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Yan Zhang

Associate Professor
Molecular Biosciences

Structural And Biophysical Studies Of phosphatases in eukaryotic transcription, Structure-Based Drug Design.


Phone: 512-471-1027

Office Location
NHB 4.126

Postal Address
100 E 24TH ST
AUSTIN, TX 78712

Ph.D., The Scripps Research Institute (2004)
B.S., Tsinghuan University, China (1997)
M.S., University of Oregon (2000)

The Salk Institute for Biological Research

Research Interests

The transcription process in eukaryotic cells is controlled by the C-terminal domain of RNA polymerase II through its post-translational modification states. However enzymes that recognize the same phosphorylation site in CTD can lead to different transcriptional outcomes. To address the central question that how gene-specific regulation was achieved by CTD regulatory enzymes, we investigate the structure function mechanism of CTD phosphatases. Specifically, a protein regulation prolyl isomerization state of the CTD proline residues can affect the transcription by controlling the availability of the substrate pools for the phosphatases. We also develop chemical compounds as tools to understand the proline isomerization state specificity of CTD binding enzymes and chemical probes to promote neuron regeneration.

Research Projects:

Combinatorial Code of CTD

The conformational states of the C-terminal domain (CTD) of eukaryotic RNA polymerase II represent a critical regulatory check point for transcription. The CTD, found only in eukaryotes, consists of 26-52 tandem hepta-peptide repeats with the general consensus sequence,1TyrSerProThrSerProSer7. The CTD can spatially and temporally recruit different regulatory and processing factors to the transcriptional machinery (Fig.1). CTD regulates the transcription through its various conformations, which are achieved through post-translational covalent modifications or prolyl isomerization (Fig. 1). Phosphorylation of serine residues at positions 2 and 5 is the primary modification sites whose patterns have been correlated to various stages of transcription.

  • The phosphatase families of CTD Ser5 phosphatases.

The phosphorylation states of CTD, namely the “CTD code”, are coordinated by CTD kinases and phosphatases. CTD phosphatases are especially difficult to study because of the high heterogeneity in endogenous CTD phosphorylation pattern. The removal of phosphorylation labels in a precise and timely manner is equally essential as placing the label for the interpretation of the CTD code during transcription regulation. For example, Ssu72 and Fcp have been reported to play key roles in general transcription, mRNA processing/termination and RNA polymerase II recycling. In contrast to those general regulators, human Scp only affects transcription of specific neuronal genes. We solved the structure of Scp and Ssu72 phosphatases which recognize the same CTD sequence but with dramatically different transcription outcome. We are further investigating the association of these phosphatases with binding partners from the transcription complexes they are involved with and how such interaction play a major role for their biological function in transcription regulation.

  • The cross-talk of Ser5 phosphorylation and Pro6 isomerization

CTD regulation of transcription is mediated both by phosphorylation of the serines and prolyl isomerization of the two prolines. Interestingly, the phosphorylation sites are typically close to prolines, thus the conformation of the adjacent proline could impact the specificity of the corresponding kinases and phosphatases. Experimental evidence of cross-talk between these two regulatory mechanisms has been elusive. Pin1 is a highly conserved phosphorylation-specific peptidyl-prolyl isomerase (PPIase) that recognizes the phospho-Ser/Thr (pSer/Thr)-Pro motif with CTD as one of its primary substrates in vivo. We provide structural snapshots and kinetic evidence that support the concept of cross-talk between prolyl isomerization and phosphorylation. We determined the structures of Pin1 bound with two substrate isosteres that mimic peptides containing pSer/Thr-Pro motifs in cis or trans conformations. The results unequivocally demonstrate the utility of both cis- and trans-locked alkene isosteres as close geometric mimics of peptides bound to a protein target. Building on this result, we identified a specific case in which Pin1 differentially affects the rate of dephosphorylation catalyzed by two phosphatases (Scp1 and Ssu72) that target the same serine residue in the CTD heptad repeat but that have different preferences for the isomerization state of the adjacent proline residue.  These data exemplify for the first time how modulation of proline isomerization can kinetically impact signal transduction in transcription regulation.

  • Chemical compounds for neural regeneration.

Scp proteins are phosphatases that target phosphorylated Ser5 (phos.Ser5) in the hepta-repeats of CTD. Identified as a modulator of neural gene silencing, Scp proteins act as evolutionarily conserved transcriptional co-repressors; and in this role, they can inhibit neuronal gene transcription in non-neuronal cells. We identified the first selective inhibitor for Scp protein, which is also the first reported selectivity inhibitor for HAD family. We are currently developing this scaffold for compounds that can promote neuron regeneration. Such compounds are not only useful as a tool to study the cascade of neuronal gene expression pattern, more importantly, it has the potential as a chemical agent promoting new neuron growth which will greatly benefit patients in neurodegenerative diseases such as Alzheimer’s.

Representative Publications

Mayfield, J.E., Robinson, M.R., Cotham, V.C., Irani, S., Matthews, W.L., Ram, A., Gilmour, D.S., Cannon, J.R., Zhang, Y. J.,* and Brodbelt, J.S*.(2016) Mapping the phosphorylation pattern of Drosophila RNA polymerase II carboxyl-terminal domain using ultraviolet photodissociation mass spectrometry. ACS Chem Biol. doi:10.1021/acschembio.6b00729

Irani S,Yogesha , Mayfield JE, Zhang M, Zhang Y, Matthews WL and Zhang Y. Crystal Structure of an atypical phosphatase. Science Signaling. doi:10.1126/scisignal.aad4805

Cramer, Saha, S.Tadi, S. Tiziani, Yan W., K. Triplett, S. Alters, D. Johnson, Y. J. Zhang,J. DiGiovanni, G. Georgiou and E. Stone Systemic Depletion of Serum L-Cyst(e)ine with an Engineered Human Enzyme Mediates Potent Induction of ROS and Cancer Ablation.  Nature Medicine doi:10.1038/nm.4232

Yan, W., Song, H., Song, F., Guo, Y., Wu, C.H., Her, A.S., Pu,Y., Wang, S., Naowarojna, N., Weitz, A., Hendrich, M.P., Costello, C.E., Zhang, L.*, Liu, P.,* and Zhang,Y.* Endoperoxide Formation by an a-Ketoglutarate-dependent Mononuclear Non-heme Iron Enzyme.  Nature. 2015. doi:10.1038/nature15519

Mayfield, J. E., Fan, S., Wei, S., Zhang, M., Li, B., Ellington, A.D., Etzkorn, F.A., and Zhang,Y. * Chemical tools to decipher the regulation of phosphatases by proline isomerization on eukaryotic RNA polymerase II.  ACS Chem Biol. 2015. doi: 10.1021/acschembio.5b00296. (Cover story)

Wei, S., Kozono, S., Kats, L., Nechama, M., Li, W., Guarnerio, J., Luo, M., You, M.H., Yao, Y., Kondo, A., Hu, H., Bozkurt, G., Moerke, N., Cao, S., Reschke, M., Chen, C.H., Rego, E.M., Lo-Coco, F., Cantley, L.C., Lee, T.H., Wu, H., Zhang, Y., Pandolfi, P.P., Zhou, X.Z., Lu, K.P. (2015). Active Pin1 is a key target of all-trans retinoic acid in acute promyelocytic leukemia and breast cancer. Nat Med. doi: 10.1038/nm.3839.

Chen, C., Li, W., Sultana, R., You, M., Kondo, A., Shahpasand, K., Kim, B., Luo, M., Nechama, M., Lin, Y., Yao, Y., Lee, T., Zhou, X., Swomley, A., Butterfield, D.,Zhang, Y.*, Lu, K.(2015). Pin1 cysteine-113 oxidation inhibits its catalytic activity and cellular function in Alzheimer's disease. Neurobiol. Dis.,(76)13-23. doi: 10.1016/j.nbd.2014.12.027 (Cover story)

Luo, Y., Yogesha, S. D., Cannon, J. R., Yan, W., Ellington, A. D., Brodbelt, J. S., & Zhang, Y. (2013). Novel Modifications on C-terminal Domain of RNA Polymerase II Can Fine-tune the Phosphatase Activity of Ssu72. ACS Chem Biol, 8(9):2042-52.doi: 10.1021/cb400229c

Shaw, J. B., Li, W., Holden, D. D., Zhang, Y., Griep-Raming, J., Fellers, R. T., Early, B. P., Thomas, P. M., Kelleher, N. L., Brodbelt, J. S. (2013). Complete Protein Characterization Using Top-Down Mass Spectrometry and Ultraviolet Photodissociation. J Am Chem Soc. 135(34):12646-51. doi: 10.1021/ja4029654

Li, W., Cantor, J. R., Yogesha, S. D., Yang, S., Chantranupong, L., Liu, J. Q., Agnello, G., Georgiou, G., Stone, E. M., Zhang, Y. (2012). Uncoupling intramolecular processing and substrate hydrolysis in the N-terminal nucleophile hydrolase hASRGL1 by circular permutation. ACS Chem Biol, 7(11), 1840-1847. doi: 10.1021/cb300232n

Zhang, M., Wang, X. J., Chen, X., Bowman, M. E., Luo, Y., Noel, J. P., Ellington, A. D., Etzkorn, F. A., Zhang, Y.* (2012). Structural and kinetic analysis of prolyl-isomerization/phosphorylation cross-talk in the CTD code. ACS Chem Biol, 7(8), 1462-1470. doi: 10.1021/cb3000887 *co-corresponding author in publication

Lee, T. H., Chen, C. H., Suizu, F., Huang, P., Schiene-Fischer, C., Daum, S., Zhang, Y., Goate, A., Chen, RH., Zhou, X. Z., Lu, K. P. (2011). Death-associated protein kinase 1 phosphorylates Pin1 and inhibits its prolyl isomerase activity and cellular function. Mol Cell, 42(2), 147-159. doi: 10.1016/j.molcel.2011.03.005

Zhang, M., Cho, E. J., Burstein, G., Siegel, D., & Zhang, Y. (2011). Selective inactivation of a human neuronal silencing phosphatase by a small molecule inhibitor. ACS Chem Biol, 6(5), 511-519. doi: 10.1021/cb100357t (Featured cover May 2011, featured story in podcast May 2011)

Zhang, Y., Zhang, M., & Zhang, Y. (2011). Crystal structure of Ssu72, an essential eukaryotic phosphatase specific for the C-terminal domain of RNA polymerase II, in complex with a transition state analogue. Biochem J, 434(3), 435-444. doi: 10.1042/BJ20101471