Expansion of DUB functionality generated by alternative isoforms – USP35, a case study

Abstract

Protein ubiquitylation is a dynamic post-translational modification that can be reversed by deubiquitylating enzymes (DUBs). It is unclear how the small number (∼100) of DUBs present in mammalian cells regulate the thousands of different ubiquitylation events. Here, we analysed annotated transcripts of human DUBs and found ∼300 ribosome-associated transcripts annotated as protein coding, which thus increases the total number of DUBs. By using USP35, a poorly studied DUB, as a case study, we provide evidence that alternative isoforms contribute to the functional expansion of DUBs. We show that there are two different USP35 isoforms that localise to different intracellular compartments and have distinct functions. Our results reveal that isoform 1 is an anti-apoptotic factor that inhibits staurosporine- and TNF-related apoptosis-inducing ligand (TRAIL; also known as TNFSF10)-induced apoptosis. In contrast, USP35 isoform 2 is an integral membrane protein of the endoplasmic reticulum (ER) that is also present at lipid droplets. Manipulations of isoform 2 levels cause rapid ER stress, likely through deregulation of lipid homeostasis, and lead to cell death. Our work highlights how alternative isoforms provide functional expansion of DUBs and sets directions for future research.This article has an associated First Person interview with the first author of the paper.

Regulatory interplay between deubiquitinating enzymes and cytokines

“…On the same line with BAP1, USP35 knockout also increased TRAIL sensitivity [74]. A study by Leznicki et al introduced three isoforms of USP3 in HEK293 cells: USP35 iso1 , USP35 iso2 and USP35 iso3 , although the focus was on the first two [74]. USP35 iso2 was revealed as an integral membrane protein on endoplasmic reticulum, while USP35 iso1 was identified as a cytosolic protein [74].…”

“…On the same line with BAP1, USP35 knockout also increased TRAIL sensitivity [74]. A study by Leznicki et al introduced three isoforms of USP3 in HEK293 cells: USP35 iso1 , USP35 iso2 and USP35 iso3 , although the focus was on the first two [74].…”

“…A study by Leznicki et al introduced three isoforms of USP3 in HEK293 cells: USP35 iso1 , USP35 iso2 and USP35 iso3 , although the focus was on the first two [74]. USP35 iso2 was revealed as an integral membrane protein on endoplasmic reticulum, while USP35 iso1 was identified as a cytosolic protein [74]. Moreover, the proteins that they interacted with also varied [74].…”

“…USP35 iso2 was revealed as an integral membrane protein on endoplasmic reticulum, while USP35 iso1 was identified as a cytosolic protein [74]. Moreover, the proteins that they interacted with also varied [74]. USP35 iso2 led to ER stress, BAP31 cleavage and activation of caspase-8 and caspase-3, resulting in apoptosis [74].…”

“…Moreover, the proteins that they interacted with also varied [74]. USP35 iso2 led to ER stress, BAP31 cleavage and activation of caspase-8 and caspase-3, resulting in apoptosis [74]. USP35 iso2 upregulated C/EBP homologous protein (CHOP) and DR5 in U2OSFIpIn and HeLa FIpIn cells [74].…”