(6v) Advancing Technologies for Protein Engineering, Metabolic Engineering, and High-Throughput Technologies

Microbial production of natural product drugs from plants offers numerous advantages over traditional synthetic chemistry, plant cell culture, or recovery from the plant. However, to realize this potential, we must tackle problems including incomplete biosynthetic pathways, poor enzyme properties, imbalance of metabolic flux, and uncontrolled cellular physiology. To address these challenges, my research aims to advance technologies that enable efficient biotransformation at the enzyme, pathway, and system level. My research will integrate computational biology, metabolic engineering, synthetic chromosome biology, and droplet microfluidics to reprogram metabolic networks and cellular processes, to guide design of protein engineering and pathway configurations, and to parse out outperformed enzyme and strain variants for maximal biosynthesis. Specifically, by consolidating statistical methods and machine learning of large-scale evolutionary data, I will establish an open-source algorithm for directed evolution of proteins. To improve pathway performance, I will create genetically encoded synthetic enzyme complexes with precise control of active site orientations and stoichiometries. I will also develop synthetic biology tools to perturb global gene expression, which ensures normal physiology for cell growth and high product yields. New modalities of biosensors capable of detecting both intracellular and extracellular metabolite concentrations will be developed to screen millions of enzymes and strain variants. In the long term, I will leverage the power of bioinformatics and large datasets of genome sequences to decipher missing enzymes in key natural product pathways, thereby promising complete biosynthesis of drugs in the microbial host.

Past research

In working with Prof. Philip Romero for postdoctoral training, I have expanded my skills of computation and statistical analysis while developing new algorithms for recombination-based protein engineering. The involvement of a deep mutational scanning project has broadened my capability to apply droplet microfluidics for high throughput biochemical analysis. My expertise rewiring cellular metabolism and reprogramming gene expression for effective microbial production has been cultivated during my postdoctoral work with Prof. Hal Alper. Under his mentorship, I have developed a CRISPR dCas9-based tool for chromosome organization, and employed CRISPR dCas9 gene regulation system for pathway engineering. As a PhD student of Prof. Ian Wheeldon, by developing synthetic protein scaffolds for organizing metabolic enzymes in S. cerevisiae, I demonstrated that the pathway efficiency could be improved via co-localization effects. In addition, my enthusiasm toward high throughput technologies has led me to develop three fluorogenic or chromogenic assays to overcome shortage of traditional analytic methods.

Teaching Interests:

Teaching interests

My training as a chemical engineer and geneticist from undergraduate and graduate studies has been supplemented with formal studies of chemical engineering and life science courses. I am enthusiastic about the opportunity to teach undergraduate courses including Transport Phenomena, Kinetics and Reaction Engineering, and Process Dynamics and Control. In addition, I look forward to the opportunity teaching upper level courses including Chemical Engineering Kinetics and Transport Phenomena.

Besides the aforementioned courses, I plan to develop and instruct an upper level course in synthetic biology for chemical engineers and bioengineers. This course will cover topics including protein engineering, metabolic engineering, gene expression, genome editing, molecular and cellular reprogramming, microbiome engineering, and high throughput technologies. My expertise in molecular and cell biology, protein and metabolic engineering, synthetic biology, and microfluidics has provided me with a unique vantage to lecture this course. Research and current challenges in the fields under the scope of these topics will be incorporated into the course structure and discussed.

Mentoring experience

My graduate and postdoctoral studies have exposed me to a wide range of teaching environments. As a teaching assistant, I have given lectures and led discussions in the classrooms of Chemical Process Analysis, Biological Unit Processes, Process Dynamics and Control, and Biochemical Engineering Principles. These teaching opportunities have taught me how to prepare course materials, cultivate student engagement, and assess the learning process. As a graduate and postdoctoral researcher, I have mentored five undergraduate and eight graduate students for their senior design or research projects. Through close interactions with my mentees, I learned to tailor my mentorship for their needs as students come with different interests and backgrounds

Selected Publications:

Lin, J.L., Bremer, B., Duan, J., Greenhalgh, J., & Romero P. Evolution-guided recombination of proteins. (in preparation)

Roychowdhury, H., Lin, J.L., & Romero, P. Sequence-function mapping for allosteric sites of caspases with droplet microfluidics. (in preparation)

Lin, J.L., Ekas, H., Deaner, M., & Alper, H. CRISPR-PIN: controlling gene position in the nucleus using dCas9-mediated tethering. (under revision).

Lin, J. L. ^†, Wagner, M. W. ^†, & Alper, H. (2017) Enabling tools for high-throughput detection of metabolites: metabolic engineering and directed evolution applications. Biotechnol. Adv. 35(8), 950-970. ^†Co-first author

Abatemarco, J. ^†, Sarhan, M. F. ^†, Wagner, J. M. ^†, Lin, J. L., Liu, L., Hassouneh, W., Yuan, S. F., Alper, H., & Abate, A. (2017) RNA-aptamers-in-droplets (RAPID) high throughput screening for secretory phenotypes. Nat. Commun. 8:332. ^†Co-first author

Lin, J. L. ^†, Zhu, J.^†, & Wheeldon, I. (2017) Synthetic protein scaffolds for biosynthetic pathway co-localization on lipid droplet membranes. Acs Synth. Biol. 6, 1534-1544. ^†Co-first author

Lin, J. L., Palomec, P., & Wheeldon, I. (2014) Design and analyis of enhanced catalysis in scaffolded multi-enzyme cascade reactions. Acs Catal. 4 (2), 505-511.

Lin, J. L. & Wheeldon, I. (2013) Kinetic enhancement in DNA-enzyme nanostructures mimic the Sabatier Principle. Acs Catal. 3, 560-564.