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: Laboratory Homepage
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 40 papers that received more than 2000 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.

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

2019

47. Xie Y, Shao X, Deng X*. (2019) Regulation of Type III Secretion System in Pseudomonas syringaeEnviron Microbiol. 2019 Aug 13. doi: 10.1111/1462-2920.14779. [Epub ahead of print]

46. Zhang Y #, Zhou C #, Pu Q, Wu Q, Tan S, Shao X, Zhang W, Xie Y, Li R, Yu X, Wang R, Zhang L, Wu M*, Deng X*. (2019) Pseudomonas aeruginosa regulatory protein AnvM controls pathogenicity in anaerobic environments and impacts host defense. mBio. 2019 Jul 23; 10(4). pii: e01362-19.

45. Huang H#, Shao X#, Xie Y#, Wang T, Zhang Y, Wang X*, Deng X*. (2019) An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosaNat Commun. 10: 2931.
https://www.sciencedaily.com/releases/2019/07/190703121423.htm
https://www.news-medical.net/news/20190704/Researchers-reveal-virulence-regulatory-mechanism-in-a-superbug.aspx

44. Shao X, Xie Y, Zhang Y, Deng X*. (2019) Biofilm Formation Assay in Pseudomonas syringaeBio-protocol. 9(10): e3237.

43. Kandimalla R, Gao F, Li Y, Huang H, Ke J, Deng X, Zhao L, Zhou S, Goel A, Wang X. (2019) RNAMethyPro: a biologically conserved signature of N6-methyladenosine regulators for predicting survival at pan-cancer level. NPJ Precis Oncol. 3: 13.

42. Peng C, Huang D, Shi Y, Zhang B, Sun L, Li M, Deng X, Wang W. (2019) Comparative transcriptomic analysis revealed the key pathways responsible for organic sulfur removal by thermophilic bacterium Geobacillus thermoglucosidasius W-2. Sci Total Environ. 676: 639-650.

41. Li K, Zhu Y, Yan W, Deng X, Xiao Y, Song L, Fang R, Jia Y, Tang X. (2019) Two components of the rhpPC operon coordinately regulate the type III secretion system and bacterial fitness in Pseudomonas savastanoi pv. phaseolicolaPLoS Pathog. 15(4): e1007673.

40. Xie Y, Shao X, Zhang Y, Liu J, Wang T, Zhang W, Hua C, Deng X*. (2019) Pseudomonas savastanoi two-component system RhpRS switches between virulence and metabolism by tuning phosphorylation state and sensing nutritional conditions. mBio. 2019 Mar 19; 10(2). pii: e02838-18.

39. Wang T#, Cai Z#, Shao X, Zhang W, Xie Y, Zhang Y, Hua C, Schuster S C, Yang L, Deng X*. (2019) The Pleiotropic Effects of c-di-GMP Content in Pseudomonas syringaeAppl Environ Microbiol. 2019 Mar 8. pii: AEM.00152-19.

38. Sun L, Huang D, Zhu L, Zhang B, Peng C, Ma T, Deng X, Wu J, Wang W. (2019) Novel thermostable enzymes from Geobacillus thermoglucosidasius W-2 for high-efficient nitroalkane removal under aerobic and anaerobic conditions. Bioresour Technol. 2019. 278: 73-81.

2018

37. Shao X#, Zhang X#, Zhang Y, Zhu M, Yang P, Yuan J, Xie Y, Zhou T, Wang W, Chen S, Liang H*, Deng X*. (2018) RpoN-dependent direct regulation of quorum sensing and the type VI secretion system in Pseudomonas aeruginosa PAO1. J Bacteriol. 2018. 200(16). pii: e00205-18.

36. Wang J#, Shao X#, Zhang Y, Zhu Y, Yang P, Yuan J, Wang T, Yin C, Wang W, Chen S, Liang H*, Deng X*. (2018) HrpS is a global regulator on T3SS and non-T3SS genes in Pseudomonas savastanoi pv. phaseolicolaMol Plant Microbe Interact. 2018. 31(12): 1232-1243.

2017

35. 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. 198 (7) 2844-2853.

34. Pu Q, Gan C, Li R, Yi L, Tan S, Li X, Wei Y, Lan L, Deng X, Liang H, Ma F, Wu M. (2017) Atg7 deficiency intensifies inflammasome activation and pyroptosis in Pseudomonas sepsis. J Immunol. 198(8), 3205.

2016

33. 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 syringaeMol Plant Microbe Interact. 29(10): 807-814.

32. 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 aeruginosaPLOS Biol. 14(4): e1002449.

31. 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.

30. 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 ArabidopsisPlant Cell Physiol. 55(9): 1568-81.

29. 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.

2015

28. 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 aeruginosaNucleic Acids Res. 43(17): 8268-82.

27. 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.

26. Zhou T, Chen K, Zhang HX, Deng X*. (2015) Genome-wide DNA binding pattern of two-component system response regulator RhpR in Pseudomonas syringaeGenomics Data. (4): 146-7.

25. 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 ChlamydomonasCell. 161(4): 879-92.

24. 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 aeruginosaMol Microbiol. 96(3): 526-47.

2014

23. 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 syringaeNucleic Acids Res. 42(18): 11472-86.

22. 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 aeruginosaNucleic Acids Res. 42 (16): 10307-10320.

21. 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 aeruginosaJ Bacteriol. 196(14): 2499-2513.

20. 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 aureusProc Natl Acad Sci U S A.111(46): E4981-90.

19. 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 aeruginosaPLOS Pathog. 10(8): e1004340.

18. 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 ArabidopsisPlant Cell Physiol. 55 (9): 1568-1581.

17. 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.

2013

16. 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.

15. 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. (2013) 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.

14. 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.

2012

13. Liang H#Deng X#, Ji Q, Sun F, Shen T, He C. (2012) The Pseudomonas aeruginosa global regulator VqsR directly inhibits QscR to control quorum-sensing and virulence gene expression. J Bacteriol. 194(12): 3098-108.

12. 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 aureusJ Bacteriol. 194(7): 1753-62.

11. 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.

10. 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.

9. 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.

8. 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. (2012) Chem. Sci. 3: 2920-2923.

7. 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 aureusJ Am Chem Soc. 134(1): 305-14.

Before 2011

6. 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 aureusChem Biol. 18(8): 1032-41.

5. 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.

4. 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.

3. 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.

2. 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.

1. 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 hrpRSMol Plant Microbe Interact. 19(9): 976-8.