Synthetic Biology I The Programming of Cells

Synthetic Biology I

The Programming of Cells

Nawwaf Kharma & Luc VarinArtificial Life GroupElec. & Comp. Engineering and Biology DepartmentsConcordia University, Montréal (QC), [email protected]

Artificial Life Group The Programming of Cells 2

Synthetic Biology- What & Why

• It is an emerging area of research that combines science and engineering to envision, design and realize novel structures and functions (mainly in cells) by (primarily) modifying the genome (within the cells)

• Cells have advantages:• They have/can have built-in

interfaces, to sense and produce many substances

• They are easy to mass produce, store and distribute

• They are generally more robust than man-made systems

• They are optimizable via directed evolution


Biological Refresher:Flow of genetic information

DNA

Transcription

RNA

RNA

Translation

Protein

Proteins

Can interact with each other


Basic Paradigm:From the ground up

• First: Basic Components

Combinatorial & Sequential

• Second: Larger Circuits

With more/larger components and/or more functionality

• Third: Communications & Pattern Formation

Leading to even greater functionality

>> Finally, future Challenges that must be met if the field is to advance >>>


Combinatorial Components I:Promoter-based Regulation

Kaern et al. (2003)

Combinatorial Components II:siRNA-based Regulation

Artificial Life Group The Programming of Cells 6Deans et al. (2007)


Combinatorial Components III:Ribozyme-based Regulation

Win et al. (2008)


Sequential Components I: First Toggle

Gardner et al. (2000)

Sequential Components II:Various Oscillators

Artificial Life Group The Programming of Cells 9Elowitz et al. (2000)Wong et al. (2006)


Sequential Components III:Mammalian Memory

Ajo-Franklin et al. (2007)

Sequential Components IV: Pulsers & Delays

Artificial Life Group The Programming of Cells 11Kaesling et al. (2006)

Delays using repressors only- how?

Combinatorial Components include: Switches Inverters Logic Gates

Sequential Components include: Oscillators (ON-OFF-ON-OFF-…)

Toggles (ON or OFF, depending on Input & State)

1-bit Memory (ON or OFF, depending on Input)

Pulse-rs (ON for a short while, then auto-OFF)

Delays (Output follows Input after a Delay)

Next: Scale-up & combine components to build circuits


Summary 1 of 3


Larger Circuits I: Combinatorial Logic (4 inputs/1 output)

Rinaudo et al. (2007)

Artificial Life Group The Programming of Cells 14Rinaudo et al. (2007)

Larger Circuits II:Sequential Logic (multi-bit memory)

Artificial Life Group The Programming of Cells 15Ham et al. (2008)


Larger Circuits III: Modular Design (- also involving intercellular communication)

Kobayashi et al. (2004)

Ex1: Larger Combinatorial Circuit with: Multi-input Logic Function with 4 (and 5) inputs and 1 output

Ex2: Multi-bit Memory that: Set precisely using a series of inputs Grows exponentially with no. of invertases

Ex3: Modular Circuit with: 3 intra-cellular modules that Sense, Process, and Output information It also communicates with other cells


Summary 2 of 3


Advanced Topics I: Pattern Formation (using inter-cellular communications)

Basu et al. (2005)Bernhardt et al. (2007)

Advanced Topics II: Inter-kingdom Communications (using another kind of inter-cellular communications)

Artificial Life Group The Programming of Cells 19Weber et al. (2007)

Advanced Topics II continued

Inter-kingdom Communications


Advanced Topics III:Applications

Artificial Life Group The Programming of Cells 21Rodrigo et al. (2007)

Ex1: Pattern Formation Is necessary for autonomous

differentiation of large collections of cells

Ex2: Inter-cellular Communications Is necessary for coordinated action by

larger collections of cells

Ex3: Applications Necessary to justify the significant cost

of investment in “blue-sky” research


Summary 3 of 3

Future Challenges I: Reliable Well-Characterized Modules

Artificial Life Group The Programming of Cells 23Canton et al. (2008)

Future Challenges II: Synchronization & Communications


How can a large number of components communicate and work synchronously across large distances? Possible answers include:

A.A large number of freely-diffusing signalsB.A much smaller number of short-distance signalsC.Isolated channels (e.g. neurons) that pass signals

As to operating synchronously: simulations have been made but no implementations yet!

Garcia-Ojalvo et al. (2004)

Future Challenges III: Interfacing with Electro/Optical Components


How can electronic devices be interfaced to the new cellular devices? Possibilities include:

A.Light at different frequenciesB.Electric fieldC.Chemical reactions, such as:

A mammalian cell-based frequency generator: DC power converts ethanol into acetaldehyde, which dose-dependently triggers expression of the BMP-2 in engineered rat cardiomyocytes (AIRNRC-BMP-2) and increases the contraction frequency


Final Summary

Cells are not like human-engineered machinesCells, if fully understood, may be treated as machinesCells are not fully understood or characterized

Researchers are starting to see potential in manipulating the genome of cells

And they are continuing to expand the frontier while simultaneously improving the reliability of existing components

There has been great progress, but still more needs to be done to:A. Build a basic repertoire of reliable well-characterized combinatorial &

sequential componentsB. Communicate and synchronize across large distances and in different

mediumsC. Establish controllable methods for growing large patterns of inter-acting

cells

References

Kaern et al. (2003): Mads Kærn,William J Blake, and J J Collins. “The Engineering of Gene Regulatory Networks.” Annual Review of Biomedical Engineering 5:179–206.

Deans et al. (2007): Tara L Deans, Charles R Cantor & James J Collins. “A Tunable Genetic Switch Based on RNAi and Repressor Proteins for Regulating Gene Expression in Mammalian Cells.” Cell 130, 363–372.

Win et al. (2008): Maung Nyan Win & Christina D Smolke. “Higher-Order Cellular Information Processing with Synthetic RNA Devices.” Science vol. 322, 456-460.

Gardner et al. (2000): Timothy S Gardner, Charles R Cantor & James J Collin. “Construction of a genetic toggle switch in Escherichia coli.” Nature vol. 403, 339-342.

Elowitz et al. (2000): Michael B Elowitz & Stanislas Leibler. “A synthetic oscillatory network of transcriptional regulators.” Nature vol. 403, 335- 338.

Wong et al. (2006): W W Wong and J C Liao. “The design of intracellular oscillators that interact with metabolism.” Cell. Mol. Life Sci. vol. 63:1215–1220.

Ajo-Franklin et al. (2007): Caroline M Ajo-Franklin, David A Drubin, Julian A Eskin, Elaine P S Gee, Dirk Landgraf, Ira Phillips & Pamela A Silver. “Rational design of memory in eukaryotic cells.” Genes and Development 21:2271–2276.

Kaesling et al. (2006): http://keaslinglab.lbl.gov/wiki/index.php/Synthetic_Biology_-_Devices_-_Pulse_Generator

Rinaudo et al. (2007): Keller Rinaudo, Leonidas Bleris, Rohan Maddamsetti, Sairam Subramanian, Ron Weiss & Yaakov Benenson. “A universal RNAi-based logic evaluator that operates in mammalian cells.” Nature Biotechnology vol. 25, No. 7: 795-801.


References continued

Ham et al. (2008): Timothy S Ham, Sung K Lee, Jay D Keasling & Adam P Arkin. “Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory.” PloS ONE, vol. 3, No. 7: 1-9.

Kobayashi et al. (2004): Hideki Kobayashi, Mads Kærn, Michihiro Araki, Kristy Chung, Timothy S Gardner, Charles R Cantor & James J Collins. “Programmable cells: Interfacing natural and engineered gene networks.” PNAS vol. 101, No. 22: 8414–8419.

Basu et al. (2005): Subhayu Basu, Yoram Gerchman, Cynthia H Collins, Frances H Arnold & Ron Weiss. “A synthetic multicellular system for programmed pattern formation.” Nature, vol. 434: 1130-1134. IET Synth. Biol., vol. 1, no. 1–2: 29–31.

Bernhardt et al. (2007): K Bernhardt, E J Carter, N S Chand, J Lee, Y Xu, X Zhu, J W Ajioka, J M Goncalves, J Haseloff, G Micklem and D Rowe. “New tools for self-organised pattern formation.”

Weber et al. (2007): Wilfried Weber, Marie Daoud-El Baba & Martin Fussenegger. “Synthetic ecosystems based on airborne inter- and intrakingdom communication.” PNAS, vol. 104, no. 25: 10435–10440.

Rodrigo et al. (2007): G Rodrigo, A Montagud, A Aparici, M C Aroca, M Baguena, J Carrera, C Edo, P Fernandez-de-Cordoba, A Ferrando, G Fuertes, D Gimenez, C Mata, J V Medrano, C Navarrete, E Navarro, J Salgado, P Tortosa, J Urchueguia and A Jaramillo. “Vanillin cell sensor.” IET Synth. Biol., vol. 1, no. 1–2: pp. 74–78.


References continued

Alexic et al. (2007): J Aleksic, F Bizzari, Y Cai, B Davidson, K de Mora, S. Ivakhno, S L Seshasayee, J Nicholson, J Wilson, A Elfick, C French, L Kozma-Bognar, H Ma & A Millar. ” Development of a novel biosensor for the detection of arsenic in drinking water.” IET Synthetic Biolology, vol. 1, no. 1–2: 87–90.

Canton et al. (2008): Barry Canton, Anna Labno & Drew Endy. “Refinement and standardization of synthetic biological parts and devices.” Nature Biotechnology, vol. 26, no. 7: 787-793.

Garcia-Ojalvo et al. (2004): Jordi Garcia-Ojalvo, Michael B Elowitz, and Steven H Strogatz. “Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing.” PNAS, vol. 101, no. 30: 10955–10960.

Weber et al. (2009): Wilfried Weber, Stefan Luzi, Maria Karlsson, Carlota Diaz Sanchez-Bustamante, Urs Frey, Andreas Hierlemann & Martin Fussenegger. “A synthetic mammalian electro-genetic transcription circuit.” Nucleic Acids Research, vol. 37, no. 4.


Synthetic Biology I The Programming of Cells

Documents

Transcript of Synthetic Biology I The Programming of Cells