E3 Ubiquitin Ligase TRIP12: Regulation, Structure, and Physiopathological Functions

Abstract

The Thyroid hormone Receptor Interacting Protein 12 (TRIP12) protein belongs to the 28-member Homologous to the E6-AP C-Terminus (HECT) E3 ubiquitin ligase family. First described as an interactor of the thyroid hormone receptor, TRIP12's biological importance was revealed by the embryonic lethality of a murine model bearing an inactivating mutation in the TRIP12 gene. Further studies showed the participation of TRIP12 in the regulation of major biological processes such as cell cycle progression, DNA damage repair, chromatin remodeling, and cell differentiation by an ubiquitination-mediated degradation of key protein substrates. Moreover, alterations of TRIP12 expression have been reported in cancers that can serve as predictive markers of therapeutic response. The TRIP12 gene is also referenced as a causative gene associated to intellectual disorders such as Clark-Baraitser syndrome and is clearly implicated in Autism Spectrum Disorder. The aim of the review is to provide an exhaustive and integrated overview of the different aspects of TRIP12 ranging from its regulation, molecular functions and physio-pathological implications.

Keywords: E3 ubiquitin ligase; TRIP12; cancers; intellectual disorders.

Figure 1

Schematic representation of Thyroid hormone Receptor Interacting Protein 12 (TRIP12) mRNA (NM_004238.3) and TRIP12 protein (isoform c, NP_004229.1) with functional domains, kinase associated-phosphorylated residues and cysteine catalytic site (yellow star). UTR: Untranslated Region, CDS: Coding Sequence, PAS: Poly-Adenylation Signal, AAA: Poly-adenylated tail, ATG: translation Start codon, Stop: translation Stop codon, NLS: Nuclear Localization Signal, S: serine residue, aa: amino acid, IDR: Intrinsically Disordered Regions, ARM: Armadillo repeats, HECT: Homologous to the E6-AP C-Terminus.

Figure 2

Schematic representation of a multiple alignment of human TRIP12 isoforms using the COBALT multiple alignment tool (see Section Software and databases). TRIP12 isoform i (2068 aa) was defined as the sequence of reference (master sequence). The two most studied isoforms b and c (and size) are written in bold. Residues in green are identical and in red are different. The different domains of TRIP12 are indicated above the alignment.

Figure 3

Schematic representation of protein domains in TRIP12 orthologues. Domain boundaries were defined using InterProScan analysis. Percentage of identity was determined by Emboss matcher (see Section Software and databases) pairwise sequence alignment (using Homo sapiens TRIP12 protein sequence as reference [43]). *: Schmidtea mediterranea cDNA sequence was manually corrected to perform the analysis.

Figure 4

Post-translational modifications of TRIP12 (isoform c) adapted from PhosphoSitePlus^® (see Section Software and databases ). Total number of references represents the number of records in which this modification site was assigned using proteomic discovery mass spectrometry and using other methods. S stands for serine, T stands for threonine, Y stands for tyrosine, and K stands for lysine.

Figure 5

Schematic representation of human TRIP12-interacting protein–protein network (n = 76) and functional enrichment analysis using STRING software (see Section Software and databases). Network nodes represent proteins. Red nodes represent proteins belonging to cellular macromolecule metabolic process (GO term: 0044260), and purple nodes represent proteins belonging to the positive regulation of the nucleobase-containing compound metabolic process (GO-term: 0045935). Edges represent protein–protein molecular actions (indicated in the figure). Line shape indicates the predicted mode of action (indicated in the figure). Active interaction sources: text mining, experiments, databases, co-expression, neighborhood and co-occurrence. Minimum required interaction score: medium confidence (0.400). Green and orange filled circles indicate proteins implicated in “transcriptional regulation” and “ubiquitination/deubiquitination system”, respectively.

Figure 6

Schematic representation of TRIP12, ARF, and P53 pathway. On the left, TRIP12 controls ARF and indirectly P53 ubiquitination degradation by proteasome, while TRIP12 participates in cell cycle progression [58,75,96,115]. On the right, ARF is protected from TRIP12 when bound to nucleophosmin (NPM)/nucleostemin (NS) and localized in the nucleolus. Moreover, in the nucleoplasm, TRIP12 is sequestered by different proteins (in the presence of NS or TRADD and in high level c-MYC condition), blocking its interaction with ARF. ARF binds and inhibits MDM2, which leads to P53 accumulation and cell cycle arrest.

Figure 7

Schematic representation of TRIP12 in the DNA damage repair (DDR) pathway in response to DNA double-strand break (DSB) [14,39,115,118,119,120,121]. In response to double-strand breaks (DSB), ATM, RNF8, and RNF168 are recruited on the damage and trigger the propagation of the ubiquitination of H2A and H2AX far from the initial DNA lesions. TRIP12 controls the nuclear pool of RNF168 for the ubiquitination of chromatin after DNA disruption. Indeed, TRIP12 ubiquitinates and induces the degradation of RNF168 by the proteasome. TRIP12 controls Ubiquitin-Specific Peptidase 7 (USP7) ubiquitination, which in turn stabilizes it.

Figure 8

Schematic illustration of published TRIP12 gene mutations in intellectual disorders. Mutations in blue are missense, mutations in orange are nonsense, mutations in black are frameshift. Mutations in green are located in splice donor sites. From [10,142,143,144,145].

Figure 9

Copy number alterations (CNA) and mutations of the TRIP12 gene in human cancers in cBioPortal (see Section Software and databases) obtained from 176 non-redundant studies containing more than 100 cases with both mutations and CNA data (27,235 patients and 28,253 samples). Only cancer types with more than 1% of altered cases are represented.

Figure 10

Schematic representation of mutations on the TRIP12 gene in human cancers in cBioPortal (see Section Software and databases) obtained from 176 non-redundant studies containing more than 100 cases with both mutations and CNA data (27,235 patients and 28,253 samples). Mutation diagram circles are colored with respect to the corresponding mutation types indicated in the legend. In case of different mutation types at a single position, the color of the circle is determined with respect to the most frequent mutation type. Truncating mutations include nonsense, nonstop, frameshift deletion, frameshift insertion, and splice site. Inframe mutations include inframe deletion and inframe insertion.

Figure 11

TRIP12 mRNA expression level in 27 different types of cancer adapted from Gepia2 website (see Section Software and databases). Only tumor/normal tissue matched pairs with more than 25 cases were considered. Each dot represents a normal (green) or a tumor (red) sample. The horizontal black bar represents the mean. The TRIP12 mRNA level was obtained by RNA-seq and expressed as transcripts per million (TPM). Cancer types in which TRIP12 mRNA is statistically differentially expressed (ANOVA test with a q value < 0.01) are marked by an asterisk.