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2004-11-23 14:55:00

施一公博士简介

生物谷

Yigong Shi, Ph.D.
Professor of Molecular Biology
yshi@molbio.princeton.edu
Schultz Lab-219
Phone: 609-258-6071
Lab Phone: 609-258-2948
Princeton University
Dept. of Molecular Biology
Lewis Thomas Laboratory
Princeton, NJ 08544 U.S.A

Research

Structural Biology of Cancer

Research in my laboratory is aimed at understanding the molecular mechanisms involved in tumorigenesis, with a focus on key regulatory components in programmed cell death (apoptosis) and TGF-b signaling. Our approaches include a variety of biochemical and biophysical methods, particularly x-ray crystallography.

Apoptosis

Apoptosis plays a central role in the development and homeostasis of all animals. Inactivation of apoptosis is a hallmark of cancer. The mechanism of apoptosis, conserved across species, involves a cascade of sequential activation of initiator and effector caspases. Caspases are a large family of cysteine proteases that cleave after an aspatate residue in their substrates. The activation of an effector caspase, such as caspase-3 or -7, is performed by an initiator caspase, such as caspase-9. The Inhibitor of Apoptosis (IAP) family of proteins suppresses apoptosis primarily by inhibiting the enzymatic activity of mature caspases.

One major caspase activation cascade is triggered by the release of cytochrome c from the mitochondria. Once in the cytoplasm, cytochrome c associates with Apaf-1 in the presence of dATP or ATP, inducing the formation of “apoptosome”, which recognizes the inactive procaspase-9 and induces its autocatalytic processing. Concurrent with cytochrome c release, Smac/DIABLO is also released from the mitochondria into the cytoplasm. Whereas cytochrome c directly activates procaspase-9 and –3 via apoptosomes, Smac eliminates the inhibitory effect of IAPs.

This mammalian paradigm of apoptosis is recapitulated in lower species. In Drosophila, the protein Dark (Apaf-1 equivalent) is critically important for the activation of Dronc (caspase-9 equivalent) whereas the processed Dronc further activates DrICE (caspase-3/-7 equivalent). The Drosophila IAP (DIAP1) suppresses cell death by inhibiting Dronc and DrICE. This suppression can be removed by the Reaper, Grim, Hid, and Sickle proteins, which are the functional homologues of the mammalian protein Smac/DIABLO.

TGF-ß signaling

Signaling through transforming growth factor ß (TGF-ß) plays a central role in regulating a diverse set of cellular processes. The intracellular mediators of the TGF-ß pathway, the Smad proteins, transduce the TGF-ß signals from the plasma membrane into the nucleus, where Smad proteins associate with specific DNA-binding proteins and activate gene expression. In response to ligand activation, the receptor-regulated Smad proteins undergo phosphorylation and hetero-oligomerize with the co-mediator Smad, Smad4. This process is antagonized by the inhibitory Smads. Since TGF-ß signaling generally triggers negative regulation on cell growth and proliferation, inactivation of this pathway has been associated with several types of cancer. In particular, inactivation of the Smad4 tumor suppressor occurs in about half of all pancreatic carcinomas.

Publications

Significant publications are indicated with asterisks “***”.

(***) Nieng Yan, Jia-Wei Wu, Jun R. Huh, Jijie Chai, Wenyu Li, Bruce A. Hay, and Yigong Shi (2004). Molecular mechanisms of DrICE inhibition by DIAP1 and removal of inhibition by Reaper, Hid, and Grim. Nature-Structural and Molecular Biology, in press.

Jun R. Huh, Stephanie Y. Vernooy, Hong Yu, Nieng Yan, Yigong Shi, Ming Guo, Bruce A. Hay (2004). Multiple apoptotic caspase cascades are required in non-apoptotic roles for Drosophila spermatid individualization. PLoS Biology 2, 43–53.

Nieng Yan and Yigong Shi (2003). Histone H1.2 as a trigger for apoptosis (News and Views). Nature-Structural Biology 10, 983-985.

(***) Jijie Chai*, Nieng Yan*, Jun R. Huh, Jia-Wei Wu, Wenyu Li, Bruce A. Hay, and Yigong Shi (2003). Molecular mechanism of Reaper/Grim/Hid-mediated suppression of DIAP1-dependent Dronc ubiquitination. Nature-Structural Biology 10, 892-898 (The single asterisk indicates equal contributions.)

Constance J. Glover, Karen Hite, Renee DeLosh, Dominic A. Scudiero, Matthew J. Fivash, Lindsey R. Smith, Robert J. Fisher, Jia-Wei Wu, Yigong Shi, Rachael A. Kipp, George L. McLendon, Edward A. Sausville and Robert H. Shoemaker (2003). A high-throughput screen for identification of molecular mimics of Smac/DIABLO utilizing a fluorescence polarization assay. Analytical Biochemistry 320, 157-169.

Yigong Shi and Joan Massagué (2003). Mechanisms of TGF-b signaling from Cell Membrane to the Nucleus. (commissioned review article) Cell 113, 685-700.

Jijie Chai, Jia-Wu Wu, Nieng Yan, Joan Massagué, Nikola P. Pavletich, Yigong Shi (2003). Features of a Smad3 MH1-DNA complex: Roles of water and zinc in DNA binding. J. Biol. Chem. 278, 20327-20331.

Yigong Shi (2003). Structural Biology of Programmed Cell Death. (Book chapter). in Essentials of Apoptosis: A Guide for Basic and Clinical Research, Humana Press, pages 47-66.

(***) Eric N. Shiozaki, Jijie Chai, Daniel J. Rigotti, Stefan J. Riedl, Pingwei Li, Srinivasa M. Srinivasula, Emad S. Alnemri, Robert Fairman, and Yigong Shi (2003). Mechanism of XIAP-mediated Inhibition of Caspase-9. Mol. Cell 11, 519-527. (COVER of the February issue).

(***) Min Hu, Pingwei Li, Muyang Li, Wenyu Li, Tingting Yao, Jia-Wei Wu, Wei Gu, Robert E. Cohen, and Yigong Shi (2002). Crystal Structure of a UBP-family Deubiquitinating Enzyme in Isolation and in Complex with Ubiquitin Aldehyde. Cell 2002 111, 1041-1054.

Yigong Shi (2002). Structural Biology of Programmed Cell Death. (Book chapter). in Essentials of Apoptosis: A Guide for Basic and Clinical Research, Humana Press, in press.

Xiaochen Wang, Chonglin Yang, Jijie Chai, Yigong Shi, Ding Xue (2002). Mechanisms of AIF-mediated apoptotic DNA degradation in Caenorhabditis elegans. Science 298, 1587-1592.

(***) Jia-Wei Wu, Ariel R. Krawitz, Jijie Chai, Wenyu Li, Fangjiu Zhang, Kunxin Luo, and Yigong Shi (2002). Structural Mechanism of a Smad4 Recognition by the Nuclear Oncoprotein Ski: Insight on Ski-Mediated Repression of TGF-b Signaling. Cell 111, 357-367.

Rachael A. Kipp, Martin A. Case, Aislyn D. Wist, Catherine M. Cresson, Maria Carrell, Erin Griner, Arun Wiita, Philip A. Albiniak, Yigong Shi, Martin F. Semmelhack, and George L. McLendon (2002). Molecular Targeting of Inhibitor of Apoptosis Proteins Based on Small Molecule Mimics of Natural Binding Partners. Biochem 41, 7344-7349.

(***) Wenyu Li, Jijie Chai, Srinivasa M. Srinivasula, Emad S. Alnemri, and Yigong Shi (2002). Structure of the Mitochondrial Serine Portease Omi/HtrA2: Insights for Its Proapoptotic Function. Nature Struct. Biol. 9, 436-441.

Eric Shiozaki, Jijie Chai, and Yigong Shi (2002). Oligomerization and Activation of Caspase-9 Induced by the CARD Domain of Apaf-1. Proc. Natl. Acad. Sci. USA 99, 4197-4202.

Yigong Shi (2002). Mechanisms of Caspase Activation and Inhibition During Apoptosis (commissioned review article). Mol Cell 9, 459-470.

Yigong Shi (2002). Apoptosome: the cellular engine for the activation of caspase-9. (Mini-review). Structure 10, 285-288.

Srinivasa M. Srinivasula, Pinaki Datta, Masatomo Kobayashi, Miki Fujioka, Jia-Wei Wu†, Ramesh Hegde, ZhiJia Zhang, Rula Mukattash, Teresa Fernandes-Alnemri, Yigong Shi, James B. Jaynes and Emad S. Alnemri (2002). Sickle, a novel Drosophila death gene in the reaper/hid/grim region encodes an IAP-inhibitory protein. Curr. Biol. 12, 125-130.

Yigong Shi (2002). A conserved tetrapeptide motif: Potentiating apoptosis through IAP-binding. Cell Death Differ. 9, 93-95.

(***) Jia-Wei Wu, Min Hu, Jijie Chai, Morgan Huse, Carey Li, Saw Kyin, Robert Fairman, Tom Muir, Joan Massagué, and Yigong Shi (2001). Crystal Structure of a Phosphorylated Smad2: Recognition of Phosphoserine Motif and Insights on Smad Function in TGF-b Signaling. Mol. Cell 8, 1277-1289. (COVER of the December issue)

Stephen W. Fesik and Yigong Shi (2001). Controlling the Caspases. (Perspectives) Science 294, 1477-1478.

(***) Jijie Chai Qi Wu, Eric Shiozaki, Srinivasa M. Srinivasula, Emad S. Alnemri, and Yigong Shi (2001). Crystal Structure of a Caspase Zymogen: Mechanisms of Activation and Substrate Binding. Cell 107, 399-407.

(***) Jia-Wei Wu, Amy Cocina, Jijie Chai, Bruce Hay, and Yigong Shi (2001). Structural Analysis of a Functional DIAP1 Fragment Bound to Grim and Hid Peptides. Mol. Cell 8, 95-104.

Jia-Wei Wu, Jack Penry, Robert Fairman, and Yigong Shi (2001). Formation of a Stable Heterodimer between Smad2 and Smad4. J. Biol. Chem. 276, 20688-20694.

Yigong Shi (2001). A Structural View of the Mitochondria-mediated Apoptosis. (Commissioned review article) Nature-Structural Biology. 8, 394-401.

(***) Jijie Chai, Eric Shiozaki, Srinivasa M. Srinivasula, Qi Wu, Pinaki Datta, Emad S. Alnemri, and Yigong Shi (2001). Structural Basis of Caspase-7 Inhibition by XIAP. Cell 104, 769-780.

Srinivasa M. Srinivasula, Ayman Saleh, Ramesh Hedge, Pinaki Datta, Eric Shiozaki, Paul D. Robbins, Teresa Fernandes-Alnemri, Yigong Shi, and Emad S. Alnemri (2001). A conserved XIAP-interaction motif in caspase-9 and Smac/DIABLO mediates opposing effects on caspase activity and apoptosis. Nature 409, 112-116 (2001).

Yigong Shi (2001). Structural Insights on Smad Function in TGF-b signaling. (Commissioned review article) BioEssays 23, 223-232 (2001).

(***) Geng Wu*, Jijie Chai*, Tomeka Suber, Jia-Wei Wu, Chunying Du, Xiaodong Wang, and Yigong Shi (2000). Structural Basis of IAP Recognition by Smac/DIABLO. Nature 408, 1008-1012. (*These authors contributed equally.)

(***) Jijie Chai, Chunying Du, Jia-Wei Wu, Saw Kyin, Xiaodong Wang, and Yigong Shi (2000). Structural and Biochemical Basis of Apoptotic Activation by Smac/DIABLO. Nature 406, 855-862. (COVER of the August 24th issue.)

Yigong Shi (2000). Survivin structure: crystal unclear. Nature-Structural Biology 7, 620-623. (News and Views article)

Sha Ha, Debbie Walker, Yigong Shi, and Suzanne Walker (2000). The 1.9 Å crystal structure of Escherichia coli MurG, a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis.. Portein Sci. 9, 1045-1052.

(***) Geng Wu, Ye-Guang Chen, Barish Ozdamar, Cassie Gyuricza, P. Andrew Chong, Jeffrey L. Wrana, Joan Massagué, and Yigong Shi (2000). Structural Basis of Smad2 Recruitment by the Smad Anchor for Receptor Activation (SARA). Science 287, 92-97.

Xianxin Hua, Zachary Miller, Geng Wu, Yigong Shi, Harvey F. Lodish (1999). Specificity in TGF-b-induced Transcription: Interactions of Promoter DNA, Smad3 and TFE3. Proc. Natl. Acad. Sci. 96, 13130-13135.

Jie-Oh Lee, Haijuan Yang, Maria-Magdalena, Antonio Di Cristofano, Tomohiko Maehama, Yigong Shi, Jack E. Dixon, Pier P. Pandolfi, and Nikola P. Pavletich (1999). Crystal Structure of the PTEN Tumor Suppressor: Implications for Its Phosphoinositide Phosphatase Activity and Membrane Association. Cell 99, 323-334.

(***) Hongxu Qin, Srinivasa M. Srinivasula, Geng Wu, Emad S. Alnemri, Yigong Shi (1999). Structural Basis of Procaspase-9 Recruitment by the Apoptotic Protease Activating Factor 1. Nature 399, 549-557.

Shi-Du Yan, Yigong Shi, et al. (1999). Role of ERAB/L-3-hydroxyacyl-coenzyme A dehydrogenase type II activity in b-Amyloid-induced cytotoxicity. J. Biol. Chem. 274, 2145-2156.

(***) Yigong Shi, Yan-Fei Wang, Lata Jayaraman, Haijuan Yang, Joan Massagué, and Nikola Pavletich (1998). Crystal Structure of A Smad MH1 Domain Bound to DNA: Insights on DNA-binding in TGF-b Signaling. Cell, 94, 585-594.

Akiko Hata, Yigong Shi, and Joan Massagué (1998). TGF-b Signaling and Cancer: Structural and Functional Consequences of Mutations in Smads. Molecular Medicine Today, 4, 257-262.

Ye-Guang Chen, Akiko Hata, Roger S. Lo, David Wotton, Yigong Shi, Nikola P.Pavletich, and , Joan Massagué (1998). Determinants of Specificity in TGF-b Signal Transduction. Genes and Development, 12, 2144-2152.

Roger S. Lo, Ye-Guang Chen, Yigong Shi, Nikola P. Pavletich, and Joan Massagué (1997) The L3 loop: a structural motif determining specific interactions between SMAD proteins and TGF-b receptors. EMBO J., 17, 996-1005.

Yang-Gyun Kim, Yigong Shi, Jeremy M. Berg, and Srinivasan Chandrasegaran (1997) Site-specific cleavage of DNA-RNA hybrids by zinc finger/Fok I cleavage domain fusions. Gene,.203, 43-49.

(***) Yigong Shi, Akiko Hata, Joan Massagué and Nikola P. Pavletich (1997) A structural basis for mutational inactivation of the tumour suppressor Smad4. Nature 388, 87-93.

Yigong Shi and Jeremy M. Berg (1996) DNA unwinding induced by zinc finger protein binding. Biochemistry 35, 3845-3848.

Jeremy M. Berg and Yigong Shi (1996) The Galvanization of Biology: A Growing Appreciation for the Roles of Zinc. Science 271, 1081-1085.

(***) Yigong Shi and Jeremy M. Berg (1995) Specific DNA-RNA Hybrid Binding by Zinc Finger Proteins. Science 268, 282-284.

Yigong Shi and Jeremy M. Berg (1995) A Direct Comparison of the Properties of Natural and Designed Zinc Finger Proteins. Chemistry and Biology, 2, 83-89.

Yigong Shi, Richard D. Beger and Jeremy M. Berg (1993) Metal Binding Properties of Single Amino Acid Deletion Mutants of Zinc Finger Peptides: Studies Using Cobalt(II) as a Spectroscopic Probe. Biophysical J. 64, 749-753.