Is the virus life? Nature: Blurring the boundaries of life

Is the virus life? Until now, the problem has worried scientists. The prevailing view is that viruses are non-living units or forms between life and non-life. Now, a new study in Nature has blurred the line between the two – a newly discovered phage not only has a very large genome, even more than bacteria, but is also far smarter and more flexible than humans think.

Is the virus life? Nature: Blurring the boundaries of life

Photo credit: UC San Diego Health

Is the virus life? The answer to this question is very complex. The scientific community is still debating the issue, but most people list viruses as non-living units, and life includes individuals with cells, protonuclear organisms, and paleontological bacteria. But in fact, viruses have undergone many defining changes in the history of science, from life to life-like, to biochemical molecules, and then in the form between chemicals and life.

Viruses that are constantly changing definitions

The virus has been discovered for just over a hundred years. As early as the end of the 19th century, researchers discovered that rabies may not be a bacterial-caused disease, and that the disease-causing molecules seem to be much smaller than bacteria, so they call edgy, a word that originated in latin , “poison”. Because these molecules can move in the human body and can also cause disease like bacteria, scientists at the time thought virus was also a life.

By 1935, the American biochemist WenDell M. Stanley purified the tobacco leaf virus, and through follow-up research by him and his colleagues, the virus was first seen in its true face , a protein-wrapped DNA/RNA nucleic acid molecule. In addition, there are no cell-like cells needed for metabolism and survival. In this way, the virus seems to be classified only as chemical molecules.

Is the virus life? Nature: Blurring the boundaries of life

Tobacco leaf virus under the microscope. Photo credit: Columbia University

However, when this “chemical molecule” enters the cell, it does not appear to be like a normal molecule at all. Viruses are activated to produce their own nucleic acid molecules and protein shells using a variety of cells and biochemical materials in the cells. In this way, the virus seems to be confined to life and non-life. In this century, Marc van Regenmortel of the University of Strasbourg in France and Brian Mahy of the CDC in the United States suggested that viruses are more like “inhabiting” life because they behave like parasites and need a cell host to replicate.

As more and more organoblasts in cells are discovered, scientists have determined that life cannot be helped by cellocells such as ribosomes, mitochondria, chlorodibodies, and viruses are the sounds of life. Most scientists also pay more attention to finding the role of viruses in molecular biology, such as using viruses to insert target fragments into specific DNA sequences, or studying the relationship between viruses and disease.

Still, there are some scientists looking for the chemistry implications of the virus and the increasingly blurred line between it and bacteria.

The boundaries between viruses and life

A 2015 study in Nature-Communications showed a range of super-tiny bacteria that used ultra-fine filters to filter water from wastewater pools, and found bacteria in the fluid that were only 9 to 2 nm3 in size, which is smaller than conventional viruses.

Is the virus life? Nature: Blurring the boundaries of life

Ultra-small bacteria under the frozen electric mirror, a figure of 100 nanometers, b figure 50 nanometers

The findings not only overturn scientists’ previous estimates that the cell’s smallest operating volume is 8 to 14 nm3, but also make the difference between viruses and bacteria smaller in volume, even with overlapping regions. As a result, the term “virus-microbial continuum” has also been derived, which blurs the line between virus escloser and bacterial.

On one side, tiny bacteria are constantly being discovered, and many studies on the other are reporting on large viruses. Some viruses contain even more genes than E. coli. For example, Frederik Schulz of the U.S. Department of Energy’s Joint Genomics Institute found unknown virus sequences in a wastewater pool in Australia in 2017 that should have been found only in cells.

During subsequent extractions, Schulz found this particular virus, Klosneuvirus, which contains far more genomes than common viruses. There are 20 aminoacettRNA syntas in normal cells, which are important for connecting amino acids to tRNA, and Klosneuvirus contains 19 genes that encode the enzyme, which means that it is almost completely independent during protein synthesis.

Is the virus life? Nature: Blurring the boundaries of life

Klosneuvirus and other virus genome size comparison

Giant phage

In addition, there is a class of bacteria prey on the virus – phage has been the focus of scientists. Phage experiences the pursuit of specific types of bacterial populations, so they can have a significant impact on the microsystems in the environment. After entering the bacteria, it can hijack the bacteria’s metabolic tools to replicate on their own, and cause bacteria to crack and lay down a generation of phages.

And these phages can cause genetic mutations in bacteria, promoting bacterial resistance, and scientists have detected specific phages in the human gut and mouth, meaning they can affect the body’s internal environment and have unintended consequences.

Jill Banfield, a professor of earth and environmental scienceats at the University of California, Berkeley, has been looking for these particular viruses. In a new study published in the journal Nature, she showed a particular class of large phages. These large phages come from more than 30 different environments, from the intestines of pregnant women to hot springs on the Tibetan Plateau, and even from biochemical reactors in South Africa.

The average phage gene is about 50 kb (kilobase, thousand base pairs), while Banfield has found 351 phages with a genome length of more than 200 kb, four times the length of a common phage, one of which is as long as 735 kb. Banfield calls this phage a “huge phage”.

These phages are not only large in the genome, but more importantly, their genes are made up of a dallin, not only the protein shells that encode packagephment phages, but also transport RNA, transport RNA synthesis, modification enzymes, transcription initiation and extension factors. “Whether or not it has ribosome and protein translation is an important condition in determining whether it is an important condition of life, and these findings of phage make it harder for us to tell if it is life. In addition, Banfield said, she found that the phage genome also has a very critical bacterial system, CRISPR/Cas.

Readers who know gene editing should be no strangers to the system, and CRISPR gained notoriety when they discovered and applied it to gene editing at the University of California, Berkeley, and applied it. This was originally used by the immune system, which bacteria use to protect against virus invasion, and can specifically target and remove gene fragments, which is why it is used as a gene editing tool. Today, the bacterial system appears in the virus’s genetic sequence.

Although this is not the first time scientists have found the CRISPR gene in a phage, Banfield has found a new bacteriophage Cas protein of the same origin as Cas9, which she calls CRISPR/Cas. When the genes of the phage enter the bacteria, the phage can intercept the bacteria’s CRISPR system to work for itself, and the CRISPR system it produces is designed to deal with other virus species.

Is the virus life? Nature: Blurring the boundaries of life

CRISPR system in giant phage, red on the left

That is, when the giant phage enters the bacteria, it can enjoy the bacteria with peace of mind, allowing the bacteria to help it produce a CRISPR system that defends itself against its competitors before replicating and multiplying itself. In this way, phages are actually much more “intelligent” than humans think.

These giant phages have made their differences between bacteria smaller and smaller, and in Banfield’s words, the line between the virus and the bacteria has narrowed. “By increasing the length of the genome is a clever way to survive, and now we find that the virus has done it,” says Banfield.

Banfield divided them into 10 populations from China, Japan, the United States, Australia and France, according to the origin of 351 giant phages. In other words, this “smart” virus has been lurking in every corner of the world. And how many smarter viruses are waiting for humandiscovery? I don’t think there’s going to be a final answer.