New & Noteworthy
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!
Using YeastMine to Access Functional Complementation Data
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.
Downloading Functional Complementation Data
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 3, 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
May 28, 2015
Breaking news: the deadline for submission of abstracts for oral presentations at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) has been extended. Abstracts may be submitted for talks in the plenary sessions or in parallel workshops until June 7th.
Abstracts for poster presentations may be submitted until July 15th. But be sure to register for the conference by June 30th to get the early registration price!
May 27, 2015
As anyone who watches a situation comedy knows, long range relationships are tricky. The longer the couple is separated, the more they drift apart. Eventually they are just too different, and they break up.
Of course if this were the end of the story, it would be the plot of the worst comedy ever. What usually happens in the sitcom is that one or both of them find someone more compatible and live happily ever after (with lots of silliness and high jinks).
Turns out that according to a new study by Hou and coworkers, our friend Saccharomyces cerevisiae could star in this sitcom. When different populations live in different environments, they drift apart. Eventually, because they accumulate chromosomal translocations and other serious mutations, they have trouble mating and having healthy offspring.
Now researchers already knew that big changes in yeast, like chromosomal translocations, affect hybrid offspring. But what was controversial before and what this study shows is that, as is known for plants and animals, smaller changes like point mutations can affect the ability of distinct populations of yeast to have healthy progeny. It is like Jerry Seinfeld being incompatible with a girl because she eats her peas one at a time (click here for other silly reasons Jerry breaks up with girlfriends).
The key to finding that yeast can be Seinfeldesque was to grow hybrid offspring in different environments. Hybrids that did great on rich media like YPD sometimes suffered under certain, specific growth conditions. Relying on the standard medium YPD masked mutations that could have heralded the beginnings of a new species of yeast.
See, genetic isolation is a powerful way for speciation to happen. One population generates a mutation in a gene and the second population has a mutation in a second gene. In combination, these two mutations cause a growth defect or even death. Now each population must evolve on its own, eventually separating into two species.
To show that this is a route that yeast can take to new species, Hou and coworkers mated 27 different Saccharomyces cerevisiae isolates with the reference laboratory strain S288C and grew their progeny under 20 different conditions. These strains were chosen because they were all able to produce spores with S288C that were viable on rich medium (YPD).
Once they eliminated the 59 pairings that involved parental strains that could not grow under certain conditions, they found that 117 out of 481 or 24.3% of crosses showed at least some negative effect on the growth of the progeny under at least some environmental conditions. And some of these were pretty bad. In 32 cases, at least 20% of the spores could not survive.
The authors decided to focus on crosses between S288C and a clinical isolate, YJM241, where around 25% of spores were inviable under growth conditions that required good respiration, such as the nonfermentable carbon source glycerol. They found that rather than each strain having a variant that affected respiration, the growth defect happened because of two complementary mutations in the clinical isolate.
The first mutation was a nonsense mutation in COX15, a protein involved in maturation of the mitochondrial cytochrome c oxidase complex, which is essential for respiration. The second was a nonsense suppressor mutation in a tyrosine tRNA, SUP7. So YJM241 was fine because it had both the mutation and the mechanism for suppressing the mutation. Its offspring with S288C were not so lucky.
Around 1 in 4 progeny got the mutated COX15 gene without SUP7 and so could not survive under conditions that required respiration. Which of course is why this was missed when the two strains were mated on YPD, where respiration isn’t required for growth.
So this is a case where the separated population, the clinical isolate YJM241, changed on its own such that it would have difficulty producing viable progeny with any other yeast strains. Like the narrator in that old Simon and Garfunkel song, it had become an island unto itself.
The researchers wondered whether this kind of change—a nonsense mutation combined with a suppressor—occurs frequently in natural yeast populations. They surveyed 100 different S. cerevisiae genome sequences and found that nonsense mutations are actually pretty common. Nonsense suppressor mutations were another story, though: they found exactly zero.
Apparently nonsense suppressor mutations are really rare in the yeast world, and Hou and colleagues wondered whether this was because they had a negative effect on growth. They added the SUP7 suppressor mutant gene to 23 natural isolates. It had negative effects on most of the isolates during growth on rich media, but it was more of a mixed bag under various stress conditions. Sometimes the mutation had negative effects and sometimes it had positive effects.
The fact that a suppressor mutation can provide a growth advantage under the right circumstances, combined with the fact that they are very rare, suggests that a new suppressor arising might help a yeast population out of a jam, but once the environment improves the yeast are free to jettison it. Suppressor mutations may be a transitory phenomenon, a momentary dalliance.
So, separate populations of yeast can change over time in subtle ways that prevent them from mating with one another. This can eventually lead to the formation of new species as the changes cause the two to drift too far apart genetically. It is satisfying to know that yeast drift apart like any other plant, animal, or sitcom character.
by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics