April 26, 2016
If you’re not already using YeastMine to answer all your questions about S. cerevisiae genes and gene products…you should be! SGD’s YeastMine is a powerful search tool that can retrieve, compare, and analyze data on thousands of genes at a time, greatly reducing the time needed to answer real, practical research questions. Through YeastMine, questions such as “What proportion of plasma membrane proteins are essential?” or “How many different gene products physically interact with the mitochondrial ribosome?” can be answered within minutes.
Next week on May 4th, 2016 at 9:30 AM PDT, we will provide a brief webinar tutorial on how to run queries and create gene lists in SGD’s YeastMine. As a practical demonstration of YeastMine, we will also showcase a research scenario in which yeast-human homology data is used to predict potential chemotherapy targets for human cancers.
Space for this webinar is limited. To reserve your spot, please register for the event using this online form: http://bit.ly/registerFor2ndSGDwebinar
This is the second episode of the SGD Webinar Series. If you missed the first one, or if you’d like to find out more about upcoming webinars, please visit our wiki page: SGD Webinar Series.
April 06, 2016
In the book Dune, the mentat Thufir Hawat is captured by the evil Harkonnens and given a residual poison. He can only stay alive by getting a constant dose of the antidote. Once it is withdrawn, he will die.
A new study in the journal GENETICS by Dodgson and coworkers shows that the same sort of thing can happen to yeast that carry an extra chromosome. In this case, certain genes on the extra chromosome turn out to be like the residual poison. And a second gene turns out to be the antidote.
Once that second gene is deleted, the yeast cell dies. It has been deprived of its antidote.
This synthetic lethal phenotype isn’t just a cool finding in yeast either. Cancer cells invariably have extra and missing chromosomes. If scientists could find similar “antidote genes” in specific types of cancers and target them, then the cancer cell would die. And this would happen without damaging the other cells of the body that have a typical number of chromosomes.
The first thing these researchers did was to make separate yeast strains each with an extra chromosome I, V, VIII, IX, XI, XII, or XVI. The next step was to see what happens when every gene was deleted individually, one at a time, from each strain.
As expected, these yeast did pretty well when a gene on the extra chromosome was deleted. So, for example, a strain with an extra chromosome I tolerated a gene deleted from chromosome I. This makes sense as this just brings that gene back to its normal copy number.
But this was not the case with chromosomes VIII and XI. Here deleting genes on the extra chromosome often had a negative effect. This suggested that the screen probably had a high number of false positives and these researchers later confirmed this.
Likely reasons for the high number of false positives include the strain with the extra chromosome being W303 and the deletion strain being S288C, errors in the deletion collection itself, and what they refer to as neighboring gene effects. Basically this last one is the effect that deleting a gene has on nearby genes.
Once Dodgson and coworkers corrected for these problems, they found two broad sets of phenotypes – general and chromosome specific.
The general ones were the ones shared by most or all of the strains. These were deletions that affected the yeast no matter which chromosome they had an extra copy of.
For the most part, these genes were enriched for the Gene Ontology (GO) term vesicle-mediated transport, indicating that they have something to do with the transportation of substances in membrane-bounded vesicles. For example, deletion of MNN10, HOC1, and MNN11, genes all involved in protein transport and membrane-related processes, had a negative effect on many of the yeast strains with an extra chromosome. Consistent with this, brefeldin A, a drug that targets protein trafficking, negatively affected most of the strains.
Another gene that affected many of these strains when deleted was TPS1. This gene encodes a subunit of trehalose-6-phosphate synthase, a key enzyme for making trehalose, a molecule that helps yeast deal with stress. Perhaps not surprisingly, having an extra chromosome is stressful!
In addition to the genes that affect many strains with an extra chromosome, there were also genes that were chromosome specific. The best characterized of these was the EDE1 gene in the strain with an extra chromosome IX. Deleting EDE1 in this strain increased its doubling time by more than 80 minutes while only causing an increase of 5 minutes in the doubling time of wild type yeast. This was a severe phenotype in their assay.
They next tried to find which gene on chromosome IX might be responsible for the severe effect of deleting EDE1. Since EDE1 is known to be involved in endocytosis, they looked for genes involved in the same process. And they found one – PRK1.
The strain with a deleted EDE1 gene and an extra chromosome IX was rescued by deleting one copy of the PRK1 gene. The extra PRK1 gene was the poison and the EDE1 gene was the antidote.
If a similar pair could be found in cancers that often have the same set of extra chromosomes, then perhaps scientists could develop drugs that target an antidote gene. Now the cancer cells would die and the “normal” cells would be fine. Thanks again, yeast, for pointing us toward new ways to treat human disease.
by Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics
November 11, 2015
Imagine what our email inboxes would look like if we didn’t have spam filters! To find the meaningful emails, we’d have to wade through hundreds of messages about winning lottery tickets, discount medications, and other things that don’t interest us.
When it comes to sorting out meaningful mutations from meaningless variation in human genes, it turns out that our friend S. cerevisiae makes a pretty good spam filter. And as more and more human genomic sequence data are becoming available every day, this is becoming more and more important.
For example, when you look at the sequence of a gene from, say, a cancer cell, you may see many differences from the wild-type gene. How can you tell which changes are significant and which are not?
SuperBud to the rescue! Because many human proteins can work in yeast, simple phenotypes like viability or growth rate can be assayed to test whether variations in human genes affect the function of their gene products. This may be one answer to the increasingly thorny problem of variants of uncertain significance—those dreaded VUS’s.
In a new paper in GENETICS, Hamza and colleagues systematically screened for human genes that can replace their yeast equivalents, and went on to test the function of tumor-specific variants in several selected genes that maintain chromosome stability in S. cerevisiae. This work extends the growing catalog of human genes that can replace yeast genes.
More importantly, it also provides compelling evidence that yeast can help us tell which mutations in a cancer cell are driver mutations, the ones that are involved in tumorigenesis, and which are the passenger mutations, those that are just the consequence of a seriously messed up cell. Talk about a useful filter!
The researchers started by testing systematically for human genes that could complement yeast mutations. Other groups have done similar large-scale screens, but this study had a couple of different twists.
Previous work from the Hieter lab had identified genes in yeast that, when mutated, made chromosomes unstable: the CIN (Chromosome INstability) phenotype. Reduction-of-function alleles of a significant fraction (29%) of essential genes confer a CIN phenotype. The human orthologs of these genes could be important in cancer, since tumor cells often show chromosome rearrangements or loss.
So in one experiment, Hamza and colleagues focused specifically on the set of CIN genes, starting with a set of 322 pairs of yeast CIN genes and their human homologs. They tested functional complementation by transforming plasmids expressing the human cDNAs into diploid yeast strains that were heterozygous null mutant for the corresponding CIN genes. Since all of the CIN genes were essential, sporulating those diploids would generate inviable spores—unless the human gene could step in and provide the missing function.
In addition to this one-to-one test, the researchers cast a wider net by doing a pool-to-pool transformation. They mixed cultures of diploid heterozygous null mutants in 621 essential yeast genes, and transformed the pooled strains with a mixture of 1010 human cDNAs. This unbiased strategy could identify unrecognized orthologs, or demonstrate complementation between non-orthologous genes.
In combination, these two screens found 65 human cDNAs that complemented null mutations in 58 essential yeast genes. Twenty of these yeast-human gene pairs were previously undiscovered.
The investigators looked at this group of “replaceable” yeast genes as a whole to see whether they shared any characteristics. Most of their gene products localized to the cytoplasm or cytoplasmic organelles rather than to the nucleus. They also tended to have enzymatic activity rather than, for example, regulatory roles. And they had relatively few physical interactions.
So yeast could “receive messages” from human genes, allowing us to see their function in yeast. But could it filter out the meaningful messages—variations that actually affect function—from the spam?
The authors chose three CIN genes that were functionally complemented by their human orthologs and screened 35 missense mutations that are found in those orthologs in colorectal cancer cells. Four of the human missense variants failed to support the life of the corresponding yeast null mutant, pointing to these mutations as potentially the most significant of the set.
Despite the fact that these mutations block the function of the human proteins, a mutation in one of the yeast orthologs that is analogous to one of these mutations, changing the same conserved residue, doesn’t destroy the yeast protein’s function. This underscores that whenever possible, testing mutations in the context of the entire human protein is preferable to creating disease-analogous mutations in the yeast ortholog.
Another 19 of the missense mutations allowed the yeast mutants to grow, but at a different rate from the wild-type human gene. (Eighteen conferred slower growth, but one actually made the yeast grow faster!)
For those 19 human variants that did support life for the yeast mutants, Hamza and colleagues tested the sensitivity of the complemented strains to MMS and HU, two agents that cause DNA damage. Most of the alleles altered resistance to these chemicals, making the yeast either more or less resistant than did the wild-type human gene. This is consistent with the idea that the cancer-associated mutations in these human CIN gene orthologs affect chromosome dynamics.
As researchers are inundated by a tsunami of genomic data, they may be able to turn to yeast to help discover the mutations that matter for human disease. They can help us separate those emails touting the virtues of Viagra from those not-to-be-missed kitten videos. And when we know which mutations are likely to be important for disease, we’re one step closer to finding ways to alleviate their effects.
by Maria Costanzo, Ph.D., Senior Biocuration Scientist, SGD
June 10, 2015
Yeast and humans diverged about a billion years ago. So if there’s still enough functional conservation between a pair of similar yeast and human genes that they can be substituted for each other, we know they must be critically important for life. An added bonus is that if a human protein works in yeast, all of the awesome power of yeast genetics and molecular biology can be used to study it.
To make it easier for researchers to identify these “swappable” yeast and human genes, we’ve started collecting functional complementation data in SGD. The data are all curated from the published literature, via two sources. One set of papers was curated at SGD, including the recent systematic study of functional complementation by Kachroo and colleagues. Another set was curated by Princeton Protein Orthology Database (P-POD) staff and is incorporated into SGD with their generous permission.
As a starting point, we’ve collected a relatively simple set of data: the yeast and human genes involved in a functional complementation relationship, with their respective identifiers; the direction of complementation (human gene complements yeast mutation, or vice versa); the source of curation (SGD or P-POD); the PubMed ID of the reference; and an optional free-text note adding more details. In the future we’ll incorporate more information, such as the disease involvement of the human protein and the sequence differences found in disease-associated alleles that fail to complement the yeast mutation.
You can access these data in two ways: using two new templates in YeastMine, our data warehouse; or via our Download page. Please take a look, let us know what you think, and point us to any published data that’s missing. We always appreciate your feedback!
YeastMine is a versatile tool that lets you customize searches and create and manipulate lists of search results. To help you get started with YeastMine we’ve created a series of short video tutorials explaining its features.
This template lets you query with a yeast gene or list of genes (either your own custom list, or a pre-made gene list) and retrieve the human gene(s) involved in cross-species complementation along with all of the data listed above.
This template takes either human gene names (HGNC-approved symbols) or Entrez Gene IDs for human genes and returns the yeast gene(s) involved in cross-species complementation, along with the data listed above. You can run the query using a single human gene as input, or create a custom list of human genes in YeastMine for the query. We’ve created two new pre-made lists of human genes that can also be used with this template. The list “Human genes complementing or complemented by yeast genes” includes only human genes that are currently included in the functional complementation data, while the list “Human genes with yeast homologs” includes all human genes that have a yeast homolog as predicted by any of several methods.
If you’d prefer to have all the data in one file, simply visit our Curated Data download page and download the file “functional_complementation.tab”.
June 03, 2015
Cars on the road today all look pretty similar from the outside, whether they’re gasoline-fueled or electric. On the inside, they’re fairly similar too. Even between the two kinds of car, you can probably get away with swapping parts like the air conditioner, the tires, or the seat belts. Although cars have changed over the years, these things haven’t changed all that much.
The engine, though, is a different story. All the working parts of that Nissan Leaf engine have “evolved” together into a very different engine from the one in that Ford Mustang. They both have engines, but the parts aren’t really interchangeable any more.
We can think of yeast and human cells like this too. We’ve known for a while that we humans have quite a bit in common with our favorite little workhorse S. cerevisiae. But until now, no one had any idea how common it was for yeast-human pairs of similar-looking proteins to function so similarly that they are interchangeable between organisms.
In a study published last week in Science, Kachroo and colleagues looked at this question by systematically replacing a large set of essential yeast genes with their human orthologs. Amazingly, they found that almost half of the human proteins could keep the yeast mutants alive.
Also surprising was that the degree of similarity between the yeast and human proteins wasn’t always the most important factor in whether the proteins could be interchanged. Instead, membership in a gene module—a set of genes encoding proteins that act in a group, such as a complex or pathway—was an important predictor.
The authors found that genes within a given module tended to be either mostly interchangeable or mostly not interchangeable, suggesting that if one protein changes during evolution, then the proteins with which it interacts may need to evolve as well. So we can trade air conditioner parts between the Leaf and the Mustang, but the Mustang’s spark plugs won’t do a thing in that newly evolved electric engine!
To begin their systematic survey, Kachroo and colleagues chose a set of 414 yeast genes that are essential for life and have a single human ortholog. They cloned the human cDNAs in plasmids for yeast expression, and transformed them into yeast that were mutant in the orthologous gene to see if the human gene would supply the missing yeast function.
They tested complementation using three different assays. In one, the human ortholog was transformed into a strain where expression of the yeast gene was under control of a tetracycline-repressible promoter. So if the human gene complemented the yeast mutation, it would be able to keep the yeast alive in the presence of tetracycline.
Another assay used temperature-sensitive mutants in the yeast genes and looked to see if the human orthologs could support yeast growth at the restrictive temperature. And the third assay tested whether a yeast haploid null mutant strain carrying the human gene could be recovered after sporulation of the heterozygous null diploid.
Remarkably, 176 human genes could keep the corresponding yeast mutant alive in at least one of these assays. A survey of the literature for additional examples brought the total to 199, or 47% of the tested set. After a billion years of separate evolution, yeast and humans still have hundreds of interchangeable parts!
That was the first big surprise. But the researchers didn’t stop there. They wondered what distinguished the genes that were interchangeable from those that weren’t. The simplest explanation would seem to be that the more similar the two proteins, the more likely they would work the same way.
But biology is never so simple, is it? While it was true that human proteins with greater than 50% amino acid identity to yeast proteins were more likely to be able to replace their yeast equivalents, and that those with less than 20% amino acid identity were least likely to function in yeast, those in between did not follow the same rules. There was no correlation between similarity and interchangeability in ortholog pairs with 20-50% identity.
After comparing 104 different types of quantitative data on each ortholog pair, including codon usage, gene expression levels, and so on, the authors found only one good predictor. If one yeast protein in a protein complex or pathway could be exchanged with its human ortholog, then usually most of the rest of the proteins in that complex or pathway could too.
All of the genes that that make the proteins in these systems are said to be part of a gene module. Kachroo and colleagues found that most or all of the genes in a particular module were likely to be in the same class, either interchangeable or not. We can trade pretty much all of the parts between the radios of a Leaf and a Mustang, but none of the engine parts.
For example, none of the tested subunits of three different, conserved protein complexes (the TriC chaperone complex, origin recognition complex, and MCM complex) could complement the equivalent yeast mutations. But in contrast, 17 out of 19 tested genes in the sterol biosynthesis pathway were interchangeable.
Even within a single large complex, the proteasome, the subunits of one sub-complex, the alpha ring, were largely interchangeable while those of another sub-complex, the beta ring, were not. The researchers tested whether this trend was conserved across other species by testing complementation by proteasome subunit genes from Saccharomyces kluyveri, the nematode Caenorhabditis elegans, and the African clawed frog Xenopus laevis. Sure enough, alpha ring subunits from these organisms complemented the S. cerevisiae mutations, while beta ring subunits did not.
These results suggest that selection pressures operate similarly on all the genes in a module. And if proteins continue to interact across evolution, they can diverge widely in some regions while their interaction interfaces stay more conserved, so that orthologs from different species are more likely to be interchangeable.
The finding that interchangeability is so common has huge implications for research on human proteins. It’s now conceivable to “humanize” an entire pathway or complex, replacing the yeast genes with their human equivalents. And that means that all of the versatile tools of yeast genetics and molecular biology can be brought to bear on the human genes and proteins.
At SGD we’ve always known that yeast has a lot to say about human health and disease. With the growing body of work in these areas, we’re expanding our coverage of yeast-human orthology, cross-species functional complementation, and studies of human disease-associated genes in yeast. Watch this space as we announce new data in YeastMine, in download files, and on SGD web pages.
by Maria Costanzo, Ph.D., Senior Biocuration Scientist, SGD
January 13, 2015
Bounce houses are a great way for kids to burn off their excess energy. They can bounce off the floor and walls and scream to their hearts’ content.
Of course, adults need to keep an eye on how many kids are in the house at any one time, to keep things safe. And if one child starts to push and kick the others, it might be easier to restore calm if the adults are careful about how many kids, and which ones, they allow inside.
The yeast mitochondrion is actually a lot like a bounce house. It’s full of energy, and it has multiple gatekeepers—protein complexes in the mitochondrial membrane that imported proteins must pass through on their way in.
And, just like a bounce house, things can go very wrong inside the mitochondrion if its proteins don’t behave properly. The end result isn’t just an upset child with a black eye, either. Genetic diseases that affect mitochondrial function are among the most severe and the hardest to treat.
Now, described in a new paper in Nature Communications, Aiyar and colleagues have used a yeast model of human mitochondrial disease to discover both a drug and a genetic means to regulate a mitochondrial import complex. Surprisingly, tweaking mitochondrial import slightly by either of these methods mitigated the disease symptoms in both yeast and human cells. They found a gatekeeper who can make sure there is the right number of kids in the bounce house and that they’re all behaving properly (at least, as well as they can!).
The researchers were interested in mitochondrial disorders that affected ATP synthase. This huge molecular machine in the mitochondrial inner membrane is responsible for generating most of the cell’s energy, so if it doesn’t work properly it can be a disaster for both yeast and human cells.
Aiyar and coworkers used a genetic trick to create a yeast model that had lower amounts of functional ATP synthase. This mimics many mitochondrial disorders.
They were able to reduce the amount of functional ATP synthase by using an fmc1 null mutant. Fmc1p is involved in assembly of the complex, so the fmc1 null mutant has lower amounts of functional ATP synthase and a reduced respiration rate.
First, they looked for a drug that would mitigate the effects of the fmc1 mutation. They tested the drugs in a collection that had already been FDA approved—a drug repurposing library—to see if any would improve the mutant’s respiratory growth.
The one candidate drug that emerged from the screen was sodium pyrithione (NaPT), which is used as an antiseptic. Not only did it improve the respiration of the yeast fmc1 mutant, it also improved the respiratory growth of a human cell line carrying the atp6-T8993G mutation found in patients with neuropathy, ataxia and retinitis pigmentosa (NARP, one type of ATP synthase disorder).
Aiyar and colleagues wondered exactly what was being affected by the NaPT. To figure this out, they used the S. cerevisiae genome-wide heterozygous deletion mutant collection. This is a set of diploid strains, each heterozygous for a null mutation of a different gene, that has been an incredibly useful resource for all kinds of studies in yeast.
They tested the effect of NaPT on each of the mutant strains and found that strains with mutations in the TIM17 and TIM23 genes were among the most sensitive. And, when they checked the data from previous chemogenomic screens, they saw that these two mutants were much more sensitive to NaPT than to any other drug, showing that the effect was specific.
TIM17 and TIM23 are both subunits of the Tim23 complex in the mitochondrial inner membrane that acts as a gate for many of the proteins that end up in mitochondria. The researchers found that NaPT specifically inhibited the function of this mitochondrial gatekeeper complex in an in vitro mitochondrial import assay, confirming its selectivity.
So, Aiyar and coworkers had found a drug that alleviates the effects of an ATP synthase disorder by modulating the function of a mitochondrial gatekeeper. This in itself was a huge advance: the discovery that a potentially useful, already-approved drug has a specific effect on this disease phenotype.
However, the scientists took things a step further by looking to see whether a genetic therapy could accomplish the same thing as the drug. It was already known that overexpressing Tim21p, a regulatory subunit of the Tim23 complex, could modulate the function of the complex similarly to the effects they had seen for NaPT.
So the researchers tested whether overexpressing Tim21p would improve respiratory growth of the fmc1 mutant. Sure enough, it did. Consistent with this, assembly of the respiratory enzyme complexes of the mitochondrial inner membrane was more efficient when Tim21p was overexpressed.
Most importantly, overexpression of Tim21p in the fmc1 mutant cells caused their total ATP synthesis to more than double. And even more exciting was the discovery that overexpressing TIMM21, the human ortholog of TIM21, in the NARP disease human cell line improved survival of those cells.
So, just like a parent deciding how many kids should be in a bounce house so that everyone has a good time, the Tim23 complex can be made to “decide” which proteins, or perhaps how many proteins, get into mitochondria, with the end result that ATP synthesis happens as efficiently as possible. The exact mechanism of this effect is still unclear, but it is clear that modulating import in this way can improve mitochondrial health even when disease mutant proteins are present.
The next step will be to translate this discovery into therapies that will help mitochondrial disease patients. People with various mitochondrial disorders may finally be able to turn their mitochondria into safe, fun places.
by Maria Costanzo, Ph.D., Senior Biocurator, SGD
January 08, 2015
What’s for dinner tonight? For many of us the answer will be “pasta with tomato sauce”, even if we don’t have Italian roots.
But as you know, there isn’t any single recipe for homemade tomato sauce. Onions and garlic, or just garlic? Pork, beef, or no meat at all? How many bay leaves go in the pot? Every cook will use a slightly different combination of ingredients, but all will end up with tomato sauce.
When it comes to combining different allele variants to survive a lethal challenge, yeast is a lot like those cooks. In a new paper in GENETICS, Sirr and colleagues used divergent yeast strains to generate a wide range of allelic backgrounds and found that there is more than one way to survive a deadly mutation in the GAL7 gene. Just as there is more than one way to make a delicious tomato sauce…
This isn’t just an academic exercise either. GAL7 is the ortholog of the human GALT gene, which when mutated leads to the disease galactosemia. And just like in yeast, people with different genetic backgrounds may do better or worse when both copies of their GALT gene are mutated.
GAL7 and GALT encode an enzyme, galactose-1-phosphate uridyl transferase, that breaks down the sugar galactose. If people with this mutation eat galactose, the toxic compound galactose-1-phosphate accumulates; this can cause serious symptoms or even death. The same is often true for yeast with a mutated GAL7 gene.
Ideally we would want to be able to predict how severe the symptoms of galactosemia would be, based on a patient’s genetic background. So far, though, it’s been a challenge to identify comprehensively the whole set of genes that affect a given human phenotype. Which is why Sirr and colleagues turned to our friend S. cerevisiae to study alleles affecting the highly conserved galactose utilization pathway.
The researchers started with two very divergent yeast strains, one isolated from a canyon in Israel and the other from an oak tree in Pennsylvania. Both were able to utilize galactose normally, but the scientists made them “galactosemic” by knocking out the GAL7 gene in each.
After mating the strains to create a galactosemic diploid, the researchers needed to let the strain sporulate and isolate haploid progeny. But its sporulation efficiency wasn’t very good, only about 20%. And they needed to have millions of progeny to get a comprehensive look at genetic backgrounds.
To isolate a virtually pure population of haploid progeny, Sirr and coworkers came up with a neat trick. They added a green fluorescent protein gene to the strain and put it under control of a sporulation-specific promoter.
Cells that were undergoing sporulation would fluoresce and could be separated from the others by fluorescence-activated cell sorting (FACS). The FACS technique also allowed sorting by size, so they could select complete tetrads containing four haploid spores and discard incomplete products of meiosis such as dyads containing only two spores.
After using this step to isolate tetrads, the researchers broke them open to free the spores and put them on Petri dishes containing galactose—an amount that was enough to kill either of the parent strains. One in a thousand spores was able to survive the galactose toxicity. Recombination between the divergent alleles from the two parent strains somehow came up with the right combination of alleles for a survival sauce.
Sirr and colleagues individually genotyped 247 of the surviving progeny, using partial genome sequencing. They mapped QTLs (quantitative trait loci) to identify genomic regions associated with survival. If they found a particular allele in the survivors more often than would be expected by chance, that was a clue that a gene in that region had a role in survival.
We don’t have the space here to do justice to the details of the results, but we can summarize by saying that a whole variety of factors contributed to the galactose tolerance of the surviving progeny. They had three major QTLs, regions where multiple alleles were over- or under-represented. The QTLs were centered on genes involved in sugar metabolism: GAL3 and GAL80, both involved in transcriptional regulation of galactose utilization genes, and three hexose transporter genes (HXT3, HXT6, and HXT7) that are located very close to each other.
It makes sense that all of these genes could affect galactosemia. Gal3p and Gal80p are regulators of the pathway, so alleles of these genes that make galactose catabolism less active would result in less production of toxic intermediates. And although the hexose transporters don’t transport galactose as their preferred substrates, they may induce the pathway by allowing a little galactose into the cell. So less active alleles of these transporters would also result in less galactose catabolism.
Another event that occurred in over half of the surviving progeny was aneuploidy (altered chromosome number), most often an extra copy of chromosome XIII where the GAL80 gene is located. The same three QTL peaks were also seen in the disomic strains, though, leading the authors to conclude that the extra chromosome alone was not sufficient for survival of galactosemia.
And finally, some rare non-genetic events contributed to survival of the progeny. The authors discovered this when they found that the galactose tolerance of some of the progeny wasn’t stably inherited. This could result from differences in protein levels between individual cells. For example, if one cell happened to have lower levels of a galactose transporter than other cells, it might be more resistant to galactose.
The take-home message here is that there are many different ways to get to the same phenotype. The new method that they developed allowed the researchers to see rare combinations of alleles in large numbers of individual progeny, in contrast to other genotyping methods where progeny are pooled and only the average can be detected.
For any disease or trait the ultimate goal is to identify all the alleles of all the genes that influence it. Imagine the impact on human health, if we could look at a person’s genotype and accurately predict their phenotype!
So far, it’s been a challenge to identify these large sets of human genes in a comprehensive way. But this approach using yeast could provide a feast of data to help us understand monogenic diseases like galactosemia, cystic fibrosis, porphyria, and many more, and maybe even more complex traits and diseases. Now that’s an appetizing prospect for human disease researchers. Buon appetito!
by Maria Costanzo, Ph.D., Senior Biocurator, SGD
October 16, 2014
A train without working brakes can cause a lot of destruction if it careens off the tracks. And it turns out that a runaway RNA polymerase II (pol II) can cause a lot of damage too. But it doesn’t cause destruction, so much as disease.
Unlike a train, which has its brakes built right in, pol II has to count on outside factors to stop it in its tracks. And one of these brakes in both humans and yeast is a helicase: Sen1 in yeast and Senataxin, the product of the SETX gene, in humans.
Mutations in SETX are associated with two devastating neurological diseases: amyotrophic lateral sclerosis type 4 (ALS4) and ataxia oculomotor apraxia type 2 (AOA2), both of which strike children and adolescents. One idea is that these mutations may short circuit the brakes on pol II, causing it to keep on transcribing after it shouldn’t. And this is just what Chen and colleagues found in a new paper in GENETICS.
The researchers used the simple yet informative yeast model system to look at some of these mutations, and found that they disrupted the helicase function of Sen1 and caused abnormal read-through of some transcriptional terminators. Looks like bad brakes may indeed have a role in causing these devastating diseases.
Some human proteins can function perfectly well in yeast. Unfortunately, Senataxin isn’t one of those; it could not rescue a sen1 null mutant yeast, so Chen and coworkers couldn’t study Senataxin function directly in yeast. But because Senataxin and Sen1 share significant homology, they could instead study the yeast protein and make inferences about Senataxin from it.
First, they sliced and diced the SEN1 gene to see which regions were essential to its function. They found that the most important part, needed to keep yeast cells alive, was the helicase domain. But this wasn’t the only key region.
Some flanking residues on either side were also important, but either the N-terminal flanking region or the C-terminal flanking region was sufficient. Looking into those flanking regions more closely, the researchers found that each contained a nuclear localization sequence (NLS) that directed Sen1 into the nucleus. This makes perfect sense of course…the brakes need to go where the train is! If we don’t put the brakes on the train, it won’t matter how well they work, the train still won’t stop.
These flanking sequences appeared to do more than direct the protein to the nuclear pol II, though. When the authors tried to use an NLS derived from the SV40 virus instead, they found that it couldn’t completely replace the function of these flanking regions even though it did efficiently direct Sen1 to the nucleus.
Next the researchers set out to study the disease mutations found in patients affected with the neurological disease AOA2. They re-created the equivalents of 13 AOA2-associated SETX mutations, all within the helicase domain, at the homologous codons of yeast SEN1.
Six of the 13 mutations completely destroyed the function of Sen1; yeast cells could not survive when carrying only the mutant gene. When these mutant proteins were expressed from a plasmid in otherwise wild-type cells, five of them had a dominant negative effect, interfering with transcription termination at a reporter gene. This lends support to the idea that Sen1 is important for transcription termination and that the disease mutations affected this function.
The remaining 7 of the 13 mutant genes could support life as the only copy of SEN1 in yeast. However, 5 of the mutant strains displayed heat-sensitive growth, and 4 of these showed increased transcriptional readthrough.
Taken together, these results show that the helicase domains of Senataxin and Sen1 are extremely important for their function. They also show that Sen1 can be used as a model to discover the effects of individual disease mutations in SETX, as long as those mutations are within regions that are homologous between the two proteins.
It still isn’t clear exactly how helicase activity can put the brakes on that RNA polymerase train, nor why runaway RNA polymerase can have such specific effects on the human nervous system. These questions need more investigation, and the yeast model system is now in place to help with that.
So, although it might not be obvious to the lay person (or politician) that brainless yeast cells could tell us anything about neurological diseases, in fact they can. Yeast may not have brains, but they definitely have RNA polymerase. And once we learn how the brakes work for pol II in yeast cells, we may have a clue how to repair them in humans.
by Maria Costanzo, Ph.D., Senior Biocurator, SGD
August 21, 2014
Say you want to send a letter to your friend on the other side of the country. First off you’ll need to put the right address and postage on the envelope. Then you’ll need the U.S. Postal Service (USPS) to take your letter and deliver it to the right person. The stamp tells the USPS to deliver the letter, and the address indicates where it should be delivered (unimpeded by snow nor rain nor heat nor gloom of night, of course!).
It turns out something similar happens in human cells with aggregated proteins. Aggregated proteins are “stamped” by attachment of the small protein ubiquitin and “addressed” to the Atg8 protein. Atg8p triggers the aggregated proteins’ incorporation into autophagosomes for eventual degradation in the lysosome.
And just as it can be devastating if your mail doesn’t get to where it needs to go, so too can it be devastating for these aggregates to accumulate instead of being properly delivered. A buildup of these aggregates is a big factor in Alzheimer’s and Huntington’s diseases.
Enter the cellular USPS. Just as is the case for a prepared letter, the human cell has a service that delivers the ubiquinated proteins to the autophagosome, in the form of the protein adaptor p62 (SQSTM1) and its relative, NBR1.
These adaptor proteins can act as a postal service because they recognize both the aggregated proteins’ stamp (ubiquitin) and their addressee (Atg8p). Specifically, they each possess an ubiquitin-conjugate binding domain (UBA) and an Atg8-interacting motif (AIM). The protein p62 in particular has been shown to associate with protein aggregates linked to neurodegenerative diseases like Huntington’s disease.
In a new paper published in Cell, Lu et al. asked whether there is a link between the ubiquitin and autophagy systems in yeast. If so, yeast might provide some clues about diseases like Huntington’s. Proteins stamped with ubiquitin are known to be addressed to the proteasome for degradation in yeast, but no link between ubiquitination and autophagy had previously been seen, even though many central components of autophagy were actually first described in yeast.
Indeed, the authors showed that cells specifically deficient in the autophagy pathway (atg8∆, atg1∆, or atg7∆), accumulated ubiquitin conjugates under autophagy-inducing conditions. This suggests that the ubiquitin and autophagy pathways are connected in yeast, as is the case for humans.
Next, the researchers looked to see if there is an adaptor in yeast analogous to p62 in humans. When they pulled down proteins that bind yeast Atg8p under starvation conditions, they found ubiquitin conjugates and, using mass spectrometry, further identified peptides from a few other proteins – one of which was Cue5p.
Could Cue5p, like p62 in humans, be the postal service that recognizes both stamped ubiquitin conjugates and the addressee Atg8p in yeast? Strikingly, Cue5p had both a CUE domain that binds ubiquitin and an Atg8p-interacting motif (AIM). The authors confirmed in vivo that Cue5p binds ubiquitin conjugates and Atg8p using these domains, particularly under starvation conditions. They also showed that it acts specifically at the stage of ubiquitin-conjugate recognition and on aggregated proteins, without affecting the process of autophagy itself.
Given that Cue5p functions similarly to p62 and p62 is known to associate with protein aggregates involved in neurodegenerative disease, Lu et al. were quick to look for Cue5p substrates. Analyzing ubiquitin-conjugated proteins that accumulated in cue5 mutant cells, they identified 24 different proteins. Although these 24 Cue5p substrates had diverse functions, the common thread was that many had a tendency to aggregate under certain conditions such as high temperature.
Could Cue5p then actually facilitate removal of cytotoxic protein aggregates in neurodegenerative diseases? Indeed, the authors showed that CUE5 helped clear cytotoxic variants of the human huntingtin protein (Htt-96Q) when it was expressed in yeast, and that Htt-96Q is ubiquitinated in yeast.
These experiments started with an observation in human cells that prompted discovery of an analogous system and adaptor protein in yeast. Now the authors turned the tables and used yeast to look for new adaptor proteins in human cells. Using bioinformatics, they identified a human CUE-domain protein, Tollip, which, although different in its domain organization from Cue5p, contains 2 AIM motifs.
To make a long story (and a lot of work!) short, they showed that Tollip binds both human Atg8p and ubiquitin conjugates and clears cytotoxic variants of huntingtin in human cells. Expressed in yeast, it similarly binds ubiquitin conjugates and Atg8p and suppresses the hypersensitivity of cue5∆ cells to the variant huntingtin protein Htt-96Q. So Tollip is a newly defined adaptor protein and functional homolog of Cue5p!
Letter carriers of one sort or another have been around for as long as human civilization has existed, from homing pigeons to FedEx. Now we know that for even longer, cells from yeast to human have been using similar ways to recognize stamped proteins and deliver them to the right address. And once again, yeast has helped us understand the inner secrets of human cells.
by Selina Dwight, Ph.D., Senior Biocurator, SGD
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
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
June 19, 2014
In the Matrix Trilogy, the delicate balance of a virtual world is upset by a rogue computer program that goes by the name of Agent Smith. This program finds and touches other agent programs, converting them into copies of itself. Eventually, all the agent programs are copies of Agent Smith and only the hero Neo can save humanity in an epic battle within the virtual world of the Matrix.
A new study out in GENETICS by Li and Du provides additional evidence that prions in the yeast Saccharomyces cerevisiae work similarly to Agent Smith, in that they spread through a direct contact model. These prions are proteins that have entered a rogue conformation, and they end up converting all copies of the same protein into a similar rogue conformation. The proteins change from a hardworking Agent Smith trying to do its job into something that mucks up the working of a cell. And the results, at least in humans, can be as catastrophic for the cell as Agent Smith was for the Matrix.
Mad cow disease, for example, is caused by prions converting the prion protein (PrP) in the brain cells of people from a useful conformation to a dangerous one that spreads. As the conformation spreads throughout the cell, these prions form amyloid fibrils that eventually kill the cell. When enough brain cells are killed, the person dies.
The authors chose to work in yeast because unlike in people, there are multiple examples of proteins in yeast that can go prion. The list includes Sup35p, Ure2p, Rnq1p, Swi1p, Cyc8p, Mot3p, Sfp1p, Mod5p and Nup100p. As you might guess from the sheer number of these prion-ready proteins, prions actually do more than kill a cell in yeast; they can serve useful functions. Scientists have yet to identify any useful functions for the prion form of PrP in people.
Having multiple prions in a cell allowed Li and Du to perform some experiments to try to distinguish between two models of prion conformation spreading. In the first, called the cross-seeding model, the prion acts very much like Agent Smith in that it needs to contact a “healthy” protein to convert it into a prion. In the second model, the titration model, factors in the cell that prevent prion formation are titrated out when prions form. As the factors are taken out of commission, prions are free to form.
The main evidence in this study that supports the cross-seeding model has to do with the localization of pre-existing prions during the de novo formation of a new prion. Li and Du found that the prion [SWI+] localized to newly forming [PSI+] prions but not to already formed [PSI+] prions. This is not the result we would expect if prion formation were due to titrating out of inhibitors of prion formation. If that were the mechanism, then there would be no reason for [SWI+] to colocalize with newly forming [PSI+]. These experiments are like having a google map of the Matrix where we could see Smiths converting other agents by touch and then moving on and touching other agents.
Work like this is important for helping to find treatments for prion associated diseases and, perhaps, other amyloid fibril forming diseases like Huntington’s or Alzheimer’s. Scientists need to focus on the amyloid fiber forming proteins themselves instead of trying, for example, to ramp up the activity of factors that inhibit formation. Scientists probably need to eliminate Agent Smith to prevent the destruction of the Matrix and all of mankind.
This is how prions turn other proteins into copies of themselves:
by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics
May 15, 2014
Imagine you are in a band and the only instruments you have are guitars. Yes, you can play some beautiful music, but there will be a whole lot of music that your band won’t be able to play.
In some ways, finding chemical leads to develop into drugs is similar to an all guitar band. The compounds in available libraries all tend to have a lot in common. They are like a vast array of subtly different guitars.
In a new study, Klein and coworkers use synthetic biology to have the yeast Saccharomyces cerevisiae make more varied libraries on its own. As an added bonus, the authors also use the yeast to assay the new leads. Not only have they expanded the range of instruments available to your band, but they’ve also made it so you can play all the instruments. You are now a one man band!
The first step in all of this is to have an assay that can easily pick out the important leads. Klein and coworkers use a galactose inducible Brome Mosaic Virus (BMV) system they had previously developed.
In this system, if one of the viral genes is on, then it produces a fusion protein that includes the Ura3 protein. When the URA3 gene is expressed, yeast die in the presence of 5-fluoroorotic acid (5-FOA). So any yeast that can make a compound that can inhibit viral expression will survive in 5-FOA.
The next step in creating these in vivo libraries was to randomly assemble various biochemical pathways into yeast artificial chromosomes (YACs) and to transform them into yeast. These pathways were chosen because they have yielded important compounds before or because they come from medically important beasts. This work was described in detail in a previous paper.
Specifically, Klein and coworkers randomly combined cDNA genes from eight biochemical pathways into YACs and transformed them into the BMV replication yeast strain. They found 74 compounds that allowed the yeast to survive in the presence of 5-FOA. Of these, 28 had activity in a secondary BMV assay.
A close look at the 74 compounds showed that by and large, most had characteristics that put them in the right ballpark to be useful leads. They had low molecular weight and the right hydrophobicity, and were chemically complex. In addition, many could easily be improved chemically (this last point is called optimizability). Most importantly, they were pretty unique from a drug lead point of view.
Over 75% of the compounds resembled nothing in known libraries. And the compounds were not similar to one another. Klein and coworkers had created a wide range of instruments other than guitars.
Of course, keeping a yeast strain alive is hardly reason to look for a new drug. But that isn’t all these compounds can do. At least some of these leads show excellent activity against two viruses related to BMV, Dengue and hepatitis C, and one looks particularly promising.
With a random combination of genes from a variety of biochemical pathways, yeast has been coaxed into synthesizing chemical leads that can target two medically relevant viruses. Scientists should be able to use a similar approach to tackle other diseases. All they need is a yeast strain with the right assay.
Yeast can make our bread rise, get us drunk, and now maybe cure us of disease. Is there anything yeast can’t do? Well, they still can’t play a guitar.
by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics
March 06, 2014
Imagine the heater at your house is run by a homemade copper-zinc battery. You are counting on a delivery of a copper solution that will keep the thing going. Unfortunately it fails to come, which means the battery doesn’t work and you are left out in the cold.
Turns out that something similar can happen in cells too. The respiratory chain that makes most of our energy needs copper to work. In a recent study, Ghosh and coworkers showed that if Coa6p doesn’t do its job delivering copper to the respiratory chain, the cell can’t make enough energy.
This isn’t just interesting biology. In this same study, the researchers showed that mutations in the COA6 gene cause devastating disease in humans and zebrafish. And their discovery that added copper can cure the “disease” in yeast just might have therapeutic applications for humans.
The respiratory chain is a group of large enzyme complexes that sit in the mitochondrial inner membrane and pass electrons from one to another during cellular respiration. This process generates most of the energy that a cell needs. Hundreds of genes, in both the nuclear and mitochondrial genomes, are involved in keeping this respiratory chain working.
Yeast has been the ideal experimental organism for studying these genes, because it can survive just fine without respiration. If it can’t respire for any reason, yeast simply switches over to fermentation, generating the alcohol and CO2 byproducts that we know and love.
Human cells aren’t as versatile though. Genes involved in respiration can cause mitochondrial respiratory chain disease (MRCD) when mutated. This is one of the most common kinds of genetic defect, with over 100 different genes known so far that can cause this phenotype.
Ghosh and colleagues wondered whether there were as-yet-unidentified human genes involved in maintaining the respiratory chain. They reasoned that any such genes would be highly conserved across species, because they are so important to life, and that the proteins they encoded would localize to mitochondria.
One of the candidates, C1orf31, caught their eye for a couple of reasons. First, some variations in this gene had been found in the DNA of a MRCD patient. And second, the yeast homolog, COA6, encoded a mitochondrial protein that had been implicated in assembly of one of the respiratory complexes, Complex IV or cytochrome c oxidase.
They first did some more detailed characterization of COA6 in yeast. They were able to verify that the coa6 null mutant had reduced respiratory growth because it had lower levels of fully assembled Complex IV.
They also looked to see what happens in human cell culture. When they knocked down expression of the human homolog, they also saw less assembly of Complex IV. This suggested that the function of this protein is conserved across species.
Next they turned to a sequencing study of an MRCD patient who had, sadly, died of a heart defect (hypertrophic cardiomyopathy) before reaching his first birthday. The sequence showed a mutation in a conserved cysteine-containing motif of COA6. To see whether this might be the cause of the defect, they created the analogous mutation in yeast COA6. The mutant protein was completely nonfunctional in yeast.
To nail down the physiological role of COA6 in a multicellular organism, they turned to zebrafish. The embryos of these fish are transparent, so it’s easy to follow organ development. Given the phenotype, the fact that they can live without a functional cardiovascular system for a few days after fertilization was important too.
When the researchers knocked down expression of COA6 in zebrafish, they found that the embryos’ hearts failed to develop normally and they eventually died. The abnormal development of the fish hearts paralleled that seen in the human MRCD patient carrying the C1orf31/COA6 mutation. And reduced levels of Complex IV were present in the fish embryos.
Going back to yeast for one more experiment, Ghosh and colleagues decided to see whether Coa6p might be involved in delivering copper to Complex IV. They knew that Complex IV uses copper ions as a cofactor, and furthermore Coa6p had similarities to several other yeast proteins that are known to be involved in the copper delivery.
They tested this by supplying the coa6 null mutant with large amounts of copper. Sure enough, its respiratory growth defect and Complex IV assembly problems were reversed. The delivery of copper kept the energy flowing in these cells. And this result showed that Coa6p is involved in getting copper to Complex IV.
These experiments showcase the need for model organism research even in the face of ever more sophisticated techniques applied to human cells. The mutation in human C1orf31/COA6 was discovered in a next-generation sequencing study, but yeast genetics established the relationship between the mutation and its phenotype. The zebrafish system allowed the researchers to follow the effects of the mutation in an embryo from the earliest moments after fertilization. And the rescue of the yeast mutant by copper supplementation offers an intriguing therapeutic possibility for some types of MRCD. Just another testament to the awesome power of model organism research!
YeastMine now lets you explore human homologs and disease phenotypes. Enter “COA6” into the template Yeast Gene -> OMIM Human Homolog(s) -> OMIM Disease Phenotype(s) to link to the Gene page for human COA6 (the connection between COA6 and disease is too new to be represented in OMIM). To browse some diseases related to mitochondrial function, enter “mitochondrial” into the template OMIM Disease Phenotype(s) -> Human Gene(s) -> Yeast Homolog(s).
by Maria Costanzo, Ph.D., Senior Biocurator, SGD
March 04, 2014
You can now use SGD’s advanced search tool, YeastMine, to find the human homolog(s) of your favorite yeast gene and their corresponding disease associations. Or, begin with your favorite human gene or disease keyword and retrieve the yeast counterparts of the relevant gene(s). As an example, you can search for the S. cerevisiae homologs of all human genes associated with disorders that contain the keyword “diabetes” (view search).
We have recently loaded data from OMIM (Online Mendelian Inheritance in Man) into our fast, flexible search resource, YeastMine, and provided 3 predefined queries (templates) that make it simple to perform the above searches. Newly updated HomoloGene, Ensembl, TreeFam, and Panther data sets are used to define the homology between S. cerevisiae and human genes. The results table provides identifiers and standard names for the yeast and human genes, as well as OMIM gene and disease identifiers and names. As with other YeastMine templates, results can be saved as lists and analyzed further. You can also now create a list of human names and/or identifiers using the updated Create Lists feature that allows you to specify the organism representing the genes in your list. The query for yeast homologs can then be made against this list.
In addition to human disease homologs, we have incorporated fungal homolog data for 24 additional species of fungi. You can now query for the fungal homologs of a given S. cerevisiae gene using the template “Gene –> Fungal Homologs.” This fungal homology data comes from various sources including FungiDB, the Candida Gene Order Browser (CGOB), and PomBase, and the results link directly to the corresponding gene pages in the relevant databases, including Candida Genome Database (CGD) and Aspergillus Genome Database (AspGD).
All of the new templates that query human and fungal homolog data can be found on the YeastMine Home page under the new tab “Homology.” These templates complement the template “Gene → Non-Fungal and S. cerevisiae Homologs” that retrieves homologs of S. cerevisiae genes in human, rat, mouse, worm, fly, mosquito, and zebrafish.
Watch the Human Disease & Fungal Homologs in SGD’s YeastMine tutorial (below) to learn how to find and use these new templates.
October 31, 2013
Folks, yeast has been on a roll lately with regard to helping to understand and finding treatments for human disease. Last week we talked about how synthetic lethal screens may find new, previously unrecognized druggable targets for cancer. And this week it is Parkinson’s disease.
Now of course yeast can’t get the traditional sort of Parkinson’s disease …it doesn’t have a brain. But it shares enough biology with us that when it expresses a mutant version of α-synuclein (α-syn) that is known to greatly increase a person’s risk for developing Parkinson’s disease, the yeast cell shows many of the same phenotypes as a diseased neuron. The yeast acts as a stand-in for the neuron.
In a new study out in Science, Tardiff and coworkers use this yeast model to identify a heretofore unknown target for Parkinson’s disease in a sort of reverse engineering process. They screened around 190,000 compounds and looked for those that rescued toxicity in this yeast model. They found one significant hit, an N-aryl-benzimidazole (NAB) compound. Working backwards from this hit they identified its target as Rsp5p, a Nedd4 E3 ubiquitin ligase.
The authors then went on to confirm this finding in C. elegans and rat neuron models where this compound halted and even managed to reverse neuronal damage. And for the coup de grace, Chung and coworkers showed in a companion paper that the compound worked in human neurons too. But not just any human neurons.
The authors used two sets of neurons derived from induced pluripotent cells from a single patient. One set of neurons had a mutation in the α-syn gene which is known to put patients at a high risk of Parkinson’s disease-induced dementia. The other set had the mutation corrected. The compound they identified in yeast reversed some of the effects in the neurons with the α-syn mutation without significantly affecting the corrected neurons. Wow.
What makes this even more exciting is that many people thought you couldn’t target α-syn with a small molecule. But as the studies here show, you can target an E3 ubiquitin ligase that can overcome the effects of mutant α-syn. It took an unbiased screen in yeast to reveal a target that would have taken much, much longer to find in human cells.
The mutant α-syn protein ends up in inclusion bodies that disrupt endosomal traffic in the cell. The NAB compound that the authors discovered restored endosomal transport and greatly decreased the numbers of these inclusion bodies. Juicing up Rsp5 seemed to clear out the mutant protein.
The next steps are those usually associated with finding a lead compound—chemical modification to make it safer and more effective, testing in clinical trial and then, if everything goes well, helping patients with Parkinson’s disease. And that may not be all.
The α-syn protein isn’t just involved in Parkinson’s disease. The dementia associated with this protein is part of a larger group of disorders called dementia with Lewy bodies that affects around 1.3 million people in the US. If everything goes according to plan, many of these patients may one day thank yeast for their treatment.
by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics
October 24, 2013
Current cancer treatments are a lot like trying to destroy a particular red plate by letting a bull loose in a china shop. Yes, the plate is eventually smashed, but the collateral damage is pretty severe.
Ideally we would want something a bit more discriminating than an enraged bull. We might want an assassin that can fire a single bullet that destroys that red plate.
One way to identify the assassin that can selectively find and destroy cancer cells is by taking advantage of the idea of synthetic lethal mutations. “Synthetic lethal” is a genetic term that sounds a lot more complicated than it really is. Basically the idea is that mutating certain pairs of genes kills a cell, although mutating each gene by itself has little or no effect.
A synthetic lethal strategy seems tailor made for cancer treatments. After all, a big part of what happens when a cell becomes cancerous is that it undergoes a series of mutations. If scientists can find and target these mutated genes’ synthetically lethal partners, then the cancer cell will die but normal cells will not.
This is just what Deshpande and coworkers set out to do in a new study in the journal Cancer Research. They first scanned a previous screen that looked at 5.4 million pairwise interactions in the yeast S. cerevisiae to find the best synthetic lethal pairs. They found 116,000 pairs that significantly affected cell growth only if both genes in the pair were mutated.
A deeper look into the data revealed that 24,000 of these pairs had human orthologs for both genes. In 500 of these pairs, at least one of the partner genes had been shown to be mutated in certain cancers. Using a strict set of criteria (such as the strength and reproducibility of the synthetic lethal effect, and the presence of clear one-to-one orthology between yeast and human), the authors narrowed these 500 down to 21 pairs that they decided to study in mammalian cell lines.
When the authors knocked down the expression of both genes in these 21 gene pairs in a mammalian cell line, they found six that significantly affected growth. They focused the rest of the work on the strongest two pairs, SMARCB1/PMSA4 and ASPSCR1/PSMC2. These mammalian gene pairs correspond to the yeast orthologs SNF5/PRE9 and UBX4/RPT1, respectively.
The authors identified two separate cancer cell lines that harbored mutated versions of the SMARCB1 gene. When this gene’s synthetic lethal partner, PMSA4, was downregulated in these cancer lines, the growth of each cell line was severely compromised. The same was not true for a cell line that had a wild type version of SMARCB1—this cell line was not affected by downregulating PMSA4. The authors used a synthetic lethal screen in yeast to identify a new cancer target which when downregulated selectively killed the cancer without killing “normal” cells.
This proof of principle set of experiments shows how the humble yeast may one day speed up the process of finding cancer treatments without all those nasty side effects (like vomiting, hair loss, anemia and so on). Yeast screens can first be used to identify target genes and then perhaps also to find small molecules that affect the activity of those gene products. Yeast may one day tame the raging bull in a china shop that is current cancer treatments.
by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics
October 10, 2013
Cheap and easy genome sequencing has been both a blessing and a curse. We are able to find an incredible wealth of variation, but for the most part we have no easy way to tell whether a difference might contribute to a disease or not.
The poster child for this problem is autism. Lots of genome wide association studies (GWAS) have been done and lots of rare variants in lots of different genes have been found – unfortunately, way too many to pick out the ones that really matter.
Luckily our friend yeast can help. Various researchers have identified a number of variants in the human cation/proton antiporter gene NHE9 that associate with autism. In a new study, Kondapalli and coworkers used the NHE9 ortholog NHX1 from S. cerevisiae as an initial screen to identify which variants impact the activity of the NHE9 protein. They found that two of the three mutations they looked at compromised the activity of yeast Nhx1p.
They then set out to confirm these results in mammalian cells. When they looked at protein activity in glial cells, they found that all three mutations compromised the activity of NHE9. This is obviously different from what they found in yeast.
Now this doesn’t mean that yeast is useless for this approach (God forbid!). No, instead it means that it is probably only useful for a subset of autism mutations. Kondapalli and coworkers had suspected this, but apparently the subset is smaller than they initially thought.
The first thing they did was to generate a rough three dimensional map of the NHE9 protein in order to see which parts the two proteins shared. The idea is that they could then do a quick screen in yeast with mutations that affect the shared structure.
While the structure of NHE9 has not been solved, we do have the structure of its distant bacterial relative, NhaA. Kondapalli and coworkers aligned the two along with the yeast ortholog Nhx1p and identified conserved regions.
Three of the NHE9 mutations associated with autism—V176I, L236S, and S438P—were all predicted to be in shared, membrane-spanning parts of the protein. The researchers introduced the equivalent mutations into NHX1—V167I, I222S, and A438P.
A yeast deleted for NHX1 grows poorly in high salt and low pH and also has increased sensitivity to hygromycin B, as compared to a yeast with a functioning NHX1. Two of the mutant genes, carrying A438P or I222S, failed to rescue these growth defects. The other mutant gene, with the V167I change, worked as well as wild type NHX1 at rescuing the yeast. So at least in yeast, two of the three mutations appear to impact protein activity.
The next step was to see if the same was true in mammals. Easier said than done! Ideally they would want to investigate whether these mutations affected the protein in the cells where NHE9 is usually active. Too bad no one knows this protein’s natural habitat. This is why the researchers starting slicing mouse brains to figure out when and where the protein is expressed.
While we don’t have time or space to go into all the details here, Kondapalli and coworkers found that when and where in the brain NHE9 was expressed made sense as far as a possible contribution to autism. They also found that glial cells had about 1.2 fold more NHE9 transcripts than did neuronal cells. They therefore did their assays of protein activity in a type of glial cells called astrocytes.
While they couldn’t completely knock out NHE9 in mouse astrocytes, they were able to knock down its expression by over 80%. When they added back the mutant NHE9 genes, they found that all three failed to mimic the effect of adding back wild type NHE9 to these cells. This is different than what they found in yeast, where only two of the mutations impacted protein activity.
When they went back to their 3D model, they saw that the mutation that differed, V167I, affected a less defined part of the structure. This points to the fact that for the quick yeast screen to work, they need to be looking at parts of the protein where the structure is shared between the yeast and the human version. In a perfect world they would have had crystal structures of each to work off of instead of having to kludge together a model.
In any event, this is the first step towards validating yeast as a quick screen for identifying mutations that can impact protein activity and so are good candidates for being involved in disease. Yeast may help scientists separate the wheat from the chaff of GWAS and so help figure out how diseases happen and maybe help find treatments or even cures. Well done yeast.
by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics
October 02, 2013
Remember in Dune when Paul Muad’Dib took a sip of the “Water of Life” and needed weeks in a coma to turn it into something that let him survive and emerge even more powerful than before? Turns out yeast sometimes have to do something similar.
Now of course the yeast aren’t consciously moving molecules around to deal with a poison like Paul did. No, instead they sometimes need to transcribe low levels of a mutated gene over a long period of time to survive in a new environment.
This process is called retromutagenesis. The idea is that a cell gets a mutation that would allow it to survive and prosper in a new environment if only it could replicate its DNA. Unfortunately the new environment is so unforgiving that the cell can’t replicate.
The cell escapes this catch-22 by transcribing the gene with the mutation so that the mutant protein can get made. Once enough of this protein is made, the cell manages to get up enough steam to power through a cell cycle. Now the mutation is established and the yeast can make lots of mutant protein and happily chug along.
In a new study in the latest issue of GENETICS, Shockley and coworkers hypothesize that something like this is happening in their experiments. They were studying oxidative damage to DNA and found that some of their mutants required many days before they could grow in the absence of tryptophan (trp). They argue that these late arising revertants were due to the cells having to wait until retromutagenesis allowed enough functional Trp5p to be made so the cell could replicate.
The authors have created strains of yeast with various mutations in the TRP5 gene that cause the yeast to be unable to grow in the absence of trp. What makes these strains so useful is that they are set up in such a way that six different, specific point reversions can result in a functional TRP5 gene. They can then analyze any Trp+ revertants to see what types of damage lead to which type of mutations.
One of the first things the authors discovered was that oxidative damage caused all six different reversions. While this was interesting, the specific mutation they wanted to focus on was a G to T transversion which occurs when G is converted to 8-oxoguanine. This is why they focused on the trp5-A149C strain.
The main way that yeast cells deal with 8-oxoguanine is by removing it with the Ogg1 protein, a DNA glycosylase. When Shockley and coworkers deleted this gene in their strain, the number of revertants increased by 20-fold. From this they concluded that most of the revertants were the result of the misreplication of an 8-oxoguanine.
This is where the yeast run into a problem. In the absence of trp, the trp5 mutants do not replicate at all…they do not go through even one cell cycle. But to revert to a functional TRP5 gene, this strain needs to go through a cell cycle. This is why the authors think that the first step towards reversion is a mutation in the TRP5 transcript.
Consistent with this idea is the fact that the mutated G in this strain is on the transcribed strand and that this is important for high revertant frequencies. It also helps to explain why revertants took so long to appear. Basically there had to be a buildup of enough functional Trp5p to allow a single cell cycle to happen. Then the G could be converted to a T and the yeast could happily grow. In this specialized case, it looks like reversion is dependent on retromutagenesis.
But retromutagenesis, also called transcriptional mutagenesis, doesn’t happen only in yeast cells. It’s being studied as a possible way that all kinds of quiescent cells, such those in the process of becoming tumor cells, or bacteria whose growth has been stopped by an antibiotic, can mutate and escape the conditions that are restricting them. Our little friend may not save the human race from destruction like Paul did, but once again yeast is proving pretty darn useful in getting results that make a difference for human health.
by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics
September 05, 2013
Huntington’s disease (HD) is a truly awful, inherited and ultimately fatal genetic disease. People with this neurodegenerative disorder typically start having trouble with their coordination and displaying mild cognitive and psychiatric problems in mid-adulthood. Their symptoms continue to worsen, with most of these folks passing away within 20 years of their diagnosis. This disease strikes down adults in their prime.
Scientists have known for decades what causes HD—too many CAG repeats in the huntingtin (htt) gene. What they haven’t been able to figure out is what to do about this misfolded protein. To date, the treatment options are very limited.
A new study out by Mason and coworkers has a chance to change all of that. Using an unbiased screen in Saccharomyces cerevisiae, these authors were able to identify a class of proteins, the glutathione peroxidases, that when overexpressed protected yeast from the harmful effects of the mutant htt protein. They then followed up and showed that these proteins had a similar effect in fruit fly and mouse HD cell models as well as in a whole fruit fly model. And this isn’t even the exciting part.
There are druggable small molecules that when added to cells (or whole animals) can upregulate the activity of glutathione peroxidases. The authors used one of these molecules, ebselen, and showed that it mimicked the effects of overexpressing various glutathione peroxidases in cells and, more importantly, in whole fruit flies. When these flies were fed ebselen, their neurons degenerated at a much slower rate. Mason and coworkers have identified a small molecule that can mitigate the effects of the mutant htt protein in model systems.
While we shouldn’t get ahead of ourselves here, this is all pretty exciting news. How cool would it be if one day people with HD lived longer, happier lives because of a drug identified using our favorite model organism? (Pay attention NIH!)
Mason and coworkers looked in S. cerevisiae for open reading frames that, when overexpressed, would lower the toxicity of the mutant htt protein. They identified 317 of these, and used a variety of bioinformatics tools to group them into different pathways and gene networks.
In the end, they decided to focus on two powerful suppressors, the glutathione peroxidases Gpx1p and Hyr1p (also known as Gpx3p), for a variety of different reasons. These proteins are powerful antioxidants, and oxidative stress is known to contribute to HD symptoms. Also, these proteins aren’t already upregulated in patients with Huntington’s disease, suggesting that it might be possible to increase their activity using drug therapy.
Now of course yeast aren’t mammals, so Mason and coworkers needed to show that having extra glutathione peroxidase activity would help in mammalian cells too. And this is just what they did: adding a mouse version of glutathione peroxidase, mGPx1, suppressed cellular toxicity in mouse cells that overexpressed the mutant form of htt.
Next they tested whether activating glutathione peroxidases would have the same effect. They focused specifically on a selenocysteine-containing molecule called ebselen because it is highly bioavailable, can cross the blood-brain barrier (critical for HD) and has been used in treating stroke and noise induced hearing loss. When added to the mouse HD model cell system, ebselen had very similar effects to overexpressing mGPx1.
So upregulating glutathione peroxidase activity by either overexpressing mGPx1 or adding the small molecule ebselen appears to help in a couple of different model cell systems. But what about a whole animal? Looks like it can help there too.
Mason and coworkers looked at HD in a fruit fly. When they added mGPx1 to this model fly, various neurons in these flies were protected from the effects of HD. And they got similar results when they fed these flies the molecule ebselen.
As a final experiment, the authors wanted to figure out whether glutathione peroxidases were really having their effect because of their antioxidant activity. In one way it makes sense that this activity is why they are so effective at mitigating the effects of the mutant HD—scientists have known for a while that oxidative stress is a major contributor to symptoms of HD. But on the other hand no antioxidant therapies have worked to date for HD. In fact, if anything they made matters worse. So one thought was that there was something special about the antioxidant activity of these proteins. For these experiments, they needed to go back to yeast.
The authors looked at a variety of antioxidant proteins, including superoxide dismutase, catalases, and glutathione reductases, and none protected the yeast from the effects of the mutant htt protein. They then checked the effects of catalase and superoxide dismutase in the HD mouse cells, and again saw no effect.
It is well known that antioxidants negatively affect autophagy and that disrupting this process can make HD symptoms worse. From this the authors reasoned that glutathione peroxidases were special because they were antioxidants that did not affect autophagy. They provided support for their idea by showing that ebselen did not affect autophagy in yeast while a control antioxidant, N-acetylcysteine, did.
Once again, yeast shows why it is such an important tool in finding potential new treatments for human disease. Without the unbiased screen, it’s difficult to imagine how scientists would have found this target. You can really only do this easily in a beast like yeast.
Symptoms like these may one day be delayed because of the awesome power of yeast genetics.
by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics