New & Noteworthy

Time Flies Like an Arrow, Fruit Flies Like a Grande Yeast

July 31, 2014

Here at SGD we tend to have a totally positive opinion of yeast.  As we have said before, they give us bread, booze, a great model organism, and even our livelihoods.  But in truth, Saccharomyces cerevisiae has a few minor faults.

For example, you can thank yeast for all those irritating fruit flies buzzing around your brown bananas.  Fruit flies aren’t attracted to the rotting fruit itself.  They are instead attracted to chemicals the yeast cells are pumping out as they nosh on that old banana.

In a new study, Schiabor and coworkers set out to identify the genetic differences that make some yeast strains more attractive to fruit flies as compared to other strains.  They found that the flies can actually tell the difference between “petite” yeast, with defective mitochondria, and “grande” yeast whose mitochondria are normal.  The mitochondria play a huge role in determining which volatile chemicals a yeast will release, and so determine which yeast are the most attractive to a fruit fly.  But the mitochondria are probably not involved in the way that you might be thinking…

In the first experiment, the authors tested a bunch of different yeast strains to find the ones that fruit flies prefer. As expected, they found a wide range of yeast attractiveness.  They decided to focus on BY4741 as the more appealing strain and BY4742 as the less appealing one.

Schiabor and coworkers chose these two strains both because they are isogenic and because they are the strains from which the systematic yeast deletion collection was made.  These two attributes mean that it should be relatively easy to track down the genetic difference in each strain’s attractiveness to fruit flies.

The first obvious candidate was the different auxotrophies in each strain. Although the strains are isogenic overall, they have a few small differences: BY4741 is a met17 mutant and is mating type a, while BY4742 is a leu2 mutant and is mating type α. Since amino acids are very important in creating various volatile chemicals, the mutations in the amino acid biosynthetic genes seemed a likely cause of the difference in the way the two strains smelled to fruit flies. However, the authors found that none of the auxotrophic mutations mattered.  When they mated the two strains and did tetrad analysis to obtain every possible genetic combination, they found that each of the eight new strains was preferred over BY4742.

Given the non-autosomal inheritance of attractiveness, an obvious candidate was the mitochondria. This hunch was confirmed in a couple of ways.  First, Schiabor and coworkers showed that every strain except BY4742 grew well on glycerol, and second, they found that an isolate of BY4742 with functional mitochondria, BY4742g, was as attractive to fruit flies as BY4741.  Apparently their stock of BY4742 had lost mitochondrial function (which can happen fairly easily for some strains), and clearly the mitochondria matter here!

Through a series of experiments we don’t have the space to describe here, the authors found that the lack of attractiveness was not due to an inability to respire.  Instead, by growing each strain on different nitrogen sources, they were able to provide evidence that mitochondrial functions like proline catabolism and/or branched amino acid anabolism were more likely to be involved.  It can sometimes be hard to remember that the mitochondrion is more than the powerhouse of the cell we all learned about in high school: a lot of very important metabolic reactions other than respiration happen within the mitochondrial compartment.

The authors think that yeast with good working mitochondria are the most useful to fruit flies, which is why fruit flies have evolved to be attracted to those yeast.  This all makes sense, as yeast and fruit flies have a mutually beneficial relationship.  Yeast serve as food for fruit fly larvae, and the ethanol they produce also protects those same fruit fly larvae from predators.  Fruit flies can open up parts of the fruit the yeast can’t get to and help move the yeast to different places.   

The bottom line is that you can blame yeast mitochondria for that swarm of fruit flies hovering over your fruit bowl.  One day maybe we can come up with a way that our fruit will only allow petite yeast to grow.  Then we’ll have a bit of time to enjoy fruit that isn’t attractive to fruit flies.  Until, of course, the flies evolve to prefer petite yeast…

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

SGD Summer 2014 Newsletter

July 28, 2014

SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This Summer 2014 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.

Look for SGD at the Yeast Genetics Meeting in Seattle!

July 23, 2014

SGD staff will be attending the GSA Yeast Genetics Meeting in Seattle, July 29 – August 2, 2014 en force! We will be hosting a Workshop, Posters, and an Exhibit Table. The Workshop, “Computational Tools at SGD,” is on Thursday, July 31 at 1:30 PM in Kane Hall, Room 220. We will be discussing our powerful search tool, YeastMine, what’s new in the realm of Strains and Sequences, and new displays in SGD. Bring your questions and comments – we love feedback!

Follow @yeastgenome and #YEAST14 on Twitter for the latest research being presented at YGM.

Find these SGD staff members, as well as those presenting posters, at the Workshop and the Exhibit table:

Maria Costanzo Workshop Speaker

Rob Nash Workshop Speaker

Ben Hitz

Workshop: “Computational Tools at SGD”

Thursday, July 31, 1:30 – 3:00 PM
Kane Hall, Room 220
Featured topics: YeastMine (our powerful search tool), Sequences and Strains update, New data displays at SGD

Posters

In addition to the Workshop, SGD curators will present 4 posters – please stop by and chat with us.

Poster	Date & Time	Poster Title	Presenter
318C	Friday, August 1 7:30 – 8:30 PM HUB Grand Ballroom	Defining the transcriptome of Saccharomyces cerevisiae	Edith Wong
387C	Friday, August 1 8:30 – 9:30 PM HUB Grand Ballroom	Yeast – it simply has a lot to say about human disease	Selina Dwight
411C	Friday, August 1 8:30 – 9:30 PM HUB Grand Ballroom	Transcriptional regulation and protein complexes in budding yeast	Stacia Engel
459C	Friday, August 1 8:30 – 9:30 PM HUB Grand Ballroom	Staying current and modern: Overhauling an actively-used model organism database website	Kelley Paskov

Exhibit Table

SGD will also have an exhibit table at the YGM. Come by to take a spin on our site, receive a prize for taking a survey, learn about various features of the database, and provide us with feedback as to what we can do to improve SGD. Look for us wearing our SuperBud fleece jackets, and feel free to flag any of us down!

Esa1p, the Balancing Artist

July 15, 2014

In the art of rock balancing, the artist positions large rocks with exquisite precision. If he or she succeeds, the rocks counterbalance each other and stay in seemingly impossible positions to make a surprising and beautiful sculpture. But a little uneven pressure is enough to make the whole thing collapse.

It turns out that the cellular acetylation state is just as precisely balanced. In a new GENETICS paper, Torres-Machorro and Pillus identify Esa1p, an acetyltransferase, as the balancing artist in Saccharomyces cerevisiae cells.

Acetylation is an important type of protein modification. Histones, the proteins that interact with DNA to provide structure to chromosomes, are acetylated by histone acetyltransferases (HATs) and deacetylated by histone deacetylases (HDACs). Some HATs and HDACs also act on non-histone proteins.

The acetylation state in a cell is a dynamic process.  All those HATs are adding acetyl groups at the same time that HDACs are removing them.  The final level of acetylation depends on the activities of each of these classes of proteins.

Acetylation of histones has been associated with increases in gene expression and deacetylation with decreases.  So to keep gene expression levels in balance, it is very important to keep acetylation balanced as well.  Throwing acetylation patterns just a bit out of whack can have profound consequences on global gene expression that can ultimately lead to cell death. 

The authors focused on one particular HAT, Esa1p, that acetylates histones H4 and H2A and also has non-histone targets. They were intrigued by the fact that yeast cells cannot survive without Esa1p, since no other HAT or HDAC subunit is essential in yeast.

An obvious explanation for lethality is that losing this protein leads to too low a level of acetylation.  They reasoned that if they also knocked out an HDAC, then the overall acetylation levels might increase and so rescue the esa1 null mutant.  And they were right.

Using a plasmid-shuffling method, they created various double mutant strains of esa1 and HDAC genes, and found that a strain that was mutant in esa1 and also in either the SDS3 or DEP1 genes was viable. SDS3 and DEP1 both encode subunits of the Rpd3L HDAC complex.

Torres-Machorro and Pillus next characterized the esa1 sds3 double mutant further.  They found that although the sds3 mutation suppressed the inviability of the esa1 mutant, it did not suppress other phenotypes such as sensitivity to high temperature and DNA damaging agents.

The authors found that the sds3 mutation subtly increased histone H4 acetylation, which was low in the absence of Esa1p.  However, acetylation levels of a different histone, H3, remained high even in the absence of Esa1p. This suggested that the fundamental problem in the esa1 null mutant was an imbalance in the global state of histone acetylation.

To test this hypothesis, the researchers used a variety of different genetic methods to tweak the balance of cellular acetylation in the esa1 sds3 mutant. They created mutations in histones H3 and H4 that made it seem as if acetylation was low or high, and they also mutated other genes for HDAC subunits. It is as if they were passers-by who decided to poke at a balanced rock sculpture to see what it took to bring the whole thing down.

Although the details are too numerous to report here, the results showed that by using these genetic methods to tweak the overall acetylation state of the cell, the fitness of the esa1 sds3 strain could be improved: phenotypes such as slow growth, sensitivity to high temperature or DNA damaging agents, or cell cycle defects were suppressed to some extent by the various manipulations.  This lends support to the hypothesis that Esa1p is the master balancer of acetylation levels in the cell and that this is its essential function.

This balancing act may happen in human cells too. Esa1p has a human ortholog, TIP60, that has been implicated in cancer and other diseases. Like Esa1p, TIP60 is essential and is involved in the DNA damage response.

So yeast teaches us that the acetylation of proteins is balanced on a knife’s edge.  Even the slightest changes can lead to a collapse in global gene regulation, which can have catastrophic effects like cancer. All that we learn about Esa1p, the acetylation balancing artist, may have much broader implications for human health.

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