Novel Bug Work Appears in Two Journals
Contact: Mary Lipton
Contact: Stephen Callister
Research results from work done by Pacific Northwest National Laboratory (PNNL) scientists and collaborators on a versatile bacterium have been accepted in two peer-reviewed journals. The researchers are studying Rhodobacter sphaeroides, a microbe that grows under a variety of conditions using a variety of electron acceptors. Its diverse abilities include metal reduction, nitrogen fixation, and the assimilation of carbon dioxide. Additionally, R. sphaeroides can produce abundant amounts of hydrogen, which could potentially prove to be a source of renewable energy. Many of these abilities are linked to R. sphaeroides' photosynthetic apparatus.
The articles, which appear in the Journal of Microbiological Methods and the Journal of Proteome Research, describe how researchers probed the photosynthetic lifestyle of R. sphaeroides on a protein level and compared their observations to those reported in published genomic analyses.
They performed a global proteomic analysis based on PNNL's accurate mass and elution time (AMT) tag approach to compare aerobic and photosynthetic R. sphaeroides proteomes. Their results highlighted proteins directly and indirectly associated with the photosynthetic lifestyle of R. sphaeroides, and the location of these proteins within cellular fractions, such as the outer membrane and cytoplasm. The AMT tag approach enabled the identification of a diverse set of proteins, which will help in developing and connecting models of photosynthetic behavior.
A greater understanding of R. sphaeroides' photosynthetic behavior is important to applying its unique abilities to, for example, hydrogen production. These studies provide a baseline for future large-scale proteomic studies using PNNL's high-throughput proteomic approach. The work was sponsored by the U.S. Department of Energy's Genomics: GTL program within the Office of Biological and Environmental Research.
The research team includes Stephen Callister, Carrie Nicora, Matt Monroe, Dick Smith, and Mary Lipton (PNNL); Xiaohua Zeng, Jung Hyeob Roh, and Sam Kaplan (University of Texas Health Center); and Miguel Dominguez, Christine Tavano, and Tim Donohue (U of Wisconsin-Madison).
Heat map (left) comparison between proteins observed in R. sphaeroides aerobic and photosynthetic cultures. Proteins shown in the heat map are involved in energy production for the cell by way of the electron transport pathway (right). Most of the proteins involved in this pathway were observed in an insoluble protein fraction extracted from the each culture during sample preparation. Increasing intensity in the positive range represents abundances that are greater than the mean abundance derived from both culture conditions and sample preparations relative to the standard deviation associated with the mean (Z-score). Decreasing intensity in the negative range represents abundances that are less than the mean abundance relative the standard deviation. Z-score values for the aerobic and photosynthetic cell cultures also suggest the growth condition in which the protein was observed with the greatest abundance. Full Image
Callister SJ, MA Dominguez, CD Nicora, X Zeng, CL Tavano, S Kaplan, TJ Donohue, RD Smith, and MS Lipton. 2006 "Application of the Accurate Mass and Time Tag Approach to the Proteome Analysis of Sub-cellular Fractions Obtained from Rhodobacter sphaeroides 2.4.1 Aerobic and Photosynthetic Cell Cultures." Journal of Proteome Research 5(8):1940-1947.
Callister SJ, CD Nicora, X Zeng, JH Roh, MA Dominguez, CL Tavano, ME Monroe, S Kaplan, TJ Donohue, RD Smith, and MS Lipton. 2006. "Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes. Accepted for publication in Journal of Microbiological Methods doi:10.1016/j.mimet.2006.04.021.