Automatic detection and measurement of viral replication compartments by ellipse adjustment

The protein composition of human adenovirus replication compartments

Human adenoviruses are double-stranded DNA viruses that replicate in the cell nucleus and induce the formation of replication compartments (RCs) that are critical in viral replication and control of virus-host interactions. RCs are specialized virus-induced subnuclear microenvironments where not only viral genome replication and expression are orchestrated but also host proteins that restrict viral replication are co-opted and subverted. The protein composition of these RCs remains largely unexplored. In this study, we isolated adenovirus RC-enriched fractions from infected cells at different times post-infection and employed a tandem mass tag-based quantitative mass spectrometry approach to identify proteins associated with RCs (data available via ProteomeXchange identifier PXD051745). These findings reveal an elaborate network of host and viral proteins potentially relevant for RC formation and function. To validate the RC-protein components identified by mass spectrometry, we employed immunofluorescence and immunoblotting techniques. Proteins previously described to colocalize in RCs in infected cells were identified in the isolated subnuclear fractions. In addition, we validated newly identified proteins associated with RCs, including the high mobility group box 1 (HMGB1), the SET nuclear proto-oncogene, the structure-specific recognition protein 1 (SSRP1), the CCCTC-binding protein (CTCF), and sirtuin 6 (SIRT6). We identified HMGB1 as a protein that binds to the viral DNA binding protein (DBP). Using shRNA knockdowns and inhibitors, we demonstrated that HMGB1 acts as a proviral factor, promoting efficient viral DNA synthesis and progeny production. Our data further suggest potential candidate targets for therapeutic intervention and provide mechanistic insights into the molecular basis of virus-host interactions.IMPORTANCEHuman adenoviruses serve as models for studying respiratory viruses and have provided critical insights into viral genome replication and gene expression, as well as the control of virus-host interactions. These processes are coordinated within virus-induced subnuclear microenvironments known as RCs. We conducted quantitative proteome analyses of RC-enriched subnuclear fractions at different times post-infection with human adenovirus species C type 5, revealing a multifaceted network of proteins that participate in the regulation of gene expression, DNA damage response, RNA metabolism, innate immunity, and other cellular antiviral defense mechanisms. Furthermore, we validated the localization of several host proteins to viral RCs using immunofluorescence microscopy and immunoblotting and identified cellular HMGB1 as a proviral factor late during infection. These findings represent the first analysis of the proteomes of isolated RCs and not only enhance our understanding of nuclear organization during infection but also shed light on the complex interplay between viral and host factors within RCs.

Sperm chemotaxis is driven by the slope of the chemoattractant concentration field

Spermatozoa of marine invertebrates are attracted to their conspecific female gamete by diffusive molecules, called chemoattractants, released from the egg investments in a process known as chemotaxis. The information from the egg chemoattractant concentration field is decoded into intracellular Ca²⁺ concentration ([Ca²⁺]_i) changes that regulate the internal motors that shape the flagellum as it beats. By studying sea urchin species-specific differences in sperm chemoattractant-receptor characteristics we show that receptor density constrains the steepness of the chemoattractant concentration gradient detectable by spermatozoa. Through analyzing different chemoattractant gradient forms, we demonstrate for the first time that Strongylocentrotus purpuratus sperm are chemotactic and this response is consistent with frequency entrainment of two coupled physiological oscillators: i) the stimulus function and ii) the [Ca²⁺]_i changes. We demonstrate that the slope of the chemoattractant gradients provides the coupling force between both oscillators, arising as a fundamental requirement for sperm chemotaxis.

Imaging the adenovirus infection cycle

Incoming adenoviruses seize control of cytosolic transport mechanisms to relocate their genome from the cell periphery to specialized sites in the nucleoplasm. The nucleus is the site for viral gene expression, genome replication, and the production of progeny for the next round of infection. By taking control of the cell, adenoviruses also suppress cell-autonomous immunity responses. To succeed in their production cycle, adenoviruses rely on well-coordinated steps, facilitated by interactions between viral proteins and cellular factors. Interactions between virus and host can impose remarkable morphological changes in the infected cell. Imaging adenoviruses has tremendously influenced how we delineate individual steps in the viral life cycle, because it allowed the development of specific optical markers to label these morphological changes in space and time. As technology advances, innovative imaging techniques and novel tools for specimen labeling keep uncovering previously unseen facets of adenovirus biology emphasizing why imaging adenoviruses is as attractive today as it was in the past. This review will summarize past achievements and present developments in adenovirus imaging centered on fluorescence microscopy approaches.

Nanoscale organization of rotavirus replication machineries

Rotavirus genome replication and assembly take place in cytoplasmic electron dense inclusions termed viroplasms (VPs). Previous conventional optical microscopy studies observing the intracellular distribution of rotavirus proteins and their organization in VPs have lacked molecular-scale spatial resolution, due to inherent spatial resolution constraints. In this work we employed super-resolution microscopy to reveal the nanometric-scale organization of VPs formed during rotavirus infection, and quantitatively describe the structural organization of seven viral proteins within and around the VPs. The observed viral components are spatially organized as five concentric layers, in which NSP5 localizes at the center of the VPs, surrounded by a layer of NSP2 and NSP4 proteins, followed by an intermediate zone comprised of the VP1, VP2, VP6. In the outermost zone, we observed a ring of VP4 and finally a layer of VP7. These findings show that rotavirus VPs are highly organized organelles.