Illinois Biological Foundry for Advanced Biomanufacturing (iBioFAB)

Huimin Zhao, University of Illinois at Urbana-Champaign zhao5@illinois.edu
Inspired by the exponential growth of the microelectronic industry, synthetic biologists have been attempting to build biological foundries for rapid prototyping and manufacturing of biological systems for synthesis of bioproducts ranging from chemicals to materials to therapeutic agents. In this talk, I will introduce the Illinois Biological Foundry for Advanced Biomanufacturing (iBioFAB) that we recently established at UIUC, which consists of (i) a computational design framework that automates the design- build-test-analyze cycle and (ii) an integrated automated robotic system that automates DNA cloning, DNA assembly, heterologous expression, and product detection (Figure 1). This iBioFAB features a 6 degree of freedom articulated robotic arm that travels on a 5-meter-long track and transfers microplates among more than 20 instruments installed on the platform; a sophisticated sample tracking system; and libraries of parts and modules for a variety of platform organisms (see video: http://youtu.be/Hwb735qZ- IQ). To demonstrate its unprecedented power, the iBioFAB was recently used to synthesize up to 1000

TALENs per day with dramatically reduced cost for large-scale genetic editing application. In addition, the iBioFAB has been used to automate the entire process of the RNA interference (RNAi)-assisted genome evolution (RAGE) method we recently developed for metabolic engineering of Saccharomyces cerevisiae (1). Through iterative cycles of creating a library of RNAi induced reduction-of-function mutants coupled with high throughput screening or selection, RAGE can continuously improve target trait(s) by accumulating multiplex beneficial genetic modifications in an evolving yeast genome. Previously, we used the manual RAGE method to improve acetic acid tolerance (1) and the furfural tolerance (2), two key traits for microbial production of chemicals and fuels from cellulosic materials. Recently, we augmented the genetic diversity
created by the RAGE method by including a library of cDNA overexpression induced enhancement-of-function mutants and further developed a fully automated modified RAGE method using the iBioFAB. We then used this new method to dramatically improve the
glycerol utilization rate and cellulase production level in addition to further increasing the acetic acid tolerance in S. cerevisiae.

Figure 1. Establishment of iBioFAB will create a new biomanufacturing paradigm.

1. T. Si, Y. Luo, Z. Bao, and H. Zhao. â??RNAi-Assisted Genome Evolution in Saccharomyces cerevisiae for Complex Phenotype Engineering.â? ACS Synthetic Biology, DOI:
10.1021/sb500074a.
2. H. Xiao and H. Zhao. â??Genome-wide RNAi Screen Reveals the E3 SUMO-protein Ligase Gene SIZ1 as a Novel Determinant of Furfural Tolerance in Saccharomyces cerevisiae.â? Biotechnology for Biofuels, 7:78 (2014).