FY2010 - Oak Ridge National Laboratory

Director’s R&D Fund—
Systems Biology and the Environment
ORNL annotation pipeline are being made using some of the methods developed in this project that will
help transition toward this eventual future.
The $3.2 million American Resource and Recovery Act (ARRA)–funded Knowledgebase R&D project
(Dr. Susan Gregurick, Program Manager for Computational Biology, DOE Office of Biological and
Environmental Research) developed the Implementation plan for the new DOE Systems Biology
Knowledgebase. There are six high-priority scientific objectives including one on Microbial Gene
Expression Regulatory Networks. Robert Cottinghamis is PI of this project and also an author of this
scientific objective, which is very likely to be part of the next phase expected to be funded in FY 2010.
We have ongoing discussions with Battelle Corporation, the Defense Department, the Department of
Homeland Security, and the University of Tennessee faculty about using RNAseq transcriptomics for
biodefense forensics, as well as an approach for studying host pathogen interactions.
Information Shared
Quest, D. J., M. L. Land , T. S. Brettin, and R. W. Cottingham. 2010. “Next Generation Models
for Storage and Representation of MicrobialBiological Annotation.” BMC Bioinformatics
11(Suppl. 6), S15.
05201
Development of Novel Biocatalysts for the Production of Fuels and
Chemicals from Synthesis Gas
James G. Elkins, Rishi Jain, Abhijeet P. Borole, Jonathan Mielenz, Zamin Koo Yang, Yunfeng Yang
(David),
and Brian H. Davison
Project Description
Biosynthesis gas (syngas) is an energy-rich feedstock produced from the gasification of lignocellulosic
biomass. Biotechnological improvements in syngas utilization have been difficult due to the lack of
industrial strains that can be manipulated at the genetic level. To tackle this, we will develop novel
biocatalysts amenable to genetic engineering. Robust genetic systems in syngas-utilizing strains would
allow manipulation of carbon fixation pathways and redirection of carbon flux towards alcohols and
potentially other high-value chemicals. For biofuel production, we plan to engineer organisms that are
capable of fixing the carbon and energy available from syngas into the 4-carbon alcohol 1-butanol.
Butanol is known to possess advantages over ethanol including a higher energy density, and it can be
blended directly with gasoline at increased concentrations. Our research plan includes these primary
goals: (1) rational engineering of Rhodospirillum rubrum to produce butanol, (2) characterization of
butanol-producing strains of R. rubrum using bench-scale fermentation and determination of solvent
tolerance and rates of production, and (3) development of genetic tools for other syngas-utilizing Grampositive
microbes. These tasks will be carried out in parallel and then integrated in year 2, depending on
our results.
Mission Relevance
The project is relevant to several current programs and the overall mission of the Biomass Program of the
DOE Office of Energy Efficiency and Renewable Energy, which has increased interest in gasification
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