Shuyi Zhang Ph.D.

Main Research Fields

Based on the research approach of ‘reductionism,’ with a long-term commitment, we study the key life processes in nature and synthetic biology, focusing on areas such as metabolic pathways, energy intake, and regulatory networks, to explore the potential diversity of biological structures and the possibilities of evolution. Related papers have been published in journals such as Science, Nature Biotechnology, and Nature Microbiology. Some research findings have rewritten and been included in classic world textbooks.

Currently, we adopt the ‘reconstructionism’ approach to biological research to break through the limitations of the ‘reductionism’ research approach. Focusing on the computer-aided rational design of high-quality protein components from scratch, high-throughput characterization empowered by automated platforms, and rapid and precise optimization assisted by continuous directed evolution systems, to establish the mapping of protein component sequences-structures-functions; as well as organically coupling these designed and modified components with gene circuits and regulatory networks to build from scratch self-replicating life systems, thereby achieving a reconstructed understanding and cognition of life structures, and effectively applying them in fields such as disease diagnosis and treatment.

Selected Publications

1. Shuyi Zhang and Donald A. Bryant. (2011). The tricarboxylic acid cycle in cyanobacteria. Science, 334, 1551-1553, DOI: 10.1126/science.1210858
- This work was featured as cover story in Chapter 3 of the classic microbiology textbook Brock Biology of Microorganisms (14th Edition)
- This work was featured by Science, along with a perspective article by Jack Meeks; this work was also covered in many media such as Faculty of 1000 Prime, ScienceDaily, Chemical and Enginerring News (C&EN), US Green Technology, Science Illustrated, Phys.org, Microbe World, Advanced Biofuels USA, Biofuels Digest, Materials Research Society, Biomedical Market Newsletter, Tumblr, Genome Web, Science and Technology Updates, Asian Network, Daily-Ondanka (Japan), Kuramae-Bioenergy(Japan), Da-Guan Weekly (China), Penn State News, Bioenergy UIUC …

2. Shuyi Zhang, Gaozhong Shen, Zhongkui Li, John H. Golbeck and Donald A. Bryant. (2014). Vipp1 is essential for the biogenesis of Photosystem I but not thylakoid membranes in Synechococcus sp. PCC 7002. Journal of Biological Chemistry, 289(23), 15904-15914, DOI: 10.1074/jbc.M114.555631

3. Fei Gan, Shuyi Zhang, Nathan C. Rockwell, Shelley S. Martin, Clark J. Lagarias and Donald A. Bryant. (2014) Extensive remodeling of a cyanobacterial photosynthetic apparatus in Far-Red light. Science, 345, 1312-1317, DOI: 10.1126/science.1256963
- This work was described as “text book changing stuff” by Professor Bill Rutherford from Imperial College London.
- Full length Science article; this work was also covered in many media such as Science World Report, Nature World News, Science 2.0, RedOrbit, ScienceDaily, JGI Science Highlight, Faculty of 1000 Prime, Mirian (Korean), BRIC (Korean), Case, Bio-Medicine, Penn State News …

4. Shuyi Zhang and Donald A. Bryant. (2014) Learning new tricks from an old cycle: the TCA cycles of cyanobacteria, algae and plants. Perspectives in Phycology, 2, 73-86, Invited review article, DOI: 10.1127/pip/2014/0016

5. Shuyi Zhang and Donald A. Bryant. (2015) Biochemical validation of the the glyoxylate cycle in the cyanobacterium Chlorogloeopsis fritschii PCC 9212, Journal of Biological Chemistry 290 (22), 14019-14030, DOI: 10.1074/jbc.M115.648170

6. Shuyi Zhang, Yang Liu and Donald A. Bryant. (2015) Metabolic engineering of Synechococcus sp. PCC 7002 to produce poly-3-hydroxybutyrate and poly-3-hydroxybutyrate-co-4-hydroxybutyrate, Metabolic Engineering, 32, 174-183, DOI:10.1016/j.ymben.2015.10.001

7. Shuyi Zhang, Xiao Qian, Shannon Chang, G Charles Dismukes and Donald A Bryant (2016) Natural and synthetic variants of the tricarboxylic acid cycle in cyanobacteria: introduction of the GABA shunt into Synechococcus sp. PCC 7002. Frontiers in Microbiology, 7, 1972, DOI: 10.3389/fmicb.2016.01972

8. Shuyi Zhang and Christopher A. Voigt. (2018) Engineered dCas9 with reduced toxicity in bacteria: implications for genetic circuit design. Nucleic Acids Research, 46, 20, 11115-11125, DOI: 10.1093/nar/gky884 

9. Jonghyeon Shin, Shuyi Zhang, Bryan S. Der, Alec A.K. Nielsen, and Christopher A. Voigt. (2020) Programming Escherichia coli to function as a digital display. Molecular Systems Biology, 16, 3, e9401, DOI: 10.15252/msb.20199401. Highlighted as Cover Article.

10. Mao Taketani, Jianbo Zhang, Shuyi Zhang, Alexander J. Triassi, Yu-Ja Huang, Linda G. Griffith & Christopher A. Voigt. (2020) Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron. Nature Biotechnology, 38, 8, 962–969, DOI: 10.1038/s41587-020-0468-5
11. Ye Chen, Shuyi Zhang, Eric M. Young, Timothy S. Jones, Douglas Densmore & Christopher A. Voigt (2020) Genetic circuit design automation for yeast. Nature Microbiology, 5, 11, 1349–1360, DOI: 10.1038/s41564-020-0757-2
12.Ye Chen & Shuyi Zhang* (2022) Editorial: Synthetic Live Biotherapeutic Products for Diseases, Frontiers in Molecular Biosciences, 9:882743, DOI: 10.3389/fmolb.2022.882743