New & Noteworthy

Finding the Right Tools for the Job

November 6, 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.

Whether you want to tinker with a classic car or a yeast genome, it’s important to use the right tools. Image from Wikimedia Commons

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