The Genomic Science program within the Office of Biological and Environmental Research (BER) supports basic, multidisciplinary research aimed at achieving a systems-level understanding of plants, microbes, and microbial communities relevant to Department of Energy (DOE) missions in bioenergy, carbon management, and the environment. To provide the scientific foundation for a bio-economy in which new biological systems can be designed to address DOE missions, it is necessary to identify and articulate fundamental biological principles that govern biology from the molecular to the community level. These principles will allow us to predict the behavior of biological systems under changing conditions. Moreover, to be able to tailor their behavior for defined purposes, it will be necessary to re-engineer these biological systems or design new ones. Novel biosystems design tools and technologies will in turn help us better understand natural systems and their response to natural or man-made environmental inputs. Technologies developed in recent years have taken engineering of living systems to a new level, but significant advances are needed to achieve a comprehensive predictive understanding of biological systems to enable re-design of novel organisms. It is also necessary to develop computer-aided design of biological systems by leveraging other activities in the computational biosciences to predict, design, construct, and test multiscale natural and hybrid biological systems that will lead to new clean energy solutions.
In 2012, BER solicited integrated interdisciplinary applications for (1) highly innovative, fundamental genomics and systems biology research and (2) technology development for biosystems design that addresses DOE missions within two focused research areas:
Optimizing oil production in oleaginous yeast by cell-wide measurements and genome-based models
This project will take advantage of an engineered strain
of the oleaginous yeast Yarrowia lipolytica that can
produce high yields of lipids from carbohydrates and
organic acids. A genome-scale dynamic metabolic
modeling approach called Ensemble Modeling, aided
by transcriptomics and metabolomics analysis of lipid
content, will be conducted to guide further re-design
and engineering of Y. lipolytica strains for increased
lipid production. Newly optimized yeast strains
showing high oil yields from sugars abundant in
biomass as well as from acetate, which can be the
product of inexpensive anaerobic cellulose degradation,
will potentially lead to new and efficient ways for
biodiesel production.
A platform for genome-scale design, redesign, and optimization of bacterial systems
Building upon genome engineering technologies
developed by the applicants' laboratories as well as
others, the researchers will engineer Escherichia coli strains with enhanced recombineering capabilities,
optimized for the production of ethylene and isobutanol
that can be directly converted into biofuels.
These strains will be used for the development of a
next-generation high-throughput synthetic biology
and genomic engineering technology platform for predictive
design of DOE-relevant bacterial systems for
biofuel production. Multiplexed mutational strategies
will be developed to induce genome-wide changes not
only in individual promoters but also in other regulatory
features and open reading frames. Iterative cycles
of metabolic modeling and high-throughput screening
will allow the optimization of re-designed biofuelproducing
strains.
Optimization of energy flow through synthetic metabolic modules and regulatory networks in a model photosynthetic eukaryotic microbe
This project will generate genome-scale metabolic
models of the diatom Phaeodactylum tricornutum informed by multiple "omics" techniques, metabolic
flux, protein localization, and protein interaction data.
Comparative modeling analysis of diatoms and other photosynthetic organisms will be used to identify key
regulatory elements that will be targeted for reprogramming
gene and metabolic networks to enhance
carbon and energy flux toward the production of lipidbased
biofuels. Genomic engineering technologies to
introduce large extrachromosomal DNA segments
into diatoms will be developed using yeast and E. coli intermediates to obtain new diatom strains with high
oil content.
Assembling reusable genetic modules for efficient biofuel production from marine macroalgae
In order to take advantage of the lack of lignin and
crystalline cellulose in the cell wall of brown macroalgae,
this project will investigate algae-associated
microbes to identify new metabolic modules capable
of degrading the brown algae carbohydrates such as
alginate, laminarin, and fucoidan, thus circumventing
the recalcitrance problem of land plants whose
lignocellulosic cell walls are very difficult to degrade.
In addition to known algae-associated candidate
microbes, uncultured microorganisms will be analyzed
by fluorescence-based screening and single-cell
genomics methods to identify new metabolic capabilities.
Genetic modules comprising selected metabolic
pathways will be engineered in yeast and E. coli using
a one-step method for the design and construction
of biosynthetic pathways that can be tuned with a
combinatorial transcriptional engineering approach for
heterologous gene expression.
Modeling and manipulating phenylpropanoid pathway flux for bioenergy
This project will develop advanced kinetic models for
the plant shikimate and phenylpropanoid/phenylalanine
pathways using Arabidopsis as a model system to
allow predictive design of experiments to modulate
fluxes toward desired products. The investigators will
carry out flux measurements in plants with altered
lignin and phenylalanine pathways, including plants
expressing a novel hydroxylase that reroutes lignin synthesis,
uncoupling it from the shikimate pool levels.
As a proof of concept, they will engineer plants for the
production of 2-phenylethanol, which is a promising
biofuel candidate due to its high energy density, low
hygroscopicity, and low volatility.
A systems-level analysis of drought and density response in the model C4 grass Setaria viridis
This multidisciplinary research team will address two
important challenges to developing high-yield bioenergy
crops that can grow in arid, marginal lands to
avoid land competition with food crops. The project
will start by conducting an extensive quantitative trait
loci (QTL) study of drought tolerance and planting
density in the model C4 grass Setaria viridis, which is
a close relative of biomass crops such as switchgrass,
sugarcane, sorghum, and Miscanthus. Extensive molecular and physiological studies will be carried out in
selected lines to build integrated metabolic and genetic
networks; candidate genes will then be analyzed in the
context of those network models. New transformation
technologies will be tailored for Setaria biodesign,
and methods for monitoring flow of transgenes will be
developed as part of this project.
Engineering CAM photosynthetic machinery into bioenergy crops for biofuels production in marginal environments
Crassulacean Acid Metabolism (CAM) is a photosynthetic
CO2 fixation mechanism common in plants that
grow in hot and arid environments to maximize water
use efficiency. This project will attempt to engineer a
functional CAM pathway in poplar and Arabidopsis.
The introduction of this metabolic machinery into a
bioenergy crop such as poplar will increase its water
use efficiency allowing cultivation in marginal lands
for biofuel production. Genomics and systems biology
analyses of monocotyledonous and dicotyledonous
CAM species will identify the necessary carbon assimilation
and stomatal control modules for engineering
C3 plants such as poplar, as well as the model plant
Arabidopsis, to acquire CAM metabolism.
Expanding the breeder's toolbox for perennial grasses
The goal of this project is to engineer the bioenergy
crop switchgrass to facilitate molecular breeding
approaches for genetic improvement, overcoming
major problems posed by its tetraploid nature and the
lack of inbred lines. Investigators will engineer new
tools to dramatically advance breeding in switchgrass
by developing homozygous plants through the generation
of double haploids. To do this, the researchers
will create a mutant in a centromere-specific histone
that produces haploid plants, which can be diploidized
upon crossing to wild type individuals. This project will
also use a perennial Brachypodium sylvaticum model
system to understand and improve drought tolerance
and nutrient use efficiency and to develop new tools
for further genomic engineering of perennial grasses.
Translation of these technologies to switchgrass will
include the development of transgenic systems to minimize
gene flow.
Dr. Pablo Rabinowicz
U.S. Department of Energy
Office of Biological and Environmental Research
Phone: 301-903-0379
E-Mail: pablo.rabinowicz@science.doe.gov