Building Microbial Machines

iGEM (International Genetically Engineered Machines) is a synthetic biology competition for teams of undergraduates. Synthetic biology takes an engineering approach by viewing genetic elements as “parts” that can be used to assemble biological devices. For example, by coupling a stationary-phase specific promoter to a methyltransferase gene, students have generated a device that will produce a wintergreen smell in stationary phase E. coli (http://parts.mit.edu/wiki/index.php/MIT_2006). iGEM actively engages students with concepts of gene structure, gene regulation and cellular communication, and lives up to its billing as “an exceptionally motivating and effective teaching method.” The iGEM website serves two important functions. First, it acts as a repository of information on these biological “parts”. The iGEM website is, therefore, a unique resource for those who wish to construct biological devices in the lab. Parts are freely accessible from iGEM and contain a standardized arrangement of restriction enzyme sites so that they can be easily combined. The iGEM website also contains a link to a Registry of Standard Biological Parts, which indexes the parts by type (promoter, protein coding sequence, terminator, etc), by function (cell motility, bacterial conjugation, cell signaling, biosynthesis) and by host organism (E. coli, yeast, B. subtilis or T7 phage). Further, the website links to iGEM instructional videos, which are very helpful and provide guidance on everything from navigating the Parts Registry to issues of biological safety. Second, the iGEM website acts as a compendium of past iGEM projects which can be used as a starting point to discuss biological systems in the classroom (available at the links to “2009 team wikis” and “Previous iGEM competitions”). As an example, the Pico-Plumber is a strain of E. coli that was engineered to migrate toward the site of a broken pipe. Once the cells reach sufficient density, they produce a peptide that lyses the cells, thereby releasing proteins that act as an adhesive to seal the breach (http://2009.igem.org/Team:Aberdeen_Scotland). Some of the most enjoyable sessions in my own course are when students use the registry to construct devices in silico. For example, students are asked to combine biological parts to design a bacterium that will fluoresce green in the presence of arsenic, a practical application of biotechnology that interests students. Students who are inspired by the design process may wish to go further and start an iGEM team to construct their device during the summer. Comprehensive information on starting a team and participating in the iGEM competition is available at the “Start-to-finish” section of the website. While the iGEM website is a valuable resource, there are also significant problems. Most notably, it is difficult to navigate the registry of biological parts until you master the engineering jargon, such as the distinction between a part, a device, and a system. Therefore, there is a substantial learning curve for most novices and the website is likely of most use to upper-level undergraduates. Selecting parts to use in a design can also be difficult as some are very poorly described, while others contain such extensive information that it can be overwhelming. In my own teaching, I preselect a subset of biological parts, but students can also be directed to a site such as EcoliHub (http://www.ecolihub.org), which serves as an entry point to information related to the bacterium, its plasmids and mobile elements. The website provides links to numerous databases, thereby providing comprehensive gene annotation, protein–protein interaction and gene expression data that can be used in the design process. Combined with the iGEM website, these two resources represent a novel, interdisciplinary approach to learning that can be highly rewarding for students.