Ancient and ongoing viral adaptation to antagonize primate SAMHD1

Thesis (Ph.D.)--University of Washington, 2015Restriction factors are components of the innate immune defense against viral pathogens. They inhibit viral replication by operating as molecular barriers to steps of the viral life cycle, and viruses have evolved mechanisms to counteract these blocks. The restriction factor SAMHD1 prevents lentiviruses such as Human Immunodeficiency Virus and the related Simian Immunodeficiency Virus (SIV) from replicating in myeloid cells and resting T-cells. Many lineages of lentiviruses, including HIV-2 and other SIVs, encode accessory proteins Vpr or Vpx that serve to abrogate host SAMHD1 restriction by causing degradation of the antiviral factor. Selective pressure for the host to escape infection and for the virus to persist result in the rapid evolution of SAMHD1 to escape viral antagonism, characteristic of a molecular arms race between host and virus. In contrast to other well-studied restriction factors, only a subset of extant lentiviruses antagonize SAMHD1. This trait evolved in one ancient ancestor of a subset of modern viruses, but was lost in SIV that infects chimpanzees, the viral precedent of HIV-1. Thus, HIV-1 that founded the pandemic does not have a method of SAMHD1 antagonism. To address the questionable necessity of SAMHD1 antagonism, I examined viral adaptation to SAMHD1 polymorphism occurring in naturally infected primates. I show that SAMHD1 antagonism must be important for viral fitness because viruses have adapted to distinct SAMHD1 variants present in their primate host population. I further examined the molecular basis of lentiviral adaptation to degrade SAMHD1 by mapping species-specificity in SAMHD1 antagonism by the viral proteins Vpr and Vpx. I show that despite high sequence diversity in vpr and vpx genes and divergent SAMHD1 targeting, Vpr and Vpx evolution is constrained by the need to bind the host ubiquitin ligase machinery used to cause SAMHD1 degradation. Capitalizing on this conservation and a structure of one crystallized Vpx protein, I designed chimeric Vpr and Vpx proteins and mapped specificity of Vpx of the SIVsmm/mac / HIV-2 lineages to two discrete regions of Vpx. I propose a model to explain how viral antagonists adapt to bind rapidly escaping targets while maintaining their function. Due to extensive and conserved interaction with a host ubiquitin ligase protein, the sequence available for Vpx and Vpr to bind target SAMHD1 is limited to dedicated regions which are evolutionary and structurally flexible, allowing sampling of great molecular diversity to reestablish target binding without compromising antagonist function and overall structure