Viruses are the Spice of Life

This week's Nature has a news article about the large and diverse role that viruses play in the ecology on this earth, and the insights about the past that we are gaining from them. If you can name an organism, there is probably a virus that infects it.

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Hints of the vast, unexplored viral world first emerged during the 1980s. Researchers at the University of Bergen in Norway, with the help of a new electron-microscopy technique, showed that viral concentrations in some aquatic habitats were up to 10 million times greater than previous estimates. Viral particles per millilitre ranged from 60,000, deep beneath the Barents Sea, to 254 million, from the surface waters of Germany's Lake Plussee.

Since then researchers have discovered huge numbers of viruses wherever they have looked, from 2,000 metres below the surface of Earth to the sands of the Sahara Desert, from acidic hot springs to polar lakes. In total there are now thought to be some 10^31 viral particles on the planet — an astronomical figure that one researcher recently described as 250 million light years' worth of viral genes laid end to end.

Then, in the mid-1990s, researchers started to grasp the dazzling variety that exists within this viral multitude. Biologists discovered that the known and cultured viruses represented just a fraction of their respective groups. From one cubic metre of seawater to the next, there was more genetic diversity in viruses than found in any other known group of organisms.

These viruses are a large reservoir of genetic diversity that can wind up in the host genome. (FYI, a phage is a virus that infects bacteria.)

A big question now is the degree to which this super-organism extends its tentacles into host genomes. It has long been known that bacteria use genes acquired from prophages — phages that insert their DNA temporarily or even permanently into the DNA of their host — to gain competitive advantage and exploit new environments. Indeed, work reaching back decades has shown that prophage genes carried by bacteria are responsible for producing the primary toxins associated with diseases such as diphtheria, scarlet fever, food poisoning, botulism and cholera.

I think this next bit is fascinating to think about.

Phage DNA has also made it into the human genome, despite the fact that phages target bacteria. The source was our mitochondria, the energy-producing capsules found in our cells and thought to be the descendants of a formerly free-living bacterium. During evolution, phage genes from the mitochondrial genome have transferred into our main genome, housed in the cell's nucleus. There, they help copy and express the few bacterial genes still present in the mitochondrial genome. Recently, this same phage DNA has been spotted in various modern bacteria belonging to the group from which mitochondria are thought to have descended. That supports the idea that the gene made its way from virus to bacterium to cell nucleus, where it now plays a key role in the molecular circuitry that drives all multicelled organisms.

The article also mentions retroviral remains in our genome, some of which appear to play a function in our physiology.

Virology isn't just about disease anymore.

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Nature 441, 683-685 (8 June 2006)