NEK9 regulates primary cilia formation by acting as a selective autophagy adaptor for MYH9/myosin IIA

Abstract

Autophagy regulates primary cilia formation, but the underlying mechanism is not fully understood. In this study, we identify NIMA-related kinase 9 (NEK9) as a GABARAPs-interacting protein and find that NEK9 and its LC3-interacting region (LIR) are required for primary cilia formation. Mutation in the LIR of NEK9 in mice also impairs in vivo cilia formation in the kidneys. Mechanistically, NEK9 interacts with MYH9 (also known as myosin IIA), which has been implicated in inhibiting ciliogenesis through stabilization of the actin network. MYH9 accumulates in NEK9 LIR mutant cells and mice, and depletion of MYH9 restores ciliogenesis in NEK9 LIR mutant cells. These results suggest that NEK9 regulates ciliogenesis by acting as an autophagy adaptor for MYH9. Given that the LIR in NEK9 is conserved only in land vertebrates, the acquisition of the autophagic regulation of the NEK9–MYH9 axis in ciliogenesis may have possible adaptive implications for terrestrial life.

Autophagy and the primary cilium in cell metabolism: What’s upstream?

“…The past several years have illuminated the cross-talk between the primary cilium and the two major cellular catabolic pathways, i.e., the autophagic pathway and the ubiquitin proteasomesystem (UPS) ( Orhon et al, 2015 ; Pampliega and Cuervo, 2016 ; Boukhalfa et al, 2019 ; Wiegering et al, 2019 ; Morel et al, 2021 ; Morleo et al, 2022 ; Senatore et al, 2022 ). Many studies have demonstrated that autophagy is engaged in the regulation of ciliogenesis by controlling the expression of factors such as IFT20 ( Pampliega et al, 2013 ), OFD1 ( Tang et al, 2013 ), MYH9/myosin 2 ( Yamamoto et al, 2021 ), CP110 ( Liu et al, 2021 ) or Kif19A ( Arora et al, 2020 ). As such, the word “ciliophagy” has been adequately introduced to designate the selective degradation of ciliary proteins by the autophagic pathway ( Cloonan et al, 2014 ).…”

Styxl2 regulatesde novosarcomere assembly by binding to non-muscle myosin IIs and promoting their degradation

“…p62/SQSTM1 and NBR1 have been shown to act as adaptors linking ubiquitinated substrates to Atg8/LC3 that is localized on the membrane of autophagosome (Kirkin et al, 2009; Pankiv et al, 2007). Interestingly, a recent study on ciliogenesis showed that MYH9 could be degraded by selective autophagy in an NEK9-mediated manner (Yamamoto et al, 2021). It remains to be tested whether NM IIs are ubiquitinated during the late stage of sarcomere assembly before their autophagy-dependent degradation and whether NEK9 is involved in this process.…”

Pathophysiology of Primary Cilia: Signaling and Proteostasis Regulation

“…An additional layer of complexity in the interplay between autophagy and ciliogenesis is represented by myosin heavy chain 9 (MYH9)/myosinIIA, a suppressor of actin dynamics and negative regulator of primary ciliogenesis ( Rao et al, 2014 ). During autophagy, NIMA-related kinase 9 (NEK9), by employing its LIR domain, binds MYH9 and facilitates its elimination through the autophagy machinery ( Yamamoto et al, 2021 ). NEK9 also controls the stability of the pericentriolar pool of OFD1, most likely acting through an unidentified adaptor-independent mechanism.…”

“…This hypothesis was supported by identification of LIR domains on OFD1 protein that directly interact with autophagosomal LC3/GABARAP proteins, mediating the elimination of the protein through the autophagy machinery ( Morleo et al, 2021 ). By promoting the autophagic removal of MYH9 and OFD1 protein complexes, NEK9 restores actin remodeling and promotes cilium elongation ( Yamamoto et al, 2021 ).…”