Viruses are both the villains and heroes of life as we know it
Viruses have a bad reputation. They are responsible for the COVID-19 pandemic and a long list of maladies that have plagued humanity since time immemorial. Is there anything to celebrate about them?
Many biologists like me believe there is, at least for one 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 enable that cell to perform new tricks.
Most phages have a rigid shell called a capsid that 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 phages have room to carry extra genetic baggage: genes that are not actually necessary for the phage’s survival that it can modify at will.
How bacteria retooled a viral switch
To see how this plays out, let’s take a deeper look at the phage life cycle.
Phages come in two main flavors: temperate and virulent. Virulent phages, like many other viruses, operate on an invade-replicate-kill program. They enter the cell, hijack its components, make copies of themselves and burst out.
Temperate phages, on the other hand, play the long game. They fuse their DNA with the cell’s and may lay dormant for years until something triggers their activation. Then they revert to virulent behavior: replicate and burst out.
Many temperate phages use DNA damage as their trigger. It’s sort of a “Houston, we have a problem” signal. If the cell’s DNA is being damaged, that means the DNA of the resident phage is likely to go next, so the phage wisely decides to jump ship. The genes that direct phages to replicate and burst out are turned off unless DNA damage is detected.
Bacteria have retooled the mechanisms controlling that life cycle to generate a complex genetic system that my collaborators and I have been studying for over two decades.
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Bacterial cells are also interested in knowing if their DNA is getting busted. If it is, they activate a set of genes that attempt to repair the DNA. This is known as the bacterial SOS response because, if it fails, the cell is toast. Bacteria orchestrate the SOS response using a switch-like protein that responds to DNA damage: It turns on if there is damage and stays off if there isn’t.
Perhaps not surprisingly, bacterial and phage switches are evolutionarily related. This prompts the question: Who invented the switch, bacteria or viruses?
It’s not just bacterial switches that appear to be phage inventions. Beautiful detective work has shown that a bacterial gene needed for cell division also arose through “domestication” of a phage toxin gene. And many bacterial attack systems, such as toxins and the genetic guns used to inject them into cells, as well as the camouflage they use to evade the immune system, are known or suspected to have phage origins.
The upside of viruses
OK, you may think, phages are great, but the viruses that infect us are certainly not cool. Yet there is mounting evidence that the viruses that infect plants and animals are also a major source of genetic innovation in these organisms. Domesticated viral genes have been shown, for instance, to play a key role in the evolution of mammalian placentas and in keeping human skin moist.