Bacteria take 'RNA mug shots' of dangerous viruses

Bacteria incorporate RNA from viruses into their own genomes as defense mechanism, which could provide insight into plant or dairy pathogens.

Scientists from The University of Texas at Austin, the Stanford University School of Medicine and two other institutions have discovered that bacteria have a system that can recognize and disrupt dangerous viruses using a newly identified mechanism involving RNA that is similar to the CRISPR/Cas system that captures foreign DNA.

The discovery might lead to better ways to thwart viruses that kill agricultural crops and interfere with the production of dairy products such as cheese and yogurt.

The research appeared online Feb. 25 in the journal Science.

In humans and other organisms, DNA molecules act as the body's blueprints, while RNA molecules read those blueprints to build the body and maintain the functions of life.

The research team found, for the first time, that bacteria can snatch bits of RNA from invaders such as viruses and incorporate the RNA into their own genomes, using this information as something akin to mug shots. They then help the bacteria recognize and disrupt dangerous viruses in the future.

"This mechanism serves a defensive purpose in bacteria. You could imagine transplanting it into other organisms and using it as a kind of virus detector," said co-senior author of the paper Alan Lambowitz, director of the University of Texas at Austin's Institute for Cellular & Molecular Biology.

The newly discovered mechanism stores both DNA and RNA mug shots from viruses in a bacterium's genome. That makes sense from an evolutionary standpoint, the researchers said, given that some viruses are DNA-based and some are RNA-based.

As a next step, Lambowitz said researchers can examine how to genetically engineer crops, such as tomatoes, so that each of their cells would carry this virus detector. Then, they could do controlled laboratory experiments in which they alter environmental conditions to see what effects the changes have on the transmission of pathogens.

"Combining these plants with the environment that they face, be it natural or involving the application of herbicides, insecticides or fungicides, could lead to the discovery of how pathogens are getting to these plants and what potential vectors could be," said Georg Mohr, a research associate at the University of Texas at Austin and co-first author of the paper.

Another application might be in the dairy industry, where viruses routinely infect the bacteria that produce cheese and yogurt, thus slowing the production process or even preventing its completion.

Currently, preventing infections is complicated and costly. Lambowitz and Mohr suggested that dairy bacteria could be engineered to record their virus interactions and defend against subsequent infections.

This RNA-based defense mechanism is closely related to a previously discovered mechanism called CRISPR/Cas in which bacteria steal bits of DNA and store them as mug shots.

That method has inspired a new way of editing the genomes of virtually any living organism, launching a revolution in biological research, but the researchers said they do not anticipate that this new discovery will play a role in that sort of gene-editing. However, the enzymatic mechanism used to incorporate RNA segments into the genome is novel and has potential biotechnological applications.

Researchers discovered this novel defense mechanism in a type of bacteria commonly found in the ocean called Marinomonas mediterranea that's part of a class of microbes called Gammaproteobacteria, which include many human pathogens such as those that cause cholera, plague, lung infections and food poisoning.

The co-senior author of the paper is Andrew Fire, a professor of pathology and of genetics at Stanford who shared the 2006 Nobel Prize in Physiology or Medicine for the discovery of RNA interference. Stanford graduate student Sukrit Silas is the co-first author.

Support for this research was provided by the National Institutes of Health and the Welch Foundation.

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