As a test of a bioenergy-related application of DNA sequencing and enzyme discovery, US Department of Energy Joint Genome Institute researchers led by the DOE JGI Director Eddy Rubin, and colleagues from the Joint BioEnergy Institute at DOE’s Lawrence Berkeley National Laboratory employed a cellulose-degrading enzyme from a salt-tolerant microbe that was isolated from the Great Salt Lake. Credit: David Gilbert, DOE JGI |
In
order to realize the full potential of advanced biofuels that are
derived from non-food sources of lignocellulosic biomass—e.g.,
agricultural, forestry, and municipal waste, and crops such as poplar,
switchgrass and miscanthus—new technologies that can efficiently and
cost-effectively break down this biomass into simple sugars are
required. Existing biomass pretreatment technologies are typically
derived from the pulp and paper industry and rely on dilute acids and
bases to break down the biomass. The treated biomass product is then
exposed to biological catalysts, or enzymes, to liberate the sugars.
A
new class of solvents, referred to as ionic liquids, have been reported
to be much more efficient in treating the biomass and enhancing the
yield of sugars liberated from it. While ionic liquids are useful for
breaking down biomass, they can also hinder the ability of the
cellulases (usually derived from fungi) used to produce sugars after
pretreatment. Ionic liquids are a liquid form of salt that will
inactivate enzymes by interfering with the folding of polypeptides—the
building-blocks of proteins. To help identify new enzymes that are
tolerant of ionic liquids, researchers from the U.S. Department of
Energy (DOE) Joint Genome Institute (JGI) and the Joint BioEnergy
Institute (JBEI) at DOE’s Lawrence Berkeley National Laboratory are
turning to those found in the complete genome sequences of halophilic
(salt-tolerant) organisms.
As
a test of this bioenergy-related application of DNA sequencing and
enzyme discovery, researchers led by the Director of the DOE JGI, Eddy
Rubin, and the Vice-President of the JBEI Deconstruction Division, Blake
Simmons, employed a cellulose-degrading enzyme from a salt-tolerant
microbe that was isolated from the Great Salt Lake. The microbe in
question, Halorhabdus utahensis, is from the branch of the tree of life
known as Archaea; H. utahensis was isolated from the natural environment
at the Great Salt Lake and sequenced at the DOE JGI as part of the
Genomic Encyclopedia of Bacteria and Archaea (GEBA) project.
“This
is one of the only reports of salt-tolerant cellulases, and the only
one that represents a true ‘genome-to-function’ relevant to ionic
liquids from a halophilic environment,” said Simmons of the study
published June 30, 2011 in Green Chemistry. “This strategy enhances the
possibility of identifying true obligatory halophilic enzymes.” Such
salt-tolerant enzymes, particularly cellulases, offer significant
advantages for industrial utility over conventional enzymes.
In
collaboration with Jerry Eichler from Ben Gurion University of the
Negev in Israel they cloned and expressed a gene from H. utahensis in
another haloarchaeal microbe, and were able to identify a salt-dependent
enzyme that can tolerate high temperatures and is resistant to ionic
liquids. “This project has established a very important link between
genomic science and the realization of enzymes that can handle very
demanding chemical environments, such as those present in a
biorefinery,” said Simmons.
The
group plans to expand this research to develop a full complement of
enzymes that is tailored for the ionic liquid process technology with
the goal of demonstrating a complete biomass-to-sugar process, one they
hope can enable the commercial viability of advanced biofuels.
Other
contributors to the project include Tao Zhang, Natalia Ivanova, Seth
Axen, Cheryl Kerfeld, Feng Chen, Nikos Kyrpides, Jan-Fang Cheng of the
DOE JGI along with Philip Hugenholtz now with The University of
Queensland, and Supratim Datta and Kenneth Sale of JBEI.
The
U.S. Department of Energy Joint Genome Institute, supported by the DOE
Office of Science, is committed to advancing genomics in support of DOE
missions related to clean energy generation and environmental
characterization and cleanup. DOE JGI, headquartered in Walnut Creek,
Calif., provides integrated high-throughput sequencing and computational
analysis that enable systems-based scientific approaches to these
challenges. Follow DOE JGI on Twitter.
