Zixin Deng
Microbial Genetics
Email: zxdeng@sjtu.edu.cn



Professor of Microbial Genetics
Head of the State Key Laboratory of Microbial Metabolism, China
President of Chinese Society for Microbiology
Member of the Chinese Academy of Sciences
Fellow of the Academy of Sciences for the Developing World
Fellow of American Academy of Microbiology


Zixin Deng was born in Hubei, China. He received his BSc in microbiology at Huazhong Agricultural University in 1982. He completed his PhD under the supervision of Professor David A. Hopwood FRS and Dr Tobias Kieser (at the John Innes Center and the University of East Anglia, Norwich, UK) on the genetics of Streptomyces. He returned to Huazhong Agricultural University in June, 1988 to start a lectureship, and has been appointed as a professor since 1992. He moved to Shanghai Jiaotong University in 2000 to begin as a professor, and now acts as the head of the State Key Laboratory of Microbial Metabolism, China. He is a Member of Chinese Academy of Sciences, a Fellow of the Science Academy for the Developing World (formally the Third World Academy of Sciences, TWAS), and a fellow of American Academy of Microbiology.

He and his colleagues have developed efficient gene cloning systems for several important antibiotics producers (notably polyene, polyether and aminoglycoside classes for medical, agricultural and veterinary uses), leading to the cloning and detailed demonstration of their biosynthetic pathways and regulatory mechanisms. He and his collaborators also worked extensively on an unusual DNA modification system by sulphur (S) in widespread bacteria of variable origin and diverse habitat. This study revealed a first DNA modification into DNA backbone to form phosphorothioate, which seemed to have opened up a fascinating new field of research with potential relevance to the understanding of interesting physiological function(s) within the context of a wide-spectrum of life systems.


Research Interests: 
1. DNA sulphur modification mechanism;
2. Biosynthesis and engineering of microbial secondary metabolites.

Figure 1. Phosphorothioation of the DNA backbone. [Zhou, et al. Nucleic Acids Res., 1988; Zhou, et al. Molecular Microbiology, 2005; He, et al. Mol Microbiol. 2007; Wang, et al. Nature Chemical Biology, 2007; Liang. et al. Nucleic Acids Res., 2007; Ou, et al. PloS One, 2009; Liu, et al. PLoS Genetics, 2010; Xie, et al. Nucleic Acids Res., 2012]

Figure 2. Incomplete beta-ketone processing as a mechanism for polyene structural variation in the FR-008/candicidin complex. [Zhou, et al. Chem Biol., 2008]



Selected Publications:

1. Gou L, Wu Q, Lin S, Li X, Liang J, Zhou X, An D, Deng Z, Wang Z. Mutasynthesis of pyrrole spiroketal compound using calcimycin 3-hydroxy anthranilic acid biosynthetic mutant. Appl Microbiol Biotechnol. 2013 May.
2. Xu F, Kong D, He X, Zhang Z, Han M, Xie X, Wang P, Cheng H, Tao M, Zhang L, Deng Z, Lin S. Characterization of streptonigrin biosynthesis reveals a cryptic carboxyl methylation and an unusual oxidative cleavage of a N-C bond. J Am Chem Soc. 2013, 135(5):1739-48.
3. Bi D, Liu L, Tai C, Deng Z, Rajakumar K, Ou HY. SecReT4: a web-based bacterial type IV secretion system resource. Nucleic Acids Res. 2013, 41:D660-5.
4. Xie X, Liang J, Pu T, Xu F, Yao F, Yang Y, Zhao YL, You D, Zhou X, Deng Z, Wang Z. Phosphorothioate DNA as an antioxidant in bacteria. Nucleic Acids Res. 2012, 40(18):9115-24.
5. Wu J, Li L, Deng Z, Zabriskie TM, He X. Analysis of the mildiomycin biosynthesis gene cluster in Streptoverticillum remofaciens ZJU5119 and characterization of MilC, a hydroxymethyl cytosyl-glucuronic acid synthase. Chembiochem. 2012, 13(11):1613-21.
6. Chen L, Wang Y, Guo H, Xu M, Deng Z, Tao M. High-throughput screening for Streptomyces antibiotic biosynthesis activators. Appl Environ Microbiol. 2012 Jun;78(12):4526-8.
7. Zhai L, Lin S, Qu D, Hong X, Bai L, Chen W, Deng Z. Engineering of an industrial polyoxin producer for the rational production of hybrid peptidyl nucleoside antibiotics. Metab Eng. 2012, 14(4):388-93.
8. Zhang W, Wang L, Kong L, Wang T, Chu Y, Deng Z, You D. Unveiling the post-PKS redox tailoring steps in biosynthesis of the type II polyketide antitumor antibiotic xantholipin. Chem Biol. 2012, 19(3):422-32.
9. Cheng L, Chen W, Zhai L, Xu D, Huang T, Lin S, Zhou X, Deng Z. Identification of the gene cluster involved in muraymycin biosynthesis from Streptomyces sp. NRRL 30471. Mol Biosyst. 2011, 7(3):920-7
10. Wang L, Chen S, Vergin KL, Giovannoni SJ, Chan SW, DeMott MS, Taghizadeh K, Cordero OX, Cutler M, Timberlake S, Alm EJ, Polz MF, Pinhassi J, Deng Z, Dedon PC. DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc Natl Acad Sci U S A. 2011, 108(7):2963-8.
11. Gu TP, Guo F, Yang H, Wu HP, Xu GF, Liu W, Xie ZG, Shi L, He X, Jin SG, Iqbal K, Shi YG, Deng Z, Szabó PE, Pfeifer GP, Li J, Xu GL. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature. 2011, 477(7366):606-10.
12. Chen S, Wang L, Deng Z. Twenty years hunting for sulfur in DNA. Protein Cell 2010, 1(1):14-21.
13. Liu G, Ou HY, Wang T, Li L, Tan H, Zhou X, Rajakumar K, Deng Z, He X. Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA. PLoS Genet. 2010, 6(12):e1001253.
14. Zhao C, Huang T, Chen W, Deng Z. Enhancement of the diversity of polyoxins by a thymine-7-hydroxylase homolog outside the polyoxin biosynthesis gene cluster. Appl Environ Microbiol. 2010, 76(21):7343-7.
15. Zhao C, Coughlin JM, Ju J, Zhu D, Wendt-Pienkowski E, Zhou X, Wang Z, Shen B, Deng Z. Oxazolomycin biosynthesis in Streptomyces albus JA3453 featuring an "acyltransferase-less" type I polyketide synthase that incorporates two distinct extender units. J Biol Chem. 2010, 285(26):20097-108.
16. Xu T, Yao F, Zhou X, Deng Z, You D. A novel host-specific restriction system associated with DNA backbone S-modification in SalmonellaNucleic Acids Res. 2010, 38(20):7133-41
17. Zhou Y, Li J, Zhu J, Chen S, Bai L, Zhou X, Wu H, Deng Z. Incomplete beta-ketone processing as a mechanism for polyene structural variation in the FR-008/candicidin complex. Chem Biol. 2008, 15(6):629-38.
18. Wang L, Chen S, Xu T, Taghizadeh K, Wishnok JS, Zhou X, You D, Deng Z, Dedon PC.Phosphorothioation of DNA in bacteria by dnd genes. Nat Chem Biol. 2007, 3(11):709-10.
19. He X, Ou HY, Yu Q, Zhou X, Wu J, Liang J, Zhang W, Rajakumar K, Deng Z. Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related bacteria. Mol Microbiol. 2007, 65(4):1034-48.
20. Liu T, Lin X, Zhou X, Deng Z, Cane DE. Mechanism of thioesterase-catalyzed chain release in the biosynthesis of the polyether antibiotic nanchangmycin. Chem Biol. 2008 May;15(5):449-58.
21. Ou HY, He X, Harrison EM, Kulasekara BR, Thani AB, Kadioglu A, Lory S, Hinton JC, Barer MR, Deng Z, Rajakumar K. MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Res. 2007, 35:W97-W104.
22. Liang J, Wang Z, He X, Li J, Zhou X, Deng Z. DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites. Nucleic Acids Res. 2007, 35(9):2944-54.
23. Deng Z, Bai L. Antibiotic biosynthetic pathways and pathway engineering--a growing research field in China. Nat Prod Rep. 2006, 23(5):811-27.
24. Liu T, You D, Valenzano C, Sun Y, Li J, Yu Q, Zhou X, Cane DE, Deng Z. Identification of NanE as the thioesterase for polyether chain release in nanchangmycin biosynthesis. Chem Biol. 2006, 13(9):945-55.
25. Zhao C, Ju J, Christenson SD, Smith WC, Song D, Zhou X, Shen B, Deng Z. Utilization of the methoxymalonyl-acyl carrier protein biosynthesis locus for cloning the oxazolomycin biosynthetic gene cluster from Streptomyces albus JA3453. J Bacteriol. 2006, 188(11):4142-7.
26. Bai L, Li L, Xu H, Minagawa K, Yu Y, Zhang Y, Zhou X, Floss HG, Mahmud T, Deng Z. Functional analysis of the validamycin biosynthetic gene cluster and engineered production of validoxylamine A. Chem Biol. 2006, 13(4):387-97.
27. Zhou X, He X, Liang J, Li A, Xu T, Kieser T, Helmann JD, Deng Z. A novel DNA modification by sulphur. Mol Microbiol. 2005, 57(5):1428-38.
28. Zhu D, He X, Zhou X, Deng Z. Expression of the melC operon in several Streptomyces strains is positively regulated by AdpA, an AraC family transcriptional regulator involved in morphological development in Streptomyces coelicolor. J Bacteriol. 2005, 187(9):3180-7

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