张数一 博士

主要科研领域与方向

基于“还原论”的研究思路，长期致力于关键生命过程和合成生物学的研究，聚焦在代谢通路、能量摄取、调控网络等领域，研究生物结构的多样性潜力和进化可能性。相关论文发表在Science，Nature Biotechnology，Nature Microbiology等。有些研究成果已经改写并被收录世界经典教科书。

目前采用“重构论”的思路进行生物学研究，从而突破“还原论”研究思路的局限。侧重在优良蛋白质元件的计算机辅助从头理性设计、自动化平台赋能的高通量表征、连续定向进化系统辅助的快速精准优化等，实现蛋白质元件序列-结构-功能映射的建立；以及将这些设计和改造后的元件有机耦合基因线路和调控网络，从头搭建能自我复制的生命系统，从而实现对生命结构的重构理解和认知，并有效地应用于疾病诊断和治疗等领域。

代表性论文

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