Proteomic analysis identifies novel binding partners of BAP1.

Roy Baas,Haico Van Attikum,Onno B Bleijerveld,Titia K Sixma,Fenna J Van Der Wal,Paul J Galardy

doi:10.1371/journal.pone.0257688

Abstract

BRCA1-associated protein 1 (BAP1) is a tumor suppressor and its loss can result in mesothelioma, uveal and cutaneous melanoma, clear cell renal cell carcinoma and bladder cancer. BAP1 is a deubiquitinating enzyme of the UCH class that has been implicated in various cellular processes like cell growth, cell cycle progression, ferroptosis, DNA damage response and ER metabolic stress response. ASXL proteins activate BAP1 by forming the polycomb repressive deubiquitinase (PR-DUB) complex which acts on H2AK119ub1. Besides the ASXL proteins, BAP1 is known to interact with an established set of additional proteins. Here, we identify novel BAP1 interacting proteins in the cytoplasm by expressing GFP-tagged BAP1 in an endogenous BAP1 deficient cell line using affinity purification followed by mass spectrometry (AP-MS) analysis. Among these novel interacting proteins are Histone acetyltransferase 1 (HAT1) and all subunits of the heptameric coat protein complex I (COPI) that is involved in vesicle formation and protein cargo binding and sorting. We validate that the HAT1 and COPI interactions occur at endogenous levels but find that this interaction with COPI is not mediated through the C-terminal KxKxx cargo sorting signals of the COPI complex.

Highlights

Ubiquitination of proteins can have a big impact on protein behavior and lifetime by affecting protein degradation, translocation and conformational change resulting in altered cellular homeostasis
We validate that the Histone acetyltransferase 1 (HAT1) and complex I (COPI) interactions occur at endogenous levels but find that this interaction with COPI is not mediated through the C-terminal KxKxx cargo sorting signals of the COPI complex
BRCA1-associated protein 1 (BAP1) becomes activated by binding to ASXL proteins to form the polycomb repressive deubiquitinase (PR-deubiquitinating enzymes (DUBs)) complex

Summary

Introduction

Ubiquitination of proteins can have a big impact on protein behavior and lifetime by affecting protein degradation, translocation and conformational change resulting in altered cellular homeostasis. Because of this major impact, protein ubiquitination and deubiquitination needs to be carefully controlled by the cell. BRCA1-associated protein 1 (BAP1) is a polycomb repressive protein that belongs to the UCH class of DUBs. Upon recruitment to polycomb repressive elements on the genome it can deubiquitinate H2AK119ub via its catalytic cysteine C91, thereby affecting gene expression [1]. BAP1 in itself has little catalytic activity but becomes activated by ASXL1 or its paralogs ASXL2 or ASXL3 (here further referred to as ASXL), forming a polycomb repressive

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