The role of ubiquitin in autophagy has so far been ascribed as a signal for cargo degradation. Ubiquitination of aggregate prone proteins, as well as bacteria and mitochondria, has been found to serve as a signal for recognition by autophagy receptors like p62 and NBR1, which are themselves also degraded together with the cargo that they associate with [83] . The in vivo specificity of p62 and NBR1 toward ubiquitin signals remains to be established under the different physiological conditions. Interestingly, it was recently found that casein kinase 2-(CK2-) mediated phosphorylation of the p62 UBA domain increases the binding affinity of this motif for polyubiquitin chains leading to more efficient targeting of polyubiquitinated proteins to autophagy [121] . CK2 overexpression or phosphatase inhibition reduced the formation of aggregates containing the polyglutamine-expanded huntingtin exon1 fragments in a p62-dependent manner. The E3 ligases involved in ubiquitination of different autophagic cargo largely remains to be identified. However, it is known that the E3 ligases Parkin and RNF185 both regulate mitophagy [122, 123] . SMURF1 (SMAD-specific E3 ubiquitin protein ligase 1) was recently also implicated in mitophagy, as well as in autophagic targeting of viral particles [79] . Interestingly, the role of SMURF1 in selective autophagy seems to be independent of its E3 ligase activity, but it rather depends on its membrane-targeting C2 domain, although the exact mechanism involved remains to be elucidated. It is also not clear whether ubiquitination could serve as a signal to regulate the activity or binding selectivity of proteins directly involved in autophagy, and whether this in some way could regulate selective autophagy. The role of ubiquitinlike proteins as SUMO and Nedd in autophagy is also unexplored.