Despite earlier presuppositions that viruses aren’t actually “alive” new research is supporting the idea they viruses are in fact living entities — just ones that are very different from other forms of known life.
The new work represents what the researchers involved say is the “first reliable method for tracing viral evolution back to a time when neither viruses nor cells existed in the forms recognized today”.
Owing to the incredible diversity observed amongst viruses (with regard to physical form, genome size, and “lifestyle”), it’s long been a challenge to classify them in any meaningful way. The new work is based on the idea that protein folds are themselves evidence that viruses are living entities, and should be placed on their own, very distinct, branch of the tree of life.
The new work supposes 7 distinct orders of viruses — based on shape/size, genetic nature, and reproductive approach.
“Under this classification, viral families belonging to the same order have likely diverged from a common ancestral virus,” the authors stated. “However, only 26 (of 104) viral families have been assigned to an order, and the evolutionary relationships of most of them remain unclear.”
A new press release provides more:
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 tiny — significantly smaller than bacteria or other microbes — and contain only a handful of genes. Others, like the recently discovered mimiviruses, 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. Folds are the structural building blocks of proteins, giving them their complex, three-dimensional shapes. By comparing fold structures across different branches of the tree of life, researchers can reconstruct the evolutionary histories of the folds and of the organisms whose genomes code for them.
The researchers 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, Caetano-Anollés said. Protein folds are better markers of ancient events because their three-dimensional structures can be maintained even as the sequences that code for them begin to change. 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,” researcher Caetano-Anollés commented.
Something I’ve long wondered about myself — how much of “evolution” is simply due to transcription “errors”, and how much is actually due to other means, such as viral or bacterial “infection”? Or for that matter (this is probably further out there to most people’s perceptions, despite growing support for the idea), how much of human/animal/plant behavior is modulated and influenced by viral and bacterial populations resident in the life in question?
The researchers 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.
In fact, the analysis revealed genetic sequences in viruses that are unlike anything seen in cells, Caetano-Anollés said. 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,” he said. Using the protein-fold data available in online databases, Nasir and Caetano-Anollés used computational methods to build trees of life that included viruses.
The data suggests “that viruses originated from multiple ancient cells … and co-existed with the ancestors of modern cells,” the researchers wrote. These ancient cells likely contained segmented RNA genomes, Caetano-Anollés stated.
“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,” Caetano-Anollés continued. “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,” Nasir stated. “This is the hallmark of parasitism.”
“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.”
“Viruses now merit a place in the tree of life. Obviously, there is much more to viruses than we once thought.”