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JBEI researchers discover gene to modify xylan for easier extraction and saccharification; most abundant biomass material after cellulose

Researchers with the US Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI) have identified a gene in rice plants the suppression of which improves both the extraction of xylan and the overall release of the sugars needed to make biofuels.

The newly identified gene—dubbed XAX1—acts to make xylan less extractable from plant cell walls. JBEI researchers, working with a mutant variety of rice plant—dubbed xax1—in which the XAX1 gene has been knocked-out found that not only was xylan more extractable, but saccharification—the breakdown of carbohydrates into releasable sugars—also improved by better than 60%. Increased saccharification is key to more efficient production of advanced biofuels.

After cellulose, xylan is the most abundant biomass material on Earth, and thus is theoretically an enormous potential source of stored solar energy for the production of advanced biofuels. A major roadblock, however, has been extracting xylan from plant cell walls. The discovery by the JBEI team marks a significant step towards removing this roadblock.

In identifying XAX1 as a xylan biosynthetic protein, the first enzyme known to be specific to grass xylan synthesis, we’ve shown that xylan can be modified so as to increase saccharification. Our findings provide us with new insights into xylan synthesis and how xylan substitutions may be modified for increased biofuel generation.

—Henrik Scheller, head of JBEI’s Feedstocks Division and director of its Cell Wall Biosynthesis group

Scheller, who also holds an appointment with Lawrence Berkeley National Laboratory, is a co-author of a paper describing this work published in Proceedings of the National Academy of Sciences (PNAS). The corresponding author is Pamela Ronald, who holds joint appointments with JBEI and the University of California (UC) Davis. Other authors were Dawn Chiniquy, Vaishali Sharma, Alex Schultink, Edward Baidoo, Carsten Rautengarten, Kun Cheng, Andrew Carroll, Peter Ulvskov, Jesper Harholt, Jay Keasling and Markus Pauly.

Xylan, like cellulose, is a major component of plant cell walls that serves as a valuable source of human and animal nutrition. Despite its importance, few of the enzymes that can synthesize xylan-type polysaccharides have been identified. It is believed that xylan plays an essential structural role in plant cell walls through cross-linking interactions with cellulose and other cell wall components.

Xylan is of particular interest for the improvement of feedstocks for the generation of cellulosic biofuels, a currently expensive and inefficient process. Xylan inhibits access of the enzymes that break down cellulose into sugars and is an additional substrate for cross-linking to lignin, all of which contributes to the recalcitrance of plant cell walls.

—Pamela Ronald

To find genes important for grass xylan biosynthesis, Ronald, Scheller and their co-authors focused on the GT61 family of glycosyltransferases. GT61 enzymes have been identified through bioinformatics as being expanded in grasses and containing grass-specific subgroups. Working with rice plants, the standard plant model for studying grasses, they conducted a reverse genetics screen of 14 genes with insertional rice mutants that are highly expressed members of the GT61 family. This led them to the identification of a mutant plant they named xax1 because its mutation resulted in the function of the XAX1 being knocked-out.

XAX1 adds a specific xylose sugar to the arabinose substitutions on the xylan chain that creates more cross-links between xylan and lignin, making the plant cell walls less amenable to the production of biofuels. Without a functioning XAX1 gene, there were fewer cross-links with lignin, which made the xylan more extractable and also increased saccharification.

—Dawn Chiniquy, first author

Subsequent assays showed the rice xax1 mutant plants to be deficient in ferulic and coumaric acid, aromatic compounds whose residues on arabinose are known to promote cross-linking between xylan chains the lignin. On the down-side, the xax1 mutant did yield a dwarf phenotype, but Scheller says he and his colleagues have already found a way to avoid the dwarf phenotype.

We can apply the same principle used to make rice plants more easily saccharified to bioenergy crops. With the ability to modify cross-linking between xylan and lignin by targeting a glycosyltransferase, we also now have a potentially important new biotechnological tool for grass biofuel feedstocks.

—Henrik Scheller

This research was primarily funded by the DOE Office of Science.


  • Dawn Chiniquy, Vaishali Sharma, Alex Schultink, Edward E. Baidoo, Carsten Rautengarten, Kun Cheng, Andrew Carroll, Peter Ulvskov, Jesper Harholt, Jay D. Keasling, Markus Pauly, Henrik V. Scheller, and Pamela C. Ronald (2012) XAX1 from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan PNAS 109 (42) 17117-17122 doi: 10.1073/pnas.1202079109



The recalcitrance of plant cell walls evolved for a reason.  How much more susceptible will this modified rice be to e.g. fungal attack?

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