New & Noteworthy

Those Yeast Got Talent

March 11, 2015

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The winners of American Idol go through quite a selection process. They start out as one of tens of thousands of people who audition, and survive each cut until they are finally crowned.

At the first cuts, those with any sort of advantage are kept in the pool and the others dropped. As the cuts continue, contestants not only need to have had that stronger initial advantage (or a bit of luck), but they also need to have picked up some new skills from all of those off- and on-air performances.

Some of these contestants start with a lot of raw talent but then progress only a little, while others are able to hone their weaker initial talent with lots of practice. Once their numbers are winnowed down to a handful, it gets close to being anyone’s game because the remaining contestants are so talented.

A new study by Levy and coworkers paints a similar sort of picture for evolving populations of yeast. Very early on a whole lot of yeast stumble upon weak, beneficial mutations that keep them going in the population. These are the yeast that make the initial cut in the hurly-burly world of the Erlenmeyer flask.

At later times a few yeast end up with strongly beneficial mutations that allow them to start to dominate. These are the pool of yeast that are the finalists of the flask.

Of course a big difference (among many) between American Idol and the yeast in this experiment is that the pool of contestants in the flask hangs around—they are not thrown off the show. This means that some cell that didn’t do too well early on can suddenly gain a strongly beneficial mutation and begin to dominate. Until, of course, that cell is usurped by another more talented yeast, in which case that finalist will fade away unless it can adapt.

And this study isn’t just a fascinating dissection of evolutionary population dynamics either. It might also have implications for treating bacterial infections and even cancer.

Bacteria and cancer cells live in large populations with each cell trying to outcompete the others. By understanding the set of mutations that allow some cells to succeed against the others and become more harmful, researchers may be able to come up with new ways to treat these devastating diseases.

One of the trickiest parts of this experiment was figuring out how to follow lots of yeast lineages all at once in a growing culture. Levy and coworkers accomplished this by adding 500,000 unique DNA barcodes to a yeast population and using high-throughput DNA sequencing to follow the lineages in real time.

They set up two replicate cultures and followed them for around 168 generations. In both cultures the researchers saw that while most of the lineages became much less common, around 5% happened upon a beneficial mutation that allowed them to increase in number by generation 112.

In other words, around 25,000 lineages ended up with beneficial mutations that let them make the first cut in both cultures. This translates to a beneficial mutation rate of around 1 X 10^-6 per cell per generation and means that around 0.04% of the yeast genome (around 5000 base pairs) can change in a way that confers a growth advantage.

But of course not all mutations are the same. Weakly beneficial mutations are very common, which means both cultures have plenty of these early on. This is why the replicate cultures behave so similarly up to around generation 80.

Eventually, though, a few yeast stumble upon stronger, more beneficial mutations. Since these are rarer and harder to get, each replicate culture gets them at different generations. This is why the cultures begin to diverge as the 100 or so of the strongest beneficial mutations begin to dominate.

The experiment did not go on for long enough to see many double mutations. In other words, it was very rare in this experiment to see a yeast lineage succeed because it had developed additive beneficial mutations. This is because there simply wasn’t enough time for a yeast cell to get a beneficial mutation and establish itself and then have one of its lineage gain and establish a second beneficial mutation. There was no Jennifer Hudson who came in 7^th but then went on to win a Grammy and an Oscar.

When a cancerous tumor is developing, however, there is plenty of time for multiple “beneficial” mutations to be established. These mutations are only beneficial for the tumor; they are devastating for the person with cancer. This is why it is so critically important to understand not only which mutations are implicated in cancer, but also the dynamics of how they accumulate in the cancer cell population during progression of the disease. Talented yeast in the hands of talented researchers are helping us figure this out.

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

Categories: Research Spotlight

Tags: cancer, evolution, Saccharomyces cerevisiae

Sweet or Salty? It’s Hard to Tell Just By Looking

March 05, 2015

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If you have ever accidentally added salt to your coffee, you know that sugar and salt are very different things even though they look pretty much the same. Turns out that genes can sometimes be this way too. They can look similar at the DNA level but have very different functions.

A great example of this can be found in a new study in GENETICS by Varshney and coworkers. They found that a protein kinase in Candida albicans, Sch9, is important for ensuring that chromosomes end up in the right place when this yeast reproduces by budding.

Turns out that the same is not true for the Sch9 ortholog in our favorite yeast Saccharomyces cerevisiae. There is no evidence that Sch9 has anything to do with chromosome segregation there, even though the Sch9 sequences in these two yeasts look very similar.

C. albicans Sch9 is very important for keeping filamentous growth at bay under certain conditions (hypoxia and high levels of carbon dioxide). To understand better how Sch9 does this, Varshney and coworkers used chromatin immunoprecipitation (ChIP) to figure out where the protein binds in the genome. They were surprised when they found that it bound mostly to centromeres.

Despite this binding, the authors saw no evidence that Sch9 was involved in stabilizing the kinetochore, the protein structure that forms at the spindle of sister chromatids. When a kinetochore is destabilized, a cell’s nuclear morphology changes, its centromeres decluster during the cell cycle, and the centromeric histone Cse4 delocalizes away from its centromeres. The authors saw none of these things in a C. albicans strain in which the SCH9 gene was deleted.

They did, however, find that C. albicans cells lacking Sch9 had anywhere from a 150 to a 750-fold increase in chromosome loss. They found this by using a strain of C. albicans that had an arginine marker on one copy of its chromosome 7 and a histidine marker on the other, and looking for how often cells lost one of the two markers. From this the authors concluded that like many other kinetochore associated proteins, Sch9 is involved in chromosome segregation.

As a final experiment, Varshney and coworkers used ChIP to see if the Sch9 protein bound to centromeres in S. cerevisiae. It did not. While the authors did not directly test whether Sch9 had any effect on chromosome segregation in S. cerevisiae, the presumption is that it didn’t, as it doesn’t appear to interact with centromeres and no such effect has been seen previously.

But Sch9 isn’t completely different in the two yeasts. A close look at the ChIP data showed that Sch9 bound the rDNA locus in both C. albicans and S. cerevisiae.

How did orthologous proteins in two budding yeasts end up with such different functions? One idea is that the ancestral gene to Sch9 was important for rDNA regulation and that it later gained a function in chromosome segregation in C. albicans. Another possibility is that the ancestral gene had both functions and that centromere binding was lost in S. cerevisiae. More work will need to be done to tell the difference.

Whichever explanation is correct, this study reminds us that, just like sugar and salt, even if two genes look similar they may have quite different functions. Assuming that similar appearance means identical function may lead to an experimental result that is just as unpleasant as salty coffee!

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

Categories: Research Spotlight

Tags: Candida albicans, chromosome segregation, ortholog, Saccharomyces cerevisiae

SGD Spring 2015 Newsletter

February 26, 2015

SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This Spring 2015 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know.

Categories: Newsletter

Mannan From Heaven

February 25, 2015

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Thousands of years ago, humans encountered very little yeast in their diet. This all changed with the invention of beer and bread.

Now of course we didn’t include the yeast as a carbon source…we just liked fluffy bread and getting hammered. But it was a different story for the bacteria in our gut. They now found the mannans in yeast cell walls raining down on them like manna from heaven.

Unlike the Israelites, who could eat manna, most of our microbiota probably couldn’t use this newfound carbon source. But at some point, the polysaccharide utilization loci (PULs) of a few species changed so that they could now digest the mannans found in yeast cell walls. And, as a new study in Nature by Cuskin and coworkers shows, it was almost certainly a great boon for them.

They found that at least one gram negative bacterium, Bacteroides thetaiotamicron, can live on just the mannans found in the yeast cell walls. This isn’t just a cool story of coevolution either. It might actually help sick people get better one day.

Glycans, like the mannans found in yeast cell walls, have been implicated in autoimmune diseases like Crohn’s disease. One day doctors may be able to treat and/or prevent diseases like this by providing bacteria that can eliminate these potentially harmful mannans: a probiotic treatment for a terrible disease.

Cuskin and coworkers identified three loci in B. thetaiotamicron, MAN-PUL1, MAN-PUL2, and MAN-PUL3, that were activated in the presence of α-mannan. Deletion experiments showed that MAN-PUL2 was absolutely required for the bacteria to utilize these mannans.

The authors next wanted to determine whether the ability to use yeast cell walls as a food source provided an advantage to these bacteria. For this work they turned to a strain of mice that lacked any of their own gut bacteria.

The authors colonized these gnotobiotic mice with 50:50 mixtures of two different strains of B. thetaiotamicron—wild type and a mutant deleted for all three PULs. They found that in the presence of mannans, the wild type strain won out over the mutant strain and that in the absence of mannans, the opposite was true.

So as we might expect, if you feed mice mannans, bacteria that can break them down do best in the mouse gut. The second result, that mutating the PULs might be an advantage in the absence of glycans, wasn’t expected. This result suggests some energetic cost of having active PULs in the absence of usable mannans.

To better mimic the real world, Cuskin and coworkers also looked at the gut bacteria of these mice when they were fed a high bread diet. In this case, the mutant still won out over wild type but not by as much. Instead of being reduced to 10% as was true in the glycan-free diet, the final proportion of wild type bacteria in guts of mice on the high bread diet was 20%. Modest but potentially significant.

We do not have the space to discuss it here, but the authors next dissected the mannan degradation pathway in fine detail. If you are interested please read it over. It is fascinating.

The authors also analyzed 250 human metagenomic samples and found that 62% of them had PULs similar to the ones found in B. thetaiotamicron. So the majority of the people sampled, but not all, had gut microbiota that could deal with the mannans in yeast cell walls.

Human microbiota have adapted to use the energy from the bits of yeast left in bread and alcoholic beverages. Given how little there is, it might be better to think of it as the filth the peasants collected in Monty Python and the Holy Grail instead of manna. Even though it isn’t much, it has given these bacteria a niche that no one else has (or probably wants).

Still, it has allowed them to at least survive. And if these bacteria can one be repurposed as a treatment for disease like Crohn’s disease, thank goodness they adapted to using these mannans.  

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

Categories: Research Spotlight

Tags: evolution, glycans, gut microbiome

Reference Genome Annotation Update R64.2.1

February 23, 2015

SGD curators periodically update the chromosomal annotations of the S. cerevisiae Reference Genome, which is derived from strain S288C. Last November, the genome annotation was updated for the first time since the release of the major S288C resequencing update in February 2011. Note that the underlying sequence of 16 assembled nuclear chromosomes, plus the mitochondrial genome, remained unchanged in annotation release R64.2.1 (relative to genome sequence release R64.1.1).

The R64.2.1 annotation release included various updates and additions. The annotations of 2 existing proteins changed (GRX3/YDR098C and HOP2/YGL033W), and 1 new ORF (RDT1/YCL054W-A) and 4 RNAs (RME2, RME3, IRT1, ZOD1) were added to the genome annotation. Other additions include 8 nuclear matrix attachment sites, and 8 mitochondrial origins of replication. The coordinates of many autonomously replicating sequences (ARS) were updated, and many new ARS consensus sequences were added. Complete details can be found in the Summary of Chromosome Sequence and Annotation Updates.

Categories: Data updates, New Data, Sequence

Message in a Bubble

February 18, 2015

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If you’re shipwrecked on a desert island, writing a message on a scrap of paper, sealing it in a bottle, and flinging it into the ocean could be your only chance at communication. As the song goes (see below), the message in a bottle is an S.O.S. to the world.

It turns out that cells may do something very similar. But instead of using a bottle, they enclose their messages in membrane-bound bubbles.

Many different mammalian cell types have been seen to form these extracellular vesicles (EVs). In mammalian cells, it’s known that EVs are used for cell-to-cell communication. They contain signals that allow cells to influence their neighbors, both for good (for example, regulating the immune response) and for bad (transmitting viruses or toxic peptides). In most cases these signals aren’t well-characterized, but the EVs may include DNAs and proteins, and they’re rich in RNAs.

Fungi have been found to produce EVs too, but they’ve been much less studied. In a new paper in Scientific Reports, da Silva and colleagues looked at the extracellular vesicles (EVs) produced by four different fungal species, including S. cerevisiae, and found that among other things, the vesicles actually include at least parts of many RNAs, both protein-coding and non-coding.

The scientists decided to look at S. cerevisiae and three species of fungal pathogens that infect humans: Cryptococcus neoformans, Paracoccidioides brasiliensis, and Candida albicans. (S. cerevisiae can be pathogenic too, but isn’t as virulent as any of those species.) They isolated EVs from each and treated the unbroken EVs with RNase to get rid of any RNA that might be contaminating their surfaces.

Then they broke open the vesicles to see what was inside. They found that the EVs contained many small RNAs, most less than 250 nucleotides in length. The scientists used RNA-seq analysis to determine the sequences of these small RNAs, and compared them to the genomic sequences that were already known for these organisms.

Many of the sequences corresponded to noncoding RNAs. For S. cerevisiae, the RNA sequences identified included the mitochondrial small and large ribosomal RNAs, RNA components of RNase enzyme complexes, a variety of small nuclear and small nucleolar RNAs, and tRNAs.

Sequences corresponding to several dozen S. cerevisiae mRNAs were also detected. There wasn’t much rhyme or reason to the kinds of proteins they encoded.  But the set of mRNA fragments didn’t correspond simply to the set of most abundant mRNAs in the cell. So it seemed like the vesicles didn’t just contain random samples of the cytoplasm, but instead had been loaded selectively with particular mRNAs.

This study raises as many questions as it answers, and there is a lot of work to be done before fungal EVs will be understood. The intriguing discovery of RNA in EVs suggests the possibility that the RNAs could influence gene expression in cells that take up the EVs, either by regulating processes like splicing or translation, or even by encoding a protein that gets translated in the recipient cell.

Being able to influence neighboring fungal cells via EVs could be an advantage for fungi in the fierce competition for biological resources. Or perhaps EVs are used to subvert gene expression in host tissues during a fungal infection. Far from being an S.O.S., these messages could be threatening.

These speculations all need much more research. Fungi are an integral part of our world, and we need to pay careful attention to the messages that they send us!

by Maria Costanzo, Ph.D., Senior Biocurator, SGD

“Message in a Bottle,” The Police, 1979

Categories: Research Spotlight

Tags: cell-cell communication, extracellular vesicles, Saccharomyces cerevisiae

Yeast Finds Needles in a Haystack to Combat Malaria

February 11, 2015

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Finding a needle in a haystack would take a long time and would be very tedious (although it’s been done!) Finding a specific drug to fight malaria by testing the effect of each drug, one at a time, on a purified protein in vitro would be at least as tedious and maybe even more so.

Luckily, we don’t have to sift through a haystack. In a new study in ACS Chemical Biology, Frame and colleagues used our friend S. cerevisiae to find nine drugs out of a collection of more than 64,000 that are promising candidates for stopping the malaria parasite in its tracks. It is as if yeast allowed them to set fire to the haystack and see nine needles gleaming in the ashes.

Malaria is a huge problem for global health. Plasmodium falciparum, the organism that causes malaria, is fast developing resistance to the few effective drugs that we have left.

But P. falciparum has an Achilles heel—it can’t make its own purine nucleotides! Since these are the building blocks of DNA and, obviously, essential for life, if we can keep P. falciparum from being able to take them up, we can kill it. 

P. falciparum imports purines via a major transporter protein, called PfENT1, located in the plasma membrane. So a drug that specifically inhibited this transporter could be a good way to attack the pathogen.

It’s possible to assay the activity of the transporter in vitro, adding different drugs one at a time and seeing which inhibits transport. But doing this for thousands of drugs might make you wish you were looking for a needle in a haystack. Frame and colleagues decided to harness the awesome power of yeast genetics to test a very large set of drugs more quickly.

The toxic nucleoside analog 5-fluorouridine (5-FUrd) is taken into yeast cells by the high-affinity uridine transporter Fui1. It kills normal yeast cells, but fui1 null mutant yeast can survive in the presence of 5-FUrd.

The researchers engineered a yeast codon-optimized version of pfENT1 and expressed it in the mutant, restoring 5-FUrd uptake. The nucleoside analog was again toxic to this strain, and the only way the yeast could survive was if the transporter activity of pfENT1 was inhibited.

This system allowed a simple and powerful screen for pfENT1 inhibitors. The yeast strain expressing pfENT1 would be able to grow in the presence of 5-FUrd only if pfENT1 transporter activity was blocked by the drug that was being tested.

Setting up the screen on a large scale, the scientists were able to test 64,560 compounds. They initially found 171 compounds that allowed the yeast to grow. They narrowed these down to 9 compounds that worked well and belonged to different structural classes of chemicals.

Because of the way the study was designed, it was likely that these compounds allowed yeast to grow because they prevented PfENT1 from pumping the toxic 5-FUrd into the cell. But what if the compounds were actually doing something different, and unexpected? To rule out this possibility, the researchers designed a secondary screen for the 9 top candidate drugs.

They used ade2 mutant yeast, which can’t make their own adenine and need to be fed it in order to survive.  These mutants can make do with the related compound adenosine, but it can’t normally get inside the cell; yeast doesn’t have a transporter that will take it up. However, PfENT1 can transport adenosine, so ade2 mutants can grow on it if they are expressing PfENT1.

With this system, if the candidate drugs are working as expected, they should prevent yeast growth. And that is exactly what the researchers found. This confirmed that the drugs are working because they specifically inhibit PfENT1 and do not allow growth by some other, indirect mechanism.

To be completely sure of the mechanism, the scientists did a direct test. They found that the nine drugs prevented PfENT1-expressing cells from taking up radiolabeled adenosine.

This was all fine, but the ultimate goal of the study was to affect growth of the malaria parasite. So Frame and colleagues tested the drugs on P. falciparum. 

In the presence of any of the nine drugs, the parasite couldn’t take up adenosine and also failed to grow. This even happened when the parasites were grown in medium containing  much higher purine concentrations than found in human blood.

Even though PfENT1 was targeted by the drugs, all nine of the drugs also killed Pfent1 null mutants. This suggested that the drugs have a secondary target or targets in addition to PfENT1. This could be a real advantage, because it could help prevent the parasites from developing resistance to the drugs.

All nine of these diverse drugs are promising candidates for the treatment of malaria. And the same approach could be used to find chemicals that affect the function of other transporters from various organisms. 

As usual, yeast is providing scientists with streamlined ways to find new treatments for serious human diseases. Instead of tediously rummaging about in a haystack, yeast lets us quickly and easily find the needles we need. 

by Maria Costanzo, Ph.D., Senior Biocurator, SGD

Categories: Research Spotlight

Tags: high throughput screen, malaria, Saccharomyces cerevisiae, transporters

Ticket to Transcribe

February 04, 2015

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tRNA_CUG may not just be for translation anymore:

Back before airplanes and cars, when times got tough people would often take trains to what they hoped were greener pastures.  And to hitch a ride on a train, they’d usually need to have a ticket. Turns out the same is true for Gln3, a transcription factor in yeast.

Basically, Gln3 stays in the cytoplasm as long as there are good sources of nitrogen available to the cell.  When these sources run out, Gln3 moves from the cytoplasm to the nucleus where it can turn on genes that can help the yeast cope with its new situation.

In a new study in GENETICS, Tate and coworkers have identified one of the tickets that lets Gln3 take the trip to the nucleus. And it was totally unexpected. To get to the nucleus, Gln3 needs a fully functional glutamine tRNA_CUG. No, really.

To get this evidence, Tate and coworkers used a reporter in which Gln3 was linked to GFP (green fluorescent protein). They tracked the location of Gln3 in the cell using fluorescence microscopy.

Using a temperature-sensitive mutant of tRNA_CUG, sup70-65, the authors showed that at the nonpermissive temperature of 30 degrees C, Gln3 could not translocate to the nucleus under a wide variety of conditions in which nitrogen was limiting. Gln3 had no problems translocating at the permissive temperature of 22 degrees C, and in wild-type cells Gln3 translocated at both temperatures. Clearly tRNA_CUG is doing something important in this process!

The next experiment showed that tRNA_CUG was more like a one-way ticket. Once Gln3 entered the nucleus under nitrogen starvation conditions at the permissive temperature, switching to the nonpermissive temperature had little effect. Gln3 stayed put.

A possible wrinkle in these experiments was that cells harboring sup70-65 formed chains reminiscent of pseudohyphae at the nonpermissive temperature no matter what the nitrogen conditions. One possible explanation for the results seen here was that many of these cells lacked nuclei. In this case, they might not see nuclear translocation because there was no nucleus to translocate to.

In the course of these studies, Tate and coworkers showed that adding rapamycin mimicked the effects of nitrogen starvation with one big difference—nuclear localization happened much more rapidly than with nitrogen starvation. This fast response allowed the authors to look at Gln3 localization while visualizing nuclei by staining DNA with DAPI (which gives a short-lived signal). They were able to use the DAPI to see that these cells did indeed have nuclei and that when they raised the temperature, Gln3 did not colocalize with the DAPI stained nuclei.  Gln3 was being kept out of nuclei at the nonpermissive temperature.

So it really looks like Gln3 needs a working tRNA_CUG to get into the nucleus. There are a couple of possible ways that this tRNA could be needed for Gln3 to make the trip.

In the first model, the tRNA is part of a complex that allows Gln3 to make the trip to the nucleus. In this model, it is almost as if Gln3 (or one of its compatriots) is clutching its ticket, tRNA_CUG. In the second, less fun model, the tRNA is required to translate a protein involved in Gln3’s transit. Which model is the correct one is still up in the air, but it will be interesting to see which is the right one.

This was the most astonishing finding in the article, but it was by no means the only one. We don’t have the time to go into the other experiments, which, among other things, teased apart differences in the four or five distinguishable pathways that work to turn on the cell’s nitrogen response.

This work highlights a recurring theme in basic research: we may think we know everything that’s going on (tRNAs just help to translate proteins, right?) but just about every time we look more closely, there is much more to see than first meets the eye. Being in the right place at the right time is essential, whether you’re escaping the Dust Bowl in The Grapes of Wrath or a transcription factor responding to the lack of a nutrient. It’s not so surprising that the cell has drafted every possible player into this process, even a lowly tRNA. 

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

Since the title has this song stuck in our heads, we thought you might want to hear it too. Enjoy!

Categories: Research Spotlight

Tags: nitrogen utilization, Saccharomyces cerevisiae, transcription factor localization, tRNA

Announcing the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)

February 01, 2015

We at SGD are happy to share this announcement from the organizers of ICYGMB 2015. We’ll keep you up to date on the latest news about the conference and important deadlines. You can also follow announcements on Twitter by searching for the hashtag #yeast2015.

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It is our great pleasure to announce the 27^th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) to be held in Levico Terme, Trento, Italy, from 6th to 12th September 2015.

The conference, initially scheduled to take place in Lviv, was moved to the heart of the Italian Alps, following the assessment of the political situation in Ukraine, and is now being co-organized by the Italian and the Ukrainian Scientific Committees under the auspices of the International Committee on Finances and Policy, together with the help of some international scientific societies such FEMS and EMBO.

The goal of the conference is to bring together investigators from around the world to present and discuss research focused on yeasts as model for the understanding of molecular biology and genetic processes, and as a paramount biotechnological microorganism.

The Conference is historically an exciting forum on yeast biology, on our web site, you will have the opportunity to appreciate the scientific program and the beautiful scenery of this magnificent part of Italy where the Conference venue is located. In addition to the exceptional selection of speakers, we kept the opportunity, for brilliant researchers, to present their most recent work, since the fourth speaker of every plenary session will be selected from the abstracts submitted to the poster sessions. The science, the surroundings, and, of course, the food will be in the best tradition of Italian professional hospitality.

The conference is also part of EXPO2015, the world exposition that will be hosted in Italy in 2015 in Milano, comprising events in every Italian region. This year, the theme is to feed the planet, and we are committed to divulge to the public the importance of yeast in food and beverage productions. For this reason, the conference will be followed by a one-day EXPO2015 Symposium on Yeast Ecology and Food Production as well as on the fundamental role of the microscopic world in nutrition and human health (12th September 2015), together with a Roundtable on science as nurturer of peace. The registration to the 27th ICYGMB Conference will also include the participation to these extra events that will take place at the Museum of Modern Art of Rovereto, Italy.

Join us in this lovely part of the Trentino Region, in Italy, from 6^th to 12^th of September 2015 for this unique international event!

Help us spread the news by word of mouth and circulate the announcement you find here because for some colleagues we may not have had the updated e-mail address in our database. 

Good science, food and location are waiting to make this a most memorable yeast Conference. 

 Yours sincerely,

Duccio Cavalieri & Andriy Sibirniy (ICYGMB Organisers), 
on behalf of the National and International Organizing Committees.

Categories: Conferences

Species Can’t Risk the New Coke

January 29, 2015

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Genome organization may protect key genes from the ravages of increased mutation rate during meiosis:

Back in 1985, Coca Cola decided to completely rejigger the flavor of their flagship soft drink, calling it the New Coke. This radical change to the product was a colossal failure. Toying with such an essential part of a key product was simply too risky a move. If only they had learned from our favorite beast, Saccharomyces cerevisiae.

In a new study in PLOS Genetics, Rattray and coworkers show that the mutation rate is higher during meiosis in yeast because of the double-strand breaks associated with recombination. This makes sense, because any new mutations need to be passed on to the next generation for evolution to happen, and germ cells are made by meiosis. But their results also bring up the possibility that key genes might be protected from too many mutations by being in recombination cold spots. Unlike the Coca Cola company, yeast (and everything else) may protect essential genes from radical change.

Previous work in the Strathern lab had suggested that when double strand breaks (DSBs) in the DNA are repaired, one result is an increased mutation rate in the vicinity. The major culprit responsible for the mutations appeared to be DNA polymerase zeta (Rev3p and Rev7p).

To test whether the same is true for the DSBs that happen during the first meiotic prophase, Rattray and coworkers created a strain that contained the CAN1 gene linked to the HIS3 gene. The idea is that mutants in the CAN1 gene can be identified as they will be resistant to canavanine. The HIS3 gene is included as a way to rule out yeast that have become canavanine resistant through a loss of the CAN1 gene. So the authors were looking for strains that were both resistant to canavanine and could grow in the absence of histidine.

The first things the authors found was that the mutation rate during meiosis was indeed increased as compared to mitosis in diploids. For example, when the reporter cassette was inserted into the BUD5 gene, the mitotic mutation rate was 5.7 X 10^-8 while the meiotic mutation rate was 3.7 X 10^-7, a difference of around 6.5 fold.

This effect was dependent on the DSBs associated with recombination, since the increased mutation rate wasn’t seen in a spo11 mutant; the SPO11 gene is required for these breaks. Using a rev3 mutant, the authors could also conclude that at least half of the increased mutation rate is due to DNA polymerase zeta. This all strongly suggests that the act of recombination increases the local mutation rate.

If recombination is associated with the mutation rate, then areas on the genome that recombine more frequently should have a higher rate of mutation during meiosis. And they do. The authors inserted their cassette into a known recombination hotspot between the BUD23 and the ARE1 genes and saw a meiotic mutation rate of 1.77 X 10^-6  as compared to a rate of 4.9 X 10^-7 when inserted into a recombination coldspot. This 3.6 fold increase provides additional evidence that recombination is an important factor in meiotic recombination.

This may be more than just an unavoidable side effect of recombination. It could be that yeast and perhaps other beasts end up with their genes arrayed in such a way as to protect important genes by placing them in recombination dead zones.

And perhaps genes where lots of variation is tolerated or even helpful are placed in active recombination areas. In keeping with this, recent studies have shown that essential S. cerevisiae genes tend to be located in recombination cold spots, and that this arrangement is conserved in other yeasts.

It is too early to tell yet how pervasive this sort of gene placement is.  But if this turns out to be a good way to protect essential genes, Coca Cola should definitely have left the Coke formula in a part of its genome with little or no recombination. Mutating that set of instructions was as disastrous as mutating an essential gene!

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

Categories: Research Spotlight

Tags: evolution, meiosis, recombination, Saccharomyces cerevisiae

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