Programmable Designer Microorganisms by Systems and Synthetic Biology Approaches

- Developing synthetic biology tools for engineering microorganisms

- Building synthetic cell factories for the production of chemicals, fuels, pharmaceuticals, and therapeutics

- Elucidation of complex regulatory networks and reconstruction of meta-structure of microorganisms

Synthetic Biology Tools

Building a synthetic metabolic pathway requires molecular tools to design DNA sequences to achieve a specific expression level (static control) and a dynamic response of expression (dynamic control). We develop various molecular tools that can control multiple layers of regulation, such as transcription, translation, and post-translation processes. Furthermore, we examine various approaches that can generate phenotypic diversity to evolve the engineered system to meet the expected performance.

Programming Cells

With various molecular tools, we program cells to solve issues in energy, environment, and biomedical applications. For example, we design and construct de novo metabolic pathways to produce chemicals and fuels from renewable biomasses. Iteration of evolutionary approaches and genome-scale comprehensive analysis of the system would generate an economically feasible bioprocess. We also integrate multiple environmental signals and implement synthetic control over biological processes for various types of environmental and biomedical applications.

Meta-structure Reconstruction

Knowing what we are dealing with is the most important strategy to successfully engineer our targets. Although it has been several decades to study E. coli, there are still plenty of unknown regulatory mechanisms, networks, and interactions between them beyond the genomic sequence. Owing to the development of innovative high-throughput technologies, we now have the potential to fully reconstruct the meta-structure of bacterial regulatory networks beyond E. coli. We use cutting-edge, high-throughput genome-scale experimental methods such as ChIP-exo, RNA-seq, TSS-seq, and Ribo-seq to build a comprehensive regulatory network of bacterial genomes. A comprehensive understanding of the meta-structure of bacteria will continue to enable applications in metabolic engineering and microbial engineering for energy, materials, and human health.