Sorting Nexins in Protein Homeostasis

Abstract

Protein homeostasis is maintained by removing misfolded, damaged, or excess proteins and damaged organelles from the cell by three major pathways; the ubiquitin-proteasome system, the autophagy-lysosomal pathway, and the endo-lysosomal pathway. The requirement for ubiquitin provides a link between all three pathways. Sorting nexins are a highly conserved and diverse family of membrane-associated proteins that not only traffic proteins throughout the cells but also provide a second common thread between protein homeostasis pathways. In this review, we will discuss the connections between sorting nexins, ubiquitin, and the interconnected roles they play in maintaining protein quality control mechanisms. Underlying their importance, genetic defects in sorting nexins are linked with a variety of human diseases including neurodegenerative, cardiovascular diseases, viral infections, and cancer. This serves to emphasize the critical roles sorting nexins play in many aspects of cellular function.

Keywords: autophagy; endosome; lysosome; proteasome; retromer; sorting nexins; ubiquitin.

Figure 1

Sorting nexins and ubiquitin coordinate the three distinct but interconnected protein proteolysis pathways. In the endo-lysosomal pathway, membrane proteins are sorted at the early endosome. Cargos destined for lysosomal degradation are marked by ubiquitination and internalized using endosomal sorting complexes required for transport pathways (ES). Cargos destined for recycling are retrieved either by the retromer or retrieval complex (R & R) coupled with various subclasses of sorting nexins (SNX- see text for details). In the autophagy-lysosome pathway (ALP) cargos are sequestered to the vacuole by double-membraned vesicles called autophagosomes by selective or non-selective mechanisms. Selective pathways in yeast are mediated by SNX-Bar heterodimers. In mammalian cells, the recognition of selective autophagy cargos is dependent upon ubiquitination (Ub). The ubiquitin-proteasomal system (UPS) targets short-lived regulatory proteins that are selectively targeted and degraded. TGN- trans-Golgi network, SNX-sorting nexin. In cells, the TGN and nucleus are in close proximity, whereas here they are drawn apart for clarity.

Figure 2

Structural classification of SNX subfamilies. The domain architecture describes the functional domains within different SNX subfamilies. The phox homology (PX) domain denotes the highly conserved lipid-binding domain that unifies the SNX protein family. It enables SNXs to bind to specific phosphoinositides (PtdIns) which mark different membrane surfaces. SNX-BAR (Bin/Amphiphysin/Rvs) proteins contain coiled-coil regions that enhance membrane binding, membrane remodeling, and protein-protein interactions. PDZ (postsynaptic density 95/discs large/zonula occludens) domains, FERM (protein 4.1/ezrin/radixin/moesin) domains, SH3 (SRC homology 3) domains, MIT (microtubule interacting and trafficking) domains, and Kinesin motor domains play a role in membrane binding, substrate recognition, kinase activity regulation, protein trafficking, and binding/movement along microtubules. The color code signifies yeast and mammalian homologs.

Figure 3

The role of SNXs in mammalian endocytosis. Transmembrane proteins are internalized into early endosomes from the plasma membrane by the endocytosis pathway. From here they are sorted through the complex and dynamic endomembrane network that consists of three different endosome vesicles (early, late, and recycling). Retrograde transport of membrane proteins requires recycling endosomes and the trans-Golgi network (TGN) for delivery back to the plasma membrane by the secretory pathway. Degradation of membrane proteins requires multiple rounds of cargo sorting and intra-luminal vesicle (ILV) biogenesis and fusion of the late endosome with the lysosome to form endo-lysosomes. Here ILVs and their accompanying cargos are degraded. The traced box at the bottom of the diagram is a zoomed-in schematic of sorting at endosomal membranes. It indicates that ubiquitinated membrane proteins destined for lysosomal proteolysis mediated by the ESCRT pathway. Transmembrane proteins are sorted by retromer and retrieval complexes aided by the actin remodeling WASH complex. Only SNX17 associates with the retriever and cooperates with the CCC complex to mediate endosomal trafficking. The retromer complex controls the recycling of a wide range of different cargos in cooperation with multiple SNX proteins including SNX3 and SNX27. Ub—Ubiquitin; CCC—CCDC22, CCDC93, and COMMD; WASH—Wiskott–Aldrich syndrome protein and SCAR homolog; ESCRT—endosomal sorting complexes required for transport.

Figure 4

Sorting nexins play critical roles in autophagy following starvation stress. (A) In mammalian cells, SNX4/SNX7 and SNX18 are required for autophagy-dependent localization of ATG16 and ATG9 from recycling endosomes to the pre-autophagosomal site (PAS). ATG9 containing vesicles are required for PAS formation and autophagosome biogenesis. (B) In yeast, Snx4-Atg20 (Snx42) and Snx4-Snx41 heterodimers regulate different forms of selective autophagy.

Figure 5

Med13 is destroyed either by the UPS or Snx4-Atg20 mediated autophagic degradation following cell death (left) or survival signals (right). Cartoon outlining stress-dependent fates of cyclin C and Med13, two members of the Cdk8 Kinase module (CKM). Here the subcellular address of cyclin C following stress mediates cell fate decisions by affecting mitochondria morphology. See text for details and [111,171,172,181].