Viruses are fully-alive organisms that share a long evolutionary history with cells, according to a new study published last week in the journal Science Advances.
Giant Acanthamoeba-infecting virus Pandoravirus salinus. Image credit: © IGS CNRS-AMU.
“Until now, viruses have been difficult to classify. In its latest report, the International Committee on the Taxonomy of Viruses recognized seven orders of viruses, based on their shapes and sizes, genetic structure and means of reproducing,” said co-author Prof. Gustavo Caetano-Anollés of the University of Illinois.
“Under this classification, viral families belonging to the same order have likely diverged from a common ancestral virus. However, only 26 of 104 viral families have been assigned to an order, and the evolutionary relationships of most of them remain unclear.”
Part of the confusion stems from the abundance and diversity of viruses. Less than 4,900 viruses have been identified and sequenced so far, even though scientists estimate there are more than a million viral species.
Many viruses are very small and contain only a handful of genes. Others, like recently discovered Acanthamoeba-infecting viruses (Pithovirus, Mollivirus, Mimiviruses and Pandoraviruses), are huge, with genomes bigger than those of some bacteria.
The new study focused on the vast repertoire of protein structures, called ‘folds,’ that are encoded in the genomes of all cells and viruses. By comparing fold structures across different branches of the tree of life, scientists can reconstruct the evolutionary histories of the folds and of the organisms whose genomes code for them.
Prof. Caetano-Anollés and his colleague, Arshan Nasir, also from the University of Illinois, chose to analyze protein folds because the sequences that encode viral genomes are subject to rapid change.
“Their high mutation rates can obscure deep evolutionary signals. Protein folds are better markers of ancient events because their 3D structures can be maintained even as the sequences that code for them begin to change,” Prof. Caetano-Anollés said.
Today, many viruses – including those that cause disease – take over the protein-building machinery of host cells to make copies of themselves that can then spread to other cells. Viruses often insert their own genetic material into the DNA of their hosts. In fact, the remnants of ancient viral infiltrations are now permanent features of the genomes of most cellular organisms, including humans.
“This knack for moving genetic material around may be evidence of viruses’ primary role as spreaders of diversity,” Prof. Caetano-Anollés said.
The team analyzed all of the known folds in 5,080 organisms representing every branch of the tree of life, including 3,460 viruses.
Using advanced bioinformatics methods, they identified 442 protein folds that are shared between cells and viruses, and 66 that are unique to viruses.
“This tells you that you can build a tree of life, because you’ve found a multitude of features in viruses that have all the properties that cells have. Viruses also have unique components besides the components that are shared with cells,” Prof. Caetano-Anollés said.
The new study uses protein folds as evidence that viruses are living entities that belong on their own branch of the tree of life. Image credit: Julie McMahon.
The analysis revealed genetic sequences in viruses that are unlike anything seen in cells. This contradicts one hypothesis that viruses captured all of their genetic material from cells.
“This and other findings also support the idea that viruses are creators of novelty,” Caetano-Anollés said.
The researchers used computational methods to build trees of life that included viruses.
“The data suggest that viruses originated from multiple ancient cells and co-existed with the ancestors of modern cells. These ancient cells likely contained segmented RNA genomes,” Prof. Caetano-Anollés said.
“The data also suggest that at some point in their evolutionary history, not long after modern cellular life emerged, most viruses gained the ability to encapsulate themselves in protein coats that protected their genetic payloads, enabling them to spend part of their lifecycle outside of host cells and spread.”
The protein folds that are unique to viruses include those that form these viral capsids. These capsids became more and more sophisticated with time, allowing viruses to become infectious to cells that had previously resisted them. This is the hallmark of parasitism,” Nasir said.
“Some scientists have argued that viruses are nonliving entities, bits of DNA and RNA shed by cellular life. They point to the fact that viruses are not able to replicate outside of host cells, and rely on cells’ protein-building machinery to function. But much evidence supports the idea that viruses are not that different from other living entities,” Prof. Caetano-Anollés said.
Many organisms require other organisms to live, including bacteria that live inside cells, and fungi that engage in obligate parasitic relationships – they rely on their hosts to complete their lifecycle. And this is what viruses do.
“The lack of translational machinery in viruses was once cited as a justification for classifying them as nonliving. This is no more. Viruses now merit a place in the tree of life. Obviously, there is much more to viruses than we once thought,” Prof. Caetano-Anollés concluded.
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Arshan Nasir & Gustavo Caetano-Anollés. 2015. A phylogenomic data-driven exploration of viral origins and evolution. Science Advances, vol. 1, no. 8, e1500527; doi: 10.1126/sciadv.1500527
