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(THE CONVERSATION) Viruses have a bad reputation. They are responsible for the COVID-19 pandemic and a long list of diseases that have plagued humanity since time immemorial. Is there something to celebrate about them?
Numerous biologists like me think there is, at least for a specific type of virus, namely, bacteriophages, or viruses that infect bacteria. When the DNA of these viruses is captured by a cell, it may contain instructions that allow that cell to perform new tricks.
The powerful power of bacterial viruses
Bacteriophages, or phages for short, control bacterial populations, both on land and at sea. They kill up to 40% of ocean bacteria every day, helping to control bacterial blooms and redistribution of organic matter.
Doctors are also enthusiastic about their ability to selectively kill bacteria. Both natural and modified phages have been successfully used to treat bacterial infections that do not respond to antibiotics. This process, known as phage therapy, could help fight antibiotic resistance.
Recent research highlights another important function of phages: they can be nature’s ultimate genetic tinkerers, creating new genes that cells can retool to acquire new functions.
Phages are the most abundant life form on the planet, with a nonillion – it’s a 1 with 31 zeros after it – of them floating around the world at any moment. Like all viruses, phages also have high replication and mutation rates, which means that they form many variations with different characteristics each time they spawn.
Most phages have a rigid shell called capsid which is filled with their genetic material. In many cases, the shell has more space than the phage needs to store the DNA essential for its replication. This means that the phages have room to carry additional genetic material: genes that are not really necessary for the survival of the phage that it can modify at will.
How bacteria reorganized a viral switch
To see how this plays out, let’s take a closer look at the phage’s lifecycle.
Phages come in two main flavors: temperate and virulent. Virulent Phages, like many other viruses, operate on an invasion-replication-elimination schedule. They enter the cell, hijack its components, copy each other and explode.
Temperate lighthouses, on the other hand, play the long game. They merge their DNA with that of the cell and can lie dormant for years until something triggers their activation. Then they return to a virulent behavior: to replicate and burst.
Many temperate phages use DNA damage as a trigger. It’s kind of a “Houston, we have a problem” signal. If the DNA of the cell is damaged, it means that the DNA of the resident phage is likely to go next, then the phage wisely decides to leave the ship. The genes that direct phages to replicate and burst are turned off unless DNA damage is detected.
Bacteria have reorganized the mechanisms controlling this life cycle to generate a complex genetic system that my collaborators and I have been studying for more than two decades.
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Bacterial cells are also interested in whether their DNA is destroyed. If so, they activate a set of genes that attempt to repair DNA. This is known as the bacterial SOS response because, if it fails, the cell is toast. Bacteria orchestrate the SOS response with the help of a switch-like protein that reacts to DNA damage: it activates if there is damage and remains extinct if there is not.
Perhaps not surprisingly, bacterial and phage switches are linked to evolution. This begs the question: who invented the switch, bacteria or viruses?
Our previous research and work of other researchers indicates that the phages got there first. In our recent report, we found that the SOS response of Bacteroidetes, a group of bacteria that include up to half of the bacteria living in your gut, is under the control of a phage switch that has been rearranged to implement the bacteria’s own complex genetic programs. This suggests that Bacterial SOS Switches are actually phage switches that were retooled eons ago.
It’s not just bacterial switches that appear to be phage inventions. Beautiful detective work has shown that a bacterial gene necessary for cell division has also appeared through “Domestication” of a phage toxin gene. And many bacterial attack systems, such as toxins and the genetic weapons used to inject them into cells, as well as camouflage they use to evade the immune system, are known or suspected to have phage origins.
The advantage of viruses
OK, you might be thinking, phages are great, but the viruses that infect us are definitely not cool. Yet there is growing evidence that viruses that infect plants and animals are also a major source of genetic innovation in these organisms. Domesticated viral genes have been shown, for example, to play a key role in the changing mammalian placentas and keeping human skin moist.
Recent evidence suggests that even nucleus of a cell, which houses DNA, could also have been a viral invention. Researchers also speculated that the ancestors of today’s viruses may have pioneered the use of DNA as the primary molecule for life. No small feat.
So while you may be used to seeing viruses as the quintessential villains, they are arguably nature’s engines for genetic innovation. Humans are probably here today because of them.
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