AbstractHuman Papilloma virus E6‐associated protein (E6‐AP), which is known as an E3 ubiquitin ligase, mediates ubiquitination and subsequent degradation of a series of cellular proteins. In this paper, we identify here trihydrophobin 1 (TH1), an integral subunit of the human negative transcription elongation factor (NELF) complex, as a novel E6‐AP interaction protein and a target of E6‐AP‐mediated degradation. Overexpression of E6‐AP results in degradation of TH1 in a dose‐dependent manner, whereas knock‐down of endogenous E6‐AP elevates the TH1 protein level. TH1 protein turnover is substantially faster, compared to controls, in cells that overexpressed E6‐AP. Wild‐type E6‐AP promotes the ubiquitination of TH1, while a catalytically inactive point mutant of E6‐AP abolishes its ubiquitination. Furthermore, in vitro ubiquitination assay also demonstrates that TH1 can be ubiquitinated by E6‐AP. The degradation is blocked by treatment with proteasome inhibitor MG132. Herein, we provide strong evidence that TH1 is a specific substrate that is targeted for degradation through E6‐AP‐catalyzed polyubiquitination. J. Cell. Biochem. 101: 167–180, 2007. © 2006 Wiley‐Liss, Inc.