The two most important biological machineries
The two most important biological machineries controlling proteostasis, PQC, and degradation are autophagy and the ubiquitin-proteasome system (UPS) (). Autophagy is a lysosome-dependent, tightly regulated catabolic process that degrades unwanted cell organelles and cytoplasmic constituents in lysosomes. Autophagy can be further distinguished as: macroautophagy, microautophagy and chaperone-assisted autophagy (including chaperone-mediated autophagy (CMA) and chaperone-assisted selective autophagy CASA)) , . Macroautophagy, often deregulated in disease conditions , involves the inclusion of cytosolic material, including cell organelles, into double-membraned vesicles termed autophagosomes , , . Autophagosomes then fuse with lysosomes or endosomes where vesicular constituents are degraded. Lysosomes are reformed and the degradation products are then released for intracellular recycling . Macroautophagy is therefore an essential mechanism for cellular indacaterol to environmental stress, for example, starvation-induced protein/lipid degradation via autophagy to mobilize diverse nutrient stores for anabolic purposes . Similar to starvation, sustained pressure overload of the heart due to biomechanical stress is also accompanied by the induction of autophagy , , . Microautophagy on the other hand refers to a direct engulfment of cytoplasmic components by lysosomes , while CMA and CASA involve chaperones like heat shock proteins such as BCL2-associated athanogene 3 (BAG3) , .
Ubiquitination, i.e. the covalent attachment of ubiquitin to the target protein, is a primary step in UPS mediated protein degradation. It is accomplished by three enzymatic steps: ubiquitin activation via the enzyme E1, ubiquitin conjugation via E2 conjugating enzyme and ubiquitin ligation by E3 ligase (). These ubiquitin marked, predominantly short-lived and misfolded proteins are subsequently degraded by 26S proteasome in ATP-dependent manner to maintain cell's youthful proteome , .
E3 ligases provide substrate recognition specificity
Ubiquitination diversity and substrate specificity in mammals is achieved by the existence of over six-hundred E3-ubiquitin ligases that catalyze the final step of ubiquitination, compared with only one E1 and very few E2 enzymes known till date . Based on their structural properties, E3 ligases are classified as: RING (really interesting new gene), HECT (homologous to E6AP C-terminus) and RBR (RING-between-RING) ligases . HECT and RBR E3 ligases carry a catalytic cysteine that accepts ubiquitin from E2∼ubiquitin complex to form an E3∼ubiquitin thioester intermediate, which subsequently transfers this ubiquitin to the substrate protein . In contrast, RING E3s, which constitute the most abundant ubiquitin ligases, catalyze the direct transfer of ubiquitin from E2∼ubiquitin complex to the substrate . Given the crucial role UPS plays in cardiac homeostasis, it is not surprising that several E3 enzymes have been implicated in various cardiac processes and pathologies like heart development, signaling cascades, ion channel regulation, autophagy regulation, protein degradation, congenital heart diseases and cardiomyopathies , .
TRIM E3 ubiquitin ligases The KEGG database shows that TRIMs belong to Ubiquitin ligases (E3), under the Single Ring-Finger type E3 class in Homo sapiens. With the concept that similar structures perform similar functions at biochemical level, the width of TRIM family grew significantly, now containing over 65 members , . The presence of numerous members in higher eukaryotes and species-specific roles of TRIMs suggest that the individual genes have evolved independently and their sequence and functions are highly maintained throughout speciation . TRIMs contain three highly conserved RING finger-B-Box-Coiled-coil domains at amino-terminal of individual members. These three motifs are highly conserved in humans in all individual member proteins, even if one of the domains is absent (Fig. 3). The remaining sequences however have evolved to acquire specific physiological functions through their carboxyl terminal motifs . The RING domain is one of the most prominent domains bestowing E3 ubiquitin ligases their property of covalently tagging specific proteins with ubiquitin from enzyme E2. This domain can recruit one or more ubiquitin moieties, resulting in mono- or poly-ubiquitination effecting different roles . As all TRIM family members contain a RING domain, they are thus potentially involved in ubiquitin conjugation to a specific substrate protein. Generally, TRIMs perform transfer of the ubiquitin by interacting with target proteins through their coiled coil domain .