A Simple Give and Take: Plant/Bacteria Symbiosis May 2005 If you scratch my back, I'll scratch yours. Researchers at Stanford University have developed a new GeneChip microarray to study the give and take relationship — or symbiosis — between plants and bacteria. The scientists discovered nearly 2,000 genes that change expression levels during the symbiosis; this new understanding may be the first step towards growing healthier plants and improving crop yields. Symbiosis is critical to the growth of legumes like alfalfa, soybeans and peanuts. Bacteria living inside the plant produce ammonia that the legume uses to grow (like fertilizer). In return, the growing plant provides the bacteria with a carbon energy source needed to live. To identify genes in the plant and bacteria involved in symbiosis, scientists typically study one gene at a time or one genome at a time, which is labor intensive and prone to experimental error. As reported in the November 23 issue of Proceedings of the National Academy of Sciences USA, Dr. Sharon Long and her research group at Stanford University used the Affymetrix dual-genome Symbiosis Chip to identify genes with expression level that change during the symbiotic relationship between Medicago truncatula (legume plant) and Sinorhizobium. meliloti (bacteria). Dr. Long and her team identified close to 2,000 genes that are expressed at different levels in the plant and bacteria during symbiosis. They determined that many bacterial genes involved in symbiosis were clustered in specific areas of the bacterial genome instead of spread throughout the genome. In addition, the Stanford group discovered that most of the roughly 400 gene expression changes in the plant were a result of the bacteria living inside the plant and not in response to ammonia production by the bacteria as speculated. In contrast, the approximately 1,300 genes whose expression was altered in the bacteria were changed in response to the bacteria's ability to produce ammonia inside the plant. The dual-genome Symbiosis Chip manufactured through the Affymetrix CustomExpress program enabled Dr. Long's group to examine gene expression changes across the entire bacterial genome and from 10,000 transcripts of the legume genome simultaneously. "This symbiosis chip thus gives us the potential to examine differentiation and response resulting from signal exchange between the two symbiotic partners simultaneously," said Long. "By placing two genomes on one chip, scientists are able to test 20,000 genes in the amount of time it previously took to test one. In addition, testing the genomes simultaneously provides a way to have internally, more consistent interpretation of data from different experiments." Contact Information: Sharon R. Long Department of Biological Sciences Stanford University Stanford, California 94305 Phone: (650)-723-3232 Fax: (650)-725-8309 srl@stanford.edu