New & Noteworthy

Turning to the Prion Expert: Yeast

February 15, 2017


You need an expert (not this guy!) for your plumbing problem. Just like you need yeast, and not some other organism, to study prions Image from flickr.

If you have a legal problem, you get a lawyer. A medical problem, a doctor. A leaky faucet, a plumber.

And if you are trying to find and figure out if a protein is a prion, you turn to the model organism where it is best understood. Yes, that is our old friend, the yeast Saccharomyces cerevisiae.

Prions became famous in the 1980’s when mad cow disease started to pop up in Britain. These are fascinating proteins that can cause an inheritable disease without affecting a cell’s DNA.

What happens is that prions can undergo a spontaneous conformational change. Now of course, this isn’t all that special. Lots of proteins can exist in different conformations.

But what makes a prion special is that the spontaneous change sets off a chain reaction where pretty much every copy of that prion protein is converted to that second conformation. And every translated prion protein thereafter both in the cell and any cells derived from that cell have that conformation too. So the new conformation along with the new traits it confers is passed on stably.

In mad cow disease, this spontaneous change causes neurological problems eventually resulting in death. But not every prion is so dangerous. Sometimes, as is the case in yeast, they can give new properties that allow survival in a new environment. Now these yeast have a new advantage in the absence of changed DNA.

Up until now prions have pretty much been confined to eukaryotes. That looks to change if a new study in Science by Yuan and Hochschild holds up.

They found that some bacteria have proteins that can and do behave as prions in a laboratory setting. The next step is to determine if they ever do so in the wild. If they do, then this would tell us that functioning prions may have evolved before the Bacteria/Eukaryota split and so be older than scientists previously thought.

The first step in finding a bacterial prion involved combing through a few bacterial genomes. Did I say a few? I meant something like 60,000 of them!

Of course you need the right tool for your search. This is where yeast’s incredibly well characterized set of prions comes in handy.

Yuan and Hochschild used an algorithm trained on known yeast prions to search through the bacterial genomes for proteins that have domains that would be predicted to be able to enter into a prion conformation. Among the proteins they found was the Rho protein in Clostridium botulinum E3 strain Alaska E43. Like the authors, I’ll call this protein Cb-Rho from here on out.

As you might remember, Rho is that famous transcription termination protein found in many different bacteria including E. coli. The E. coli version, however, does not look particularly like a prion nor did the authors find that it acts like one either.

A hallmark of prions is that one of the conformations involves their ability to form amyloid aggregates. These authors used a bacterial assay to show that this happened with Cb-Rho.

They next checked whether the prion portion of the protein behaved as a prion in a yeast cell. They substituted the prion domain from Cb-Rho with that of the one from Sup35p, a yeast prion. This chimeric protein behaved similarly to wild type Sup35p.

pipe

If you have a broken pipe, you find a plumber. But if you want to find and characterize a prion, you turn to yeast. Image from flickr.

They next tested their protein in E. coli. Often the prion conformation of the prion protein results in decreased activity of the protein. This is true in the Sup35p case, for example.

Sup35 acts as a translation release factor – it is an important factor in stopping translation at a stop codon. It is less active in its prion form meaning that there is now more read through of stop codons.

Rho is a transcription termination factor and so it would make sense that the prion conformation of Rho would result in lower levels of transcription termination. This is just what the authors found when they tested Cb-Rho in E. coli.

They used a reporter in which a transcription termination site was placed upstream of the lacZ gene. The idea is that if transcription termination is compromised, more lacZ will get made making the colonies a darker blue. And since termination is not 100% efficient, if Rho is doing its job, the colonies will be light blue.

When they plated out E. coli containing an engineered form of Cb-Rho, they got two classes of colonies, light blue and dark blue. And more importantly, this colony color was inheritable. In other words, light blue colonies gave more light blue colonies and dark blue colonies gave more dark blue colonies.

This isn’t to say that the colony color was a permanent state. It wasn’t. A bit under 1% of the colonies would spontaneously revert to the other form, as you’d expect from a prion protein.

So with the invaluable help of yeast, these authors were able to find and validate a protein from bacteria that can act as a prion. If they find a function for this in the wild, then yeast will have helped us better understand the evolution of life on Earth. Again. #APOYG!

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

Categories: Research Spotlight

Tags: lacZ, protein aggregate, bacterial prion, amyloid

Yeast with Dementia

January 04, 2012

Even though it doesn’t have a brain, yeast is teaching us a lot about Alzheimer’s.  Researchers are using this simple eukaryote to figure out what previously identified Alzheimer’s-related genes may be doing in humans as well as to identify new genes that might be involved in this terrible disease.  Studies like this may even one day help scientists find better treatments.

Alzheimer’s is a form of dementia that hits about 50% of people over 85.  The video below has a great summary of the how the disease progresses:

As the video states, plaques and tangles are linked to the memory loss that is associated with Alzheimer’s.  Scientists know that the plaques are  amyloids of misfolded AΒ peptides and that AΒ peptides that come from the amyloid precursor protein (APP).  What they don’t know is how AΒ peptides cause their damage and if it can be stopped.  And so far, genome wide association studies (GWAS) in humans have not shed much light on this problem either.

That isn’t to say that GWAS have been a waste of time.  They haven’t.  These studies have identified a number of alleles of a few genes that impact a person’s risk for ending up with Alzheimer’s.  They just haven’t been able to link the build up of plaques with the identified genes.  This is where yeast comes in.

Treusch and coworkers created a strain of yeast in which the AΒ peptide was sent to the endoplasmic reticulum.  This mimics what happens to the peptide in the cells of Alzheimer’s patients.  These yeast grew more slowly and developed protein complexes reminiscent of plaques.

They then added each of 5532 yeast open reading frames to this strain to identify genes that specifically affected its growth rate.  Of the 40 different yeast genes they found, two (YAP1802 and INP52) were yeast homologs of human genes (PICALM and SYNJ1) that had already been identified to be important in Alzheimer’s risks.  These results validated the screen and gave the researchers the confidence to dive deeper into their results.

The researchers decided to focus on the 12 genes that had very close human homologs.  Of these 12 genes, 10 dealt with endocytosis and the cytoskeleton and at least three had been implicated in previous genome wide association studies in humans.  Further work by these authors validated four of these genes by showing that they had similar effects on AΒ cell toxicity in the worm model C. elegans.

In one of the most interesting parts of the study, the researchers used the yeast strain to show why the GWAS-identified gene PICALM affects Alzheimer’s patients.  Rather than modifying APP trafficking as had been previously proposed, their results support a model where PICALM lessens the impact of misfolded AΒ plaques on the cell. 

This study is another example of the awesome power of yeast genetics.  Who would have thought that a brainless yeast could teach us so much about Alzheimer’s?

Simple explanation of the genetics of Alzheimer’s

More information about Alzheimer’s

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

Categories: Research Spotlight, Yeast and Human Disease

Tags: plaque, PICALM, amyloid, alzheimer's, model organism, APP, yeast

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