**3.2 Ubiquitin (Ub): proteasome pathway (UPP)**

Intracellular proteins are degraded by the ubiquitin (Ub)–proteasome pathway (UPP). The UPP consists of enzymes, which attach polypeptide cofactor, Ub onto proteins, and tags them for degradation. This tagging process enables their recognition by the 26S proteasome (large multicatalytic protease complex that degrades ubiquitinated proteins to small peptides). The UPP selectively eliminates misfolded and damaged proteins that arise by missense or nonsense mutations, biosynthetic errors, or damage by oxygen radicals or by denaturation [25]. Three enzymatic components E1, E2, and E3 are required to link chains of Ub onto proteins destined for degradation. E1 or Ub-activating enzyme and E2s or Ub-carrier or conjugating proteins prepare Ub for conjugation and E3 or Ub-protein ligase, recognize specific protein substrate, and catalyze the transfer of activated Ub to it. The initial step in conjugation is activation of Ub at its C-terminus by the enzyme E1. After activation, Ub bound to E1 through thioester linkage is transferred to a sulfhydryl group. The E2s generally are small proteins, containing the cysteine that forms a thioester linkage with the activated Ub. The large number of E2s helps to generate the specificity of the ubiquitination system because specific E2s function in the degradation of various types of substrates, and they can conjugate with various E3s (**Figure 3**) [24, 26, 27].

#### **3.3 Autophagy**

Autophagy is a clearance mechanism that degrades damaged organelles and proteins. Normally, it is activated under stress conditions as a protective mechanism to ensure survival and cellular homeostasis by protein turnover. Autophagy is classified in three different categories, chaperone-mediated autophagy (CMA), microautophagy, and macroautophagy, depending on the mechanism used for the capture and degradation of substrates.

In CMA, proteins contain the pentapeptide KFERQ, which is recognized by the chaperone viz., heat shock protein 70 and transported to the lysosome for its hydrolysis. Lysosomes are sites for intracellular protein degradation, which involves uptake of secretory vesicles, portions of the cytoplasm, or whole organelles by lysosomes followed by enzymatic degradation. Microautophagy refers to a process in which some portions of the cytosol are trapped directly by the lysosome without the intervention of chaperones and macroautophagy involves sequestration of damaged organelles or large protein aggregates into cargo vesicles known as autophagosomes that transport the contents to the lysosome for its degradation (**Figure 4**) [28].

**Figure 3.**

*Picture depicting the process of misfolding protein correction using the ubiquitin (Ub)–proteasome pathway (UPP).*

#### **Figure 4.**

*The picture depicting the role of chaperones or heat shock protein in encountering the misfolding of protein and resolving it through different pathway.*
