Yihong Ye, Ph.D.
Photo of Yihong Ye
Scientific Focus Areas: Cell Biology, Chemical Biology, Molecular Biology and Biochemistry, Neuroscience, Genetics and Genomics


A selection of recent and significant publications can be viewed below.

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Unconventional secretion of misfolded proteins promotes adaptation to proteasome dysfunction in mammalian cells.
Lee JG, Takahama S, Zhang G, Tomarev SI, Ye Y.
Nat Cell Biol (2016 Jul) 18:765-76. Abstract/Full Text
UFMylation of RPL26 links translocation-associated quality control to endoplasmic reticulum protein homeostasis.
Wang L, Xu Y, Rogers H, Saidi L, Noguchi CT, Li H, Yewdell JW, Guydosh NR, Ye Y.
Cell Res (2020 Jan) 30:5-20. Abstract/Full Text
A myosin-7B-dependent endocytosis pathway mediates cellular entry of α-synuclein fibrils and polycation-bearing cargos.
Zhang Q, Xu Y, Lee J, Jarnik M, Wu X, Bonifacino JS, Shen J, Ye Y.
Proc Natl Acad Sci U S A (2020 May 19) 117:10865-10875. Abstract/Full Text
Filamentous recombinant human Tau activates primary astrocytes via an integrin receptor complex.
Wang P, Ye Y.
Nat Commun (2021 Jan 4) 12:95. Abstract/Full Text
Abnormal triaging of misfolded proteins by adult neuronal ceroid lipofuscinosis-associated DNAJC5/CSPα mutants causes lipofuscin accumulation.
Lee J, Xu Y, Saidi L, Xu M, Zinsmaier K, Ye Y.
Autophagy (2023 Jan) 19:204-223. Abstract/Full Text

Additional Publications

Safeguarding Lysosomal Homeostasis by DNAJC5/CSPα-Mediated Unconventional Protein Secretion and Endosomal Microautophagy.
Lee J, Xu Y, Ye Y.
Front Cell Dev Biol (2022) 10:906453. Abstract/Full Text
Graph Convolutional Network-Based Screening Strategy for Rapid Identification of SARS-CoV-2 Cell-Entry Inhibitors.
Gao P, Xu M, Zhang Q, Chen CZ, Guo H, Ye Y, Zheng W, Shen M.
J Chem Inf Model (2022 Apr 25) 62:1988-1997. Abstract/Full Text
Mitoxantrone modulates a heparan sulfate-spike complex to inhibit SARS-CoV-2 infection.
Zhang Q, Radvak P, Lee J, Xu Y, Cao-Dao V, Xu M, Zheng W, Chen CZ, Xie H, Ye Y.
Sci Rep (2022 Apr 15) 12:6294. Abstract/Full Text
Clearing Traffic Jams During Protein Translocation Across Membranes.
Wang L, Ye Y.
Front Cell Dev Biol (2020) 8:610689. Abstract/Full Text
Chaperoning transmembrane helices in the lipid bilayer.
Zhang Q, Ye Y.
J Cell Biol (2021 Jan 4) 220. Abstract/Full Text
Heparan sulfate assists SARS-CoV-2 in cell entry and can be targeted by approved drugs in vitro.
Zhang Q, Chen CZ, Swaroop M, Xu M, Wang L, Lee J, Wang AQ, Pradhan M, Hagen N, Chen L, Shen M, Luo Z, Xu X, Xu Y, Huang W, Zheng W, Ye Y.
Cell Discov (2020 Nov 4) 6:80. Abstract/Full Text
A spiral path to unfolding.
Ye Y, Xia D.
Nat Struct Mol Biol (2019 Sep) 26:763-765. Abstract/Full Text
AAGAB Controls AP2 Adaptor Assembly in Clathrin-Mediated Endocytosis.
Gulbranson DR, Crisman L, Lee M, Ouyang Y, Menasche BL, Demmitt BA, Wan C, Nomura T, Ye Y, Yu H, Shen J.
Dev Cell (2019 Aug 19) 50:436-446.e5. Abstract/Full Text
Discovery of Irreversible p97 Inhibitors.
Ding R, Zhang T, Wilson DJ, Xie J, Williams J, Xu Y, Ye Y, Chen L.
J Med Chem (2019 Mar 14) 62:2814-2829. Abstract/Full Text
To Build by Destruction.
Wang L, Ye Y.
Mol Cell (2018 Nov 15) 72:605-607. Abstract/Full Text
The Roles of Endo-Lysosomes in Unconventional Protein Secretion.
Lee J, Ye Y.
Cells (2018 Nov 3) 7. Abstract/Full Text
Regulation of protein homeostasis by unconventional protein secretion in mammalian cells.
Ye Y.
Semin Cell Dev Biol (2018 Nov) 83:29-35. Abstract/Full Text
Secretion of misfolded cytosolic proteins from mammalian cells is independent of chaperone-mediated autophagy.
Lee J, Xu Y, Zhang T, Cui L, Saidi L, Ye Y.
J Biol Chem (2018 Sep 14) 293:14359-14370. Abstract/Full Text
Proteomic characterization of endogenous substrates of mammalian ubiquitin ligase Hrd1.
Ye Y, Baek SH, Ye Y, Zhang T.
Cell Biosci (2018) 8:46. Abstract/Full Text
Nonenzymatic acetylation of ubiquitin Lys side chains is modulated by their neighboring residues.
Lee SY, Choi YS, Kim EH, Cheong HK, Lee YJ, Lee JG, Ye Y, Ryu KS.
FEBS J (2018 Apr) 285:1277-1289. Abstract/Full Text
DNAJC5 facilitates USP19-dependent unconventional secretion of misfolded cytosolic proteins.
Xu Y, Cui L, Dibello A, Wang L, Lee J, Saidi L, Lee JG, Ye Y.
Cell Discov (2018) 4:11. Abstract/Full Text
The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress.
Wang X, Chemmama IE, Yu C, Huszagh A, Xu Y, Viner R, Block SA, Cimermancic P, Rychnovsky SD, Ye Y, Sali A, Huang L.
J Biol Chem (2017 Sep 29) 292:16310-16320. Abstract/Full Text
A Mighty "Protein Extractor" of the Cell: Structure and Function of the p97/CDC48 ATPase.
Ye Y, Tang WK, Zhang T, Xia D.
Front Mol Biosci (2017) 4:39. Abstract/Full Text
Ufd2p synthesizes branched ubiquitin chains to promote the degradation of substrates modified with atypical chains.
Liu C, Liu W, Ye Y, Li W.
Nat Commun (2017 Feb 6) 8:14274. Abstract/Full Text
The HECT domain ubiquitin ligase HUWE1 targets unassembled soluble proteins for degradation.
Xu Y, Anderson DE, Ye Y.
Cell Discov (2016) 2:16040. Abstract/Full Text
Lunapark Is a Component of a Ubiquitin Ligase Complex Localized to the Endoplasmic Reticulum Three-way Junctions.
Zhao Y, Zhang T, Huo H, Ye Y, Liu Y.
J Biol Chem (2016 Aug 26) 291:18252-62. Abstract/Full Text
Doa1 is a MAD adaptor for Cdc48.
Zhang T, Ye Y.
J Cell Biol (2016 Apr 11) 213:7-9. Abstract/Full Text
gp78 functions downstream of Hrd1 to promote degradation of misfolded proteins of the endoplasmic reticulum.
Zhang T, Xu Y, Liu Y, Ye Y.
Mol Biol Cell (2015 Dec 1) 26:4438-50. Abstract/Full Text
In Search of a Cure for Proteostasis-Addicted Cancer: A AAA Target Revealed.
Xia D, Ye Y.
Cancer Cell (2015 Nov 9) 28:550-552. Abstract/Full Text
Bag6 complex contains a minimal tail-anchor-targeting module and a mock BAG domain.
Mock JY, Chartron JW, Zaslaver M, Xu Y, Ye Y, Clemons WM Jr.
Proc Natl Acad Sci U S A (2015 Jan 6) 112:106-11. Abstract/Full Text
Cleaning up in the endoplasmic reticulum: ubiquitin in charge.
Christianson JC, Ye Y.
Nat Struct Mol Biol (2014 Apr) 21:325-35. Abstract/Full Text
Role of HERP and a HERP-related protein in HRD1-dependent protein degradation at the endoplasmic reticulum.
Huang CH, Chu YR, Ye Y, Chen X.
J Biol Chem (2014 Feb 14) 289:4444-54. Abstract/Full Text
Dimeric Ube2g2 simultaneously engages donor and acceptor ubiquitins to form Lys48-linked ubiquitin chains.
Liu W, Shang Y, Zeng Y, Liu C, Li Y, Zhai L, Wang P, Lou J, Xu P, Ye Y, Li W.
EMBO J (2014 Jan 7) 33:46-61. Abstract/Full Text
USP13 antagonizes gp78 to maintain functionality of a chaperone in ER-associated degradation.
Liu Y, Soetandyo N, Lee JG, Liu L, Xu Y, Clemons WM Jr, Ye Y.
Elife (2014) 3:e01369. Abstract/Full Text
A ubiquitin-like domain recruits an oligomeric chaperone to a retrotranslocation complex in endoplasmic reticulum-associated degradation.
Xu Y, Liu Y, Lee JG, Ye Y.
J Biol Chem (2013 Jun 21) 288:18068-76. Abstract/Full Text
Bag6/Bat3/Scythe: a novel chaperone activity with diverse regulatory functions in protein biogenesis and degradation.
Lee JG, Ye Y.
Bioessays (2013 Apr) 35:377-85. Abstract/Full Text
Roles of p97-associated deubiquitinases in protein quality control at the endoplasmic reticulum.
Liu Y, Ye Y.
Curr Protein Pept Sci (2012 Aug) 13:436-46. Abstract/Full Text
TorsinA participates in endoplasmic reticulum-associated degradation.
Nery FC, Armata IA, Farley JE, Cho JA, Yaqub U, Chen P, da Hora CC, Wang Q, Tagaya M, Klein C, Tannous B, Caldwell KA, Caldwell GA, Lencer WI, Ye Y, Breakefield XO.
Nat Commun (2011 Jul 12) 2:393. Abstract/Full Text
Proteostasis regulation at the endoplasmic reticulum: a new perturbation site for targeted cancer therapy.
Liu Y, Ye Y.
Cell Res (2011 Jun) 21:867-83. Abstract/Full Text
The ERAD inhibitor Eeyarestatin I is a bifunctional compound with a membrane-binding domain and a p97/VCP inhibitory group.
Wang Q, Shinkre BA, Lee JG, Weniger MA, Liu Y, Chen W, Wiestner A, Trenkle WC, Ye Y.
PLoS One (2010 Nov 12) 5:e15479. Abstract/Full Text
The p97 ATPase dislocates MHC class I heavy chain in US2-expressing cells via a Ufd1-Npl4-independent mechanism.
Soetandyo N, Ye Y.
J Biol Chem (2010 Oct 15) 285:32352-9. Abstract/Full Text
Multilayered mechanism of CD4 downregulation by HIV-1 Vpu involving distinct ER retention and ERAD targeting steps.
Magadán JG, Pérez-Victoria FJ, Sougrat R, Ye Y, Strebel K, Bonifacino JS.
PLoS Pathog (2010 Apr 29) 6:e1000869. Abstract/Full Text
Role of intramembrane charged residues in the quality control of unassembled T-cell receptor alpha-chains at the endoplasmic reticulum.
Soetandyo N, Wang Q, Ye Y, Li L.
J Cell Sci (2010 Apr 1) 123:1031-8. Abstract/Full Text
Building ubiquitin chains: E2 enzymes at work.
Ye Y, Rape M.
Nat Rev Mol Cell Biol (2009 Nov) 10:755-64. Abstract/Full Text
Ubiquilin and p97/VCP bind erasin, forming a complex involved in ERAD.
Lim PJ, Danner R, Liang J, Doong H, Harman C, Srinivasan D, Rothenberg C, Wang H, Ye Y, Fang S, Monteiro MJ.
J Cell Biol (2009 Oct 19) 187:201-17. Abstract/Full Text
Mechanistic insights into active site-associated polyubiquitination by the ubiquitin-conjugating enzyme Ube2g2.
Li W, Tu D, Li L, Wollert T, Ghirlando R, Brunger AT, Ye Y.
Proc Natl Acad Sci U S A (2009 Mar 10) 106:3722-7. Abstract/Full Text
ERAD inhibitors integrate ER stress with an epigenetic mechanism to activate BH3-only protein NOXA in cancer cells.
Wang Q, Mora-Jensen H, Weniger MA, Perez-Galan P, Wolford C, Hai T, Ron D, Chen W, Trenkle W, Wiestner A, Ye Y.
Proc Natl Acad Sci U S A (2009 Feb 17) 106:2200-5. Abstract/Full Text
The zinc finger protein A20 targets TRAF2 to the lysosomes for degradation.
Li L, Soetandyo N, Wang Q, Ye Y.
Biochim Biophys Acta (2009 Feb) 1793:346-53. Abstract/Full Text
Inhibition of p97-dependent protein degradation by Eeyarestatin I.
Wang Q, Li L, Ye Y.
J Biol Chem (2008 Mar 21) 283:7445-54. Abstract/Full Text
Structure and function of the yeast U-box-containing ubiquitin ligase Ufd2p.
Tu D, Li W, Ye Y, Brunger AT.
Proc Natl Acad Sci U S A (2007 Oct 2) 104:15599-606. Abstract/Full Text
Last Reviewed June 2023