New & Noteworthy
New SGD Help Video: Yeast-Human Functional Complementation Data
June 30, 2015
Yeast and humans diverged about a billion years ago, but there’s still enough functional conservation between some pairs of yeast and human genes that they can be substituted for each other. How cool is that?! Which genes are they? What do they do?
This two-minute video explains how to find, search, and download the yeast-human functional complementation data in SGD. You can find help with many other aspects of SGD in the tutorial videos on our YouTube channel. And as always, please be sure to contact us with any questions or suggestions.
The Sounds of Silencing
June 17, 2015
For centuries, we thought of the universe as an empty, eerily silent place. Turns out we were dead on when it came to the emptiness, not so much when it came to the silence.
Despite more and more powerful equipment, SETI has yet to find any meaningful radio signals coming from the stars. Yeast research is in a better position: new techniques applied to telomeric gene expression now make sense of the signals. Image by European Southern University (ESO) via Wikimedia Commons
Once we invented devices that could detect electromagnetic radiation—starting with the Tesla coil receiver in the 1890s—we began to realize what a noisy place the universe really is. And now with modern radio telescopes becoming more and more sensitive, we know there is a cacophony of signals out there (although the Search for Extraterrestrial Intelligence has yet to find any non-random patterns).
The ends of chromosomes, telomeres, have also long thought to be largely silent in terms of gene expression. But a new paper in GENETICS by Ellahi and colleagues challenges that idea.
Much like surveying the universe with a high-powered radio telescope, the researchers used modern techniques to make a comprehensive survey of the telomeric landscape–and saw that the genes were not so silent. Their work revealed that there’s a lot more gene expression going on at telomeres than we thought before.
It also gave us some fascinating insights into the role of the Sir proteins, founding members of the conserved sirtuin family that is implicated in aging and cancer.
Telomeres are special structures that “cap” the ends of linear chromosomes to protect the genes near the ends from being lost during DNA replication, something like aglets, those plastic tips that keep the ends of your shoelaces from fraying. They have characteristic DNA sequence elements that we don’t have space to describe here (but you can find a short summary in SGD).
Classical genetics experiments in Drosophila fruit flies showed that telomeres had a silencing effect on the genes near them, and early work in yeast seemed to confirm this. Reporter genes became transcriptionally silenced when they were placed near artificial constructs that mimicked telomere sequences.
This early work was solid, but had a few limitations. The artificial telomere constructs were, well, artificial; some of the reporter genes encoded enzymes that had an effect on overall cellular metabolism, such as Ura3; and the studies tended to look at just one or a few telomeres.
To get the whole story, Ellahi and colleagues decided to look very carefully at the telomeric universe of S. cerevisiae. First, they used ChIP-seq to look at the physical locations of three proteins, Sir2, Sir3, and Sir4, on chromosomes near the telomeres.
These proteins, first characterized and named Silent Information Regulators for their role in silencing yeast’s mating type cassettes, had been seen to also mediate telomeric silencing. Scientists had hypothesized that they might be present at telomeres in a gradient, strongly repressing genes close to the chromosomal ends and petering out with increasing distance from the telomere.
Ellahi and coworkers re-analyzed recent ChIP-seq data from their group to find where the Sir proteins were binding within the first and last 20 kb regions of every chromosome. These 20 kb regions included the telomere and the so-called subtelomeric region where genes are thought to be silenced. They found all three Sir proteins at all 32 natural telomeres.
However, the Sir proteins were not uniformly distributed across the telomeres, but rather occupied distinct positions. Typically, all three were in the same position, as would be expected since they form a complex. And they were definitely not in a gradient along the telomere.
Next the researchers asked whether gene expression was truly silenced in that subtelomeric region. They used mRNA-seq to measure gene expression from the ends of chromosomes in wild type or sir2, sir3, or sir4 null mutants.
They found that contrary to expectations, there is actually a lot of transcription going on near telomeres, even in the closest 5 kb region. The levels are lower than in other parts of the genome, but that can be partly explained by the fact that open reading frames are less dense in these regions. And only 6% of genes are silenced in a Sir-dependent manner.
The sensitivity of mRNA-seq allowed Ellahi and colleagues to uncover new patterns of gene expression in this work. They were able to detect very low-level transcription from some of the telomeric repetitive elements. Also, because the SIR genes are involved in mating type regulation, the mRNA-seq data from the sir mutants revealed a whole new set of genes that are differentially expressed in different cell types (haploids of mating types a and α, or a/α diploids).
The researchers point out that their work raises the question of why the cell would use the Sir proteins to repress transcription of a few subtelomeric genes. Wouldn’t it be more straightforward if these genes just had weaker promoters to keep their expression low?
They hypothesize that Sir repression could actually be part of a stress response mechanism, allowing a few important genes to be turned on strongly when needed. This idea could have intriguing implications for the role of Sir family proteins in aging and cancer in larger organisms.
So, neither the universe nor the ends of our chromosomes are as silent as we thought. But unlike the disappointed SETI researchers, biologists studying everything from yeast to humans can now build on this large quantity of meaningful data from S. cerevisiae telomeres.
by Maria Costanzo, Ph.D., Senior Biocuration Scientist, SGD
Yeast-Human Functional Complementation Data Now in 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!
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.
Gene –> Functional Complementation template
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.
Human Gene –> Functional Complementation template
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”.
Yeast are People Too
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.
Just like these cars, yeast and human cells have some big differences under the hood but still share plenty of parts that are interchangeable. Nissan Leaf image via Wikimedia Commons; Ford Mustang image copyright Bill Nicholls via Creative Commons
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.
This budding yeast-human drives home the point that humans and yeast share a lot in common: so much, that yeast continues (and will continue) to be the pre-eminent tool for understanding the fundamental biology of being human. Image courtesy of Stacia Engel
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