New & Noteworthy

How to Make A Safe and Fun Mitochondrion

January 13, 2015

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Influencing mitochondrial import to treat disease:

Bounce houses are a great way for kids to burn off their excess energy. They can bounce off the floor and walls and scream to their hearts’ content.

Of course, adults need to keep an eye on how many kids are in the house at any one time, to keep things safe. And if one child starts to push and kick the others, it might be easier to restore calm if the adults are careful about how many kids, and which ones, they allow inside.

The yeast mitochondrion is actually a lot like a bounce house. It’s full of energy, and it has multiple gatekeepers—protein complexes in the mitochondrial membrane that imported proteins must pass through on their way in.

And, just like a bounce house, things can go very wrong inside the mitochondrion if its proteins don’t behave properly. The end result isn’t just an upset child with a black eye, either. Genetic diseases that affect mitochondrial function are among the most severe and the hardest to treat.

Now, described in a new paper in Nature Communications, Aiyar and colleagues have used a yeast model of human mitochondrial disease to discover both a drug and a genetic means to regulate a mitochondrial import complex. Surprisingly, tweaking mitochondrial import slightly by either of these methods mitigated the disease symptoms in both yeast and human cells.  They found a gatekeeper who can make sure there is the right number of kids in the bounce house and that they’re all behaving properly (at least, as well as they can!).

The researchers were interested in mitochondrial disorders that affected ATP synthase. This huge molecular machine in the mitochondrial inner membrane is responsible for generating most of the cell’s energy, so if it doesn’t work properly it can be a disaster for both yeast and human cells.

Aiyar and coworkers used a genetic trick to create a yeast model that had lower amounts of functional ATP synthase. This mimics many mitochondrial disorders.

They were able to reduce the amount of functional ATP synthase by using an fmc1 null mutant. Fmc1p is involved in assembly of the complex, so the fmc1 null mutant has lower amounts of functional ATP synthase and a reduced respiration rate.

First, they looked for a drug that would mitigate the effects of the fmc1 mutation. They tested the drugs in a collection that had already been FDA approved—a drug repurposing library—to see if any would improve the mutant’s respiratory growth.

The one candidate drug that emerged from the screen was sodium pyrithione (NaPT), which is used as an antiseptic. Not only did it improve the respiration of the yeast fmc1 mutant, it also improved the respiratory growth of a human cell line carrying the atp6-T8993G mutation found in patients with neuropathy, ataxia and retinitis pigmentosa (NARP, one type of ATP synthase disorder).

Aiyar and colleagues wondered exactly what was being affected by the NaPT. To figure this out, they used the S. cerevisiae genome-wide heterozygous deletion mutant collection. This is a set of diploid strains, each heterozygous for a null mutation of a different gene, that has been an incredibly useful resource for all kinds of studies in yeast.

They tested the effect of NaPT on each of the mutant strains and found that strains with mutations in the TIM17 and TIM23 genes were among the most sensitive. And, when they checked the data from previous chemogenomic screens, they saw that these two mutants were much more sensitive to NaPT than to any other drug, showing that the effect was specific.

TIM17 and TIM23 are both subunits of the Tim23 complex in the mitochondrial inner membrane that acts as a gate for many of the proteins that end up in mitochondria. The researchers found that NaPT specifically inhibited the function of this mitochondrial gatekeeper complex in an in vitro mitochondrial import assay, confirming its selectivity.

So, Aiyar and coworkers had found a drug that alleviates the effects of an ATP synthase disorder by modulating the function of a mitochondrial gatekeeper. This in itself was a huge advance: the discovery that a potentially useful, already-approved drug has a specific effect on this disease phenotype.

However, the scientists took things a step further by looking to see whether a genetic therapy could accomplish the same thing as the drug.  It was already known that overexpressing Tim21p, a regulatory subunit of the Tim23 complex, could modulate the function of the complex similarly to the effects they had seen for NaPT.

So the researchers tested whether overexpressing Tim21p would improve respiratory growth of the fmc1 mutant. Sure enough, it did. Consistent with this, assembly of the respiratory enzyme complexes of the mitochondrial inner membrane was more efficient when Tim21p was overexpressed.

Most importantly, overexpression of Tim21p in the fmc1 mutant cells caused their total ATP synthesis to more than double.  And even more exciting was the discovery that overexpressing TIMM21, the human ortholog of TIM21, in the NARP disease human cell line improved survival of those cells.

So, just like a parent deciding how many kids should be in a bounce house so that everyone has a good time, the Tim23 complex can be made to “decide” which proteins, or perhaps how many proteins, get into mitochondria, with the end result that ATP synthesis happens as efficiently as possible. The exact mechanism of this effect is still unclear, but it is clear that modulating import in this way can improve mitochondrial health even when disease mutant proteins are present.

The next step will be to translate this discovery into therapies that will help mitochondrial disease patients. People with various mitochondrial disorders may finally be able to turn their mitochondria into safe, fun places.

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

Categories: Research Spotlight, Yeast and Human Disease

Tags: ATP synthase, mitochondria, respiration, Saccharomyces cerevisiae, yeast model for human disease

Yeast Genetics Makes Awesome Sauce

January 08, 2015

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What’s for dinner tonight? For many of us the answer will be “pasta with tomato sauce”, even if we don’t have Italian roots.

But as you know, there isn’t any single recipe for homemade tomato sauce. Onions and garlic, or just garlic? Pork, beef, or no meat at all? How many bay leaves go in the pot? Every cook will use a slightly different combination of ingredients, but all will end up with tomato sauce.

When it comes to combining different allele variants to survive a lethal challenge, yeast is a lot like those cooks. In a new paper in GENETICS, Sirr and colleagues used divergent yeast strains to generate a wide range of allelic backgrounds and found that there is more than one way to survive a deadly mutation in the GAL7 gene.  Just as there is more than one way to make a delicious tomato sauce…

This isn’t just an academic exercise either.  GAL7 is the ortholog of the human GALT gene, which when mutated leads to the disease galactosemia. And just like in yeast, people with different genetic backgrounds may do better or worse when both copies of their GALT gene are mutated.  

GAL7 and GALT encode an enzyme, galactose-1-phosphate uridyl transferase, that breaks down the sugar galactose. If people with this mutation eat galactose, the toxic compound galactose-1-phosphate accumulates; this can cause serious symptoms or even death. The same is often true for yeast with a mutated GAL7 gene.

Ideally we would want to be able to predict how severe the symptoms of galactosemia would be, based on a patient’s genetic background. So far, though, it’s been a challenge to identify comprehensively the whole set of genes that affect a given human phenotype. Which is why Sirr and colleagues turned to our friend S. cerevisiae to study alleles affecting the highly conserved galactose utilization pathway.

The researchers started with two very divergent yeast strains, one isolated from a canyon in Israel and the other from an oak tree in Pennsylvania. Both were able to utilize galactose normally, but the scientists made them “galactosemic” by knocking out the GAL7 gene in each.

After mating the strains to create a galactosemic diploid, the researchers needed to let the strain sporulate and isolate haploid progeny. But its sporulation efficiency wasn’t very good, only about 20%. And they needed to have millions of progeny to get a comprehensive look at genetic backgrounds.

To isolate a virtually pure population of haploid progeny, Sirr and coworkers came up with a neat trick. They added a green fluorescent protein gene to the strain and put it under control of a sporulation-specific promoter.

Cells that were undergoing sporulation would fluoresce and could be separated from the others by fluorescence-activated cell sorting (FACS). The FACS technique also allowed sorting by size, so they could select complete tetrads containing four haploid spores and discard incomplete products of meiosis such as dyads containing only two spores.

After using this step to isolate tetrads, the researchers broke them open to free the spores and put them on Petri dishes containing galactose—an amount that was enough to kill either of the parent strains. One in a thousand spores was able to survive the galactose toxicity. Recombination between the divergent alleles from the two parent strains somehow came up with the right combination of alleles for a survival sauce.

Sirr and colleagues individually genotyped 247 of the surviving progeny, using partial genome sequencing. They mapped QTLs (quantitative trait loci) to identify genomic regions associated with survival. If they found a particular allele in the survivors more often than would be expected by chance, that was a clue that a gene in that region had a role in survival.

We don’t have the space here to do justice to the details of the results, but we can summarize by saying that a whole variety of factors contributed to the galactose tolerance of the surviving progeny. They had three major QTLs, regions where multiple alleles were over- or under-represented. The QTLs were centered on genes involved in sugar metabolism: GAL3 and GAL80, both involved in transcriptional regulation of galactose utilization genes, and three hexose transporter genes (HXT3, HXT6, and HXT7) that are located very close to each other.

It makes sense that all of these genes could affect galactosemia. Gal3p and Gal80p are regulators of the pathway, so alleles of these genes that make galactose catabolism less active would result in less production of toxic intermediates. And although the hexose transporters don’t transport galactose as their preferred substrates, they may induce the pathway by allowing a little galactose into the cell. So less active alleles of these transporters would also result in less galactose catabolism.

Another event that occurred in over half of the surviving progeny was aneuploidy (altered chromosome number), most often an extra copy of chromosome XIII where the GAL80 gene is located. The same three QTL peaks were also seen in the disomic strains, though, leading the authors to conclude that the extra chromosome alone was not sufficient for survival of galactosemia.

And finally, some rare non-genetic events contributed to survival of the progeny. The authors discovered this when they found that the galactose tolerance of some of the progeny wasn’t stably inherited. This could result from differences in protein levels between individual cells. For example, if one cell happened to have lower levels of a galactose transporter than other cells, it might be more resistant to galactose.

The take-home message here is that there are many different ways to get to the same phenotype. The new method that they developed allowed the researchers to see rare combinations of alleles in large numbers of individual progeny, in contrast to other genotyping methods where progeny are pooled and only the average can be detected.

For any disease or trait the ultimate goal is to identify all the alleles of all the genes that influence it. Imagine the impact on human health, if we could look at a person’s genotype and accurately predict their phenotype!

So far, it’s been a challenge to identify these large sets of human genes in a comprehensive way. But this approach using yeast could provide a feast of data to help us understand monogenic diseases like galactosemia, cystic fibrosis, porphyria, and many more, and maybe even more complex traits and diseases. Now that’s an appetizing prospect for human disease researchers. Buon appetito!

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

Categories: Research Spotlight, Yeast and Human Disease

Tags: galactosemia, Saccharomyces cerevisiae, yeast model for human disease

Mother Yeast Keeps Daughters Tidy

December 18, 2014

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Yeast need translation and organelle tethering to sequester misfolded proteins away from the cytoplasm:

Sometimes parents feel like they’re constantly nagging their kids to clean things up. Eventually, some parents just give in and do it themselves. It turns out that yeast cells aren’t all that different.

And it is even more important for cells to clean up their cellular trash than it is for that sullen teenager. If trash like misfolded or damaged proteins is not sequestered from the rest of the cytoplasm, it can cause other proteins to change their conformation or interfere with metabolic processes. This is obviously much worse than having a smelly room!

One way that cells bin their trash is by compacting it into globs, or aggregates. While this works in the short run, as cells age these aggregates build up, and in human cells, they’re hallmarks of diseases like ALS and Alzheimer’s.

In a new study published in Cell, Zhou and colleagues looked at the process of protein aggregation in S. cerevisiae. A number of other studies had already suggested that just like human parents, mother yeast cells clean up trash for their daughters. The researchers confirmed this and also made a couple of very surprising findings.

Zhou and coworkers discovered that although aggregates are mostly composed of previously translated proteins, they don’t form without new translation. And they found that aggregates aren’t littered around the cytoplasm, but instead are collected in very specific trash bins located on the surface of cellular organelles.

To do these studies, the scientists assembled a toolkit of ways to induce and visualize protein aggregation.  They used stresses like heat shock or various chemicals to stimulate aggregate formation.

They visualized the aggregates by using GFP-labeled Hsp104p, which binds to them specifically. They also had some thermally unstable reporter proteins fused to different colored fluorescent markers that helped them track aggregation. And they created time-lapse videos to watch the whole process.

They first looked in detail at aggregate formation, creating two different kinds of cellular trash (aggregates of distinct sets of marker proteins) at different times to ask whether they would all end up in the same aggregates or in separate ones. These experiments showed that in general, newly aggregated proteins will join existing aggregates rather than creating new ones. And intriguingly, these results also hinted that new translation was needed to start the aggregation process.

Zhou and coworkers tested this directly by adding cycloheximide, an inhibitor of translation, to their aggregation experiments. Sure enough, cycloheximide prevented all of the treatments from causing aggregation, and other treatments and conditions that blocked translation did the same thing.

So just as the threat of taking away the car keys may get that sullen teenager off the couch to start cleaning up, newly synthesized polypeptides are the inducer for the cellular clean-up. Without them, all the trash just stays littered around the cell.

The researchers guessed that if aggregation starts at sites where translation is occurring, it might be concentrated at the surface of the endoplasmic reticulum (ER), where a large proportion of ribosomes are bound. They used several different sophisticated microscopy techniques to confirm that most aggregates were in fact associated with the ER.

But they also got a surprise: in addition to the ER, many aggregates were associated with the mitochondrial surface and some even formed directly on it.* The authors also observed aggregates that formed at the ER but migrated along it to ER-mitochondrial contact points and eventually to mitochondria. So, cells don’t litter their trash just anywhere; they start specific collection points on the surfaces of organelles. And much of the trash seems to end up attached to mitochondria.

The researchers noticed something else when they looked at aggregates in cells that were dividing. When a bud forms, mitochondria are actively transported into it. However, the aggregates that were on mitochondria didn’t go into buds. They stayed on mitochondria that remained in the mother cell. Mom protects her daughter from any trash that mom created!

To figure out what controls this asymmetric segregation, Zhou and colleagues tested a panel of 72 mutant strains, each with a deletion in a mitochondrial outer membrane protein. One strain, the fis1 null mutant, was markedly defective: aggregates often went into the bud. Fis1p is known to be involved in mitochondrial fission, but this result suggests it may have an entirely separate role in making sure that trash-bearing mitochondria stay in the mother cell.

And finally, the authors saw that as mother cells got older, they got less and less able to keep aggregates out of their daughters’ cytoplasm. Towards the end of the mothers’ lives, aggregates were distributed more or less randomly between mother and daughter.

Trash build up is a big problem in teenagers’ rooms and in cells. Just like mom, the cell packs the trash away into bins where it will do less harm. Unfortunately, as the cell (and mom) get older, this gets harder and harder to do. In both cases, the daughter is saddled with more and more trash as mom struggles to keep up. And this is bad for the daughter as well as for the mom.

So, there’s actually a very good reason behind all that nagging to clean up your room. The secret to a long life is to always pick up your trash!

*New data from the Weissman lab, described here in a recent blog post, dovetail nicely with this finding since they establish that a lot of translation takes place on the mitochondrial surface.

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

Categories: Research Spotlight

Tags: mitochondria, protein aggregation, Saccharomyces cerevisiae

Telomerator is the Chromosomal Terminator

December 10, 2014

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A simple tool for adding telomeres to linear DNA:

First there was the Terminator. Now, in a new study published in PNAS by Mitchell and Boeke, we have the telomerator.

Instead of being a homicidal robot from the future bent on killing Sarah Connor, the telomerator is a tool that lets scientists easily turn circular DNA into stable chromosomes in the yeast Saccharomyces cerevisiae. While less splashy, this bit of synthetic biology is definitely cool in its own way (and much less dangerous!).

The system that Mitchell and Boeke created is very clever. They first inserted the intron from the ACT1 gene into the middle of the URA3 gene. The URA3 gene was still functional, as ura3 mutants could use it to grow on medium lacking uracil.  

They next inserted a sequence into the middle of the intron that consisted of an 18 base pair I-SceI cleavage site flanked on each side by around 40 base pairs of yeast telomere repeats (called Telomere Seed Sequences or TeSSs). This construct still allowed ura3 mutants to grow in the absence of added uracil.

The final step was to introduce the homing endonuclease I-SceI to the cell so that it cut the circular DNA precisely between the two TeSSs. The idea is that when you add the homing endonuclease, the newly linearized piece of DNA ends up with the telomere seeds on each end. Telomerase adds more repeats to the seeds until the DNA has proper telomeres. Voilà, a chromosome is born.

The URA3 gene part of the plasmid is important for selecting cells with the linearized DNA. Basically a circularized DNA will grow on medium lacking uracil but fail to grow on medium with 5-FOA, while the linearized DNA will do the opposite. In other words, the process of linearization should destroy the URA3 gene. And that’s just what they found.

Previous work had shown that to be stable in yeast, a chromosome needs to be at least 90 kilobases (kb) or so long. This is why they tested their new telomerator in synIXR, a synthetic yeast chromosome that is about 100 kb in length. This chromosome has 52 genes from the right arm of chromosome 9, two genes from the left arm, around 10 kb of nonessential BAC DNA, the native centromere CEN9, and a LEU2 marker. 

Mitchell and Boeke inserted the telomerator sequence into two different locations in the BAC part of the circularized synIXR and found that adding I-SceI appeared to linearize the DNA. In both cases they found that around 100 out of 200 cells were resistant to 5-FOA and unable to grow in the absence of uracil but could still grow in the absence of leucine. This is just what we would predict if we cut the DNA in the middle of the URA3 gene and created a stable piece of linear DNA.

They next wanted to use this tool to study the effects of telomeric DNA on nearby genes. We would predict that because of telomeric silencing, genes near a telomere will be downregulated. Any genes that affect growth when turned down should quickly become evident.

To accomplish this they inserted the telomerator three base pairs downstream of each of the 54 genes on synIXR, generating 54 new plasmids. After activating the telomerator by expressing the I-SceI nuclease, they used pulsed field gel electrophoresis to confirm that 51 of the 54 synthetic chromosomes had indeed been linearized.

As expected, they found that putting a telomere near a gene sometimes has profound effects. For example, when they linearized DNA where the telomerator was 3’ of either YIR014W, MRS1, or YIR020C-B, they got no growth. They also found many more effects on the growth rate at both 30° C and 37° C at many different, “telomerized” genes. The implication is that when these genes are near telomeric DNA, they no longer function at a high enough level for the yeast to grow well or in some cases to even survive.

To confirm that the effects they saw were due to telomeric silencing, Mitchell and Boeke tested each linearized DNA in a sir2 mutant, a key player in this form of silencing. Mutating sir2 reversed the effects of placing a telomere near the gene, further supporting the idea that the newly created chromosome ends are like normal telomeres because they undergo the same Sir2-mediated silencing.

Finally, the researchers tested the stability of the newly created chromosomes by selecting for Ura⁺ revertants from six individual cultures with different linearized molecules. They failed to select any revertants in which the DNA had recircularized, showing that the linear chromosomes are stable.

So in contrast to the Terminator, who sliced and diced his victims randomly, the telomerator will allow synthetic biologists to create linear chromosomes with precisely positioned telomeres. This study proved the concept, and this tool will be incredibly useful in the future, both in yeast and potentially in other eukaryotes. Both the Terminator and the telomerator can say, “I’ll be back”!

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

Categories: Research Spotlight

Tags: Saccharomyces cerevisiae, synthetic biology, telomere

New Alternative Reference Genomes

December 08, 2014

At SGD, we are expanding our scope to provide annotation and comparative analyses of all major budding yeast strains, and are making progress in our move toward providing multiple reference genomes. To this end, the following new S. cerevisiae genomes have been incorporated into SGD as “Alternative References”: CEN.PK, D273-10B, FL100, JK9-3d, RM11-1a, SEY6210, SK1, Sigma1278b, W303, X2180-1A, Y55. These genomes are accessible via Sequence, Strain, and Contig pages, and are the genomes for which we have curated the most phenotype data, and for which we aim to curate specific functional information. It is important to emphasize that we are not abandoning a standard sequence; S288C is still in place as “The Reference Genome”. However, we do recognize that it is helpful for students and researchers to be able to ‘shift the reference’, selecting the genome that is most appropriate and informative for a specific area of study.

These new genome sequences have been also been added to SGD’s BLAST datasets, multiple sequence alignments, the Pattern Matching tool, and the Downloads site. Please explore these new genomes, and send us your feedback.

Categories: Data updates, New Data, Sequence

Tags: reference genome, Saccharomyces cerevisiae, strains

A Lot Hinges on Ndc80

December 04, 2014

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A collapsible protein complex makes sure that dividing cells get the right number of chromosomes:

The invention of collapsible tent poles was a boon to backpackers everywhere. These long, rigid poles provide strong support for a tent, but when it’s time to pack up and go, they fold up into a short package. The secret? Flexible regions in between the rigid sections.

Although the inventors of these poles couldn’t have known it, something similar already existed in nature. In a new paper in GENETICS, Tien and colleagues used the awesome power of yeast genetics, along with some cool biochemistry, to look at the shape of the S. cerevisiae Ndc80 complex in vivo. They found that, just like a tent pole, it bends sharply at a flexible region to fold two rigid sections next to each other. And this ability to fold is critical for accurate chromosome segregation.

During cell division, chromosomes must be correctly attached to the mitotic spindle so that the mother and daughter cells each get one, and only one, copy of each. If a yeast cell doesn’t get this process right, it can become sick or even die. And if it happens in an animal cell, it can lead to cancer.

The Ndc80 complex, which is conserved from yeast to humans, is an integral part of this process because it connects the chromosomes to the spindle during mitosis. It consists of four subunits and has an elongated middle and globular parts on each end, sort of like a dumbbell. The Ndc80 protein, one of the subunits, has an unstructured  “loop” region in the middle of its elongated section.

Previous work had shown that the loop region of Ndc80 is flexible in vitro, and in vivo experiments had shown that the whole complex can change its conformation. Tien and colleagues wanted to know whether the Ndc80 loop region was important for the shape of the complex during mitosis, and whether flexibility in this region was important for function.

They started with a genetic approach, and isolated mutations in NDC80 that caused heat sensitivity. One particular allele, ndc80-121, was especially interesting. The mutant protein had two amino acid changes, near each other and near the loop region. The Ndc80 complex containing the mutant protein was just as stable, and bound to microtubules just as tightly, as the wild-type complex. So why did the cells die at higher temperatures?

Tien and colleagues visualized mitosis in the mutant cells using fluorescence microscopy. They could see that when they raised the temperature, dividing mutant cells had lots of aberrant attachments between chromosomes and the spindle. Because of these attachments, proceeding through mitosis caused their spindles to break—a lethal event.

However, if they timed the temperature shift to happen later in the cell cycle, the ndc80-121 mutant cells were fine. If chromosomes had already been lined up correctly on the spindle before the temperature was raised, then the rest of mitosis could go on without a problem.

Tien and coworkers wondered whether the mutation might disrupt the binding of some other protein to the complex at high temperatures. To look for interactions, they selected mutations that suppressed the heat-sensitive phenotype of ndc80-121. But they didn’t find any suppressor mutations in other genes. However, they did find an intragenic suppressor mutation within the ndc80-121 gene.

Interestingly, this mutation affected a residue that was on the other side of the loop relative to the original two changes. If the Ndc80 complex is a dumbell, imagine that the dumbell is collapsible like a two-segment tent pole, with the loop region of Ndc80 as the elastic between the sections. If you folded the complex in this way, the amino acids changed in the ndc80-121 mutant protein would be positioned close to the amino acid that the suppressor mutation affected—an intriguing explanation for how these mutations might affect each other.

Of course, genetic interactions don’t prove a direct physical interaction. So the researchers looked to see whether they could detect physical interactions between these regions. They treated the complex with a reagent that would permanently cross-link amino acids that were close to each other. Then they chopped the complex into smaller peptides using a protease, and analyzed the cross-linked peptides using mass spectrometry to locate the linked residues.

Sure enough, they were able to detect multiple cross-links within the complex, and their locations confirmed that the complex folds much like a tent pole. Based on their mutant phenotypes, the researchers think it’s likely that the original ndc80-121mutation destabilizes folding of the complex and that the intragenic suppressor mutation makes folding tighter. Consistent with this idea, the intragenic suppressor mutation alone confers a slow-growth phenotype, as if it makes the complex fold just a little too tightly to support vigorous growth.

These experiments as a whole establish that the Ndc80 complex folds tightly early in mitosis. So, creative inventors and Mother Nature have arrived at similar solutions for the tent pole and for this important complex. And just as collapsible tent poles have become ubiquitous in the backpacking world, so too has the collapsible Ndc80 complex been conserved throughout evolution: even the specific residues that mediate the folding are highly conserved. Since this work has shown that correct folding of the yeast complex is necessary for its role in helping chromosomes to line up accurately on the spindle, the same is almost certainly true in mammalian cells.

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

Categories: Research Spotlight

Tags: mitosis, Ndc80 complex, protein structure, Saccharomyces cerevisiae

Ribosomes Caught in the Act

November 24, 2014

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If you want to see what animals really do out in the wild, first you need to hide a camera and a trip-wire so well that the jungle seems totally undisturbed. Then, if you’re lucky, you’ll be able to catch them in the middle of the night as they pass by. Now you can surprise that tiger and find out what he is doing at that specific spot.

In two companion Science articles from the Weissman group at UCSF, Jan et al. and Williams et al. did essentially the same thing to S. cerevisiae ribosomes. They hid a molecular tag and the enzyme that recognizes it at various interesting places within yeast cells, so cleverly that the cells had no idea anything was different. Instead of a flash of light, they used a pulse of the small molecule biotin to find out which mRNAs were being translated at specific locations in the cell.

What they found was that when ribosomes are translating proteins that are targeted to a particular organelle, they hang around the surface of that organelle—way more frequently than was previously thought. And the exquisite specificity of this technique, allowing them to pinpoint one particular mRNA within the cell, uncovered a fascinating case of dual protein localization.

Pinpointing Translation Locations

The researchers needed to develop a technique for catching ribosomes in the act of translation. One part of this had already been worked out in the same group: ribosomal profiling, a method that allows you to map very precisely the positions of ribosomes on mRNAs.

Briefly, cells are lysed and translating ribosomes are treated with nucleases that nibble away mRNAs, except for the 30 nucleotides or so that are protected within the ribosome. Then those protected fragments are analyzed by deep sequencing. This shows, at the single nucleotide level, where ribosomes are sitting on each individual mRNA.

Ribosomal profiling tells us where translating ribosomes are in relation to mRNAs, but not where they are in relation to the rest of the cell. To get this location information, the researchers came up with a clever tagging strategy.

They started with a bacterial gene, E. coli BirA, that encodes a biotin ligase—an enzyme that can attach biotin to specific acceptor peptides. They fused BirA to various yeast genes in order to target biotin ligase to different places in the cell.

Next they tagged ribosomes by putting a biotin acceptor, called the AviTag, on ribosomal proteins such that the tag would be sticking out on the ribosomal outer surface. They tested both the BirA and AviTag fusions to make sure that they didn’t interfere with the functions of any proteins. Just like the camera hidden in the jungle, the tags didn’t perturb yeast cells in the least.

Now the researchers were set to surprise ribosomes with a pulse of biotin. Any ribosomes that were close to BirA would become biotinylated. The tagged ribosomes could then be isolated, and the mRNA sequences being translated in those ribosomes could be identified. The method as a whole is termed proximity-specific ribosomal profiling.

Jan and coworkers set up and validated this method in their paper, and used it to look at translation of secretory proteins at the surface of the endoplasmic reticulum (ER), while Williams and colleagues used the method to look closely at translation at the mitochondrial surface. Import into both of those organelles has previously been studied intensively, but often in vitro and mostly for just a few model protein substrates. In contrast, proximity-specific ribosomal profiling gives us the ability to look at translation of the entire proteome in vivo.

While it was known before that proteins targeted towards a certain organelle tended to be translated near that organelle, these researchers found that it was much more common than previously believed. For example, they found that most mitochondrial inner membrane proteins were translated at the mitochondrial surface and imported cotranslationally, in contrast to the previous view that mitochondrial import is predominantly posttranslational.

Both studies discovered many more details than we can summarize here. But the comparison between the ER and mitochondrial studies led to a special insight about one protein.

Osm1p Goes Both Ways

Osm1p, fumarate reductase, was thought to be a mitochondrial protein (although results from a few high-throughput studies had hinted at a link to the ER). But proximity-specific ribosomal profiling showed very clearly that it was translated at both the ER and mitochondrial surfaces. Williams and coworkers went on to confirm by fluorescence microscopy of an Osm1p-GFP fusion that Osm1p is indeed present in both ER and mitochondria.

Both of these organelles have pretty strict criteria for the signal sequences of proteins they import, so how could it be possible that the same protein goes to both locations? The researchers found that in fact, it’s not! They repeated the ribosomal profiling on the OSM1 mRNA, this time adding the drug lactimidomycin which makes ribosomes pile up at translational start sites. This showed that OSM1 actually has two start codons and produces two different proteins targeted to the two locations.

The OSM1 methionine codon currently annotated as the start would produce a protein with an ER targeting signal. Ribosomes piled up there, but also at another methionine codon 32 codons downstream. Starting translation at this codon would produce a protein with a mitochondrial targeting signal. Williams and colleagues confirmed this idea by showing that mutating the first Met codon made all of the Osm1p go to mitochondria, while mutating the Met codon at position 32 sent all of it to the ER.

The mutant form of Osm1p that couldn’t go to the ER conferred an intriguing phenotype: the inability to grow in the absence of oxygen. Osm1p generates oxidized FAD, which is necessary for oxidative protein folding, and it also interacts genetically with ERO1, which is involved in this process. Taken together, this all suggests that Osm1p activity drives oxidative protein folding in the ER.

The traditional ways of determining where a protein is in the cell, microscopic visualization or physical fractionation, can both be difficult and imprecise. Proximity-specific ribosomal profiling gets around those challenges, and gives a very precise picture of exactly where proteins are being created and how ribosomes are oriented with respect to organelles.

The example of Osm1p localization gives just a hint of the insights that are waiting for scientists who exploit this technique further. And we’re not just talking about yeast: the authors tested and validated the method in mammalian cells. Just like that tiger, surprised ribosomes in many different cell types will be giving up their secrets about where they roam and what they do.

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

Categories: Research Spotlight

Tags: endoplasmic reticulum, mitochondria, protein targeting, Saccharomyces cerevisiae, translation

Lots of Ways to Get to the Same Place

November 13, 2014

 

How Bad Mutations Can Help Yeast Thrive in New Environments:

If you’ve ever asked for directions from more than one person, you know there are many ways to get to the same place. But not all routes are created equal. You might be trying to get to the post office, but on some routes you’ll pass by the zoo, while on others you might pass the museum or the bus station.

Turns out that something like this may be happening with individuals in a population too. Each may be well adapted for its environment, but each may have arrived there in different ways. And although they may seem similar, they might actually be more different than they look on the surface.

In a new study in PLOS biology, Szamecz and coworkers show that a lot of these different routes to the same place happen in yeast because of bad mutations. They found that when a yeast gets a deleterious mutation, it is sometimes able to mutate its way back to being competitive with wild type again. But the evolved strain is genetically distinct from the original wild type strain. Similar phenotype, distinct genotype.

And this isn’t just an interesting academic exercise either. As any biologist knows, bad mutations are much more common than are good ones. This means that populations may often be evolving to overcome the effects of these bad mutations. This process may help to explain the wide range of diverse genotypes seen in any wild population. 

The authors started out by focusing on 187 yeast strains in which a single gene had been deleted. Each strain grew more poorly than wild type under the tested conditions.

They then took 4 replicates of each mutant along with the wild type strain and grew them for 400 or so generations. They looked for strains that had evolved to overcome the growth defect caused by the mutation. 

To take into account the fact that every strain would probably evolve a bit to grow better in the environment, they only looked for those that had gained more growth advantage than the wild type had. Around 68% of the strains showed at least one replicate that met this criterion.

So as we might expect, it is possible for a strain that grows poorly to mutate its way closer to a wild type growth rate. The next question was whether these mutant strains had mutated back to something close to wild type or to something new.

The authors decided to answer this question by doing a gene expression analysis of the wild type, the eight mutant strains, and a corresponding evolved line from each of these eight. After doing transcriptome analysis, they found that for the most part the evolved lines did not simply revert back to the original gene expression pattern of the wild type strain. Instead, they generated a novel gene expression pattern to deal with the consequences of having lost the original gene. And in the next set of experiments, the authors showed that this matters when the evolved strains are put in a new environment.

The researchers took 237 evolved lines that grew nearly as well as the original wild type strain and tested how well they each did in 14 different environments. In other words, they tested genetically distinct, phenotypically similar strains in new environments.

They found that even though the original mutant strains grew poorly in all the environments tested, the evolved ones sometimes did better. Fitness improved in 52% of the strains and declined in 8%. What is even more interesting is that a few stumbled upon genotypes that were significantly better than the evolved wild type in a particular environment.

A couple of great examples are the rpl6b or atp11 deletion mutant strains. Strains evolved from either mutant did around 25% better than the evolved wild type strain in high salt, even though both of the original mutants did significantly worse than the wild type strain. By suffering a bad mutation, the evolved strain had been rerouted so that it now grew better than wild type. 

So it looks like getting a bad mutation may not be all bad after all. It might just give you that competitive edge you need when things change. Sometimes the best way to get from point A to point B is not a straight line. 

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

Categories: Research Spotlight

Tags: evolution, Saccharomyces cerevisiae

Finding the Right Tools for the Job

November 06, 2014

 

Researchers Create a New Gene Editing Tool for Prototrophs and Diploids:

If you like spending your weekends tinkering with your beautiful 1957 Ford Thunderbird that only leaves the garage on sunny days, then you probably own a set of “standard” wrenches, sized in inches.  But if you wanted to tune up the trusty 2008 Subaru that gets you to work every day, you’d be out of luck. The standard wrenches are no use and you’d need a set of metric wrenches to fit the Subaru parts.

Molecular tools can be like that too. The genetic engineering toolkit that has been used on Saccharomyces cerevisiae for many years has been terrifically handy, but it only works for strains that have specific nutritional requirements, termed auxotrophs. It’s not so useful for so-called prototrophic strains that are already able to make all the compounds that they need. And some of the non-cerevisiae Saccharomyces strains that are being studied more and more these days happen to be prototrophic.

But in a new GENETICS paper, Alexander and colleagues describe a new toolkit that works on the prototrophic wild and industrial Saccharomyces species and even works efficiently on diploid strains. This sets the stage for faster and more versatile modification of these strains that are becoming useful models for molecular evolution, as well as helping us to make wine, brew beer, and produce chemicals. 

The “standard” toolkit for S. cerevisiae is based on nutritional markers that can be selected. For example, a ura3 mutant strain can’t grow without added uracil in the medium, but when it is transformed with the wild-type URA3 gene it doesn’t need uracil any more.

Importantly, URA3 can also be selected against: ura3 mutants can survive in the presence of 5-fluoroorotic acid (5-FOA), but wild-type URA3 strains cannot. So, starting with a ura3 mutant you can replace any desired sequence with the URA3 gene, selecting for growth in the absence of uracil; then you can tinker with a gene of interest and add the modified version back into the cell to replace URA3, now selecting for 5-FOA resistance. 

Another tool in the classic toolkit is a site-specific nuclease like SceI that can encourage any added fragments to end up in the right spot in the yeast genome. Free DNA ends at a chromosomal break stimulate integration of a transformed fragment if its ends are homologous to the chromosome near the break.

To do this kind of tinkering with prototrophic strains, the researchers needed a marker that could be selected both positively and negatively like URA3. Using a gene that has no equivalent in yeast would be an added plus, since it would be easy to detect and follow. They turned to thymidine kinase (TK), which was lost from the fungal lineage a billion years ago.

TK from Herpes simplex virus had already been expressed in yeast and was known to confer resistance to antifolate drugs. And it had already been shown in other organisms that TK makes cells sensitive to 5-fluorodeoxyuridine (FUdR). The researchers tried it in yeast, and sure enough, only cells that had lost the added TK gene were able to grow in the presence of FUdR.

Alexander and colleagues next created a gene cassette, which they named HERP (Haploid Engineering and Replacement Protocol). The cassette contained the TK gene, a galactose-inducible version of the SCEI gene, and an SceI cleavage site.

As a test case, they decided to replace the S. cerevisiae ADE2 gene with the ADE2 orthologs from seven Saccharomyces species. Transforming with a mixture of seven different sequences and retrieving all seven desired constructs would be a proof of concept showing that this procedure could be used to transform with pools of different sequences and generate a whole library of different strains. And it worked.

They first replaced the ADE2 gene in S. cerevisiae with the HERP cassette, selecting for resistance to antifolates. Next they transformed the HERP-containing strain with a mixture of seven fragments, in the presence of galactose (to turn on SceI and cut the chromosome at that location) and FUdR (to select against cells in which the HERP cassette was not replaced with ADE2). The strategy worked perfectly and efficiently: they got transformants carrying each of the genes, integrated at the correct location.

This work in haploids was all well and good, but most wild type and industrial strains are diploid. And these sorts of strategies tend to work badly in diploids because the cell uses the other gene copy for homologous recombination instead of the DNA fragments scientists put in. To be really useful, HERP would need to work in diploids too.

Alexander and coworkers managed to get HERP to work efficiently in diploids by setting up a situation where both homologous chromosomes had HERP cassettes with SceI recognition sites. Now, when they induced SceI with galactose, both chromosomes of the diploid strain were cut. This dramatically increased the efficiency of transformation: 14 out of 15 strains carried the transformed sequence on both chromosomes instead of the more typical 4% seen with other methods.

So now we have a versatile toolkit that can be used on many different makes and models of yeasts. With a little modification, it could also be applied to many other fungi. And although you can’t use the metric wrench set on your Thunderbird, these HERP cassettes work just as well on S. cerevisiae as on other Saccharomyces species.

The ability to work with prototrophic strains could be a big advantage even in lab strains of S. cerevisiae, since auxotrophic strains sometimes grow slower than wild type even when supplemented with the nutrients they need. So now we have an even larger set of tools to choose from when we want to take that old Thunderbird out for a spin. 

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

Categories: Research Spotlight

Tags: genetic engineering, Saccharomyces cerevisiae, selectable marker

If Yeast Can’t Stand the Heat, Our World May Be in Trouble

October 23, 2014

In case there were still any doubters, the world is definitely heating up. April to September 2014 were the warmest these months have ever been since we started keeping records in 1880. And about 35,000 walruses were forced ashore this summer in Alaska because there wasn’t enough room left for them on the sea ice where they normally hang out. Unfortunately, the trend looks to be more record breaking heat for as long as we can see in the future.

This is bad news for us, and even worse news for nature.  But all is not lost! Our hero yeast may be able to swoop in and make us biofuels to replace gasoline.  This won’t stop global warming, but it might at the very least slow it down.

But yeast in its current form probably couldn’t make enough biofuels to make a difference without using too much precious food in the process. Like the X-men, it will need a helpful mutation or two to increase its efficiency to the point where it can make a real dent in slowing down the relentless rise in global temperatures. And ironically, one new trait yeast needs to pull this off is to be able to survive better in the heat.

To efficiently turn the parts of the plants we can’t use (mostly anything to do with cellulose) into biofuels, we need for yeast to grow in cultures where enzymes are chopping cellulose into bite sized pieces at the same time.  These enzymes work best at temperatures that are a real struggle for wild type yeast.

In a new study in Science, Caspeta and coworkers isolated mutants better able to tolerate high temperatures by simply growing Saccharomyces cerevisiae at around 39.5° C for over 300 generations.  They did this in triplicate and ended up with strains that grew on average about 1.9 times faster than wild type yeast at these temperatures.

The next step was to use genome sequencing and whole-genome transcription profiling to figure out why these mutant strains were heat tolerant. This is where things got really interesting.

They found many genes that were affected, but identified ERG3 as the most important player. All of the thermotolerant strains that they selected contained a nonsense mutation in ERG3. And in fact, when they introduced an erg3 nonsense mutation into wild type yeast, they found that this engineered strain grew 86% as well as the original mutant strain at high temperatures. In other words, most of the heat tolerance of these strains came from mutations in the ERG3 gene.

This makes sense, as membrane fluidity is a key factor in dealing with higher temperatures, and ERG3 codes for a C-5 sterol desaturase important for membrane composition.  When Caspeta and coworkers looked at the membranes of the mutant strains, they found a buildup of the “bended” sterol fecosterol.  Since “bended” sterols have been shown to protect the membranes of plants and Archaea from temperature swings, this could be the reason that the mutant strains dealt with the heat so well.

So as we might predict, changing the composition of the cell membrane affects how the yeast respond to temperature. What we couldn’t predict is that in order to get to this point via artificial selection, the yeast had to have a second mutation in either the ATP2 or the ATP3 genes that actually make yeast less able to grow at higher temperatures.

Because ATP2 and ATP3 are needed for yeast to grow on nonfermentable carbon sources, the authors hypothesized that perhaps thermotolerance could not evolve while oxidative respiration worked at full speed. Consistent with this, Caspeta and coworkers found that their evolved thermotolerant strains were more susceptible to oxidative stress and could not grow on nonfermentable carbon sources. This was not true of the strain they engineered to only have the mutation in the ERG3 gene—it grew well at 40° C and could use nonfermentable carbon sources.

So not only have these authors found a mutant yeast with the superpower of growing at higher temperatures, but they also showed that sometimes engineering works better than natural selection at creating the mutant they want. Evolving sometimes requires passing through an intermediate that makes the final product less useful than it could have been. In this case it worked best to use a combination of artificial selection and engineering to build a better mutant.   

Even this super engineered yeast mutant won’t stop global warming in its tracks, but it might help us to slow it down enough so that natural systems have a chance to adapt. A superhero indeed… 

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

Categories: Research Spotlight

Tags: biofuel, evolution, Saccharomyces cerevisiae, thermotolerance

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