Dr Xin Deng (鄧新博士)

PhD (Kansas State University)

Assistant Professor

Dr Xin Deng

Contact Information

Office: 1B-106, 1/F, Block 1,
To Yuen Building
Phone: +852 3442-5693
Fax: +852 3442-0549
Email: xindeng@cityu.edu.hk
Web: CityU Scholars

Research Interests

  • Virulence regulation in pathogenic bacteria
  • Antibiotic resistance
  • Host-pathogens interactions
  • RNA epigenetics

Dr Deng is a microbiologist. He received his PhD in Genetics at Kansas State University in 2009. He did his postdoctoral training at University of Chicago. In 2015, he began his independent career at Nankai University before joined the City University of Hong Kong in 2017. Dr Deng has published more than 30 papers that received more than 900 citations.

Research Interests

The emergence and spread of various multidrug-resistant bacterial strains have posed alarming challenges to public health and agriculture worldwide. Public demand for new antibiotics is enormous, yet drug development pipelines of the pharmaceutical industry started to run dry with limited targets available for inventing new bactericidal antibiotics. It is important to uncover potential therapeutic targets. Our group has been working on virulence regulation in the human pathogen Pseudomonas aeruginosa and plant pathogen Pseudomonas syringae, which are of world-wide importance. These pathogens rely on quorum sensing (QS) systems and type III secretion system (T3SS) to invade their hosts. However, how these systems are regulated remains largely unknown. Research in our group has led to the identification of a variety of new virulence factors and mechanisms. Tuning their expression and developing inhibitors are key for the development of strategies to control Pseudomonas infections.

The other topic in my group is RNA epigenetics in bacteria. N6-methyladenosine (m6A) is the most abundant messenger RNA (mRNA) modification in eukaryotic organisms. Identification of demethylases, methyltransferase and m6A-specific binding proteins in eukaryotes indicates regulatory functions of this RNA modification. However, very little was known on m6A in bacterial mRNA. We have mapped the first m6A methylome in bacteria, and found a unique pattern other than eukaryotes. Our work demonstrates that m6A exists in a wide-range of bacteria, which might play important roles in gene regulation.

Position Availability

PhD students, postdoctoral fellows, and research assistant positions are available. Candidates who have a strong interest in our research and meet the basic requirements of the University and BMS department are encouraged to apply. Interested candidates can send CV and a short summary of past research experience to Dr Deng (xindeng@cityu.edu.hk). Undergraduate students who seek for lab experience are welcome to contact Dr Deng directly by email, phone or office visit.

Publications (#corresponding author, *co-first author)

  1. Ye Y, Lin P, Zhang W, Tan S, Zhou X, Li R, Pu Q, Koff JL, Dhasarathy A, Ma F, Deng X, Jiang J, Wu M. (2017) DNA repair interacts with autophagy to regulate inflammatory responses to pulmonary hyperoxia. J Immunol. In press.
  2. Zhou T, Yin C, Zhang Y, Shi H, Wang J, Sun L, Shao X, Gao R, Wang W#, Deng X#. (2016) Lon protease is involved in RhpRS-mediated regulation of type III secretion in Pseudomonas syringae. Mol Plant Microbe Interact. 29(10):807-814.
  3. Zhao J, Yu X, Zhu M, Kang H, Ma J, Wu M, Gan J#, Deng X# and Liang H#. (2016) Structural and molecular mechanism of CdpR involved in quorum-sensing and bacterial virulence in Pseudomonas aeruginosa. PLOS Biol. 14(4):e1002449.
  4. Yu P, Yuan J, Zhang H, Deng X, Ma M, Zhang H. (2016) Engineering metal-binding sites of bacterial CusF to enhance Zn/Cd accumulation and resistance by subcellular targeting. J Hazard Mater. 302:275-85.
  5. Yu P, Yuan J, Deng X, Ma M, Zhang H. (2016) Subcellular targeting of bacterial CusF enhances Cu accumulation and alters root to shoot Cu translocation in Arabidopsis. Plant Cell Physiol. 55(9):1568-81.
  6. Luo GZ, Wang F, Weng X, Chen K, Hao Z, Yu M, Deng X, Liu J, He C. (2016) Characterization of eukaryotic DNA N6-methyladenine by a highly sensitive restriction enzyme-assisted sequencing. Nat Commun. 7:11301.
  7. Kong W, Zhao J, Zhu M, Kang H, Zhou T, Deng X#, Liang H#. (2015) ChIP-seq reveals molecular mechanisms of global regulator AlgR mediating cyclic di-GMP synthesis and biofilm formation in Pseudomonas aeruginosa. Nucleic Acids Res. 43(17):8268-82.
  8. Deng X#*, Chen K*, Luo GZ, Weng X, Ji Q, Zhou T, He C#. (2015) Widespread occurrence of N6-methyladenosine in bacterial mRNA. Nucleic Acids Res. 43(13):6557-67.
  9. Zhou T, Chen K, Zhang HX, Deng X#. (2015) Genome-wide DNA binding pattern of two-component system response regulator RhpR in Pseudomonas syringae. Genomics Data. (4):146-7.
  10. Fu Y, Luo GZ, Chen K, Deng X, Yu M, Han D, Hao Z, Liu J, Lu X, Dore LC, Weng X, Ji Q, Mets L, He C. (2015) N6-methyldeoxyadenosine marks active transcription start sites in Chlamydomonas. Cell. 161(4):879-92.
  11. Yang N, Ding S, Chen F, Zhang X, Xia Y, Di H, Cao Q, Deng X, Wu M, Wong CC, Tian XX, Yang CG, Zhao J, Lan L. (2015) The Crc protein participates in down-regulation of the Lon gene to promote rhamnolipid production and rhl quorum sensing in Pseudomonas aeruginosa. Mol Microbiol. 96(3):526-47.
  12. Deng X*, Liang H*, Chen, K, He C, Lan L, Tang X. (2014) Molecular mechanisms of two-component system RhpRS regulating type III secretion system in Pseudomonas syringae. Nucleic Acids Res. 42(18):11472-86.
  13. Liang H*, Deng X*, Li X, Ye Y, Wu M. (2014) Molecular mechanisms of master regulator VqsM mediating quorum-sensing and antibiotic resistance in Pseudomonas aeruginosa. Nucleic Acids Res. 42 (16): 10307-10320.
  14. Deng X, Liang H, Ulanovskaya O, Ji Q, Zhou T, Sun F, Lu Z, Hutchison A, Lan L, Wu M, Cravatt B, He C. (2014). Steady-state hydrogen peroxide induces glycolysis in Staphylococcus aureus and Pseudomonas aeruginosa. J Bacteriol. 196(14):2499-2513.
  15. Ding Y, Liu X, Chen F, Di H, Xu B, Zhou L, Deng X, Wu M, Yang CG, Lan L. (2014) Metabolic sensor governing bacterial virulence in Staphylococcus aureus. Proc Natl Acad Sci U S A. 111(46):E4981-90.
  16. Cao Q, Wang Y, Chen F, Xia Y, Lou J, Zhang X, Yang N, Sun X, Zhang Q, Zhuo C, Huang X, Deng X, Yang CG, Ye Y, Zhao J, Wu M, Lan L. (2014) A novel signal transduction pathway that modulates rhl quorum sensing and bacterial virulence in Pseudomonas aeruginosa. PLoS Pathog. 10(8):e1004340.
  17. Yu P, Yuan J, Deng X, Ma M, Zhang H. (2014) Subcellular targeting of bacterial CusF enhances Cu accumulation and alters root to shoot Cu translocation in Arabidopsis. Plant Cell Physiol. 55 (9): 1568-1581.
  18. Liu J, Yue Y, Han D, Wang X, Fu Y, Zhang L, Jia G, Yu M, Lu Z, Deng X, Dai Q, Chen W, He C. (2014) A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat Chem Biol. 10:93-95.
  19. Deng X, Weerapana E, Ulanovskaya O, Sun F, Liang H, Ji Q, Ye Y, Fu Y, Zhou L, Li J, Zhang H, Wang C, Alvarez S, Hicks ML, Lan L, Wu M, Cravatt B, He C. (2013) Proteome-wide quantification and characterization of oxidation-sensitive cysteines in pathogenic bacteria. Cell Host Microbe. 13 (3): 358-70.
  20. Ji Q, Zhang L, Jones MB, Sun F, Deng X, Liang H, Cho H, Brugarolas P, Gao NY, Peterson NS, Lan L, Bae T, He C. Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR. Proc Natl Acad Sci U S A. 110(13):5010-5.
  21. Liang H, Deng X, Bosscher M, Ji Q, Jensen MP, He C. (2013) Engineering bacterial two-component system PmrA/PmrB to sense lanthanide ions. J Am Chem Soc. 135(6):2037-9.
  22. Liang H*, Deng X*, Ji Q, Sun F, Shen T, He C. Regulatory mechanism of global regulator VqsR to quorum-sensing systems and virulence factors in Pseudomonas aeruginosa. J Bacteriol. 194(12):3098-108.
  23. Deng X, Sun F, Ji Q, Liang H, Missiakas D, Lan L, He C. (2012) Expression of multidrug resistance efflux pump gene norA is iron-responsive in Staphylococcus aureus. J Bacteriol. 194(7):1753-62.
  24. Sun F, Ding Y, Ji Q, Liang Z, Deng X, Wong CC, Yi C, Zhang L, Xie S, Alvarez S, Hicks LM, Luo C, Jiang H, Lan L, He C. (2012) Protein cysteine phosphorylation of SarA/MgrA family transcriptional regulators mediates bacterial virulence and antibiotic resistance. Proc Natl Acad Sci U S A. 109(38):15461-6.
  25. Sun F, Liang H, Kong X, Xie S, Cho H, Deng X, Ji Q, Zhang H, Alvarez S, Hicks LM, Bae T, Luo C, Jiang H, He C. (2012) Quorum-sensing agr mediates bacterial oxidation response via an intramolecular disulfide redox switch in the response regulator AgrA. Proc Natl Acad Sci U S A. 109(23):9095-100.
  26. Ji Q, Zhang L, Sun F, Deng X, Liang H, Bae T, He C. (2012) Staphylococcus aureus CymR is a new thiol-based oxidation-sensing regulator of stress resistance and oxidative response. J Biol Chem. 287(25):21102-9.
  27. Qian Y, Zhang L, Ding S, Deng X, He C, Zheng EX, Zhu HL, Zhao J. A fluorescent probe for rapid detection of hydrogen sulfide in blood plasma and brain tissues in mice. Chem. Sci. 3:2920-2923.
  28. Sun F, Ji Q, Jones MB, Deng X, Liang H, Frank B, Telser J, Peterson SN, Bae T, He C. (2012) AirSR, a [2Fe-2S] cluster-containing two-component system, mediates global oxygen sensing and redox signaling in Staphylococcus aureus. J Am Chem Soc. 134(1):305-14.
  29. Sun F, Zhou L, Zhao BC, Deng X, Cho H, Yi C, Jian X, Song CX, Luan CH, Bae T, Li Z, He C. (2011). Targeting MgrA-mediated virulence regulation in Staphylococcus aureus. Chem Biol. 18(8):1032-41.
  30. Deng X, Lan L, Kennelly M, Zhou JM, Tang X. (2010). Pseudomonas syringae two-component response regulator RhpR regulates genes under an inverted repeat element promoter. Mol Plant Microbe Interact. 23(7):927-39.
  31. Deng X, Lan L, Xiao Y, Zhou JM, Tang X. (2009). Pseudomonas syringae pv. phaseolicola mutants compromising type III secretion system. Mol Plant Microbe Interact. 22(8):964-76.
  32. Lan L, Deng X, Xiao Y, Zhou JM, Tang X. (2007). Mutation of Lon protease differentially affects the expression of Pseudomonas syringae type III secretion system genes in rich and minimal media and reduces pathogenicity. Mol Plant Microbe Interact. 20(6):682-96.
  33. Xiao Y, Lan L, Yin C, Deng X, Baker D, Zhou JM, Tang X. (2007). Two-component sensor RhpS promotes induction of Pseudomonas syringae type III secretion system by repressing negative regulator RhpR. Mol Plant Microbe Interact. 20(3):223-34.
  34. Lan L, Deng X, Zhou JM, Tang X. (2006). Genome-wide gene expression analysis of Pseudomonas syringae pv. tomato DC3000 reveals overlapping and distinct pathways regulated by hrpL and hrpRS. Mol Plant Microbe Interact. 19(9):976-8.