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Historicizing HIV

Historicizing HIV
Biologist Sara Sawyer has used phylogenetic analysis to help answer a key question about the evolution of the primate retroviral defense system. Photo: Scott Shulz

Biologist Sara Sawyer has used phylogenetic analysis to help answer a key question about the evolution of the primate retroviral defense system. Photo: Scott Shulz

Sara Sawyer’s eureka moment, as a young scientist, came when thinking about how to apply her interest in the long sweep of evolutionary theory to one of the big questions in HIV research: why do humans get infected by HIV but monkeys don’t?

In particular, she wanted to understand why a single protein, TRIM5α, is able to help successfully prevent HIV infection when it’s part of certain monkey genomes but is blind to the virus when it’s part of the human genome.

What she found, by delving tens of millions of years into the primate family’s evolutionary history, is an answer that lies on one small patch of amino acids on TRIM5α that evolved differently in humans than in monkeys.

“When retroviruses enter a cell in your body, they have to insert themselves into your chromosome in order to replicate,” says Sawyer, an assistant professor of molecular genetics and microbiology. “As a result, there are more than half a million historical retroviruses that are frozen in our genome, creating a fossil record of past infections. We are interested in mining human and primate genomes for evidence of how we overcame these previous infections.”

In order to reconstruct the evolutionary history of TRIM5α, Sawyer and her colleagues took genetic samples from 17 primates and sequenced the gene for each of them. Using statistical modeling, they were then able to reconstruct a phylogeny—a family tree—of the TRIM5α protein.

They traced the evolution of TRIM5α as it spread out from the genome of an ancient primate ancestor to become an essential part of the retroviral defense system in, among other primates, humans, chimpanzees, pygmy marmosets, Bolivian howler monkeys, African green monkeys, and Sumatran orangutans.

TRIM5α, they believed, had been locked in an evolutionary arms race with various retroviruses for all this time. Every time it mutated to destroy a particular retrovirus, another retrovirus (or a mutated version of the old one), emerged that could make its way past TRIM5α’s attack. And then TRIM5α adapted again, and so on and so on.

At some point over this long history the monkey TRIM5α acquired, or the human TRIM5α lost, the ability to defend against HIV, or against a retrovirus similar in its function to HIV.

What Sawyer hoped to identify wasn’t that particular moment in evolutionary history, but rather where on the TRIM5α  protein this long-running arms race was occurring.

“Human genes tend to evolve very slowly, like a slow turning cog,” says Sawyer, “but if our hypothesis was correct, there would be one part of the protein that was engaged with the very fast moving cog of the virus, and its evolution would be sped up. And, in fact, we found this 13-amino acid patch that had that signature.”

With that precise knowledge in hand, Sawyer and her colleagues went to the lab and created two mutants, one a monkey TRIM5α with the human version of that 13-amino acid patch, and one a human TRIM5α with the monkey patch. They exposed these mutants to HIV. As they’d predicted, the human version was suddenly able to “see” HIV and react to it, and the monkey version was now “blind” to it.

“Our paper,” says Sawyer, “showed that very small sequence changes can affect the ability of TRIM5α to see HIV.”

The distance is considerable, says Sawyer, between her finding and the development of new treatments for HIV infection. We’re a still a long way, for instance, from a therapy that can simply alter the TRIM5α sequence in our genome so that we’re naturally resistant to HIV infection. But identifying the precise molecular mechanism through which TRIM5α interacts (or doesn’t) with HIV is significant, and may lead to other kinds of research.

More significant, perhaps, has been Sawyer’s methodological innovation. The traditional approach to finding the key sequence on TRIM5α would have been essentially a trial-and-error one. Scientists would identify a bunch of places where the parallel sequences differed, and they’d synthesize mutants of the proteins in which those sequences were altered. Then they’d expose the different mutant proteins to HIV and see if they reacted differently.

“The problem with that approach,” says Sawyer, “is that it’s very laborious. It takes a long time and a lot of hands in the lab to find the right one. We decided to take a completely different approach based on evolutionary theory.”

Her paper, which was published in 2005 in the Proceedings of the National Academy of Sciences (PNAS), has been influential in the field, and other HIV researchers are now taking phylogenetic approaches to locating important sequences.

Sawyer herself is now using the same approach to look for proteins that have historically been enabling, rather than combating, retroviruses. In theory, these proteins should also show rapid evolution, as they’ve been attempting to mutate away from retroviruses for millions of years.

These “pro-viral” proteins offer a more promising therapeutic target, says Sawyer, because it should be easier to block the function of a human protein that’s already working (i.e. allowing HIV in to infect it) than to activate a defensive protein (like TRIM5-alpha) that’s not.

For Sawyer, part of the excitement of working in the HIV field is the potential to help in some way to develop treatments. As big a part of it, however, is just the chance to peer into the human past in a novel way.

“You have more sequence in your genome that encodes for viruses than you do that encodes for the proteins that physically make you into you. Eight percent of the human genome is retroviruses. You’re part virus, part human.”

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Saturday, 04 February 2023

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