The interaction of enzymes with environmental factors and their effect on function

In eukaryotic cells, a large number of proteins are transported to the 26S proteasome after modification with ubiquitin by special substrate receptors. The AAA-ATPase CDC48, its cofactors and other ubiquitin-binding factors appear to be involved in this process. However, the exact function of CDC48 and the interaction of the factors in degradation processes are not yet sufficiently understood. In this work, it was shown for the first time that the factors of substrate recruitment, multiubiquitylation and substrate transfer to the proteasome physically interact and form a network that specifically directs substrates to the proteasome. CDC48 plays a central role in this degradation pathway, as it works with the help of the cofactors UFD1/NPL4 in the recognition and transfer of the substrate to the E4 enzyme UFD2. Furthermore, CDC48 terminates ubiquitylation, which counteracts excessive formation of non-linear ubiquitin chains and thus optimizes the degradation process. Multiubiquitylation by UFD2 is coupled to the proteasome via the receptor proteins RAD23 and DSK2. The substrate is transported to the proteasome in a concerted mechanism that occurs via ternary complexes of RAD23, UFD2 and CDC48 or through association of the ubiquitin-binding factors involved on the proteasome. The substrate ubiquitylated by UFD2 in the presence of CDC48 can be specifically bound via the UBA domains of the receptors RAD23 and DSK2 and transferred to the proteasome. In vivo, the degradation pathway shown controls the inactivation of the transcription factor SPT23, which is significantly degraded via this UFD2-dependent degradation pathway. In addition, SPT23 appears to be degraded via a parallel degradation pathway using the protein RPN10. The proteolysis of misfolded proteins of the endoplasmic reticulum (ERAD) also occurs via the degradation pathway shown here.