The National Institute of Diabetes & Digestive & Kidney Diseases

The endoplasmic reticulum (ER) is the major site of protein biosynthesis in eukaryotes. Polypeptides entering the ER may frequently encounter folding problems, resulting in aggregation-prone, misfolded proteins. To preserve ER homeostasis, eukaryotes have evolved a conserved quality control pathway termed retrotranslocation or dislocation, which eliminates unwanted proteins in the ER by exporting them into the cytosol for degradation by the ubiquitin proteasome system. Defect in retro-translocation results in the accumulation of misfolded proteins and causes ER stress, which has been implicated in the pathogenesis of many human diseases including type 2 diabetes and several types of neurodegenerative diseases. The retro-translocation pathway is also hijacked by certain viruses to destroy folded cellular proteins required for anti-viral defense. This allows viruses to evade host immune surveillance. The molecular mechanism of retrotranslocation is not well understood. For example, it is not well understood how cells can distinguish misfolded polypeptides from those that are in the folding process. How misfolded substrates are selectively targeted to the site of translocation in the ER membrane, and subsequently transferred across the membrane are completely unknown. The identity of the protein-conducting channel for retro-translocation is still under debate. In addition, how viruses exploit this cellular pathway during their invasion into host cells is unclear. We have previously identified a cytosolic ATPase called p97, which provides the driving force to move substrates into the cytosol during retro-translocation. We also discovered a membrane protein complex that interacts with p97 to mediate the transport of substrates into the cytosol. The central component of this complex is Derlin-1, a conserved multi-spanning membrane protein postulated to form a protein channel. We are currently investigating the mechanism by which p97 act in retrotranslocation. We are also interested in identifying additional function of p97 by searching for novel p97 interaction partners.

Another project in the lab is to dissect the mechanism by which Lys48-linked polyubiquitin chains are formed on a substrate, a process essential for the degradation of misfolded ER proteins as well as many short-lived proteins in eukaryotes. It is known that ubiquitination requires the concerted action of three types of enzymes, an activating enzyme (E1), a conjugating enzyme (E2), and a ligase (E3). Most ubiquitin ligases use either a HECT (Homologous to E6-associated protein C-Terminus) or a RING (Really Interesting New Gene) domain to catalyze polyubiquitination, but the mechanism of E3 catalysis is poorly defined. We have established an in vitro ubiquitination system using recombinant Ube2g2 (E2) and gp78 (E3). We are investigating how these enzymes act to assemble Lys48-linked polyubiquitin chains.

Wang Q, Mora-Hensen H, Weniger M, Perez-Galan P, Wolford C, Hai T, Ron D, Chen W, Trenkle W, Wiestner A*, Ye Y* ERAD inhibitors integrate ER stress with an epigenetic mechanism to activate BH3-only protein NOXA in cancer cells Proc Natl Acad Sci U S A(106): 2200-2205, 2009. [Full Text/Abstract]

Li L, Soetandyo N, Ye Y The zince finger protein A20 targets TRAF2 to the lysosomes for degradation Biochim Biophys Acta (1793): 346-353, 2009. [Full Text/Abstract]

Wang Q, Li L, Ye Y Inhibition of p97-dependent protein degradation by Eeyarestatin I. J Biol Chem (283): 7445-7454, 2008. [Full Text/Abstract]

Li L, Hailey DW, Soetandyo N, Li W, Lippincott-Schwartz J, Shu HB, Ye Y Localization of A20 to a lysosome-associated compartment and its role in NFkappaB signaling. Biochim Biophys Acta (1783): 1140-1149, 2008. [Full Text/Abstract]

Lu Y, Lv Y, Ye Y, Wang Y, Hong Y, Fortini ME, Zhong Y, Xie Z A role for presenilin in post-stress regulation: effects of presenilin mutations on Ca2 currents in Drosophila. FASEB J, 2007. [Full Text/Abstract]

Li W, Tu D, Brunger AT, Ye Y A ubiquitin ligase transfers preformed polyubiquitin chains from a conjugating enzyme to a substrate. Nature(446): 333-337, 2007. [Full Text/Abstract]

Tu D, Li W, Ye Y, Brunger AT Inaugural Article: Structure and function of the yeast U-box-containing ubiquitin ligase Ufd2p. Proc Natl Acad Sci U S A(104): 15599-15606, 2007. [Full Text/Abstract]

Ye Y Diverse functions with a common regulator: Ubiquitin takes command of an AAA ATPase. J Struct Biol (156): 29-40, 2006. [Full Text/Abstract]

Seidner GA, Ye Y, Faraday MM, Alvord WG, Fortini ME Modeling clinically heterogeneous presenilin mutations with transgenic Drosophila. Curr Biol (16): 1026-1033, 2006. [Full Text/Abstract]

Wang Q, Li L, Ye Y Regulation of retrotranslocation by p97-associated deubiquitinating enzyme ataxin-3. J Cell Biol (174): 963-971, 2006. [Full Text/Abstract]

Ye Y, Shibata Y, Kikkert M, van Voorden S, Wiertz E, Rapoport TA Inaugural Article: Recruitment of the p97 ATPase and ubiquitin ligases to the site of retrotranslocation at the endoplasmic reticulum membrane. Proc Natl Acad Sci U S A (102): 14132-14138, 2005. [Full Text/Abstract]

Ye Y The role of the ubiquitin-proteasome system in ER quality control. Essays Biochem (41): 99-112, 2005. [Full Text/Abstract]

Ye Y, Shibata Y, Yun C, Ron D, Rapoport TA A membrane protein complex mediates retro-translocation from the ER lumen into the cytosol. Nature (429): 841-847, 2004. [Full Text/Abstract]

Ye Y, Meyer HH, Rapoport TA Function of the p97-Ufd1-Npl4 complex in retrotranslocation from the ER to the cytosol: dual recognition of nonubiquitinated polypeptide segments and polyubiquitin chains. J Cell Biol (162): 71-84, 2003. [Full Text/Abstract]

Tsai B#, Ye Y#, Rapoport TA Retro-translocation of proteins from the endoplasmic reticulum into the cytosol. Nat Rev Mol Cell Biol (3): 246-255, 2002. [Full Text/Abstract]

Ye Y, Meyer HH, Rapoport TA The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol. Nature (414): 652-656, 2001. [Full Text/Abstract]

Ye Y, Fortini ME Apoptotic activities of wild-type and Alzheimer''s disease-related mutant presenilins in Drosophila melanogaster. J Cell Biol (146): 1351-1364, 1999. [Full Text/Abstract]

Ye Y, Lukinova N, Fortini ME Neurogenic phenotypes and altered Notch processing in Drosophila Presenilin mutants. Nature (398): 525-529, 1999. [Full Text/Abstract]

Ye Y, Fortini ME Characterization of Drosophila Presenilin and its colocalization with Notch during development. Mech Dev (79): 199-211, 1998. [Full Text/Abstract]

# co-first author
* co-corresponding author