New & Noteworthy

Another Small Victory for Lamarck

July 29, 2015

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Examples of various ways that the environment affects gene expression have become so commonplace that new examples don’t make much of a splash anymore. It is as if Lamarck and Darwin had never argued about how natural selection works.

The main reason we aren’t surprised anymore is that we have a pretty good handle on how most of these changes are happening. Something in our environment causes chemical groups to be added or removed from our DNA and/or its associated proteins, causing a change in gene expression. These kinds of epigenetic changes happen a lot and are now seen as the norm.

What doesn’t happen much at all is that the underlying DNA gets changed in a predictable way to change gene expression in response to something in the environment. Which is why a recent study in PNAS by Jack and coworkers makes you stand up and take notice.

In this study the researchers provide evidence that suggests that yeast will expand the number of copies of its rDNA locus to match the level of nutrients in the environment (presumably to make more ribosomes to take advantage of all those nutrients). The yeast is responding to the environment by changing the content of its genome rather than just changing how it is used.

This is big. It is almost as if Lamarck was right about some part of natural selection. Oh wait, that’s exactly what it is! 

What makes this so cool is that it suggests that natural selection doesn’t necessarily just happen when a random genetic variant wins out in a population. Sometimes the environment itself can induce the winning genome change–and these aren’t just epigenetic changes. (Go Lamarck!)

Jack and coworkers focused on the rDNA locus of the yeast Saccharomyces cerevisiae. This is a fairly fluid part of the yeast genome that consists of multiple copies of the 35S and 5S pre-rRNA genes. The average yeast cell has around 180 copies of this locus and there is a normal range of 150-200 per cell. If a yeast somehow ends up with 80 or fewer copies, it quickly increases the number back to that golden 150-200 range via a Fob1 dependent mechanism.

The authors created a strain of yeast that lacked Fob1 and had only 35 tandem repeats in its rDNA region. This strain, rDNA₃₅, could not expand its rDNA unless Fob1 was added back. They now had a strain in which they could test what affected rDNA expansion, by transforming the strain with a plasmid expressing Fob1 and growing the transformants under different conditions.

The most surprising experiment was the final one of the paper. The authors grew the rDNA₃₅ strain in either 2% or 0.5% glucose and found that rDNA amplification was slowed significantly in low glucose. The authors interpret this to mean that the genome change, the expansion of rDNA, is dependent on nutrient availability. A signaling pathway is able to adjust the rate of rDNA expansion.

Yeast will, of course, grow more slowly at low levels of glucose than they will at higher levels. But the authors were able to show that slow growth was not the reason for the slowed expansion of rDNA at low glucose. They were able to separate the two effects by overexpressing Pnc1, a nicotinamidase.

Overexpression of Pnc1 led to a decreased rate of copy number increase even at the higher glucose levels without affecting growth rate. So rDNA expansion can be separated from slow growth under the right conditions. And as you’ll see below, Pnc1 makes perfect sense given how at least part of nutrient level-dependent rDNA amplification works.

In looking for factors that might affect the rate of rDNA expansion, Jack and coworkers focused on the TOR signaling pathway, since previous work had suggested that it might be important in this process and it is known to respond to nutrient availability. The authors confirmed it was a key player by showing that rapamycin, a TOR inhibitor, kept the rDNA₃₅ strain from expanding its rDNA in the presence of FOB1.

Again they ran into the problem of disentangling cell growth and the rDNA expansion, as rapamycin slows cell growth. The next set of experiments showed that the lack of expansion was almost certainly not due to the slower growth rate.

It is known that rapamycin affects histone deacetylases (HDACs) including Sir2. Jack and coworkers found that nicotinamide, a Sir2 inhibitor, increased the rate of expansion of rDNA without affecting growth rate. So rDNA amplification was not dependent on growth rate.

Which brings us back to Pnc1, that enzyme that cleaves nicotinamide! Presumably endogenous levels of nicotinamide are able to inhibit Sir2 and so encourage the rDNA expansion. Overexpressing Pnc1 releases Sir2 which can then impede the expansion of rDNA.

While that was a bit complicated, the idea is simple and potentially profound. Yeast can sense the level of nutrients in their environment at least partially through the TOR signaling pathway and adjust the actual content of their genome accordingly.

The involvement of nicotinamide in this regulatory process makes this result even cooler, as it has important roles in aging and cellular metabolism from yeast to man. For example, it plays a key role in the life extending properties of caloric restriction in yeast and possibly in more complicated eukaryotes as well. (Click here for a fascinating look at NAD, a compound that contains nicotinamide.)

So, in the presence of low nutrient levels, yeast expand their rDNA much more slowly than they would at higher nutrient levels. Yeast can tailor its genome in response to its environment so it can better utilize that environment.

This work raises the fascinating possibility that this process might even happen at genomic regions other than the rDNA locus. Yeast still has plenty of surprises in store—including giving a Lamarck a little boost.

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

SGD Help Videos: Working with Lists in YeastMine

July 28, 2015

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Understanding lists and knowing how to work with them is crucial to getting the most out of YeastMine. This set of short videos explains everything you need to know.

YeastMine allows you to save objects in lists. Typically, these objects are genes, but you can also make lists of other objects such as Gene Ontology terms or PubMed IDs. One way to create a list in YeastMine is to run a query and save the results in a list. Another way is to type in or upload your own list.

Whenever you create a list in YeastMine, you’re immediately presented with information about the genes in the list, such as Gene Ontology and pathway enrichment, interactions, orthologs, and more. This can help you decide what kind of further analysis you’d like to do. 

And what if you create a list but then realize that you forgot to include a gene? No worries. It’s easy to edit your saved lists.

Once you have a list of genes, you can feed it into any template query whose name begins with “Gene” to get results for all of the genes in the list. This powerful feature lets you run successive queries to narrow down your results. For example, you could make a list of all the proteins in a given size range, then query that list to see which ones are located in the nucleus, and finally ask how many of these nuclear proteins have human homologs.

And finally, once you’ve created and saved lists you can do a lot of different things with them: combine them, find their intersection, find genes that are not shared between two lists, or find genes that are in one list but not another. This provides a powerful way to combine or compare results from different YeastMine queries.

As always, please contact us if you have any questions about YeastMine. We’re happy to help!

Saving Search Results as a List

Creating and Using Gene Lists

Adding Objects to a Saved List

Feeding Lists into Templates

List Operations

Two Tales of Two Tails

July 22, 2015

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Tails let animals sense and interact with their environment at a distance from their bodies. It turns out that some proteins use their “tails” in a similar way. Except they take it one step further.

In addition to sensing the environment, they can also use their tails as sort of fishing poles to catch proteins they need to interact with. And they do this with great specificity…it is like having that perfect lure that always catches one type of fish.

A great example of this is the septin family of proteins which includes many members that are “tailed” proteins. Septins are highly conserved proteins that typically have a globular GTP-binding domain adjacent to an elongated C-terminal extension.

Septins form structures that act as the boundaries between different cellular parts. In budding yeast cells, they form the septum that separates the mother and bud, and recruit the cytokinesis machinery that allows the daughter cell to separate from the mother cell. In larger animals, they can be found in places such as the dendritic spines of neurons, sperm flagella, or cilia. And in humans, septin mutations have been linked to cancer and neurological diseases.

Until now, the details of how septins recruit other proteins to boundary sites have been elusive. But in two new papers in GENETICS, Finnigan and coworkers in the Thorner lab at Berkeley dove into this question and gained real insight into the lures these proteins use.

In their first paper they reported an extremely comprehensive genetic analysis to dissect the functions of two of the least characterized septins, Shs1 and Cdc11. In the second paper they used both genetic and physical methods to show how these septins recruit myosin to the septum to form the contractile ring that pinches off the bud from the mother.

The bottom line: their C-terminal tails are extremely important. They intertwine with other proteins’ tails like love-struck seahorses. And their specificity comes from these same tails—certain tails only coil around other tails.  

The S. cerevisiae genome encodes a family of septins that assemble with each other to form octameric rods that consist of four different septins. The rods have both end-to-end and side-to-side interactions with each other, forming a ladder-like superstructure.

The septins Cdc11 and Shs1 are the most closely related members of the septin family, and the most recently evolved. They cap the ends of the septin rods. In otherwise wild-type cells, Cdc11 is essential for life while Shs1 is not.

Because SHS1 can be deleted without causing a major phenotype, the first step in investigating its function was to find genetic conditions under which its function becomes more obvious. The authors created four different genetic backgrounds in which the function of other septins was compromised by different mutations. Cells that had mutations in both SHS1 and in other septin genes had obvious problems, such as elongated buds or the inability to grow at high temperatures.

Now Finnigan and colleagues were set to do a detailed genetic analysis to figure out what different parts of Shs1 do by testing mutant versions in these different backgrounds. We can’t possibly recapitulate all the results here, but we’ll do our best to cover the highlights.

Almost all septins, whether in yeast or mammals, end with a tail: a long stretch called the C-terminal extension (CTE) that contains sequence patterns characteristic of a coiled-coil structure. The researchers found that the coiled coil regions of Shs1 and Cdc11were essential to their functions. (And no, they didn’t create any mutations by writing their names in the coiled coil sequence!)

Finnigan and colleagues tried swapping CTEs between different septins. When Cdc11 carried the Shs1 CTE and vice versa, the cells grew just fine. However, this swappability didn’t extend to other septins that are positioned internally in the septin rods. The CTEs of the end subunits Cdc11 and Shs1 could be exchanged for each other, but these CTEs only worked when they were on the ends of the rods.

Since coiled coils are often involved in interactions between proteins, Finnigan and colleagues wondered whether the essential function of the Cdc11 and Shs1 CTEs might be to recruit other proteins to the bud neck.

To test this, they searched published data to identify proteins that are well-known to be localized to the bud neck at the time in the cell cycle when septins are present. They found 30 such proteins, and overexpressed GFP-tagged versions of each in a strain where both Cdc11 and Shs1 lacked their CTEs.

Of the 30 proteins, only overexpressed Bni5 suppressed the growth defect of this strain. To test directly whether binding to Bni5 is a critical function of Shs1, Finnigan and colleagues fused the two genes to each other, so that Bni5 replaced the CTE of Shs1. This fusion protein could compensate for the lack of both Cdc11 and Shs1 CTEs.

To confirm that the important function of the CTEs is to hold Bni5 in the right place, they came up with an alternative test using a “nanobody”, which is a very small, very high-affinity single-chain antibody. They replaced the CTE of either Cdc11 or Shs1 with a nanobody that recognized GFP, and expressed a GFP-Bni5 fusion in these strains. In both cases, tethering Bni5 to the septin via the nanobody obviated the need for the CTE.

Finally, the authors asked why it is important for Bni5 to be located on the septin rods. Previous work had suggested that Bni5 recruits Myo1 (myosin), an important component of the contractile ring at the bud neck. They used the same nanobody constructs to test this, simply expressing GFP-Myo1 in the strains where the nanobody replaced the CTEs of Cdc11 or Shs1. Sure enough, tethering Myo1 to the terminal septins eliminated the need for Bni5.

So we now know that tails are absolutely essential for the functions of the alternative terminal septins Shs1 and Cdc11. These fishing poles let them hold on to the Bni5 “bait,” which in turn catches Myo1 to provide the muscle for cytokinesis to occur. Since septins are so highly conserved, it’s probable that these results will be directly applicable to higher organisms: there are mammalian septins that also occupy the end positions of septin rods, analogous to Cdc11 and Shs1. And that’s no fish story!

Not only septins use their tails to fish.

by Maria Costanzo, Ph.D., Senior Biocuration Scientist, SGD

SGD Help Video: Gene Name Reservation

July 13, 2015

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The eminent Drosophila geneticist Michael Ashburner famously said: “Biologists would rather share their toothbrush than share a gene name.” It’s true that assigning names to genes is often a sticky subject.

In the Saccharomyces cerevisiae community we’re very lucky to have well-defined guidelines for genetic nomenclature, an established system for reserving gene names, and criteria for making them “standard,” or official, names. This system was agreed upon by yeast researchers nearly two decades ago and has served the community well.

Take a look at this video to get an overview of how the gene naming system works. And as always, please contact us with any questions or suggestions.