Eukaryotic cells harbor a conglomerate of different genetic entities, each locked in conflict with other genetic entities for evolutionary dominance, often within the same genome. Still other groups of genes have been shaped by evolutionarily ancient conflicts with infectious pathogens, often emerging as victors from such conflicts with compromised housekeeping functions in the cell. My lab is interested in understanding how eukaryotic genetics and epigenetics have been shaped by such events. We study causes, mechanisms, and consequences of two forms of genetic conflict: extrinsic (between genomes) conflicts that shape genes involved in host-pathogen interactions, and intrinsic (within genome) conflicts that shape eukaryotic genome architecture.
Evolution as a Tool to Describe and Discover Antiviral Strategies
In the past decade, virologists have revealed a novel arm of intracellular, cell-autonomous immunity that mammalian cells mount against a variety of viral infections. For instance, the TRIM5alpha gene was discovered in a functional screen because it confers resistance to HIV infection in rhesus macaques but not in humans. In collaboration with Michael Emerman (Fred Hutchinson Cancer Research Center), we have used an evolutionary approach that identifies potential antiviral genes based on evolutionary signatures that suggest that they have been locked in antagonistic conflict with viruses throughout primate evolution. These conflicts result in higher than expected rates of amino acid changes that are fixed by selection (positive selection). Despite their discovery due to their activity against young, extant viruses like HIV-1, our analyses of the evolutionary histories of intracellular immunity genes have revealed that they have acted as antiviral genes throughout mammalian evolution. Several immunity genes, such as TRIM5alpha and APOBEC3G, represent some of the fastest evolving genes in the human genome.
We have used the signature of positive selection to identify the amino acid residues in antiviral proteins that are responsible for specific recognition of viral components. This was one of the first instances where positive selection guided the functional analysis of host-pathogen interfaces. For example, the signature of positive selection in TRIM5alpha identified a patch of only a few amino acids that turned out to be responsible for determining the recognition of specific retroviral capsids, including HIV. Likewise, positive selection identified a novel poly(ADP-ribose) polymerase domain on the antiviral protein ZAP that might represent a novel host-virus interaction interface.
Our analyses have revealed that even single–amino acid changes could determine the outcome of such host-virus conflicts. We postulated that viruses much older than those in the present day have driven selection for our current antiviral specificities. For example, PtERV is a retroviral lineage that was active 4 million years ago and left more than a hundred proviral imprints in both chimp and gorilla genomes, but none in the human genome. Using these "fossilized" imprints, we reconstructed the putative ancestral PtERV capsid gene, and showed that a single–amino acid change in TRIM5alpha that conferred a protective benefit against PtERV could lead to increased susceptibility to HIV-1, implying a fitness trade-off in these evolutionary conflicts.
Our survey of polymorphisms in antiviral genes in human populations also showed that retention of antiviral defense could be quite labile. We found alleles associated with impaired antiviral activity in both TRIM5alpha and APOBEC3H in certain human populations, suggesting that demography and relaxed selective pressures may have led to a significant reduction in the antiviral repertoire in many human populations. Thus, evolution can provide a means for identifying potential antiviral genes, revealing the functional sites of host-virus antagonism, and understanding differences in human susceptibility to infectious diseases.
Confronting Viral Mimicry
One highly successful strategy employed by both viral and bacterial pathogens to subvert host cell machinery for their own purposes is mimicry. For instance, the K3L gene from a lineage of poxviruses (that includes smallpox) resulted from the acquisition of a host translation gene, eIF2alpha. K3L aids poxviruses in defeating the antiviral response mounted by the PKR (protein kinase R) gene. PKR phosphorylates eIF2alpha on detecting viral infection to block protein production. We discovered that positive selection of PKR can allow it to overcome the challenge imposed by viral mimicry. This positive selection is most pronounced at the interaction surface between PKR and its substrate eIF2alpha. This is intriguing because eIF2alpha is highly conserved in eukaryotes, whereas PKR is among the fastest evolving genes in primate genomes. Our analyses reveal that host genes can employ evolutionary strategies to overcome mimicry by pathogens.
As a counterpoint to the viral mimicry challenge imposed by K3L, we also study the functional consequences of host genomes usurping viral genes to their own advantage. For example, "domesticated" retroviruses are ancient copies of retroviral insertions in the genome that now perform essential functions for the host. I discovered that the Iris gene of Drosophila is an envelope gene that had been domesticated from the Kanga lineage of insect retroviruses. We found that Iris has been subject to positive selection, and my lab is exploring whether Iris provides a degree of protection to Drosophila species against retroviruses.
Genetic Conflict as a Basis for Centromere Complexity (and Speciation?)
Centromeres are the DNA sites of attachment of microtubules that orchestrate the orderly movement of chromosomes during cell division. However, there is a range of complexity and rapid evolution of centromeric DNA in various eukaryotes that is hard to explain for a process that seems so central to eukaryotic replication. Steven Henikoff (HHMI, Fred Hutchinson Cancer Research Center) and I proposed the "centromere-drive" hypothesis to resolve this apparent paradox. We proposed that centromeres actively compete with each other for evolutionary survival. In the process of female meiosis, only one of four meiotic chromosomes "wins," i.e., is chosen in the oocyte in both plants and animals. The other three chromosomes are eliminated. We postulated that centromeres, by virtue of their microtubule attachment, are under direct selection for inclusion in the egg, which provides a robust impetus for evolutionary changes and expansions at the centromere.
Although success in female meiosis would be a significant advantage for the winning centromere, the ensuing imbalances in centromere strength could result in either sex-ratio distortion of male sterility. Thus, other genes of the genome would be predicted to evolve to suppress these evolutionary costs of the driving centromere. Consistent with this prediction, we found that several centromeric and heterochromatin proteins evolve under positive selection. Thus, although chromosome segregation is essential and despite the fact that centromeric proteins and DNA are both required for this process, they are nonetheless locked in an evolutionary conflict playing out with dynamics similar to those of host-virus interactions. Current work is aimed at determining if incompatibilities between centromeric components can provide a reproductive barrier between closely related species.
Using centromeric competition as a starting point, we have begun investigating other noncoding DNA components of eukaryotic genomes that are poorly understood yet participate in essential cellular processes. These include heterochromatic DNA (required for chromosome segregation and transposon silencing), dosage compensation (required to equilibrate the transcriptional output between one versus two X chromosomes), and origins of DNA replication (required to ensure efficient replication of the genome). We have found that components of all three processes show evidence of being shaped by episodes of positive selection. We aim to understand whether and how genetic conflicts may shape these essential processes that profoundly influence the character of our genomes.