Developing Original Functional Microbial Genomics Projects for Undergraduate Courses

RM 208

Genomics research provides both the DNA sequence of all the genes in an organism and the potential functions of the proteins encoded by the genes. However, this information does not provide definitive evidence about the functions of the proteins. Instead, functional genomics research is used to directly test the function of proteins that were predicted from deduced amino acid sequences. We have successfully employed functional genomics in undergraduate courses to identify for the first time the genes from three separate strains of Agrobacterium (A. radiobacter K84, A. tumefaciens C58, and A. vitis S4) that encode proteins that are actually involved in the biosynthesis of the amino acids proline and, in overlapping pathways, leucine, isoleucine and valine. We now seek to expand this research into the biosynthetic pathways of other amino acids. Towards this end, we are analyzing the published biosynthetic pathways of several amino acids in E. coli cells to identify appropriate candidate enzymes. The amino acid sequences of these previously identified proteins in E. coli are then used to identify potential proteins with the same functions in the three Agrobacterium strains. In future courses, the actual functions of these proteins will be tested. In addition to providing evidence for or against genome database predictions and valuable information on gene and protein evolution, this endeavor provides original research experiences to numerous undergraduates, many of whom could not otherwise participate in original research.