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