Applied Synthetic Biology for Engineering Metabolism and Synthetic Microbial Communities

            Applied Synthetic Biology for Engineering Metabolism and Synthetic Microbial Communities

Charles David Rutter, University of Illinois, Urbana-Champaign

2^nd Year Postdoctoral Fellow

Research Interests:

Synthetic Biology is a multi-disciplinary field focused of design and construction of biological devices for a desired application. Work is this field has led to development of tools that allow manipulation of microbial species beyond simple overexpression or knockout of protein function. Particularly, it has demonstrated the applicability of synthetic genetic constructs in both rational and combinatorial approaches involving manipulation of microbes at the genetic, transcript, and protein levels to improve performance. As such, these approaches are well suited for application to complex systems such as improved engineering of metabolism by addition of metabolite sensor elements and development of optimized synthetic microbial communities for enhanced lignocellulosic biomass degradation or complex biotransformations.

Postdoctoral Project: “Metabolic Engineering and Systems Biology of Oleaginous Yeasts”

Under supervision of Christopher V. Rao, Chemical and Biomolecular Engineering, Univeristy of Illinois, Urbana-Champaign

PhD Dissertation: “Engineering E. coli Toward Consolidated Bioprocess of Cellulose”

Under supervision of Rachel R. Chen, Chemical and Biomolecular Engineering, Georgia Institute of Technology

Undergraduate Thesis: “Characterization of Cellulosic Sugars by the Microalgae C. reinhardtii”

Under supervision of John Morgan, Chemical Engineering, Purdue University

Research Experience:

My research experience falls within the fields of synthetic biology, systems biology, and metabolic engineering. I have had the opportunity to work with all types of industrially relevant microorganisms (bacteria, yeast, and algae). As a PhD student I gained expertise in the relevant processing and metabolism of cellulosic substrates, approaches for improvement of protein secretion in bacteria as well as relevant metabolic engineering strategies for conversion of cellulose into a variety of valuable products. As a postdoctoral researcher I have had the opportunity to extend my knowledge to include the metabolism of traditional and oleaginous yeasts as well as their mechanisms for regulation at the genetic, transcript, and posttranscriptional level. This has left me with extensive knowledge in the fields of metabolic engineering, synthetic biology, molecular biology, microbial genetics, and fermentation technologies.

Teaching Experience:

In addition to my time spent as a researcher, I have gained substantial teaching experience. As an undergraduate at Purdue University I spent 3 semesters as a TA for the undergraduate math modelling and statistical analysis course. As a member of the Zeta Chapter of Omega Chi Epsilon I organized and led supplement instruction sessions for core courses in the undergraduate curriculum including momentum transfer, thermodynamics, and reaction kinetics across 5 semesters. I also worked as a tutor through the Purdue Athletic department to provide one-on-one and group tutoring for student-athletes in courses such as Spanish, chemistry, calculus, and differential equations. As a graduate student I had the opportunity to TA the Senior Operations Laboratory, which involved instruction of senior Chemical Engineering students in the lab as well as the Senior Capstone Design course in which I worked with professors and other TAs so create a problem statement and evaluate the designs submitted by students. In additional to these more formal teaching assignments, I have served as a mentor for younger students in the lab as both a graduate student and a postdoctoral research helping researchers to understand molecular and synthetic biology principles, analytical techniques, and experimental design.

Future Direction:

As a faculty I would like to continue my research in metabolic engineering by employing the synthetic biology techniques I have learned as well as those which I plan to develop. Firstly I would like to develop systems that are capable of sensing the metabolic and redox state of microbial cell factories to differentially regulate metabolism post-transcriptionally to remove inhibitory compounds and improve flux through rate limiting steps to improve product formation. This will require development of a variety of biosensors, which will be capable of sensing metabolites and reacting to regulate transcript levels dynamically.

Additionally I would like to continue to develop systems for consolidated bioprocessing of lignocellulosic substrates using synthetic microbial communities to leverage the natural capabilities of different organisms to create a cost-effective system for utilization of the most abundant biomass on the planet. This will require development of synthetic biology tools to manipulate various types of microbes including bacteria, cyanobacteria, fungi, and algae to cooperatively degrade substrates and application of creative metabolic engineering approaches to maximize product formation

Selected Publications:

C. Rutter, Z. Mao, and R. Chen. 2013. Periplasmic expression of a Saccharophagus cellodextrinase enables E. coli to ferment cellodextrin. Applied microbiology and biotechnology (2013): 1-10.

C. Rutter, R. Chen. 2014. Improved cellobiose utilization in E. coli by including both hydrolysis and phosphorolysis mechanisms. Biotechnology Letters. 36:301-307

HD Shin, SH Yoon, J Wu, C Rutter, SW Kim, R Chen. 2012. High-yield production of meso-2,3-butanediol from cellodextrin by engineering E. coli biocatalysts. Bioresource Biotechnology. 118:367-73

C Rutter, C.V. Rao, S. Zhang. 2015. Engineering Yarrowia lipolytica for Production of Medium-Chain Fatty Acids. In Preparation.