New & Noteworthy

Red Ink for the S. cerevisiae Genome

April 2, 2015


Text editing has come a long way since the fountain pen, and genome editing is now almost as easy, thanks to the CRISPR/Cas system. Image by Nic McPhee via Flickr.com

Editing is an essential part of producing good writing. You might cringe when your masterpiece comes back covered in red ink, but in the end your paper is better for it.

These days, computers have made editing much, much faster and easier than using ink on paper. Some of us remember when cutting and pasting literally mean cutting the piece of paper on which your manuscript was typed and pasting the sections in a different order!

The same kind of revolution has happened when it comes to editing genomes. A seemingly obscure system used by bacteria to defend against invading phages, discovered in the 1950s, led to the development of restriction enzymes as the reagents that have enabled virtually all modern molecular biology. And now, an equally “obscure” system of bacterial immunity has opened the door to genome editing that is as precise and nearly as fast as your thesis advisor using Microsoft Word to edit your dissertation (maybe faster!).

This bacterial system is called CRISPR/Cas. Bacteria use it to defend against the foreign DNA—from infecting phages, bacteria that transfer plasmids via conjugation, or other sources—that constantly assaults them. And now scientists are using it to edit the genomes of most any beast they want, including our favorite yeast.

What makes this technique so powerful is that it is easily programmable. You can make virtually any sequence change that you wish, and even more impressively, make lots of changes all at once. CRISPR/Cas may be one of those technological leaps that changes everything.

The incredible potential of this approach, and the ethics of its use in humans, are hot topics right now. But while researchers and philosophers are hammering out guidelines for using the CRISPR/Cas system in larger organisms, yeast researchers are free to forge ahead and edit the S. cerevisiae genome to their hearts’ content. This has now been made much easier with the availability of a whole toolkit, created at the Delft University of Technology and described in a new paper by Mans et al. 

The yeast system has three essential components. The first is a plasmid that will express a specific guide RNA (gRNA). The gRNA leads a nuclease to the right place in the genome.  Mans and colleagues made a whole set of plasmids, with different nutritional and antibiotic resistance markers, that can express one or more gRNAs.

The second component of the system is the nuclease that binds to the gRNA and makes a double-stranded cut in the target DNA. The researchers used the Cas9 nuclease from Streptococcus pyogenes, and engineered a set of yeast strains that had the cas9 gene stably integrated into a chromosome and expressed from a strong yeast promoter.

The third component is one or more repair fragments: pieces of DNA that specify the modified sequence that the researcher wants to engineer into the genome.

So, for example, if a scientist wants to delete a gene precisely, she can create a gRNA that targets the gene, and then co-transform a Cas9-expressing yeast strain with both the plasmid expressing the gRNA and a repair fragment that corresponds to the gene’s upstream and downstream flanking sequences, fused together. When the gRNA is expressed in the transformant, it leads Cas9 to the gene, where it makes a double-stranded cut at a precise position in the DNA.

Now the researcher can let yeast do the rest of the work. S. cerevisiae has a powerful homologous recombination system, and it’s greatly stimulated by double-stranded breaks in DNA.

After Cas9 cuts the gene, yeast will repair the break, using as a template the repair fragment that the researcher designed. In this case, the upstream and downstream sequences will recombine with the homologous sequences in the chromosome, but since the coding sequence is missing from the repair fragment, the resulting strain will have a precise deletion of the gene of interest.

This example illustrates one of the simplest uses of the technique. Mans and colleagues tried successively more complicated tasks and were able to accomplish some amazing feats.

They were able to precisely delete six genes in one step by transforming with repair fragments for all six, along with three plasmids that each expressed two gRNAs. Also in one step, they replaced one yeast gene with six Enterococcus faecalis genes encoding subunits of the pyruvate dehydrogenase complex and other enzymes in the pathway. The E. faecalis genes were specified on six overlapping repair fragments that were cotransformed into the strain.

The CRISPR/Cas9 system designed by Mans and colleagues can do much more than gene deletions and replacements. By designing repair fragments specifying particular mutations, the method can also be used to create point mutations or other modifications.

For this technique to work, it’s important that there are no mismatches between the gRNA sequence and the chromosomal target sequence, and other sequence characteristics can influence the efficiency of the method.  So the authors created an online tool that helps researchers select optimal Cas9 targets in regions of interest and design gRNA sequences. Since they incorporated the sequences of 33 different S. cerevisiae strains into the tool, researchers can specify a strain and retrieve information on the best sequences for targets and gRNAs for their gene(s) of interest based on sequences found in that particular strain.

Importantly, the CRISPR/Cas9 technique allows researchers to make multiple changes in a single step. This is a big advantage, since transformation itself can be mutagenic. For example, a strain that has been commonly used to investigate the function of hexose transporters was engineered to carry multiple deletions in the conventional manner, using successive rounds of transformation and selection.  Its genomic sequence, which was recently determined, reveals that its genome is a complete mess, with many rearrangements and deletions. 

With the development of this toolkit, editing the S. cerevisiae genome is beginning to be almost as easy as editing a text document. And since Mans and colleagues have made all of the strains, plasmids, and online tool freely available to the world, everyone will be able to take advantage of them. Just think of the stories that yeast researchers will be able to write!

CRISPR/Cas in Bacteria

Way before this became a powerful tool for researchers, it was a very cool immune system for bacteria, allowing them to defend against assaults from foreign invaders. 

Bacteria collect foreign DNA sequences from invaders that threaten them, just like collecting mug shots of notorious criminals. They store these mug shots in a special place in their genome, integrated between blocks of a repeated sequence. (The CRISPR acronym refers to these repeats.) This region is transcribed, and the RNA is chopped into pieces containing individual mug shots. Because these mug shots, called crRNAs, are complementary to the DNA sequences of invaders, they can recognize and hybridize with those invading sequences.

Bacteria have an additional small RNA, the tacrRNA, that binds to both the crRNA and to a CRISPR-associated (Cas) nuclease. This forms a RNA-DNA-protein complex on the foreign DNA and allows the nuclease to do its work, cutting both strands of the DNA and neutralizing the invader.

To use this system for genome engineering, scientists have fused the two RNAs of the bacterial system into a single RNA, the guide RNA (gRNA).  It contains both the mug shot (with sequences complementary to the target) and the RNA sequence that recruits the nuclease. The gRNA, a Cas nuclease, and a repair fragment are the essential components of the system.

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

Conformity Preferred in Yeast

March 25, 2015


In a classic Apple ad, the world is a gray, dreary place where everyone is the same. In charges a woman dressed in brightly colored clothing who hurls a hammer into a big black and white screen, smashing the old conformist world order. Individuality can now blossom.

Mother Nature frowns on mutations that add to cell to cell variation in gene expression. Image by SUNandMooN363 via Creative Commons

This is a powerful story for people, but it turns out that if Mother Nature had her druthers, she would like that woman to either stay at home or dress and act like everyone else. At least this is true if we are talking about individuals that are genetically identical. In this case, alleles that cut down on cell to cell variation tend to be the ones that prosper.

This is confirmed in a new study in Nature in which Metzger and colleagues in the Wittkopp lab showed that there is a selection against mutations that cause increased variation between individuals in the S. cerevisiae TDH3 gene. In other words, mutations that cause more “noise” are selected against. The squeaky wheel is eliminated.

The TDH3 gene encodes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), an important metabolic enzyme. Yeast cells can survive a deletion of this gene, but their fitness is greatly reduced. Overexpression of the gene also has noticeable effects. This suggested to the researchers that the level of TDH3 expression would be under selection pressure during evolution.

Metzger and coworkers compared the promoters of the TDH3 gene from 85 different strains of S. cerevisiae and found that the promoter had undergone selection out in the wild. The authors were interested in why certain polymorphisms were selected for and why others were selected against. To try to tease this out, they compared the activities of evolved changes to randomly selected ones.

The authors first used the sequences of the 27 haplotypes they saw in the 85 strains to predict what the original, ancestral promoter probably looked like. They then re-created this sequence and also sequences that represented the most likely intermediates on the way to the current promoters. They linked each of these promoter sequences to a yellow fluorescent protein (YFP) reporter and looked at mean activity and expression noise. In other words, they looked at how much promoter activity there was in aggregate and how much it varied between individual cells for the 10,000 cells in each culture.

They next set out to generate a pool of polymorphisms that didn’t make the cut during evolution, so they could compare these to the successful ones. To do this, they individually mutated 236 G:C to A:T transitions throughout the promoter region. They chose this transition because these are the most common spontaneous mutations seen in yeast and the most common SNP seen in this promoter out in the wild.

Now they were ready to do their experiment! Comparing the randomly created mutations to the evolved changes, they looked at both the overall level of expression and how much variation there was between each of the 10,000 individual cells in the tested culture.

What they found was that the effects on the mean level of activity were pretty comparable between the “selected” mutations and the random ones. But the same was not true for individual variation. The random mutations were much more likely to increase expression noise compared to the “selected” mutations.

From these results the authors conclude that there is a selection against mutations that increase the level of noise. In fact, they go a step further and conclude that at least for the TDH3 promoter, there was more of a selection against noise than there was a selection for a particular level of activity. It was more important that individuals had consistent activity than it was to have some mean level of activity.

This makes some sense, as a cell is a finely tuned machine where all the parts need to work in harmony together to succeed. If one part is erratic and shows different levels of activity in different individuals, then some of those individuals won’t do as well and so won’t survive.

This also means that certain paths to a more fit organism will be selected over others. And it could be that organisms miss out on some potential fitter states because they can’t survive the dangerous evolutionary journey that would be needed to get there.

So the cell prefers that all the parts work together in a predictable way. When you’re a population of individuals that are more or less genetically identical, nonconformists are dangerous.  The gray sameness of the Nineteen Eighty-Four world is preferable to a more bohemian atmosphere where diversity is celebrated.

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

  

From Sourdough Bread to Chemotherapeutic Drugs

March 18, 2015


Microbes can achieve great things when they work together:

Microbiologists in the lab spend a lot of time and effort keeping each microbial strain and species separate. The conventional wisdom is that if you want to really understand an organism, you need to study it in isolation, as a pure culture. If contaminating colonies of some other bug appear on your Petri dishes, you’d better melt down those plates in the autoclave and trash them!

When microbes work together, the results range from delicious to life-saving. Image by Hillarywebb via Wikimedia Commons

On the other hand, amateur microbiologists have known for centuries that mixtures of microbes can do great things. Sourdough bread, for example, is made using a culture of Lactobacilli and yeasts. They complement each other during the fermentation: the bacteria metabolize sugars that the yeast can’t use, and make new compounds that can be fermented by the yeast. The result is extremely tasty. 

A new study from Zhou and colleagues brings a microbial community into the lab to make a medicine called paclitaxel that is used to treat cancer. Yes, bread bowls for your clam chowder are cool, but this is obviously way more important for human health.

Paclitaxel is an incredibly successful drug for treating breast and ovarian cancer, but unfortunately there isn’t an easy way to make it.  It can be purified from the bark of the Pacific yew (killing the trees in the process), synthesized by plant cells cultured in vitro, or synthesized chemically. But all of these processes are expensive and complicated, which means this life saving drug is always in short supply.

The researchers wanted to produce it more cheaply and easily, and an obvious solution was to let microbes do most of the work. But neither of the most commonly used microbial workhorses, S. cerevisiae and E. coli, was exactly right for the job.

E. coli had already been engineered to overproduce the compound taxadiene. The taxadiene then needs to be oxidized to create oxygenated taxanes, which are paclitaxel precursors. This oxidation can be done by membrane-bound oxidoreductase enzymes called cytochrome P450s. But these enzymes are not found naturally in bacteria, and getting them expressed and functional in E. coli is challenging.

The researchers decided to see whether they could coax these two microbes into cooperating to produce oxygenated taxanes. After creating an E. coli strain that produced taxadiene and an S. cerevisiae strain that produced a P450 oxidoreductase, they grew them together in the same culture, with glucose as the carbon source. 

As planned, the E. coli pumped out taxadiene and it was able to diffuse into the yeast cells, where it became oxygenated. However, the two species weren’t as happy together as the researchers had hoped. 

One of the things that humans love about yeast is that when it grows on glucose, it produces ethanol. However, the E. coli cells didn’t love being bathed in ethanol: their yield of taxadiene went way down as the ethanol levels in the culture went up.

So Zhou and coworkers switched the carbon source to xylose. S. cerevisiae cannot consume xylose, but E. coli can. When growing on xylose, E. coli produces acetate, which the yeast can use—and they don’t produce ethanol under these conditions.

Growing the microbes in xylose doubled the yield of oxygenated taxanes over that of the glucose-grown culture. But still, only 8% of the taxadiene that was produced was getting oxygenated.

To be sure that the yeast cells were producing the P450 enzyme as efficiently as possible, the researchers tried driving transcription of the gene using several different promoters. Using the promoter that was strongest in the co-culture conditions made a significant difference in the proportion of taxadiene that was oxygenated.

The researchers guessed that another factor limiting the final yield was that the yeast cells were not growing as well as they could. Tweaking the ratio of the two species in culture and the contents of the media resulted in a three-fold increase in oxygenated taxanes. But Zhou and colleagues hoped to improve things even more.

Thinking that the limiting step in yeast growth might be the supply of acetate, the researchers tried to beef up the acetate synthesis pathway in E. coli. They engineered the bacteria to overproduce several of the enzymes in the acetate biosynthesis pathway, but this didn’t make a large difference. 

Scientists came up with expensive ways to stop using the Pacific yew tree to make paclitaxel. Now we might be able to do this more cheaply with yeast and bacteria. Image by Jason Hollinger via Wikimedia Commons

They reasoned that if they forced the E. coli to rely on the acetate biosynthesis pathway for energy, the cells might ramp up their acetate production. To do this they blocked oxidative phosphorylation by deleting the the atpFH gene that encodes a subunit of ATP synthase. Now more acetate was produced, the yeast cells grew better, and 75% of the taxadiene that was produced got oxygenated. They were in business!

Zhou and coworkers went on to show that the co-culture environment could be modified to generate several other isoprenoids. This class of naturally-occurring molecules includes some that are in use, or in development, as pharmaceuticals (paclitaxel, and others currently in clinical trials) and compounds that have other applications, from fragrances to fuels. 

There’s much more work to be done, and the potential of microbial communities is just beginning to be realized. Harnessing the power of multiple organisms means that different steps of pathways can be optimized separately and then mixed and matched for a desired result. This approach could turn out to be the best thing since sliced bread! But then again, sourdough bakers already knew that.

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

Those Yeast Got Talent

March 11, 2015


Thriving in a yeast culture is a lot like becoming a finalist on American Idol—you need some minor advantage to hang around and then a big finish to dominate. Image by Michael Tanne via Wikimedia Commons

The winners of American Idol go through quite a selection process. They start out as one of tens of thousands of people who audition, and survive each cut until they are finally crowned.

At the first cuts, those with any sort of advantage are kept in the pool and the others dropped. As the cuts continue, contestants not only need to have had that stronger initial advantage (or a bit of luck), but they also need to have picked up some new skills from all of those off- and on-air performances.

Some of these contestants start with a lot of raw talent but then progress only a little, while others are able to hone their weaker initial talent with lots of practice. Once their numbers are winnowed down to a handful, it gets close to being anyone’s game because the remaining contestants are so talented.

A new study by Levy and coworkers paints a similar sort of picture for evolving populations of yeast. Very early on a whole lot of yeast stumble upon weak, beneficial mutations that keep them going in the population. These are the yeast that make the initial cut in the hurly-burly world of the Erlenmeyer flask.

At later times a few yeast end up with strongly beneficial mutations that allow them to start to dominate. These are the pool of yeast that are the finalists of the flask.

Of course a big difference (among many) between American Idol and the yeast in this experiment is that the pool of contestants in the flask hangs around—they are not thrown off the show. This means that some cell that didn’t do too well early on can suddenly gain a strongly beneficial mutation and begin to dominate. Until, of course, that cell is usurped by another more talented yeast, in which case that finalist will fade away unless it can adapt.

And this study isn’t just a fascinating dissection of evolutionary population dynamics either. It might also have implications for treating bacterial infections and even cancer.

Bacteria and cancer cells live in large populations with each cell trying to outcompete the others. By understanding the set of mutations that allow some cells to succeed against the others and become more harmful, researchers may be able to come up with new ways to treat these devastating diseases.

One of the trickiest parts of this experiment was figuring out how to follow lots of yeast lineages all at once in a growing culture. Levy and coworkers accomplished this by adding 500,000 unique DNA barcodes to a yeast population and using high-throughput DNA sequencing to follow the lineages in real time.

They set up two replicate cultures and followed them for around 168 generations. In both cultures the researchers saw that while most of the lineages became much less common, around 5% happened upon a beneficial mutation that allowed them to increase in number by generation 112.

In other words, around 25,000 lineages ended up with beneficial mutations that let them make the first cut in both cultures. This translates to a beneficial mutation rate of around 1 X 10-6 per cell per generation and means that around 0.04% of the yeast genome (around 5000 base pairs) can change in a way that confers a growth advantage.

But of course not all mutations are the same. Weakly beneficial mutations are very common, which means both cultures have plenty of these early on. This is why the replicate cultures behave so similarly up to around generation 80.

Eventually, though, a few yeast stumble upon stronger, more beneficial mutations. Since these are rarer and harder to get, each replicate culture gets them at different generations. This is why the cultures begin to diverge as the 100 or so of the strongest beneficial mutations begin to dominate.

The experiment did not go on for long enough to see many double mutations. In other words, it was very rare in this experiment to see a yeast lineage succeed because it had developed additive beneficial mutations. This is because there simply wasn’t enough time for a yeast cell to get a beneficial mutation and establish itself and then have one of its lineage gain and establish a second beneficial mutation. There was no Jennifer Hudson who came in 7th but then went on to win a Grammy and an Oscar.

When a cancerous tumor is developing, however, there is plenty of time for multiple “beneficial” mutations to be established. These mutations are only beneficial for the tumor; they are devastating for the person with cancer. This is why it is so critically important to understand not only which mutations are implicated in cancer, but also the dynamics of how they accumulate in the cancer cell population during progression of the disease. Talented yeast in the hands of talented researchers are helping us figure this out.

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

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