Research Summary
1) My first research project focuses on the physiological function of bacterial DNA phosphorothioate modification. My colleagues and I collaborated to show that many bacteria contain DNA that is stereo-specifically and sequence-specifically sulfur-modified (phosphorothioate). Because of its sequence-specificity, we hypothesized that it is related to the function of the modification. The search for a biological function of DNA S-modification resulted in the discovery that the modification can function as a restriction endonuclease inhibitor in trans. I will next use structural biology techniques to uncover the related mechanism of the inhibition. An insight into this mechanism would hopefully provide a new theory for phosphorothioate DNA based inhibitor design.
2) I am also conducting research to discover the active form of the enzyme that separates the strands of DNA during the process of DNA replication. The eukaryotic helicase, known as “CMG,” is a protein complex composed of eleven different subunits and its structure is believed to be conserved in all eukaryotes from yeast to humans. Using recombinant DNA methods, I am working to over-express the eleven proteins to eventually purify CMG to homogeneity and examine its structure at the atomic level using X-ray crystallographic diffraction methods. A detailed structure of the CMG will ultimately provide a deeper understanding of how chromosomes organize the replication machine during cell division and will help in the design of chemotherapy drugs which often target DNA replication factors.
Impact in China
Science and technology in China are developing rapidly, supported by large financial investments. There is a great need not only for more scientific activity, but also for an ever increasing level of scientific excellence. Interacting directly with great scientists, as Tang Scholars can do here at Berkeley, provides Chinese scholars with an opportunity to strengthen our connection to the world’s leading scientists and also share our knowledge with the expanding scientific community in China.
Publications
Wu Q, Gou L, Lin S, Liang J, Yin J, Zhou X, Bai L, An D, Deng Z*, Wang Z*. Characterization of the N-methyltransferase CalM involved in calcimycin biosynthesis by Streptomyces chartreusis NRRL 3882. Biochimie. 2013 Jul.95 (7):1487-93.
Gou L, Wu Q, Lin S, Li X, Liang J, Zhou X, An D*, Deng Z*, Wang Z*. Mutasynthesis of Pyrrole Spiroketal Compound by Using Calcimycin 3-Hydroxy Anthranilic Acid Biosynthetic Mutant. Applied Microbiology and Biotechnology，2013 Sep;97(18):8183-91.
Xie X, Liang J, Pu T, Xu F, Yao F, Yang Y, Zhao Y, You D, Zhou X, Deng Z*, Wang Z*.Phosphorothioate DNA as an antioxidant in bacteria. Nucleic Acids Research. 2012 Oct; 40(18):9115-24.
Wu Q, Liang J, Lin S, Zhou X, Bai L *, Deng Z and Wang Z*. Characterization of the Pyrrole Polyether Antibiotic Calcimycin (A23187) Biosynthetic Gene Cluster from Streptomyces chartreusis NRRL 3882. Antimicrobial Agents and Chemotherapy (AAC)，2011 Mar; 55(3):974-82.
An X, Xiong W, Yang Y, Li F, Zhou X, Wang Z, Deng Z, Liang J. A novel target of IscS in Escherichia coli: participating in DNA phosphorothioation. PLoS One. 2012; 7(12):e51265.
Zhang Y, Liang J, Lian P, Han Y, Chen Y, Bai L, Wang Z, Liang J, Deng Z, Zhao YL. Theoretical study on steric effects of DNA phosphorothioation: B-helical destabilization in Rp-phosphorothioated DNA. J Phys Chem B. 2012 Sep 6;116(35):10639-48.
Chen F, Zhang Z, Lin K, Qian T, Zhang Y, You D, He X, Wang Z, Liang J, Deng Z, Wu G. Crystal structure of the cysteine desulfurase DndA from Streptomyces lividans which is involved in DNA phosphorothioation. PLoS One. 2012; 7(5):e36635.
Hu W, Wang C, Liang J, Zhang T, Hu Z, Wang Z, Lan W, Li F, Wu H, Ding J, Wu G, Deng Z, Cao C. Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification. Cell Res.2012 Jul;22(7):1203-6.
F. Chen, K. Lin, Z. Zhang, L. Chen, X. Shi, C. Cao, Z. Wang, J. Liang, Z. Deng, G. Wu. Purification, crystallization and preliminary X-ray analysis of the DndE protein from Salmonella enterica serovar Cerro 87, which is involved in DNA phosphorothioation. Acta Crystallogr Sect F Struct Biol Cryst Commun.2011 Nov 1; 67(Pt 11):1440-2.
Q. Wu, J. Liang, S. Lin, X. Zhou, L. Bai*, Z. Deng* and Z. Wang*. Characterization of the Pyrrole Polyether Antibiotic Calcimycin (A23187) Biosynthetic Gene Cluster from Streptomyces chartreusis NRRL 3882. (2011) Antimicrobial Agents and Chemotherapy, 55(3): 974-982.
He, Y, Wang Z, Bai L, Liang J, Zhou X, Deng Z. Two pHZ1358-derivative Vectors for Efficient Gene Knockout in Streptomyces. J. Microbiol. Biotechnol. 2010 4; 20(4): 678-682.
Zhao C, Coughlin JM, Ju J, Zhu D, Wendt-Pienkowski E, Zhou X, Wang Z, Shen B, Deng Z.(2010) Oxazolomycin biosynthesis in Streptomyces albus JA3453 featuring an “acyltransferase-less” type I polyketide synthase that incorporates two distinct extender units. J Biol Chem. 2010 Apr 20.
Liang J, Niu Q, Xu X, Luo Y, Zhou X, Deng Z*, Wang Z*. (2009) Effective elimination of nucleic acids from bacterial protein samples for optimized blue native polyacrylamide gel electrophoresis. Electrophoresis, 30(14): 2454-9.
Xu T, Liang J, Chen S, Wang L, He X, You D, Wang Z, Li A, Xu Z, Zhou X, Deng Z. (2009) DNA phosphorothioation in Streptomyces lividans: Mutational analysis of the dnd locus. BMC Microbiol. 2009 Feb 20; 9(1): 41.
Xu X*, Wang Z*, Fan K, Wang S, Jia C, Han H, Ramalingam E & Yang K. 2008, Localization of the ActIII actinorhodin polyketide ketoreductase to the cellwall, FEMS Microbiology Letters. 287(1): 15-21.
Liang J*, Wang Z*, He X, Li J, Zhou X, Deng Z (2007). DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites. Nucleic Acids Res 35, 2944-2954.
He Y, Fan K, Jia C, Wang Z, Pan W, Huang L, Yang K, Dong Z (2007). Characterization of a hyperthermostable Fe-superoxide dismutase from hot spring. Appl Microbiol Biotechnol 75, 367-376.
Wang Z, Xu X, Fan K, Jia C, Yang K (2007). Sample preparation for two-dimensional blue native/SDS polyacrylamide gel electrophoresis in the identification of Streptomyces coelicolor cytoplasmic protein complexes. J Biochem Biophys Methods 70, 565-572.
(*Co-first author)