Background:Streptococcus mutans is a key cariogenic bacterium. Current antimicrobials lack species specificity, while phage-based approaches remain experimental and require more S. mutans phage isolates. Objective:To profile the diversity of S. mutans-associated phages and strain-level heterogeneity in phage exposure using genome-informed CRISPR spacer and prophage analyses. Materials and methods:We compiled 944 publicly available S. mutans genomes and dereplicated them into 735 non-redundant strains. CRISPR-Cas systems, spacers, spacer targets, and putative prophages were identified, quality-assessed, and functionally annotated. Phylogenetic relationships of (pro)phages were evaluated using terminase large subunit proteins, and comparative genomics compared spacer-positive and spacer-negative strains. Results:CRISPR systems were detected in 548/735 strains, yielding 14,263 spacers, 1,864 phage-targeting spacers mapped to 110 viral genomes, including 41 cultured isolates, 51 metagenome-assembled phages, and 18 uncultured viral genomes. The most frequently targeted cultured phage was phiKSM96, whereas metagenome-assembled Caudoviricetes ctNo011 showed broader targeting. Prophage mining identified 186 regions in 130 strains, including 37 of ≥ medium quality and elements related to ctNo011 and phiKSM96. TerL phylogeny showed that most high-quality endogenous prophages clustered with phiKSM96 and ctNo011. Conclusion:These findings reveal a vast, uncultivated phage repertoire targeting S. mutans, providing a critical genomic roadmap to guide the future isolation of novel phages for caries prevention.

Understanding the acid resistance mechanism of S. mutans is crucial for preventing dental caries. FtsZ is the core protein for cell division in bacteria that can polymerize into Z-rings and drive cytokinesis. Our previous study revealed that the FtsZ in S. mutans (SmFtsZ) has higher self-assembly and GTPase activity under acidic stress, which may be responsible for acid resistance and cariogenesis of S. mutans. However, the functional structure mechanism of SmFtsZ under low pH conditions is still unclear. Here, we further reported the crystal structure of S. mutans FtsZ, revealing a unique lateral interface. Through protein polymerization and GTPase activity assay, we experimentally demonstrated that the mutation of Arg68 on this lateral interface significantly reduced the functional activity of FtsZ in an acidic environment. The phenotype assay and rat caries model further showed that the mutation of Arg68 effectively inhibited the acid resistance of S. mutans and the occurrence and progress of dental caries in vivo. By employing a molecular dynamics simulation analysis, we conclude that the mutation of Arg68 disrupts the conformation change necessary for SmFtsZ polymerization under acidic conditions. Our study proposes a novel mechanism to maintain FtsZ function in bacteria and could be a potential target for antimicrobial drugs to inhibit the growth of S. mutans in acidic environments.

Maintaining carbon/nitrogen (C/N) metabolic balance is essential for cellular homeostasis, allowing microorganisms to adapt to fluctuating environmental conditions. In the autotrophic cyanobacteria, the C/N balance is achieved through a sophisticated network that coordinates the uptake of inorganic carbon and nitrogen, including the ATP-binding cassette (ABC) transporters CmpABCD and NRT that import bicarbonate and nitrate, respectively. Notably, both transporters possess an extra C-terminal regulatory domain (CRD) that is fused to one of the nucleotide-binding domains (NBDs). Via structure guided site-directed mutagenesis and bicarbonate transport activity assays, we found that CmpABCD is tightly regulated by the nitrate-binding CRD. At a low intracellular nitrate concentration, CmpBCD adopts an auto-inhibited conformation, in which the CRD locks the two NBDs of CmpC and CmpD. Upon binding to the nitrate, the CRD is released from NBDs and becomes highly flexible, thus restoring the transport activity of CmpABCD. We propose a distinct regulatory mechanism of ABC transporters, which may be broadly applicable to those fused with a regulatory domain. Moreover, these findings combined with previous reports establish a direct link between the inorganic carbon uptake and intracellular nitrate level through an ABC importer, providing a straightforward and economic strategy that coordinates the C/N homeostasis.

Ethylene (C2H4) functions both as a key phytohormone regulating plant growth and development and as an essential feedstock in organic chemical synthesis. Reliable detection of C2H4 is critical for monitoring emissions during crop cultivation and ensuring safety in industrial transportation. However, most existing C2H4 sensors rely on noble-metal catalysts and/or high-operating temperature, which significantly constrain their practical applications. Moreover, achieving high specificity in C2H4 recognition remains a major challenge. Inspired by the signal transduction mechanism of plant C2H4 receptor, this study propose a biomimetic sensing strategy based on a facilely synthesized cuprous-cystine complex (Cu2Cyt), which features a sulfur-bridged Cu+ coordination center that mimics the biological binding site for C2H4 recognition. The noble-metal-free wearable sensor was fabricated by depositing a Cu2Cyt/MXene composite onto a flexible interdigital electrode, enabling room-temperature detection of C2H4 emitted from fruits or leaked from transport pipelines of chemical industries. It exhibits a detection range (0.05-5 ppm), an ultra-low detection limit of 1.07 ppb, fast response/recovery (51/92 s), high sensitivity of 3.64%·ppm-1 in trace concentration range of 0-0.5 ppm, and good reversibility and reproducibility. Overall, this work offers a bioinspired design strategy for low-cost, high-performance, noble-metal-free, and wearable sensors, capable of trace-level C2H4 monitoring.

Many invertebrates lack erythrocytes and instead rely on extracellular hemoglobin assemblies, termed erythrocruorins, for oxygen transport. Here we report a 2.84 Å cryo-electron microscopy (cryo-EM) structure of Perinereis linea erythrocruorin (PlEc). PlEc is a ∼3.3 MDa megacomplex composed of 180 polypeptide chains organized into 12 protomers, forming a hexagonal bilayer with D6 symmetry. Each protomer consists of 12 globin subunits and three linker subunits, adopting a mushroom-like architecture. The cap of the mushroom is formed by a globin dodecamer associated with a heterotrimeric linker head, and the stem consists of a triple-stranded coiled coil derived from the N-terminal helices of three linker subunits. Biochemical assays show that PlEc has thermal stability and auto-oxidation rate comparable to those of other erythrocruorins, but displays relatively lower oxygen-binding affinity. These findings provide mechanistic insights into the quaternary assembly of invertebrate erythrocruorins and lay the groundwork for the potential biomedical applications.

In plants, peroxisomal β oxidation is essential for energy production, sugar metabolism and the regulation of hormonal signaling. The Arabidopsis COMATOSE (CTS) gene, which encodes the peroxisomal ATP-binding cassette transporter ABCD1 (also known as CTS or PAX1), mediates the import of various fatty acyls and hormones into peroxisomes for β oxidation. Although physiological evidence has demonstrated that defects in CTS impair plant development and growth, the underlying molecular mechanisms remain poorly understood. In this study, biochemical assays confirm that CTS transports a broad range of fatty acyl-CoAs, as well as indole-3-butyric acid (IBA), an auxin and precursor to indole-3-aceditc acid, and auxin herbicide 2,4-dichlorophenoxy butyric acid (2,4-DB). We further solve five cryo-EM structures of CTS: the apo form, ATP-bound, and three substrate-bound states (C12:0-, IBA- and 2,4-DB-CoA) at near-atom resolutions. These structures reveal that CTS binds a single substrate molecule in a characteristic U-shaped conformation. Moreover, physiological studies using point mutations of key substrate-binding residues identify critical residues essential for its function. Our findings reveal the molecular principles by which CTS integrates lipid metabolism, hormone regulation, and xenobiotic activation throughout the plant life cycle, as well as underscore its potential as a target for crop improvement and herbicide development.

Gastric mucosal inflammation is a critical precondition of various gastric diseases, and development of safe and effective anti-inflammatory agents for prompt resolution of acute inflammation at early stage is vital to preventive medicine. B vitamins are essential water-soluble nutrients with reported anti-inflammatory properties, yet their potent regulatory effects in gastric mucosal inflammation are not systemically assessed. In this study, we adopted a lipopolysaccharide (LPS)-induced inflammatory mouse gastric organoid model to screen for anti-inflammatory B vitamin family members. With the anti-inflammatory effect of vitamin B12 (VB12) being validated in this gastric organoid model, which is consistent with the roles in other biological settings, further screening of the rest B vitamin members identified vitamin B6 (VB6) as the most potent anti-inflammatory agent as it preventatively ameliorated LPS-induced organoid collapse and preserved gastric epithelial polarity in the inflammatory organoids. Functional assays confirmed that VB6 significantly downregulated the expressions of key pro-inflammatory Tnf, Cxcl1, and Il1b genes, and inhibited TNF-α and IL-1β protein secretions. Further mechanistic exploration revealed that VB6 antagonized LPS-induced inflammatory responses by targeting the transcription of positive regulatory genes in core LPS-mediated inflammatory signaling pathways. These findings provide important experimental evidence for the development of nutrition-based intervention strategies for gastric inflammatory diseases in human.

Viral infections pose ongoing threats to human health, emphasizing the continued need for effective antivirals. Antiviral drug discovery often relies on phenotype-based drug discovery (PBDD) and target-based drug discovery (TBDD). However, current computational approaches focus solely on predicting compounds that bind to specific antiviral-related targets, overlooking the biological relevance of antiviral phenotypes. Here, we propose DeepAVC, a large language model-powered framework that integrates DeepPAVC for PBDD and DeepTAVC for TBDD. As a result, DeepAVC outperforms existing baselines in antiviral compound prediction and provides high interpretability by identifying key atoms and residues involved in compound-protein interactions. Moreover, we demonstrate that DeepPAVC and DeepTAVC complement each other and can be used synergistically. We further confirm DeepAVC's power through both in vitro and in vivo experiments. Finally, we identify MNS as a novel broad-spectrum antiviral compound with greater efficacy than Sisunatovir. All these results suggest that DeepAVC is a valuable tool for antiviral drug discovery.

Dear Editor, Accurate segregation of replicated chromosomes during mitosis relies on the coordination between kinetochore attachment to spindle microtubules and cell cycle progression.The spindle assembly checkpoint(SAC)serves as the primary surveillance mechanism that senses the faulty kinetochore-microtubule attachment and catalyzes the assembly of the mitotic checkpoint complex(MCC).

Efficient genome packaging is a critical step in the phage life cycle, directly influencing the viral maturation and infectivity. In tailed phages, this process is driven by a packaging motor composed of a portal protein and a terminase complex. The terminase complex usually consists of a large subunit (TerL) and a small subunit (TerS), which cooperate to recognize, cleave, and translocate genomic DNA into the capsid. However, due to the remarkable diversity and complexity of phage packaging systems, the molecular mechanisms governing TerS-mediated DNA recognition remain poorly understood. Here, we report the 3.51 Å cryo-electron microscopy structure of the TerS from the short-tailed cyanophage Pam5, which infects the host Pseudanabaena mucicola Chao 1806. Pam5 TerS assembles into a nonameric ring with a radially symmetric spiral architecture. Biochemical assays show that Pam5 TerS recognizes the genomic DNA via a specific interaction between the N-terminal helix-turn-helix (HTH) domain of TerS and a 21-bp DNA sequence within the terS gene. In contrast, the TerS from another short-tailed cyanophage, Pam1, which infects the same host, binds to DNA in a sequence-independent manner. These findings reveal that cyanophages, even infecting the same host, could adopt two distinct DNA recognition strategies: HTH-mediated sequence-dependent or sequence-independent modes. This work provides structural and mechanistic insights into the diverse DNA-recognition strategies of TerS and advances our understanding of the evolutionary plasticity of viral genome packaging mechanisms.

Autoimmune hepatitis (AIH) is a progressive and currently incurable inflammatory liver disorder. Accumulating evidence suggests that intestinal Klebsiella pneumoniae may contribute to AIH. However, the specific bacterial features underlying its role remain unclear. We isolated 32 strains of K. pneumoniae from both healthy and AIH patients. Genomic and phenotypic analyses identified a unique strain, KpA4-1 from an AIH patient, distinguished by its production of membrane vesicles (MVs) encapsulating plasmid DNA (p2). Administration of p2-containing MVs in mice elevated serum liver enzymes and antinuclear antibodies (ANA), indicating liver injury and autoimmune activation. Oral administration of KpA4-1 in AIH mice exacerbated AIH pathology, evidenced by elevated liver enzymes, increased ANA titers, and enhanced hepatic CD8 + T cell infiltration. Mechanistically, KpA4-1 activated the cGAS-STING signaling pathway that potentiated hepatic inflammation in AIH mice. The pivotal role of the p2 was further validated by attenuated AIH pathology in mice treated with KpA4-1Δp2 or bacteriophage therapy targeting KpA4-1. Collectively, these findings uncover a novel mechanism by which the intestinal K. pneumoniae exacerbates AIH via DNA-encapsulated MVs, highlighting their potential as diagnostic or therapeutic targets.

Carboxysomes are self-assembled bacterial microcompartments (BMCs) that encapsulate the enzymes RuBisCO and carbonic anhydrase into a proteinaceous shell, enhancing the efficiency of photosynthetic carbon fixation. The chaperone CcmS was reported to participate in the assembly of β-carboxysomes; however, the underlying molecular mechanism remains elusive. We report the crystal structure of CcmS from Synechocystis sp. PCC 6803, revealing a monomer of α/β fold. Moreover, its complex structures with two types of BMC hexamers, CcmK1 homohexamer and CcmK1-CcmK2 heterohexamer, reveal a same pattern of CcmS binding to the featured C-terminal segment of CcmK1. Upon binding to CcmS, this C-terminal segment of CcmK1 is folded into an amphipathic α-helix protruding outward that might function as a hinge to crosslink adjacent BMC-H hexamers, thereby facilitating concerted and precise assembly of the β-carboxysome shell. Deletion of the ccmS gene or the 8-residue C-terminal coding region of ccmK1 resulted in the formation of aberrant and fewer carboxysomes, suppressed photosynthetic capacity in Synechocystis sp. PCC 6803. These findings enable us to propose a putative model for the chaperone-assisted assembly of β-carboxysome shell and provide clues for the design and engineering of efficient carbon fixation machinery.

The human ATP-binding cassette (ABC) transporter ABCA7 participates in the lipidation of apolipoprotein ApoE, a commonly recognized risk factor for Alzheimer’s disease (AD). How ABCA7 is involved in the molecular pathogenesis of AD remains poorly understood. Using cryoelectron microscopy (cryo-EM), we determined ABCA7 structures in the apo and substrate-bound forms, respectively. Combined with activity assays, we assigned the residues that specifically bind two molecules of phosphatidylserine (PS) that are arranged in a “tail-to-tail” manner. Pull-down assays confirmed that ApoE directly interacts with ABCA7; and moreover, both ATPase and lipid transport activities of ABCA7 were significantly enhanced in the presence of ApoE. We also measured the activities of a familial AD variant and a protective clinically reported variant in the ABCA7 gene. Our findings not only give structural insights into ABCA7-mediated PS translocation, but we also provide first biochemical evidence for its link to AD by forwarding lipids to ApoE.

Cyanophages, which are bacteriophages that specifically infect host cyanobacteria, also utilize the tail to initiate host recognition and adsorption. Owing to the limited structural information on cyanophages, our understanding of the mechanism by which cyanophages specifically recognize their hosts remains largely unknown. Here, we determined the intact cryoelectron microscopy structure of a freshwater cyanopodophage Pan3, which consists of an icosahedral shell and a short tail comprising four modular components: the dodecameric adaptor, hexameric nozzle, trimeric needle, and six heterohexameric tailspikes. Notably, each tailspike features an SGNH esterase domain fused to a lectin domain, forming a continuous groove complementary to the host lipopolysaccharide. These findings provide insights into the receptor engagement in Podoviridae, and establish a structural framework for cyanophage and host interactions that may guide future antibacterial interventions against harmful blooms.

Root caries present a significant challenge in dentistry. The unsatisfactory prognosis of restorative treatments requires novel, noninvasive preventive strategies. Here, we developed an amelogenin-derived peptide-modified poly(amidoamine), PAMAM-C11, to prevent demineralization in caries lesions and control periodontal destruction. PAMAM can induce dentin remineralization, whereas the C11 peptide strongly binds hydroxyapatite. When C11 is modified on the surface groups of PAMAM, it anchors the entire molecule on demineralized dentin surfaces, thereby resisting washout and enhancing the mineralization efficiency, especially in the presence of collagenase in the cariogenic environment. PAMAM-C11 also inhibits matrix metalloproteinases in dentin and periodontal tissues, protecting the necessary mineralization templates and controlling periodontal destruction. Furthermore, PAMAM-C11 can promote the proliferation and osteogenic differentiation of periodontal ligament stem cells, indicating its potential use in periodontal regeneration. These findings were ultimately validated in an in vivo rat caries model. It can be concluded that PAMAM-C11 has great potential for clinical applications on root caries prevention.

Streptococcus mutans is recognized as the primary etiological agent of dental caries, one of the most prevalent infectious diseases globally. Its remarkable acid tolerance enables survival and proliferation in the low-pH biofilm microenvironment, establishing S. mutans as the dominant species in dental plaque and a key contributor to cariogenesis. Although numerous studies have identified genes linked to acid tolerance mechanisms, the full set of essential acid tolerance genes within its genome remains incompletely characterized, largely due to the lack of systematic, genome-scale investigations. To address this knowledge gap, we constructed a genome-wide pooled CRISPR interference (CRISPRi) library targeting 95% of the predicted S. mutans genes and employed next-generation sequencing to identify acid tolerance determinants systematically. Our screen revealed 95 acid tolerance-associated genes, a subset of which were functionally validated through gene knockout studies. Functional enrichment analysis demonstrated significant associations with metabolic pathways (including cofactor biosynthesis and amino/nucleotide sugar metabolism), tRNA modification, and transcriptional regulation. Protein-protein interaction (PPI) network analysis identified critical interactors (ComYC, SMU\_1979c, DeoC, AcpP, NadD, and SMU\_1988c) and two functionally cohesive modules. These findings provide novel mechanistic insights into the acid adaptation strategies of S. mutans and highlight potential therapeutic targets for caries prevention.

Background Dental caries is a bacterial-mediated infectious disease that affects the hard tissues of the tooth, with Streptococcus mutans being the primary cariogenic pathogen due to its robust biofilm-forming ability. Controlling biofilm formation is essential for caries prevention. Recent studies have indicated that D-amino acids, which are not incorporated into proteins, play regulatory roles in bacterial processes such as growth inhibition and biofilm dispersal. However, whether D-amino acids can inhibit the growth of S. mutans remains controversial. This study aimed to investigate the effects of D-amino acids on S. mutans growth and biofilm formation in vitro, as well as their anti-caries efficacy in a rat caries model.Materials and Methods This study utilized Streptococcus mutans UA159 to screen 15 D-amino acids for growth inhibition, identifying D-histidine (D-His) as the most effective. Minimum inhibitory concentration, growth curves, biofilm assays, and transcriptomic analysis were performed in vitro. Anti-caries efficacy was evaluated in a rat model using Micro-CT and Keyes scoring.Results D-His significantly inhibits the planktonic growth of S. mutans and delays biofilm formation, particularly in the early stages. Furthermore, RNA sequencing revealed 417 upregulated genes and 394 downregulated genes in D-His-treated S. mutans, with significant alterations in pathways related to carbohydrate utilization, protein biosynthesis, and transmembrane transport. Moreover, D-His exhibited effective caries prevention in an in vivo rat model.Conclusion These findings suggest that D-His has potential as an anti-caries agent by targeting S. mutans growth and biofilm dynamics.

FtsZ is the core protein for cell division in bacteria that can polymerize into Z-rings and drive cytokinesis. Understanding how bacteria maintain the correct function of FtsZ under various environmental stresses is crucial for novel antibacterial drug discovery. Our previous study revealed that the FtsZ in S. mutans has higher self-assembly and GTPase activity under acidic stress, which may be responsible for the cariogenesis of S. mutans. However, the mechanism is still unknown. Here, we further reported the crystal structure of S. mutans FtsZ, revealing a unique lateral interface. Through protein polymerization and GTPase ability assay, we experimentally demonstrated that mutation of Arg68 on this lateral interface significantly reduced the functional activity of FtsZ in an acidic environment. The phenotype assay and rat caries model further showed that mutation of Arg68 effectively inhibited the acid resistance of S. mutans and the occurrence and progress of dental caries in vivo. By employing a molecular dynamics simulation analysis, we conclude that mutation of Arg68 disrupts the conformation change necessary for SmFtsZ polymerization under acidic conditions. Our study proposes a novel mechanism to maintain FtsZ function in bacteria and could be a potential target for antimicrobial drugs to inhibit the growth of S. mutans in an acidic environment. ### Competing Interest Statement The authors have declared no competing interest.

Structural variation (SV) typically refers to alterations in DNA fragments at least 50 base pairs long in the human genome. It can alter thousands of DNA nucleotides and thus significantly influence human health, disease, and clinical phenotypes. There is a shared and growing recognition that the emergence of effective computational tools and high-throughput technologies such as short-read sequencing and long-read sequencing offers novel insight into SV and, by extension, diseases affecting planetary health. However, numerous available SV tools exist with varying strengths and weaknesses. This is currently hampering the abilities of scholars to select the optimal tools to study SVs. Here, we reviewed 175 tools developed in the past two decades for SV detection, annotation, visualization, and downstream analysis of human genomics. In this expert review, we provide a comprehensive catalog of SV-related tools across different technology platforms and summarize their features, strengths, and limitations with an eye to accelerate systems science and planetary health innovations.

Recent language models have significantly accelerated our understanding on the massive biological data, using protein or DNA/RNA sequences as a single-language modality. Here we present a dual-language foundation model, which integrates both protein and coding sequences (CDS) for pre-training. Compared to the benchmark models, it shows a superior performance up to ~20% on both protein and mRNA-related discriminative tasks, and gains the capacity to de novo generate coding sequences of ~50% increased protein yield. Moreover, the model also possesses the knowledge transferability from the pre-training data to the upstream 5' untranslated regions. These findings indicate the intrinsic correlations between protein and its CDS, as well as the coding region and beyond. It provides a new paradigm that leverages the multiple-language foundation model to interpret the hidden context of distinct corpora/biological languages, which could be further applied to mine the yet-unknown biological information/correlation beyond the Central Dogma. ### Competing Interest Statement C.-Z.Z., H.-R.Z. and Y.C. have submitted a patent application related to this language model. Other authors have declared no conflicts of interest.