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As the national push for alternative energy sources heats up, researchers at
the University of Rochester have for the first time identified how genes
responsible for biomass breakdown are turned on in a microorganism that
produces valuable ethanol from materials like grass and cornstalks, March
2007.

Waste products such as grass clippings and wood chips - once thought too
difficult to turn into ethanol - may soon be fodder for hungry, gene-tweaked
bacteria. The findings in the Proceedings of the National Academy of
Sciences may empower scientists to engineer ethanol-producing
super-organisms that can make clean-burning fuel from the nation's one
billion unused tons of yearly biomass production.

"This is the first revelation of how a bacterium chooses from its more than
100 enzymes to break down a particular biomass," says David H. Wu, professor
in the Department of Chemical Engineering at the University of Rochester.
"Once we know how a bacterium targets a particular type of biomass, we
should be able to boost that process to draw ethanol from biomass far more
efficiently that we can today."

Ethanol holds the promise of a clean, renewable alternative to fossil fuels,
but deriving it from plants is difficult. Producing it from corn is the
easiest method, but doing so on a large scale would drive up the price of
corn, corn starch, and even tangential foods like beef, since cows are fed
on corn - not to mention all the energy spent fertilizing, maintaining, and
harvesting a crop like corn. Conversely, deriving ethanol from plant
materials such as the corn stalks and wood chips is challenging because the
plants - cellulose is a very tough substance to break down, making for an
inefficient process.

Wu's technique may prove much more effective than traditional methods.
Instead of using separate steps to break down biomass into glucose and
ferment the glucose into ethanol, as is currently done, Wu is working on a
way to make a bacterium break down and ferment plant biomass efficiently in
just one step.

Wu investigated C. thermocellum, which is a microorganism that has that
ability to turn biomass into ethanol in one step, but is not used at the
industrial scale yet because the first step, breaking down the plant's
cellulose, is much too inefficient. The key, Wu surmised, is to find out
what enzymes the bacterium uses to accomplish its feat, and then boost its
ability to produce those enzymes. The problem, however, lies in the fact
that C. thermocellum uses more than 100 enzymes, and any of the millions of
combinations of them may be the magic mixture to break down a particular
biomass.

So, Wu decided to make the bacterium do the work for him.

"The bacteria know how to express just the right genes to break down any
particular biomass substrate, and we wanted to know how they know to turn on
and off just the right genes at the right time to do the trick," says Wu.
"We found the bacterium essentially throws the whole bowl of spaghetti at
the wall, sees what sticks, and then makes a lot of that particular noodle."

C. thermocelllum produces low levels of many of its enzymes at any one time.
When the bacterium comes in contact with wood, for instance, a few of its
enzymes break down some of that wood. A product of that tiny reaction is a
sugar called laminaribiose that diffuses into the cell. There it deactivates
a repressor for two genes, which wake up and start pumping out the two
triggers the full production of wood-degrading enzymes CelC and LicA.

Wu's paper shows the first time the triggering pathway for enzyme production
in this bacterium has been revealed, and it was only possible because C.
thermocellum genome was just recently sequenced, thanks to Wu's
collaboration with the U. S. Department of Energy. With its 100 busy
enzymes, the entire genome had to be observed as a whole, since fiddling
with combinations of two, three, or more enzymes at a time would have taken
"more than our lifetime," Wu says.

Wu is now working to re-engineer C. thermocellum to express an abundance of
particular genes so it can readily and efficiently produce ethanol from a
particular biomass. He's also continuing the genome-wide search for enzyme
combinations that will degrade and ferment grasses, corn stovers, and even
food waste.

"I don't think this is the revolution that makes ethanol a mainstay," says
Wu, "but I believe this is a part of what will lead to the revolution." This
research, also authored by Wu's graduate students Michael Newcomb and
Chun-Yu Chen, is funded by the U. S. Department of Energy.

[www.rochester.edu]