(6gt) 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.