QB3 Berkeley / Hongjun Dong

Hongjun Dong

Ph.D., 2011, Institute of Microbiology, Chinese Academy of Sciences

Berkeley host: Professor Michelle C. Chang

Research Summary

Microorganisms have long been used for studying basic bioscience such as DNA replication and protein synthesis. They are also exploited as cell factories for producing many chemicals, antibiotics, and amino acids due to their metabolic diversity and fermentation properties. However, overproduction of one particular metabolite cannot be achieved mostly in wild type strains. Through modern techniques of genetic manipulation, we are able to make microbes to fulfill our need for efficient industrial production.

In my research I explore the genetic construction of a microbial cell factory. There are two aspects for strain development, one is to create a novel pathway for producing natural or unnatural products, and the other is to engineer the host to support the production of target products efficiently. Particularly, the following steps are included:

  • Build an artificial novel pathway. For producing a selected target compound, the possible biochemical synthetic routes are proposed with the computer assistant design from current biochemical reactions databases, and the related enzymes are mined from public protein and gene databases. Then the new genes from different sources are assembled together to form a novel functional pathway. In this process, which relies on directed evolution or computer design, the desired genes could be chemically synthesized, enabling enzyme function that does not exist in nature.
  • Optimization of target pathway. The regulation principles of the target pathway are established and tested. The expression levels of each gene in the pathway are fine-tuned through promoter replacement or RBS modification, to maximize the catalysis efficiency. Advanced synthetic biology tools will be employed for this aim.
  • Strain improvement. For efficient production of target metabolite, the host needs to be modified in order to support the heterologous target pathway. The genome-scale metabolic network model will be used to predict the related pathways, and system biology techniques will be used to study the mechanisms. Laboratory adaptive evolution will be employed to increase the cellular growth and improve the tolerance against toxicity because of the overproduction. Finally, a strain with high yield, productivity, and titer of target product will be developed.

Impact in China

My goal is to construct a new generation of microbial cell factories by combining deep insights of life mechanisms and advanced manipulation tools. With the training of the Tang Scholar Program at UC Berkeley, I hope to contribute to the development of the fermentation industry in China by providing new engineered strains for the production of valuable natural or unnatural compounds.

Publications

  1. Hongjun Dong, Chunhua Zhao, Tianrui Zhang, Zhao Lin, Yin Li and Yanping Zhang*. Engineering Escherichia coli cell factories for n-butanol production. Advances in Biochemical Engineering/Biotechnology, 2015, DOI 10.1007/10_2015_306.
  2. Zhao Lin, Hongjun Dong*, Yin Li*. Improvement of butanol production by Escherichia coli using Tn5 transposon (in Chinese). Chinese Journal of Biotechnology, 2015, 31(12): 1711−1719.
  3. Fuyu Gong, Guanhui Bao, Chunhua Zhao, Yanping Zhang*, Yin Li, Hongjun Dong*. Fermentation and genomic analysis of acetone-uncoupled butanol production by Clostridium tetanomorphum. Applied Microbiology and Biotechnology, 2015, 1-7.
  4. Hongjun Dong, Wenwen Tao, Fuyu Gong, Yin Li, Yanping Zhang*. A functional recT gene for recombineering of Clostridium. Journal of Biotechnology, 2014, 173: 65-67.
  5. Guodong Luan#, Hongjun Dong#, Tianrui Zhang, Zhao Lin, Yanping Zhang, Yin Li, Zhen Cai*. Engineering cellular robustness of microbes by introducing the GroESL chaperonins from extremophilic bacteria. Journal of Biotechnology, 2014, 178: 38–40.
  6. Liejian Yang, Guanhui Bao, Yan Zhu, Hongjun Dong*, Yanping Zhang, Yin Li*. Discovery of a novel gene involved in autolysis of Clostridium cells. Protein & Cell, 2014, 4(6): 467-474.
  7. Hongjun Dong#, Wenwen Tao#, Yanping Zhang, Yin Li*. Development of an anhydrotetracycline-inducible gene expression system for solvent-producing Clostridium acetobutylicum: A useful tool for strain engineering. Metabolic Engineering, 2014, 14(1): 59-67.
  8. Hongjun Dong#, Wenwen Tao#, Linjiang Zhu, Yanping Zhang, Yin Li*. CAC2634-disrupted mutant of Clostridium acetobutylicum can be electrotransformed in air. Letters in Applied Microbiology, 2011, 53(3): 379-382.
  9. Hongjun Dong, Wenwen Tao, Zongjie Dai, Liejian Yang, Fuyu Gong, Yanping Zhang, Yin Li*. Biobutanol. Advances in Biochemical Engineering-Biotechnology, 2011, doi: 10.1007/10_2011_128.
  10. Hongjun Dong, Yanping Zhang, Zongjie Dai, Yin Li*. Engineering Clostridium strain to accept unmethylated DNA. PloS ONE, 2010, 5: e9038.
  11. Hongjun Dong, Yanping Zhang, and Yin Li*. The genetic manipulation systems for Clostridium acetobutylicum (in Chinese). Chinese Journal of Biotechnology, 2010, 26(10): 1372-1378.
  12. Hongjun Dong, Lixian Wu, Sanfeng Chen*. Cloning and expression of ethylene-forming enzyme gene from Pseudomonas syringae pv. glycinea ICMP2189 (in Chinese). Journal of Agricultural Biotechnology, 2017, 15(4): 698-701.
  13. Hongjun Dong, Yanping Zhang, Yan Zhu, Guodong Luan, Runjiang Wang, Wenwen Tao, and Yin Li*. Biofuels and Bioenergy: Acetone and Butanol. Comprehensive Biotechnology (2nd Edition), Elsevier Science Publishers Ltd, 13153 words, 2011. (Book chapter)
  14. Guanhui Bao, Hongjun Dong, Yan Zhu, Shaoming Mao, Tianrui Zhang, Yanping Zhang, Zugen Chen, Yin Li*. Comparative genomic and proteomic analyses of Clostridium acetobutylicum Rh8 and its parent strain DSM 1731 revealed new understandings on butanol tolerance. Biochemical and Biophysical Research Communications, 2014, 450(4): 1612-1618.
  15. Zongjie Dai, Hongjun Dong, Yan Zhu, Yanping Zhang, Yin Li*, Yanhe Ma. Introducing a single secondary alcohol dehydrogenase into butanol-tolerant Clostridium acetobutylicum Rh8 switches ABE fermentation to high level IBE fermentation. Biotechnology for Biofuels, 2012, 5(1): 44.
  16. Shaohua Wang, Yanping Zhang, Hongjun Dong, Shaomin Mao, Yan Zhu, Runjiang Wang, Guodong Luan, and Yin Li*. Formic Acid Triggers the “Acid Crash” of Acetone-Butanol-Ethanol Fermentation of Clostridium acetobutylicum. Applied and Environmental Microbiology, 2011, 77: 1674-1680.
  17. Linjiang Zhu, Hongjun Dong, Yanping Zhang, and Yin Li*. Engineering the Robustness of Clostridium acetobutylicum by Introducing Glutathione Biosynthetic Capability. Metabolic Engineering, 2011, 13(4): 426–434.
  18. Zuojun Wu, Hongjun Dong, Liangdong Zou, Diannan Lu, Zheng Liu*. Enriched Microbial community in bioaugmentation of petroleum-contaminated soil in the presence of wheat straw. Applied Biochemistry and Biotechnology, 2011, 164(7): 1071-1082.
  19. Li Tao, Hongjun Dong, Xi Chen, Sanfeng Chen*, Tianhong Wang. Expression of ethylene-forming enzyme (EFE) of Pseudomonas syringae pv. glycinea in Trichoderma viride. Applied Microbiology and Biotechnology, 2008, 80(4): 573-578.

(#equal contribution, *corresponding author)