Researchers see breakthrough in building better biofuels 

Source: Niina Heikkinen, E&E reporter • Posted: Monday, January 12, 2015

A recent study is bringing scientists a step closer to determining how plants regulate their cell wall thickness and strength, an advance that could make biofuel production more efficient.

Two groups of researchers at the University of Massachusetts, Amherst, and the University of California, Davis, have found the gene regulatory networks that are responsible for the synthesis of the secondary cell wall components, cellulose, hemicellulose and lignin in the model plant Arabidopsis thaliana.

Learning how to control the composition of secondary cell walls is an area of intense interest among advanced biofuel researchers because the structures make up the bulk of the plant matter that is broken down into biofuels. The researchers focused on the secondary cell walls in a type of plant tissue called xylem from the Arabidopsis plant’s roots.

Of the three cell wall components, lignin is the most troublesome for the biofuel industry because it limits the extraction of cellulose and hemicellulose for biofuel production, according to Siobhan Brady, an assistant professor in the Department of Plant Biology and Genome Center at UC Davis and a co-author of the study.

Eliminating lignin from secondary cell walls isn’t an option, since the rigid polymer plays an essential role in the plant’s waterproofing, stability and protection. “It’s a Catch-22,” Brady said.

Instead, “biofuel researchers would like to breed plants with differing amounts of cellulose, hemicellulose or lignin. Ideally, with less lignin,” she said.

Until this study, researchers weren’t able to manipulate production of the different components independently of each other, since many of the transcription factors, proteins that bind to the plant’s DNA and regulate gene expression, are redundant.

Solving a puzzle of plant manipulation

Rather than try to isolate single genes related to secondary cell wall production, the researchers looked at the function of hundreds of transcription factors working within the root xylem’s regulatory network. Using both computer modeling and laboratory experiments, they discovered that it was possible to enhance the production of individual components of the cell wall under certain stress conditions by regulating different transcription factors.

“Now that we have shown that the transcriptional control of these enzymes can be uncoupled, we want to try to subtly control differing ratios of each of these compounds using predictions made from our network,” Brady said.

The researchers identified a network of more than 240 genes and more than 600 interactions between protein and DNA that researchers had not known existed, according to Samuel Hazen, a plant geneticist at UMass Amherst and a co-author of the study.

The findings were published in the journal Nature.

“What was really cool about this research was we’ve known for a long time that a lot of different transcription factors were involved, but it was hard to understand how all the pieces fit together,” said Jenny Mortimer, director of plant systems biology at the Joint BioEnergy Division, a part of the Department of Energy. “They screened for lots and lots of interactions, and what they pulled out was really surprising.”

The study showed that “the control of the secondary cell wall is incredibly complex and detailed, which is important for plant biologists who want to change it to make biofuels,” she said. “This gives us a way to really tweak the system to the way we want.”

The researchers also found that instead of acting as a series of on-off switches for genes, many of the transcription factors are part of feed-forward loops. In gene regulation, this means that when X activates Y, X and Y both can activate Z. This type of regulation allows for a diverse array of responses to environmental stressors like high salinity or drought, according to the researchers.

Having that level of complexity is a benefit for biofuel researchers because it gives them more options to work with, Mortimer said.

Looking for weedy candidates

The research represents just one of several ways scientists are altering plants to maximize their ability to produce cellulose and hemicellulose for biofuels, said Laura Bartley, an assistant professor in the Department of Microbiology and Plant Biology at the University of Oklahoma.

“One way is to make biomass denser, so you have bigger plants on the same amount of land. The second is to reduce the impact of the plants, by using plants that can grow on very poor soils, that don’t need as much nitrogen or water. The third is a study like this one to improve lignocellulosic materials so you can get as much fuel as possible,” she said.

In addition to looking at transcription factors, researchers have studied the genes that code for the enzymes responsible for building up the plant’s biomass. While previous research had identified the presence of feed forward loops in plant gene regulation, “this study increases the scale enormously,” said Bartley.

That does not mean that scientists will necessarily be able to use this research to create plants with more easily digestible complex sugars in the very near future.

“One of the things that’s important to note is that Arabidopsis is a little weed that won’t be used as a biofuel,” said Barley. “We want to know how this system works in all different cell types and in plants that we are interested in for biofuels.”

Bartley is among a number of researchers investigating how research on plants can be applied to grasses like sorghum and switchgrass.

Through genetic mapping, her lab has found that many of the genes in Arabidopsis are also conserved in grasses; however, that does not guarantee that transcription factors in the plant would work the same way.

A few more years to go

On the West Coast, Brady’s lab is also looking at transcription factors in sorghum. In Massachusetts, Hazen’s lab is researching Brachypodium distachyon, a type of wild grass that is an evolutionary intermediary between Arabidopsis and grasses used for biofuels.

Even if researchers discover how to regulate complex sugars in secondary cell walls in biofuel feedstocks, the next challenge will be finding how much lignin the plants can do without and still remain healthy. Plants without enough lignin can have problems with their xylem tissues collapsing, inhibiting water and nutrient transfer from the plant’s roots.

One strategy, which has already been successfully tested by Dominique Loque’s research team at the Lawrence Berkeley National Laboratory, could be to rewire plants to get rid of lignin in places where it is not as necessary, while also increasing the amount of cellulose, said Bartley.

Mortimer predicted that it could take roughly 10 to 15 years before scientists are able to use transcription factor regulatory networks to control secondary cell wall composition. According to Brady, it will be at least a few more years before transcription factors in grasses like sorghum and switchgrass are identified.

To Hazen, it is “absolutely realistic” that researchers will be able to use their research to create better biofuel feedstocks. “We’re making excellent progress,” he said.

Funding for the study was provided by DOE’s Joint BioEnergy Division.