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Links to DRYGIN added to SGD Locus Summary and Interactions pages

June 23, 2012

SGD now provides links from both the Locus Summary and Interactions pages for each S. cerevisiae ORF to DRYGIN (Data Repository of Yeast Genetic Interactions), a database of quantitative genetic interactions of S. cerevisiae (Koh et al., 2010). These genetic interactions were determined from SGA double-mutant arrays conducted in Charles Boone’s laboratory at the University of Toronto, and include both published data (Costanzo et al., 2010) and new interactions released by the Boone laboratory as they become available. Clicking on a DRYGIN link in SGD from an ORF’s Locus Summary or Interactions page goes directly to the DRYGIN search results page for that ORF, which lists both positive and negative genetic interactions as well as any genetic correlations for the given ORF.

Ethanol from Waste

June 16, 2012

Scientists are coming up with ways for yeast to use waste like this to generate ethanol.

Biofuels hold the promise to significantly slow down global warming.  But this will only be the case if they come from something besides corn.

We don’t want them to come from the parts of other plants we eat, either.  Shunting food towards fuel will only jack up food prices and put the lives of the poorest at risk.  Policy makers should not have to decide between feeding the poor and running their cars.

No, to make biofuels worth our time, we need to be able to turn agricultural waste, grass, saplings, etc. into ethanol.  Unfortunately this stuff is mostly cellulose and lignin and we don’t have anything that can efficiently ferment this “lignocellulosic biomass.” 

Many groups are working towards creating strains of Saccharomyces yeast, the predominant fungal organism used for large-scale industrial processes, to do this job.  None have yet been created that can do the job well enough to be industrially viable. They are either poor fermentors or are genetically modified so that they include non-yeast genes.  Ideally any strain would include only Saccharomyces genes, to avoid the public’s fear and loathing of genetically modified organisms.  

This is where a new study in GENETICS by Schwartz and coworkers comes in.  This group is working towards engineering a yeast that can ferment the pentoses like xylose that make up a good chunk of this otherwise inedible biomass, using genes that are naturally occurring in Saccharomyces.  They haven’t yet created such a yeast, but they have at least identified a couple of key genes involved in utilizing xylose.

The researchers took what seemed to be a straightforward approach.  Collect and screen various yeast strains for their ability to grow on xylose and isolate the relevant gene(s) from the best of them.  Sounds easy enough except that most of the strains they’ve found are terrible sporulators.  This means that they couldn’t use conventional methods to isolate the genes they were interested in and so had to come up with new methods.

First they needed to find some way to get the strain to sporulate.  They were able to force sporulation by creating a tetraploid intermediate between the xylose fermenting strain, CBS1502, and the reference strain, CBS7001, by adding an inducible HO gene.  During this process, they noticed that the ability to utilize xylose segregated in a 3:1 pattern.  This usually means that two genes are involved.

They next needed a way to identify these two genes.  What they did was to pool 21 spores that could ferment xylose and 21 that could not.  They then purified the DNA from each pool and compared them using high throughput sequencing.  They eventually found two genes that were key to getting this yeast to use xylose as its carbon source.  (They also found at least two other “bonus” genes that seemed to boost its ability to use xylose).

One of the genes, GRE3, was a known member of a xylose utilization pathway.  But the other gene, the molecular chaperone APJ1, was not known to be involved in metabolizing xylose.  The authors hypothesize that APJ1 might stabilize the GRE3 mRNA.

These two genes may not be enough to create an industrially viable, xylose fermenting Saccharomyces just yet.  But the novel methods of gene isolation presented in this study may allow researchers to find additional genes that might one day get them there.  Then we will have a way to get ethanol without the large carbon footprint and without the human cost.

 

A genetic engineering approach to getting yeast to ferment agricultural waste

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

Cancer’s Chromosomal Chaos Explained (Partly)

June 1, 2012

Because they have the wrong number of chromosomes, cancers can sample many different genetic combinations.

One reason cancer is so tricky to treat has to do with its adaptability.  It can quickly try out new genetic combinations until it hits upon one that can survive whatever treatment a doctor is currently throwing at it.  The result is return of the cancer after remission.

One way cancer is able to change its genetics so rapidly has to do with chromosome instability.  The number of chromosomes in a cancer cell is much less stable than in a normal cell.  This allows the cancer cell to constantly explore a wide range of chromosomal combinations.

It is still an open question how this dynamic instability happens.  The gene-centric theory suggests that mutations in key genes are the main driving force.  The chromosome-centric model says that having the wrong number of chromosomes is the critical component.

Distinguishing between these two models using cancer cells has proven difficult because these cells always have mutated genes.  There is simply no way to look at just chromosome numbers in this system.  This is where yeast can help.

In a recent paper published in PLoS Genetics, Zhu and coworkers used yeast to explore whether altered chromosome number was sufficient to explain chromosome instability.  They found that chromosome numbers alone can explain some but not all of chromosomal instability.

The authors created various chromosomal combinations in yeast by sporulating isogenic triploid yeast cells.  These cells had different numbers of genetically identical chromosomes.  They then explored the stability of each chromosome number combination using both FACS and qPCR.

What they found was that chromosome number certainly impacted chromosomal stability.  Chromosome number became less and less stable as the chromosome number veered further and further from the haploid state.  Of course, once the cells became diploid, stability returned. 

The authors explain this with the idea that there is only so much cellular machinery to move chromosomes to the proper place during mitosis.  As more and more chromosomes are added to the cell, the machinery becomes increasingly taxed, resulting in more and more errors. 

But once the diploid state is reached, all the genes are present to make twice as much mitotic machinery.  Now stable chromosome segregation can happen.

This was the broad pattern Zhu and coworkers observed but it certainly wasn’t the whole story.  The authors found islands of stability in the chromosomal chaos. 

For example, very often when there were equal numbers of chromosome VII (ChrVII) and chromosome X (ChrX), the chromosome number was more stable than predicted.   They explored this further and found evidence that suggested that at least part of this was due to the MAD1 gene on ChrVII and the MAD2 gene on ChrX. 

Stable chromosome numbers required that these genes be present in a 1:1 ratio.  Once the ratio strayed from one, chromosomal instability increased.  But these genes don’t explain everything.  There were unstable combinations where the MAD1/MAD2 ratio was correct.  As might be expected, there are other gene combinations that can lead to instability as well.

So incorrect chromosome number alone can explain the chromosomal instability seen in cancer cells.  But genes clearly play a role too, as evidenced by the islands of stability and the MAD1 gene and MAD2 genes.  As usual, reality is probably a combination of the two models. 

So it looks like chromosome number does play an important role in chromosomal instability.  Too many chromosomes may overtax the mitotic machinery so that chromosomes end up mis-segregated.

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