Browse Articles
Discover research articles across all indexed journals
State-dependent motion of a genetically encoded fluorescent biosensor
Genetically encoded biosensors can measure biochemical properties such as small-molecule concentrations with single-cell resolution, even in vivo. Despite their utility, these sensors are “black boxes”: Very little is known about the structures of their low- and high-fluorescence states or what features are required to transition between them. We used LiLac, a lactate biosensor with a quantitative fluorescence-lifetime readout, as a model system to address these questions. X-ray crystal structures and engineered high-affinity metal bridges demonstrate that LiLac exhibits a large interdomain twist motion that pulls the fluorescent protein away from a “sealed,” high-lifetime state in the absence of lactate to a “cracked,” low-lifetime state in its presence. Understanding the structures and dynamics of LiLac will help to think about and engineer other fluorescent biosensors.
<i>Dux</i> cluster duplication ensures full activation of totipotent genes
Zygotic genome activation (ZGA) confers to the mouse two-cell (2C) embryo a unique transcriptional profile characterized by transient up-regulation of many totipotency-related genes and MERVL retrotransposons. Intriguingly, those genes are duplicated and clustered in the genome during evolution, including Dux cluster, Obox, and Zscan4 family members in mice. However, the contribution and biological significance of the totipotency-related gene duplication events in early embryo development remain poorly understood. Here, we focus on Dux cluster, the master regulator of ZGA that is necessary and sufficient for the induction of 2C-like cells and activation of totipotency-related genes in mouse embryonic stem cells (mESCs). By reducing Dux gene copies from 31 to 0 or 1 through CRISPR-Cas9 technology, we generate Dux -KO and Dux (n = 1) mESC lines, respectively. We uncover that the totipotency-related gene transcriptional profile is awakened to a much lesser extent in Dux (n = 1) mESCs compared to wild type mESCs following global DNA demethylation reprogramming or induction of DNA damage, mimicking the intrinsic events in preimplantation development. Together, Dux cluster duplication is critically required for full activation of ZGA transcripts.
Systematic identification of allosteric effectors in <i>Escherichia coli</i> metabolism
Recent physical binding screens suggest that protein–metabolite interactions are more extensive than previously recognized. To elucidate the functional relevance of these interactions, we developed a mass spectrometry–based screening method for higher throughput in vitro enzyme assays. By systematically quantifying the effects of 79 metabolites on the activity of 20 central Escherichia coli enzymes, we not only assess functional relevance but also gauge the depth of the current understanding of regulatory interactions within one of the best-characterized networks. Our identification of 50 inhibitors and 14 activators not only expands the range of known input signals but also uncovers novel regulatory logic. For instance, we observed that AMP inhibits malic enzyme to safeguard the cyclic operation of the tricarboxylic acid cycle, and erythrose-4-phosphate inhibits 6-phosphogluconate dehydrogenase to redirect flux from the pentose phosphate pathway into the Entner–Doudoroff pathway. Discrepancies between our standardized assays and existing database entries suggest that many previously reported interactions might occur only under specific, often nonphysiological conditions. Our dataset represents a systematically determined functional protein–metabolite interaction network, establishing a baseline for allosteric regulation in central metabolism. These results enhance our understanding of the regulatory logic governing metabolic processes and underscore its significance in cellular adaptation and growth.
Molecular mechanism of Arp2/3 complex activation by nucleation-promoting factors and an actin monomer
Arp (actin-related protein) 2/3 complex nucleates actin filament branches on the sides of preexisting actin filaments during cell and organelle movements. We used computer simulations of mammalian Arp2/3 complex to address fundamental questions about the mechanism. Metadynamics and umbrella free energy sampling simulations of the pathway revealed that a clash between the D-loop of Arp2 and Arp3 produces an energy barrier of 20 ± 6 kcal/mol between the inactive splayed and active short-pitch conformations of Arp2/3 complex. Atomistic molecular dynamics simulations showed that binding the CA motif of the nucleation-promoting factor Neuronal Wiskott-Aldrich Syndrome Protein (N-WASp) to inactive, splayed Arp2/3 complex shifts it toward the short-pitch active conformation and opens a binding site for an actin monomer on Arp3. Other simulations showed that this actin monomer stabilizes a transition state of Arp2/3 complex. These observations together with prior experimental work provide insights required to propose a physically grounded pathway for actin filament branch formation.
Evidence for a possible quantum effect on the formation of lithium-doped amorphous calcium phosphate from solution
Differential isotope effects are an emerging tool for discovering possible nontrivial quantum mechanical effects within biological systems. However, it is often nearly impossible to elucidate the exact mechanisms by which a biological isotope effect manifests due to the complexity of these systems. As such, one proposed in vitro system of study for a quantum isotope effect is calcium phosphate aggregation, where symmetric calcium phosphate molecular species, known as Posner molecules, have been theorized to have phosphorus nuclear spin–dependent self-binding rates, which could be differently modulated by doping with stable lithium isotopes. Here, we present in vitro evidence for such a differential lithium isotope effect on the formation and aggregation of amorphous calcium phosphate from solution under certain conditions. Experiments confirm that lithium incorporates into amorphous calcium phosphate, with 7 Li found to promote a greater abundance of observable calcium phosphate particles than 6 Li under identical solution preparations. These in vitro results offer a potential explanation for in vivo biological studies that have shown differential lithium isotope effects. Given the importance of calcium phosphate in biological systems—ranging from mitochondrial signaling pathways to key biomineralization processes, as well as the proposed role of Posner molecules as a “neural qutrit”—these results present an important step in understanding calcium phosphate nucleation as well as the potential role of calcium phosphate for quantum biology and processing.
Characterizing sliding and rolling contacts between single particles
Contacts between particles in dense, sheared suspensions are believed to underpin much of their rheology. Roughness and adhesion are known to constrain the relative motion of particles, and thus globally affect the shear response, but an experimental description of how they microscopically influence the transmission of forces and relative displacements within contacts is lacking. Here, we show that an innovative colloidal-probe atomic force microscopy technique allows the simultaneous measurement of normal and tangential forces exchanged between tailored surfaces and microparticles while tracking their relative sliding and rolling, unlocking the direct measurement of coefficients of rolling friction, as well as of sliding friction. We demonstrate that, in the presence of sufficient traction, particles spontaneously roll, reducing dissipation and promoting longer-lasting contacts. Conversely, when rolling is prevented, friction is greatly enhanced for rough and adhesive surfaces, while smooth particles coated by polymer brushes maintain well-lubricated contacts. We find that surface roughness induces rolling due to load-dependent asperity interlocking, leading to large off-axis particle rotations. In contrast, smooth, adhesive surfaces promote rolling along the principal axis of motion. Our results offer direct values of friction coefficients for numerical studies and an interpretation of the onset of discontinuous shear thickening based on them, opening up ways to tailor rheology via contact engineering.
Structural basis for dimerization and activation of UvrD-family helicases
UvrD-family helicases are superfamily 1A motor proteins that function during DNA replication, recombination, repair, and transcription. UvrD family monomers translocate along single-stranded (ss) DNA but need to be activated by dimerization to unwind DNA in the absence of force or accessory factors. However, prior structural studies have only revealed monomeric complexes. Here, we report the first structures of a dimeric UvrD-family helicase, Mycobacterium tuberculosis UvrD1, both free and bound to a DNA junction. In each structure, the dimer interface occurs between the 2B subdomains of each subunit. The apo UvrD1 dimer is observed in symmetric compact and extended forms indicating substantial flexibility. This symmetry is broken in the DNA-bound dimer complex with leading and trailing subunits adopting distinct conformations. Biochemical experiments reveal that the Escherichia coli UvrD dimer shares the same 2B–2B interface. In contrast to the dimeric structures, an inactive, autoinhibited UvrD1 DNA-bound monomer structure reveals 2B subdomain–DNA contacts that are likely inhibitory. The major reorientation of the 2B subdomains that occurs upon UvrD1 dimerization prevents these duplex DNA interactions, thus relieving the autoinhibition. These structures reveal that the 2B subdomain serves a major regulatory role rather than participating directly in DNA unwinding.
Broken time-reversal symmetry in visual motion detection
Our intuition suggests that when a movie is played in reverse, our perception of motion at each location in the reversed movie will be perfectly inverted compared to the original. This intuition is also reflected in classical theoretical and practical models of motion estimation, in which velocity flow fields invert when inputs are reversed in time. However, here we report that this symmetry of motion perception upon time reversal is broken in real visual systems. We designed a set of visual stimuli to investigate time reversal symmetry breaking in the fruit fly Drosophila ’s well-studied optomotor rotation behavior. We identified a suite of stimuli with a wide variety of properties that can uncover broken time reversal symmetry in fly behavioral responses. We then trained neural network models to predict the velocity of scenes with both natural and artificial contrast distributions. Training with naturalistic contrast distributions yielded models that broke time reversal symmetry, even when the training data themselves were time reversal symmetric. We show analytically and numerically that the breaking of time reversal symmetry in the model responses can arise from contrast asymmetry in the training data, but can also arise from other features of the contrast distribution. Furthermore, shallower neural network models can exhibit stronger symmetry breaking than deeper ones, suggesting that less flexible neural networks may be more prone to time reversal symmetry breaking. Overall, these results reveal a surprising feature of biological motion detectors and suggest that it could arise from constrained optimization in natural environments.
Cryo-EM meets crystallography: A model-independent view of the heteronuclear Mn <sub>4</sub> Ca cluster structure of photosystem II
Photosynthesis converts solar energy to chemical energy by splitting water molecules and carbon dioxide to produce oxygen and carbohydrates with an efficiency that engineers working on solar energy device can only dream of. Photosystem II (PSII) is the enzyme that catalyzes the light-driven oxidation of water that occurs during photosynthesis. This oxygen-producing reaction occurs in the Mn 4 Ca cluster found inside the enzyme’s oxygen-evolving center (OEC). Even though the structure and mechanism of action of the OEC have been intensively investigated for many decades, questions still remain about both. The Mn 4 Ca cluster stores the high-energy oxidizing equivalents required for water oxidation so that its own oxidation state depends on its chemical composition, i.e., the number of its oxygen ligands. The issue addressed here is the number of oxygen ligands associated with the Mn 4 Ca cluster after PSII has been exposed to two of the four flashes of light necessary for it to produce an oxygen molecule, PSII 2F. Comparisons of recently published cryo-EM maps and crystallographic OEC-omit maps described here reveal the OEC structure of PSII 2F contains only five internal oxygen ligands, and that the sixth O ligand identified earlier in PSII 2F crystal structures is an artifact caused by model bias. This finding should have a significant impact on our understanding of the mechanism of water oxidation that is catalyzed by PSII because it is incompatible with prevailing high valence paradigm (HVP) models for this process.
Allosteric inhibition of the IZUMO1–JUNO fertilization complex by the naturally occurring antisperm antibody OBF13
Sperm IZUMO1 binds to egg JUNO, and this interaction is essential for mammalian fertilization. Isolated from a female mouse immunized with syngeneic sperm, the antisperm antibody OBF13 recognizes IZUMO1 and inhibits murine fertilization. How OBF13 interferes with sperm–egg interactions was unknown. Here, we present the X-ray crystal structure of IZUMO1 in complex with OBF13. OBF13 binds to the apex of the four-helix domain of IZUMO1, distant from the JUNO-binding site. Our crystal structure of OBF13-bound IZUMO1 resembles apo-IZUMO1 and differs from the structure of IZUMO1 in complex with JUNO. We identify that OBF13 carries a low level of somatic hypermutation, and through deep mutational scanning, we engineer an affinity-enhanced OBF13 variant. This OBF13 variant single-chain fragment variable decreases the apparent affinity of IZUMO1 for membrane-bound murine JUNO and blocks the binding of acrosome-reacted sperm to eggs, thereby preventing fertilization. We propose allostery between the OBF13 epitope and the JUNO-binding site. OBF13 inhibits a conformational change in IZUMO1, preventing fusion-competent sperm from adhering to murine eggs during fertilization. Surprisingly, murine IZUMO1 binds to hamster JUNO with an affinity ~20-fold higher than to murine JUNO. The decreased affinity caused by OBF13 of murine IZUMO1 for hamster JUNO is sufficient for murine sperm to bind to and fuse with hamster eggs. Our studies provide a structural and mechanistic framework for species-specific, allosteric inhibition of IZUMO1 by a naturally occurring antisperm antibody and offer insights into the development of immunocontraceptives.
A WRKY transcription factor confers broad-spectrum resistance to biotic stresses and yield stability in rice
Plants are subject to attack by diverse pests and pathogens. Few genes conferring broad-spectrum resistance to both insects and pathogens have been identified. Because of the growth–defense tradeoff, it is often challenging to balance biotic stress resistance and yield for crops. Here, we report that OsWRKY36 suppresses the resistance to insects and pathogens via transcriptional repression of Phenylalanine Ammonia Lyases ( PALs ), a key enzyme in phenylpropanoid pathway in rice. Knocking out OsWRKY36 causes elevated lignin biosynthesis and increased sclerenchyma thickness of leaf sheath, leading to enhanced resistance to multiple pests and pathogens. Additionally, loss of OsWRKY36 also derepresses the transcription of Ideal Plant Architecture 1 ( IPA1 ) and MONOCULM2 ( MOC2 ), resulting in increased spikelet number per panicle and tiller number. These findings provide mechanistic insights into biotic stress tolerance in rice and offer a promising strategy to breed rice cultivars with broad-spectrum resistance to insects and pathogens while maintaining stable yield.
BIN1 reduction ameliorates <i>DNM2</i> -related Charcot–Marie–Tooth neuropathy
Charcot–Marie–Tooth (CMT) disease, the most common inherited neuromuscular disorder, manifests as progressive muscle weakness and peripheral nerve defects. Dominant mutations in DNM2 , encoding the large GTPase dynamin 2, result in CMT without any suggested therapeutic strategy. Different dominant mutations in DNM2 also cause centronuclear myopathy (CNM), and increasing BIN1 (amphiphysin 2), an endogenous modulator of DNM2, rescued CNM in mice. Here, we found that increasing BIN1 level exacerbated the phenotypes of the Dnm2 K562E/+ mouse carrying the most common DNM2 -CMT mutation. Conversely, whole-body reduction of Bin1 expression level, through the generation of Dnm2 K562E/+ mice with heterozygous loss of BIN1, restored motor performance and ameliorated muscle organization and structural defects of peripheral nerves. The rescue of motor defects was maintained at least up to 1 y of age. BIN1 inhibited the GTPase activity of DNM2, and the rescue was driven by an increased activity of the K562E DNM2 -CMT mutant, and a normalization of integrin localization in muscle. Overall, this study highlights BIN1 as a modifier of DNM2 -CMT, and its reduction as a potential therapeutic strategy. It also revealed an opposite pathological mechanism and inverse therapeutic concepts for DNM2 -CMT peripheral neuropathy versus DNM2 -CNM myopathy.
Adeno-associated viruses for efficient gene expression in the axolotl nervous system
Axolotls are amphibian models for studying nervous system evolution, development, and regeneration. Tools to visualize and manipulate cells of the axolotl nervous system with high-efficiency, spatial and temporal precision are therefore greatly required. Recombinant adeno-associated viruses (AAVs) are frequently used for in vivo gene transfer of the nervous system but virus-mediated gene delivery to the axolotl nervous system has not yet been described. Here, we demonstrate the use of AAVs for efficient gene transfer within the axolotl brain, the spinal cord, and the retina. We show that serotypes AAV8, AAV9, and AAVPHP.eB are suitable viral vectors to infect both excitatory and inhibitory neuronal populations of the axolotl brain. We further use AAV9 to trace retrograde and anterograde projections between the retina and the brain and identify a cell population projecting from the brain to the retina. Together, our work establishes AAVs as a powerful tool to interrogate neuronal organization in the axolotl.
HCV NS3/4A protease relocalizes CCTα to viral replication sites, enhancing phosphatidylcholine synthesis and viral replication
Positive-sense single-stranded RNA [(+)RNA] viruses constitute more than one-third of all virus genera, including numerous pathogens of clinical significance. All (+)RNA viruses reorganize cellular membranes from organelles to establish replication compartments (RCs). These RCs are thought to form a platform for membrane-associated replicases, in addition to protecting the viral RNAs from cytosolic innate immune signaling and RNA-degradation machinery. Previous work demonstrated that three families of (+)RNA viruses, namely Bromoviridae , Picornaviridae , and Flaviviridae , commonly induce the accumulation of phosphatidylcholine (PC) at their RCs. This phenomenon suggests a potential avenue for a broad-spectrum antiviral strategy targeting PC metabolism. Our study elucidates three key observations: i) hepatitis C virus (HCV) infection prompts the relocalization of CCTα, the rate-limiting enzyme in PC synthesis, to the RCs; ii) the enhancement of PC synthesis is contingent upon the protease activity of the NS3/4A protein; and iii) utilizing click chemistry, we demonstrate that HCV infection stimulates de novo PC synthesis at the viral replication site through the Kennedy pathway. These findings provide significant insights into the manipulation of lipid metabolism by HCV during RC formation, a mechanism likely conserved across various (+)RNA virus families.
Monitoring chalcogenide ions–guided in situ transform active sites of tailored bismuth electrocatalysts for CO <sub>2</sub> reduction to formate
Although bismuth catalysts enable accelerated electrochemical CO 2 -to-formate conversion, the intrinsic active sites and forming mechanisms under operating conditions remain elusive. Herein, we prepared Bi 2 O 2 NCN, Bi 2 O 3 , and Bi 2 O 2 S as precatalysts. Among them, Bi 2 O 2 NCN-derived catalyst possesses optimum performance of electrochemical CO 2 -to-formate, exhibiting an upsurge of Faradaic efficiency to 98.3% at –0.6 V vs. reversible hydrogen electrodes. In-situ infrared and electrochemical impedance spectra trace and interpret the superior performance. Multimodal structural analyses utilizing quasi-in-situ X-ray diffraction, in-situ X-ray absorption near edge structure and in-situ Raman spectra provide powerful support to monitoring the catalysts’ in-situ transforms to metallic Bi, identifying the formation of the active sites influenced by the chalcogenide ions-guided: Carbodiimide promotes to form of the dominant Bi(003) facet exposure, which distinguishes from sulfide- and oxide-preferred dominant Bi(012) facets exposure. Concurrently, theoretical insights garnered from multiscale/multilevel computational analyses harmoniously corroborate the experimental findings. These findings show the pivotal role of chalcogenide in tailoring bismuth electrocatalysts for selective CO 2 reduction to formate, illuminating the significance of controlling structural chemistry in designing catalysts toward high-efficiency renewable energy conversion.
Core dimensions of human material perception
Visually categorizing and comparing materials is crucial for everyday behavior, but what organizational principles underlie our mental representation of materials? Here, we used a large-scale data-driven approach to uncover core latent dimensions of material representations from behavior. First, we created an image dataset of 200 systematically sampled materials and 600 photographs (STUFF dataset, https://osf.io/myutc/ ). Using these images, we next collected 1.87 million triplet similarity judgments and used a computational model to derive a set of sparse, positive dimensions underlying these judgments. The resulting multidimensional embedding space predicted independent material similarity judgments and the similarity matrix of all images close to the human intersubject consistency. We found that representations of individual images were captured by a combination of 36 material dimensions that were highly reproducible and interpretable, comprising perceptual (e.g., grainy, blue) as well as conceptual (e.g., mineral, viscous) dimensions. These results provide the foundation for a comprehensive understanding of how humans make sense of materials.
Phase transitions in the rolling of irregular cylinders and spheres
When placed on an inclined plane, a perfect 2D disk or 3D sphere simply rolls down in a straight line under gravity. But how is the rolling affected if these shapes are irregular or random? Treating the terminal rolling speed as an order parameter, we show that there are qualitative transitions in the speed as a function of the dimension of the state space and inertia. We calculate the scaling exponents and the macroscopic lag time associated with the presence of first- and second-order transitions and describe the regimes of coexistence of stable states and the accompanying hysteresis. Experiments with rolling cylinders corroborate our theoretical results on the scaling of the lag time. Experiments with spheres reveal closed orbits and their period-doubling in the overdamped and inertial limits, respectively, providing visible manifestations of the hairy ball theorem and the doubly connected nature of S O ( 3 ) , the space of 3D rotations. Going beyond simple curiosity, our study might shed light on a number of natural and artificial systems that involve the rolling of irregular objects, ranging from nanoscale cellular transport to robotics.
Phased ERK responsiveness and developmental robustness regulate teleost skin morphogenesis
Elongation of the vertebrate embryonic axis necessitates rapid expansion of the epidermis to accommodate the growth of underlying tissues. Here, we generated a toolkit to visualize and quantify signaling in entire cell populations of the periderm, the outermost layer of the epidermis, in live developing zebrafish. We find that oriented cell divisions facilitate growth of the early periderm during axial elongation rather than cell addition from the basal layer. Activity levels of Extracellular signal-regulated kinase (ERK), a downstream effector of the MAPK pathway, gauged by a live biosensor, predict cell cycle entry, and optogenetic ERK activation regulates cell cycling dynamics. As development proceeds, rates of peridermal cell proliferation decrease, and ERK activity becomes more pulsatile and functionally transitions to promote hypertrophic cell growth. Targeted genetic blockade of cell division generates animals with oversized periderm cells, yet, unexpectedly, development to adulthood is not impaired. Our findings reveal stage-dependent differential responsiveness to ERK signaling and marked developmental robustness in growing teleost skin.
Nanoscale distribution of bioactive ligands on biomaterials regulates cell mechanosensing through translocation of actin into the nucleus
Cells respond to adhesive ligands such as arginine-glycine-aspartate (RGD) through integrins, which regulates cellular activities via influencing cytoskeleton assembly. Herein, we report that the nanoscale distribution of active ligands on biomaterials regulates cells through not only cytoplasmic tension but also nuclear tension. This is particularly related to translocation of actin into nucleus and highlighted in our interpretation of an “abnormal” phenomenon that large RGD nanospacing (>70 nm) disassembles integrin clusters, inhibits cell adhesion, but promotes osteogenic differentiation of mesenchymal stem cells. Our studies reveal that the unstable adhesion at the 150 nm RGD distance increases actin dynamics, resulting in the nuclear translocation of globular (G) actin. The compartment polymerization of more G-actins to filamentous actins in nucleus increases nuclear tension, facilitating transcription activity and releasing calcium ions from the endoplasmic reticulum. This noncanonical mechanotransduction process sheds insight into mechanotransduction pertinent to cell–material interactions.
A general framework for interpretable neural learning based on local information-theoretic goal functions
Despite the impressive performance of biological and artificial networks, an intuitive understanding of how their local learning dynamics contribute to network-level task solutions remains a challenge to this date. Efforts to bring learning to a more local scale indeed lead to valuable insights, however, a general constructive approach to describe local learning goals that is both interpretable and adaptable across diverse tasks is still missing. We have previously formulated a local information processing goal that is highly adaptable and interpretable for a model neuron with compartmental structure. Building on recent advances in Partial Information Decomposition (PID), we here derive a corresponding parametric local learning rule, which allows us to introduce “infomorphic” neural networks. We demonstrate the versatility of these networks to perform tasks from supervised, unsupervised, and memory learning. By leveraging the interpretable nature of the PID framework, infomorphic networks represent a valuable tool to advance our understanding of the intricate structure of local learning.