Yingming Zhao, Ph.D.

Research Summary


Laboratory of Proteomics and Protein Post-translational modifications

Overview

Laboratory of Proteomics and Protein Modifications

Post-translational modifications (PTMs) represent a major vehicle to diversify a cellular proteome, the inventory of all protein species in an organism. PTMs have critical roles in all the major cellular pathways and diseases. A protein can be potentially modified by more than 200 types of post-translational modifications, which are catalyzed by enzymes encoded by more than 5% of the genome in higher eukaryotes. A combination of a dozen PTM sites in a substrate protein could lead to more than a million possible protein structures with potentially different functions. Given the high abundance and diversities of PTMs, they are likely the most complex regulatory mechanisms in cells. Despite their critical roles in cells, little is known about their biology, except several most extensively studied PTMs. Functional characterizations of PTMs at the molecular level have been slow, largely due to a lack of suitable information infrastructure and technology infrastructure.

Our research aims to develop mass spectrometry-based proteomics technologies, and to use them to dissect PTM pathways. We are developing new mass spectrometry and bioinformatics tools for reliable, sensitive, and comprehensive analysis of proteins and PTMs. We are interested in dynamics analysis of diverse PTMs in order to understand their functions. We are using proteomics approach to characterize lysine acetylation, lysine propionylation, and lysine butyrylation pathways, the last two of which were recently discovered by us. We have begun applying a new bioinformatics tool, PTMap, also recently developed by us, to investigate PTM cross-talks. We also use powerful proteomics technologies in conjunction with biochemistry, molecular biology, and cell biology to decode PTM networks that have major implications for human health and are not amenable to conventional techniques. 

 

Recent Publications


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2014

Huang H, Sabari BR, Garcia BA, Allis CD, Zhao Y, SnapShot: Histone Modifications. Cell. 2014 Oct 9;159(2):458-458.e1. doi: 10.1016/j.cell.2014.09.037.

Dai L, Peng C, Montellier E, Lu Z, Chen Y, Ishii H, Debernardi A, Buchou T, Rousseaux S, Jin F, Sabari BR, Deng Z, Allis CD, Ren B, Khochbin S, Zhao Y, Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark. Nat Chem Biol. 2014, doi: 10.1038/nchembio.1497.

Tan M, Peng C, Anderson KA, Chhoy P, Xie Z, Dai L, Park J, Chen Y, Huang H, Zhang Y, Ro J, Wagner GR, Green MF, Madsen AS, Schmiesing J, Peterson BS, Xu G, Ilkayeva OR, Muehlbauer MJ, Braulke T, Mühlhausen C, Backos DS, Olsen CA, McGuire PJ, Pletcher SD, Lombard DB, Hirschey MD, Zhao Y, Lysine Glutarylation Is a Protein Posttranslational Modification Regulated by SIRT5. Cell Metab. 2014, 19, 605-17.

Tang S, Huang G, Fan W, Chen Y, Ward JM, Xu X, Xu Q, Kang A, McBurney MW, Fargo DC, Hu G, Baumgart-Vogt E, Zhao Y, Li X. SIRT1-Mediated Deacetylation of CRABPII Regulates Cellular Retinoic Acid Signaling and Modulates Embryonic Stem Cell Differentiation. Mol Cell. 2014 Aug 20. pii: S1097-2765(14)00604-2. doi: 10.1016/j.molcel.2014.07.011.

Kazgan N, Metukuri MR, Purushotham A, Lu J, Rao A, Lee S, Pratt-Hyatt M, Lickteig A, Csanaky I, Zhao Y, Dawson PA, Li X. Intestine-specific Deletion of Sirt1 in Mice Impairs DCoH2-HNF1α-FXR Signaling and Alters Systemic Bile Acid Homeostasis. Gastroenterology, 2014, 146, 1006-16.

Xu G, Wang J, Wu Z, Qian L, Dai L, Wan X, Tan M, Zhao Y, Wu Y., SAHA regulates histone acetylation, butyrylation and protein expression in neuroblastoma. J Proteome Res. 2014, DOI: 10.1021/pr500497e

 Luo X, Wang B, Tang F, Zhang J, Zhao Y, Li H, Jin Y. Wwp2 targets SRG3, a scaffold protein of the SWI/SNF-like BAF complex, for ubiquitination and degradation. Biochem Biophys Res Commun, 2014, 443, 1048-53.

Sun H, Chen X, Yuan F, Liu J, Zhao Y, Chen SY. Involvement of seven in absentia homolog-1 in ethanol-induced apoptosis in neural crest cells. Neurotoxicol Teratol. 2014 Sep 3;46C:26-31. doi: 10.1016/j.ntt.2014.08.006.

Zhang Y, Wu Z, Wan X, Liu P, Zhang J, Ye Y, Zhao Y, Tan M, Comprehensive Profiling of Lysine Acetylome in Staphylococcus aureus. Sci China Chem. In Press.

2013

Park J, Chen Y, Tishkoff DX, Peng C, Tan M, Dai L, Xie Z, Zhang Y, Zwaans BM, Skinner ME, Lombard DB, Zhao Y, SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways. Mol Cell, 2013, 50, 919-30.

Colak G, Xie Z, Zhu AY, Dai L, Lu Z, Zhang Y, Wan X, Chen Y, Cha YH, Lin H, Zhao Y, Tan M. Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in Escherichia coli. Mol Cell Proteomics, 2013, 12, 3509-20.

Chen Y, Colak G, Zhao Y, SILAC-Based Quantification of Sirt1-Responsive Lysine Acetylome. Methods Mol Biol, 2013, 1077, 105-20.

Dobbin MM, Madabhushi R, Pan L, Chen Y, Kim D, Gao J, Ahanonu B, Pao PC, Qiu Y, Zhao Y, Tsai LH, SIRT1 collaborates with ATM and HDAC1 to maintain genomic stability in neurons. Nat Neurosci, 2013, 16, 1008-15.

Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Krajewski K, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S, Recombinant antibodies to histone post-translational modifications. Nat Methods, 2013, 18. doi: 10.1038/nmeth.2605.

Montellier E, Boussouar F, Rousseaux S, Zhang K, Buchou T, Fenaille F, Shiota H, Debernardi A, Héry P, Curtet S, Jamshidikia M, Barral S, Holota H, Bergon A, Lopez F, Guardiola P, Pernet K, Imbert J, Petosa C, Tan M, Zhao Y, Gérard M, Khochbin S., Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B. Genes Dev, 2013, 27, 1680-92.

Lee S, Tan M, Dai L, Kwon OK, Yang JS, Zhao Y, Chen Y, MS/MS of synthetic peptide is not sufficient to confirm new types of protein modifications. J Proteome Res, 2013, 12, 1007-13.

 Liao B, Zhong X, Xu H, Xiao F, Fang Z, Gu J, Chen Y, Zhao Y, Jin Y, Itch, an E3 ligase of Oct4, is required for embryonic stem cell self-renewal and pluripotency induction. J Cell Physiol, 2013, 228, 1443-51.

 

2012

Xie, Z., Dai, J., Dai, L., Tan, M., Cheng, Z., Wu,Y., Boeke, J. D., Zhao, Y., Lysine succinylation and lysine malonylation in histones. Mol Cell Proteomics, 2012, 11, 100-7. 

Chen, Y., Zhao, W., Yang, J.S., Cheng, Z., Luo, H., Lu, Z., Tan, M., Gu, W., and Zhao, Y., Quantitative acetylome analysis reveals the roles of SIRT1 in regulating diverse substrates and cellular pathways. Mol Cell Proteomics, 2012, 11, 1048-62.

Li, N., Kon, N., JIang, L., Tan, M., Ludwig, T., Zhao, Y., Baer, R., W., G., Tumor suppression in the absence of p53-mediated cell cycle arrest, apoptosis, and senescence. Cell, 149, 1269-83

Qiang, L., Wang, L., Kon, N., Lee, S., Zhao, Y., Gu, W., Farmer, S.R., Accili, D., Brown remodeling of white adipocytes by SirT1-dependent deacetylation of PPARγ. Cell, 2012, 150, 620-32.

Choi, M.C., Cohen, T.J., Barrientos, T., Wang, B., Simmons, B.J., Li, M., Yang, J.S., Cox, G.A., Zhao, Y., Yao, T.P., A direct HDAC4-MAP kinase crosstalk activates neurogenic muscle atrophy. Mol Cell, 2012, 47, 1-11.

Liu, J., Yan, J., Jiang, S., Wen, J., Chen, L., Zhao, Y., Lin, A., Site-specific ubiquitination is required for relieving the transcription factor Miz1-mediated suppression on TNF-α-induced JNK activation and inflammation. Proc Natl Acad Sci U S A, 2012, 109, 191-6.

Montellier, E., Rousseaux, S., Zhao, Y., Khochbin S. Histone crotonylation specifically marks the haploid male germ cell gene expression program. Bioessays, 2012, 34, 187-93.

 

2011

Tan, M., Luo, H., Lee, S., Jin, F., Yang, J.-S., Montellier, E., Buchou,T., Cheng, Z., Rousseaux, S., Rajagopal, N., Lu, Z., Ye, Z., Zhu, Q., Wysocka, J., Ye, Y., Khochbin, S., Ren, B., Zhao, Y., Identification of 67 histone marks and histone lysine crotonylation as a new type of Histone modification. Cell, 2011, 146, 1016-28.

Zhang, Z., Tan, M., Xie, Z., Dai, L., Chen, Y., and Zhao, Y., Identification of lysine   succinylation as a new post-translational modification. Nat Chem Biol, 2011, 7, 58-63.

Peng, C., Lu, Z., Xie, Z., Cheng, Z., Chen, Y., Tan, M., Luo, H., Zhang, Y., He, W., Yang, K., Zwaans, B.M. M., Tishkoff, D., Ho, L., Lombard, D., He, T.-C., Dai, J., Verdin, E., Ye, Y., Zhao, Y., The first identification of lysine malonylation substrates and its regulatory enzyme. Mol Cell Proteomics, 2011, 10, M111.012658.

Lu, J.-Y., Lin, Y.-Y., Sheu, J.-C., Wu, J.-T., Lee, F.-J., Chen, Y., Lin M.-I, Chiang, F.-T., Tai, T.-Y., Berger, S. L., Zhao, Y., Tsai K.-S., Zhu, H., Chuang, L.-M., and Boeke, J. D., Acetylation of Yeast AMPK Controls Intrinsic Aging Independently of Caloric Restriction. Cell, 2011, 146, 969-979.

Ghosh, S., Zhang, J., Zhao, Y., DePamphilis, M.L., and Vassilev, A.P., Assembly of the human origin recognition complex occurs through independent nuclear localization of its components. J Biol Chem, 2011, 286, 23831-41.

Samant, S.A., Courson, D.S., Sundaresan, N.R., Pillai, V.B., Tan, M., Zhao, Y., Shroff, S.G., Rock, R.S. and Gupta, M.P., HDAC3-dependent reversible lysine acetylation of cardiac myosin heavy chain isoforms modulates their enzymatic and motor activity. J Biol Chem, 2011, 286, 5567-77.

He, B.-C., Gao, J.-L., Zhang, B.-Q., Luo, Q., Shi, Q., Kim, S.H., Huang, E., Gao, Y., Yang, K., Wagner, E.R., Wang, L., Tang, N., Luo, J., Liu, X., Li, M., Shen, J., Luther, G., Hu, N., Zhou, Q., Luu, H.H., Haydon, R.C., Zhao, Y., He, T.C.,  Tetrandrine Inhibits Wnt/b-Catenin Signaling and Suppresses Tumor Growth of Human Colorectal Cancer. Mol Pharmacol2011, 79, 211-9.

Chu,C., Hou, H., Zhang, J., Phu, L., Loktev, A.V.,  Kirkpatrick, D.S.,  Jackson, P.J., Zhao, Y., Zou, H., A novel acetylation of β-tubulin by San modulates microtubule polymerization via down-regulating tubulin incorporation, Mol Biol Cell, 2011, 22, 448-56.

Lu, Z., Cheng, Z., Zhao, Y., Volchenboum ,S.L., Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation. PLoS One, 2011, 6, e28228.

Li, X., Wang, Q., Pan, N., Lee, S., Zhao, Y., Chait, B., Yue, Z. Phosphorylation-Dependent 14-3-3 Binding to LRRK2 Is Impaired by Common Mutations of Familial Parkinson’s Disease. PLoS One, 2011, 6, e17153.

Song, H., Li, C.-W., Labaff, A.M., Lim, S.-O., Li, L., Kan, S.-F., Chen, Y., Zhang, K., Lang, J., Xie, X., Wang, Y., Huo, L., Hsu, S.-C., Chen, X.,Zhao, Y., Hung, M.-C., Acetylation of EGF receptor contributes to tumor cell resistance to Histone deacetylase inhibitors. Biochem Biophys Res Commun, 2011, 404, 68–73.