Structural conservation and diversity in retroviral capsid

Retroviruses cause life-long infections for which no cure is available. Two members of the retrovirus family, HIV- 1 (human immunodeficiency virus 1) and HTLV-1 (human T-cell lymphotropic virus 1) are important human pathogens. HIV-1 is the causative agent of AIDS (acquired immunodeficiency syndrome), while HTLV-1 infection can cause severe diseases with poor prognosis, such as Adult T-cell leukemia/lymphoma (ATLL). Therefore these viruses and other non-human retroviruses need to be extensively studied to understand common features of the retrovirus lifecycle, and to potentially find ways to treat or prevent viral infection. Retroviruses exist in two forms, immature and mature, with retroviruses initially assembling into the immature non-infectious form. Upon maturation, the virus undergoes a dramatic structural rearrangement of its internal constituents, only then gaining infectivity. Understanding the process of assembly and maturation from a structural viewpoint is of great interest, as interference with assembly and maturation causes the virus to remain non-infectious and therefore harmless. It was also recently revealed that naturally occurring small molecules promote assembly and maturation of HIV-1. By using state-of-the-art cryo-electron tomography methods combined with sophisticated image processing techniques, we will provide unprecedented insights into the structure of different retroviral Gag assemblies and decipher the role of small molecules in more detail. Comparing structures from different retroviruses will help us to understand which mechanisms are important to virus assembly and maturation.

Retroviruses are important pathogens in humans and animals. They cause life-long infections for which no cure is available. One example for such virus is HIV the main causative agent of AIDS. Retroviruses exist in two forms, immature and mature, with retroviruses initially assembling into the immature, non-infectious form. Upon maturation, the virus undergoes a dramatic structural rearrangement of its internal constituents. Understanding the process of assembly and maturation from a structural viewpoint is of great interest, as interference with assembly and maturation causes the virus to remain non-infectious. Previous work revealed that retroviruses use similarly shaped building blocks, so-called capsid proteins, to assemble. Different retroviruses do not use these capsid proteins identically to assemble their virus particles. Instead, they put these building blocks together with substantial variation. One major question of this project was to better understand the conserved and divergent structural mechanisms in retroviruses when assembling their capsid protein lattices. Recently, it was also found that a naturally occurring small molecule called inositol-hexakiphosphate (or in short IP6) promotes assembly and maturation of HIV-1. We set out to understand if this molecule also plays a role in retroviruses beyond HIV-1. By using cryo-electron tomography (cryo-ET), a technique to look at extremely small samples in their natural state, combined with sophisticated image processing techniques, we were able to provide unprecedented insights into the structure of different retroviral assemblies and decipher the role of IP6 in more detail. Specifically, we could show that a close relative of HIV-1, the horse retrovirus Equine infectious Anaemia virus (EIAV) employs similar assembly strategies as HIV-1. We could clearly delineate which areas of capsid protein are important for both retroviruses and hence were kept identical or changed over the course of evolution. Importantly, we could also show that the role of IP6 is conserved among lentiviruses (the genus to which both HIV-1 and EIAV belong). We then also studied Rous Sarcoma virus (RSV) using high-resolution cryo-ET and could show that also in this retrovirus, which is distantly related to HIV-1, IP6 plays a crucial role in its lifecycle. By developing new image processing tools we also revealed that RSV displays an unexpected flexibility in the way it assembles its capsid to form a protective shell around its genetic information. In summary, our results provide new fundamental insights into important assembly and maturation mechanisms in retroviruses and show for the first time that IP6 plays an important role in other retroviruses beyond HIV-1. This work lays the foundation for new research to better understand retrovirus biology and to identify mechanisms to interfere with retrovirus infectivity.