FY2010 - Oak Ridge National Laboratory

Director’s R&D Fund—
Systems Biology and the Environment
Objective 3. Structural analysis and modeling of the Ignicoccus–Nanoarchaeum system. We have
performed detailed structural modeling and molecular dynamics simulations of two major proteins
identified by proteomics. One of the two proteins, Igni_1226, is particularly important as it forms pores in
the outer membrane. Ongoing analyses are directed at understanding its potential role in metabolite
exchange with Nanoarchaeum, as well as in the overall bioenergetic processes of Ignicoccus, and the
results will be published as a stand-alone study.
Program Development
“From genomes to metabolomes: Understanding mechanisms of symbiosis and cell-cell signaling using
the archaeal system Ignicoccus–Nanoarchaeum.” Grant proposal submitted to DOE, September 2010.
Information Shared
Campbell, J., G. Flores, A. L. Reysenbach, and M. Podar. 2010. “A global biodiversity study of marine
and terrestrial hyperthermophilic nanoarchaea.” Poster at ISME 13 Meeting, Seattle, August.
Giannnone, R., M. Podar, and R. Hettich. 2010. “Elucidating the parasitic/symbiotic association between
the archaea Ignicoccus hospitalis and Nanoarchaeum equitans via differential proteomics.” Poster at
American Society of Mass Spectrometry Meeting, Salt Lake City, June.
Podar, M. 2010. “Functional genomics and diversity of hyperthermophilic Nanoarchaea.” Thermal
Biology Institute 2nd Annual Research Associates Meeting, Bozeman, MT, June 9.
Podar, M. 2010. “Functional genomic and evolutionary insights into the Nanoarchaeum–Ignicoccus
relationship.” ISME 13 Meeting, Seattle, August.
Podar, M. 2010. “Integrated proteomic and transcriptomic analysis of the Ignicoccus hospitalis–
Nanoarchaeum equitans relationship.” Extremophiles Meeting, Azores, September.
05256
Developing a Systems Biology Approach for Linking Genetic and
Environmental Constraints to Primary Productivity in Model and
Nonmodel Species
David J. Weston, Yunfeng Yang (David), Rich Norby, Stan Wullschleger, and Christopher W. Schadt
Project Description
Global warming is expected to drive major shifts in species composition in the coming decades, and these
community-level changes will greatly affect many important processes in terrestrial ecosystems. Given
the importance of this issue, it is unfortunate that we are still unable to associate specific genetic attributes
to the physiological traits that drive subsequent species compositional shifts. Using three plant model
species (Arabidopsis, soybean, and poplar), we will use a comparative network approach to identify
groups of genes that are conserved among species and that are associated with net CO 2 assimilation and
energy absorbance. These conserved genes or gene networks (i.e., modules) will provide a scaffold by
which orthologous genes from non-model species can be further evaluated for associations with net CO 2
and energy gain. We will test this approach using switchgrass, an important non-model species that is
adapted to a wide range of environments. Cultivars from contrasting habitats will be collected and used to
evaluate within-module gene sequences and expression variation to net CO 2 and energy gain under heat
stress and recovery conditions. Completion of the proposed work will provide a systematic framework for
identifying genetic and environmental constraints on plant productivity in non-model organisms.
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