Lecture 12. Synthetic Microbial Communities - Engineering communities 1 Flashcards
What are the two main approaches to synthetic community building?
Rationally engineer links (i.e. create to study and apply)
Exploit natural links or tendencies (i.e. learn from nature)
What are the possible benefits/motivations for synthetic community engineering?
Might allow for more robust implementation of desired genetic circuit output (less affected by noise and heterogeneity?)
Might increase efficiency (e.g. by elimination of toxic byproducts)
Might act as model systems to understand natural multi-cell communities (e.g. as seen in gut or cancer tumour)
Might allow for functions to be implemented that could not be possible within a single organism (complex metabolism, functional materials, higher signal amplification, computing?)
What is the rational for engineering synthetic communities
Use Signalling: Most of the cases will have two different types of cells from two different species
Use Metabolism
Use Physical Interaction: Can one cell physically do something to another cell (not many examples of this actually)
How does an engineered minicellulosome function?
4 engineered yeast strains producing different cellulose-degrading enzymes and their scaffold
Only when four different species come together you get an enzyme complex that can breakdown cellulose
How can “prey vs predator’ cycles appear in signalling-based engineering?
One circuitry has toxin, one has antitoxin. When one cell is activated the other one dies
What is an example of a “prey” and “predator” mechanism?
Both ‘prey’ and ‘predator’ express ccdB (suicide gene) Prey express LuxI, which activates ccdA (suicide gene inhibitor) in predator
Predator expresses LasI, which activates ccdB in prey
What is an example of a negative feedback loop intertwined with a positive feedback loop?
LuxR is constitutively produced for synchronisation
AHL is produced via luxI gene product. AHL is degraded via aiiA gene product. AHL-LuxR activate both genes
AHL activates expression of both genes, but aiiA has a repression effect as it degrades AHL
What occurs in metabolite-based engineering of synthetic communities?
Cross-feeding of metabolites increase productivity (in biomass and recombinant protein)
What does cross-feeding allow in regards to pyruvate?
Cross-feeding of metabolites allows independent optimisation of conflicting pathways that both derive from pyruvate
Can metabolite-based engineering occur between species that photosynthesise and those that don’t?
Yes: species that can photosynthesise, coupling photosynthesis to metabolic pathways utilises capabilities of both species
Light - sucrose cross feeding engineered in S. elongatus (cyanobacteria) / H. Boliviensis
What is two way cross-feeding also known as?
Syntrophy, can enable both N and C fixation (depending on bacteria used)
What are the key challenges in the engineering of synthetic communities?
Limited choice of ‘wires”
Diffusion limits
Cross-talk
Population dynamics
Evolutionary stability
How does nature overcome diffusion challenge?
Coupling by gaseous substances or ionic (electrical) signals
What is an example of gaseous coupling in synthetic communities?
H₂O₂ effectively makes luxI promoter more sensitive to LuxR- AHL
Could oscillators be used as biosensors?
Additional signals and genes introduced to modulate promoters in the original circuit, allowing sensitivity of circuit dynamics to external signals (arsenite in this case)
What applications for synthetic pathways are there?
Using SCs to implement pattern formation
Functionalised biofilms with patterned production
Metabolically linked SCs to improve bioproduction
Signal-linked SCs to improve biosensing
Using SCs to understand natural interactions; build to understand
How can SCs be used to implement pattern formation?
Attempts to implement a Turing mechanism using differences in diffusion rate of signals
How can SCs be used to functionalise biofilms with patterned production?
Culture mixed with gold nanoparticles under amyloid fibril (curli subunit) expression control
How can SCs be used to improve biopoduction via metabolic link?
Cross-feeding to improve bioproduction
Coupling phototrophs to heterotrophs
How can SCs be used to understand natural interactions?
Cross-feeding auxotrophs can outcompete WT through metabolic “division of labour”
