Publications#co-first authors               *(co)corresponding authors

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59. Shao X#, Tan M#, Xie Y, Yao C, Wang T, Huang H, Zhang Y, Ding Y, Liu J, Han L, Hua C, Wang X*, Deng X*. (2021) Integrated regulatory network in Pseudomonas syringae reveals dynamics of virulence. Cell Reports. 2021 DOI:10(2). 34:108920.

58. Wang T#, Sun W#, Fan L#, Hua C#, Wu N, Fan S, Zhang J, Deng X*, Yan J*. (2021) An atlas of the binding specificities of transcription factors in Pseudomonas aeruginosa directs prediction of novel regulators in virulence. eLife. 2021 DOI:10:e61885.


57. Fan L#, Wang T#, Hua C#, Sun W#, Li X, Grunwald L, Liu J, Wu N, Shao X, Yin Y, Yan J*, Deng X*. (2020) A Compendium of DNA-Binding Specificities of Transcription Factors in Pseudomonas syringae. Nature Commun. 2020 DOI:10.1038/s41467-020-18744-7.

56. Chen G, Gan J, Yang C, Zuo Y, Peng J, Li M, Huo W, Xie Y, Zhang Y, Wang T, Deng X, Liang H. (2020) The SiaA/B/C/D signaling network regulates biofilm formation in Pseudomonas aeruginosa. EMBO J. 2020 DOI:16;39(6):e103412.

55. Hou C, He W, Wang Z, Yi B, Hu Z, Wang W, Deng X, Yao X. (2020) Particulate-Aggregated Adhesives with Exudate-Sensitive Properties and Sustained Bacteria Disinfection to Facilitate Wound Healing. ACS Appl Mater Interfaces. 2020 Jul 15. DOI: 12(28):31090-31098.

54. Qin S, Li J, Zhou C, Privratsky B, Schettler J, Deng X, Xia Z, Zeng Y, Wu H, Wu M. (2020) SHIP-1 Regulates Phagocytosis and M2 Polarization Through the PI3K/Akt-STAT5-Trib1 Circuit in Pseudomonas aeruginosa Infection. Front Immunol. 2020 Mar 18;11:307.

53. Xie Y, Liu W, Shao X, Zhang W, Deng X*. (2020) Signal transduction schemes in Pseudomonas syringae. Comput Struct Biotechnol J. 2020. DOI: 10.1016/j.csbj.2020.10.039.

52. Cao Q, Yang N, Wang Y, Xu C, Zhang X, Fan K, Chen F, Liang H, Zhang Y, Deng X, Feng Y, Yang C, Wu M, Bae T, Lan L. (2020) Mutation-induced remodeling of the BfmRS two-component system in Pseudomonas aeruginosa clinical isolates. Sci Signal. 2020 Nov 3. DOI: 10.1126/scisignal.aaz1529.

51. Shao X, Xie Y, Zhang Y, Liu J, Ding Y, Wu M, Wang X, Deng X*. (2020) Novel therapeutic strategies for treating Pseudomonas aeruginosa infection. Expert Opinion on Drug Discovery. 2020. DOI: 10.1080/17460441.2020.1803274.

50. Hua C, Wang T, Shao X, Xie Y, Huang H, Liu J, Zhang W, Zhang Y, Ding Y, Jiang L, Wang X, Deng X*. (2020) Pseudomonas syringae dual-function protein Lon switches between virulence and metabolism by acting as both DNA-binding transcriptional regulator and protease in different environments. Environ Microbiol. 2020.

49. Shao X#, Zhang W#, Umar M#, Wong H, Seng Z, Xie Y, Zhang Y, Yang L, Kwok C*, Deng X*. (2020) RNA G-quadruplexes structures mediate gene regulation in bacteria. mBio. 2020 Jan 21; 10(2). 11(1): e02926-19.


48. Yang Z, Yang Y, Wang M, Wang T, Fok HK, Jiang B, Xiao W, Kou S, Guo Y, Yan Y, Deng X, Zhang WB, Sun F. Dynamically Tunable, Macroscopic Molecular Networks Enabled by Cellular Synthesis of 4-Arm Star-like Proteins. Matter. 2019 Oct 9.

47. Xie Y, Shao X, Deng X*. (2019) Regulation of Type III Secretion System in Pseudomonas syringae. Environ Microbiol. 2019 Aug 13. doi: 10.1111/1462-2920.14779.

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 aeruginosa. Nat Commun. 10: 2931.

44. Shao X, Xie Y, Zhang Y, Deng X*. (2019) Biofilm Formation Assay in Pseudomonas syringae. Bio-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. phaseolicola. PLoS 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 syringae. Appl 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.


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. phaseolicola. Mol Plant Microbe Interact. 2018. 31(12): 1232-1243.


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.


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 syringae. Mol 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 aeruginosa. PLOS 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 Arabidopsis. Plant 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.


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 aeruginosa. Nucleic 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 syringae. Genomics 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 Chlamydomonas. Cell. 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 aeruginosa. Mol Microbiol. 96(3): 526-47.


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 syringae. Nucleic 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 aeruginosa. Nucleic 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 aeruginosa. J 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 aureus. Proc 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 aeruginosa. PLOS 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 Arabidopsis. Plant 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.


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.


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 aureus. J 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 aureus. J 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 aureus. Chem 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 hrpRS. Mol Plant Microbe Interact. 19(9): 976-8.