Genomes to Life Contractor-Grantee Workshop III
February 6-9, 2005, Washington, D.C.
Genomics:GTL Program Projects
Sandia National Laboratories
16
The Transcriptome of a Marine Cyanobacterium—Analysis Through Whole Genome Microarray Analyses
Brian Palenik1* (bpalenik@ucsd.edu), Ian Paulsen2* (ipaulsen@tigr.org), Bianca Brahamsha1, Rob Herman1, Katherine Kang2, Ed Thomas3, Jeri Timlin3, and Dave Haaland3
1Scripps Institution of Oceanography, La Jolla, CA; 2The Institute for Genomic Research, Rockville, MD; and 3Sandia National Laboratories, Albuquerque, NM
Nitrogen and phosphorus abundance and type are thought to control photosynthesis and carbon sequestration in large areas of the world’s oceans. Little is known about the regulation in cyanobacteria of nitrogen and phosphorus metabolism and their interaction with other environmental variables such as light and micronutrients. We are using a whole genome microarray of Synechococcus sp. WH8102 to examine these issues.
We have used whole genome microarrays in a number or experiments, initially to compare cells grown with nitrate and cells grown with ammonia. We found that 247 genes were down-regulated during growth under ammonia compared to nitrate. This included the NtcA transcriptional regulator known to control growth when ammonia is low and nitrogen sources other than ammonia are used. We also found that the use of a number of alternative nitrogen sources were down regulated (e.g. nitrate metabolism, cyanate transport, and urea metabolism). Some of these clearly have ntcA binding sites upstream although a complete comparison of the microarray results with ntcA binding site predictions are still in progress by Zhengchang Su and Ying Xu (UGA) as part of our GTL project. In addition, a number of genes associated with stress conditions are down regulated. These include glutathione peroxidase and a number of proteases and heat shock like proteins. This supports our hypothesis that growth under nitrate is actually more stressful than on ammonia due to the requirement of additional electron transport activity (and electron leakage) to reduce nitrate to nitrite to ammonia. Thus, we currently hope to analyze and model these results as a combination of NtcA regulation and stress response regulation. Interestingly a number of hypotheticals and conserved hypotheticals are down regulated, giving us an initial clue as to their possible functions in the cell.
In addition, we have also characterized phosphate limitation in WH8102 and made knockout mutants in a number of the two-component regulatory systems of the cell. We are also examining these phosphate limitation experiments with the wild type and mutant cells using whole genome microarray analyses. Because of its relatively small number of regulatory systems compared to many microbes, Synechococcus sp. WH8102 is an ideal model system for preparing a complete picture of the regulatory networks of an environmentally significant microbe.
Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under Contract DE-ACO4-94AL85000.
This work was funded by the U.S.Department of Energy’s Genomics: GTL program (genomicsgtl.energy.gov) under project, “Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling,” (www.genomes-to-life.org) and by its Microbial Genome Project under “Transport and its regulation in marine microorganisms—a genomics-based approach.”
* Presenting author
