(12i) Engineering the Spatial Organization of Proteins for Applications in Synthetic Biology and Beyond

in Synthetic Biology and Beyond

Christopher Jakobson¹, Marilyn F. Slininger¹, Edward Y. Kim¹, Jeff E. Glasgow², Michael A. Asensio³, Norma M. Morella⁴, Emily C. Hartman², Alex Chien⁵, Yiqun Chen¹, Elias Valdivia⁴, Matthew B. Francis², Niall M. Mangan⁶, and Danielle Tullman-Ercek⁷

¹Dept. of Chemical Engineering, UC Berkeley

²Dept. of Chemistry, UC Berkeley

³Dept. of Bioengineering, UC Berkeley

⁴Dept. of Plant and Microbial Biology, UC Berkeley

⁵Biophysics Graduate Group, UC Berkeley

⁶Dept. of Applied Mathematics, U. of Washington

⁷Dept. of Chemical Engineering, Northwestern University

Research Interests:

Protein encapsulation, the storage of biologically active molecules inside protein containers to enhance cargo function, is ubiquitous in nature. My graduate research with Prof. Danielle Tullman-Ercek focused on two examples of this strategy: (i) bacterial microcompartments, subcellular organelles of Salmonella, Yersinia, and other pathogens, and (ii) virus-like particles, such as those based on bacteriophage MS2. By engineering these systems as platform technologies for synthetic biology, we also discover biological design principles that can guide the development of therapeutics and vaccines.

Bacterial microcompartments are protein-bound containers that house specialized metabolic pathways, allowing invading pathogens to proliferate in the host gut [1]. We have focused on engineering these structures to improve the performance of heterologous biosynthetic pathways encapsulated in the organelles. We have learned how to control organelle formation [2,3], control small molecule transport across the protein membrane [4], and localize heterologous cargo using a variety of cellular zip codes [5]. We have identified surprising plasticity in microcompartment-mediated ­metabolism and used mathematical models to understand microcompartment function in detail [6]. This toolbox allows us orchestrate the formation of custom subcellular organelles in bacteria and to encapsulate heterologous pathways in a well-controlled manner.

Using the bacteriophage MS2, another protein container, we have explored the possibility of using protein membranes to control the diffusion of small molecules. We have demonstrated that changes to the chemical character of the pores of the MS2 virus-like particle can influence the kinetic behavior of an encapsulated enzyme [7]. We have also devised a selection for MS2 virus-like particle assembly in order to comprehensively characterize the mutational landscape of the MS2 coat protein gene, and we have identified a single point mutant that mediates a stable conversion of the viral capsid structure from a 27 nm to a 17 nm icosahedron [8].

Our studies are but two examples of the growing intersection of synthetic biology and the study of host-pathogen interactions, demonstrating that the knowledge gained from engineering complex biological systems is broadly applicable to understanding their function and evolution. My independent research will focus on engineering probiotics to deplete the small molecules metabolized in microcompartment organelles, characterizing the mutational landscapes of complex systems such as viral capsids to understand their evolution, and designing spatial organization strategies to optimize the performance of heterologous biosynthetic pathways. My laboratory will combine chemical engineering expertise with experimental biology and mathematical modeling to take a unique approach to these questions.

Teaching Interests:

I have teaching experience on the instructional teams for the undergraduate Fluid Mechanics and Heat & Mass Transfer courses at Cornell University, as well as the graduate Protein Engineering course at UC Berkeley. In each of these courses, our focus as teachers was on student-driven learning in the form of guided problem-solving sessions, group projects, and facilitated discussion of primary literature [9]. I also serve as a scientific advisor to the K-12 Alliance professional development program for science teachers in California. I am part of a teaching team that leads a weeklong summer institute for teacher leaders from districts throughout the state, providing instruction on science content and modeling effective science pedagogy [10]. I will combine the lessons I have learned from teaching at the university and secondary levels to continue to improve my instruction of core chemical engineering courses.

As an independent investigator, I also plan to develop a course on Mathematical Methods in Biological Engineering for graduate and upper-level undergraduate students. The course will provide students with the analytical and numerical tools required to address chemical and biological phenomena at the molecular, organism, and population scales using models of chemical kinetics, cellular metabolism, and disease epidemiology. A key student outcome will be proficiency in the use of MATLAB as a numerical toolkit to address nonlinear dynamics in biological systems.

1. Jakobson and Tullman-Ercek, PLoS Pathogens (2016).

2. Kim*, Jakobson*, and Tullman-Ercek, PLoS ONE(2014)

3. Jakobson, Chen, Slininger, Valdivia, Kim, and Tullman-Ercek, in revision.

4. Slininger, Jakobson, and Tullman-Ercek, submitted.

5. Jakobson, Kim, Slininger, Chien, and Tullman-Ercek, J. Biol. Chem.(2015)

6. Jakobson, Slininger, Tullman-Ercek, and Mangan, in preparation.

7. Glasgow, Asensio, Jakobson, Francis, and Tullman-Ercek, ACS Synth. Biol. (2015).

8. Asensio*, Morella*, Jakobson, Hartman, Glasgow, Sankaran, Zwart, and Tullman-Ercek, submitted.

*These authors contributed equally.

Manuscripts in preparation and submitted available upon request.

9. Sample syllabi, schedules, and course materials for Protein Engineering available upon request.

10. See: https://www.wested.org/service/k-12-alliance-science-content-institutes/