A new study of giant viruses supports the idea that viruses are ancient living organisms and not inanimate molecular remnants. The study may reshape the universal family tree, adding a fourth major branch to the three that most scientists agree represent the fundamental domains of life.
Rather than comparing genetic sequences, which are unstable and change rapidly over time, the researchers looked for evidence of past events in the three-dimensional, structural domains of proteins. These structural motifs – folds – are relatively stable molecular fossils. Some protein folds appear only in one group or in a subset of organisms, while others are common to all organisms. According to reserach leader Gustavo Caetano-Anollés, “We make a very basic assumption that structures that appear more often and in more groups are the most ancient structures.”
A census was made of all protein folds occurring in more than 1,000 organisms representing viruses, bacteria, archaea, and eukarya. Giant viruses were included because they are large and complex, with genomes that rival or exceed those of the simplest bacteria. That complexity includes enzymes involved in translating the genetic code into proteins. Finding these enzymes in viruses was surprising, since viruses lack all other known protein-building machinery and must commandeer host proteins to do the work for them.
The researchers mapped evolutionary relationships between the protein endowments of hundreds of organisms and used the information to build a new universal tree of life that included viruses and had four clearly differentiated branches. Giant viruses formed the fourth branch of the tree, alongside bacteria, archaea and eukarya. Many of the most ancient protein folds – those found in most cellular organisms – were also present in the giant viruses. This suggests that these viruses appeared quite early in evolution, near the root of the tree of life. It also suggests that giant viruses were originally much more complex than they are today and experienced a dramatic reduction in their genomes over time. This likely explains their eventual adoption of a parasitic lifestyle. The researchers suggest that giant viruses are more like their original ancestors than smaller viruses with pared down genomes.