Quality control mechanisms that protect nuclear envelope identity and function

Abstract

The nuclear envelope (NE) is a specialization of the endoplasmic reticulum with distinct biochemistry that defines inner and outer membranes connected at a pore membrane that houses nuclear pore complexes (NPCs). Quality control mechanisms that maintain the physical integrity and biochemical identity of these membranes are critical to ensure that the NE acts as a selective barrier that also contributes to genome stability and metabolism. As the proteome of the NE is highly integrated, it is challenging to turn over by conventional ubiquitin-proteasome and autophagy mechanisms. Further, removal of entire sections of the NE requires elaborate membrane remodeling that is poorly understood. Nonetheless, recent work has made inroads into discovering specializations of cellular degradative machineries tailored to meeting the unique challenges imposed by the NE. In addition, cells have evolved mechanisms to surveil and repair the NE barrier to protect against the deleterious effects of a breach in NE integrity, in the form of either a ruptured NE or a dysfunctional NPC. Here, we synthesize the most recent work exploring NE quality control mechanisms across eukaryotes.

Figure 1.

The NE in metazoans and S. cerevisiae. A schematic of the NE and associated proteins in metazoan (left) and S. cerevisiae cells (right). Relative positions of nups mentioned in the text shown within the NPC scaffold, which consists of the inner ring (yellow) and outer ring (green). Cytosolic filaments (blue) and nuclear basket (red) also shown. SPB, spindle pole body.

Figure 2.

ERAD and INMAD. (A) Schematic of ERAD of a hypothetical substrate. (1) Upon binding the substrate, Hrd1 receives multiple ubiquitin moieties (sequentially) from an E2 such as Ubc7 and transfers them to the substrate (black). (2) The substrate is retrotranslocated from the ER membrane into the cytosol in a manner dependent on the Cdc48/p97 complex and a retrotranslocon channel formed by Hrd1. (3) The substrate is recruited to the proteasome, where it is degraded. (B) INMAD is required for clearing INM proteins through a mechanism similar to ERAD, but instead of Hrd1, the Asi complex or other E3 ubiquitin ligase/retrotranslocon channels are used. INMAD is also used to degrade orphan subunits (light blue) of ER complexes as depicted: (1) Multiprotein complexes are too large to diffuse past the peripheral channels between the NPC and the POM, but orphan subunits can. (2) Asi2 then binds the orphaned substrate via its transmembrane domain; Asi1 receives a ubiquitin moiety from an E2 such as Ubc7 and transfers it to the substrate. (3) The orphaned substrate is retrotranslocated from the INM into the nucleus in a manner dependent on the Cdc48/p97 complex and a retrotranslocon channel likely formed by the Asi complex. (4) The orphaned substrate is recruited to the proteasome, where it is degraded.

Figure 3.

Proposed models of nucleophagy and NPC-phagy. (A) Schematic of two proposed models of Atg39-mediated nucleophagy. Model 1: (1) Atg39 binds the INM through its lumenal amphipathic helices (red and orange) and condenses, which contributes to both INM and ONM remodeling to evaginate the INM. (2) An INM fission event (depicted by red arrows) generates an intralumenal vesicle containing nuclear (purple hexagons)/INM cargo (Heh1 as model INM cargo shown). (3) ONM scission releases a double-membrane NE-fragment containing the lumenal vesicle that is (4) recognized by the phagophore membrane by direct engagement between Atg8 and the AIM (blue) of Atg39. (5) The autophagosome fuses with the vacuole, releasing the NE fragment into the lumen of the vacuole. Model 2: (1) Atg39 condensation drives INM and ONM remodeling and the evagination of the INM. (2) Scission of the ONM and INM occur simultaneously, resulting in an NE-derived vesicle that can be (3) captured by a phagophore. (4) The autophagosome fuses with the vacuole, releasing the NE fragment into the lumen of the vacuole. (B) (a) A schematic of nucleoporinophagy. A free pool of Nup159 is selectively targeted by the phagophore via the binding of Atg8 to the AIM on Nup159 (blue). (b) A schematic of a proposed model of membrane remodeling during NPC-phagy. (1) NPCs cluster, and the NE herniates toward the cytosol. (2 and 3) In one or two membrane fission steps (red arrows), an NE-derived vesicle with multiple NPCs is released from the nucleus. This structure can be selectively recognized by a phagophore via Atg8 and the AIM on Nup159.