bioRxiv Science⌕ Search

bioRxiv · 10.1101/2025.09.15.676328

Endocytic motif on HIV Env regulates cleavage status and antibody neutralization of cell-free and cell-to-cell infection

Abstract

Antibodies inhibit human immunodeficiency virus type 1 (HIV-1) infection by targeting the envelope glycoprotein (Env). Env cleavage is a key determinant of antibody binding, as cleavage reduces Env flexibility and alters glycosylation. Given the greater abundance of uncleaved Env on the cell surface compared to virions, we investigated whether Env endocytosis, initiated through a membrane-proximal tyrosine motif in its cytoplasmic tail, regulates the abundance of cleaved Env at the cell surface. We hypothesize that such a shift would alter the cleavage and glycosylation profile of cell surface Env, affecting the sensitivity of cell-to-cell infection to neutralizing antibodies. To address this, we generated an endocytic mutant (ASPI-Env) and compared its antigenic properties to a cleavage-site mutant (SEKS-Env). Immunoprecipitation and ratiometric antibody binding studies of cell surface Env demonstrated that the ASPI mutation increases the amount of uncleaved Env on the cell surface. Consequently, ASPI-Env in cell-free infection was more sensitive to NAbs recognizing uncleaved Env. Notably, only b12, which can engage both cleaved and uncleaved Env but has a higher affinity for uncleaved Env, showed increased inhibition of ASPI-Env during cell-to-cell infection. This mirrors the enhanced neutralization of SEKS-Env during the cell-to-cell transfer assay and supports a model in which uncleaved Env participates in CD4-dependent virion transfer. Finally, the ASPI mutation altered lectin binding and differentially affected cell-to-cell and cell-free infections. Together, these findings indicate that Env endocytosis modulates the abundance of cleaved Env at the cell surface, thereby influencing antibody neutralization and lectin recognition in distinct modes of HIV-1 transmission. IMPORTANCEWe find that Env endocytosis modulates the antigenicity of Env on both the cell surface and virions. Blocking internalization increased uncleaved Env on the cell surface, thereby reshaping HIV-1 neutralization due to enhanced binding of antibodies that preferentially recognize uncleaved Env. We further show that uncleaved Env on the cell surface can initiate CD4-dependent transfer of virions across virological synapses. These findings demonstrate that Env endocytosis shapes cleavage-associated antigenicity in a manner that can differentially impact the recognition and neutralization of cells and viruses. The impact of uncleaved Env on neutralization indicates that a broader spectrum of cleaved and uncleaved Env conformations may be relevant when designing vaccines and cure strategies that must contend with a diverse antigenic landscape.

Source connections

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Figueroa Acosta, D. M., Li, H., Chen, B. K.. 2025-09-15. Endocytic motif on HIV Env regulates cleavage status and antibody neutralization of cell-free and cell-to-cell infection. https://doi.org/10.1101/2025.09.15.676328

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

Rapid and largely reversible shifts in the canine fecal metabolome during dietary change

Diet can rapidly change the fecal metabolome, but less is known about recovery after the original diet is restored. We used untargeted UPLC-MS metabolomics to analyze 72 fecal samples from nine Pumi dogs during an owner-managed switch from dry food to raw food and back to dry food. Diet phase accounted for a large proportion of variation in both ionization modes. More than 13,000 LC-MS features changed at the first sampling point after the switch to raw food, with a similarly large response after return to dry food. Among features significant in both comparisons, more than 99% changed in opposite directions. At the final sampling point, no positive-mode (ESI+) features and only 13 negative-mode (ESI-) features differed from the second dry-food baseline under the same threshold. BARF-associated patterns persisted in analyses excluding individual dogs and in pedigree-adjusted candidate models, although individual feature effects depended on normalization. Putative metabolites from several biochemical classes differed in their response and recovery. The fecal metabolome therefore changed rapidly and returned largely toward baseline, with differences among dogs.

microbiology↗

Taxonomic and functional concordance between full-length ONT 16S and ONT shotgun metagenomics in the canine gut microbiome

Background: Full-length Oxford Nanopore Technologies (ONT) 16S rRNA sequencing provides a scalable view of microbial community composition and can support phylogeny-based functional prediction, but it is not equivalent to shotgun metagenomics. We asked which biological conclusions are preserved when the same canine fecal specimens are profiled by full-length ONT 16S and ONT whole-genome shotgun (WGS) sequencing, and how their agreement depends on analytical scale, reference representation and classifier. Methods: Ninety-seven fecal specimens from 51 dogs were profiled with both assays from the same DNA extract. Functional profiles predicted from NanoASV/NanoPredict with PICRUSt2 were compared with WGS-supported KEGG Ortholog (KO) profiles generated by Kadath. Taxonomy was benchmarked in a source-genome-matched RefSeq universe and in a host-specific DogMAG universe using minitax and Kraken2. Agreement was evaluated at whole-profile, feature-abundance, detection, between-sample structure and biological-inference scales. Age-associated transfer was assessed with dog-aware continuous mixed models, grouped signed-score analyses and paired/dog-blocked PERMANOVA. Results: Functional whole-profile concordance was high: median within-sample CLR Spearman correlations ranged from 0.781 to 0.860 across developmental strata, while between-sample functional structure remained significant by Mantel (rho=0.543) and Procrustes (r=0.693; both p=0.001). Feature-wise transfer was substantially weaker (median KO-wise CLR Spearman=0.318). Continuous age-associated KO slopes showed substantial cross-assay concordance (Spearman=0.727; signed-score Spearman=0.753; direction agreement=77.9%), although 1,290/5,258 eligible KOs retained significant assay-by-age interactions. Taxonomically, exact genus/species abundance agreement was much lower than agreement in between-sample ecological structure. Host-specific DogMAG improved species-level median Spearman from 0.261 to 0.656 for minitax SpeciesEstimate and from 0.181 to 0.512 for Kraken2. The classifier effect was independent of reference choice: under both RefSeq and DogMAG, minitax yielded stronger 16S-WGS concordance than Kraken2, with all eight prespecified RefSeq paired genus/species endpoints and all 10 DogMAG primary paired endpoints significant after BH correction. The same ordering extended to developmental inference, with DogMAG genus/species age-slope concordance of 0.795/0.799 for SpeciesEstimate versus 0.693/0.702 for Kraken2. Taxonomic Aitchison PERMANOVA detected age-associated structure in every assay/reference/classifier/rank combination, whereas age-by-assay interactions were consistently significant but small (R2 approximately 1.1 to 2.2%). Stricter NanoASV identity thresholds removed substantial 16S abundance without improving species-level agreement. Conclusions: The extent of cross-assay agreement depends on the level of analysis. Full-length ONT 16S preserves broad functional organization, ecological structure and much of the direction of age-associated change, but exact fine-rank composition, individual-feature abundance and effect magnitude remain assay dependent. Host-specific reference representation substantially narrows the taxonomic gap, and classifier choice exerts an additional independent effect: within the same matched reference set, minitax consistently yields stronger 16S-WGS concordance than Kraken2 across abundance, detection, ecological-distance and developmental-inference endpoints. Full-length ONT 16S is therefore well suited to broad ecological screening and hypothesis generation, whereas WGS remains preferable when conclusions depend on quantitative fine-rank composition, directly supported gene content or precise feature-level effect estimates.

microbiology↗

Matrix-controlled emergence of biofilm architecture shapes antimicrobial survival

Biofilms are structured microbial communities whose extracellular matrix is widely regarded as a basis of their protection against antimicrobial compounds. Yet how matrix production by individual bacteria gives rise to collective architecture and antimicrobial protection remains poorly understood. Here, we systematically varied expression of the master biofilm regulator csgD in Salmonella enterica and found that increasing matrix production reorganizes biofilms from dense, isotropic packings into sparse, nematically aligned communities by altering cell-cell interactions. By combining experimentally measured biofilm architectures with reaction-diffusion modeling, we show that these structural changes produce distinct patterns of antimicrobial killing, ranging from preferential killing near the liquid-biofilm interface to more uniform killing throughout the community. Consequently, increasing matrix production unexpectedly reduces antimicrobial survival by shifting the biofilm into different transport regimes, while strain-specific physiological differences further modulate antimicrobial depletion. Rather than acting as a passive barrier, EPS therefore shapes antimicrobial susceptibility by reorganizing biofilm architecture and its transport properties. EPS thus provides a physical link between molecular regulation, collective architecture and antimicrobial survival, providing a quantitative framework for understanding how cellular matrix production generates emergent biofilm function.

microbiology↗