Regulated degradation of the inner nuclear membrane protein SUN2 maintains nuclear envelope architecture and function

Abstract

Nuclear architecture and functions depend on dynamic interactions between nuclear components (such as chromatin) and inner nuclear membrane (INM) proteins. Mutations in INM proteins interfering with these interactions result in disease. However, mechanisms controlling the levels and turnover of INM proteins remain unknown. Here, we describe a mechanism of regulated degradation of the INM SUN domain-containing protein 2 (SUN2). We show that Casein Kinase II and the C-terminal domain Nuclear Envelope Phosphatase 1 (CTDNEP1) have opposing effects on SUN2 levels by regulating SUN2 binding to the ubiquitin ligase Skp/Cullin1/F-BoxβTrCP (SCFβTrCP). Upon binding to phosphorylated SUN2, SCFβTrCP promotes its ubiquitination. Ubiquitinated SUN2 is membrane extracted by the AAA ATPase p97 and delivered to the proteasome for degradation. Importantly, accumulation of non-degradable SUN2 results in aberrant nuclear architecture, vulnerability to DNA damage and increased lagging chromosomes in mitosis. These findings uncover a central role of proteolysis in INM protein homeostasis.

A ubiquitin-proteasome pathway degrades the inner nuclear membrane protein Bqt4 to maintain nuclear membrane homeostasis

“…As homologs of Asi proteins are absent in S. pombe as in other species, INMAD mechanisms may be diverse among organisms. However, increasing evidence has shown that the degradation of INM proteins in plants and mammals also employs the UPS and Cdc48/p97 (Tsai et al, 2016; Huang et al, 2020; Krshnan et al, 2022), raising a general mechanism for INM protein degradation.…”

Dynamic regulation of LINC complex composition and function across tissues and contexts

“…However, numerous studies have identified mechanoresponsive post‐transcriptional control over SUN2 levels, suggesting a role for regulated protein degradation pathway. Interestingly, insight into the possible mechanisms at play came from other experimental angles: the study of integral INM protein turnover [41] and crosstalk between lipid composition at the INM and the nuclear envelope proteome [42] (Fig. 3).…”

“…3). Carvalho and colleagues, focusing on defining mechanisms of protein turnover at the INM, honed in on predicted binding sites for degradation by the Skp1/Cullin/F‐Box family of ubiquitin ligase complexes, specifically containing the F‐Box member βTrCP, in SUN2 [41]. Importantly, SCF βTrCP typically requires phosphorylation of its recognition site in client proteins, opening up an attractive avenue by which signaling pathways could impinge of SUN2 protein levels.…”

“…(1) When SUN2 (perhaps as a monomer or trimer) engages the INM with its amphipathic helix (AH, orange) in its nucleoplasmic domain (which may prefer regions with membrane packing defects [42]), it is stabilized. (2) Loss of engagement of the AH may permit phosphorylation of nearby ‘site 2’ (and possibly ‘site 1’) by casein kinase II (CK‐II), which is antagonized by the phosphatase CTDNEP1 [41]. (3) Phosphorylation of ‘site 2’ leads to binding of SCF βTrCP , engagement of p97, and extraction and proteasome‐mediated turnover of SUN2.…”

Differential reliance of CTD-nuclear envelope phosphatase 1 on its regulatory subunit in ER lipid synthesis and storage

“…We had previously shown that ER expansion interferes with chromosome segregation causing higher rates of micronuclear formation (Merta et al, 2021), suggesting a link between dysregulated lipid synthesis and chromosomal instability in cancer cells. CTDNEP1 influences the lipid profile of the inner nuclear membrane (INM) as well as the stability of the inner nuclear envelope protein Sun2 through direct membrane sensing mechanism (Krshnan et al, 2022; Lee et al, 2023). CTDNEP1 has been implicated in regulating BMP signaling (Satow et al, 2006; Sakaguchi et al, 2013; Hayata et al, 2015; Darrigrand et al, 2020), which also involves nuclear envelope-associated proteins (Bengtsson, 2007).…”