E ligases provide substrate recognition specificity

E3 ligases provide substrate recognition specificity Ubiquitination Science Daily 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 [23]. 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 [25]. 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 [26]. In contrast, RING E3s, which constitute the most abundant ubiquitin ligases, catalyze the direct transfer of ubiquitin from E2∼ubiquitin complex to the substrate [26]. 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 [27], [28].
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 [29], [30]. 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 [31]. 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 [32]. 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 [33]. 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 [34]. All known vertebrate TRIMs are categorized in 11 distinct subclasses depending on the types of domains present at their carboxyl-terminals (Fig. 3) [29], [35]. Beyond conserved N-terminal domains, it is the C-terminal that provides specificity of interactions with other proteins. The subclass IV forms almost two third of the TRIM/RBCC family, possessing RFP- like B30.2 (PRY and SPRY) domains at C-terminal. While this ancient family has been reported to greatly diversify in vertebrates, in fish the B30.2 containing subclass appears prominent as well, with other human TRIMs having limited numbers of orthologues [36]. Moreover, Meroni and Diez-Roux (2005) have reported almost 20 members of TRIM family also in invertebrates. The TRIM E3 ubiquitin ligase family has emerged as a critical component in various cellular processes from cell development to apoptosis. For example, TRIM36 plays central role in arranging somites during Xenopus embryogenesis [37]; TRIM59 and TRIM44 promotes proliferation in colorectal cancer and testicular germ tumor, respectively [38], [39]; TRIM24, TRIM28 and TRIM33 are well established transcriptional intermediary factors α, β and γ, respectively [40], [41], [42]; TRIM13, TRIM21, and Muscle Ring Fingers (MuRFs) are involved in autophagy [43], [44], [45], [46]; TRIM5α trimerizes to induce defense against HIV [34], whereas, TRIM21 negatively regulates IFN beta production after pathogen-recognition via degradation of IRF3 [47]. Moreover, many TRIMs have been emerged as markers of carcinogenesis through their interaction with tumor protein p53 like TRIM24, TRIM28, TRIM29, and TRIM32 [48], [49], [50], [51]. Interestingly, we found that TRIM is the major ‘single ring finger family’ that is known to be involved in cardiac pathophysiology including cardiomyocyte differentiation, signaling, apoptosis, cardiac hypertrophy/atrophy/ischemia, and dilated cardiomyopathy (Supplementary Table 1 and Supplementary Fig. 1).