Reading, Writing and Editing a Genome: An Emerging Frontier in Synthetic Biology

Advances in reading, writing and editing genomes have greatly expanded our ability to reprogram biological systems at the resolution of a single nucleotide and on the scale of a whole genome.  Such capacity has drastically accelerated the cycle of design, build and test in synthetic biology to construct organisms for both basic and applied biological research and medicine.  In this presentation, I will highlight our recent work in the development of new strategies and tools for genome editing and our attempt in automating the design, build and test cycle.  Examples include but are not limited to: (a) automated design and synthesis of TALENs and their applications in treatment of sickle-cell disease and mitochondrial diseases (1-4); (b) CRISPR based multiplexed genome engineering in Saccharomyces cerevisiae and Streptomycetes (5-6); and (c) rapid cellular prototyping of S. cerevisiae via genome-scale engineering based on either RNAi or CRISPR technologies (7-9).

References:

1. N. Sun, J. Liang, Z. Abil, and H. Zhao. “Optimized TAL Effector Nucleases (TALENs) for Use in Treatment of Sickle Cell Disease.” Molecular Biosystems, 8, 1255 – 1263 (2012).
2. J. Liang, R. Chao, Z. Bao, N. Sun, Z. Abil, and H. Zhao.“FairyTALE: A High-throughput TAL Effector Synthesis Platform.” ACS Synthetic Biology, 3, 67-73 (2014).
3. L. Cuculis, Z. Abil, H. Zhao, and C. Schroeder. “Direct Observation of TALE Protein Dynamics Reveals a Two-state Search Mechanism.” Nature Communications, 6: 7277 (2015).
4. P. Reddy, A. Ocampo, K. Suzuki, J. Luo, S. R. Bacman, S. L. Williams, A. Sugawara, D. Okamura, Y. Tsunekawa, D. Lam, X. Xiong, N. Monsterrat, C. Rodriguez, I. Sancho-Martinez, D. Manau, S. Civico, M. del Mar O’callaghan, J. Campistol, H. Zhao, J. M. Campistol, C. T. Moraes, J. C. Izpisua-Belmonte. “Selective Elimination of Mitochondrial Mutations in the Germline by Genome Editing.” Cell, 161, 459–469 (2015).
5. Z. Bao, H. Xiao, J. Liang, X. Xiong, N. Sun,T. Si, and H. Zhao. “Homology Integrated CRISPR-Cas (HI-CRISPR) System for One-step Multi-gene Disruptions in Saccharomyces cerevisiae.” ACS Synthetic Biology, 4, 585−594 (2015).
6. R.E. Cobb, Y. Wang, and H. Zhao. “High-efficiency Multiplex Genome Editing of Streptomyces Species using an Engineered CRISPR/Cas System.” ACS Synthetic Biology, 4, 723–728 (2015).
7. T. Si, H. Xiao, and H. Zhao. “Rapid Prototyping of Microbial Cell Factories via Genome-scale Engineering.” Biotechnology Advances, 33, 1420–1432 (2015).
8. T. Si, Y. Luo, Z. Bao, and H. Zhao. “RNAi-Assisted Genome Evolution in Saccharomyces cerevisiae for Complex Phenotype Engineering.” ACS Synthetic Biology, 4, 283−291 (2015).
9. Z. Bao, R.E. Cobb, and H. Zhao. “Accelerated Genome Engineering through Multiplexing.” Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 8, 5–21 (2016).