Sphingosine-1-phosphate (S1P), a key metabolite of sphingolipids, plays crucial roles in a wide range of physiological and pathological processes. S1P primarily exerts its functions by binding to G protein-coupled sphing...Sphingosine-1-phosphate (S1P), a key metabolite of sphingolipids, plays crucial roles in a wide range of physiological and pathological processes. S1P primarily exerts its functions by binding to G protein-coupled sphingosine-1-phosphate receptors (S1PRs), which comprise five subtypes (S1PR1-5) in humans, thereby activating these receptors and their downstream signaling pathways. Understanding the molecular determinants that govern agonist selectivity among different S1PR subtypes is vital for the rational and precise development of targeted therapeutic agents. Here, four cryo-electron microscopy structures of agonist-bound S1PR1-Gi1 complexes are reported. Through an integrated approach combining structural analysis, molecular dynamics simulations, and pharmacological assays, the molecular basis for the selectivity of CYM5442, HY-X-1011, Ponesimod, and SAR247799 toward S1PR1 over S1PR2-S1PR5 is uncovered. Nonconserved residues within the ligand-binding pocket and at the Gi1-protein interface contribute to S1PR1 selectivity by these agonists. A distinct agonist binding orientation toward transmembrane helices 5-7, combined with branched substituents that increase the agonist's molecular width, results in steric clashes with residues in S1PR3. Additionally, branched moieties located at the tail portions of the agonist restrict its deep insertion into the binding pocket of both S1PR3 and S1PR5. These structural features collectively enhance its selectivity for S1PR1 over S1PR3 and S1PR5. Furthermore, polar interactions with conserved polar residues in the top region of the binding pocket also influence agonist selectivity. Besides, the relatively broad molecular width of the agonist sterically hinders its binding into S1PR2 and S1PR4 pocket by nonconserved residue pairs bearing bulky side chains. These findings establish a structural framework for the rational design of next-generation S1PR1 highly selective agonists with improved therapeutic potential.
How animals allocate resources between growth, maintenance, and reproduction is a fundamental question. In this issue of PLOS Biology, Pradhan and colleagues show that maternal nutrient sensing regulates ribosome deposit...How animals allocate resources between growth, maintenance, and reproduction is a fundamental question. In this issue of PLOS Biology, Pradhan and colleagues show that maternal nutrient sensing regulates ribosome deposition into embryos, shaping the early growth dynamics in the next generation.
Cells adjust their proteome to their environment. Most prominently, ribosome expression often scales near linearly with the cellular growth rate to provide sufficient translational capacity while preventing metabolically...Cells adjust their proteome to their environment. Most prominently, ribosome expression often scales near linearly with the cellular growth rate to provide sufficient translational capacity while preventing metabolically wasteful ribosomal excess. In microbes, such proteome adjustments can passively perpetuate through symmetric cell division. However, in animals, a passive propagation is hindered by the separation between soma and germline. This separation raises the question whether the proteome of animals is reset at every generation or can be propagated from parent to offspring across this barrier. We addressed this question for the intergenerational effects of dietary restriction in Caenorhabditis elegans, combining proteomics and live imaging. Under ad libitum feeding, the offspring of dietarily restricted mothers grew more slowly than progeny of well-fed mothers. However, this growth disparity was attenuated when mTORC1 signaling in the progeny was inhibited, creating conditions in which the protein-synthesis capacity at hatching is less limiting. Maternal inhibition of mTORC1 signaling, either ubiquitously or specifically in the pharynx, similarly reduced growth and ribosomal protein levels in offspring, whereas other growth-reducing perturbations, such as reduced insulin signaling or mTORC1 inhibition in the epidermis, did not reduce progeny ribosomal protein levels. We conclude that maternal physiology shapes ribosomal protein provisioning across the soma-germline boundary, thereby modulating early offspring growth in accordance with post-hatching ribosome demand.
Cyclic-di-GMP (c-di-GMP) is a ubiquitous second messenger in bacteria and regulates a variety of cell activities. Many bacteria contain multiple enzymes involved in c-di-GMP synthesis or degradation; however, how they co...Cyclic-di-GMP (c-di-GMP) is a ubiquitous second messenger in bacteria and regulates a variety of cell activities. Many bacteria contain multiple enzymes involved in c-di-GMP synthesis or degradation; however, how they coordinate with each other to orchestrate c-di-GMP homeostasis remains unclear. Here, using the cyanobacterium Anabaena PCC 7120 as a model, we created cdG0 and cdGmax strains by deleting all 8 and 14 genes, respectively, that encode enzymes with c-di-GMP degradation and synthesis domains, alongside a collection of mutants with various numbers of these genes deleted. Our findings demonstrate that c-di-GMP in Anabaena not only modulates cell size but is also indispensable for cell viability. Quantitative analysis established two critical physiological thresholds in vivo: a minimal c-di-GMP level required for cell size maintenance and a lower, lethal threshold essential for survival. We show that the 16 enzymes involved in c-di-GMP turnover in Anabaena function as an electromechanical-like dual relay to control c-di-GMP dynamics, with different modules contributing to c-di-GMP homeostasis or responding as an SOS alarm when the c-di-GMP concentration drops below the lethal threshold. Both effects of c-di-GMP on cell size reduction and cell viability are mediated by the cyclic-di-GMP receptor (CdgR), depending on the amount of the c-di-GMP-free form of CdgR available because of titration by c-di-GMP in the cells. The system, with the two concentration thresholds of c-di-GMP that dictate cell size and viability, respectively, enables dynamic cellular adaptation while preventing lethal effects.
Experiences reshape our internal representations of the world. However, the neural and cognitive dynamics of this process are largely unknown. Here, we investigated how sequence learning reorganizes neural representation...Experiences reshape our internal representations of the world. However, the neural and cognitive dynamics of this process are largely unknown. Here, we investigated how sequence learning reorganizes neural representations and how sleep-related consolidation mechanisms contribute to this transformation. Using high-density electroencephalography and multivariate decoding, we found that learning temporal sequences of visual information led to the incorporation of successor representations during a subsequent perceptual task, despite temporal information being task-irrelevant. Importantly, individuals with better sequence memory performance exhibited stronger successor incorporation during the perceptual task. Representational similarity analyses comparing neural patterns with different layers of a deep neural network revealed a learning-induced shift in representational format, from low-level visual features to higher-level abstract properties. Critically, both the strength and transformation of successor representations correlated with the neurophysiological hallmarks of slow-wave sleep during a post-learning nap, particularly the coupling between slow oscillations and spindles. These findings support the idea that sequence learning induces lasting changes in visual representational geometry and that sleep physiology strengthens these changes, providing mechanistic insights into how the brain updates internal models after exposure to environmental regularities.
Osteogenesis depends on the self-renewal and differentiation of mesenchymal stem cells (MSCs). Emerging research underscores the regulatory functions of RNA methylation on bone homeostasis. Here, we show PCIF1, the N6,2'...Osteogenesis depends on the self-renewal and differentiation of mesenchymal stem cells (MSCs). Emerging research underscores the regulatory functions of RNA methylation on bone homeostasis. Here, we show PCIF1, the N6,2'-O-dimethyladenosine (m6Am) methyltransferase, is essential for maintaining bone mass and promoting osteogenic differentiation of MSCs. Multiple complementary analyses-including GWAS, TWAS, and single-cell transcriptomics-collectively point to PCIF1 as a regulator of human bone mineral traits and early-stage mesenchymal differentiation. Global or MSC-specific Pcif1 deletion elicits osteoporotic pathology in mice, although myeloid cell-specific Pcif1 knockout does not induce femur bone alterations. Mechanistically, Pcif1 knockout decreases m6Am signals of Wnt-related genes (Wnt11, Fzd4, and Fgfr2) and accelerates mRNA degradation. This down-regulates active β-Catenin protein, and thus impairs osteogenic function of MSCs. Additionally, the WNT agonist attenuates the osteoporosis-like phenotype induced by Pcif1 deletion. These findings highlight the crucial role of PCIF1-mediated m6Am modification in regulating osteogenesis and suggest potential therapeutic implications for bone disorders.
The competitive research funding system is at a breaking point. Innovations to address ongoing problems are needed on a grander scale than ever before, but even this will not suffice to fix a struggling system. What we n...The competitive research funding system is at a breaking point. Innovations to address ongoing problems are needed on a grander scale than ever before, but even this will not suffice to fix a struggling system. What we need is a whole system transformation.
Coronaviruses (CoVs) rely heavily on host lipid metabolism for efficient replication, but the specific host pathways involved remain incompletely defined. Here, we identify the non-vesicular cholesterol transport protein...Coronaviruses (CoVs) rely heavily on host lipid metabolism for efficient replication, but the specific host pathways involved remain incompletely defined. Here, we identify the non-vesicular cholesterol transport protein GRAMD1C as a key host factor required for the replication of multiple coronaviruses across α, β, and δ genera, including TGEV, PEDV, HCoV-229E, SARS-CoV-2, MHV, and PDCoV. Mechanistically, GRAMD1C is recruited to the replication factory through its interaction with the viral nonstructural proteins 3 and 4 (nsp3 and nsp4). Transmission electron microscopy (TEM) analysis revealed that GRAMD1C facilitates the formation of replication double-membrane vesicles (DMVs). Further domain rescue and inhibitor experiments demonstrated that GRAMD1C's cholesterol transport activity is essential for viral replication. Moreover, GRAMD1C-deficient and inhibitor-treated mice exhibited reduced viral replication, underscoring its critical role in vivo. Collectively, our findings expand the current understanding of the importance of non-vesicular cholesterol transport in viral replication and highlight GRAMD1C as a promising broad-spectrum antiviral target.
A unifying framework of the brain's representation and manipulation of negative emotional experiences has been elusive. A new study in PLOS Biology describes how different brain systems correspond to emotion regulation a...A unifying framework of the brain's representation and manipulation of negative emotional experiences has been elusive. A new study in PLOS Biology describes how different brain systems correspond to emotion regulation and suggests a key dimension that explains how we feel.
ADP-ribosylation (ADPr) is a post-translational modification that has regulatory roles in multiple cellular pathways including the DNA damage response and in innate immunity. Recently, it has been uncovered that ADP-ribo...ADP-ribosylation (ADPr) is a post-translational modification that has regulatory roles in multiple cellular pathways including the DNA damage response and in innate immunity. Recently, it has been uncovered that ADP-ribose can be further modified by a family of ubiquitin E3 ligases, the DELTEXES, which catalyze ubiquitin transfer directly onto ADP-ribose, creating a hybrid ADPr-Ub modification which can be recognized by proteins with dedicated ADPr-Ub binding domains. With this hybrid modification recently been identified in cellular systems, we use a series of in vitro and cellular assays in human cells to investigate the amino acid preference for ADPr-Ub production as well as conditions required for reversal of the modification. We show that ADPr on both serine and glutamate-linked peptides can be ubiquitinated by the RING-DTC domains of DTX2 and DTX3L in vitro and that this can be recognized by RNF114, RNF138 and RNF166 for ubiquitin chain elongation. Finally, we demonstrate that DTX2 rather than DTX3L plays a role in ADPr-Ub production at sites of DNA damage to promote the recruitment of RNF114, RNF138, and RNF166 in an HPF1-independent manner.
Macrophages rely on efficient chemotaxis to locate sites of infection and tissue damage. One general strategy that enhances chemotactic accuracy is the use of self-generated gradients, where cells locally deplete attract...Macrophages rely on efficient chemotaxis to locate sites of infection and tissue damage. One general strategy that enhances chemotactic accuracy is the use of self-generated gradients, where cells locally deplete attractants to create or sharpen guidance cues. Here, we show that mouse bone marrow-derived macrophages (BMDMs) migrate toward the complement component C5a using this strategy. Cells actively deplete C5a from their surroundings, establishing local gradients as fresh attractant diffuses inward. We visualized this process in real time with fluorescent C5a and reproduced its dynamics using computational models. C5a depletion is mediated primarily by C5aR1-dependent endocytosis. This mechanism produces complex responses, with different C5a concentrations inducing temporally distinct waves of migration, and maximal chemotaxis occurring below 10 nM C5a. As expected, increasing C5a concentrations recruit more cells. In contrast, human macrophages inactivate C5a mainly through carboxypeptidase-mediated degradation, yielding a higher optimal concentration (~30 nM) and distinct migratory dynamics. Both species also deplete externally-imposed C5a gradients, sharpening them and enhancing guidance. These findings identify C5a degradation as a critical mechanism by which macrophages extract directional information from their environment. Self-generated gradient formation, despite different mechanisms across species, emerges as a conserved and versatile strategy for immune navigation.
Emotion regulation is essential for well-being and mental health, yet individuals vary widely in their emotion regulation success. Why? Traditional neuroimaging studies of emotion regulation often focus on localized neur...Emotion regulation is essential for well-being and mental health, yet individuals vary widely in their emotion regulation success. Why? Traditional neuroimaging studies of emotion regulation often focus on localized neural activity or isolated networks, overlooking how large-scale brain organization relates to the integration of distributed systems and sub-processes supporting regulatory success. Here, we applied a novel system-level framework based on spatial gradients of macroscale brain organization to study variance in emotion regulation success. Using two large functional magnetic resonance imaging (fMRI) datasets (n = 358, n = 263), we projected global activation patterns from a laboratory emotion regulation task onto principal gradients derived from independent resting-state fMRI data from the Human Connectome Project. These gradients capture low-dimensional patterns of neural variation, providing a topographical framework within which complex mental phenomena, such as emotion regulation, emerge. In both datasets, individual differences in regulation success were associated with systematic reconfiguration along Gradient 1-a principal axis differentiating unimodal and heteromodal brain areas. This gradient-based neural reconfiguration also associates with lower negative affect in daily life, as measured via smartphone-based experience sampling in a subset of participants (n = 55). Meta-analytic decoding via Neurosynth revealed that Gradient 1 and regulation success align with multiple psychological processes, including social cognition, memory, attention, and negative emotion, suggesting this gradient reflects diverse, integrative demands during effective emotion regulation. These findings introduce a gradient-based perspective on emotion regulation success that is biologically grounded in well-established large-scale brain organization and ecologically valid through its links with real-world emotional experience. Such gradient-based dynamics may serve as predictive biomarkers of regulatory success and inform targeted interventions in clinical populations.
Viruses face selective pressure to evade cellular antiviral responses to control the outcome of an infection. However, due to their limited genome size, viruses must adopt unique strategies to confront cellular sensors....Viruses face selective pressure to evade cellular antiviral responses to control the outcome of an infection. However, due to their limited genome size, viruses must adopt unique strategies to confront cellular sensors. Since its emergence in humans, SARS-CoV-2 accrued many mutations; however, the functional consequence of many such genetic changes remains unexplored. Here, we show that SARS-CoV-2 produces a truncated form of the nucleocapsid protein, called N*M210. Due to the acquisition of a viral transcription regulatory sequence (TRS) in the N gene, certain variants like Omicron produce a new viral mRNA that markedly increases N*M210 production. We show that N*M210 is a double-stranded RNA (dsRNA)-binding protein. Using its dsRNA binding motif, N*M210 inhibits multiple antiviral responses, supressing interferon, triggering processing body disassembly, and potently blocking G3BP1 foci, including stress granules and RNase L-dependent bodies. Using a panel of recombinant SARS-CoV-2 viruses (rSARS-2), we show that enhanced N*M210 production increases virus fitness in primary human cells and in mice. Furthermore, we show that during infection N*M210 improves virus fitness, in part, due to its ability to potently block G3BP1 foci. We propose a model where, to evade the cellular antiviral response, SARS-CoV-2 has evolved a mechanism to increase the production of a truncated form of the N protein, which limits activation of dsRNA-induced antiviral responses, tipping the balance in favor of the virus in the battle for control of the cell.
Overactivation of memory networks and pathways can induce post-traumatic stress disorders and memory generalization, where memories are recalled in inappropriate situations. Here, we demonstrate that age-related defects...Overactivation of memory networks and pathways can induce post-traumatic stress disorders and memory generalization, where memories are recalled in inappropriate situations. Here, we demonstrate that age-related defects in long-term memories in Drosophila are also caused by memory generalization. Aversive memory engram cells are formed in both young and old flies trained in an odor avoidance task. However, while engrams in young flies are activated specifically by odors previously paired with electrical shocks, engrams in old flies are activated by shock-paired, unpaired, and novel odors. This enhancement of engram cell activation occurs because of increased activity of dopaminergic neurons during memory consolidation in old flies. Increased dopamine signaling results from an inability of old flies to inhibit glutamatergic activation and leads to increased activation of dopamine D2 receptors on engram cells. Our data suggest that increased dopaminergic activity after training generalizes the responsiveness of engram cells to disrupt appropriate memory recall.
Obligately lytic (virulent) phages always lyse host cells to release progeny viruses, while temperate phages can either lyse their hosts or integrate into host genomes as prophages, forming lysogens. There is a rich hist...Obligately lytic (virulent) phages always lyse host cells to release progeny viruses, while temperate phages can either lyse their hosts or integrate into host genomes as prophages, forming lysogens. There is a rich history of work studying the relative advantages and disadvantages of these two phage life history strategies, but little of this work has addressed the spatial constraints common to biofilm environments. We developed a live imaging system to track lytic infections, lysogenic infections, and uninfected cells at single-cell resolution within three-dimensional Escherichia coli biofilms. We find that biofilm structure substantially impacts the ecological success of different phage infection strategies. Temperate phages have the unique capacity to release phages from lysogens that have undergone lytic induction from within the interior of mature biofilms. When this occurs in biofilm contexts that do not limit phage diffusion, lytic infections expand rapidly, but lysogenic infections are favored as phage mobility declines in densely packed biofilm architectures. In matrix-replete biofilms that do limit phage mobility, lytic phage infection is more limited, favoring lysogenic growth. Direct competition assays between lysogenized host bacteria and obligately lytic phages-with or without the ability to superinfect lysogens-revealed that spatial structure and superinfection potential together greatly impact phage competition outcomes during co-invasion into pre-existing, phage-susceptible biofilm populations. Highly packed, phage diffusion-impeding biofilms disproportionately favored temperate phages in the lysogenic cycle over obligate lytic phages, highlighting how biofilm architecture can constrain lytic phage infection and promote vertical phage genome transmission strategies.
Females influence offspring paternity through diverse pre- and post-copulatory mechanisms. Sperm discrimination-the differential physiological response to ejaculates based on male or sperm characteristics-can bias fertil...Females influence offspring paternity through diverse pre- and post-copulatory mechanisms. Sperm discrimination-the differential physiological response to ejaculates based on male or sperm characteristics-can bias fertilization outcomes, but in vivo evidence of this process in large-bodied mammals is lacking. Here, in a study of nine females and four males, we tested whether two aspects of female physiology that affect sperm survival-vaginal immune response and pH-are modulated by male genetic makeup in a non-human primate, the olive baboon (Papio anubis). Our findings suggest post-copulatory differences in vaginal gene expression and pH, with the strongest immune responses and largest pH decreases, harmful to sperm, exhibited by females mating with genetically similar males. These findings are consistent with genetically-based post-copulatory mate discrimination, offering new insights into how interactions between male gametes and the female reproductive tract may shape conception probability in primates.
Most theoretical work on the origin of heredity has focused on how genetic information can be maintained without mutational degradation in the absence of error-proofing systems. A simple and parsimonious solution assumes...Most theoretical work on the origin of heredity has focused on how genetic information can be maintained without mutational degradation in the absence of error-proofing systems. A simple and parsimonious solution assumes the first gene sequences evolved inside dividing protocells, which enables selection for functional sets. But this model of information maintenance does not consider how protocells acquired their genetic information in the first place. Clues to this transition are suggested by patterns in the genetic code, which indicate a strong link to autotrophic metabolism, with early translation based on direct physical interactions between amino acids and short RNA polymers, grounded in their hydrophobicity. Here, we develop a mathematical model to investigate how random RNA polymers inside autotrophically growing protocells could evolve better coding sequences for discrete functions. The model tracks a population of protocells that evolve towards two essential functions: CO2 fixation (which drives monomer synthesis and cell growth) and copying (which amplifies replication and translation of sequences inside protocells). The model shows that distinct coding sequences can emerge from random RNA sequences driving increased protocell division. The analysis reveals an important restriction: growth-supporting functions such as CO2 fixation must be more easily attained than informational processes such as RNA copying and translation. This uncovers a fundamental constraint on the emergence of genetic heredity: growth precedes information at the origin of life.
The human glucose-6-phosphate transporter (G6PT/SLC37A4) mediates the translocation of glucose-6-phosphate (G6P) from the cytoplasm into the endoplasmic reticulum, a process essential for glucose production and the maint...The human glucose-6-phosphate transporter (G6PT/SLC37A4) mediates the translocation of glucose-6-phosphate (G6P) from the cytoplasm into the endoplasmic reticulum, a process essential for glucose production and the maintenance of blood glucose homeostasis between meals. Dysfunction of G6PT causes glycogen storage disease type Ib (GSD-Ib), a severe metabolic disorder characterized by hypoglycemia, hepatomegaly, and neutropenia. Despite its physiological and clinical significance, the structural basis of G6P recognition and the molecular mechanisms underlying GSD-Ib have remained elusive. Here, we present cryo-electron microscopy structures of human G6PT, revealing a monomer in an outward-open state at 3.1 Å and a homodimeric assembly in a face-to-face topology at 3.3 Å. By combining computational modeling of the G6P-G6PT complexes with functional characterization, we have uncovered the key molecular elements that govern the alternating-access mechanism: an electropositive substrate-binding pocket tailored for phosphorylated sugars; conserved aromatic residues that seal the cytosolic gate; and a dynamic inter-domain salt bridge that regulates the conformational transition. Our work provides fundamental insights into the transport cycle of the organophosphate:phosphate antiporter (OPA) family, offers a framework for interpreting GSD-Ib pathology at the molecular level, and establishes a foundation for advancing the mechanistic understanding of the human SLC37 family.
Studies of human social behavior indicate stronger social affinity in matched-neurotype dyads (e.g., two individuals with autism or two without) compared to mixed-neurotype dyads (e.g., one individual with autism paired...Studies of human social behavior indicate stronger social affinity in matched-neurotype dyads (e.g., two individuals with autism or two without) compared to mixed-neurotype dyads (e.g., one individual with autism paired with one without). Is this dyad matching phenomenon also quantifiable in nonhuman animals? Using deep learning tools, we analyzed dyadic male-female interactions in prairie voles, a socially monogamous rodent species. To simulate "neurotypes", voles were exposed to either control conditions or early-life sleep disruption (ELSD) during a critical neurodevelopmental period (post-natal days 14-21), recapitulating the influence of developmental sleep quality on later-life social behavior. Analogous to human studies, voles showed signs of reduced social affinity in mixed dyads compared to matched dyads, including sex-specific changes in aggression and body orientation toward the conspecific. These findings advance our understanding of social affinity between potential partners, providing a framework for new studies in both animal models and humans.