Brainstorming Session Overview:
Useful Applications of Synthetic Biology
Medical / Human Applications
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)
BioEnergy
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)
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)
Powering Implantable Medical Devices
Light sensitive Proton Pump (Pseud. Putida)
Biological Based Fuel Cells (Sammy)
Bacterial Biosensors
- Sense and Sequester Toxic Compounds (arsenic) (Sammy)
- Quorum Sensing
Bridging Applications
- Radon Sensor
E. coli that resists mutations (Alex)
Biofilms and Vascularization (Harris and Sammy)
Cellular Computation (George)
Microfluidics (George)
Recombination (Harris)
DNA transfer using virus (Shaunak)
Combinatorial Constructions and Selections
BioBricks (Nick)
Pathway / Metabolic Engineering
Microbial Therapy, BioEnergy
Input
(Import)
Set of genes (reasonable #)
Source/
Availability
Output / Product
(Export)
Assay
Optimization
Clone or Make Synthetically
RBS
RBS
RBS
Promoter
Cellulose to EtOH -> 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
Artemisinin example, Malaria Drug, Keasling Lab
Could couple to a sensor (make when needed)
Use BioBrick Strategy
Pathway / Metabolic Engineering
Microbial Therapy, BioEnergy
Input
(Import)
Set of genes (reasonable #)
Source/
Availability
Output / Product
(Export)
Assay
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): 2979–2988
Cellulose to EtOH -> 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)
glycolysis
Use BioBrick Strategy
Sensors
Biosensor, Quorum Sensing, BioEnergy
RBS
Sensor
RBS Response Element
Assay
Optimization
Sensors
-respond to external commands
-Can be used to turn genes on and off
1. Cytoplasmic Regulatory Proteins
2. Two-Component Systems
3. Environment Responsive Promoter
4. Regulatory RNAs
Sense EtOH buildup -> Trigger protective measure
Sense Deficiency -> Trigger Synthesis of vitamin
Sense Arsenic -> Detectable output or
Trigger Sequestration
Triggered “Kill Switch” for safety
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
Cellular Targeting
Surface Display: Fusions to Membrane Proteins
Fusion Protein
OmpA
Autotransporters
Want to Coat Bacteria with
Proteins of Interest
Streptavidin
Strep Binding Peptides
Histidine Tag
Random Library (Peptides)
Surface Display: OmpA – Outer Membrane Protein A
Llp
Leader
Llp
Leader 2
OmpA
BioBrick
Insertion Site
OmpA
BioBrick
Insertion Site
Pautsch A, Schulz GE. High-resolution
structure of the OmpA membrane domain. J
Mol Biol. 2000 Apr 28;298(2):273-82.
OmpA Outer Membrane Protein
Georgiou G, Stephens DL, Stathopoulos C, Poetschke
HL, Mendenhall J, Earhart CF.
Display of beta-lactamase on the Escherichia coli
surface: outer membrane phenotypes conferred by
Lpp'-OmpA'-beta-lactamase fusions. Protein Eng. 1996
Feb;9(2):239-47.
Surface Display: Autotransporter System: AIDA-1
Leader
Sequence
Linker Autotransporter
BioBrick
Insertion Site
Jose J. Autodisplay: efficient bacterial surface display of
recombinant proteins. Appl Microbiol Biotechnol. 2006
Feb;69(6):607-14. Epub 2005 Dec 20. Review.
Maurer J, Jose J, Meyer TF. J Bacteriol. 1997 Feb;179(3):794804.
Oomen CJ, van Ulsen P, van Gelder P, Feijen M,
Tommassen J, Gros P.
Structure of the translocator domain of a bacterial
autotransporter.
EMBO J. 2004 Mar 24;23(6):1257-66. Epub 2004 Mar 11.
NalP Autotransporter
Jain S, van Ulsen P, Benz I, Schmidt MA, Fernandez R,
Tommassen J, Goldberg MB. Polar localization of the
autotransporter family of large bacterial virulence proteins. J
Bacteriol. 2006 Jul;188(13):4841-50.