General

Principal Investigator

De-Feng Li, Ph. D., Professor

E-mail: lidefeng@im.ac.cn


Research Areas

Molecular mechanisms of bacterial adaptation and antibiotics resistances

Education

1997-2001  Wuhan University, B.S.

2001-2006  Institute of Biophysics, Chinese Academy of Sciences, Ph.D


Experience

   
Work Experience

2006-2017  Institute of Biophysics, Chinese Academy of Sciences.

2018-          Institute of Microbiology, Chinese Academy of Sciences.


Publications


Papers

Hong Y#, Huang Z#, Guo L, Ni B, Jiang CY, Li XJ, Hou YJ, Yang WS, Wang DC, Zhulin IB, Liu SJ*, Li DF*. The ligand-binding domain of a chemoreceptor from Comamonas testosteroni has a previously unknown homotrimeric structure. Mol Microbiol. 2019 Sep;112(3):906-917.

Zhao F, Hou YJ, Zhang Y, Wang DC*, Li DF*. The 1-β-methyl group confers a lower affinity of l,d-transpeptidase LdtMt2 for ertapenem than for imipenem. Biochem Biophys Res Commun. 2019 Mar 5;510(2):254-260.

Yang WS, Hong Y, Zhang Y, Wang DC*, Li DF*, Hou YJ*. A potential substrate binding pocket of BdcA plays a critical role in NADPH recognition and biofilm dispersal. Biochem Biophys Res Commun. 2018 Mar 11;497(3):863-868.

Feng N#, Qi C#, Hou YJ, Zhang Y, Wang DC*, Li DF*. The C2'- and C3'-endo equilibrium for AMP molecules bound in the cystathionine-beta-synthase domain. Biochem Biophys Res Commun. 2018 Mar 4;497(2):646-651.

Gao YR#, Li DF#, Fleming J#, Zhou YF, Liu Y, Deng JY, Zhou L, Zhou J, Zhu GF, Zhang XE, Wang DC*, Bi LJ*. Structural analysis of the regulatory mechanism of MarR protein Rv2887 in M. tuberculosis. Sci Rep. 2017 Jul 25;7(1):6471.

Zheng X#, Feng N#, Li D*, Dong X*, Li J*. New molecular insights into an archaeal RNase J reveal a conserved processive exoribonucleolysis mechanism of the RNase J family. Mol Microbiol. 2017 Nov;106(3):351-366.

Yang K#, Li DF#, Wang X, Liang J, Sitia R, Wang CC*, Wang X*. Crystal Structure of the ERp44-Peroxiredoxin 4 Complex Reveals the Molecular Mechanisms of Thiol-Mediated Protein Retention. Structure. 2016 Oct 4;24(10):1755-1765.

Miao LL#, Hou YJ#, Fan HX, Qu J, Qi C, Liu Y, Li DF*, Liu ZP*. Molecular Structural Basis for the Cold Adaptedness of the Psychrophilic β-Glucosidase BglU in Micrococcus antarcticus. Appl Environ Microbiol. 2016 Jan 22;82(7):2021-30.

Qi C#, Li DF#, Feng L, Hou Y, Sun H, Wang DC*, Liu W*. Biochemical and structural characterization of a novel ubiquitin-conjugating enzyme E2 from Agrocybe aegeria reveals Ube2w family-specific properties. Sci Rep. 2015 Nov 3;5:16056.

Zhang XL#, Li DF#, Fleming J, Wang LW, Zhou Y, Wang DC, Zhang XE*, Bi LJ*. Core component EccB1 of the Mycobacterium tuberculosis type VII secretion system is a periplasmic ATPase. FASEB J. 2015 Dec;29(12):4804-14.

Fan S#, Li DF#, Wang DC, Fleming J, Zhang H, Zhou Y, Zhou L, Zhou J, Chen T, Chen G*, Zhang XE*, Bi L*. Structure and function of Mycobacterium smegmatis 7-keto-8-aminopelargonic acid (KAPA) synthase. Int J Biochem Cell Biol. 2015 Jan;58:71-80.

Li WJ#, Li DF#, Hu YL, Zhang XE, Bi LJ*, Wang DC*. Crystal structure of L,D-transpeptidase LdtMt2 in complex with meropenem reveals the mechanism of carbapenem against Mycobacterium tuberculosis. Cell Res. 2013 May;23(5):728-31.

Li DF#, Zhang JY#, Hou YJ, Liu L, Hu Y, Liu SJ*, Wang DC*, Liu W*. Structures of aminophenol dioxygenase in complex with intermediate, product and inhibitor. Acta Crystallogr D Biol Crystallogr. 2013 Jan;69(Pt 1):32-43.

Zhang X#, Zhang J, Zhang R, Guo Y, Wu C, Mao X, Guo G, Zhang Y, Li D*, Zou Q*. Structural, enzymatic and biochemical studies on Helicobacter pylori arginase. Int J Biochem Cell Biol. 2013 May;45(5):995-1002.

Zhang J#, Zhang X, Zhang R, Wu C, Guo Y, Mao X, Guo G, Zhang Y, Wang DC, Li D*, Zou Q*. Modeling studies with Helicobacter pylori octaprenyl pyrophosphate synthase reveal the enzymatic mechanism of trans-prenyltransferases. Int J Biochem Cell Biol. 2012 Dec;44(12):2116-23.

Bian CF#, Zhang Y, Sun H, Li DF*, Wang DC*. Structural basis for distinct binding properties of the human galectins to Thomsen-Friedenreich antigen. PLoS One. 2011;6(9):e25007.

Li DF#, Zhang N#, Hou YJ, Huang Y, Hu Y, Zhang Y, Liu SJ*, Wang DC*. Crystal structures of the transcriptional repressor RolR reveals a novel recognition mechanism between inducer and regulator. PLoS One. 2011 May 3;6(5):e19529.

Zhang J#, Zhang X, Wu C, Lu D, Guo G, Mao X, Zhang Y, Wang DC, Li D*, Zou Q*. Expression, purification and characterization of arginase from Helicobacter pylori in its apo form. PLoS One. 2011;6(10):e26205.

Feng L, Sun H, Zhang Y, Li DF* & Wang DC*. Structural insights into the recognition mechanism between an antitumor galectin AAL and the Thomsen-Friedenreich antigen. FASEB J. 2010 Oct;24(10):3861-8.

Yang N#, Li DF#, Feng L, Xiang Y, Liu W*, Sun H*, Wang DC*. Structural basis for the tumor cell apoptosis-inducing activity of an antitumor lectin from the edible mushroom Agrocybe aegerita. J Mol Biol. 2009 Apr 3;387(3):694-705.

 

 


Research Interests

To address some health related problems, such as degrading the pollutant via microbes and overcoming bacterial antibiotics resistances, we must understand the response of bacteria to environmental conditions. We are interested in the mechanisms of bacteria adaptation to pollutant. As well, we are interested in the mechanisms of bacteria adaption to extreme environments and resisting antibiotics.

Current research includes:

1) The mechanisms of bacteria sensing, moving towards or away from and degrading environmental chemicals, such as aromatic compounds, substrates in Calvin cycle and so on.

2) The regulation mechanism of bacterial movement during biofilm formation and dispersal.

3) The mechanism of bacteria fighting against antibiotics and the way to overcome bacterial antibiotic resistance.

4) Structural study on proteins involved in bacterial adaptation to extreme environments.


Students

现指导学生

韩群  硕士研究生  085238-生物工程  

秦亚玲  博士研究生  071010-生物化学与分子生物学