Location, Location, Location: Directing Biology through Synthetic Assemblies and Organelles
We have taken a new and exciting approach to the iGEM challenge this year. Because UCSF is without an undergraduate program, we chose to take on 7 exceptional students (6 high school students and 1 undergraduate) from the bay area. The students' participation was conceived with help from UCSF's SEP program — the Science and Health Education Partnership between UCSF and the San Francisco Unified School District, designed to help boost student science literacy in the city. Using iGEM as a guiding framework, we created an educational program to introduce them to Synthetic Biology and experimental science. As part of this, the students worked as a team with a post-baccalaureate instructor and a group of graduate students and post-doctoral researchers to actively create an interesting and fun project. This year, we are using synthetic approaches to engineer and manipulate novel cellular microenvironments into Eukaryotic cells. It is widely appreciated that the efficiency and specificity of many cellular processes frequently depend on spatial localization, which can be achieved in different ways. For example, multiple enzymes involved in a given process frequently co-localize by binding to a common scaffold. Processes can also be localized in larger and more specialized microenvironments, such as whole organelles, through physical separation into distinct membrane compartments. Co-localization and compartmentalization allow molecular components to function in concert more effectively, and can protect the process from the external environment. Conversely, if the process involves any harmful intermediates (e.g. degradation, oxidation, etc.), compartmentalization can protect the rest of the cell. This summer, our team is creating novel microenvironments in yeast through (a) protein-scaffold interactions and (b) membrane compartmentalization. In the first project, we are reengineering the pathway output of the yeast mating response through the recruitment of exogenous pathway modulators to the Ste5 scaffold via synthetic leucine zippers. Our approach uses a new combinatorial cloning method based on type IIs restriction enzymes, allowing multi-step ligations to be consolidated into one. In a second project, we are using the same signaling pathway to engineer a new organelle in yeast. We are exploiting the observation that a unique code of modified phosphoinositide lipids is usually used to confer distinct identities to membranous compartments (i.e. organelles). Therefore, our project is based on conferring a distinct phosphoinositide composition to endosomes containing the mating receptor Ste2 by recruiting mammalian phosphoinositide phosphatases (MTMRs) or kinases (PI3K) able to produce phosphoinositides that normally do not exist in yeast. Through this, we hope to arrest trafficking of Ste2-specific endosomes to the yeast vacuole, creating a new stable organelle labeled with a unique and orthogonal molecular identity code. Creation of a new organelle could have unlimited engineering potential and a wide array of applications, such as creation of a segregated compartment dedicated to the synthesis of drugs or biofuels.