Patrolling the nucleus: inner nuclear membrane-associated degradation

Abstract

Protein quality control and transport are important for the integrity of organelles such as the endoplasmic reticulum, but it is largely unknown how protein homeostasis is regulated at the nuclear envelope (NE) despite the connection between NE protein function and human disease. Elucidating mechanisms that regulate the NE proteome is key to understanding nuclear processes such as gene expression, DNA replication and repair as NE components, particularly proteins at the inner nuclear membrane (INM), are involved in the maintenance of nuclear structure, nuclear positioning and chromosome organization. Nuclear pore complexes control the entry and exit of proteins in and out of the nucleus, restricting movement across the nuclear membrane based on protein size, or the size of the extraluminal-facing domain of a transmembrane protein, providing one level of INM proteome regulation. Research in budding yeast has identified a protein quality control system that targets mislocalized and misfolded proteins at the INM. Here, we review what is known about INM-associated degradation, including recent evidence suggesting that it not only targets mislocalized or misfolded proteins, but also contributes to homeostasis of resident INM proteins.

Keywords: Asi complex; ERAD; INMAD; Inner nuclear membrane; Protein quality control.

Fig. 1

Post-translational mechanisms of INM homeostasis. a The diffusion retention model supports the idea that a NET (blue) is able to freely diffuse in and out of the nucleus as long as its cytoplasmic/nucleoplasmic domain is small enough to travel through the peripheral channel of NPCs (~ 60 kDa). NETs accumulate inside the nucleus by tethering to other nuclear factors such as chromatin (yellow) and/or lamins (green). b Using a sequence to signal a truncated version of karyopherin-α (green), an INM-bound NET (purple) is translocated through an NPC, followed by release of the karyopherin by association with Nup50/Nup2 (orange) or by other mechanisms. c Piecemeal nuclear autophagy (PMNA) occurs in the nuclei of yeast under nutrient deprivation, when sections of the INM are pinched off into the vacuole (yeast equivalent of the lysosome). PMNA is not known to occur in higher eukaryotes although there is evidence of autophagy of NE proteins (Dou et al. 2015). d Similar to ERAD, the INMAD pathway involves the ubiquitination of targets (yellow) by an E3 ligase containing a RING domain (blue–purple). Degradation of soluble targets may occur inside the nucleus by nuclear-localized proteasomes (gray). For membrane-bound targets, the Cdc48 AAA-ATPase may be involved in removal of the protein from the INM for degradation. Alternatively, retrotranslocation of the targets back to the ER for removal and processing by cytoplasmic ERAD machinery may occur

Fig. 2

INMAD is an extension of ERAD. Membrane-bound E3 ligases of budding yeast are depicted at the ER only (Hrd1, dark red), at the ER and INM (Doa10, green) and at the INM only (Asi complex, green–blue–purple). The Asi complex is composed of the RING domain-containing proteins Asi1 and Asi3, as well as an accessory protein, Asi2. ERAD components, such as the E2 conjugating enzymes Ubc6 (yellow) and Ubc7 (blue) as well as the AAA-ATPase Cdc48 (brown) participate in the targeting of substrates to proteasomes (gray) for degradation. These components are also found inside the nucleus and likely contribute to INMAD. Ubc6 and Ubc7 have been shown to be associated with Asi1 and Asi3 through bimolecular fluorescence complementation (Khmelinskii et al. 2014). Proteasomes and Cdc48 have also been localized to the nucleus (Chen et al. ; Gallagher et al. 2014)

Fig. 3

INMAD ubiquitination of Pom33 drives its INM distribution. a A pool of Pom33 (magenta) is ubiquitinated (yellow), and contributes to its INM distribution. b When ASI1 is deleted, Pom33 aggregates into one or more foci at the INM. These foci colocalize with a subset of Nups, such as Nup188 (purple). c When a single ubiquitin was added back to Pom33 at its N-terminus, Pom33 re-distributed in the INM, even in the absence of Asi1