(4ar) Toward Orthogonal Organelles for Engineered Cellular Processes

To carry out functions and chemical reactions that may be incompatible with existing conditions and hosts is a fundamental obstacle in both natural biological systems and engineered biotechnological applications. To overcome this challenge, nature has evolved specialized subcellular compartments called organelles. These compartments can execute functions and reactions that would be inefficient or even impossible in a homogenous intracellular environment. The emergence of organelles marked a significant evolutionary leap from prokaryotes to eukaryotes, unlocking new possibilities to explore functions that were otherwise inaccessible. Inspired by this development, my research focuses on engineering both natural and synthetic organelles to perform specialized functions. I envision creating orthogonal organelles designed to compartmentalize, insulate, and provide optimal local conditions for executing specific biochemical reactions within a host cell. This approach opens doors for advancements in metabolic engineering and synthetic biology applications.

Recent studies have demonstrated the benefits and potential of moving reactions into both natural and engineered organelles. However, challenges such as interference with existing processes within the organelles and transport issues remain significant obstacles to implementing this approach broadly. Current strategies focus on identifying and removing specific native reactions and components that interfere with desired reactions, an often-tedious process prone to side effects such as reduced cell growth. In contrast, creating an orthogonal organelle—whether by repurposing a non-essential organelle or building one from synthetic components—offers the advantage of excluding host machinery while providing an optimized local environment for desired functions that may be incompatible with the rest of the cell. The capability to create such a synthetic organelle promises not only to enhance the efficiency of naturally found reactions but also offers havens for artificial reactions and functions that were previously inaccessible to recombinant hosts.

Developing engineering tools to create orthogonal organelles requires expertise in rewiring natural pathways and introducing foreign factors to control their biogenesis. It also demands the ability to predict and characterize how these organelles will behave within host systems. My research vision integrates my previous work in engineering both native organelles (i.e. the yeast peroxisome) and synthetic organelles formed through liquid-liquid phase separation. My initial research goals include:

i) Repurposing yeast peroxisomes by engineering their import machineries to exclude native components.

ii) Investigating and manipulating interactions between organelles and other cellular components through the formation of artificial film-like condensates on native organelles.

iii) Using both existing and engineered organelles to compartmentalize non-native metabolic pathways.

This approach will expand the touted design-build-test-learn framework to organelle engineering, with immediate applications in improving the biosynthesis of high-valued chemicals and implementing challenging heterologous metabolic pathways.

Teaching Interests:

While I am confident of my ability to teach specific subjects that are integral to the chemical engineering discipline such as kinetics and transport phenomena, I am particularly interested in shaping how students think critically and broadly. The process of critical thinking in the form of the scientific process, after all, is how I was drawn to my career in the first place. Throughout my academic training, I’ve had the fortune of having mentors with excellent critical thinking skills who continue to serve as my role models. I aspire to do the same for my students and look forward to becoming an active mentor myself in helping less experienced minds become more accustomed to the process of critical thinking and problem solving. This is the most important skill that I believe I can teach beyond any one single fact or concept and one that I intend to make into the central focus for any course or training in my group and classroom.

I also believe that teaching is a two-way process that helps both students and teachers to continue learning. I have often found that my grasp on the concepts that I need to teach a student becomes firmer both in the lab and in the classroom. Because of this, I particularly enjoy more interactive learning experiences such as hands-on experiments in lab courses and group discussions, where I can not only share my knowledge, but also engage students to share their thought process and occasionally take on the role of teachers themselves. I hope to show students that learning need not be a trickle-down, passive process but rather an active exchange of ideas.