A new data analysis supports the hypothesis that viruses are living organisms that have extensive evolutionary commonality with living cells. New research provides the first reliable method to trace the evolution of viruses back to an era when both viruses and living cells were in different forms than they are today
![The variety of physical features, the size of the genomes and the lifestyles of viruses all make their classification difficult. New research uses protein folding as evidence that viruses are living creatures that belong in their own branch of the branch of life. [Courtesy of Julie McMahon]](https://www.hayadan.org.il/images/content3/2015/11/742001-500x357.png)
A new data analysis supports the hypothesis that viruses are living things with extensive evolutionary commonality with living cells. A new study provides the first reliable method to trace the evolution of viruses back to an era when both viruses and living cells were in different forms than they are today.
A new data analysis supports the hypothesis that viruses are living things with extensive evolutionary commonality with living cells. A new study provides the first reliable method to trace the evolution of viruses back to an era when both viruses and living cells were in different forms than they are today. The research findings have long been published in the scientific journal Science Advances.
Until now, it has been problematic to classify the viruses, said Professor Gustavo Caetano-Anollés of the University of Illinois, the researcher who conducted the new analysis. As part of the study, the researchers found 7 groups of viruses, based on their structures, sizes, genetic composition and reproduction possibilities. "In light of this classification, virus families belonging to the same group are those that most likely diverged from a common ancestral virus," explains the lead researcher. "At the same time, only 26 (out of 104) of the virus families were classified under a defined group, and the evolutionary relationships between them still remain unclear."
Part of the lack of recognition is due to the wealth and variety of viruses. Fewer than 4900 viruses have been identified and their genomes sequenced so far, despite the fact that scientists estimate that there are more than a million virus species. Many types of viruses are extremely tiny - much smaller than bacteria or other microorganisms - and contain only a handful of genes. Others, such as the recently discovered mimiviruses, are gigantic, containing genomes larger than some bacteria. The new study focuses on the extensive collection of protein structures known as "protein folds", encoded within the genomes of all cells and viruses. The folds are the structural building blocks of proteins, and they are the ones that provide them with their complex and three-dimensional shapes. By comparing the structures of the folds across the different branches of the tree of life, researchers are able to reconstruct the evolutionary history of the folds and even of the organisms themselves.
The researchers chose to analyze the folding pattern of the proteins in light of the fact that the sequences that code the genomes of the viruses are exposed to rapid changes; Their high mutation rate may mask hidden evolutionary signals, explains the lead researcher. It turns out that protein folds are better markers of past events, because their three-dimensional structures are preserved over generations even when their coding sequences begin to change. Today, many viruses - including those that cause diseases - take over the protein building mechanism of the cells that host them in order to replicate their own copies and spread them to other cells. Usually the viruses insert their genetic material into the DNA of their hosts. In fact, the remnants of the ancient viruses that penetrated cells are now permanent features of the genomes of most cellular organisms, including humans. This talent for transferring genetic material may be evidence of the initial role of viruses as "propagators of diversity," says the lead researcher.
The researchers examined all known folds in 5080 organisms representing each branch of the tree of life, including 3460 viruses. Thanks to advanced bioinformatics methods, the researchers were able to identify 442 protein folds common to both living cells and viruses, with only 66 of them unique to viruses. "This finding means that a tree of life can be built, since many characteristics have been found in viruses that are also included in living cells," explains the lead researcher. "Viruses also have unique characteristics that are not shared by living cells." In fact, the data analysis revealed genetic sequences in viruses that do not resemble any sequences in cells, the researcher notes. This finding contradicts the hypothesis that viruses absorbed all their genetic material from the host cells. This finding and others also support the idea that viruses are "producers of innovation", adds the researcher. Thanks to the data available to researchers in online databases of protein folding, the scientists used computerized methods to build trees of life that also include viruses. The data show that "viruses originate from several primitive cells... and were found together with the ancestors of modern cells", explains the researcher. These primitive cells probably contained genomes of RNA parts, the researcher explains.
The data also show that at a certain point in their evolutionary history, not long after the appearance of modern cellular life, most viruses achieved the ability to insert themselves through the protein envelope, replicate copies of them and spread outside the host cell, explains the researcher. "The viruses protected themselves with the help of protein boxes that became more and more sophisticated over the years, which allowed the viruses to infect the cells that until then were immune to the viruses" says one of the researchers. "This is the seal of quality of parasites".
Some scientists believe that viruses are not living things, but only pieces of DNA and RNA protected by cellular life. They emphasize the fact that viruses are unable to replicate on their own (proliferate) outside the host cells, and rely entirely on the protein building mechanism of the cells themselves in order to function. However, much evidence supports the idea that viruses are not so different from other living things, claims the lead researcher. "Many organisms need other organisms to live, including bacteria that live inside cells, and fungi that must use parasitic relationships - they all rely on their hosts to complete their life cycle," he adds. "And that's exactly what viruses do." The discovery of the superviruses of the mimiviruses in the early XNUMXs challenged the traditional hypotheses regarding the nature of viruses, the researcher adds. "These large viruses are very different from the tiny Ebola viruses, which include only seven genes. These superviruses are large and diverse in their genetic makeup," said the researcher. "Some of them are physically large and have genomes as large as or even larger than those of parasitic bacteria." Some of these large viruses also have genes that encode proteins that are essential for the transcription phase, the same process by which cells read the sequences of the genome and thereby build proteins. The lack of a replication mechanism in viruses used to be one of the strongest arguments for classifying viruses as non-living creatures. "The situation is no longer like that," says the chief researcher. "Viruses deserve a place in the tree of life today. Obviously, there is much more to viruses than we know about them today."
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