A new study by a multinational team of scientists supports the idea that viruses are ancient living organisms and not inanimate molecular remnants run amok, as some scientists have argued.
The study of giant viruses, described in a paper in the journal BMC Evolutionary Biology, may reshape the universal family tree, adding a fourth major branch to the three that most scientists agree represent the fundamental domains of life.
The researchers used a relatively new method to peer into the distant past. Rather than comparing genetic sequences, which are unstable and change rapidly over time, they looked for evidence of past events in the three-dimensional, structural domains of proteins.
“These structural motifs, called folds, are relatively stable molecular fossils that – like the fossils of human or animal bones – offer clues to ancient evolutionary events,” said Prof Gustavo Caetano-Anollés of the University of Illinois, and the Institute for Genomic Biology, who led the analysis.
“Just like paleontologists, we look at the parts of the system and how they change over time,” he said. “Some protein folds appear only in one group or in a subset of organisms, he said, while others are common to all organisms studied so far. We make a very basic assumption that structures that appear more often and in more groups are the most ancient structures.”
“Most efforts to document the relatedness of all living things have left viruses out of the equation.”
“We’ve always been looking at the Last Universal Common Ancestor by comparing cells,” Prof Caetano-Anollés said. “We never added viruses. So we put viruses in the mix to see where these viruses came from.”
The team conducted a census of all the protein folds occurring in more than 1,000 organisms representing bacteria, viruses, the microbes known as archaea, and all other living things. The researchers included giant viruses because these viruses are large and complex, with genomes that rival – and in some cases exceed – the genetic endowments of the simplest bacteria.
“The giant viruses have incredible machinery that seems to be very similar to the machinery that you have in a cell,” Prof Caetano-Anollés said. “They have complexity and we have to explain why.”
Part of that complexity includes enzymes involved in translating the genetic code into proteins, he said. Scientists were startled to find these enzymes in viruses, since viruses lack all other known protein-building machinery and must commandeer host proteins to do the work for them.
In the new study, 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.
The resulting tree had four clearly differentiated branches, each representing a distinct ‘supergroup.’ The giant viruses formed the fourth branch of the tree, alongside bacteria, archaea and eukarya (plants, animals and all other organisms with nucleated cells).
The researchers discovered that 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,” Prof Caetano-Anollés said.
“The new analysis adds to the evidence that giant viruses were originally much more complex than they are today and experienced a dramatic reduction in their genomes over time,” he added. “This reduction 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. They also found that viruses appear to be key ‘spreaders of information.’
“The protein structures that other organisms share with viruses have a particular quality, they are (more widely) distributed than other structures,” Prof Caetano-Anollés explained. “Each and every one of these structures is an incredible discovery in evolution. And viruses are distributing this novelty.”
“Most studies of giant viruses are pointing in the same direction. And this study offers more evidence that viruses are embedded in the fabric of life,” Prof Caetano-Anollés concluded.
Bibliographic information: Arshan Nasir et al. Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. BMC Evolutionary Biology 2012, 12:156; doi: 10.1186/1471-2148-12-156