New & Noteworthy

Budding Yeast Diversifies its Phosphatase Portfolio

March 10, 2016


Putting all your eggs in one basket can be dangerous! So too can putting all your activity in a single protein. Image from Andrew McDowell via Flickr.

You’ve probably heard the old saying, “Don’t put all your eggs in one basket.” The idea of course is that the wise thing to do is to spread out your possessions so when something happens to one set, you still have the rest. (See what Homer and Marge Simpson think of this saying.)

If it really is wise to follow this saying, then according to the results of a new study just published in GENETICS by Kennedy and coworkers, the budding yeast S. cerevisiae is wiser than the fission yeast S. pombe. Well, at least as far as for one part of entry into mitosis.

To enter mitosis, every eukaryote tested so far needs to increase the activity of cyclin dependent kinase 1 (Cdk1). Dephosphorylation of a key tyrosine residue in Cdk1 is an important part of this increased activity.

One of the big players in this dephosphorylation is the phosphatase Cdc25 in S. pombe or Mih1p in S. cerevisiae. In fact, it is so important in S. pombe, that deleting it is lethal. These poor cells arrest in G2 and eventually die.

The same is not true for S. cerevisiae. Deleting MIH1 has only mild effects—a slight delay in entering mitosis and starting anaphase. The phosphorylation on the key tyrosine on Cdk1p, Y19, remains for a longer period of time in this strain, but does eventually clear, explaining the delayed mitotic entry.

One interpretation of this result is that S. cerevisiae has spread its Cdk1 phosphatase activity over multiple proteins. Knocking out MIH1 still leaves enough Cdk1 activity to allow the cell to enter mitosis, albeit more slowly.

One likely suspect in S. cerevisiae is Ptp1p. Previous work had shown that in S. pombe, Pyp3, the homologue of Ptp1p, can also dephosphorylate Cdk1-Y19.

Kennedy and coworkers found that deleting both MIH1 and PTP1 in S. cerevisiae had a more severe effect on mitotic entry and exit from anaphase compared to deleting only MIH1. In addition, the level of Y19 phosphorylation on Cdk1p remained for an even longer period in the mih1 ptp1 deletion strain. But it was still not lethal and the cells did eventually manage to pass through mitosis.

These results suggest there is still another player involved. The next suspect these researchers focused on was protein phosphatase 2A (PP2A). Previous work had shown that mutation of the B-regulatory subunits of PP2A, Cdc55p and Rts1p, both affect Cdk1p phosphorylation.

Because of the multiple routes by which PP2A can affect entry into mitosis, the authors designed an in vivo phosphatase assay to accurately measure the level of phosphorylation of Y19 of Cdk1p. The results of this assay suggested that PP2ARts1 and not PP2ACdc55 affected the phosphorylation state of Y19.

Kennedy and coworkers finally managed to kill off their yeast by deleting MIH1, PTP1, and PP2ARts1! They had finally found enough of this yeast’s phosphatase activity to mimic the effects of just Cdc25 in the fission yeast S. pombe.

Fission yeast keeps all of its Cdk1 phosphatase eggs in the same basket, while budding yeast has at least three different options. Image from websuccessteam.com.

Using immunopurified protein complexes, Kennedy and coworkers were able to show that both Mih1p and Ptp1p could dephosphorylate Y19 of Cdk1. They could not, however, see dephosphorylation by PP2ARts1. It could be that their in vitro assay did not detect it for this protein or that PP2ARts1 works on a different phosphatase that affects Cdk1.

Bottom line is that the budding yeast has evolved such that the phosphatase activity needed to enter mitosis is spread out over multiple proteins. The fission yeast evolved in a way that kept all of its phosphatase eggs in the same basket, Cdc25. We’ll let you decide which yeast you think is the wiser.

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

The Benefits of Sex

March 3, 2016


It is a good thing for lion-kind that these cubs weren’t budded off their mom asexually! Image from Stephanie Cornell via Pinterest.

While you doggedly swipe right and left or wait night after night at that club, you may be wondering whether it is all worth it. Biologists have been wondering something similar.

Now they haven’t been wondering about the value of sex…since everything from amoebas to zebras has sex, it must be pretty important. No, the hard part has been figuring out why it is so beneficial.

On balance it can seem that the minuses of disease risk and passing on only half of your DNA outweighs the benefits of the combining two individual sets of DNA for some brand new combination. A new study by McDonald and coworkers in Nature using our old friend S. cerevisiae provides compelling evidence for a couple of ways that sex is good for a species.

First it is a way of combining individual beneficial mutations into a single individual. Now rather than having a couple of well adapted individuals battling for supremacy, the mutations can merge into one super beast that can outcompete everyone else.

This benefit, recombination speeds adaptation by eliminating competition among beneficial mutations, had been predicted and goes by the name of the Fisher-Muller effect. But this is the first time scientists have actually seen it playing out at the DNA level.

The second big benefit of sex is freeing good mutations from a bad genetic background. Now the beneficial mutation is not weighed down by other negative mutations. It’s like finally getting rid of that concrete block tied around your ankle.

Yeast is an ideal system for studying the benefits of sex because it can happily exist as a sexual or asexual creature. This means that researchers can directly compare the two in the same experiment. Which is just what McDonald and coworkers did.

They followed 6 sexual and 12 asexual populations through about 1000 generations of adaptation. The only difference between the asexual and sexual populations was, as you might have guessed, sex.

The sexual populations included 11 bouts of sex. In other words, every 90 generations or so, an ‘alpha’ cell would swipe left and find an ‘a’ cell to hook up with.

As expected and has been seen before, the sexual populations were much better adapted to their environment than were the asexual populations. Sex is clearly a good thing! The next step was to tally up the mutations in each population to try to figure out why.

What McDonald and coworkers found was that there wasn’t a lot of difference in the mutations that crop up in each. Over time, both groups had about the same number and ratio of intergenic, synonymous, and nonsynonymous mutations.

The big difference between the asexual and the sexual populations was in the mutations that became fixed. In the sexual group, most mutations were weeded out over time. In their experiment, 78% of mutations became fixed in the asexual population while only 16% hung around in the sexual population.

Even the birds and the bees do it! Image from blog.beeminder.com.

Sheer numbers wasn’t the only difference between the two either. The kinds of mutations that became fixed differed significantly in both as well.

In the asexual population, each of the three kinds of mutations fixed at around the same rate. Around 75-80% of intergenic, synonymous and nonsynonymous mutations became established in this population.

It was a different story in the sexual population. Here, 22% of the nonsynonymous, 11% of the intergenic and none of the synonymous mutations became fixed. It seems like only mutations that make a difference end up getting selected for.

Further analysis revealed two big reasons why the two populations differed. First, good mutations ended up getting stuck with other bad mutations in the asexual population. This blunted the positive effects of the beneficial mutation.

And second, the various good mutations tended to be spread out among different groups in the asexual population. The end result was that instead of working together, these groups battled each other for supremacy resulting in some beneficial mutations being lost.

So no need to wonder anymore about the benefits of sex to a species. It is a strong purifier, weeding out unimportant or damaging mutations and a powerful aggregator, squirrelling all the good ones into one group. No wonder most every beast does it!

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

Join SGD at The Allied Genetics Conference

February 29, 2016


TAGC 2016 imageSGD will be attending The Allied Genetics Conference (TAGC) in Orlando, Florida, July 13–17, 2016! For the first time ever, the meetings of the yeast, C. elegans, ciliate, Drosophila, mouse, and zebrafish model organism communities will be united under one roof, along with a new meeting on population, evolutionary, and quantitative genetics.

Submit your abstracts now! Abstract submission will be open until March 23, 2016. If you want GREAT science and access to the leaders of the field, then TAGC is the place for you. SGD will be there, will you?

Not Quite The Same

February 24, 2016


From a first glace you might think these images are the same but they aren’t. Just like the gene expression pattern of a yeast auxotroph grown in complete media is not the same as that of the wild type strain. Image from Wikimedia Commons.

Imagine a world where you either make your own bread from scratch or have it delivered to your doorstep. Not much of a difference, right? Either way you’re eating bread.

Except of course that the two are pretty different. Having your bread delivered frees up time to do other things.

It turns out that something similar may be going on in our old friend, Saccharomyces cerevisiae. According to a new study in Nature Microbiology by Alam and coworkers, a yeast able to make its own amino acids or nucleobases works very differently than one that can’t but is supplied all the nutrients it can use.

This is important for yeast studies because these sorts of auxotrophic markers are used all the time. It means researchers need to be very careful about comparing a wild type yeast strain with a yeast strain deleted for, say, URA3, but grown in the presence of plenty of uracil. The two are not equivalent.

And the study may even have implications for other folks as well. For example, cancer cells have many mutations, some of which can be in metabolic genes. These mutations may affect how these cancers respond to drug treatment.

This all might not matter much if the effects were small. But they weren’t in this study. The changes were profound.

Alam and coworkers compared 16 different strains that were identical except that four different metabolic genes were deleted in various combinations. These genes included HIS3, LEU2, URA3 and MET15 (also known as MET17).

Using mRNA sequencing, they found that 5,011 out of 5,923 transcripts were affected in one strain or the other. This is 85% of the coding genome of yeast!

While not all of these changes were huge, 573 of them differed by 2-fold or more. In other words, around 10% of the genome is significantly affected when a yeast cell is provided a nutrient instead of having to make it itself. Not surprisingly, the affected genes were enriched for those involved in metabolic activity and enzymatic function.

The authors next looked at some publically available gene expression experiments that used auxotrophs in the same BY4741 background. These studies primarily looked at the how the knocking out of a specific gene affected global gene expression. The vast majority of deleted genes were not metabolic.

Alam and coworkers found that a sizeable minority of changes overlapped with the ones they saw with deleting HIS3, LEU2, URA3 or MET15. In other words, on average, at least 18% of the changes in the genes identified in these studies were not due to the gene deletion they were studying. They were instead due to the deletion of a “housekeeping” metabolic gene.

This all might be less of a big deal if the affected genes were always the same. Then you could just be on the lookout for these genes when using a specific auxotroph.

Not all replacements are equal to the original. Image from PopCultureBeast.com.

Unfortunately, it isn’t so easy. Different combinations of deleted metabolic genes yield different changes in gene expression patterns with very little overlap.

So, for example, when the authors compared a his3 deletion strain to one deleted for both HIS3 and URA3, a very different set of genes was affected. And these were different from a strain deleted for HIS3 and MET15, and so on. Looking at all the possible combinations confirmed that universal gene targets were rare.

The bottom line from these experiments is that researchers need to be very careful about the strains they compare because they may not be as equivalent as they think. Just because the older Star Trek films and the newer ones have a Spock, that doesn’t mean the half Vulcan is the same in both. Just ask Uhura.

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

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