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


Research Direction


Research Unit

National Key Laboratory of Plant Molecular Genetics

Peng Zhang

Personal Profile

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.


Research Work

We are a structural biology group focusing on plant cross-membrane transport and signaling. Using macromolecular X-Ray crystallography and cryo-EM techniques, we determine the 3D-structures of proteins/complexes involved in plant nutrient/hormone transport and plant-environment signaling. Combining with biochemical, biophysical and physiological methods, we aim to understand the underlying molecular mechanism in these processes, and provide creative ideas to plant/crop design and engineering.


Main Achievements

1)Structural mechanism of plant membrane transporters

Plant membrane transporters play essential roles by absorbing inorganic nutrients from soil, delivering metabolites, nutrients and active small molecules to target microenvironment. A number of transporter-mutants failure in growth, development and biotic resistance have been identified. Meanwhile, introduction or engineering of functional transporters to reinforce the quality traits in plants are widely accepted. Therefore, understanding the structural mechanism underlying the membrane transport process is of great importance. For a long-term goal, we study plant nutrient and hormone transporters, emphasizing their structural and regulatory mechanism under certain physiological scenarios.

We determined the 3D structure of the plant hormone ABA/JA transporter ABCG25/16 in different conformations (Nat Plants, 2023, 2024). The substrate binding residues were revealed through structure analysis; together with biochemical and physiological analysis, the ABA/JA transport model was suggested. This structural information of ABA/JA transporter not only reveals the molecular mechanism underlying substrate-binding specificity and dynamic transport process of plant hormone, but also diversifies the transport mechanism among ABC transporters.

We carried out structural and mechanistic study of plant nutrient membrane transporters. We determined the 3D structures of BicA and SbtA/B that are key bicarbonate transporters in cyanobacterial CO2-concentration mechanisms (CCM) (Nat Plants, 2019; Proc Natl Acad Sci, 2021), and the CNGC Ca2+ channel (Nat Plants, 2025b), the GORK K+ channel (Nat Communs, 2025) and the nitrate/proton transporter ClCa (Nat Communs, 2023) that regulate the stomatal movement; and also the first plant inorganic phosphate transporter PHO1 and its regulation by inositol pyrophosphate (Nat Plants, 2025a). These advanced our knowledge of the plant nutrient cross-membrane transporter and regulatory mechanism of photosynthetic efficiency and would inform strategies to boost photosynthesis.

We studied the structural and molecular mechanism of a unique family of ABC transporters widely distributed in bacteria and plants, the Energy-Coupling Factor (ECF) transporters, which are responsible for the uptake of micronutrients (vitamin-Bs, metals etc.) from the environment. 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, 2020; 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.


2)Structural mechanism of plant cross-membrane signaling

Plants encounter more complicated environmental circumstances than animals. Biotic and abiotic factors including light, drought, temperature, microbes etc are perceived and responded through signal cascades existing at plant plasma and organelle membranes. A number of proteins or active small molecules have been identified functioning as receptor/sensor molecules. Elucidating the cross-membrane signaling mechanism using crystallographic and cryo-EM techniques is another research interest.

In plants, the well-studied cryptochrome (CRY) photoreceptors, activated by blue light, mediate various light responses in plants including plant growth and development, temperature sensing, etc. However, the molecular mechanism of activation and signaling through interaction with downstream effectors remains largely unknown. We determined the oligomeric structures of the blue-light-perceiving PHR domain of Zea mays CRY1 and an Arabidopsis CRY2 constitutively active mutant which reveals a molecular mechanism of plant CRY activation (Nat Struct Mol Biol, 2020). A low-resolution complex structure of an active CRY with its downstream effector CIB1 was also determined which suggests downstream light signaling mechanism (Plant Commun, 2023).


Phosphatidic acid (PA) serves as a vital second messenger molecule to regulate various biological events, ranging from plant drought responses to cell proliferation. PA is mainly produced by the hydrolysis of phospholipids by Phospholipase D (PLD). We determined the first crystal structure of the eukaryotic PLD, plant PLD1, 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; Prog Lipid Res. 2021.). 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. By determining the 3D structure of Ups1-Mdm35 in complex with and without PA, the underlying mechanism of PA trafficking and its feedback regulation by CL was revealed. (EMBO Rep. 2015. Recommended by Faculty-1000 Biology).


In addition, we are also interested in the structural and catalytic mechanism of plant metabolic enzymes, especially those involved in the biosynthesis of physiological or drug functional active metabolites. (Nat Commun. 2021a, b; Plant Commun, 2019; Proc Natl Acad Sci, 2016; Mol Plant. 2016)


Publications

ORCID: 0000-0003-0408-2923

1. Zhang X.#, Carroll W.#, Nguyen T.B.#, Nguyen T.H., Yang Z., Ma M.L., Huang X.W., Hills A., Guo H., Karnik R., Blatt M.R.*, Zhang P. *. GORK K+ channel structure and gating vital to informing stomatal engineering. Nat Commun. 2025. doi:10.1038/s41467-025-57287-7.

2. Wang J.P.#, Du B.Y.#, Zhang X.#, Qu X.M., Yang Y., Yang Z., Wang Y.F.*, Zhang P.*. Cryo-EM structures of Arabidopsis CNGC1 and CNGC5 reveal molecular mechanisms underlying gating and calcium selectivity. Nat Plants. 2025b. doi:10.1038/s41477-025-01923-z

3.Fang S.#, Yang Y.#, Zhang X.#, Yang Z., Zhang M.H., Zhao Y., Zhang C.S., Yu F., Wang Y.F.*, Zhang P.*. Structural mechanism underlying PHO1;H1 mediated phosphate transport in Arabidopsis. Nat Plants. 2025a. doi:10.1038/s41477-024-01895-6.

4. Tan X.H. # , Wang D.P. # , Zhang X.W., Zheng S., Jia X.J., Liu H. , Liu Z.L. , Yang H. , Dai H.L. , Chen X., Qian Z.X. , Wang R. , Ma M.L. , Zhang P., Yu N. , Wang E.T. A pair of LysM receptors mediates symbiosis and immunity discrimination in Marchantia. Cell. 2025. S0092-8674(24)01466-1. doi: 10.1016/j.cell.2024.12.024.

5. Hao Y., Zeng Z., Yuan M, Li H., Guo S., Yang Y., Jiang S., Hawara E., Li J., Zhang P., Wang J., Xin X., Ma W., Liu H. The blue-light receptor CRY1 serves as a switch to balance photosynthesis and plant defense. Cell Host Microbe. 2025. 33(1):137-150.e6. doi:10.1016/j.chom.2024.12.003.

6. An N.#, Huang X.W.#, Yang Z., Zhang M.H., Ma M.L., Yu Fang., Jing L.Y., Du B.Y., Wang Y.F., Zhang X.*, Zhang P.*. Cryo-EM structure and molecular mechanism of the jasmonic acid transporter ABCG16. Nat Plants. 2024. 10: 2052-2061. doi:10.1038/s41477-024-01839-0.

7. Zhou C.M.#, Li J.X.#, Zhang T.Q., Xu Z.G., Ma M.L., Zhang P.*, Wang J.W.*. The structure of B-ARR reveals the molecular basis of transcriptional activation by cytokinin. Proc Natl Acad Sci U S A. 2024. 121. e2319335121. doi: 10.1073/pnas.2319335121.

8. Huang X.W.#, Zhang X.#, An N., Zhang M.H., Ma M.L., Yang Y., Jing L.Y., Wang Y.F., Chen Z.G.*, Zhang P.*. Cryo-EM structure and molecular mechanism of abscisic acid transporter ABCG25. Nat Plants. 2023.9(10):1709-1719. doi:10.1038/s41477-023-01509-7

9. Yang Z.#, Zhang X.#, Ye S.W.#, Zheng J.T., Huang X.W., Yu F., Chen Z.G.*, Cai S.Q.*, Zhang P.*. Molecular mechanism underlying regulation of Arabidopsis CLCa transporter by nucleotides and phospholipids. Nat Commun. 2023. 14(1): 4879. doi: 10.1038/s41467-023-40624-z

10. Wang C.#, Yu L.Y.#, Zhang J.Y.#, Zhou Y.X. #, Sun B., Xiao Q.J., Zhang M.H., Liu H.Y., Li J.H., Li J.L., Luo Y.Z., Xu J., Lian Z., Lin J.W., Wang X., Zhang P., Guo L.*, Ren R.B.*, Deng D.*. Structural basis of the substrate recognition and inhibition mechanism of Plasmodium falciparum nucleoside transporter PfENT1. Nat Commun. 2023. 14(1): 1727. doi: 10.1038/s41467-023-37411-1.

11. Li L.Z., Xu Z.G., Chang T.G., Wang L., Kang H., Zhai D., Zhang L.Y., Zhang P., Liu H.T., Zhu X.G., Wang J.W. Common evolutionary trajectory of short life-cycle in Brassicaceae ruderal weeds. Nat Commun. 2023. 14(1):290. doi: 10.1038/s41467-023-35966-7.

12. Ha Y.H. #, Zhang X. #, Liu Y.Q., Ma M.L., Huang X.W., Liu H.T., Zhang P. Cryo-EM structure of the CRY2 and CIB1 fragment complex provides insights into CIB1-mediated photosignaling. Plant Commun. 2023. 4(2):100475. doi: 10.1016/j.xplc.2022.100475.

13.Liu H.Y. #, Lin J.S. #, Luo Z.P. #, Sun J. #, Huang X.W. #, Yang Y., Xu J., Wang Y.F., Zhang P., Oldroyd G.E., Xie F. Constitutive activation of a nuclear-localized calcium channel complex in Medicago truncatula. Proc Natl Acad Sci U S A. 2022.119 (34): e2205920119. doi: 10.1073/pnas.2205920119.

14.Fang S. #, Huang X.W.#, Zhang X.#,*, Zhang M.H., Hao YH, Guo H., Liu L.N., Yu F., Zhang P. Molecular mechanism underlying transport and allosteric inhibition of bicarbonate transporter SbtA. Proc Natl Acad Sci U S A. 2021.118 (22) e2101632118. doi: 10.1073/pnas.2101632118.

15.Xiao Y. #, Shao K. #, Zhou J.W. #, Wang L., Ma X.Q., Wu D., Yang Y.B., Chen J.F., Feng J.X., Qiu S., Lv Z.Y., Zhang L.*, Zhang P.*, and Chen W.S.*. Structure-based engineering of substrate specificity for pinoresinol-lariciresinol reductases. Nat Commun. 2021.12 (1) 2828. doi: 10.1038/s41467-021-23095-y.

16.Liu G.Q.#, Zhao Y.L.#, He F.Y., Zhang P., Ouyang X.Y., Tang H.Z.*, Xu P.*. Structure-guided insights into heterocyclic ring-cleavage catalysis of the non-heme Fe (II) dioxygenase NicX. Nat Commun. 2021.12 (1) 1301. doi: 10.1038/s41467-021-21567-9.

17.Yang G.H. #, Hong S.#, Yang P.J.#, Sun Y.W., Wang Y., Zhang P., Jiang W.H. *, Gu Y.*. Discovery of an ene-reductase for initiating flavone and flavonol catabolism in gut bacteria. Nat Commun. 2021.12 (1) 790. doi: 10.1038/s41467-021-20974-2.

18. Yao Y. #, Li J. #., Lin Y. #, Zhou J., Zhang P.*, Xu Y.*. Structural insights into phospholipase D function. Prog Lipid Res. 2021. 81: 101070. doi: 10.1016/j.plipres.2020.101070.

19. Shao K. #, Zhang X. #, Li X. #, Hao Y.H., Huang X.W., Ma M.L., Zhang M.H., Yu F., Liu H.T.*, Zhang P.*. The oligomeric structures of plant cryptochromes. Nat. Struct. Mol. Biol. 2020. 27(5): 480-488. doi: 10.1038/s41594-020-0420-x.（Views and News in NSMB）

20. 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. 2020.30(1): 61-69. doi: 10.1038/s41422-019-0244-6.

21. Thomas C., Aller SG, Beis K., Carpenter E.P., Chang G., Chen L., Dassa E., Dean M., Duong Van Hoa F., Ekiert D., Ford R., Gaudet R., Gong X., Holland I.B., Huang Y., Kahne D.K., Kato H., Koronakis V., Koth C.M., Lee Y., Lewinson O., Lill R., Martinoia E., Murakami S., Pinket H.W., Poolman B., Rosenbaum D., Sarkadi B., Schmitt L., Schneider E., Shi Y., Shyng S.L., Slotboom D.J., Tajkhorshid E., Tieleman D.P., Ueda K., Váradi A., Wen P.C., Yan N., Zhang P., Zheng H., Zimmer J., Tampé R. Structural and functional diversity calls for a new classification of ABC transporters. FEBS Lett. 2020.594(23) :3767-3775. doi: 10.1002/1873-3468.13935.

22. Chen Q.W. #, Li J.X. #, Liu Z.X., Mitsuhashi T., Zhang Y.T., Liu H.L., Ma Y.H., He J., Shinada T., Sato T., Wang Y., Liu H.W., Abe I., Zhang P.*, Wang G.D*. Molecular Basis for Sesterterpene (C25) Diversity Produced by Plant Terpene Synthases. Plant Communications. 2020. 1(5), 100051.doi: 10.1016/j.xplc.2020.100051.

23. 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. 2020 1(1), 100004. doi: 10.1016/j.xplc.2019.100004.

24. 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. Nat Plants. 2019. 5(11):1184-1193. doi: 10.1038/s41477-019-0538-1.

25. He J, Zhang C, Dai H, Liu H, Zhang X, Yang J, Chen X, Zhu Y, Wang D, Qi X, Li W, Wang Z, An G, Yu N, He Z, Wang YF, Xiao Y, Zhang P, Wang E. A LysM receptor heteromer mediates perception of arbuscular mycorrhizal symbiotic signal in rice. Mol Plant. 2019. 12(12):1561-1576. doi: 10.1016/j.molp.2019.10.015.

26. Sun Y.W., Chen Z., Li J.X., Li .JH., 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. 2018.11(10):1308-1311. doi.10.1016/j.molp.2018.05.010

27. Yang Y, Liang T, Zhang L, Shao K, Gu X, Shang R, Shi N, Li X, Zhang P, Liu H. (2018) UVR8 interacts with WRKY36 to regulate HY5 transcription and hypocotyl elongation in Arabidopsis. Nat Plants. 4(2):98-107. doi: 10.1038/s41477-017-0099-0.

28. 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. 2017a. 114(31):8235-8240. doi: 10.1073/pnas.1620183114.

29. 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. doi: 10.1042/BCJ20170060.

30. 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. 2017b.114(26):6866-6871. doi:10.1073/pnas.1705689114.

31. 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 JW. *, Zhang P.*. Structure and mechanism of a group‐I cobalt energy coupling factor transporter. Cell Res. 2017. 27(5):675-687. doi: 10.1038/cr.2017.38.

32. 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. doi: 10.1073/pnas.1523614113.

33. 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(2):195-204. doi: 10.1016/j.molp.2015.10.010. (Cover & Highlight)

34. 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. doi: 10.1038/ncomms8661.

35. 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). 813-823. doi: 10.15252/embr.201540137. (Recommended by Faculty 1000, Biology)

36. 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):827-833. doi: 10.1038/ng.3305.

37. 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):18560-18565. doi: 10.1073/pnas.1412246112.

38. 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. doi: 10.1093/nar/gku907.

39. 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. doi: 10.1074/jbc.M114.559716.

40. 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. doi: 10.1074/jbc.M113.543504.

41.Zhang P. Structure and mechanism of energy-coupling factor transporters. Trends Microbiol. 2013. 21(12):652-659. doi: 10.1016/j.tim.2013.09.009.（Invited review）

42.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):268-271. doi: 10.1038/nature12046. (Recommended by Faculty 1000, Biology; Highlighted by Nature China.)

43. 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):417-426. doi: 10.1042/BJ20130041.

44.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. doi: 10.1038/nature09488. (Recommended by Faculty 1000, Biology)

45.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(1):133-43. doi: 10.1042/BJ20090336.

46. 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(1):45-56. doi: 10.1042/BJ20080242.

47.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(10):2423-2434. doi: 10.1110/ps.062397806.

48.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(22):6621-6628. doi: 10.1093/nar/gkl989.