N Nature Microbiology · Dec 03, 2025 Transcription co-inhibition alters drug resistance evolution and enhancesMycobacterium tuberculosisclearance from granulomas Mycobacterium tuberculosis(Mtb), the causative agent of tuberculosis, remains the deadliest human pathogen. Treatment is hampered by drug resistance and the persistence of slow-growing or non-replicating populations. Rifampicin, a cornerstone of first-line therapy, inhibits transcription during promoter escape, but resistance mutations undermine efficacy and drive resistance spread. We revisited the transcription cycle as an antibacterial target by characterizing AAP-SO2, an RNA polymerase inhibitor with whole-cell activity against Mtb. AAP-SO2slows the nucleotide addition cycle, disrupting elongation and termination. Rifampicin-resistant mutations impose fitness costs by perturbing the balance of these steps, creating exploitable weaknesses. Inhibition of transcription with AAP-SO2reduced the evolution of rifampicin resistance and was especially effective against the most common resistant mutant. Combination treatment with rifampicin and AAP-SO2synergistically killed non-replicating Mtb in an ex vivo rabbit granuloma model. These findings show that exploiting functional vulnerabilities of the transcription cycle can counter rifampicin resistance and improve clearance of recalcitrant Mtb populations. Antibiotics Cryoelectron microscopy Pathogens Transcription biology
N Nature Microbiology · Nov 04, 2025 Structural and mechanistic insights into herpesvirus helicase–primase and its therapeutic inhibitors The herpes simplex virus (HSV) helicase–primase (HP) complex is a promising anti-herpes therapeutic target. However, progress in developing highly effective small-molecule HP inhibitors (HPIs) for the treatment of genital herpes has been hindered by the lack of structural information on the HP complex and the incomplete understanding of the mechanism of action of HPIs. Here we present the cryogenic electron microscopy structure of the HSV-1 HP apo-complex (3.8 Å), along with structures bound to pritelivir (3.2 Å) and amenamevir (3.2 Å)—two clinically active, chemically distinct HPIs. The potency of both inhibitors against HSV variants bearing mutations within the HPI binding pocket supports the high-resolution mapping of key molecular interactions while revealing residues that govern their antiviral spectrum against alphaherpesviruses. Our results provide important insight into the unique architecture of the HP complex and the mechanism of inhibition of HPIs, paving the way for the development of next-generation antivirals to treat herpesvirus infections. Cryoelectron microscopy Herpes virus Structure-based drug design
N Nature Microbiology · Oct 31, 2025 Prefusion structure, evasion and neutralization of HSV-1 glycoprotein B Glycoprotein B (gB) refolds between prefusion and postfusion conformations to facilitate herpesvirus entry into host cells. However, the isolation of prefusion-specific neutralizing antibodies, effective against other viral entry machines, has been challenging. Here we describe stabilization of the prefusion gB ectodomain from herpes simplex virus 1 (HSV-1), determine ectodomain structures at 2.9- to 4.1-Å resolution using cryogenic electron microscopy (cryo-EM) and isolate a prefusion-specific gB-neutralizing antibody termed WS.HSV-1.24. Murine immunization with gB stabilized in the prefusion conformation induced high titres of antibodies binding to both prefusion and postfusion gB, but—most notably—without measurable serum neutralization. Accessibility analysis revealed iso-surface exposure, with accessible surfaces on prefusion HSV-1 gB also exposed on postfusion gB. Structural analysis suggested substantial plasticity, with regions that refolded between pre- and postfusion conformations relegated to domain interfaces with limited accessibility; indeed, WS.HSV-1.24 recognized a domain-interface refolding region to facilitate neutralization. We propose that prefusion HSV-1 gB evades neutralization by most antibodies through an iso-surface display that is coupled to structural plasticity. Cryo-EM structures of the stabilized prefusion conformation of the glycoprotein B ectodomain—the HSV-1 entry machine—identify a prefusion-specific neutralizing antibody and reveal how prefusion glycoprotein B may evade antibody-mediated neutralization. Antibodies Cryoelectron microscopy Herpes virus Vaccines Viral immune evasion biology mouse experiments
N Nature Microbiology · Oct 31, 2025 Structures of the sheathed flagellum reveal mechanisms of assembly and rotation inVibrio cholerae Motility promotes the complex life cycle and infectious capabilities ofVibrio choleraeand is driven by rotation of a single polar flagellum. The flagellar filament comprises four flagellin proteins (FlaA–D) and is covered by a membranous sheath continuous with the outer membrane. Here we combine in situ cryo-electron microscopy single-particle analysis, fluorescence microscopy and molecular genetics to determine 2.92–3.43 Å structures of the sheathed flagellar filament from intact bacteria. Our data reveal the spatial arrangement of FlaA–D, showing that FlaA localizes at the cell pole and functions as a template for filament assembly involving multiple flagellins. Unlike unsheathed flagellar filaments, the sheathed filament fromV. choleraepossesses a highly conserved core but a smooth, hydrophilic surface adjacent to the membranous sheath. A tiny conformational change at the single flagellin level results in a supercoiled filament and curved membranous sheath, supporting a model wherein the filament rotates separately from the sheath, enabling the distinct motility ofV. cholerae. Bacterial structural biology Cryoelectron microscopy biology
N Nature Microbiology · Oct 10, 2025 Dipeptidase 1 is a functional receptor for a porcine coronavirus Coronaviruses of the subgenusEmbecovirusinclude several important pathogens, such as the human seasonal coronaviruses HKU1 and OC43, bovine coronavirus and porcine haemagglutinating encephalomyelitis virus (PHEV). While sialic acid is thought to be required for embecovirus entry, protein receptors remain unknown for most of these viruses. Here we show that PHEV does not require sialic acid for entry and instead uses dipeptidase 1 (DPEP1) as a receptor. Cryo-electron microscopy at 3.4–4.4 Å resolution revealed that, unlike other embecoviruses, PHEV displays both open and closed conformations of its spike trimer at steady state. The spike receptor-binding domain (RBD) exhibits extremely high sequence variability across embecoviruses, and we found that DPEP1 usage is specific to PHEV. In contrast, the X-ray structure of the RBD–DPEP1 complex at 2.25 Å showed that the structural elements involved in receptor binding are conserved, highlighting the remarkable versatility of this structural organization in adopting novel receptor specificities. Cryoelectron microscopy Viral evolution Virus–host interactions Virus structures X-ray crystallography biology
N Nature Microbiology · Oct 01, 2025 Structure of a distinct β-barrel assembly machinery complex in the Bacteroidota The Gram-negative β-barrel assembly machinery (BAM) complex catalyses the folding and membrane insertion of newly synthesized β-barrel outer membrane proteins. The BAM is structurally conserved, but most studies have focused on Gammaproteobacteria. Here, using single-particle cryogenic electron microscopy, quantitative proteomics and functional assays, we show that the BAM complex is distinct within the Bacteroidota. Cryogenic electron microscopy structures of BAM complexes from the human gut symbiontBacteroides thetaiotaomicron(3.3 Å) and the human oral pathogenPorphyromonas gingivalis(3.2 Å) show similar, seven-component complexes of ~325 kDa. The complexes are mostly extracellular and comprise canonical BamA and BamD; an integral, essential outer membrane protein, BamG, that associates with BamA; and four surface-exposed lipoproteins: BamH–K. Absent from the BAM in Pseudomonadota, BamG–K form a large, extracellular dome that may confer additional functionality to enable the folding and assembly of β-barrel–surface-exposed lipoprotein complexes that are a hallmark of the Bacteroidota. Our findings develop our understanding of fundamental biological processes in an important bacterial phylum. Bacterial structural biology Cryoelectron microscopy Microbiology Structural Biology Cryo-EM Proteomics Human
