns in cancer including a marked loss in the B compartment, result primarily from a global imbalance in the process of CpG methylation and its erasure. Our results suggest that the resulting altered methylation and impaired function of ProB RepSeqs globally weaken the B compartment, rendering it more plastic, which in turn may confer fate plasticity to the cancer cell.Competing Interest StatementThe authors have declared no competing interest.
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Space-Scale Hybrid Continuous-Discrete Sliding Frank-Wolfe Method
- Journal : IEEE Signal Processing Letters
- 2024
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Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization.
- Journal : Nat Commun
- 2024
- Although our understanding of the involvement of heterochromatin architecturalfactors in shaping nuclear organization is improving, there is still ongoingdebate regarding the role of active genes in this process. In this study, weutilize publicly-available Micro-C data from mouse embryonic stem cells toinvestigate the relationship between gene transcription and 3D gene folding. Ouranalysis uncovers a nonmonotonic - globally positive - correlation betweenintragenic contact density and Pol II occupancy, independent of cohesin-basedloop extrusion. Through the development of a biophysical model integrating therole of transcription dynamics within a polymer model of chromosome organization,we demonstrate that Pol II-mediated attractive interactions with limited valencybetween transcribed regions yield quantitative predictions consistent withchromosome-conformation-capture and live-imaging experiments. Our work providescompelling evidence that transcriptional activity shapes the 4D genome throughPol II-mediated micro-compartmentalization.
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Mechanism of homology search expansion during recombinational DNA break repair in Saccharomyces cerevisiae.
- Journal : Mol Cell
- 2024
- Homology search is a central step of DNA double-strand break (DSB) repair byhomologous recombination (HR). How it operates in cells remains elusive. Wedeveloped a Hi-C-based methodology to map single-stranded DNA (ssDNA) contactsgenome-wide in S. cerevisiae, which revealed two main homology search phases.Initial search conducted by short Rad51-ssDNA nucleoprotein filaments (NPFs) isconfined in cis by cohesin-mediated chromatin loop folding. Progressive growth ofstiff NPFs enables exploration of distant genomic sites. Long-range resectiondrives this transition from local to genome-wide search by increasing theprobability of assembling extensive NPFs. DSB end-tethering promotes coordinatedsearch by opposite NPFs. Finally, an autonomous genetic element on chromosome IIIengages the NPF, which stimulates homology search in its vicinity. This workreveals the mechanism of the progressive expansion of homology search thatis orchestrated by chromatin organizers, long-range resection,end-tethering, and specialized genetic elements and that exploits the stiff NPFstructure conferred by Rad51 oligomerization.
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A new type of non-Mendelian segregation.
- Journal : Nat Ecol Evol
- 2024
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Mechanism of homology search expansion during recombinational DNA break repair in Saccharomyces cerevisiae
- Journal : Molecular Cell
- 2024
- Homology search is a central step of DNA double-strand break (DSB) repair by homologous recombination (HR). How it operates in cells remains elusive. We developed a Hi-C-based methodology to map single-stranded DNA (ssDNA) contacts genome-wide in S. cerevisiae, which revealed two main homology search phases. Initial search conducted by short Rad51-ssDNA nucleoprotein filaments (NPFs) is confined in cis by cohesin-mediated chromatin loop folding. Progressive growth of stiff NPFs enables exploration of distant genomic sites. Long-range resection drives this transition from local to genome-wide search by increasing the probability of assembling extensive NPFs. DSB end-tethering promotes coordinated search by opposite NPFs. Finally, an autonomous genetic element on chromosome III engages the NPF, which stimulates homology search in its vicinity. This work reveals the mechanism of the progressive expansion of homology search that is orchestrated by chromatin organizers, long-range resection, end-tethering, and specialized genetic elements and that exploits the stiff NPF structure conferred by Rad51 oligomerization.
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The C. elegans SET1 histone methyltransferase SET-2 is not required for transgenerational memory of silencing.
- Journal : MicroPubl Biol
- 2024
- The SET-2 /SET1 histone H3K4 methyltransferase and RNAi pathway components arerequired to maintain fertility across generations in C. elegans . SET-2 preservesthe germline transcriptional program transgenerationally, and RNAi pathways relyon small RNAs to establish and maintain transgenerational gene silencing. Weinvestigated whether the functionality of RNAi-induced transgenerationalsilencing and the composition of pools of endogenous small RNA are affected bythe absence of SET-2 . Our results suggest that defects in RNAi pathways are notresponsible for the transcriptional misregulation observed in the absence ofSET-2 .
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Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation
- Journal : Biophysical Journal
- 2023
- The RNA-binding protein TDP-43 is associated with mRNA processing and transport from the nucleus to the cytoplasm. TDP-43 localizes in the nucleus as well as accumulating in cytoplasmic condensates such as stress granules. Aggregation and formation of amyloid-like fibrils of cytoplasmic TDP-43 are hallmarks of numerous neurodegenerative diseases, most strikingly present in >90% of amyotrophic lateral sclerosis (ALS) patients. If excessive accumulation of cytoplasmic TDP-43 causes, or is caused by, neurodegeneration is presently not known. In this work, we use molecular dynamics simulations at multiple resolutions to explore TDP-43 self- and cross-interaction dynamics. A full-length molecular model of TDP-43, all 414 amino acids, was constructed from select structures of the protein functional domains (N-terminal domain, and two RNA recognition motifs, RRM1 and RRM2) and modeling of disordered connecting loops and the low complexity glycine-rich C-terminus domain. All-atom CHARMM36m simulations of single TDP-43 proteins served as guides to construct a coarse-grained Martini 3 model of TDP-43. The Martini model and a coarser implicit solvent C⍺ model, optimized for disordered proteins, were subsequently used to probe TDP-43 interactions; self-interactions from single-chain full-length TDP-43 simulations, cross-interactions from simulations with two proteins and simulations with assemblies of dozens to hundreds of proteins. Our findings illustrate the utility of different modeling scales for accessing TDP-43 molecular-level interactions and suggest that TDP-43 has numerous interaction preferences or patterns, exhibiting an overall strong, but dynamic, association and driving the formation of biomolecular condensates.
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AlphaFold2 Predicts Whether Proteins Interact Amidst Confounding Structural Compatibility
- Journal : Journal of Chemical Information and Modeling
- 2024
- Predicting whether two proteins physically interact is one of the holy grails of computational biology, galvanized by rapid advancements in deep learning. AlphaFold2, although not developed with this goal, is promising in this respect. Here, I test the prediction capability of AlphaFold2 on a very challenging data set, where proteins are structurally compatible, even when they do not interact. AlphaFold2 achieves high discrimination between interacting and non-interacting proteins, and the cases of misclassifications can either be rescued by revisiting the input sequences or can suggest false positives and negatives in the data set. AlphaFold2 is thus not impaired by the compatibility between protein structures and has the potential to be applied on a large scale.
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Dynamics of Protein–RNA Interfaces Using All-Atom Molecular Dynamics Simulations
- Journal : The Journal of Physical Chemistry B
- 2024
- Facing the current challenges posed by human health diseases requires the understanding of cell machinery at a molecular level. The interplay between proteins and RNA is key for any physiological phenomenon, as well protein–RNA interactions. To understand these interactions, many experimental techniques have been developed, spanning a very wide range of spatial and temporal resolutions. In particular, the knowledge of tridimensional structures of protein–RNA complexes provides structural, mechanical, and dynamical pieces of information essential to understand their functions. To get insights into the dynamics of protein–RNA complexes, we carried out all-atom molecular dynamics simulations in explicit solvent on nine different protein–RNA complexes with different functions and interface size by taking into account the bound and unbound forms. First, we characterized structural changes upon binding and, for the RNA part, the change in the puckering. Second, we extensively analyzed the interfaces, their dynamics and structural properties, and the structural waters involved in the binding, as well as the contacts mediated by them. Based on our analysis, the interfaces rearranged during the simulation time showing alternative and stable residue–residue contacts with respect to the experimental structure.
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