Development of microbial cell factories for consolidated bioprocessing by engineering biology platform

Akihiko Kondo^1,2,3

¹Graduate School of Science, Technology and Innovation, Kobe University,

²Department of Chemical Science and Engineering, Graduate School of Engineering,

Kobe University, 1 -1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan.

³Cell Factory Research Team, RIKEN Center for Sustainable Resource Science,

1-7-22 Suehirocho, Tsurumiku, Yokohama, 230-0045, Japan

In order to construct sustainable biorefineries, which produce variety of biofuels and bio-based chemicals from non-food biomass, consolidated bioprocessing (CBP), which integrates enzyme production, saccharification and fermentation into a single process, is a promising strategy. One of the key technologies to develop microbial cell factories for CBP is cell surface engineering, which is a powerful tool to express enzymes on the cell surface for conversion of biomass into sugars [1]. We have developed various cell surface display systems in yeast, bacteria and fungus and showed the direct fermentation of biomass. To design novel metabolic pathways for conversion of sugars to target chemicals, we have developed computer simulation tools [2]. To efficiently construct cell factories by re-write genome based on designs, we have developed the platform technologies such as genome editing and a large gene cluster synthesis systems and are going to integrate to set up the automated systems. By tethering the DNA deaminase activity to nuclease-deficient CRISPR/Cas9 system, a genome editing tool that enables targeted point mutagenesis [3, 4] have developed (termed Target-AID or Base Editor). In addition, an efficient DNA assembly method, namely,OrderedGeneAssembly inB. subtilis(OGAB) method have developed. OGAB method can assemble more than 50 DNA fragments to construct up to 100 kb DNA in one-step usingB. subtilis[5]. An automated metabolomics analysis system has also been developed to analyze the performance of cell factories in more accurate and high throughput manner. We have integrated these technologies to construct engineering biology platform to quickly construct microbial cell factories for CBP. We are applying this platform for construction of various cell factories [6-8].

References

[1] Hasunuma T. et al.,Biotechnology advances30 (6), 1207-1218 (2012)

[2] Araki M., et al.,Bioinformatics,31(6), 905-911 (2015)

[3] Nishida K. et al.Science,353, aaf8729 (2016).

[4] Shimatani Z. et al.,Nature Biotechnology,35(5), 441-443 (2017).

[5] Tsuge, K. et al.,Scientific Reports,5, 10655 (2015).

[6] Noda S et al.,Nature Communications, 8(1): 1153 (2017)

[7] Vavricka, CJ., ey al.,Nature Communications,10 (1), 2015 (2019)

[8] Vavricka, CJ., ey al.,Trends in Biotechnology,in press(2019)

Akihiko Kondo^1,2,3

¹Graduate School of Science, Technology and Innovation Kobe University

²Department of Chemical Science and Engineering, Kobe University

1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan

³Cell Factory Research Team, Center for Sustainable Resource Science, RIKEN

1-7-22 Suehirocho, Tsurumiku, Yokohama, 230-0045, Japan

Tel&Fax: +81-78-803-6196 E-mail: akondo@kobe-u.ac.jp

Akihiko Kondo received his Ph.D. from Kyoto University in Chemical Engineering (1988). He was appointed as full professor of Kobe University in 2003 and also appointed as a team leader of the cell factory research team at RIKEN Center for Sustainable Resource Science in 2012. He became a member of Science Council Japan in 2017.

A. Kondo has developed various platform technologies such as cell surface display systems, metabolic pathway design tools, metabolic analysis technologies, genome editing and long chain DNA synthesis technologies. He also has applied these platform technologies for construction of various microbial cell factories for production of biofuels and various chemicals from biomass, and cyanobacteria and microalgae for production of starch, oil and chemicals from CO₂.

A. Kondo has been appointed as editor or editorial board members of many Journals such as Journal of Biotechnology, Metabolic Engineering, Biotechnology for Biofuels, Bioresource Technology, etc. He has published more than 630 peer reviewed international papers.