Viruses are Alive

A new analysis supports the hypothesis that viruses are living entities that share a long evolutionary history with cells. The study offers the first reliable method for tracing viral evolution back to a time when neither viruses nor cells existed in the forms recognized today.

Until now, viruses have been difficult to classify because of 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 and their high mutation rates can obscure deep evolutionary signals. 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. 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. This contradicts one hypothesis that viruses captured all of their genetic material from cells. This along with other findings support the idea that viruses are creators of novelty.

Using the protein-fold data available in online databases researchers used computational methods to build trees of lifethat included virus sizes, genetic structure and means of reproducing.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.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.” they 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 (reproduce) 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.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 discovery of the giant mimiviruses in the early 2000s challenged traditional ideas about the nature of virus. These giant viruses were not the tiny Ebola virus, which has only seven genes. These are massive in size and massive in genomic repertoire. Some are as big physically and with genomes that are bigger than bacteria that are parasitic.Some giant viruses also have genes for proteins that are essential to translation, the process by which cells read gene sequences to build proteins. The lack of translational machinery in viruses was once cited as a justification for classifying them as nonliving.

Viruses now merit a place in the tree of life and there is much more to viruses than we once thought

 

 

For more information please visit: www.igb.illinois.edu

 

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