Rodriguez, Z. | Search bioRxiv

bioRxiv2026

Cryoelectron tomography of HIV-1 cell-cell transmission conjugates reveals a secluded environment for viral assembly and transfer

Cell-cell transmission of HIV-1 (CCT) is a highly efficient mode of intrahost transmission that provides viral particles broad protection from antiretroviral agents including antiretroviral drugs, host restriction factors, and broadly neutralizing antibodies. Interestingly, the exact factors that grant viral particles increased protection and efficiency during intrahost spread remain unclear. Using a T cell co-culturing system and correlative cryoelectron tomography (cryoET) workflow, we investigated the architecture of HIV-1 CCT sites in a near-native, in situ context to address why CCT is efficient and grants this resistance. Contrary to previous models which suggest large, virus-packed sites, our 3D reconstructions reveal that CCT occurs within small intercellular spaces containing on average 1-5 viral particles. Surrounding these spaces are long, tight membrane interfaces that seclude the viral particles from the remaining extracellular environment. These observations suggest a model where spatial isolation may limit accessibility of antiretroviral agents to the virus-containing spaces thereby conferring protection to viral particles during transmission. To functionally validate these structural insights, we developed a quantitative flow cytometry strategy that decouples CCT conjugate formation from successful CCT infection through the analysis of multicell events. This methodology allows us to systematically compare the impact different molecules such as Env and CD4 have on HIV-1 CCT in a quantitative and population-level manner. Using this approach, we determined that initial HIV-1 CCT conjugate formation is partially dependent on CD4, but the Env involved in conjugate formation may differ from Env used for viral entry. Overall, these findings may prompt a rethinking of intervention strategies for HIV-1 CCT and have further implications with cytoplasmic trafficking, nuclear import, and host restriction factors.

microbiology↗

bioRxiv2023

Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection

Many eukaryotic viruses require membrane-bound compartments for replication, but no such organelles are known to be formed by prokaryotic viruses1-3. Bacteriophages of the Chimalliviridae family sequester their genomes within a phage-generated organelle, the phage nucleus, which is enclosed by a lattice of the viral protein ChmA4-10. Previously, we observed lipid membrane-bound vesicles in cells infected by Chimalliviridae, but due to the paucity of genetics tools for these viruses it was unknown if these vesicles represented unproductive, abortive infections or a bona fide stage in the phage life cycle. Using the recently-developed dRfxCas13d-based knockdown system CRISPRi-ART11 in combination with fluorescence microscopy and cryo-electron tomography, we show that inhibiting phage nucleus formation arrests infections at an early stage in which the injected phage genome is enclosed within a membrane-bound early phage infection (EPI) vesicle. We demonstrate that early phage genes are transcribed by the virion-associated RNA polymerase from the genome within the compartment, making the EPI vesicle the first known example of a lipid membrane-bound organelle that separates transcription from translation in prokaryotes. Further, we show that the phage nucleus is essential for the phage life cycle, with genome replication only beginning after the injected DNA is transferred from the EPI vesicle to the newly assembled phage nucleus. Our results show that Chimalliviridae require two sophisticated subcellular compartments of distinct compositions and functions that facilitate successive stages of the viral life cycle.

cell biology↗