Rhomboid Family Pseudoproteases Use the ER Quality Control Machinery to Regulate Intercellular Signaling

Abstract

SummaryIntramembrane proteolysis governs many cellular control processes, but little is known about how intramembrane proteases are regulated. iRhoms are a conserved subfamily of proteins related to rhomboid intramembrane serine proteases that lack key catalytic residues. We have used a combination of genetics and cell biology to determine that these “pseudoproteases” inhibit rhomboid-dependent signaling by the epidermal growth factor receptor pathway in Drosophila, thereby regulating sleep. iRhoms prevent the cleavage of potential rhomboid substrates by promoting their destabilization by endoplasmic reticulum (ER)-associated degradation; this mechanism has been conserved in mammalian cells. The exploitation of the intrinsic quality control machinery of the ER represents a new mode of regulation of intercellular signaling. Inactive cognates of enzymes are common, but their functions are mostly unclear; our data indicate that pseudoenzymes can readily evolve into regulatory proteins, suggesting that this may be a significant evolutionary mechanism.

A Conserved Protein with AN1 Zinc Finger and Ubiquitin-like Domains Modulates Cdc48 (p97) Function in the Ubiquitin-Proteasome Pathway

“…Rhomboid proteases are polytopic membrane proteins bearing a protease active site deep within the lipid bilayer (56). It may be relevant in this context that some eukaryotic rhomboid and pseudorhomboid proteins function in ERAD (57,58). In eukaryotes, Zf_AN1 domains are commonly part of proteins that also contain ubiquitin, polyubiquitin, or ubiquitinlike sequences; however, the domain order in the protein is often permuted relative to Cuz1.…”

ERAD‐dependent control of the Wnt secretory factor Evi

“…Following coordinated recognition and delivery to membrane‐embedded ubiquitination machineries, ERAD substrates are retrotranslocated across the ER membrane into the cytosol through the AAA‐ATPase VCP (also known as p97) and degraded by 26S proteasomes (Ye et al , 2001; Vembar & Brodsky, 2008; Smith et al , 2011; Olzmann et al , 2015). Since ERAD‐dependent quality control has been linked to a range of cellular processes and human diseases (Zettl et al , 2011; Guerriero & Brodsky, 2012; Perrody et al , 2016), understanding its molecular mechanisms is an important step to develop potential treatment strategies (Tsai & Weissman, 2010; Hetz et al , 2013). In addition to its role in protein quality control of nascent polypeptides, ERAD has been implicated in regulating the abundance of mature proteins in response to changes in physiological conditions (Wiertz et al , 1996a,b; Sever et al , 2003; Brodsky & Fisher, 2008; Adle et al , 2009; Foresti et al , 2013; Avci et al , 2014; van den Boomen et al , 2014).…”

New insights into parasite rhomboid proteases

“…The iRhom family of pseudoproteases, which evolved from rhomboid proteases that lost their catalytic activity but retained their localization and the ability to bind their substrates, may provide additional regulatory functions. These pseudoproteases were recently shown to regulate the function of their active counterparts by promoting endoplasmic reticulum-associated degradation of the substrates [9]. Phylogeny studies revealed that the iRhoms are highly conserved in all animal species and are hence under selective pressure [23].…”

“…The most recent classification of the rhomboid family in eukaryotes [5] proposed an organisation into three groups: Rhomboid-like proteases (active rhomboids); iRhoms (inactive rhomboids) harbouring three specific features [9] -a longer Nterminal cytoplasmic domain, a large and conserved loop 1 domain (corresponding to the iRhom homology domain IRHD), and an invariant proline residue N-terminus to the predicted catalytic serine (GPxx replacing the GxSx rhomboid catalytic motif usually present in the transmembrane domain 4); and other inactive rhomboid-like proteins that cannot be assigned to either of the previous groups. The rhomboid-like proteases can be further classified according to their intracellular localization in the secretory pathway or mitochondria.…”