fundamentals of synthetic biology. introduction definition the “abstraction hierarchy” ...
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Fundamentals of Synthetic Biology
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Introduction
Definition The “abstraction hierarchy” Orienting Examples Basic Procures
Basic Manufacture Parts: proteins/etc. Devices: Scaffolds and more Systems: Therapeutic Bacteria Characterization Future of Manufacture Future Applications
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Introduction
Definition The “abstraction hierarchy” Orienting Examples Basic Procures
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Synthetic BiologyAn engineering science to develop the standards, abstractions, characterization protocols, and parts lists to make genetic engineering of new, complex, biological functions cheaper, faster, scalable and reliable.
NSF ERChttp://www.synberc.org (Berkeley, Harvard, MIT, Prairie View, UCSF)
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Review of Central Dogma
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The Rosetta Stone
In the reign of the young one who has succeeded his father in the kingship, lord of diadems, most glorious, who has established Egypt and is pious towards the gods, triumphant over his enemies, who has restored the civilized life of men, lord of the Thirty Years Festivals, even as Ptah the Great, a king like Ra, great king of the Upper and Lower countries, offspring of the Gods Philopatores…
Egyptian
Demotic
Greek
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Human
Fly
Bacterium(Plasmid)
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Deciphering the language
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Percent of Total Number of Types Cell Weight of Each Molecule
Water 70 1 Inorganic ions 1 20 Sugars and precursors 1 250 Amino acids and precursors 0.4 100 Nucleotides and precursors 0.4 100 Fatty acids and precursors 1 50 Other small molecules 0.2 ~300 Macromolecules (proteins, nucleic 26 ~8000 acids, and polysaccharides)
Total ~11000
Bacteria Have ~1e10 Molecules
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Non-ideal Cellular EnvironmentA small box 100 nm on a side
~450 proteins~30 ribosomes~340 tRNAsSeveral mRNAs30,000 small organics50,000 ions70% water
In bacteria: 1nM=1 molecule
In E. coli: >80% of proteins < 100 nM
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Review of Central Dogma
The Genome of an organism is its
“program”
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DNA Codes for RNA
Aacggtggtcgatatgctgagactagctagactacgactttacgactttagcact.
transcript (RNA)
transcription factor
RNAPgene
promoter
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RNA codes for Protein
Aacggtggtcgatatgctgagactagctagactacgactttacgactttagcact.
Ribosome Binding Site GeneProtein
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Proteins Form Chemical Reaction Networks
Folded Protein
Other Folded Proteins
Organics and ions
Aacggtggtcgatatgctgagactagctagactacgactttacgactttagcact.
DNA and RNA
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Synthetic Biology Abstraction
Parts
Devices
Systems Chasses Devices made of devices Applications
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Parts
“Atoms” of function
Most commonly: All parts encoded in DNA Some parts are DNA: promoters, etc. Some parts are expressed
RNA Protein
Some parts are synthesized metabolitrd
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Promoters
Ribosome Binding Sites
Open Reading Frames
Terminators
Basic Parts
DevicesA GFP Producing Device
tetR RBS GFP Ter. Ter.
Standardization of Part manufacture and the Biobrick Language
Drew Endy Tom Knight
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The Parts Registry
http://parts.mit.eduDrew Endy, Tom Knight, Randy Rettberg
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Part functions Binding
DNA, Scaffolds, etc. Targeting
Secretion signals (parts on parts) Activity
RNAP activation/inhibition Macromolecular modification:phosphorylation, etc. Metabolite consumption/production Immune response triggering Luminescence/fluorescence Photoenergy conversion Redox …
No common currency really. Classes of mechanisms and physics of function
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How many functions/part?
More than we usually think Energetic and time cost of
production is a “function” Non-specific binding is a “function” Uncontroled cross-reaction is a
“function” Promiscuity of activity is a (possibly
very useful) “function.”
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Sensors Processors Actuators
Reporter Genes
Signal Integrators
Biosynthetic Genes
Digital SwitchesVirulence Genes
Categorization of parts?
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Devices?
Groups of parts that create a new function.
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
A possible pulse generator. C-terminal domain of Spo0AComplexed to DNA
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Devices?
Groups of parts that create a new function.
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
A possible pulse generator.
100 200 300 400
500
1000
1500
2000
Basic function of PG
Time (min)
G fluorescence/OD
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Devices?
Groups of parts that create a new function.
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
A possible pulse generator.Models of function
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
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Systems Assemblages of Devices
Fuzzy hierarchy… Systems are large scale devices in
some ways… But also think of them as
applications. Or maybe designs in their
environment.
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Device: quorum sensor
Part: anaerobic-activated promoter
Part: adhesion-activated promoter
Part: radiation-activated promoter
Part: amber suppressor
Part: transcriptional activator
Part: two-component sensing domains
Part: adhesion-specificity domains
Part: ribosome binding site
Part: TTSS secretion domain
Device: promoter-driven AND gate
Device: directed motility (Tar chimeras)
Part: invasin
Device: intracellular timer
Device: Effector-less TTSS needle for heterologous protein secretion into eukaryotic cytosol
Chassis: modified lipid A to reduce septic shock
Chassis: E. coli chassis with reduced genome
Testbed: tumor-targeting microbe
Systems Design
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Systems Design
Define Problem “Modularize Solution” Selection things to sense, logic, and actuators
needed Select/Design chassis Select/Design parts Predict/Measure how composition works Make many test compositions at once. (library) Measure performance of pieces and systems
at different levels (how?) Try again (and again, and again, and…)
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Classical metabolic engineeringGoal: produce more arginine
Ubiquitous pathway(often we are making new chemicals)
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How do we make more?
Strategies Overexpress New pathways for
production of L-glutamate and acetyl-CoA
More active enzymes from other species.
Removal of bleed-off of other pathways
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The context is important.
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Regulation and Timing is Critical
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
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Systems Questions 1
Is arginine biosynthesis “factorable” Can it be buffered from the cell’s own
metabolism (not likely) How critical is it’s regulation? Will it be maintained in a bioreactor?
(selective pressure) Is it cost effective, scalable, uncontaminable?
This is just for the classical work… What if our systems are WAY more
complicated?
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Systems 2: Engineering Beyond the Bioreactor
Therapeutic Bacteria and Viruses Remediation of water, soil and air
by engineered microbes Soil management and agricultural
optimization with microbial and plant GMOs
Environmental sensing and “Plant” protection (naval ship hulls, oil pipelines, etc.)
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Systems 2: Engineering Beyond the Bioreactor
Engineering for complex behavior
Uncertainty in the operation of the system and in the environment
Engineering for ecological stability and minimal perturbation
Engineering for safety and containment
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Cause of “Hamburger Disease”Enterohaemorrhagic E. coli (EHEC)
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“Devices” of Bacterial Pathogenesis
LEE Cluster: Formation of Adhering/Effacing Lesions upon adhesion
bfpA Locus: Adhesion via bundle-forming pili
Stx1 prophage: Secrete shiga toxin to induce haemorrhaging
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Complex Regulation of Bacterial Virulence
Genetic Regulation: Controls the when, where, and how much of gene expression
Sensing in the LEE Cluster
pH gastrointestinal location
autoinducer bacterial density
membrane control surface proteinstress expression
Epinephrine host state
ppGpp starvation
Control of Gene Timing
Cascades of Gene Expression
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A Snapshot of Regulation at a Complex Promoter
Multiple regulatory proteins can interact with each other, small molecules, and the DNA to induces changes in transcription or translation
Other regulatory elements affect protein activity post-translationally
DNA Binding
A protein-protein interaction
DNA Upstream of LEE Genes
DNA Binding
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Challenges
Complexity is higher Factorization not as obvious Uncertainty in mechanisms much
higher Measurements and selections are
much harder Risks higher Selection and “sex” more of a
problem.
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Needs
Multiscale Design High throughput construction of parts and
systems. Design for abstraction and predictability Experimental Testing Risk Assessment framework.
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Agenda
Classical Manufacture Parts: Protein design Devices: Scaffold design Systems: Therapeutic Bacteria Characterization Future Manufacture
Wrap up.