Office of Biological and Environmental Research Weekly Report

April 13, 2009

Comparing Genomes of Two Algae Strains Highlights Genes for Carbon Capture. Scientists from the Monterey Bay Aquarium Research Institute, led by Alexandra Z. Worden, have decoded the genomes of two algal strains, highlighting the genes enabling them to capture carbon and maintain the delicate balance of carbon in the oceans. The study sampled two geographically diverse isolates of the photosynthetic algal genus Micromonas—one from the South Pacific, the other from the English Channel. Surprisingly, the two isolates had about 90% of their genes in common compared to about 98% for humans and some primates. Algae such as Micromonas were among the first cells on Earth to acquire the capacity to fix CO₂ and use the energy from sunlight to generate biomass (the essential process of photosynthesis). Worden said that the differences between these algae may make them more resilient compared to more closely related species, enabling them to better survive environmental change and their geographically diverse locations. These results help illuminate cellular processes that could be used to produce algae-derived biofuels. Scientists at DOE’s Joint Genome Institute (JGI) played an essential role in the research by carrying the DNA sequencing and participating in the interpretation of the results. These findings are published in the April 10 edition of the journal Science.

Media Interest: No

Contact: Daniel Drell, SC-23.2 (301) 903-4742

New Insights From Computer Simulations May Improve Biomass Deconstruction.

Scientists at the DOE BioEnergy Science Center (BESC) have made a significant step in understanding the recalcitrance of biomass to microbial deconstruction. Microbes that break down plant biomass have large extracellular enzyme complexes, known as cellulosomes, that break down plant cell walls. The BESC team used computational simulations to understand the binding dynamics of two cellulosome proteins that play critical roles in the assembly of the cellusome. The simulations included a typical cellulosome complex and one with mutant proteins that cause a major change in protein-protein recognition sites needed for normal assembly of the cellulosome. This information will help BESC researchers re-design cellulosomal modules that can degrade biomass more efficiently than normal cellulosomes. The research, made possible with computational time on the ORNL Kraken Cray XT5 Supercomputer, has just been published on-line in the journal Protein Science, in a paper titled: “Building a foundation for structure-based cellulosome design for cellulosic ethanol: Insight into cohesin-dockerin complexation from computer simulation”, by Jiancong Xu, Michael Crowley, and Jeremy C. Smith.

Media Interest:   No

Contact:  Susan Gregurick, SC-23.2, (301) 903-7672

Defining the Role of Predictive Modeling for Rational Biological Engineering. The field of genomics is moving towards rational re-engineering of microbes that could provide new technologies for DOE’s energy and environment missions. Nitin Baliga and co-authors at the Institute for Systems Biology (ISB) have just published an article in Nature Reviews Microbiology (Volume 7, pages 297-305, April 2009) that discusses current research in genomics and the opportunities for significant advances provided by the integration of new technologies such as synthetic biology, systems biology, and predictive modeling. The authors point out that biological systems do not readily adapt to large changes in their metabolic or regulatory systems that alter the balance of energy or resources. New strategies are needed to overcome this obstacle that bring together separate efforts in systems biology and synthetic biology using simultaneous global modeling and systems optimization.  This multi-scale approach to experimental characterization and redesign of microbial cells and microbial communities will provide a foundation for applying microbial biology to achieve new sources of energy and to solve problems in environmental contamination.

Media Interest:  No

Contact: Susan Gregurick, SC-23.2, (301) 903-7672, Arthur Katz, SC-23.2. (301) 903-4932