New & Noteworthy

Runaway Polymerases Can Wreak Havoc in Cells

October 16, 2014

A train without working brakes can cause a lot of destruction if it careens off the tracks. And it turns out that a runaway RNA polymerase II (pol II) can cause a lot of damage too.  But it doesn’t cause destruction, so much as disease.

Working brakes are important for both large and small machines, including RNA polymerase. Image from Wikimedia Commons

Unlike a train, which has its brakes built right in, pol II has to count on outside factors to stop it in its tracks. And one of these brakes in both humans and yeast is a helicase: Sen1 in yeast and Senataxin, the product of the SETX gene, in humans. 

Mutations in SETX are associated with two devastating neurological diseases: amyotrophic lateral sclerosis type 4 (ALS4) and ataxia oculomotor apraxia type 2 (AOA2), both of which strike children and adolescents.  One idea is that these mutations may short circuit the brakes on pol II, causing it to keep on transcribing after it shouldn’t. And this is just what Chen and colleagues found in a new paper in GENETICS.

The researchers used the simple yet informative yeast model system to look at some of these mutations, and found that they disrupted the helicase function of Sen1 and caused abnormal read-through of some transcriptional terminators.  Looks like bad brakes may indeed have a role in causing these devastating diseases.

Some human proteins can function perfectly well in yeast. Unfortunately, Senataxin isn’t one of those; it could not rescue a sen1 null mutant yeast, so Chen and coworkers couldn’t study Senataxin function directly in yeast. But because Senataxin and Sen1 share significant homology,  they could instead study the yeast protein and make inferences about Senataxin from it.

First, they sliced and diced the SEN1 gene to see which regions were essential to its function. They found that the most important part, needed to keep yeast cells alive, was the helicase domain. But this wasn’t the only key region.

Some flanking residues on either side were also important, but either the N-terminal flanking region or the C-terminal flanking region was sufficient. Looking into those flanking regions more closely, the researchers found that each contained a nuclear localization sequence (NLS) that directed Sen1 into the nucleus. This makes perfect sense of course…the brakes need to go where the train is!  If we don’t put the brakes on the train, it won’t matter how well they work, the train still won’t stop.

These flanking sequences appeared to do more than direct the protein to the nuclear pol II, though.  When the authors tried to use an NLS derived from the SV40 virus instead, they found that it couldn’t completely replace the function of these flanking regions even though it did efficiently direct Sen1 to the nucleus.

Next the researchers set out to study the disease mutations found in patients affected with the neurological disease AOA2.  They re-created the equivalents of 13 AOA2-associated SETX mutations, all within the helicase domain, at the homologous codons of yeast SEN1.

Six of the 13 mutations completely destroyed the function of Sen1; yeast cells could not survive when carrying only the mutant gene. When these mutant proteins were expressed from a plasmid in otherwise wild-type cells, five of them had a dominant negative effect, interfering with transcription termination at a reporter gene. This lends support to the idea that Sen1 is important for transcription termination and that the disease mutations affected this function.

The remaining 7 of the 13 mutant genes could support life as the only copy of SEN1 in yeast. However, 5 of the mutant strains displayed heat-sensitive growth, and 4 of these showed increased transcriptional readthrough.

Taken together, these results show that the helicase domains of Senataxin and Sen1 are extremely important for their function. They also show that Sen1 can be used as a model to discover the effects of individual disease mutations in SETX, as long as those mutations are within regions that are homologous between the two proteins.

It still isn’t clear exactly how helicase activity can put the brakes on that RNA polymerase train, nor why runaway RNA polymerase can have such specific effects on the human nervous system. These questions need more investigation, and the yeast model system is now in place to help with that.

So, although it might not be obvious to the lay person (or politician) that brainless yeast cells could tell us anything about neurological diseases, in fact they can. Yeast may not have brains, but they definitely have RNA polymerase. And once we learn how the brakes work for pol II in yeast cells, we may have a clue how to repair them in humans.

by Maria Costanzo, Ph.D., Senior Biocurator, SGD

Categories: Research Spotlight, Yeast and Human Disease

Tags: transcription, RNA polymerase II, helicase, ALS, Saccharomyces cerevisiae

Using Yeast to Discover Treatments for ALS

November 01, 2012

What do Lou Gehrig, Stephen Hawking, David Niven and Mao Zedong have in common?  They all suffered (or in Hawking’s case, continue to suffer) terribly from a disease called amyotrophic lateral sclerosis or ALS.  And now the humble yeast S. cerevisiae may help scientists find new treatments so that others do not need to suffer similarly.

Patients with ALS gradually lose use of their motor neurons and generally die within 3-5 years of diagnosis.  While there are some rare forms that run in families, most are sporadic.  There is no history of the disease in the family and then suddenly, it just appears.

cowboy with lariat

Lariats can also rustle up some TDP-43!
(Image: Rodeo Star sculpture by Clay Hoffman, clayhoffman@frontier.com)

The causes of ALS have remained a mystery for many years but recent work has suggested that RNA binding proteins and RNA processing pathways are somehow involved.  In particular, an RNA-binding protein called TDP-43 appears to be a key player.  Mutations in its gene are associated with ALS, and aggregates of the protein are found in damaged neurons of ALS patients. Unfortunately, since this protein is needed for cell survival it is not an easy target for therapies.  This is where yeast can help.

Scientists have managed to mimic the effects of TDP-43 in yeast.  When this protein is overexpressed, the yeast cells die just like the motor cell neurons do. In a recent Nature Genetics paper, Armakola and coworkers use this model system for finding better therapeutic targets.  And it looks like they may have succeeded.

These authors used two different screens to systematically look for proteins that when deleted or expressed at lower levels rescued yeast overexpressing TDP-43.  They found plenty.  One screen yielded eight suppressors while the other yielded 2,056 potential suppressors.  They decided to focus on one of the stronger suppressors, DBR1.

The first thing they wanted to do was to make sure this wasn’t a yeast specific effect.  If lowering the amount of DBR1 has no effect in mammalian models, it is obviously not worth pursuing!

To answer this question, they created a mammalian neuroblastoma cell line with an inducible system for making a mutant version of TDP-43, TDP-43 Gln331Lys, found commonly in ALS patients.  As expected, these cells quickly died in the presence of inducer.  They could be rescued, though, when DBR1 activity was inhibited with siRNA.  The authors confirmed that decreasing the activity of DBR1 in primary neurons decreased TDP-43 toxicity as well.

So decreasing the amount of DBR1 appears to rescue cells that die from the effects of mutant TDP-43.  This suggests that targeting DBR1 may be useful as a therapy for ALS.  But this study doesn’t stop there.  It also tells us a bit about how lowering DBR1 levels might be rescuing the cells.

DBR1 is an RNA processing enzyme involved in cleaning up the mess left behind by splicing.  It cleaves the 2’-5’ phosphodiester bond of the spliced-out intron (called a lariat).  Previous studies in yeast have shown that when Dbr1p levels are reduced or its catalytic activity is disrupted by a mutation, there is a build up of these lariats. This study showed directly that the accumulated lariats interact with TDP-43 in the cytoplasm to suppress its toxicity. So in ALS, the accumulated lariats may serve as a decoy for the mutant TDP-43 protein, preventing it from binding to and interfering with more essential RNAs.

This last result may also suggest another potential therapy.  If scientists can find other ways to increase the amount of decoy RNA, then they may not need to depend on reducing levels of DBR1.  There may be many possible approaches to soaking up rogue TDP-43.

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

Categories: Research Spotlight, Yeast and Human Disease

Tags: RNA binding, Lou Gehrig's Disease, DBR1, yeast model for human disease, Saccharomyces cerevisiae, ALS

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