CRL4AMBRA1 targets Elongin C for ubiquitination and degradation to modulate CRL5 signaling

Si‐Han Chen; Gwendolyn M Jang; Ruth Hüttenhain; David E Gordon; Dan Du; Billy W Newton; Jeffrey R Johnson; Joseph Hiatt; Judd F Hultquist; Tasha L Johnson; Yi‐Liang Liu; Lily A Burton; Jordan Ye; Kurt M Reichermeier; Robert M Stroud; Alexander Marson; Jayanta Debnath; John D Gross; Nevan J Krogan

doi:10.15252/embj.201797508

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Author Affiliations

Si‐Han Chen¹,²,³,⁴,
Gwendolyn M Jang¹,³,⁴,
Ruth Hüttenhain¹,³,⁴,
David E Gordon¹,³,⁴,
Dan Du⁵,
Billy W Newton¹,³,⁴,
Jeffrey R Johnson¹,³,⁴,
Joseph Hiatt⁶,⁷,⁸,⁹,
Judd F Hultquist¹,³,⁴,
Tasha L Johnson¹,³,⁴,
Yi‐Liang Liu¹⁰,
Lily A Burton¹¹,
Jordan Ye¹²,¹³,
Kurt M Reichermeier¹⁴,
Robert M Stroud³,¹⁰,
Alexander Marson³,⁸,⁹,¹⁵,¹⁶,¹⁷,
Jayanta Debnath¹²,¹³,
John D Gross³,¹¹ and
Nevan J Krogan (nevan.krogan{at}ucsf.edu)*,¹,³,⁴,¹³

¹Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, USA
²Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
³Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA
⁴Gladstone Institutes, San Francisco, CA, USA
⁵Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
⁶Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
⁷Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
⁸Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
⁹Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
¹⁰Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
¹¹Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
¹²Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
¹³Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
¹⁴California Institute of Technology, Pasadena, CA, USA
¹⁵Division of Infectious Diseases and Rheumatology, University of California, Berkeley, Berkeley, CA, USA
¹⁶Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
¹⁷Chan Zuckerberg Biohub, San Francisco, CA, USA

↵*Corresponding author. Tel: +1 415 476 2980; E‐mail: nevan.krogan{at}ucsf.edu

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Abstract

Multi‐subunit cullin‐RING ligases (CRLs) are the largest family of ubiquitin E3 ligases in humans. CRL activity is tightly regulated to prevent unintended substrate degradation or autocatalytic degradation of CRL subunits. Using a proteomics strategy, we discovered that CRL4^AMBRA¹ (CRL substrate receptor denoted in superscript) targets Elongin C (ELOC), the essential adapter protein of CRL5 complexes, for polyubiquitination and degradation. We showed that the ubiquitin ligase function of CRL4^AMBRA¹ is required to disrupt the assembly and attenuate the ligase activity of human CRL5^SOCS³ and HIV‐1 CRL5^VIF complexes as AMBRA1 depletion leads to hyperactivation of both CRL5 complexes. Moreover, CRL4^AMBRA¹ modulates interleukin‐6/STAT3 signaling and HIV‐1 infectivity that are regulated by CRL5^SOCS³ and CRL5^VIF, respectively. Thus, by discovering a substrate of CRL4^AMBRA¹, ELOC, the shared adapter of CRL5 ubiquitin ligases, we uncovered a novel CRL cross‐regulation pathway.

Synopsis

The ubiquitin E3 ligase CRL4^AMBRA¹ targets Elongin C (ELOC), the shared adapter of CRL5 ubiquitin ligases, for polyubiquitination and degradation, thereby modulating IL‐6/STAT3 signaling and HIV‐1 infectivity that are regulated by CRL5^SOCS³ and HIV‐1 CRL5^VIF, respectively.

Quantitative proteomics identifies ELOC as a novel substrate of CRL4^AMBRA1.
ELOC mediates the interaction between AMBRA1 and multiple CRL5 substrate receptors.
ELOC targeting by CRL4^AMBRA1 attenuates the ligase activity of CRL5^SOCS3 and HIV‐1 CRL5^VIF.
CRL4^AMBRA1 modulates CRL5^SOCS3‐ and HIV‐1 CRL5^VIF‐regulated functions.