New & Noteworthy

Pinpointing Peroxisomes

August 14, 2014

One way to think about the cell is that organelles float around in it like those globs in a lava lamp.  This is obviously a simplification, but it’s also true that organelles aren’t locked into place.  As usual, the real picture lies somewhere in between these two extremes.

What we know about the architecture of the cell has mostly been discovered using classical cell biology and genetic techniques. But in a paper published in Molecular BioSystems, Cohen et al. uncovered some very interesting small details using a very large-scale approach.

The authors were interested in peroxisomes, where a lot of critical metabolic reactions happen (or fail to happen, in several human diseases). The researchers were able to see that peroxisomes not only interact with other organelles, but they contact the endoplasmic reticulum (ER) and mitochondria in a way that could be extremely important for cellular metabolism. And surprisingly, it was by combining a variety of different high-throughput techniques that Cohen and colleagues could uncover this fine structure.

The first step was to set up two reporter constructs to look for genes involved in two different peroxisomal processes.

One reporter was a red fluorescent protein, mCherry, modified to carry a peroxisomal targeting signal and show whether import into peroxisomes was normal. Another reporter, a peroxisomal membrane protein (Ant1p) tagged with green fluorescent protein (GFP), would show whether peroxisomal membranes were normal.

The reporters were crossed into mutant collections, creating one strain for each gene in the genome that had either a complete deletion (for nonessential genes) or a knock-down allele (for essential genes), plus both reporters. Now the researchers could systematically test for genes that, when mutated, affected one or both of these aspects of peroxisomal biogenesis.

To visualize the mutant phenotypes, they used a sophisticated technique termed “high-content screening.” This is an automated way to analyze micrographs that both pinpoints the intracellular location of a fluorescent reporter and measures its quantity. Screening the mutant collection in this way showed that 56 strains had altered distribution of the two different reporter proteins.  Some had a reduction in peroxisomal protein import (mCherry fluorescence), while some had fewer or no peroxisomes and some had peroxisomes that were smaller than normal (GFP fluorescence).

One result that caught the researchers’ eyes was that one of the strains with smaller peroxisomes had a mutation in the MDM10 gene. Mdm10p is part of the ERMES (ER-Mitochondria Encounter Structure) complex that tethers mitochondria to the ER, and this wasn’t previously known to have any connection with peroxisomes. Strains that were mutant in other ERMES subunits had the same phenotype, confirming that the complex has something to do with peroxisome structure.  Other results from the screens added weight to the idea of a three-way connection between peroxisomes, the ER, and mitochondria, and the authors went on to show that peroxisomes often sit at the ERMES complex where mitochondria contact the ER.

Next, to test whether mitochondria might have specific subdomains where peroxisomes interact, the authors used yet another large-scale screen. In the C-terminal GFP fusion library, where each yeast open reading frame is C-terminally tagged with GFP, 96 strains showed a punctate pattern of the fluorescent signal – meaning that the protein was concentrated in spots, rather than evenly distributed.  They labeled the mitochondria with a red fluorescent marker protein in these strains and, again using the high-content screening system, identified protein spots that co-localized with mitochondria. The most intense hit was for Pda1p, a subunit of the mitochondrial enzyme pyruvate dehydrogenase (PDH), and a similar result was obtained for another PDH subunit. So PDH isn’t distributed uniformly in the mitochondrion, but is instead concentrated in clusters.

Looking more closely using the various reporter constructs in their collections, the authors found that peroxisomes and the ERMES complex most often co-localized with those mitochondrial globs of PDH. It would make metabolic sense for peroxisomes to hang out near PDH on mitochondria because this could increase the local concentration of metabolites that they both use.

Intriguingly, Cohen et al. also found that mitochondria and peroxisomes co-localized in mammalian cells. Given that many diseases are linked to peroxisomal metabolism, this is an important avenue to investigate.

So while organelles don’t float around in the cell quite as fluidly as the globs in a lava lamp, the data generated from large-scale approaches boiled down to learning some very fine-grained detail about cellular architecture. We think that’s, like, groovy.

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

Categories: Research Spotlight, Yeast and Human Disease

Tags: endoplasmic reticulum, mitochondria, peroxisomes, Saccharomyces cerevisiae

Shmoos Lost in Translation

August 07, 2014

To mate, the yeast Saccharomyces cerevisiae needs to shmoo — to generate a projection that reaches out to a nearby yeast of the opposite sex, until the yeast cell is shaped like the Al Capp cartoon character.  And to shmoo yeast needs, among other things, polyamines like spermidine.

Spermidine is important for one of the most interesting proteins in the world, the translation initiation and elongation factor eIF5A.  Not only is this protein pretty much conserved in just about every living thing, but it is also the only protein to have the unique amino acid hypusine.  And to make things even more fascinating, there are two other conserved proteins whose only job is to convert a single lysine residue of eIF5A into hypusine, using polyamines like spermidine.  Simply mind boggling.

In a new study in GENETICS, Li and coworkers provide compelling evidence that spermidine is important in yeast shmooing because of its involvement in the hypusinylation of eIF5A.   They also found that one reason eIF5A is so important in this process is that it is necessary for translating Bni1p, a formin needed to organize the actin cables of the shmoo.  Without these actin cables, the shmoo can’t form.

It looks like yeast needs eIF5A to translate Bni1p because of the long stretches of prolines found in this protein.  This suggests that like its bacterial ortholog EF-P, a key job for eIF5A is to help the cell deal with polyproline stretches in proteins.

To show this the researchers made a set of targeted mutations to check whether hypusinylation of eIF5A is necessary for shmooing.  When they knocked out LIA1, one of the enzymes that uses spermidine to convert lysine to hypusine, the resulting yeast failed to shmoo.  Since the only known target of the Lia1 protein is eIF5A, this suggests that hypusinylation of eIF5A is critical to its function in shmooing.

They also used temperature sensitive mutants of eIF5A to show that this gene (HYP2, also known as TIF51A) is involved in shmooing.  At the nonpermissive temperature, only 7.7% of yeast with the less severe mutant allele, tif51A-1, shmooed, while none of the yeast with the more severe mutation, tif51A-3, were able to shmoo.  These two results taken together establish the importance of eIF5A in shmooing.

Because eIF5A was known to be important for translating polyproline regions, the researchers looked for yeast proteins with such stretches, with the idea that their failure to be translated may be behind the need for eIF5A in shmooing.  They found 549 such proteins, and a comparison of their Gene Ontology (GO) annotations showed four overrepresented categories including “mating projection” (shmoo).  They focused on a protein from this group, Bni1p, because it was known to be involved in shmoo formation and it was one of only two proteins with ten or more prolines in a row. 

Bni1p is important for organizing the actin cables that are needed to make a shmoo.  Li and coworkers showed that the temperature sensitive mutants of eIF5A and bni1 mutants had similar phenotypes in terms of actin organization in the shmoo.

So the idea here is that yeast need eIF5A to shmoo because they need eIF5A to translate Bni1p, and Bni1p is needed to set up the actin framework of the shmoo.  In this hypothesis, it is the indirect action of eIF5A that prevents the shmooing. To test this hypothesis, the authors generated a bni1 mutant that lacked the polyproline regions. 

They compared the transcript levels of wild type BNI1 and the mutant lacking the polyproline stretches using RT-qPCR and found that the presence of eIF5A didn’t matter much.  The transcript levels of the mutant and wild type BNI1 were pretty much the same.

It was a different story for the protein levels.  Using Western blots Li and coworkers saw very little wild type Bni1p, but lots of the mutant protein.  The yeast cells struggled to translate wild type Bni1p but had no trouble with the mutant.  The easiest explanation is that eIF5A is needed to help the yeast translate polyproline regions of proteins, including Bni1p. 

Finally, to confirm the eIF5A and Bni1p connection, they showed that additional Bni1p could partially overcome the shmoo defect of the temperature sensitive mutants of eIF5A.  Since this suppression was only partial, and since the mutant phenotype of the eIF5A mutant is more severe than that of the bni1 mutant, there are probably other proteins involved in shmooing that require eIF5A for translation. Some likely candidates are those proteins containing polyproline stretches that are annotated to the GO term “mating projection”.

Although a connection between oddly-shaped yeast cells and human fertility and/or disease may not seem obvious, there might indeed be one. It turns out that eIF5A is so highly conserved  that human eIF5A works just fine when expressed in yeast, and mammalian formins, like Bni1p, are also proline-rich. Formins are necessary for polarized growth, which is a feature of both reproductive cell and cancer cell growth, and spermidine is required for fertilization.

Hard to believe that yeast channeling a cartoon character can teach us so much about the most fascinating of proteins, eIF5A.  And maybe even shed light on our own fertility. 

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

Categories: Research Spotlight

Tags: eIF5A, hypusine, Saccharomyces cerevisiae, translation

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

Categories: Research Spotlight

Tags: Drosophila, mitochondria, Saccharomyces cerevisiae

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.

Categories: Newsletter

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:</p?

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!

Categories: Conferences, News and Views

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

Categories: Research Spotlight, Yeast and Human Disease

Tags: histone acetylation, Saccharomyces cerevisiae, yeast model for human disease

Adding Introns to Synthetic Biology’s Toolbox

July 03, 2014

As any good handyman knows, the more tools you have in your tool chest, the better the chance that you can find what you need to solve a problem.  The same goes for synthetic biologists.  The more parts they can mix and match, the more likely they are to engineer the exact level of gene expression they need.

In the last few years synthetic biologists have amassed a wide variety of transcription and translation elements that can be combined in different ways to exquisitely tune the level of expression of their gene of interest.  And now, in a new study out in PLOS Genetics, Yofe and coworkers have added introns to the list of parts available for our favorite yeast Saccharomyces cerevisiae.

Yeast isn’t loaded with introns, but it does have a reasonable number that can be co-opted for synthetic biology.  The authors inserted 240 of these introns individually into the same position near the 5’ end of the yellow fluorescent protein (YFP) gene and monitored the level of fluorescence of each individual strain over a 24 hour period.  They chose the 5’ end of the gene because yeast has a bias for introns being located there.

The authors found that these reporters spanned a 100-fold range of gene expression, that every intron caused a decrease in the level of gene expression, and that even though many of these introns respond to environmental stimuli in their natural context, their effect on gene expression here was immune to the environmental changes the authors tested.  Taken together, these results suggest that introns could be used in yeast systems for dampening over-exuberant gene expression in ways that are independent of growth conditions.  If all of this holds up, introns will prove to be very useful tools indeed.

Yofe and coworkers next wanted to use this library to figure out some of the rules for why some introns cause lowered activity compared to others.  The simplest possibility, that longer introns cause a larger decrease in gene expression, turned out not to be true.  There was no correlation between the size of the intron and its effect on the level of fluorescence. 

Next they scanned the sequences of their constructs to look for elements that might increase or decrease splicing efficiency.  These splicing regulatory elements (SREs) are better understood in larger eukaryotes, but there is evidence that they are important in yeast as well.  The authors identified a number of intron splicing enhancers (ISEs) and intron splicing silencers (ISSs) that were highly enriched near the splice sites. 

To confirm that these sequences did in fact affect splicing efficiency (and hence gene expression), they showed that mutating the enhancer motif TTTATGCT to the silencer motif TTTGTGTA in two reporters resulted in a 22% and a 13% decrease in gene expression.  This proof of principle experiment suggests that future synthetic biologists may be able to further tweak the expression of their genes by manipulating these SREs.

In a final set of experiments the authors used the library to identify rules that can be used to predict how inserting various introns into different positions will affect a gene’s activity.  They found that the most important features were the presence of SREs and the RNA structures at the intron-exon junction.  Synthetic biologists should be able to use these rules to intelligently design their reporter systems.

These experiments are the first step towards adding introns to the ever growing set of tools available to synthetic biologists for modulating gene expression.  We are getting closer to figuring out how genes are controlled and being able to use that knowledge to our advantage.  Or to put it another way, we have taken another baby step towards being able to control a gene as well as a yeast cell does.

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

Categories: Research Spotlight

Tags: Saccharomyces cerevisiae, splicing, synthetic biology

Polygamous DNA Replication

June 26, 2014

Once someone is married, there are lots of things that keep them from starting a second marriage at the same time.  Laws, fear of losing the first spouse, social mores and so on all create a situation where the vast majority of people have only a single spouse at any one time. 

As each of these inhibitions is lifted, people will be more or less inclined towards polygamy, depending on who they are and the culture they live in.  For example, if having multiple spouses becomes acceptable socially, then some people might dive right in while others might hold off.

It turns out that origins of replication are similar.  There are many layers of control that keep an origin from firing more than once during any cell cycle.  But just like people and polygamy, when a few inhibitory layers are removed, some origins are more likely to fire more than once in a cell cycle than are others.

In a new study out in PLOS Genetics, Richardson and Li have identified a DNA sequence that makes nearby origins of replication fire more than once during a cell cycle when certain regulatory mechanisms have been disabled.  The authors hypothesize that these reinitiation promoters (RIPs) may be important for promoting genetic diversity by causing genomic duplication of specific regions under certain circumstances. 

This lab had previously shown that the origin ARS317 reinitiates more frequently when global regulation is removed from some key players in initiation: Cdc6p, the Mcm2-7 complex, and the origin recognition complex (ORC).  They disabled the regulation of all three of these by mutating each to prevent their recognition by the master regulator cyclin-dependent kinase (CDK, whose catalytic subunit is Cdc28p). In this study, they identified a second origin, ARS1238, that also reinitiated more often under these conditions.  The authors next set out to identify why these origins reinitiated under these conditions.

The first thing they found was that chromosomal context didn’t matter a whole lot.  Both origins reinitiated at around the same rate when they were in their natural context or when moved to other chromosomes.  The ability to reinitiate must be contained in the sequence of the DNA that was moved.

They next showed through deletion and linker scanning analysis that the two origins both required an AT-rich, ~60 base pair sequence to reinitiate.  This sequence needed to be within around 35-75 base pairs of the origin to promote reinitiation. Not any old stretch of AT-rich DNA would do; a specific DNA sequence was necessary, suggesting that this DNA is not required for reinitiation just because it is more easily unwound. 

These authors have shed light on a key process in the life of a cell—the firing of an origin of replication once and only once during any cell cycle.  It is critical for a cell that origins do not routinely reinitiate to prevent widespread genomic duplications that left unchecked would be very dangerous to the cell.

Richardson and Li have shown that not all origins are created equally, in that some are more likely to reinitiate under certain conditions than are others. If similar regions in mammalian cells turn out to be hotspots for genetic changes in cancers, then scientists may be able to target them to prevent the cancer’s genetic progression.  We may be able to reintroduce laws to keep polygamy at bay.

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

Categories: Research Spotlight

Tags: DNA replication, replication origin, Saccharomyces cerevisiae

Shared Domains and Phosphorylation Sites on Protein Pages

June 24, 2014

We have redesigned the Protein page to include a new tabular display of protein domains. This table provides the identifier for each domain and illustrates the respective locations of the domains within the protein. In addition to this new table, the domains are displayed in an interactive network diagram that presents the proteins that share these domains with your protein of interest (see figure below, left).

Another new feature on the Protein page is the display of phosphorylation sites within the protein’s sequence (as curated by BioGRID). This feature is available for both the reference strain S288C and other commonly used S. cerevisae strains, using the pull-down to select the desired strain view (see figure below, right) .

Left: Proteins (gray circles) that share domains (colored squares) with Fas1p (yellow circle). Right: an example of some of the phosphorylation sites in Swe1p (red residues).

Categories: New Data, Website changes

YGM Early Registration Deadline is Approaching!

June 23, 2014

There are only a few days left to register for the Yeast Genetics Meeting at the early registration rate. After midnight on Thursday, June 26, the fees will increase by $75. Conference housing is filling up fast too. This is a meeting you don’t want to miss, so don’t delay!

Categories: Conferences

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