Microbial Therapy (Steph, Alex, Sammy) Pathway Engineering

1
Brainstorming Session Overview Useful
Applications of Synthetic Biology
Medical / Human Applications
BioEnergy
Microbial Therapy (Steph, Alex, Sammy) Pathway
Engineering - make product body needs
(possibly sense deficiency) - Synthetic
Symbiosis (E. coli natural gut environment)
- Vitamin B Production (Steph and Alex) -
Fibrin (clotting) (Sammy) - Insulin (Harris)
- Degrade Plaque - Implantable Devices that
release or synthesize drugs - Off-switch for
safety, competitive concerns (Alex) Cellular
Targeting - Aptamers (Steph) - Bacterial
Surface Display / Fusion Prot. (Perry) - Target
Bact to certain tissues (actuator or product) -
Targeting Microbial Factories - Sequestration
of Toxic Compounds (Sammy) Bacterial Biosensors
- Sense and Sequester Toxic Compounds
(arsenic) (Sammy) - Quorum Sensing - Radon
Sensor Biofilms and Vascularization (Harris and
Sammy) Recombination (Harris)
Producing a Renewable Energy Source Cellulose to
EtOH (Shaunak, Steph, Alex) Fatty Acid
production and degradation for energy Synthesis,
Tolerance, and Export of EtOH or
alkanes Alternative organisms for Energy Prod.
Yeast (Shaunak) Bacteria as Energy Source Light
Powering E. coli w/ Photorhodopsin
(Alex) Powering Implantable Medical
Devices Light sensitive Proton Pump (Pseud.
Putida) Biological Based Fuel Cells (Sammy)
Bridging Applications
E. coli that resists mutations (Alex) Cellular
Computation (George) Microfluidics (George) DNA
transfer using virus (Shaunak) Combinatorial
Constructions and Selections BioBricks (Nick)
2
Pathway / Metabolic Engineering Microbial
Therapy, BioEnergy
Input (Import)
Output / Product (Export)
Assay
Set of genes (reasonable )
Source/ Availability
Optimization
Clone or Make Synthetically
RBS
RBS
RBS
Promoter
Cellulose to EtOH -gt Sugar (Xylose) to EtOH
(pdc and adhB genes, L. Ingram) pyruvate
decarboxylase, alcohol dehydrogenase II Vitamin
Production (operon structure) Natural Product
Production (Fibrin, Insulin) Plaque
Degradation Synthesis of an antibiotic Fatty
Acid Production or alkanes Could couple to a
sensor (make when needed) Use BioBrick Strategy
Artemisinin example, Malaria Drug, Keasling Lab
3
Pathway / Metabolic Engineering Microbial
Therapy, BioEnergy
Input (Import)
Output / Product (Export)
Assay
Set of genes (reasonable )
Source/ Availability
Optimization
Clone or Make Synthetically
RBS
RBS
RBS
Promoter
conversion of six molecules of xylose into 10
molecules each of ethanol and CO2 J Bacteriol.
2001 May 183(10) 29792988
Cellulose to EtOH -gt Sugar (Xylose) to EtOH
(pdc and adhB genes, L. Ingram) pyruvate
decarboxylase, alcohol dehydrogenase II Vitamin
Production (operon structure) Natural Product
Production (Fibrin, Insulin) Plaque
Degradation Synthesis of an antibiotic Fatty
Acid Production or alkanes Could couple to a
sensor (make when needed) Use BioBrick Strategy
glycolysis
4
Sensors Biosensor, Quorum Sensing, BioEnergy
Sensor
Response Element
RBS
RBS
Assay
Optimization
Sensors -respond to external commands -Can be
used to turn genes on and off
Sense EtOH buildup -gt Trigger protective
measure Sense Deficiency -gt Trigger Synthesis of
vitamin Sense Arsenic -gt Detectable output or
Trigger Sequestration Triggered Kill
Switch for safety
1. Cytoplasmic Regulatory Proteins
2. Two-Component Systems
3. Environment Responsive Promoter
4. Regulatory RNAs
5
Cellular Targeting Bacterial Surface Display and
Aptamers (Potential Applications)
Bind Viruses
Bind Toxins
Bind Surface
Bind Proteins
Microscale patterning
Bind Other Cells
Bind DNA
Bind Tissue Types
Streptavidin
Cell-cell Interactions Cell-cell targeting
Tissue Targeting
Combinatorial Constructions and Selections Many
New BioBricks
6
Cellular Targeting
Surface Display Fusions to Membrane Proteins
Fusion Protein
OmpA
Want to Coat Bacteria with Proteins of Interest
Autotransporters
Streptavidin Strep Binding Peptides Histidine
Tag Random Library (Peptides)