Walnut Creek, California
August 13, 2008
Genomics is accelerating
improvements for converting plant biomass into biofuel—as an
alternative to fossil fuel for the nation's transportation
needs, reports Eddy Rubin, Director of the
U.S. Department of Energy Joint
Genome Institute (DOE JGI), in the August 14 edition of the
journal Nature. In "Genomics of cellulosic biofuels," Rubin lays
out a path forward for how emerging genomic technologies will
contribute to a substantially different biofuels future as
compared to the present corn-based ethanol industry—and in part
mitigate the food-versus-fuel debate. The Nature Review is
available for download (by subscription) at
http://www.nature.com/.
"The Apollo moon shot and the Human Genome Project rallied
support for massive R&D efforts that created the capabilities to
overcome obstacles that were not contemplated at the outset of
these initiatives," says Rubin. "Similarly, today's barriers to
improving biofuels are significant, but genetics and genomics
can catalyze progress towards delivering, in the not-too-distant
future, economically-viable and more socially acceptable
biofuels based on lignocellulose."
While Rubin acknowledges that this strategy is in its infancy,
rapid progress is being made.
"Over the past 10,000 years, wild plant species were selected
for their desirable traits resulting in today's highly
productive food crops. We simply don't have thousands of years
in the face of the energy and climate challenges, so by applying
the power of genomics to these problems, we are seeking to speed
up the domestication of energy crops and the technologies for
converting them to suitable biofuels as a more carbon-neutral
approach to meeting part of our transportation needs."
In the Nature Review, Rubin describes the processes entailed in
biofuel production from lignocellulose: the harvesting of
biomass, pretreatment and saccharification, which results in the
deconstruction of cell wall polymers into component sugars, and
then the conversion of those sugars into biofuels through
fermentation. Each step, he says, offers an opportunity for
genomics to play a significant role.
"With the data that we are generating from plant genomes we can
home in on relevant agronomic traits such as rapid growth,
drought resistance, and pest tolerance, as well as those that
define the basic building blocks of the plants cell
wall—cellulose, hemicellulose and lignin. Biofuels researchers
are able to take this information and design strategies to
optimize the plants themselves as biofuels feedstocks—altering,
for example, branching habit, stem thickness, and cell wall
chemistry resulting in plants that are less rigid and more
easily broken down."
For microbial biomass breakdown, Rubin says that many candidates
have already been identified. These include Clostridia species
for their ability to degrade cellulose, and fungi that express
genes associated with the decomposition of the most recalcitrant
features of the plant cell wall, lignin, the phenolic "glue"
that imbues the plant with structural integrity and pest
resistance. The white rot fungus Phanerochaete chrysosporium
produces unique extracellular oxidative enzymes that effectively
degrade lignin by gaining access through the protective matrix
surrounding the cellulose microfibrils of plant cell walls.
Another fungus, the yeast Pichia stipitis, ferments the
five-carbon "wood sugar" xylose abundant in hardwoods and
agricultural harvest residue. Rubin says that Pichia's recently
sequenced genome has revealed insights into the metabolic
pathways responsible for this process, guiding efforts to
optimize this capability in commercial production strains.
Pathway engineering promises to produce a wider variety of
organisms able to ferment the full repertoire of sugars derived
from cellulose and hemicellulose and tolerate higher ethanol
concentrations to optimize fuel yields.
Rubin also touches on the emerging technology of
metagenomics—characterizing, without the need for laboratory
culture, the metabolic profile of organisms residing in an
environmental sample—for the identification of enzymes suitable
for industrial-scale biofuel production.
"Using this prospecting technique, we can survey the vast
microbial biodiversity to gain a better picture of the metabolic
potential of genes and how they can be enlisted for the
enzymatic deconstruction of biomass and subsequent conversion to
high energy value fuels."
As an example, Rubin cites an analysis of the hindgut contents
of nature's own bioreactor, the termite, (published in Nature
(450, 560-565 [22 November 2007]), which has yielded more than
500 genes related to the enzymatic deconstruction of cellulose
and hemicellulose.
The Nature Review goes on to list the feedstock genomes,
microbial "biomass degraders," and "fuel producers" completed or
in progress. These include the first tree genome completed—that
of the poplar Populus trichocarpa and other plants in the
sequencing queue, such as soybean, switchgrass, sorghum,
eucalyptus, cassava, and foxtail millet. In addition, Rubin
points to oil-producing algae as an alternative source for
biodiesel production—with the alga Chlamydomonas reinhardtii, as
just one of several algal species that has been characterized
for their ability to efficiently capture and convert sunlight
into energy.
"Given the daunting magnitude of fossil fuel used for
transportation, we will likely have to draw from several
different sources to make an appreciable impact with cellulosic
biofuels, all of which will in some significant way will be
informed by genomics," says Rubin.
"Toward this end, rapid new sequencing methods and the
large-scale genomics previously applied to sequencing the human
genome are being exploited by bioenergy researchers to design
next-generation biofuels, higher-chain alcohols and alkanes,
with higher energy content than petroleum and more adaptable to
existing infrastructure."
The U.S. Department of Energy Joint Genome Institute,
supported by the DOE Office of Science, unites the expertise of
five national laboratories -- Lawrence Berkeley, Lawrence
Livermore, Los Alamos, Oak Ridge, and Pacific Northwest -- along
with the Stanford Human Genome Center to advance genomics in
support of the DOE missions related to clean energy generation
and environmental characterization and cleanup. DOE JGI's Walnut
Creek, CA, Production Genomics Facility provides integrated
high-throughput sequencing and computational analysis that
enable systems-based scientific approaches to these challenges.
Additional information about DOE JGI can be found at:
http://www.jgi.doe.gov/.
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