Principal Investigator
Researcher
Email:pengzhang01@cemps.ac.cn
Personal Web: http://pzhangxtal.sippe.ac.cn

National Key Laboratory of Plant Molecular Genetics

Professional experience  

Oct.2010-Present.  PI of Structural Biology. National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, SIBS, CAS. Shanghai, China.  

Feb. 2008-Oct.2010.  Postdoctoral research associate. Department of Molecular Biology, Princeton University; Princeton, NJ, USA.  

Jul.2007-Jan.2008.  Research Assistant. Institute of Biochemistry and Cell Biology, SIBS, CAS. Shanghai, China.  

Education  

Sept. 2002-Jul. 2007.  Ph.D. in Biochemistry and Molecular Biology. Institute of Biochemistry and Cell Biology (IBCB), SIBS, CAS.  Shanghai, China. (Advisor: Dr. Jianping Ding, Professor.)  

Sept. 1998-Jul. 2002.  B.S. in Biochemistry and Molecular Biology. Shandong University. Jinan, China.  

We are a structural biology group mainly focusing on the synthesis, cross-membrane transport and signaling of plant bioactive small molecules.  

A wealth of bioactive small molecules are synthesized and required in plants, which form the pool of metabolites and nutrients. Plant small molecules not only constitute the valuable source of pharmaceutical leading compounds, but also play essential roles in plant physiological and pathological processes. Using macromolecular crystallography and cryo-EM techniques, we determine the 3D-structures of proteins/complexes involved in the synthesis, cross-membrane transport and signaling of these small molecules. Combining with biochemical, biophysical and physiological methods, we aim to understand the underlying molecular mechanism in these processes, and provide creative ideas to plant or crop engineering.  

Our ongoing projects include the structural and mechanistic study of plant membrane transporters (nutrient and hormone), bioactive small molecules involved cross-membrane signaling, and plant metabolite biosynthesis & engineering.  

1) Structural mechanism of membrane transporters 

Plant membrane transporters play essential roles by absorbing nutrients from soil, delivering metabolites, nutrients and signal molecules to target microenvironment. A number of transporter-mutants failure in growth, development and biotic resistance have been identified. Meanwhile, introduction of functional transporters to reinforce the quality traits in plants are generally accepted. Therefore, understanding the molecular mechanism underlying the membrane transport process is of great importance. Currently, we are carrying out structural and mechanistic study of transporters mediating the cross-membrane transport of plant active small molecule (Vitamin, HCO₃^-, metabolites, and plant hormone)  

Energy coupling factor (ECF) transporters are a new family of ATP-binding cassette (ABC) transporters widely distributed in bacteria and plants. Responsible for the uptake of micronutrients (vitamin-Bs, metals etc.) from the environment, ECF transporters are composed of an ECF module consisting of a transmembrane T protein (EcfT) and two nucleotide-binding proteins EcfA and EcfA’, and a transmembrane substrate-specific binding protein EcfS. We determined the representative 3D structures of ECF transporter complexes, the folate/pantothenate/Co²⁺ ECF transporters (Nature, 2013 Recommended by Faculty-1000 Biology; Proc Natl Acad Sci, 2014; Nature Commun, 2015; Cell Res, 2017.) and proposed a working-model (Trends Microbiol, 2013). This model was supported by many studies and cited by a number of reviews (Annu Rev Biochem,2019; Curr Opin Struct Biol, 2018; Nat Struct Mol Biol, 2016; Nature Review Microbiol, 2014; Crit Rev Biochem Mol Bio, 2014; Faculty-1000 Biology), and was generally recognized as a novel ABC transporter mechanism in the field.  

In another study, we determined the 3D structure of a bicarbonate transporter (BicA) involved in the cyanobacterial CO₂-concentrating mechanisms (CCM) (Nature Plants, 2019.). It advanced our knowledge of the structure and function of cyanobacterial bicarbonate transporters, and would inform strategies for bioengineering functional BicA in heterologous organisms to boost CO₂ assimilation. 

2) Molecular mechanism of cross-membrane signaling 

Plants encounter more complicated environmental circumstances than animals. During evolution, a large number of plant metabolites are produced of physiological and pathological roles through function as signaling molecules to adapt environmental changes (light, microbes, temperature, …). Such metabolites include lipids, vitamin derivatives, and plant hormones. Elucidating the cross-membrane signaling mechanism using crystallographic and cryo-EM techniques is another research interest.  

In eukaryotic cells, Phosphatidic acid (PA) serves as not only a structural intermediate lipid for membrane lipid synthesis but also a vital second messenger molecule binding with downstream targets to regulate various biological events, ranging from cell proliferation, plant stress responses to roles in human cancers. PA is mainly produced by the hydrolysis of phospholipids by Phospholipase D (PLD). We determined the first crystal structure of the eukaryotic PLD, plant PLDa1, in the apo state and in complex with PA, which not only revealed catalytic and regulatory mechanisms, but also provided structural insights for PLD-targeted inhibitor/drug design (Cell Res, 2019). PA is mainly produced at the ER membrane, and transported to mitochondria. Ups1-Mdm35 is a highly conserved protein complex mediating the transport of PA in the mitochondrial intramembrane space, and this transport is feedback regulated by CL. We determined the crystal structure of Ups1-Mdm35 in complex with and without PA, and built a theoretical model of CL binding with Ups1-Mdm35, which enlightened the transport process and regulatory mechanism (EMBO Rep. 2015. Recommended by Faculty-1000 Biology).  

In another study, the structure of the membrane two-component protein complex, XylFII-LytS, which regulates the D-xylose transport in bacteria, was determined with and without ligand. The conformational changes revealed by the structures allowed a mechanistic proposal of signal perception and transport regulation of D-xylose (Proc Natl Acad Sci, 2017).  

3) Plant metabolite synthesis and engineering 

We are also working on the biosynthesis and engineering of plant metabolites, especially of physiological or pharmaceutical functions (mainly through collaborations). (Plant Commun, 2019; Proc Natl Acad Sci, 2016; Mol Plant. 2016; Biochem J. 2013) 

1. Wang C.C., Sun B., Zhang X., Huang X.W., Zhang M.H., Guo H., Chen X., Huang F., Chen T.Y., Mi H.L., Yu F., Liu L.N., Zhang P.*. Structural mechanism of the active bicarbonate transporter from cyanobacteria. Nature Plants. 2019 (In press) 

2. Li J.X.^#, Yu F. ^#, Guo H., Xiong R.X., Zhang W.J., He F.Y., Zhang M.H., Zhang P.*. Crystal structure of plant PLDα1 reveals catalytic and regulatory mechanisms of eukaryotic phospholipase D. Cell Res. 2019 (In press) 

3. Liu Z.F.^#, Li J.X.^#, Sun Y.W., Zhang P.*, Wang Y.*. Structural insights into the catalytic mechanism of a plant diterpene glycosyltransferase SrUGT76G1. Plant Communications. 2019 (In press) 

4. Sun Y.W., Chen Z., Li J.X., Li .J.H., Lv H.J., Yang J.Y., Li W.W., Xie D.A., Xiong Z.Q., Zhang P., Wang Y.*. Diterpenoid UDP-glycosyltransferases from Chinese Sweet Tea and Ashitaba Complete the Biosynthesis of Rubusoside. Mol Plant. 2018. doi.10.1016/j.molp.2018.05.010 

5. Yang Y, Liang T, Zhang L, Shao K, Gu X, Shang R, Shi N, Li X, Zhang P, Liu H.*. UVR8 interacts with WRKY36 to regulate HY5 transcription and hypocotyl elongation in Arabidopsis. Nature Plants. 2018. 4:98-107 

6. Li J.X. ^#, Wang C.Y. ^# , Yang G.H., Sun Z., Guo H., Shao K., Gu Y., Jiang W.H.*, Zhang P.*. Molecular mechanism of environmental D-xylose perception by a XylFII-LytS complex in bacteria. Proc Natl Acad Sci U S A. 2017. 114(31):8235-8240.  

7. Fang X., Li J.X., Huang J.Q., Xiao Y.L., Zhang P., Chen X.Y.*. Systematic identification of functional residues of Artemisia annua amorpha-4,11- dienesynthase.  Biochem J. 2017. 474(13):2191-2202.  

8. Zhou F. ^#, Wang C.Y. ^# , Gutensohn M. ^#, Jiang L, Zhang P., Zhang D.B., Dudareva N.*, Lu S.*. A Novel Recruiting Protein of Geranylgeranyl Diphosphate Synthase Controls Metabolic Flux towards Chlorophyll Biosynthesis in Rice. Proc Natl Acad Sci U S A. 2017. 114(26):6866-6871. 

9. Bao Z.H. ^#, Qi X.F. ^#, Hong S., Xu K., He F.Y., Zhang M.H., Chen J.G., Chao D.Y., Zhao W., Li D.F., Wang J.W. *, Zhang P.*. Structure and mechanism of a group‐I cobalt energy coupling factor transporter. Cell Res. 2017. 27(5):675-687.  

10. Qi X.F., Lin W., Ma M.L., Wang C.Y., He Y., He N.S., Gao J., Zhou H., Xiao Y.L., Wang Y., and Zhang P.*. Structural basis of rifampin inactivation by rifampin phosphotransferase. Proc Natl Acad Sci U S A. 2016. 113 (14) 3803-3808. 

11. Wang C. ^#, Chen Q. ^#, Fan D., Li J., Wang G.*, and Zhang P.*. Structural analyses of short-chain prenyltransferases identify an evolutionarily conserved GFPPS clade in Brassicaceae plants. Mol Plant. 2016.  9:195–204. (Cover & Highlight) 

12. Zhao Q. ^#, Wang C.C. ^#, Wang C.Y., Guo H., Bao Z.H., Zhang M.H., Zhang P. *. Structures of FolT at substrate-bound and substrate-released conformations reveal a gating mechanism of ECF transporters. Nat Commun. 2015. 6:7661. 

13.  Yu F. ^#, He F.Y. ^#, Yao H.Y., Wang C.Y., Wang J.C., Li J.X., Qi X.F., Xue H.W.*, Ding J.P.*, Zhang P.*. Structural basis of intramitochondrial phosphatidic acid transport mediated by Ups1-Mdm35 complex. EMBO Rep. 2015. 16 (7). 813-23. (Recommended by Faculty 1000, Biology) 

14. Li X.M., Chao D.Y., Wu Y., Huang X.H., Chen K., Cui L.G., Su L., Ye W.W., Chen H., Chen H.C., Dong N.Q., Guo T., Shi M., Feng Q., Zhang P., Han B., Shan J.X.*, Gao J.P.*, Lin H.X.*. Natural alleles of a proteasome α2 subunit gene contribute to thermotolerance and adaptation of African rice.  Nat Genet.  2015. 47(7):827-33.  

15. Zhang M.H.^#, Bao Z.H.^#, Zhao Q., Guo H., Xu K., Wang C.C., Zhang P.*. Structure of a pantothenate transporter and implications for ECF module sharing and energy coupling of group II ECF transporters.  Proc Natl Acad Sci U S A. 2014. 111(52):18560-5. 

16. Yang X., Ren W.Q., Zhao Q.X., Zhang P, Wu F.J., He Y.K.*.  Homodimerization of HYL1 ensures the correct selection of cleavage sites in primary miRNA. Nucleic Acids Res. 2014. 42(19):12224-12236. 

17. Zhang Z.L., Wu J., Lin W., Wang J., Yan H., Zhao W., Ma J., Ding J.P.*, Zhang P.*., and Zhao G.P.*. Subdomain II of alpha-isopropylmalate synthase is essential for activity: Inferring a mechanism of feedback inhibition. J Biol Chem. 2014. 289(40): 27966-27978. 

18. Lin W., Wang Y., Han X.B., Zhang Z.L.,Wang C.Y., Wang J., Yang H.Y., Lu Y.H., Jiang W.H., Zhao G.P.*., Zhang P.*. Atypical OmpR/PhoB subfamily response regulator GlnR of actinomycetes functions as a homodimer, stabilized by the unphosphorylated conserved Asp-focused charge. J Biol Chem. 2014. 289(22): 15413-15425. 

19. Zhang P.*. Structure and mechanism of energy-coupling factor transporters. Trends Microbiol. 2013. 21(12):652-9. （Invited review） 

20. Xu K. ^#, Zhang M.H. ^#, Zhao Q. ^#, Yu F. ^#, Guo H., Wang C.Y., He F.Y., Ding J.P., Zhang P.*. Crystal structure of a folate energy-coupling factor transporter from Lactobacillus brevis. Nature. 2013. 497(7448):268-71. (Recommended by Faculty 1000, Biology; Highlighted by Nature China.) 

21. Li J.X. ^#, Fang X. ^#, Zhao Q., Ruan J.X., Yang C.Q., Wang L.J., Miller D.J., Faraldos J.A., Allemann R.K., Chen X.Y.*, Zhang P.*. Rational engineering of plasticity residues of sesiquiterpene synthases from Artemisia annua: product specificity and catalytic efficiency.  Biochem J. 2013. 451(3):417-26.  

22. Zhang P., Wang J.W. and Shi Y.*. Structure and mechanism of the S component of a bacterial ECF transporter. Nature. 2010; 468(7324): 717-720. (Recommended by Faculty 1000, Biology) 

23. Zhang P.^#, Ma J.^#, Zhang Z., Zha M., Xu H., Zhao G., Ding J.*. Molecular basis of the inhibitor selectivity and insights into the feedback inhibition mechanism of citramalate synthase from Leptospira interrogans. Biochem J. 2009; 421:133-43.  

24. Ma J.^#, Zhang P.^#, Zhang Z.L., Zha M.W., Xu H., Zhao G..P., and Ding J.*. Molecular basis of the substrate specificity and the catalytic mechanism of citramalate synthase from Leptospira interrogans. Biochem J. 2008; 415:45-56.  

25. Zhang P., Zhao J., Wang B., Du J., Lu Y., Chen J. and Ding J.*. The MRG domain of human MRG15 uses a shallow hydrophobic pocket to interact with the N-terminal region of PAM14. Protein Sci. 2006; 15:2423-34. 

26. Zhang P.^#, Du J.^#, Sun B., Dong X., Xu G.., Zhou J., Huang Q., Liu Q., Hao Q. and Ding J.*. Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3. Nucleic Acids Res. 2006; 34:6621-8.