Virus Evolution Through Horizontal Gene Transfer

Project Summary Horizontal gene transfer (HGT) is a well characterized phenomenon driving the evolution and genetic diversity of bacteria but its underlying mechanisms and consequences in the context of viral evolution are far less well- understood. Poxviruses and other large DNA viruses encode numerous genes of clear cellular origin. I aim to investigate how they get there and evolve following their acquisition. We have demonstrated that LINE-1 (L1) retrotransposons play a key role in the transfer of cellular genes into poxvirus genomes but do not yet understand the dynamics of how this occurs without inducing catastrophic insertional mutagenesis. How newly acquired genes evolve proviral functions and avoid deletion due to functional redundancy with their cellular ancestor. The central hypothesis of this proposal is that L1 insertions into poxvirus genomes are enriched in distal regions of the genome, avoiding disruption of essential core genes, where they can evolve to benefit the virus. I will focus on two major outstanding questions emerging from this hypothesis. In Aim 1 I will characterize the interaction between virus replication and cellular L1 machinery. This will comprise spatially defining the interaction within the cytoplasm, understanding if and how L1 activity impacts viral replication, and comprehensively characterizing the frequency and distribution of L1-mediated insertions into the viral genome. To do so I will use a combination of experimental and computational techniques spanning molecular biology, biochemistry, genetics, and next-generation sequencing. In Aim 2 I will seek to elucidate the origin and evolution of poxvirus K3L, a host-derived inhibitor of the antiviral effector PKR. K3L is a structural homolog of vertebrate eIF2 that competitively inhibits PKR-induced translational shutoff. Compared to eIF2 K3L is dramatically truncated and lacks a phosphorylation site, and so cannot mediate the antiviral functions downstream of PKR. Despite this homology, computational and phylogenetic analysis suggests K3L is most closely related to the aIF2 protein of methanogenic archaea and may not have been acquired from the host cell of an ancestral poxvirus but rather from microbes occupying similar or overlapping ecological space. Since my original submission, I have generated new preliminary data that M. fervens aIF2 inhibits vertebrate PKR, giving experimental support to my computational work. I will confirm and expand on these results in mammalian cell culture, and use experimental evolution to model the adaptation of newly acquired viral genes. The recent identification of archaeal-origin genes in other DNA viruses, provides further support for my hypothesis, but K3L would be the first known example in viruses of multicellular eukaryotes. A picture is emerging of viruses as melting pots in nodes of diverse genetic exchange and my proposed studies will illuminate the participation of a new family of viruses in these ecological spaces. These studies will advance our understanding of the process of viral co-option of cellular genes as well as explore unexpected mechanisms underlying the genetic diversity of viruses and the ecological spaces they occupy.