Advances in the understanding and development of CRISPR-Cas systems have revolutionized the gene editing methods in biology and medicine. However, the imperfect properties of current CRISPR-Cas technology, such as a high off-target rate, a strict PAM requirement, high cell toxicity, and large gene size, restrict its diverse applications. We aim to discover, characterize, and engineer new CRISPR-Cas systems with superior properties compared with current CRISPR-Cas systems. In addition, we leverage different CRISPR-Cas systems to develop rapid and efficient gene editing tools in major human pathogens to facilitate fundamental understanding of infection and drug-resistance mechanisms. Finally, we aim to develop CRISPR-based antimicrobial strategies to counter infections caused by drug-resistant human pathogens.
CRISPR-Cas characterization and engineering: One potential way to overcome the limitation of current CRISPR-Cas technologies is to discover, characterize, and engineer new CRISPR-Cas systems from other bacteria that may possess rich and distinct biochemical properties for gene editing. We explore and study new CRISPR-Cas systems using multiple approaches, including bioinformatics, biochemical, structural biology, and molecular evolution methods. In addition, we study the fundamental molecular mechanism of current CRISPR-Cas9 systems to evolve PAM-expanded and high-fidelity versions of these enzymes (PLoS Biol, 2019; Nat Catal, 2020). Ultimately, we aim to develop compact CRISPR-Cas systems with low off-target rate and expanded targeting sites.
Gene editing in major human pathogens: The rapid emergence of drug-resistant human pathogens has posed a severe public health crisis worldwide, emphasizing the desperate need to identify new drug targets and develop new therapeutic strategies. Genetics is the key means to study bacterial physiology. However, traditional genetic manipulation methods in major human pathogens remain as time-consuming and laborious endeavors. We have created rapid and highly efficient genetic manipulation tools in multiple major human pathogens, including Staphylococcus aureus (JACS, 2017; Chem Sci, 2018; Chem Sci, 2020), Pseudomonas aeruginosa (iScience, 2018), Klebsiella pneumoniae (Appl Environ Microbiol, 2018; Antimicrob Agents Chemother, 2019), and Acinetobacter baumannii (Cell Chem Biol, 2019; STAR Protocols, 2020) by engineering the powerful CRISPR/Cas9 genome editing technology and deaminase-mediated base editing systems. These tools have been requested and utilized by numerous research groups worldwide and are available in Addgene (http://www.addgene.org/Quanjiang_Ji/). We utilize protein engineering and synthetic biology approaches to develop genome-wide screening tools in multiple human pathogens. The development of these tools will advance fundamental physiology studies as well as novel drug-target exploration (PNAS, 2018; Mol Microbiol, 2018).
CRISPR-based antimicrobial therapy: We aim to develop CRISPR engineered bacteriophages to counter infections caused by drug-resistant bacterial pathogens using the CRISPR systems developed by ourselves. The engineered bacteriophages are not only able to species-specifically kill target bacterial cells, but also capable of sequence-specifically eliminating certain genes. Therefore, both resistance attenuation and bacterial killing can possibly be achieved using the engineered phages.
1. Chen, W. & Ji, Q. (2020) Genetic manipulation of MRSA using CRISPR/Cas9 technology. Methods in Molecular Biology 2069:113-124.
Research Articles and Reviews
18. Zhang, Y., Zhang, H., Xu, X., Wang, Yuj, Chen, W., Wang, Ya., Wu, Z., Tang, N., Wang, Yu, Zhao, S., Gan, J.*, Ji, Q.* (2020) Catalytic-state structure and engineering of Streptococcus thermophilus Cas9. Nature Catalysis 3: 813-823.
17. Yu, H.#, Wu, Z.#, Chen, X., Ji, Q.*, Tao, S.* (2020) CRISPR-CBEI: a designing and analyzing tool kit for cytosine base editor-mediated gene inactivation. mSystems 5: e00350-20.
16. Wang, Y.*, Wang, Z., Ji, Q.* (2020) CRISPR-Cas9-based genome editing and cytidine base editing in Acinetobacter baumannii. STAR Protocols DOI: 10.1016/j.xpro.2020.100025.
15. Pi, Y., Chen, W., Ji, Q.* (2020) Structural basis of Staphylococcus aureus surface protein SdrC. Biochemistry 59: 1465-1469.
14. Zhang, Y., Zhang, H., Wang, Z., Wu, Z., Wang, Y., Tang, N., Xu, X., Zhao, S., Chen, W.*, Ji, Q.* (2020) Programmable adenine deamination in bacteria using a Cas9-adenine-deaminase fusion. Chemical Science 11: 1657-1664.
13. Wu, Z., Wang, Y., Zhang, Y., Chen, W., Wang, Y., Ji, Q.* (2020) Strategies for developing CRISPR-based gene editing methods in bacteria. Small Methods 4: 1900560.
12. Chen, W., Zhang, H., Zhang, Y., Wang, Y., Gan, J.*, Ji, Q.* (2019) Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease. PLoS Biology 17: e3000496.
11. Wang, Y., Wang, Z., Chen, Y., Hua, X., Yu, Y., Ji, Q.* (2019) A highly efficient CRISPR-Cas9-based genome engineering platform in Acinetobacter baumannii toward the understanding of H2O2-sensing mechanism of OxyR. Cell Chemical Biology 26: 1732-42.
10. Zhang, Y., Sun, X., Qian, Y., Yi, H., Song, K., Zhu, H., Zonta, F., Chen, W., Ji, Q., Miersch, S, Sidhu, S.S.*, Wu, D.* (2019) A potent anti-SpuE antibodyallosterically inhibits type III secretion system and attenuates virulence of Pseudomonas aeruginosa. Journal of Molecular Biology 431:4882-4896.
9. Fu, T., Liu, L., Yang, Q.L., Wang, Y., Xu, P., Zhang, L., Liu, S., Dai, Q., Ji, Q., Xu, G.L., He, C., Luo, C.*, Zhang, L.* (2019) Thymine DNA glycosylase recognizes the geometry alteration of minor grooves induced by 5-formylcytosine and 5-carboxylcytosine. Chemical Science 10: 7407-17.
8. He, T., Wang, R., Liu, D., Walsh, T.R., Zhang, R., Lv, Y., Ke, Y., Ji, Q., Wei, R., Liu, Z., Shen, Y., Wang, G., Sun, L., Lei, L., Lv, Z., Li, Y., Pang, M., Wang, L., Sun, Q., Fu, Y., Song, H., Hao, Y., Shen, Z., Wang, S., Chen, G., Wu, C., Shen, J., Wang, Y. (2019) Emergence of plasmid-mediated high-level tigecycline resistance genes in animals and humans. Nature Microbiology 4: 1450-6.
7. Sun, Q. #, Wang, Y. #, Dong, N., Shen, L., Zhou, H., Hu, Y., Gu, D., Chen, S., Zhang, R.*, Ji, Q.* (2019) Application of CRISPR/Cas9-based genome editing in studying the mechanism of pandrug resistance in Klebsiella pneumoniae. Antimicrobial Agents and Chemotherapy 63: e00113-19.
6. Wang, Y., Wang, S., Chen, W., Song, L., Shen, Z., Yu, F., Li, M., Ji, Q.*(2018) Precise and efficient genome editing in Klebsiella pneumoniae using CRISPR-Cas9 and CRISPR-assisted cytidine deaminase. Applied and Environmental Microbiology 84: e01834-18.
5. Chen, W., Zhang, Y., Zhang, Y., Pi, Y., Gu, T., Song, L., Wang, Y., Ji, Q.* (2018) CRISPR/Cas9-based genome editing in Pseudomonas aeruginosa and cytidine deaminase-mediated base editing in Pseudomonas species. iScience 6: 222-31.
4. Wei, W.#, Zhang, Y.#, Gao, R., Li, J., Xu, Y., Wang, S., Ji, Q.*, Feng, Y.* (2018) Crystal structure and acetylation of BioQ suggests a novel regulatory switch for biotin biosynthesis in Mycobacterium smegmatis. Molecular Microbiology 109: 642-62.
3. Song, L., Zhang, Y., Chen, W., Gu, T., Zhang, S.Y., Ji, Q.* (2018) Mechanistic insights into staphylopine-mediated metal acquisition. PNAS 115: 3942-7.
2. Gu, T.#, Zhao, S.#, Pi, Y., Chen, W., Chen, C., Liu, Q., Li, M., Han, D.*, Ji, Q.* (2018) Highly efficient base editing in Staphylococcus aureus using an engineered CRISPR RNA-guided cytidine deaminase. Chemical Science 9: 3248-53.
1. Chen, W., Zhang, Y., Yeo, W.S., Bae, T., Ji, Q.* (2017) Rapid and efficient genome editing in Staphylococcus aureus by using an engineered CRISPR/Cas9 system. JACS 139: 3790-5.
Tianmu Lake (10/2019)
Dishui Lake (10/2020)
|Current Group Members|
Associate Research Fellow
Associate Research Fellow, ShanghaiTech University,2020-Current;
Assistant Research Fellow, ShanghaiTech University,2018-2020;
Postdoc., ShanghaiTech University, 2016-2018;
Postdoc., ShanghaiTech University, 2018-Current;
Ph.D., Northwest A&F University, 2014-2018;
Postdoc., ShanghaiTech University, 2020-Current;
Ph.D., Northwest A&F University, 2015-2020;
Tongnian Gu （顾桐年）
Yishuang Pi （皮义双）