DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis.

Amr Nassrallah ,Dominique Eeckhout ,Ikhlak Ahmed ,Gérald Zabulon ,Vanessa Masson ,Anne Flore Deton-Cabanillas ,David Stroebel ,Sandra Fonseca ,Bérangère Lombard ,Auguste Genovesio ,Vicente Rubio ,Cécile Breyton ,Elisa Iniesto ,Clara Bourbousse ,Chris Bowler ,Kris Gevaert ,Damarys Loew ,Martin Rougée ,Stéphanie Drevensek ,Ouardia Aït-Mohamed ,Geert De Jaeger ,Frédy Barneche

doi:10.7554/elife.37892

Abstract

DE-ETIOLATED 1 (DET1) is an evolutionarily conserved component of the ubiquitination machinery that mediates the destabilization of key regulators of cell differentiation and proliferation in multicellular organisms. In this study, we provide evidence from Arabidopsis that DET1 is essential for the regulation of histone H2B monoubiquitination (H2Bub) over most genes by controlling the stability of a deubiquitination module (DUBm). In contrast with yeast and metazoan DUB modules that are associated with the large SAGA complex, the Arabidopsis DUBm only comprises three proteins (hereafter named SGF11, ENY2 and UBP22) and appears to act independently as a major H2Bub deubiquitinase activity. Our study further unveils that DET1-DDB1-Associated-1 (DDA1) protein interacts with SGF11 in vivo, linking the DET1 complex to light-dependent ubiquitin-mediated proteolytic degradation of the DUBm. Collectively, these findings uncover a signaling path controlling DUBm availability, potentially adjusting H2Bub turnover capacity to the cell transcriptional status.

Highlights

DE-ETIOLATED 1 (DET1) is an evolutionarily conserved factor in multicellular organisms, acting in most instances to regulate gene expression through ubiquitin-mediated protein degradation
Our study further reveals that Arabidopsis SGF11 physically links deubiquitination module (DUBm) to the DDA1 C3D subunit in vivo and is subject to DET1-dependent ubiquitin-mediated degradation
To investigate how DET1 impacts on chromatin status, we tested whether histone post-translational modifications (PTMs) were affected in det1-1 mutant plants by conducting label-free quantitative mass spectrometry analysis of purified histones (Figure 1—figure supplement 1)

Summary

Introduction

DE-ETIOLATED 1 (DET1) is an evolutionarily conserved factor in multicellular organisms, acting in most instances to regulate gene expression through ubiquitin-mediated protein degradation. A currently accepted model in both plants and animals is that DET1 is an atypical DAMAGED DNA BINDING PROTEIN 1 (DDB1)-CULLIN4 (CUL4) Associated Factor (DCAF) acting with the small DDA1 (DET1-DDB1-Associated 1) protein to provide specificity to one or more E3 CUL4-RING ubiquitin ligases (CRL4) (Chory, 2010; Lau and Deng, 2012) For this activity, DET1 and DDA1, together with DDB1 and CONSTITUTIVE PHOTOMORPH OGENIC 10 (COP10) proteins, constitute a substrate adaptor module (COP10-DET1-DDB1-DDA1; hereafter termed C3D) within CRL4 complexes (Irigoyen et al, 2014; Pick et al, 2007). We first provide evidence that DET1 is essential for the regulation of H2Bub levels over most genes by controlling the light-dependent degradation of a plant H2Bub deubiquitination module (DUBm) This DUBm comprises SGF11, UBP22 and ENY2, the Arabidopsis orthologous proteins of yeast Sgf, Ubp and Sus, respectively, which, in the absence of a predictable plant Sgf73-like subunit, appears to act independently from SAGA. This study uncovers a signaling path controlling global H2Bub levels, potentially fine-tuning gene transcriptional capacity or ‘regulatability’ during developmental responses to external cues

Results

Discussion

Methods and materials