Using Functional Genomics and Metagenomics in the Undergraduate Classroom as a Bride to Research Experiences

Event Center A & B

In Fall 2013, a course titled Functional Genomics in Bacteria was taught at CSU San Bernardino. This small, laboratory-focused course allowed students to pursue two distinct group projects in functional genomics and metagenomics. The students participated in all stages of development of both projects. One project focused on identifying elements of the Variovorax paradoxus EPS flagellar apparatus by heterologous host complementation. The polar flagellum of this microorganism has been identified biochemically, but the genes were not identified in the genome annotation process. Several non-motile flagellum knockout strains in E. coli were received from the CGSC (New Haven) and libraries of genomic DNA from V. paradoxus EPS were generated in pBAD24 and pBBR1MCS5. The construction and evaluation of these libraries was carried out during the quarter, and then followed up by students from the class after the term ended. A second project focused on enriching for Aminocyclopropane-1-carboxylate (ACC) deaminase activity from the soil metagenome. ACC deaminase is a key enzyme involved in plant growth promotion by disrupting the ethylene stress hormone synthesis pathway. ACC can also serve as a nitrogen source in culture, as the enzymatic activity yields ammonium and alpha-ketoglutarate. On this basis an enrichment strategy was devised. Soils were collected and DNA extracted. The DNA was introduced into E. coli using a Fosmid library (CopyControl, Epicentre) and the library was validated and sampled for ACC deaminase activity by growth on medium containing ACC as sole carbon source. Students in this course learned advanced molecular techniques as well as the use of bioinformatics resources and tools, and were directly involved in the planning and execution of an original, publishable research project. Four of the five students involved in this project are currently pursuing graduate degrees, suggesting that “real-world” research experiences in the classroom may stimulate increased participation in STEM careers.