New & Noteworthy

Personalized Essential Genes

November 02, 2016


Like a smartphone, a gene can have both essential and specialized functions. XRN1 may be an example of such a gene.Image from Wikimedia Commons.

Every smartphone has a few, key functions. For example, they all let you make calls, send texts, take pictures, and search the web. But smartphones also have their own specialized functions depending on who owns them.

Maybe you’re an avid Candy Crusher and so you have every iteration of that game on your phone. Or maybe you have an ESPN app that lets you watch football highlights. There are pretty much an infinite number of possible combinations to personalize your phone.

A new study out in PLOS Pathogens finds something similar for the XRN1 gene in yeast. Rowley and coworkers found that in terms of basic function, they could swap one XRN1 gene for another across 4 different Saccharomyces species. All these different versions of the XRN1 did their main job of degrading RNA just fine no matter which yeast species they were in.

But a closer look revealed that each version of this key gene had a personalized function that did not swap as well. And this specialization wasn’t something trivial like Apple Music vs. Spotify. The personalized XRN1 genes protected their own species of yeast against species-specific viruses better than the XRN1 genes from other species.

It will be interesting to see if something similar happens in people. Perhaps the human version of XRN1, which also plays a role in taming RNA viruses, works better with human-specific RNA viruses too. This might help to explain our poor response to viruses that move from one species to ours.

Rowley and coworkers used four different assays to show that XRN1 from Saccharomyces species cerevisiae, mikatae, kudriavzevii and bayanus were all interchangeable for rescuing a variety of growth defects present in a S. cerevisiae strain deleted for XRN1. These XRN1 genes are indistinguishable in terms of the basic function of degrading damaged or old RNA in the cell.

The same was not true of each gene’s ability to deal with RNA viruses.

The main virus that infects Saccharomyces goes by the name of the L-A virus. These RNA viruses are a little different from many other viruses in that they don’t spread from one yeast cell to another. Instead, they stay within their host cell and spread only when the infected yeast cell buds off a new daughter.

These researchers used three different assays to show that the XRN1 genes from different species worked less well than the cerevisiae XRN1 to reduce the viral load in Saccharomyces cerevisiae. All three assays were consistent with the S. cerevisiae version working best.

First, they used an assay that looked directly at the dsRNA of the L-A virus. In a cerevisiae strain deleted for XRN1, they saw a fat, juicy band on their gel. This band was unaffected when they added back a dead version of XRN1 (either E176G or Δ1206-1528) and severely reduced when they added back the complete XRN1 gene from S. cerevisiae.

The effect of XRN1 from other species depended on how closely related they were to S. cerevisiae. For example, the XRN1 from the more closely related S. mikatae was able to reduce the band a bit while the genes from the more distantly related S. kudriavzevii and S. bayanus had no discernible effect.

The second assay took advantage of a very cool RNA virus known as “killer”. It basically has the instructions for making a secreted toxin that kills any yeast around the host cell while sparing the host. It is completely dependent on the L-A virus.

Previous research showed that XRN1 affects how well yeast carrying both viruses kill off surrounding yeast. They measured this with something called a kill zone. The idea was to put a spot containing 6×105 killer S. cerevisiae on a lawn of S. cerevisiae lacking the killer virus and to measure how big the “death” circle was that surrounded the spot.

Consistent with the results looking directly at the double stranded RNA of the L-A virus, Rowley and coworkers found that XRN1 from other Saccharomyces species were less able to negatively affect the ability of the killer virus to kill. This is presumably because they are less likely to degrade the virus meaning there is more of it around.

When they used S. cerevisiae XRN1, the kill zone averaged about 0.68 cm2. S. mikatae, S. kudriavzevii, and S. bayanus average 0.92 cm2, 0.96 cm2, and 0.97 cm2. S. cerevisiae harboring XRN1 from a different species were better killers.

The final experiment tested the ability of overexpressed XRN1 to cure S. cerevisiae of the L-A virus. In the absence of XRN1, 0/103 yeast managed to get rid of their virus. This number rose to 49% (78/159) when the XRN1 from S. cerevisiae was overexpressed. The XRN1 genes from other species fared much worse: only 12% (20/129) were cured with S. mikatae, 9% (11/123) with S. kudriavzevii, and 8% (10/120) with S. bayanus.

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XRN1 can keep the L-A virus in check…now if we could only get it to do something about that LA traffic! Image from pixabay.com.

So it looks like the S. cerevisiae XRN1 gene has evolved to combat the L-A viruses that infect S. cerevisiae best. But is the reverse true? Are the XRN1 genes from the other species also specialized in their viral attacks? Looks like the answer is yes, at least for S. kudriavzevii.

The tricky part of answering this question is the only well characterized L-A virus is from S. cerevisiae. So their first experiment was to find a virus in another Saccharomyces species. With a little work they found one in S. kudriavzevii FM1138. The experiments they did with this strain weren’t as clean as the ones they did with S. cerevisiae because S. kudriavzevii is a trickier yeast to work with, but they found that XRN1 from S. kudriavzevii did best at reducing the amount of S. kudriavzevii-specific virus compared to the XRN1 genes from the other species.

So XRN1 does some important basic things in the cell like clearing out old and damaged RNA and these functions are pretty similar no matter which Saccharomyces species they come from. However, the same is not true for its role in keeping viruses in check. At least in S. cerevisae, its XRN1 does a way better job at keeping its endemic viruses manageable than do the XRN1 genes from three other Saccharomyces species.

by Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: ribonuclease , virus , pathogen