Grand challenge seeks carbon sequestration, hydrogen production solutions

Cyanobacterium sequenced in just six months

In just six months of collaboration, a Department of Energy grand challenge led by Washington University in St. Louis has resulted in the sequencing and annotation of a cyanobacterium that could yield clues to how environmental conditions influence key carbon fixation processes at the gene-mRNA-protein levels in an organism.

Two of the most critical environmental and energy science challenges of the twenty-first century are being addressed in a system biology program funded by the W.R. Wiley Environmental Molecular Sciences Laboratory (EMSL) , a National User facility managed by the Pacific Northwest National Laboratory for the Department of Energy (DOE). This program features an elaborate international collaboration involving six university laboratories and ten national laboratory groups. The challenges are carbon sequestration and hydrogen production. The organisms that could provide answers are cyanobacteria (blue-green algae). The leader of the program is Himadri Pakrasi, Ph.D., Washington University professor of biology in Arts & Sciences.

Pakrasi is leading a Grand Challenge Project in membrane biology that is using a systems approach to understand the network of genes and proteins that govern the structure and function of membranes and their components responsible for photosynthesis and nitrogen fixation in two species of unicellular cyanobacteria, specifically Cyanothece and Synechocystis. This is one of two Grand Challenge projects recently funded by EMSL-PNNL. Another project, not involving Washington University, is led by PNNL laboratory fellows and chief scientists John Zachara and Jim Fredrickson, is probing the fundamental question of how subsurface metal-reducing bacteria interact with and transfer electrons to the mineral surfaces on which they live. Pakrasi spoke Feb. 17, 2007, at the annual meeting of the American Association for the Advancement of Science in St. Louis.

According to Pakrasi, the team has made extraordinary progress in five key areas. Through Washington University’s Genome Sequencing Center, researchers have sequenced and annotated 99 percent of the Cyanothece 51142 genome, designed a microarray for global transcriptional analysis of the organism and have completed half of a proteomic map – some 2,400 proteins. A novel photobioreactor has been designed for mass balance analysis of Cyanothece cells during circadian cycles, and atomic structures for five proteins involved in sequestering such key nutrients as iron, nitrate and bicarbonate have been determined through X-ray crystallography.

According to Pakrasi, this kind of work cannot be done without access to a DOE user facility such as EMSL “Cyanobacteria have played an influential role in the evolution of the terrestrial environment,” said Pakrasi. “They precede chloroplasts in evolution and are largely responsible for today’s oxygen-rich environment. They make significant contributions to harvesting solar energy, sequestering carbon, bio-assimilating metals and the production of hydrogen in marine and freshwater ecosystems. Cyanobacteria also are model microorganisms for studying the fixation of carbon dioxide and nitrogen at the biomolecular level. Learning the intricacies of these organisms could lead to breakthroughs in the understanding of both biological carbon sequestration and hydrogen production.”

A systems approach integrates all available temporal information into a predictive, dynamic model to understand the function of a cell and the cellular membranes. Because Cyanobacteria make significant contributions to harvesting solar energy, planetary carbon sequestration, metal acquisition, and hydrogen production in marine and freshwater ecosystems, the genetics and biochemistry of these organisms are particularly suitable for such an approach.

Specifically, Pakrasi and his collaborators are focusing on the amazing cyanobacterium Cyanothece, a one-celled marine cyanobacterium, which is a bacterium with a well-defined circadian rhythm, or biological clock. In particular, Cyanothece have the uncanny ability to produce oxygen and assimilate carbon through photosynthesis during the day while fixing nitrogen through the night, all within the same cell. Incredibly, even though the organism has a circadian rhythm, its cells grow and divide in ten to fourteen hours.

To unravel the mystery, Pakrasi and his collaborators are growing Cyanothece cells in photobioreactors, testing cells every hour to try to understand the cycles at different times of the day. With the combined diverse expertise of 16 different laboratories, the Grand Challenge scientists and engineers are examining numerous biological aspects of the organism. The results of this Grand Challenge project will provide the first comprehensive systems level understanding of how environmental conditions influence key carbon fixation processes at the gene-mRNA-protein levels in an organism.