Post-translational modification and protein sorting to small extracellular vesicles including exosomes by ubiquitin and UBLs

Abstract

Exosomes, a type of small extracellular vesicles (sEVs), are secreted membrane vesicles that are derived from various cell types, including cancer cells, mesenchymal stem cells, and immune cells via multivesicular bodies (MVBs). These sEVs contain RNAs (mRNA, miRNA, lncRNA, and rRNA), lipids, DNA, proteins, and metabolites, all of which mediate cell-to-cell communication. This communication is known to be implicated in a diverse set of diseases such as cancers and their metastases and degenerative diseases. The molecular mechanisms, by which proteins are modified and sorted to sEVs, are not fully understood. Various cellular processes, including degradation, transcription, DNA repair, cell cycle, signal transduction, and autophagy, are known to be associated with ubiquitin and ubiquitin-like proteins (UBLs). Recent studies have revealed that ubiquitin and UBLs also regulate MVBs and protein sorting to sEVs. Ubiquitin-like 3 (UBL3)/membrane-anchored Ub-fold protein (MUB) acts as a post-translational modification (PTM) factor to regulate efficient protein sorting to sEVs. In this review, we focus on the mechanism of PTM by ubiquitin and UBLs and the pathway of protein sorting into sEVs and discuss the potential biological significance of these processes.

Keywords: Exosome; Multivesicular body; Post-translational modification; Small extracellular vesicle; Ubiquitin; Ubiquitin-like protein.

Fig. 1

Types of extracellular vesicles. Extracellular vesicles (EVs) are divided into two types: microvesicles that are directly secreted from the plasma membrane and exosomes that are secreted via multivesicular bodies (MVBs). Microvesicles are relatively larger EVs with a diameter of 1000 nm. In contrast, exosomes are nanometer-sized vesicles with a diameter of ≤ 150 nm [–3]. MVBs may be released extracellularly as exosomes or fuse with lysosomes, which degrade the contents of the MVBs [3, 33]

Fig. 2

Protein sorting to small extracellular vesicles (sEVs) via ubiquitin-like protein 3 (UBL3) modification. UBL3 is a novel post-translational modification factor, specifically localised in MVB, and released in sEVs. Of the 1241 UBL3-interacting proteins identified through a comprehensive proteomics analysis, 29% were annotated as ‘extracellular vesicular exosomes’. The sorting of UBL3 target proteins is enhanced by UBL3 modification [32]

Fig. 3

Schematic illustration of small extracellular vesicle (sEV) sorting and secretion through multivesicular bodies (MVBs) by UBLs. UBLs (Ubiquitin, Nedd8, SUMO, ISG15, ATG12, and UBL3) are depicted as small ovals. Each UBL has various functions for the regulation of MVB formation and sEV secretion. The proteins of sEV undergo post-translational modification such as ubiquitination, SUMOylation and UBL3 modification [32, 85, 92, 95, 129, 130]. Sorting of a subset of proteins is controlled by these modifications. Compared with ubiquitin and SUMO, UBL3 is more specifically localised to MVB and enriched in sEV [32]. The formation of intraluminal vesicles (ILVs) and MVBs is also regulated by a subset of UBLs. TSG101 is modified by ISG15 [138], while Alix is interacted with ATG12-ATG3 [149]. These complexes influence the biogenesis of ILVs and MVB formation [, –153]. Crosstalk between these molecules plays an important role in the regulation of MVB and extracellular secretion to sEV [–38, 41]