Synthetic Biology A Brief Survey Isaac Larkin 01112016

Synthetic Biology: A Brief Survey Isaac Larkin 01/11/2016 http: //news. mit. edu/topic/synthetic-biology 1

What is Synthetic Biology? Synthetic biology is programming biological matter. Schwille, P. Science 333, 1252– 4 (2011).

The Synthetic Biology Stack Biomolecular Circuit/“Device” Characterization and Design Biomolecule “Part” Characterization and Design DNA Insertion/ Genome Manipulation DNA Assembly DNA Sequencing and Synthesis Level of Abstraction

Falling Cost of DNA Sequencing and Synthesis Facilitates Synthetic Biology IDT oligo synthesis (i. Buy): 15 -60 bp for $0. 01 -$0. 03 /base/nmole synthesis. cc/2014/02/time-for-new-costcurves-2014. html

Falling Cost of DNA Sequencing and Synthesis Facilitates Synthetic Biology Twist’s Price: 10¢ / base 1. Elizabeth Segran, Fast Company, 2015 (goo. gl/l 4 JGn. P) 2. http: //www. incubizz. de/index. php/twist-bioscience

Advances in DNA Assembly Enable Whole Genome Synthesis Assembly strategy for synthetic genomes Holt, R. A. Nat. Biotechnol. 26, 296– 7 (2008).

Advances in DNA Assembly Enable Whole Genome Synthesis Gibson Assembly Up to 10 fragments at once One pot, 50ºC, 15 -60 min neb. com/products/ synbio. tsl. ac. uk/gibson-assembly/

Advances in DNA Assembly Enable Whole Genome Synthesis Mycoplasma laboratorium jcvi. org, 2010

Advances in DNA Assembly Enable Whole Genome Synthesis Synthetic Yeast Project syntheticyeast. org

Advances in DNA Assembly Enable Whole Genome Synthesis Synthetic Yeast Project Science 344, 55– 8 (2014).

Genome Manipulation Leads to Rewriting the Genetic Code MAGE: Multiplex Automated Genome Engineering in E. coli MAGE enables rapid, introduction of ~10 simultaneous mutations in E. coli Wang, H. H. et al. Nature 460, 894– 8 (2009).

Genome Manipulation Leads to Rewriting the Genetic Code Only 314 UAG in the whole E. coli genome! Ma, N. J. , Moonan, D. W. & Isaacs, F. J. Nat. Protoc. 9, 2285– 300 (2014)

Genome Manipulation Leads to Rewriting the Genetic Code CAGE enables genome-wide UAG UAA codon reassignment (Science 2013) Ma, N. J. , Moonan, D. W. & Isaacs, F. J. Nat. Protoc. 9, 2285– 300 (2014)

Genome Manipulation Leads to Rewriting the Genetic Code Genomically Recoded Organisms (GROs) enable efficient NSAA incorporation Lajoie, M. J. et al. Science 342, 357– 60 (2013)

Genome Manipulation Leads to Rewriting the Genetic Code Azides Photo-Crosslinker Alkynes Fluorophores Quast, R. B. et al. FEBS Lett. 589, 1703– 12 (2015)

Prediction and Programming of Biomolecule Structure is Improving Predicted Structure Crystal Structure Marks, D. S. , Hopf, T. A. & Sander, C. Nat. Biotechnol. 30, 1072– 80 (2012)

Prediction and Programming of Biomolecule Structure is Improving Baker Lab designs 2 -component, tetrahedral protein nanoparticles King, N. P. et al. Nature 510, 103– 8 (2014)

Prediction and Programming of Protein Structure is Improving Baker Lab designs 2 -component, tetrahedral protein nanoparticles King, N. P. et al. Nature 510, 103– 8 (2014)

Design of Biomolecule Function Produces Novel “Parts” for Synthetic Biologists DNA promoter libraries enable tuning of maximum expression 1. http: //2011. igem. org/Team: DTU-Denmark/ Project_improving_ara. BAD

Design of Biomolecule Function Produces Novel “Parts” for Synthetic Biologists Spinach: An RNA mimic of GFP 1. Paige, J. S. , Wu, K. Y. & Jaffrey, S. R. Science 333, 642– 6 (2011).

Design of Biomolecule Function Produces Novel “Parts” for Synthetic Biologists 1. Paige, J. S. , Wu, K. Y. & Jaffrey, S. R. Science 333, 642– 6 (2011).

Design of Biomolecule Function Produces Novel “Parts” for Synthetic Biologists Enzyme engineering: still really hard, but not impossible Engineered formolase (FLS): -Incorporates formaldehyde into central metabolism -Potentially, a new CO 2 fixation route 1. Siegel, J. B. et al. Proc. Natl. Acad. Sci. 112, 3704– 9 (2015).

From Parts to Complex Devices: Design of Genetic Circuits Origin of the field! 1. Cameron, D. E. , Bashor, C. J. & Collins, J. J. Nat. Rev. Microbiol. 12, 381– 90 (2014).

From Parts to Complex Devices: Design of Genetic Circuits Origin of the field! 1. Cameron, D. E. , Bashor, C. J. & Collins, J. J. Nat. Rev. Microbiol. 12, 381– 90 (2014).

From Parts to Complex Devices: Design of Genetic Circuits Circuit fidelity has improved 1. Elowitz, M. B. & Leibler, S. Nature 403, 335– 8 (2000).

From Parts to Complex Devices: Design of Genetic Circuits Circuit fidelity has improved 1. Danino, T. et al. Nature 463, 326– 30 (2010).

Therapeutic Genetic Circuits Cellular system to sense and repress psoriasis in mice 1. Schukur, L. et al. Sci. Transl. Med. 7, 318 ra 201– 318 ra 201 (2015).

Programming Metabolic Circuits to Make Useful Small Molecules 1 st triumph: Artemisinic Acid Production 1. Paddon, C. J. et al. Nature 496, 528– 32 (2013).

Programming Metabolic Circuits to Make Useful Small Molecules ~700 -fold better than first strain’s yield! 1 st triumph: Artemisinic Acid Production At an economically viable scale! (After 7 years of optimizing). 1. Paddon, C. J. et al. Nature 496, 528– 32 (2013).

Programming Metabolic Circuits to Make Useful Small Molecules Complete Opiate Biosynthesis in Yeast (Currently tiny yields) 1. Galanie, S. et al. Science (80 -. ). 349, 1095– 1100 (2015).

The Synthetic Biology Stack Biomolecular Circuit/“Device” Characterization and Design Biomolecule “Part” Characterization and Design DNA Insertion/ Genome Manipulation DNA Assembly DNA Sequencing and Synthesis Level of Abstraction

Thanks! Sarah Joe Weston Mike Jewett The NU Synthetic Biology Center 1. http: //www. tsienlab. ucsd. edu/HTML/Images/IMA GE%20 -%20 PLATE%20 -%20 Beach. jpg