New & Noteworthy

SGD Help: Interaction Overview and Network

August 24, 2015


SGD includes data on many thousands of genetic and physical interactions between the genes and proteins of Saccharomyces cerevisiae, as curated by our friends at the BioGRID database. We provide two different graphical displays that help you get a very quick and intuitive overview of known interactions for a particular gene or protein.

All interactions for a gene and its product are listed on its interactions page (see an example). At the top of the page, the Interactions Overview shows at a glance how many interactions have been curated and whether they are physical or genetic. This video explains the details of the Interactions Overview diagram:

Farther down on the Interactions page, the Interaction Network is a visual representation of genetic interactions for a particular gene and the protein-protein interactions for its gene product. The network is interactive, allowing you to choose to view either genetic or physical interactions or both. Using the slider, you can set a minimum number of experiments supporting the interactions displayed. Learn how to use the interactive features of the Interaction Network by watching this brief video:

Categories: Tutorial

Tags: protein-protein interactions, genetic interactions, BioGRID

If it Swims Like a Duck…

May 06, 2015


It may swim like a duck, but this beast is obviously not a duck. Just like the glycine patch of Pxr1 looks like an interaction region when it isn’t. Image by Yotujonoo via Creative Commons

Back in the 1980’s some U.S. politicians were proposing to raise money by something they called “revenue enhancements”. Richard Darman, the budget director at the time, correctly pointed out that a revenue enhancement really is just a tax increase by another name. 

To make his point, he used the expression, “If it looks like a duck and quacks like a duck, it’s a duck.” In other words, just because politicians call it something else, if a revenue enhancement does everything a tax increase does then it really is just a tax increase.

This same reasoning is often used in biology. If two regions of a protein look the same (are homologous) and the proteins do similar things, then the two similar regions do the same thing. Except, of course, when they don’t.

This probably isn’t what Conan O’Brien had in mind when he changed the famous expression a bit to say, “If it looks like a duck and quacks like a duck, it’s a little person dressed as a duck,” but as is often the case with Team Coco, he was right in both biology and life. Not everything that looks and quacks like a duck is a duck, and not every homologous region in proteins that do similar things does the same thing.

Conan’s point is borne out in a new study out in GENETICS where Banerjee and coworkers show that even though the yeast Prp43 RNA helicase shares glycine patches with three of the proteins with which it interacts, this doesn’t mean the glycine patches are used the same way in each case. They may all look and act like ducks, but they are not all ducks! 

Glycine patches are short, glycine-rich protein motifs that are thought to help proteins recognize other proteins or RNAs. Two of the proteins that the researchers looked at, Spp382 and Sqs1, have glycine patches that are only subtly different from that of Prp43. In both of these, the glycine patch is important for interacting with Prp43, but that isn’t its only role. The patches really are ducks in this case, just different kinds of ducks—maybe a mallard and a mandarin duck.

In the case of the third protein, Pxr1, the glycine patch seems to have a completely different (albeit important) role. In this case, it really is a little person in a duck costume!

Prp43 is involved in two different kinds of RNA processing in the yeast cell—pre-mRNA splicing and rRNA maturation. It is one of the few proteins shared between the two complexes involved in each process.

Previous work had shown that different factors in each complex are important for bringing Prp43 to each party. For rRNA maturation, Sqs1 and Pxr1 are the critical players, while for pre-mRNA splicing, Spp382 is key. Since all four proteins share little else beyond a shared weakly conserved, 45-50 amino acid glycine-rich patch, one idea was that all of these proteins use the patch to interact with one another. As is true of much in life, the real answer is a bit more complicated than that.

The first set of experiments was to determine how well Prp43 interacts with each of the other glycine patches, using yeast two-hybrid assays. With full length proteins, the authors found that Spp382 interacted most strongly with Prp43, Pxr1 was the weakest, and Sqs1 was intermediate. They got a similar order of interaction when using just the glycine patches of each of these three proteins, with one small difference: the Pxr1 glycine patch did no better than the empty vector control.

This last result suggested that the glycine patch of Pxr1 was insufficient on its own to interact with Prp43. This was confirmed when they found no difference in the interaction of full length Pxr1 and Pxr1 deleted for the glycine patch.

The Pxr1 glycine patch apparently plays no role in interacting with Prp43—it really isn’t a duck at all. But that doesn’t mean it is dispensable! They showed later that it is critical for snoRNA processing, an important step needed for rRNA maturation.

Mandarins and mallards look like ducks and quack like ducks…and they are ducks. Like these ducks, the glycine patches of Spp82 and Sqs1 look and act like interaction regions, and in fact they are interaction regions. Image via Wikimedia Commons

Of course, sometimes if it looks and quacks like a duck, it is indeed a duck. This was the case for Sqs1 and Spp382.

As shown by two-hybrid and glycine patch swap assays, each of these glycine patches do seem to be important for interacting with Prp43. But each patch was more than just a way for two proteins to hook up.

To show this, Banerjee and coworkers looked for chimeras of Spp382, Pxr1, and Sqs1 that could rescue the lethal phenotype of a Spp382 deletion. First off, they showed that deleting the glycine patch from Spp382 was equivalent to deleting the whole protein—it was a lethal event. And as expected, replacing the Spp382 glycine patch with the one from Pxr1 was still lethal. But the Sqs1 glycine patch was able to rescue the deletion strain although it grew more slowly. So the Spp382 and Sqs1 glycine patches could to some extent substitute for one another.

One way to interpret the difference in growth rates is that it has to do with the fact that the glycine patch of Spp382 bound more strongly to Prp43 than did the one from Sqs1. The glycine patch from Sqs1 can’t fully rescue the Spp382 deletion strain because it is a weaker binder. But a set of mutagenesis experiments suggests that this is not the case.

The authors basically took the Spp382/Pxr1 chimera in which the Pxr1 glycine patch replaced the one from Spp382 and made a series of point mutations that slowly converted the glycine patch back to the one from Spp382. What they found was that the strength of interaction in the two-hybrid assay does not correlate with the level of rescue in the complementation assay. One interpretation is that the Spp382 glycine patch is doing more than recruiting Prp43.

Taken together, these results are a bit of a biological cautionary tale. Just because a protein region looks like another one, do not assume they are doing the same thing. Sometimes what looks and acts like a duck is just a man dressed as a duck.

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

Categories: Research Spotlight

Tags: glycine patch, Saccharomyces cerevisiae, protein-protein interactions

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