Cell Discovery

Bifidobacteriaceae and Lactobacillaceae are key probiotic families and widely used in food production, yet a comprehensive understanding of strain functions and their gut microbial interactions based on complete genomes remain understudied. Here we constructed a complete-genome dataset of 3,300 strains from these two families, including 1,151 newly isolated from China. Compared with draft assemblies, complete genomes substantially recovered a gene functional landscape encompassing stress tolerance, surface exopolysaccharide synthesis, nutrient utilization, and mobile genetic elements. Major species from both families exhibited a prevalence >60% in the Chinese population, far higher than that in US/Dutch cohorts. Notably, as a core probiotic species with remarkable genomic plasticity and gut-adaptive potential, Lactiplantibacillus plantarum stood out in our dataset for its enriched functional profile and was particularly abundant in the Chinese population. Moreover, compared with non-Chinese genomes, our isolates of key species displayed less metabolic complementarity and stronger competition with potentially pathogenic keystone species in the gut, thereby linking strain origin to enhanced probiotic potential and ecological fitness to benefit human gut health.

Mixed-lineage leukemia translocated to 3 (MLLT3) is vital for maintaining the stemness of hematopoietic stem cells. Loss of MLLT3 in megakaryocyte (MK)-erythrocyte progenitor (MEP) cells leads to its differentiation into MKs. Despite its significance in stemness, the regulatory mechanism of MLLT3 during differentiation remains elusive. In this study, we investigate the regulatory role of histone deacetylase 6 (HDAC6) in modulating MLLT3 levels via heat shock protein 90 (Hsp90) activation during myeloid lineage differentiation into MKs, monocytes, and macrophages. We found that HDAC6 activates Hsp90 through deacetylation, enabling Hsp90 to retain MLLT3 in the cytoplasm where protein kinase C (PKC) phosphorylates MLLT3 at serine residues; leading to loss of MLLT3 during MK and macrophage differentiation but not during monocyte differentiation. This research provides valuable insights into the regulatory mechanisms underlying myeloid lineage commitment and opens new avenues for future investigations into stem cell biology and therapeutic applications.

Heterogeneous nuclear ribonucleoprotein U (HNRNPU) deficiency is a rare genetic cause of neurodevelopmental disorders (NDDs) lacking targeted therapies. Here, we developed a transcriptomic-guided compound prioritization pipeline using Connectivity Map (CMap) analysis on multi-model transcriptomic signatures from HNRNPU-deficient human cells and mouse models. Ten compounds were selected through manual curation and functionally screened in patient-derived HNRNPU-deficient neuroepithelial stem (NES) cells with earlier observed cellular phenotypes. Two of the compounds, AS601245 and Lenalidomide, significantly reduced the elevated neural progenitor population during differentiation, and their combination further decreased primary cilia incidence, indicating partial rescue of the patient-specific cellular phenotypes. To understand the mechanisms underlying the partial rescue, we employed proteome integral solubility alteration (PISA) and expression proteomics. PISA assay identified TMEM150C and GSK3A as proximal targets of combined treatment. Additionally, we observed reversal of multiple biological pathways including downregulation of Wnt signalling and upregulation of mitochondrial pathways and transmembrane proteins. Altogether, we established a computational-experimental pipeline for transcriptomic-guided drug repurposing for a monogenic NDD, and demonstrated that the network-level modulation partially rescues the delayed neural differentiation in HNRNPU-deficient neural cells.

Aberrant activation of type I interferon (IFN-I) is closely related to the development of autoimmune diseases. The metabolic regulation of cytokine signaling is essential for immune homeostasis. In this study, we characterized Urolithin A(UA), a natural gut-derived metabolite, as an inhibitor of Janus kinase (JAK) signaling. UA was found to broadly dampen JAK phosphorylation and the downstream signaling induced by cytokines such as type I interferons (IFN-I), type II interferons (IFN-II), and interleukin-6 (IL-6). UA can directly bind to JAK1 JH1 domain and treatment with UA attenuated autoimmune pathogenesis in Trex1-KO mice, IMQ-induced SLE and psoriasis models. Our findings unveil that UA is an anti-inflammatory metabolite that promotes immune homeostasis and could be used to treat inflammatory and autoimmune diseases.

Bacteria have evolved multiple immune systems to resist phage invasion, however, only a small part of the defensive mechanisms have been clearly uncovered. In this study, we report a type III Druantia two-component defense system, DruH-DruE, identified from Mycobacterium smegmatis. The DruH-DruE prevents phage DNA cyclization and replication.DruE can be replaced from the defense system by either homolog in M. tuberculosis or M. smegmatis. The physical interaction between this two components is essential for fighting against phage infection. Mutations in the interaction sites led to the loss of phage-defending function of the system. The broad-spectrum antiphage ability of the defense system could be activated by the small tail protein Gp25 of phage A10ZJ24. This study fills a major gap in current knowledge of antiphage mechanism of type III Druantia defense system, expanding our understanding of the immune mechanisms in prokaryotic cells.

The Rcs phosphorelay regulates gene expression in response to cell envelope stress and is critical for the virulence of pathogenic bacteria, including Klebsiella pneumoniae, due to its regulation of genes related to extracellular capsule, cell division, and motility. The RcsC histidine kinase, RcsD phosphotransfer protein and RcsB response regulator, which form the core of the Rcs phosphorelay, are negatively regulated by the unique inner membrane protein IgaA via interaction with RcsD. An outer membrane lipoprotein, RcsF, activates signaling by interaction with IgaA, but the precise activation mechanisms remain unclear. In this study, we determined the structures of IgaA and the IgaA/RcsF complex using Cryo-electron microscopy (Cryo-EM). We also determined the structures of RcsC and RcsD, which both form homodimers stabilized by hydrophobic interactions, creating ladder-like structures. Combining the Cryo-EM structures, AlphaFold3 structure predictions of IgaA/RcsD and RcsF/IgaA/RcsD, and genetic studies, we describe a model for how RcsF modifies the IgaA/RcsD interaction, lifting negative regulation and activating the Rcs phosphorelay. Our findings provide a high-resolution depiction of the Rcs stress response system and suggest potential targets for small molecule inhibitors.

The developmental program governing meibomian gland (MG) morphogenesis and proliferation remains poorly understood, largely due to the lack of physiologically relevant model systems. Here, we established a novel high-fidelity, three-dimensional organoids model derived from mouse meibomian gland (mMGO) epithelium. Transcriptomic and phenotypic analyses demonstrated that mMGOs faithfully recapitulate postnatal gland development in vivo, including dynamic transcription program, branching morphogenesis, lineage differentiation, and functional lipid accumulation. Leveraging this model, we identified the Hippo-YAP pathway as a pivotal regulator of MG epithelial proliferation and homeostasis for the first time. YAP inhibition severely impaired organoids growth, while pharmacological inhibition of Hippo pathway with XMU-MP-1 enhanced proliferation and progenitor clonogenicity. Crucially, in inflammation-induced atrophic organoids, XMU-MP-1 treatment rescued YAP nuclear localization and stimulated regrowth and functional restoration. Our study provided new mechanistic insights and a robust organoids platform for MG development research, and nominated targeted Hippo pathway inhibition as a promising strategy to reverse glandular atrophy in meibomian gland dysfunction.

Translation efficiency remains a major limitation for RNA therapeutics. Conventional optimization targets the 5 untranslated region (5 UTR), while the 3 UTR is viewed mainly as a stabilizing element. Here, we demonstrate that the 3 UTR can be rationally engineered to actively enhance translation. Using an intracellular directed-evolution platform based on the SINEB2 element, we identified RNA modules P51 and its compact variant P51t3,which markedly increased protein output without affecting mRNA levels. P51t3 consistently boosted expression two- to six-fold across plasmid, in vitro transcribed mRNA, and recombinant AAV systems. Mechanistic studies revealed that P51t3 binds ribosomal protein RPL39, recruiting 60S subunits to the initiation site through the natural closed-loop translation model. By integrating evolutionary selection with 3 UTR design, this work redefines the 3 UTR as an active translational enhancer and provides a broadly applicable regulatory element for next-generation mRNA and gene-delivery therapeutics.

Orthohantaviruses cause severe human diseases including hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS), with case fatality rates up to 40%. No FDA-approved therapeutics are currently available, highlighting urgent need for drug development following recent outbreak events. We systematically examined host protease dependencies in hantavirus replication, focusing on Signal Peptidase (SP) and Signal Peptide Peptidase (SPP) essential for viral glycoprotein maturation. Through comprehensive database mining and molecular docking analysis, we identified six potential protease inhibitors, with Compound E achieving the highest binding confidence score (-0.28) against SPP. Our analysis reveals that targeting host ER proteases represents a viable antiviral strategy, providing a systematic framework for protease-targeted antihantavirus drug development and identifying specific lead compounds for experimental validation.

Human genetic studies have identified defects in multiple mechanisms that predispose the risk of developing inflammatory bowel diseases (IBD), which include alterations in adaptive and innate immune responses, epithelial integrity and regulation of the intestinal mucus layer. Despite the importance of intestinal barrier integrity in the pathogenesis of IBD, essentially all current therapies modulate the immune responses. In this study, we determined the high resolution cryo-EM structure of human NXPE1, a IBD associated protein. Based on the structural homology, we identified NXPE1 as an O-acetyltransferase. Since NXPE1 is a pseudo gene in mouse, we generated knockout mouse model that lacked two of the mouse NXPE1 homologs, Nxpe2 and Nxpe4. The O-acetylation of sialic acid on red blood cells was abolished in the double knockout mice, confirming the sialic acid O-acetyltransferase function of NXPE1 family members. These findings underscore the potential of NXPE1 as a novel therapeutic target of the intestinal barrier functions for the treatment of IBD.

PUF60 is a splicing factor related to the polypyrimidine-tract binding protein U2AF2. PUF60 is deleted in developmental disorders such as Verheij syndrome and amplified in approximately 8% of cancers. Thus, both increases and decreases in PUF60 expression can have profound physiological effects. However, little is known about how changes in PUF60 expression impact global splicing patterns. Here, we created a model system of CRISPRa/i in mouse stem cells (mESCs) to transcriptionally upregulate or downregulate Puf60. Our results uncovered extensive transcriptional, post-transcriptional, and post-translational regulation of Puf60 protein expression. We observed that Puf60 protein levels in normal mESCs drop dramatically at a critical cell density, leading to cell death. Puf60 is very essential in stem cells, and its repression causes cell death and impacts specific splicing events, including its own splicing autoregulation, providing valuable insights into the functional consequences of PUF60 dysregulation. Analysis of phosphoprotein data revealed phosphorylation of threonine at the N-terminus of PUF60. Our results showed that mutating threonine to glutamate downregulates the protein and alters its localization. Thus, our study reveals a novel regulatory mechanism of Puf60 phosphorylation that mediates its function and may be related to its frequent overexpression in cancer cells.

In Plasmodium falciparum, DNA replication and asynchronous nuclei formation precede cytokinesis during intraerythrocytic schizogony. Inhibition of fatty acids (FAs) import and impaired membrane biogenesis led to the arrest of mitosis through the inhibition of DNA replication and nuclei formation. On the iRBC surface, parasite ribosomal protein P2 (PfP2) complex mediated FAs import and membrane biogenesis, seemingly prior events before the commitment for DNA replication and nuclei formation. The inhibition of FAs import led to the degradation of histones by the evolutionarily conserved bacterial serine protease ClpP/ClpR in the parasite nucleus. Noncanonical arginine hyperphosphorylation by a novel arginine kinase in the nucleus was subjected for proteostasis and marks histones for degradation by ClpP/ClpR machinery. Inhibition of de novo FAs biosynthesis by an anti-cancer drug, Cerulenin and C75, in HEK293T and HCT116 carcinoma mammalian cells showed histone degradation. Lipid (L) induced histone proteostasis by ClpP/ClpR, seemingly an indispensable L-checkpoint before mitotic commitment.

Mitochondria and lipid droplets (LDs) are functionally coupled to coordinate fatty acid utilization and storage. However, a comprehensive understanding of mitochondria-LD alliances remains elusive. We have identified a previously unrecognized role for optical atrophy 1 (OPA1), a mitochondrial fusion factor, in the regulation of fatty acid release from LDs. We demonstrated that OPA1s exon 4 adapts an amphipathic helix to target OPA1 to LDs. OPA1 localized to LDs promote fatty acid release by facilitating the recruitment of lipases to LDs. In addition, OPA1s residence on LDs competes with its mitochondrial entry, influencing mitochondria fusion and connectivity. Furthermore, the S158N polymorphism within OPA1s exon 4 exhibiting attenuated fatty acid release from LDs is associated with changes in metabolic traits in pediatric cancer survivors. Altogether, our findings reveal that OPA1 actively mediates fatty acid release from LDs and provide a mechanistic link between OPA1 and human metabolism.

Rhinoviruses are the leading cause of acute respiratory illnesses and comprise more than 170 types that constantly circulate in humans worldwide. Beyond common colds, rhinoviruses can trigger severe symptoms, particularly in young children, older adults and people with asthma or chronic obstructive pulmonary disease. Despite their clinical and socio-economic impact, no approved vaccine or antiviral treatment exist. Here, we uncovered the interaction of the host AAA+ ATPase RUVBL1/2 with rhinovirus non-structural protein 2C and we demonstrated that RUVBL1/2 is strictly and specifically required for the replication of the viral RNA of the most prevalent and pathogenic rhinovirus species. Pharmacological inhibition of RUVBL1/2 ATPase activity efficiently inhibited rhinovirus replication in a human nasal epithelium model, even post-infection. Moreover, serial viral passaging in the presence of a RUVBL1/2 inhibitor did not lead to the emergence of resistance. These findings reveal an unexpected and strong host dependency with promising potential for antiviral targeting.

Transmembrane (TM) proteins play essential roles in biology as transporters, ion channels, chaperones, enzymes, and mediators of signal transduction. However, membrane proteins often suffer from inefficient folding and intrinsic instability. Misfolding in cells can cause numerous loss-of-function pathologies. Likewise, denaturation upon purification in the laboratory is a critical barrier to structure determination and characterization of key biochemical mechanisms. Generalizable strategies to stabilize membrane proteins remain limited. Here, we developed an informatics-based de novo design strategy to create synthetic auxiliary subunits that interact with the TM helices of a model pentameric ion channel, thereby bolstering folding while maintaining channel function. Biochemical and structural characterization reveal the synthetic TM subunits can also be used to create larger multi-spanning designer proteins of custom topology. This proof-of-concept motivates the feasibility of computationally designed accessory TM helices as potential pharmacological chaperone "folding correctors" of membrane proteins in disease and as tools in structural biology.

Acinetobacter baumannii is a top-priority, ESKAPE pathogen that poses a major challenge to human health. The pathogen is difficult to combat due to its extensive arsenal of antibiotic resistance and its protective polysaccharide capsule. In addition, A. baumannii isolates are highly heterogeneous, which complicates the development of rapid detection methods or novel targeted therapeutic approaches. Here, we discovered and characterized a new biotechnological tool, the nanobody H7 (NbH7), along with its conserved target, the surface-exposed Omp25 protein of A. baumannii, and elucidated their interaction at the molecular level. Moreover, we demonstrate that NbH7-functionalized magnetic beads enable selective and efficient capture of A. baumannii from bacterial mixtures, including non-pathogenic intestinal bacteria. This provides proof of concept for a new targeting system that remains effective across diverse A. baumannii clinical isolates and capsule types and holds potential for use in diagnostic cell enrichment and targeted therapies.

Deep-sea corals are vital in maintaining coral ecosystem biodiversity, yet their genetic characteristics remain largely unexplored. Here, we present 11 deep-sea coral genome assemblies, including four Hexacorallia and seven Octocorallia species, significantly contributing new genomic information across two orders. Our analysis reveals the historical dynamics of coral speciation and the influence of environmental factors on the evolution of coral reef ecosystems.Total of 126 horizontal gene transfer (HGT) events were detected, among which genes from the ancestor of symbiodiniaceae indicate that the ancestors of deep-sea corals may have inhabited shallow-sea environments. Notably, several of these HGTs are involved in phosphorus (PhnX/PhnW) and cholesterol (DHCR7) metabolisms within corals, indicating that HGTs may serve as an adaptive survival strategy for the coral holobionts. Deep-sea corals also rely on symbiotic bacteria to synthesize 10 essential amino acids (such as valine and tyrosine), retaining only partial amino acid synthesis capacity. In addition, we investigated the evolution of key biological rhythm genes and temperature adaptation in corals. The loss of key rhythm genes (e.g., clock and cry) in deep-sea corals and copy number difference of genes related to heat stress (e.g., Cbl-b and Rchy) revealed genetic difference between deep-sea and shallow-sea corals. Our new genome assemblies enhance the understanding of deep-sea coral evolution, biodiversity, and adaptation, providing a genetic foundation for coral conservation.

Oncolytic virotherapy is an innovative approach to cancer treatment that uses replication-competent viruses to selectively target and destroy cancer cells while leaving healthy tissues largely unaffected. Zika virus (ZIKV), a neurotropic orthoflavivirus, has recently gained attention as a potential oncolytic agent due to its ability to infect neural-derived cells and suppress tumor growth in preclinical models. Although existing studies have examined ZIKVs oncolytic effects, the mechanisms underlying these effects remain largely unexplored. Additionally, the roles of individual ZIKV proteins and their interactions with host factors remain incompletely understood. Here, we used RNA sequencing, affinity purification-mass spectrometry, and functional assays to uncover previously unidentified mechanisms underlying ZIKVs oncolytic activity in pediatric neural tumors. We found that the ZIKV non-structural proteins NS4A and NS5 exert oncolytic effects, reducing tumorsphere size. ZIKV-host protein-protein interaction networks were characterized and showed that integrin 3 (gene: ITGA3), a mediator of cell-matrix adhesion, interacts with ZIKV NS2B and NS4A. Integrin 3 was further shown to be involved in ZIKV- and NS4A-induced tumorsphere size reduction, while ITGA3 knockdown and ZIKV infection additively inhibited 3D invasion. These findings provide critical mechanistic insights that could inform the rational design of ZIKV-based virotherapies and highlight opportunities for combination treatment strategies.

Dopamine is a neurotransmitter essential for cognition, and its dysregulation is associated with neurological diseases1,2. Historically, dopamine has been understood to signal exclusively through metabotropic receptors3. Delta-type ionotropic glutamate receptors (GluDs), which have recently been established as ligand-gated ion channels4,5, are fundamental for synaptic maintenance, are implicated in neurological disorders, and co-localize with dopaminergic machinery. Here, we report that dopamine is a direct agonist of GluDs, eliciting ionotropic activity, as visualized by cryo-electron microscopy (cryo-EM), bilayer recordings, mutagenesis, and patch clamp recordings. Dopamine binds to the GluD ligand binding domain, inducing clamshell closure and channel activation through a distinct molecular interface. GluD channel activity is tightly regulated by G-proteins, which act as molecular switches to tune GluD activity: free G{beta}{gamma} inhibits ligand-gating, while G or inactive G-protein heterotrimers enable dopamine-induced GluD currents. This tuning of GluD activity by G-proteins is uncoupled in a point mutation associated with neurodegeneration. These findings expand mechanisms of neuronal dopaminergic signaling, uncover how G-proteins tune GluD channel activity, and provide a framework for targeting GluDs in neurological diseases.

Airway epithelial homeostasis relies on multiple specialized cell types, with club cells playing central roles in maintaining epithelial integrity and regulating inflammation. Environmental insults such as allergens, viral infections, or pollutants preferentially damage club cells, impairing epithelial repair and contributing to pulmonary diseases. However, the functional properties of club cells remain incompletely defined, and tractable human models are lacking. Herein, we establish a robust platform to differentiate human pluripotent stem cells (hPSCs) into club cells exhibiting their hallmark secretory features, appropriate epithelial organization, and functional properties. Single-cell transcriptomic analyses and lineage trajectory inference revealed unexpected epithelial plasticity: hPSC-derived club cells give rise to multiciliated epithelial cells through a deuterosomal intermediate--a previously uncharacterized trajectory. Additionally, a distinct club cell subset exhibited transcriptional features indicative of neuroendocrine and goblet cell differentiation potential. This study uncovers club cell plasticity and establishes a hPSC-based platform for studying airway development, regeneration and disease modeling.