Genomes to Life Contractor-Grantee Workshop III
February 6-9, 2005, Washington, D.C.
Genomics:GTL Program Projects
Lawrence Berkeley National Laboratory
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VIMSS Functional Genomics Core: Analysis of Stress Response Pathways in Metal-Reducing Bacteria
Aindrila Mukhopadhyay1, Steven Brown4, Swapnil Chhabra2, Brett Emo3, Weimin Gao4, Sara Gaucher2, Masood Hadi2, Qiang He4, Zhili He4, Ting Li4, Yongqing Liu4, Alyssa Redding1, Joseph Ringbauer, Jr.3, Dawn Stanek4, Jun Sun5, Lianhong Sun1, Jing Wei5, Liyou Wu4, Huei-Che Yen3, Wen Yu5, Grant Zane3, Matthew Fields4, Martin Keller5 (mkeller@diversa.com), Anup Singh2 (aksingh@sandia.gov), Dorothea Thompson4, Judy Wall3 (wallj@missouri.edu), Jizhong Zhou4 (zhouj@ornl.gov), and Jay Keasling1* (keasling@socrates.berkeley.edu)
1Lawrence Berkeley National Laboratory, Berkeley, CA; 2Sandia National Laboratories, Livermore, CA; 3University of Missouri, Columbia, MO; 4Oak Ridge National Laboratory, Oak Ridge, TN; and 5Diversa Inc., San Diego, CA
The Functional Genomics Core is part of the VIMSS project and there is a separate overview presentation of the VIMSS project. Environmental contamination by metals and radionuclides constitutes a serious problem in many ecosystems. Bioremediation schemes involving dissimilatory metal ion-reducing bacteria are attractive for their cost-effectiveness and limited physical detriment and disturbance on the environment. Desulfovibrio vulgaris, Shewanella oneidensis, and Geobacter metallireducens represent three different groups of organisms capable of metal and radionuclide reduction whose complete genome sequences were determined under the support of DOE-funded projects. Utilizing the available genome sequence information, we have focused our efforts on the experimental analysis of various stress response pathways in D. vulgaris Hildenborough using a repertoire of functional genomic tools and mutational analysis.
Originally isolated in 1946, from the clay soils in Hildenborough, Kent (UK), Desulfovibrio vulgaris Hildenborough belongs to a class of sulfate reducing bacteria (SRB) that are found ubiquitously in nature. As with most soil bacteria that do not live permanently in hyperosmotic environments, a NaCl salt stress in a D .vulgaris can be expected to result in at least two primary responses, osmotic and that towards Na+ ions. The genomic sequence of D. vulgaris indicates that a variety of mechanisms may be employed to counter these two stresses. In order to understand these mechanisms at the physiological level an integrated functional genomics analysis was conducted. Data from microarray analysis of the transcriptome, quantitative and qualitative proteomic analysis, PLFA profiling and IR studies reveal many interesting responses to stress. For example, with respect to hyperosmotic stress, the three gene operon that regulates the uptake of the osmoprotectant, glycine betaine is highly up-regulated. With respect to Na+ stress, Na+/H+ antiporters such as the dehydrogenase mnhA show upregulation in mRNA levels. As might be expected with cellular physiology, a myriad of other relevant responses were observed such as upregulation in ATP synthesis, down-regulation in flagellar systems. IR studies also indicate changes in cell wall composition. Moreover, several genes of unknown function were observed to be significantly and reproducibly changing, and may lead to the annotation of additional candidates involved in Salt stress. The study also attempts to understand the general correlation of proteomics vs. transcriptomics data. Results from this work will lead to further studies with metabolic profiling, and gene deletion mutants.
* Presenting author
