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Wood-eating Gribbles Could Show How to Convert Waste to Biofuel

Wed, 06/26/2013 - 1:42pm
Skip Derra

Limnoria—the wood-eating gribble. (Source: Laura Michie, Portsmouth University, with assistance from Alex Ball from the Natural History Museum)The gribble, a wood-boring marine isopod long has been considered nothing more than a nautical nuisance. Its specialty is boring its way into the wooden hulls of ships, turning seafaring into an even more perilous undertaking.

But new research that shows how the gribble digests wood could hold a key to the production of carbon-neutral fuels from waste.

Simon McQueen-Mason has seen the destructive power of the tiny gribble first hand. Before he became a plant scientist, McQueen-Mason—who today works in the Centre for Novel Agricultural Products at the University of York, Heslington, York, UK—was a commercial fisherman who owned his own wooden-hulled fishing boat.

“Gribbles thrive on a diet of wood, a notoriously hard to digest material,” McQueen-Mason said. “I’m very familiar with their destructive power. So I thought they might be interesting to study.”

Specifically, McQueen-Mason and his team have been studying an enzyme found in the gribble that could show the way to breaking down wood into simple sugars. Their work could lead the way in turning waste—paper, scrap wood and straw—into liquid fuel.

The research team—from University of York, University of Portsmouth, Hampshire, UK, and the National Renewable Energy Laboratory, Golden, Colo.—have used advanced biochemical analysis and x-ray imaging techniques to determine the structure and function of the enzyme used by the gribble.

Simon McQueen-MasonTo create liquid fuel from woody biomass, the polysaccharides (sugar polymers) that make up the bulk of these materials have to be broken down into simple sugars. These sugars are then fermented to produce liquid biofuels. Current methods of breaking down the woody biomass are very expensive, so some scientists are studying natural organisms that can break down wood in the hope of developing industrial processes that can do the same.

This is where the gribble comes in.

“Gribbles are unusual because they have a microbe-free digestive system, unlike other animals,” he explained. “This means they do not (as found in termites, etc.) have microbial assistance in digesting wood.”

This was an advantage in the research, McQueen-Mason said.

“This provides an opportunity to identify a relatively smaller set of digestive enzymes than in animals working with microbes,” he said. “We surveyed the genes expressed in the digestive system and found 25 percent of these encode likely glycosyl hydrolases—enzymes that convert polysaccharides into simple sugars. Of these, the most abundant encoded a predicted cellulase of a class not seen before in animals but used by wood-degrading fungi.”

“We cloned the gene encoding of this cellulase and expressed it in a fungus to produce enough of the enzyme to characterize it at biochemical and structural levels,” McQueen-Mason explained.

He added that the biochemical studies measured how quickly the enzyme converts cellulose to simple sugars under various conditions. The structural work involved making crystals of the proteins and shooting powerful x-ray beams at them. They then recorded the x-ray scattering and developed a 3-D image of what the enzyme looks like in atomic detail to help understand how it breaks down cellulose.

The 3-D structure shows the tunnel where the enzyme feeds in the cellulose chains for digestion. The red color represents the highly acidic surface that allows it to be stable and active in very high salt condition. (Source: John McGeehan, the University of Portsmouth)John McGeehan, team member and a structural biologist from the University of Portsmouth said that once they made the crystals they transported them to the Diamond Light Source, a UK national synchrotron facility.

“The Diamond synchrotron produced such good data that we could visualize the position of every single atom in the enzyme,” McGeehan said. “Our U.S. colleagues then used powerful supercomputers to model the enzyme in action. Together these results help to reveal how the cellulose chains are digested into glucose.”

“This is the first fully functional characterized animal enzyme of this type and provides us with a previously undiscovered picture of how they work,” McQueen-Mason added.

“While this enzyme looks superficially similar to equivalent ones from fungi, closer inspection highlights structural differences that give it special features. For example, the enzyme has an extremely acidic surface and we believe that this is one of the features that contribute to its robustness,” he explained.

“The enzyme is very stable in the presence of salt, something not seen in fungal equivalents, and this may be associated with an unusual acid coating on the enzyme,” McQueen-Mason said. “This unusual property may make it useful for processing in seawater (cheaper and more environmentally sustainable than fresh water) or in conjunction with ionic liquids.”

The team has transferred the genetic blueprint of the enzyme to an industrial microbe that can produce it in large quantities, in the same way enzymes for biological washing detergents are made.

"The robust nature of the enzymes makes it compatible for use in conjunction with sea water, which would lower the costs of processing,” McQueen-Mason said. “Lowering the cost of enzymes is seen as critical for making biofuels from woody materials cost effective. Its robustness would also give the enzymes a longer working life and allow it to be recovered and re-used during processing."

McQueen-Mason added that the industrial partner, Novozymes, could scale up the process in a year or less.

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