New & Noteworthy

Ghosts of Centromeres Past

January 28, 2013

Every cell needs to correctly divvy up its chromosomes when it divides.  Otherwise one cell would end up with too many chromosomes, the other with too few and they’d both probably die.

Cells have developed elaborate machinery to make sure each daughter gets the right chromosomes.  One key part of the machinery is the centromere.  This is the part of the chromosome that attaches to the mitotic spindle so the chromosome gets dragged to the right place. 

Given how precise this dance is, it is surprising how sloppy the underlying centromeric DNA tends to be in most eukaryotes.  It is very long with lots of repeated sequences which make it very tricky to figure out which DNA sequences really matter.  An exception to this is the centromeres found in some budding yeasts like Saccharomyces cerevisiae.  These centromeres are around 125 base pairs long with easily identifiable important DNA sequences.

The current thought is that budding yeast used to have the usual diffuse, regional centromeres but that over time, they evolved these newer, more compact centromeres.  Work in a new study published in PLOS Genetics by Lefrançois and coworkers lends support to this idea.

These authors found that when they overexpressed a key centromeric protein, Cse4p (or CenH3 in humans), new centromere complexes formed on DNA sequences near the true centromeres. The authors termed these sequences CLR’s or Centromere-Like Regions.  And they showed that these complexes are functional.

When Lefrançois and coworkers kept the true centromere from functioning on chromosome 3 in cells overexpressing Cse4p, 82% of the cells were able to properly segregate chromosome 3.  This compares to the 62% of cells that pull this off with normal levels of Cse4p.  The advantage disappeared when the CLR on chromosome 3 was deleted.

A close look at the CLRs showed that they had a lot in common with both types of centromeres.  They had an AT-rich 90 base pair sequence that looked an awful lot like the kind of sequence that Cse4p prefers to bind and a lot like the repeats found within more traditional centromeres.  They also tended to be in areas of open chromatin and close to true centromeres. The obvious conclusion is that these are remnants of the regional centromeres budding yeast used to have. 

The hope is that the yeast CLRs might make studying regional centromeres easier.  They are so long and complicated that it is very difficult to pick out which sequences matter and which don’t, but the yeast CLRs could be a simpler model system.  Even better, the CLRs might shed some light on the process of neocentromerization – the formation of new centromeres outside of centromeric regions, which happens a lot in cancer cells. Once again, simple little S. cerevisiae may hold the key to understanding what’s going on in much larger organisms.

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

Categories: Research Spotlight, Yeast and Human Disease

Tags: centromeres, evolution, Saccharomyces cerevisiae, yeast model for human disease

Autophagy’s (Atg)9th Symphony

January 17, 2013

(Please click the musical note and listen to the music while reading.) The music you’re listening to starts off with a marimba. Then a flute joins in and as the marimba fades, in comes a shamisen. The piece progresses similarly with a harp, and then ends with the reappearance of the marimba. A nice, jaunty little piece of music.

This song is actually a tool for learning about autophagy in the yeast S. cerevisiae. Autophagy is a way to break down damaged or no longer useful proteins and recycle their components for later use. It is a very important pathway in keeping starving yeast alive. Many of the proteins involved in autophagy are highly conserved, and autophagy defects are implicated in several kinds of human disease.

As described in a recent paper, Takahashi and coworkers converted the sequences of four proteins involved in a step in autophagy – Atg9, Sso1, Sec9, and Sec22 – into pieces of music using UCLA’s Gene2Music program. Each protein was then assigned a musical instrument. Atg9 was played with the marimba, Sso1 with the flute, Sec9 with the shamisen, and Sec22 with the harp. The orchestrated piece of music reflects how each protein interacts with the others in the autophagy pathway.

Atg9 is a transmembrane protein that is key to making the vesicles that carry the damaged or unused proteins to the lysosome for destruction. But it, like the marimba, is not enough. Atg9 is recruited into service by at least three other proteins, Sso1, Sec9, and Sec22. These appear in succession in the musical piece as a flute, shamisen, and harp. Just like all four are needed for the orchestral piece, all four are also needed for successful autophagy.

Now listen to the music again. With this background, did you find the piece more illuminating? If you didn’t, it may simply be because it doesn’t fit your learning style, or match the type of intelligence that is your strength. Some people may respond to music better than they do to pictures of pathways or memorizing the steps involved. It may be that these people’s understanding of complicated pathways is enhanced with a musical component.

There will need to be more research on musical representation of complex pathways to see if they actually help students and even the public better understand science. If they do, I am looking forward to hearing the Krebs Cycle put to music. Or the assembly of the RNA polymerase II preinitiation complex. Which pathways do you want put to music?

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

Categories: Research Spotlight

Tags: autophagy, music, Saccharomyces cerevisiae, teaching

P is for Protection (not Processing)

January 11, 2013

Growing and dividing are dangerous work for a cell. Making all that energy throws off free radicals that mutate DNA and wreak havoc with delicate intracellular machinery. Given this it might seem surprising that just sitting there, not growing, is dangerous too. And yet it looks like it is.

When a cell runs out of food and goes into a quiescent state, it creates ribonucleoprotein (RNP) complexes called processing bodies (P bodies). In a new study out in GENETICS, Shah and colleagues were able to control how well yeast cells could make these P bodies. What they found was that cells that had trouble making P bodies didn’t survive the quiescent state as well as those cells that were great P body makers. It looked like P bodies were doing something to protect the cell when it wasn’t growing. In other words, being quiescent is dangerous too.

The key discovery made by the authors that allowed them to do these experiments was the fact that the Ras/PKA signaling system works specifically through the Pat1 protein to make P bodies. So by controlling the sensitivity of Pat1p to the signaling system, they could control the number of P bodies in the cell.

The Ras/PKA pathway phosphorylates two serine residues on Pat1p. When they are phosphorylated, P bodies are disrupted and/or are prevented from forming. The Pat1-EE mutation replaces the serine residues with glutamic acids, mimicking the phosphorylated state. The authors found that yeast cells carrying Pat1-EE produced fewer, smaller P bodies than did yeast carrying the wild type version of Pat1.

The authors then used this constitutively active mutant to ask whether P bodies helped cells survive the quiescent state. They compared the survival rate of cells carrying either the wild type version or the Pat1-EE protein and found that cells carrying the wild type version of Pat1 were more likely to survive after quiescence than were those cells carrying the constitutive form. More P bodies led to better survival.

The authors don’t yet know why this is, but one idea is that proteins and RNAs critical for survival after quiescence are stored in these particles. The idea would be that cells that have these key components squirreled away and protected survive better than those cells where these proteins and RNAs have degraded.

As a final point, it is important to mention why this matters (besides the excitement of figuring out how things work). Quiescent yeast cells are used as models for aging in higher eukaryotes like us. Perhaps by understanding how to make a yeast cell better survive this non-growing state, we can learn something about how to make people live longer too.

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

Categories: Research Spotlight

Tags: P bodies, quiescence, Saccharomyces cerevisiae

Be Good, For Adaptation’s Sake

December 17, 2012

You may never have herded cows. But in one way or another, you’ve certainly experienced the tragedy of the commons.

This happens when a village shares a pasture that can only feed a certain number of cows. For the system to work, everyone has to cooperate and keep the total number of cows under that limit. But inevitably, one cheater comes along and adds extra cows to his herd. At no immediate cost to himself, he gets all the benefits of the extra cows. But then tragedy kicks in as the pasture is overgrazed until no one can have any cows.

This doesn’t just happen out in the village. We can see it in the overfishing of the oceans, the production of carbon dioxide contributing to global warming, the milking of investors on Wall Street, and many other aspects of modern life. But perhaps surprisingly, we can even see it in cultures of the humble yeast S. cerevisiae.

In a recent issue of the Proceedings of the National Academy of Sciences, Waite and Shou set up a yeast system to look at the factors influencing the tragedy of the commons. In human society, sometimes cheaters cause a collapse, but other times, cooperators get together and exile the cheaters from the village. You might think that since yeast aren’t quite as smart as humans, in yeast “society” the cheaters would always win. However, Waite and Shou found that sometimes the cheaters were marginalized or even driven out, and the cooperators thrived!

To do these experiments, the researchers set up a very clever pasture in miniature. They engineered three strains, each marked with a different-colored fluorescent marker so they could be distinguished from each other.

The two “cooperator” strains needed each other to survive on minimal medium: one required lysine and produced excess adenine, while the other required adenine and produced excess lysine. The “cheater” strain required lysine but it didn’t provide any nutrients. So the cheater needed one of the cooperators to survive, but didn’t contribute anything to the common good.

As we might expect, being cooperative has a cost. The generous production of extra nutrients made the cooperator grow slower than the otherwise identical cheater strain. So you would predict that if you mixed the cooperators and the cheater in equal numbers and grew them together, the cheater would take over and collapse the culture every time.

However, when the researchers mixed all three strains in a 1:1:1 ratio and grew lots of replicate cultures, they found that cheaters didn’t always prosper. Sometimes the nice guys finished first.

Of course some of the cultures did collapse under the influence of the rapacious cheaters. After a while these cultures stopped growing and turned out to be made up of mostly dead or dying cheater cells. The cheaters had taken over the culture, selfishly using up the lysine until eventually there was not enough to continue growing.

But unexpectedly, other replicate cultures were growing much faster, at rates similar to cultures without any cheaters. In these cultures, the two cooperator strains had either dominated the culture or even driven the cheaters extinct!

To explain this, the researchers proposed that the intense selection pressure led to an adaptive race between cooperators and cheaters. In surviving cultures, the rare cooperator with a small advantage had outcompeted the cheaters.

To confirm this, they took a close look at the winning cooperators. They found that the fitness advantage could be inherited, so they used whole-genome resequencing to find out why the cooperators were outcompeting the cheaters. They kept finding mutations in the same five genes.

These genes all made sense, as mutating them would help in an environment with limited amounts of lysine. For example, most of the mutations were found in ECM21 and DOA4. Both of these gene products are important in pathways that break down proteins like permeases. Knocking them out would keep the permeases around longer, making for better lysine uptake. But this newfound advantage did not come without a price.

The researchers tested directly whether the adaptive mutations improved growth in limiting amounts of lysine. Without exception, they did. But almost all these strains grew more slowly in abundant lysine than did their ancestor strains. That explains why these mutant strains only became a significant proportion of the population late in the life of the culture, when lysine levels were very low.

The same mutations can arise in both cooperators and cheaters, of course. But when cheaters become better at growing in low lysine levels, they just become that much better at making themselves extinct. When cooperators get better at growing in low lysine levels, they are better able to keep growing and keep the cheaters at bay.

So the take-home lesson is that cooperation does pay, after all. Especially in a constantly changing environment, cooperators can often win the adaptive race and squelch the cheaters. Maybe we should take a hint from little S. cerevisiae that being kind to each other is not only a nice thing to do, it’s in all of our best interests!

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

Categories: Research Spotlight

Tags: adaptation, evolution, Saccharomyces cerevisiae

As Good as the Original

December 07, 2012

If you got to choose between an original and a copy of that original, you’d undoubtedly choose the original. Because of mistakes during the copying process, the original is bound to be superior.

Cairns was the first scientist to try to apply the same logic to cells like mother cells of the budding yeast S. cerevisiae, or stem cells. The idea is that since these cells make lots of copies of themselves, they might have some mechanism for keeping the original DNA and sending the copies to the new cells. This would protect the original DNA from building up mutations.

While this seems reasonable, the many studies done to date have failed to provide any compelling evidence to support the idea. When scientists look at a cell’s DNA in bulk, they see it randomly dividing between mother and daughter. But this is not the end of the story.

Another idea people have had is that one of the strands of the double helix is kept in its original form in the mother while the other is free to be passed on to the daughter. There is mounting evidence in yeast and mammalian cells that there is some strand-specific selection going on. But in a new study out in GENETICS, Keyes and coworkers show that this selection is not dependent on a strand being an original as opposed to a copy.

They use a couple of cool tricks to be able to follow specific strands of DNA in specific cell types in these experiments. First, they engineered a strain that would incorporate BrdU (bromodeoxyuridine) into newly synthesized DNA, so that they could distinguish between the original and copied strands. Second, they used a technique to separate mother cells from daughter cells that involves arresting the mother cells with alpha factor, labeling them with biotin, and then allowing them to divide: the mothers can be pulled away from the daughters by their biotin labels.

As you can see from the image on the right, Keyes and coworkers let a population of biotin-labeled mother cells divide once in the presence of BrdU. Next they separated mothers (M) from daughters (D) and biotinylated the daughters.

Next they let the two populations divide separately one more time in unlabeled thymidine (TdR) instead of BrdU, and separated mothers from daughters again. As shown in the figure, this allowed them to isolate four different cell populations:

1) MM: the original mother cells
2) MD: daughters of the original mothers
3) DM: mother cells derived from the first daughter
4) DD: daughters of the first daughter

The image shows the prediction if the Watson strand is preferentially kept by the mother. As you follow along, remember that the red strand represents the labeled DNA.

If mother cells inherit the Watson strand specifically and the daughter cell always gets the Crick strand (C), then we would predict that only MD and DM cells should have BrdU DNA. The other two cell types should only have unlabeled DNA.

Let’s follow the mother side to see why. The mother cell would inherit the unlabeled Watson strand and a labeled Crick strand because she would keep the original from the first division. The labeled and so copied Crick strand would then be passed preferentially to the daughter.

The same sort of logic applies to the daughter cell. The daughter inherited the labeled Crick strand. Since this daughter now becomes the mother in the next division, the labeled strand now becomes the Watson strand. She would keep this labeled strand and pass the unlabeled Crick strand to her daughter.

These are not the results they got. Instead, all the cell types had pretty close to the same amounts of BrdU. The moms did not preferentially hang on to either the original Watson or Crick strand.

They then followed this up with a separate, similar experiment that looked at each individual chromosome on a microarray. The results were that there was no bias for either strand for any of the chromosomes.

It seems that mom doesn’t hang onto the original DNA even at a single chromosome. In the cases of strand-specific selection that are now being studied, there are most likely other ways to pick a strand that have nothing to do with whether it is an original or a copy. Another great idea foiled by data…

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

Categories: Research Spotlight

Tags: chromosome segregation, Saccharomyces cerevisiae

I See Dead Yeast (in My Beer Foam)

November 19, 2012

A study by Blasco and coworkers confirms that beer foam is littered with corpses of dead yeast. Or at least with bits of their cell walls.

This has been known for awhile. But what these researchers did was to identify one of the key proteins in the cell wall important for maintaining a good head on beer.

The authors knew from previous studies that certain mannose binding proteins play an important role in beer foam. So they used primers that lined up with the 5’ and 3’ ends of one of the known foam-related genes from S. cerevisiae, AWA1, to look for similar genes in the brewing yeast S. pastorianus. This allowed them to PCR out the CFG1 gene.

To show that this protein was involved in the foaminess of beer, they next knocked the gene out of S. pastorianus and used this deletion strain to do some brewing. What they found was that while beer made with this strain had about the same amount of foam, it didn’t last as long. This strongly suggested that CFG1 was involved in maintaining a good head on a mug of beer, earning the gene its name: Carlsbergensis Foaming Gene.

As a final experiment, they added the gene back to a strain of S. cerevisiae, M12B, that makes beer without foam. When this strain expressed CFG1 and was used to brew up some beer, that beer was foamless no more. This suggests that CFG1 may be important for foam formation as well as stabilization.

What is probably happening is that during fermentation, yeast cells are autolysing, releasing their cell wall proteins into the beer. Since Cfg1p is hydrophilic on one end and hydrophobic on the other, it forms very stable bubbles. And foam is simply a bunch of stable bubbles.

Hopefully scientists can use this information to tweak the amount of foam a given beer yields. Then a drinker can choose lots or little foam, long lasting or short lived foam, or any combination he or she wants.

Root beer foams for a different reason

NPR’s take on this study

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

Categories: Research Spotlight

Tags: beer, brewing, Saccharomyces cerevisiae, Saccharomyces pastorianus

Identifying the Unstable

November 08, 2012

One of the many stumbling blocks in finding better treatments for genetic diseases is figuring out the cause of the disease.  These days, this doesn’t necessarily mean simply identifying the gene with the mutation.  No, nowadays it can mean figuring out what each specific mutation does to the gene it damages.

See, many genetic diseases are not caused by single mutations.  Instead, lots of different mutations can all damage the same gene in different ways.  And each class of mutation may require different treatments.

Cystic fibrosis (CF) is a great example of this.  While most cases of this ultimately fatal disease are caused by mutations in the CFTR gene, not every mutation does the same thing to the CFTR protein.  Because of this, scientists have found different drugs to treat people with different classes of CFTR mutations.

So one drug, Ivacaftor, targets CFTR proteins that can’t open up as well as they should, while another investigative drug, PTC124, targets prematurely stopped CFTR proteins.  Each only treats a specific subset of CF patients who have the correct CFTR mutation.

All of this screams out for a quick and easy assay to figure out how a mutation actually disables a certain protein.  And this is where a new study by Pittman and coworkers just published in the journal GENETICS can help.

The authors have come up with a sensitive in vivo assay in S. cerevisiae that allows scientists to quickly identify mutations that lead to unstable proteins.  This kind of instability isn’t rare in human disease either.  Some of the more famous examples include a kidney disease called primary hyperoxaluria type 1 (PH1), Lou Gehrig’s disease (ALS), Parkinson’s disease, spinal muscular atrophy (SMA), and even some forms of cancer.

The assay basically inserts wild type and mutant versions of the gene of interest into the middle of the mouse dihydrofolate reductase (DHFR) gene, individually adds these chimeric genes to yeast lacking DHFR, and then measures growth rates.  The idea is that if the mutation leads to instability, the DHFR chimeric protein will be unstable too and the yeast will show growth defects under certain conditions.  This is just what they found.

Initially they focused on a gene involved in PH1, the AGT gene encoding alanine: glyoxylate aminotransferase.  They were able to show that disease causing mutations known to affect protein stability affected growth in this assay.  Not only that, but there was a strong correlation between growth and level of protein stability.  In other words, the more unstable the protein, the more severe the growth defect.

They then expanded their assay beyond known AGT mutations.  First they were able to identify a subset of disease-causing AGT mutations as affecting the stability of the AGT protein.  But the assay ran into trouble when they switched to the more stable SOD1 protein.  This protein, which is involved in most cases of ALS, is so stable that mutations that destabilized it were invisible in the assay.  The authors solved this problem by introducing a mutation into DHFR that destabilized it.  Now they could identify mutants that destabilized SOD1.

As a final step, they used their assay to screen a library of stabilizing compounds to identify those that specifically stabilized their mutant proteins.  Unfortunately, in this first attempt they only found compounds that stabilize DHFR, but the assay has the potential to find drugs that stabilize disease-related proteins as well.

Whether or not that potential is realized, this technique should still be a very useful way to determine whether a mutation affects protein stability.  Then, when drugs that stabilize the protein have been found, using this or other screens, doctors will know which patients can be helped by these compounds.  And this will be a boon for scientists and patients alike.

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

Categories: Research Spotlight, Yeast and Human Disease

Tags: protein stability, Saccharomyces cerevisiae, yeast model for human disease

Using Yeast to Discover Treatments for ALS

November 01, 2012

What do Lou Gehrig, Stephen Hawking, David Niven and Mao Zedong have in common?  They all suffered (or in Hawking’s case, continue to suffer) terribly from a disease called amyotrophic lateral sclerosis or ALS.  And now the humble yeast S. cerevisiae may help scientists find new treatments so that others do not need to suffer similarly.

Patients with ALS gradually lose use of their motor neurons and generally die within 3-5 years of diagnosis.  While there are some rare forms that run in families, most are sporadic.  There is no history of the disease in the family and then suddenly, it just appears.

The causes of ALS have remained a mystery for many years but recent work has suggested that RNA binding proteins and RNA processing pathways are somehow involved.  In particular, an RNA-binding protein called TDP-43 appears to be a key player.  Mutations in its gene are associated with ALS, and aggregates of the protein are found in damaged neurons of ALS patients. Unfortunately, since this protein is needed for cell survival it is not an easy target for therapies.  This is where yeast can help.

Scientists have managed to mimic the effects of TDP-43 in yeast.  When this protein is overexpressed, the yeast cells die just like the motor cell neurons do. In a recent Nature Genetics paper, Armakola and coworkers use this model system for finding better therapeutic targets.  And it looks like they may have succeeded.

These authors used two different screens to systematically look for proteins that when deleted or expressed at lower levels rescued yeast overexpressing TDP-43.  They found plenty.  One screen yielded eight suppressors while the other yielded 2,056 potential suppressors.  They decided to focus on one of the stronger suppressors, DBR1.

The first thing they wanted to do was to make sure this wasn’t a yeast specific effect.  If lowering the amount of DBR1 has no effect in mammalian models, it is obviously not worth pursuing!

To answer this question, they created a mammalian neuroblastoma cell line with an inducible system for making a mutant version of TDP-43, TDP-43 Gln331Lys, found commonly in ALS patients.  As expected, these cells quickly died in the presence of inducer.  They could be rescued, though, when DBR1 activity was inhibited with siRNA.  The authors confirmed that decreasing the activity of DBR1 in primary neurons decreased TDP-43 toxicity as well.

So decreasing the amount of DBR1 appears to rescue cells that die from the effects of mutant TDP-43.  This suggests that targeting DBR1 may be useful as a therapy for ALS.  But this study doesn’t stop there.  It also tells us a bit about how lowering DBR1 levels might be rescuing the cells.

DBR1 is an RNA processing enzyme involved in cleaning up the mess left behind by splicing.  It cleaves the 2’-5’ phosphodiester bond of the spliced-out intron (called a lariat).  Previous studies in yeast have shown that when Dbr1p levels are reduced or its catalytic activity is disrupted by a mutation, there is a build up of these lariats. This study showed directly that the accumulated lariats interact with TDP-43 in the cytoplasm to suppress its toxicity. So in ALS, the accumulated lariats may serve as a decoy for the mutant TDP-43 protein, preventing it from binding to and interfering with more essential RNAs.

This last result may also suggest another potential therapy.  If scientists can find other ways to increase the amount of decoy RNA, then they may not need to depend on reducing levels of DBR1.  There may be many possible approaches to soaking up rogue TDP-43.

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

Categories: Research Spotlight, Yeast and Human Disease

Tags: ALS, DBR1, Lou Gehrig's Disease, RNA binding, Saccharomyces cerevisiae, yeast model for human disease

When Polymerases Collide

October 25, 2012

Lots of recent studies are showing that transcription happens over way more DNA than anyone previously thought. For example, the ENCODE project has shown that most of a genome gets transcribed into RNA in humans, fruit flies and nematodes. This transcriptional exuberance was recently confirmed in the yeast S. cerevisiae as well.

There is also a whole lot of antisense transcription going on. Taken together, these two observations suggest that there are lots of opportunities for two polymerases to run headlong into each other. And this could be a big problem if polymerases can’t easily get past one another.

Imagine that the two polymerases clash in the middle of some essential gene. If they can’t somehow resolve this situation, the gene would effectively be shut off. Bye bye cell!

Of course this is all theoretical at this point. After all, smaller polymerases like those from T3 and T4 bacteriophages manage to sneak past one another. It looks like this isn’t the case for RNA polymerase II (RNAPII), though.

As a new study by Hobson and coworkers in Molecular Cell shows, when two yeast RNAPII molecules meet in a head on collision on the same piece of DNA, they have real trouble getting past each other. This is true both in vitro and in vivo.

For the in vivo experiments, the authors created a situation where they could easily monitor the amount of transcription close in and far away from a promoter in yeast. Basically they pointed two inducible promoters, from the GAL10 and GAL7 genes, at one another and eliminated any transcription terminators between them. They also included G-less cassettes (regions encoding guanine-free RNA) at different positions relative to the GAL10 promoter, so that they could use RNAse T1 (which cleaves RNA at G residues) to look at how much transcription starts out and how much makes it to the end.

When they just turned on the GAL10 promoter, they saw equal amounts of transcription from both the beginning and the end of the GAL10 transcript. But when they turned on both GAL10 and GAL7, they saw only 21% of the more distant G-less cassette compared to the one closer to the GAL10 promoter.

They interpret this result as meaning the two polymerases have run into each other and stalled between the two promoters. And their in vitro data backs this up.

Using purified elongation complexes, they showed that when two polymerases charge at each other on the same template, transcripts of intermediate length are generated. They again interpret this as the polymerases stopping dead in their tracks once they run into one another. Consistent with this, they showed that these stalled polymerases are rock stable using agarose gel electrophoresis.

Left unchecked, polymerases that can’t figure out how to get past one another would obviously be bad for a cell. Even if it were a relatively rare occurrence, eventually two polymerases would clash somewhere important, with the end result being a dead cell. So how do cells get around this thorny problem?

One way is to get rid of the polymerases. The lab previously showed that if a polymerase is permanently stalled because of some irreparable DNA lesion, the cell ubiquitinates the polymerase and targets it for destruction. In this study they used ubiquitin mutants to show that the same system can work at these paused polymerases too. Ubiquitylation-compromised yeast took longer to clear the polymerases than did their wild type brethren.

The authors think that this isn’t the only mechanism by which polymerases break free though. They are actively seeking factors that can help resolve these crashed polymerases. It will be interesting to see what cool way the cell has devised to resolve this dilemma.

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

Categories: Research Spotlight

Tags: RNA polymerase II, Saccharomyces cerevisiae, transcription, ubiquitin-mediated degradation

Better Beer Through Beards

October 16, 2012

Small time craft brewers are always looking for ways to push the envelope of beer taste.  They are trying to find variations in beer’s fundamental ingredients — hops, barley, and yeast — that will make their beer distinctive.  Of these three, the most important is probably yeast (of course, we’re biased here at SGD!).

Something like 40-70% of beer taste comes from the yeast used to make it alcoholic.  This is why brewers search high and low for new strains of yeast that will give their beer that special something which will make it stand out.  They have looked on Delaware peaches, ancient twigs trapped in amber, Egyptian date palms, and in lots and lots of other places. 

But brewers don’t always have to go far away because sometimes the best yeast is right under their noses.  Literally.

A brewery in Oregon found the yeast they were looking for in one of their master brewers’ beards.  They are now using this yeast to brew a new beer!  This seems uniquely revolting but the beer supposedly is quite tasty.  Perhaps if they don’t advertise the source of their yeast, this beer could become popular.

They aren’t sure where the yeast in his beard came from, but they think it may have come from some dessert he ate in the last 25 years or so (he hasn’t shaved his beard since 1978).  What would be fun is if his beard wasn’t just an incubator, but a breeding ground for new yeast.  Maybe yeast from a dessert from 1982 hooked up with a beer yeast blown into his beard while he was working at the brewery.  The end result is a new improved hybrid yeast! 

Of course we won’t have any real idea about this yeast until we get some sequence data from it.  And all kidding aside, the more yeast that are found that are good for making beer, the better the chances that scientists can home in on what attributes make them beer worthy.  So this beard borne yeast may help many beers in the years to come despite its troubling beginning.

Perhaps brewers also need to start searching through more beards to look for likely beer yeast candidates.  Beard microbiome project anyone?

More information

About beard yeast

What’s in a beer, anyway?

Original lager yeast found in Patagonia

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

Categories: Research Spotlight

Tags: beer, fermentation, Saccharomyces cerevisiae

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