June 16, 2012
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
Categories: Research Spotlight
Tags: biofuel, biomass, ethanol, fermentation, lignocellulosic biomass, Saccharomyces, Saccharomyces cerevisiae, yeast