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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A ubiquitin ligase-associated chaperone holdase maintains polypeptides in soluble states for proteasome degradation.
Wang Q, Liu Y, Soetandyo N, Baek K, Hegde R, Ye Y.
Mol Cell (2011 Jun 24) 42:758-70. Abstract/Full Text
Reversible inactivation of deubiquitinases by reactive oxygen species in vitro and in cells.
Lee JG, Baek K, Soetandyo N, Ye Y.
Nat Commun (2013) 4:1568. Abstract/Full Text
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

Additional Publications

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
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
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
Derlin2 protein facilitates HRD1-mediated retro-translocation of sonic hedgehog at the endoplasmic reticulum.
Huang CH, Hsiao HT, Chu YR, Ye Y, Chen X.
J Biol Chem (2013 Aug 30) 288:25330-9. 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
The E3 ubiquitin ligases Hrd1 and gp78 bind to and promote cholera toxin retro-translocation.
Bernardi KM, Williams JM, Kikkert M, van Voorden S, Wiertz EJ, Ye Y, Tsai B.
Mol Biol Cell (2010 Jan 1) 21:140-51. 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
Polyubiquitin chains: functions, structures, and mechanisms.
Li W, Ye Y.
Cell Mol Life Sci (2008 Aug) 65:2397-406. Abstract/Full Text
Localization of A20 to a lysosome-associated compartment and its role in NFkappaB signaling.
Li L, Hailey DW, Soetandyo N, Li W, Lippincott-Schwartz J, Shu HB, Ye Y.
Biochim Biophys Acta (2008 Jun) 1783:1140-9. 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
A role for presenilin in post-stress regulation: effects of presenilin mutations on Ca2+ currents in Drosophila.
Lu Y, Lv Y, Ye Y, Wang Y, Hong Y, Fortini ME, Zhong Y, Xie Z.
FASEB J (2007 Aug) 21:2368-78. Abstract/Full Text
A ubiquitin ligase transfers preformed polyubiquitin chains from a conjugating enzyme to a substrate.
Li W, Tu D, Brunger AT, Ye Y.
Nature (2007 Mar 15) 446:333-7. Abstract/Full Text
Regulation of retrotranslocation by p97-associated deubiquitinating enzyme ataxin-3.
Wang Q, Li L, Ye Y.
J Cell Biol (2006 Sep 25) 174:963-71. Abstract/Full Text
Modeling clinically heterogeneous presenilin mutations with transgenic Drosophila.
Seidner GA, Ye Y, Faraday MM, Alvord WG, Fortini ME.
Curr Biol (2006 May 23) 16:1026-33. Abstract/Full Text
Recruitment of the p97 ATPase and ubiquitin ligases to the site of retrotranslocation at the endoplasmic reticulum membrane.
Ye Y, Shibata Y, Kikkert M, van Voorden S, Wiertz E, Rapoport TA.
Proc Natl Acad Sci U S A (2005 Oct 4) 102:14132-8. Abstract/Full Text
A membrane protein complex mediates retro-translocation from the ER lumen into the cytosol.
Ye Y, Shibata Y, Yun C, Ron D, Rapoport TA.
Nature (2004 Jun 24) 429:841-7. Abstract/Full Text
Function of the p97-Ufd1-Npl4 complex in retrotranslocation from the ER to the cytosol: dual recognition of nonubiquitinated polypeptide segments and polyubiquitin chains.
Ye Y, Meyer HH, Rapoport TA.
J Cell Biol (2003 Jul 7) 162:71-84. Abstract/Full Text
The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol.
Ye Y, Meyer HH, Rapoport TA.
Nature (2001 Dec 6) 414:652-6. Abstract/Full Text
Apoptotic activities of wild-type and Alzheimer's disease-related mutant presenilins in Drosophila melanogaster.
Ye Y, Fortini ME.
J Cell Biol (1999 Sep 20) 146:1351-64. Abstract/Full Text
Neurogenic phenotypes and altered Notch processing in Drosophila Presenilin mutants.
Ye Y, Lukinova N, Fortini ME.
Nature (1999 Apr 8) 398:525-9. Abstract/Full Text