A new big-data analysis conducted by four scientists from the Stanford University, USA, has found an astonishing 30 percent of all protein adaptations since the time our species diverged from chimpanzees to have been driven by viruses.
While the struggle between pathogens and their hosts has long been recognized as a major player in evolution, this is the first time researchers had been able to look at the pattern across different genomes at a global scale.
“When you have a pandemic or an epidemic at some point in evolution, the population that is targeted by the virus either adapts, or goes extinct. We knew that, but what really surprised us is the strength and clarity of the pattern we found,” said David Enard, Ph.D., a postdoctoral fellow at Stanford University and the study’s first author.
A sweeping view of how small tweaks in protein shape and composition have helped humans and other mammals respond to viruses, as well as determining which parts of the cell are involved in the process, could eventually help scientists develop new therapeutics against viral outbreaks the world is facing today.
The big advancement of the study is in showing for the first time that at least as much adaptation takes place outside the immune system as within it – an achievement that resulted from abandoning the usual practice of focusing exclusively on proteins directly involved in the immune response.
First, Enard and his colleagues scoured the literature for all known proteins that physically interact with viruses, identifying about 1,300 candidates from a set of 9,900, and then funnelling them through a tailor-made big-data algorithm, which uses all available genomic databases to compare the evolution of virus-interacting proteins to that of their “neutral” counterparts.
As it turns out, the interacting proteins underwent changes three times as frequently as other proteins, which isn’t all too surprising given that viruses hijack nearly every function of a host organism’s cells in order to replicate and spread, prompting it to adapt.
The study sheds light on some longstanding biological mysteries, such as why closely-related species have evolved different machinery to perform identical cellular functions, like DNA replication or the production of membranes.
“This paper is the first with data that is large enough and clean enough to explain a lot of these puzzles in one fell swoop,” said the senior author on the paper Dmitri Petrov.