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A new study finds that viruses share some genes exclusively with cells that are not their hosts, viruses swap genes with a variety of cellular organisms and are agents of diversity. The study looked at protein structures in viruses and across all domains of life: from the single-celled microbes known as bacteria and archaea, to eukaryotes, a group that includes animals, plants, fungi and all other living things.
Viruses that infect archaea and bacteria, for example, are not known to infect eukarya. However, they may still interact in non harmful ways with organisms they do not infect. The team used a bioinformatics approach to analyze the genomes of organisms and the viruses that infect them. Rather than focusing on genetic sequences, which can change over the generations, the team examined the functional components of proteins, which they call folds.
There are more than 1,400 of folds across all domains of life-has a unique 3-D structure that performs a specific operation. Because folds are critical to protein function, they remain stable even as the sequences that code for them change as a result of mutations or other processes.This makes protein folds reliable markers of evolutionary changes over vast time periods, especially for viruses that mutate notoriously fast.
The researchers found hundreds of folds that are present across all domaind of life and in all types of viruses, which suggests that they came from an ancient ancestor of all life forms. Some folds, however, occur only within a single domain and the viruses that infect it, suggesting a transfer of genetic material only between that group of viruses and their hosts. Out of a total of about 2,000 superfamilies of folds, the team found one that was exclusive to archaea and the viruses that infect archaea, 29 shared only by bacteria and the viruses that infect them, and 37 that are exclusive to eukaryotes and their viruses.
The data also point to other, as yet unknown, mechanisms that allow viruses to exchange genetic material with cells, many virus-hallmark genes in cellular organisms those viruses are not known to infect. People tend to think only about viruses that infect and kill their hosts, we have known for decades that a virus will sometimes enter into a cell and incorporate its genetic material into the cell without killing it. In the case of single-celled organisms, those genes are sometimes passed along to future generations. Human DNA, too, contains remnants of viruses.
Some retroelements and transposons are believed to have originated in ancient viruses. Retroelements are sequences copied from RNA viruses into DNA and inserted into the genomes of nonviral organisms. Transposons, also known as “jumping genes,” can move from one part of the genome to another.The team also discovered a large subset of virus-specific protein folds that were not present in any cellular genomes. This suggests that viruses can create new genes and, potentially, transfer those genes to cellular organisms.
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