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Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs

September 24, 2018


poison_ivy__batman__by_flo_moshi

In the Batman comics, Poison Ivy is resistant to all natural toxins and diseases (from deviantart)

Resistance to poisoning is a good thing in the cartoon world, where both good and bad guys and gals often have superpowers that render them resistant to all sorts of toxins and poisons. But does that happen in the “real” world that we live in?

Well, some people would say that Keith Richards and cockroaches are the ultimate examples of earthly organisms resistant to every known toxin! But there are other more mundane examples of humans that are resistant or tolerant to certain chemical or organic compounds.

For example, almost everyone knows someone (or themselves) who can’t drink milk, because if they do, they feel really sick, with uncomfortable or even severe gastrointestinal symptoms. These people are said to be “lactose intolerant” (which is NOT an allergy to milk), because their gut can’t digest a sugar called lactose found only in milk and milk-based products.

Interestingly, all humans have the “lactase” gene that allows their body to digest lactose, but lactose intolerant folks have a particular “switch” sequence in their DNA that causes the gene to get totally turned off once they’re not babies anymore.

Hydrolysis_of_lactose

The lactase enzyme splits the disaccharide lactose into galactcose (1) plus glucose (2) (from wikimedia)

However, people who CAN drink milk as adults (“lactose tolerant” people) have a change in their DNA sequence that inactivates the switch. So these people have the lactose-digesting gene turned on and functioning for their whole lives and can consume milk and dairy products even as adults.

This is an example of genomic diversity among human beings, where people’s individual genome sequences have differences that can make them resistant to the negative effects of some foods or chemicals, while other people have little or no tolerance at all.

This type of DNA sequence variation across all the members of a species is called “standing genetic variation” and it’s a very good thing. Why? Because when a changing or novel environment challenges a population, standing genetic variation increases the chance that some individuals can adapt to new types of foods (like what happened with the lactase gene) or have other characteristics that make them better suited to survive in the new environment…or even be resistant to new diseases!

PlanetOfTheApes

In the Planet of the Apes series, “simian flu” kills almost all humans except for those few who are resistant (from deviantart)

But what does all of this have to do with yeast? Well, just like lactose intolerant humans, yeast can get sick when they try to “eat” certain things too, and will fail to grow well in the presence of such compounds. But could there be some yeast individuals somewhere in the world that have tolerance to certain normally-toxic compounds?

This is exactly the question that Higgins and co-workers asked, and in the September issue of Genetics they describe how they found naturally occurring yeast that can tolerate high levels of compounds called “ionic liquids.” And they also discovered the underlying naturally-occurring genetic variations in two genes that make the yeasts more tolerant to these compounds!

So what are ionic liquids and why were these investigators interested in them? Ionic liquids are a type of salt that can exist in a liquid state at temperatures under the boiling point of water or even at room temperature.

One type in particular, “imidizolium ionic liquids” (IILs) are often used in production of biofuels because they efficiently solubilize plant biomass cellulose and help turn it into glucose. The glucose can then be fermented (often by our yeast friend Saccharomyces cerevisiae) into bioethanol or other biofuels.

However, most commonly used S. cerevisiae strains, when grown in the presence of IILs, get very ill. But if IIL-tolerant yeasts could be found, they could help improve the production of cellulosic ethanol and other bioproducts.

Exxon_desert_tanker

Cellulosic biofuels may help decrease worldwide carbon emissions by reducing fossil fuel use (from wikimedia)

Higgins and co-workers decided to make use of the standing genetic variation within the S. cerevisiae species by taking hundreds of different strains of S. cerevisiae, isolated from around the world, and seeing if any of them could grow better in the presence of IILs.

And indeed they found some strains that were extremely IIL-tolerant compared to other S. cerevisiae strains such as beer, wine or lab strains, or even those commonly used in biofuel production! The yeast strain that was the most IIL-tolerant was, surprisingly, a clinical isolate from Newcastle, England.

The researchers then took genomic DNA from this IIL-tolerant strain and chopped it up into large pieces and put the pieces (carried on special plasmids called fosmids) into the common S288C lab strain (which is intolerant to high IILs) to see which regions could allow the lab strain to now grow in the presence of high levels of IILs.

They found two genes that conferred tolerance to the IILs: the SGE1 gene, plus a previously unnamed gene, YDR090C, which had not been studied very much. The proteins made from both genes appear to be located in the plasma membrane of the cell. The authors propose that the tolerant version of the SGE1 protein, already known to be a multidrug efflux pump that exports toxic cationic dyes out of the cytoplasm, is directly involved in the pumping the IILs out of the cells to help yeast tolerate these toxic compounds.

MDR_pump

The Sge1 protein is a multidrug transporter. Similar proteins in humans can cause resistance to anti-cancer drugs (from wikimedia)

The researchers were not able to exactly figure out what YDR090C is doing in the membrane to help cells be resistant to the bad effects of IILs, but they did find out that cells with a deletion of the gene were less tolerant to IILs. They thus named this gene “ILT1” for “Ionic Liquid Tolerant”.

The authors also found that the SGE1 gene from the IIL-resistant “wild” strain from England had a change in its protein sequence relative to the lab strain, but rather than making the protein more efficient at pumping, it looks like the changed protein is more abundant in the cell and thus can just pump out more of the obnoxious IILs.

Whenever they put this resistant gene version into an IIL-intolerant yeast, it did the trick of allowing the strain to grow better in high IILs concentration. This discovery might allow greater use of IIL-treated biomass for the production of biofuels, as it shows one powerful method of increasing the tolerance of biofuel-producing yeast to toxic IILs.

So this is indeed a case where looking at the “standing genetic variation” of a species has helped discover new and useful biotechnological functions in yeast, and also shown us that resistance (to IILs at least) is NOT futile, and may indeed help us make yeast more efficient at making more biofuels!

Resistance might be futile if you’re up against the Borg, but at least yeast can resist IILs!

by Barbara Dunn, Ph.D. and Kevin MacPherson, M.S.

Categories: Research Spotlight

Tags: lignocellulosic biomass, biofuels, variation

Prions Let Yeast Take Traits for a Test Drive

August 27, 2012

For the most part, prions have a bad rep. They are the proverbial bad apple that spoils the whole bunch.

One bad apple can spoil the whole bunch...

A prion is a protein that misfolds in a certain way that creates a chain reaction to misfold many additional copies of that particular protein in a cell. This misfolding en masse can cause severe problems like mad cow disease or Alzheimer’s.

As if that weren’t bad enough, this misfoldedness can spread from one organism to another. Once a prion gets into a cell and/or a part of the body, it will cause many of its properly folded brethren to misfold too. This is true even though the prion gene in the new host is happily churning out properly folded protein.

These things look like a nightmare. Why on Earth are prions still around? Because in addition to their bad side, they can sometimes be an advantage too (at least in yeast).

In a study published in Nature in February 2012, Halfmann and coworkers provide compelling evidence that prions can help both laboratory and wild yeast strains to adapt rapidly to a changing environment, by unlocking survival traits hidden in yeast DNA. In other words, prions are a way for a yeast population to hedge its bets against a world of changing environments.

The authors focused on the most famous prion in yeast, the translation termination protein Sup35p. When Sup35p switches to prion mode ([PSI+]), it becomes bound up in insoluble fibers, causing translation termination to become leaky. Now normally untranslated parts of mRNAs become part of their respective proteins. And this can change these proteins’ functions.

Sure, most of this newfound variation will have no effect or maybe even be harmful, but occasionally the prion will reveal a beneficial trait. This yeast can then go on to survive and even thrive in this new environment.

This mechanism may apply to other prions in addition to Sup35p. Prions tend to come from proteins that are global regulators of transcription or translation. In the non-prion form, these proteins do their usual job making sure transcription and translation are following the rules. But when these proteins become misfolded into a prion, they can no longer perform their usual function. This uncovers previously silent bits of DNA or RNA for transcription or translation.

These authors also convincingly showed that prions are not some weird phenomenon found only in laboratory strains of yeast. They found evidence for prions in 255 out of the 690 wild strains they surveyed (although only ten had Sup35p based prions). Not only that, but many of these prions also conferred new traits on the yeast that could be beneficial in certain circumstances. It looks like prions may serve an important function in yeast.

A more surprising result from the study is that these prion-derived traits carry on in later generations even after the prion has been removed. For example, the authors looked at the wine yeast UCD978. They found that when Sup35p was in its prion form in this strain, UCD978 could effectively penetrate agar surfaces and that this trait was lost when the prion was cured, reverting Sup35p to its functional form.

They then took the study further and showed that after meiosis and sporulation, 5/30 haploid progeny of UCD978 retained the trait even after the prion was removed. These five had fixed the new trait and no longer required the prion to maintain it. They got all the benefits with none of the costs.

It isn’t obvious how this trait became independent of the original inducing prion. But that is for another study (or two or ten).

If the results of this study pan out, they show that prions are not just part of a disease but are really just another way to adapt to environmental changes and to pass them down to future generations. Maybe these apples aren’t so bad after all!

Prions allow yeast cells to take various traits out for a test drive.

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

Categories: Research Spotlight

Tags: evolution, S. cerevisiae, prions, variation, SUP35

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