New & Noteworthy

Now Yeast Even Finds Fungal Pathogens!

July 27, 2017


Some products have lots and lots of uses. Sometimes they are designed that way like the hypothetical Shimmer, a floor wax and dessert topping from Saturday Night Live. And sometimes they can be used in more situations than they were originally designed for like Windex in the movie My Big Fat Greek Wedding, or the most versatile thing out there in real life, duct tape. (Click here and here for some fun duct tape uses).

Positive Pregnancy test results

Yeast might one day be used to identify fungal pathogens with an assay as easy to use as a pregnancy test. from Wikimedia Commons

Wait, did I say duct tape was the most versatile thing out there? Maybe I spoke too soon.

Our friend Saccharomyces cerevisiae is in contention with duct tape for that title. Of course it is used to make bread, beer and wine, but it has lots of other uses too. Just a very few include using it to: make antimalarial drugs, understand how our cells and a surprising variety of human diseases work, understand how evolution can happen, understand how cancer forms and progresses, and make ambergris (whale puke). In the near future, it may even help deal with climate change by making biofuels out of agricultural waste, and pain management by making opioids.

And now a new study by Ostrov and coworkers adds another use—the simple and inexpensive detection of fungal pathogens. This is a big deal because if it works the way the authors think it will, this new use could one day save the lives of a significant fraction of the two million or so people who die from fungal pathogens each year.

In a nut shell, these authors have engineered S. cerevisiae to be attracted to different kinds of fungus by monkeying with its pheromone detection system.

S. cerevisiae comes in two mating types, a and α. The a-type cells make the secreted mating pheromone “a-factor” and STE2, a receptor that responds to “α-factor.” And α-type cells make the secreted mating pheromone “α-factor” and a receptor, STE3, that responds to the “a-factor.” So, thea-type cell makes something that makes it attractive to α-type cells and vice versa.

The end result of the factor/receptor interaction is that a number of genes are regulated so that the two haploid cells, a-type and α-type, can merge to become an a/α diploid. Fertilization yeast-style.

What these authors have done is to switch out the STE2 receptor from S. cerevisiae with the receptors from other fungal species in a-type cells so that the newly engineered cell responds to the presence of the new fungal species’ pheromone. For example, they replaced S. cerevisiae STE2 with the STE2 from Candida albicans so that the newly engineered cell now responds to pheromones from C. albicans.

Now of course that doesn’t make much of a sensor! No, they also need a readout to know that the engineered yeast has detected the presence of C. albicans.

They started out using a fluorescent reporter to see whether their engineered system responded to C. albicans mating pheromone. The cells fluoresced when the C. albicans mating pheromone was around at low levels but not with any of nine other fungal mating pheromones. So the system is definitely working—it can specifically identify C. albicans.

But to make it more useful in the developing countries where fungal pathogens are the biggest problem, they wanted to create a system with a more visible readout. For this they turned a bright red pigment called lycopene.    

They needed to add three genes from Erwinia herbicola to get yeast to make lycopene: crtE, crtB, and crtI. They placed the first two under constitutive promoters (pADH1 for crtE and pTEF1 for crtB) and the third gene, crtI, under the control of the pheromone-inducible promoter from FUS1. So, lycopene is not made unless the appropriate pheromone is around to turn on the crtI gene.

This new system worked as well as the fluorescent one.

For the next step, they replaced the S. cerevisiae STE2 with STE2 genes from nine other fungal species involved in human disease and/or food or agricultural spoilage and showed that their system worked for all of them. These new pathogens included: Candida glabrata, Histoplasma capsulatum, Lodderomyces elongisporus, Botrytis cinerea, Fusarium graminearum, Magnaporthe oryzae, Zygosaccharomyces bailii, and Zygosaccharomyces rouxii.

And they didn’t stick to just the well-characterized fungal species either. They were also able to create a system that worked for Paracoccidioides brasiliensis, a less-well studied fungus that causes paracoccidioidomycosis (PCM), a disease endemic to Latin America.

It may be that just understanding a fungal species’ mating system is enough to create this sort of biosensor. More species will have to be tested to see just how universal the simple swapping out of a single gene will be.

hammock made of duct tape

Yeast is giving duct tape a run for its money in terms of versatility (although it can’t yet be used to make a hammock like this). From Ally’s Place (http://moonshadowangel.blogspot.com/2007/01/duct-tape-ho.html).

In their final step, Ostrov and coworkers tested whether they could create a simple, inexpensive dipstick test by spotting their engineered strains onto filter paper. For the initial test, they focused on two of their engineered strains: the one that detects the presence of C. albicans and the one that detects the presence of P. brasiliensis. They found that the system worked by simply putting the yeast-spotted filter paper into soil, urine, serum, and blood that had been supplemented with synthetic pheromone.

The yeast with C. albicans STE2 turned red with C. albicans pheromone, but not with P. brasiliensis pheromone and vice versa. And to increase its utility further, the authors found that the filter paper stayed functional even after being stored for 38 weeks at room temperature.

The impact of fungal pathogens on human health is understudied and underappreciated despite the toll they take on people’s lives, especially in the developing world. For example, as one recent review points out, “…at least as many, if not more, people die from the top 10 invasive fungal diseases than from tuberculosis or malaria.”

The basic research done on S. cerevisiae has allowed these scientists to devise an ingenious way to identify fungal pathogens. That magical combination of basic research and the most versatile eukaryote out there, S. cerevisiae, is poised to help humanity yet again.  #APOYG

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

Categories: Research Spotlight

Tags: crtI , MATALPHA , crtB , fungal pathogens , crtE , STE2 , STE3 , MATA , mating

Of Medieval Market Townes and Wasp Guts

February 03, 2016


As market towns like this one were a place where isolated medieval Europeans could find partners to take back home, so to are a wasp’s gut for yeast. Image from Wikimedia Commons.

Back before trains, planes and automobiles, people didn’t get around as much. And for the people of medieval Europe, this could be a real problem genetically.

At this time there were a lot of small, isolated villages scattered across Europe. If people in these villages stayed put, inbreeding might have gotten as bad as the poor Spanish Hapsburgs. Their last king, Charles II, was infertile, riddled with genetic diseases and his royal line died out with him.

One reason (among many) that this didn’t happen to people all over Europe was market towns. These were centrally located places where villagers came to sell goods. And where they also found partners to bring home to freshen up the gene pool.

Turns out that out in the wild, our friend yeast is in an even worse predicament than medieval Europeans. Because they are all clones of each other, they exist in isolated colonies with almost no genetic diversity.

Yeast are also way less mobile than people. They do have spores but these don’t tend to travel very far without help.

And yet, looking at yeast DNA shows that yeast definitely get around. There are all sorts of signs of various DNA mixing over time. So where are all these yeast hooking up?

A new study by Stefanini and coworkers in PNAS suggests that yeasts’ market towns are in the guts of wasps. It is there that various yeasts can meet and mate before heading back to their “villages.”

This makes sense in a lot of ways. First off, as we described in an earlier blog, there is good evidence that yeast winter in wasp guts.

So there are definitely a variety of yeast hanging around for months, waiting for warmer weather. The gut is also the kind of harsh place where spore dissolution, the first step in yeast mating, can happen.

When the authors looked at the yeast isolates from a wasp’s gut they saw a lot more outbreeding compared to other sources. This suggests that a lot of mating is indeed going on there.

The next step was to directly test how much mating can actually happen in a wasp gut. Stefanini and coworkers tested this by having the wasps eat five different yeast strains and then analyzing the isolates genetically over time. They compared the results from this experiment to the amount of mating that happens in wine must and under ideal lab conditions.

What they found was a whole lot of mating going on.

After two months, around 1/3 of the yeast in the wasp’s gut were outcrossed. This is OK but pretty comparable to what is found in wine must.

It was a different story after four months. Now 90% of the yeast were outcrossed. This is an even better result than scientists typically get in the lab. Clearly the wasp gut is a great place for a yeast to find a partner.

The authors also found that the S. paradoxus strain had to mate to survive in the gut. The only time they found this strain in yeast isolates was in hybrids with S. cerevisiae.

The next steps will be to see if this kind of mating actually has a big effect on yeast diversity in the wild. And of course what, if anything, the wasp gets out of hosting these cavorting yeast.

A market town was great for both the town and the visitors. People met up, sold goods, found partners and the towns prospered from all of this traffic. I can’t wait to find out if the wasp/yeast situation is so mutually beneficial as well.

Jerry Lee Lewis has a whole lot of shakin’ going on, just like a wasp’s gut has a whole lot of matin’ going on.

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

Categories: Research Spotlight

Tags: inbreeding , Saccharomyces cerevisiae , mating , Saccharomyces paradoxus , outcrossing

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