Abstract
TRIM proteins constitute a large, diverse and ancient protein family which play a key role in processes including cellular differentiation, autophagy, apoptosis, DNA repair, and tumour suppression. Mostly known and studied through the lens of their ubiquitination activity as E3 ligases, it has recently emerged that many of these proteins are involved in direct RNA binding through their NHL or PRY/SPRY domains. We summarise the current knowledge concerning the mechanism of RNA binding by TRIM proteins and its biological role. We discuss how RNA-binding relates to their previously described functions such as E3 ubiquitin ligase activity, and we will consider the potential role of enrichment in membrane-less organelles.
Introduction
The control of gene products at the RNA and protein levels is an essential mechanism governing cellular fate. This post-transcriptional regulatory layer determines the location, quantity and time constraints of effector molecules required to respond to stimuli. Perturbations in the levels of these molecules caused by mutations in RNA-binding proteins (RBPs) often lead to diseases such as neurological disorders and cancer (Cooper et al., 2009). In recent decades, systems biology and the ‘omics’ revolution have greatly advanced our understanding of the global post-transcriptional changes that occur during various biological processes, including cell development and immune responses (Ahmad and Lamond, 2014; Angerer et al., 2017). In addition, methodological advances in the RNA field have expanded the number of putative RBPs (Baltz et al., 2012; Castello et al., 2012; Gerstberger et al., 2014; Dominguez et al., 2018; Hentze et al., 2018) and put a spotlight on low-affinity and multivalent protein-RNA interactions at the core of many important regulatory mechanisms (Jankowsky and Harris, 2015; Falkenberg et al., 2017). Among the newly identified RBPs, many lack classical RNA-binding domains (RBDs) such as the RNA recognition motif (RRM), the cold shock domain (CSD) and K-homology (KH) domain (Hentze et al., 2018). Instead, these proteins feature domains hitherto only known to be involved in protein-protein and protein-DNA interactions and include both structured and disordered regions (Hentze et al., 2018). The mechanisms of RNA association for the large number of newly identified RBPs remain to be elucidated, creating exciting new questions about the basis of RNA recognition in the cell. Several of the newly identified RBPs are members of the tripartite motif (TRIM) protein family, which will be the focus of this review.
From a biochemical point of view, TRIM proteins constitute one of the largest subfamilies of ubiquitin E3 ligases found in the animal kingdom (Crawford et al., 2018) (Figure 1). Although first thought to be metazoan-specific, members of this family have now been identified in plants and fungi, highlighting its long evolutionary history (Sardiello et al., 2008; Marín, 2012; Crawford et al., 2018). The TRIM family is characterised by the presence of three distinct N-terminal domains: the RING domain, one or two B-boxes, and a coiled-coil region (RBCC), invariably ordered in this sequence from N- to C-terminus (Reymond et al., 2001) (Figure 2). To date, at least 77 TRIM proteins have been identified in humans, some of which lack components of the RBCC region but are evolutionarily closely related (Hatakeyama, 2017). In addition, 18 TRIM family members have been identified in Caenorhabditis elegans, seven in Drosophila melanogaster and more than 200 in zebrafish, underscoring the functional adaptability of this tripartite domain arrangement across species (Reymond et al., 2001; Sardiello et al., 2008; Langevin et al., 2019).
Phylogeny of human TRIM proteins.
A phylogenetic tree based on the tripartite motif alone mostly reflects the natural classification of TRIM proteins based on the C-terminal domains. Proteins with an incomplete tripartite motif (except for loss of B-box1) were excluded from the analysis. Within the PRY/SPRY family, branches coloured in brown represent those where B-box1 is lost while it is maintained within those coloured in red. *Note that TRIM45 has a Filamin domain but no NHL domain.
The TRIM family includes more than 70 proteins in humans.
Shown are the RBCC (A) and BCC (B) motif-containing TRIM proteins, with numbers corresponding to individual TRIM genes. Members of the RBCC group were structurally classified into 11 subfamilies (I–XI) by Ozato et al. (2008) and are shown schematically. Asterisks (*) indicate the NHL and PRY/SPRY subfamilies discussed in this review that have clear RNA-binding evidence. (1): TRIM19 has isoform specific C-terminal domains (Nisole et al., 2005). (2): TRIM56 does not contain a canonical NHL domain (Liu et al., 2016).
RNA related functions have long been known for certain TRIM proteins (Fridell et al., 1995; Frank and Roth, 1998; Slack et al., 2000; Sonoda and Wharton, 2001) with the C-terminal domain playing a key role in these interactions (Sonoda and Wharton, 2001; Loedige et al., 2013). In 2014, in vitro evidence of direct RNA binding by TRIM proteins was presented for BRAT (BRAin Tumour), a member of the TRIM-NHL subfamily in Drosophila (Loedige et al., 2014). A few months earlier, mRNA interactome capture studies of HEK293, HeLa, and mouse embryonic stem cells (mESCs) had identified TRIM25, TRIM28, TRIM56 and TRIM71 as being RBPs (Baltz et al., 2012; Castello et al., 2012; Kwon et al., 2013). Recently, a more unbiased protein-RNA crosslinking capture study also added TRIM33, TRIM44 and TRIM26 to those above (Trendel et al., 2019), see Table 1). Mounting evidence of RNA binding in this family, in combination with the ubiquitination function of TRIM proteins, points to an involvement in systems that rapidly alter protein levels, stability and function in response to the presence of regulatory and scaffolding RNA molecules.
Table of all candidate RNA-binding human TRIM proteins covered in this review with relevant orthologs, biological functions and RNA binding domains.
| Name | Relevant orthologs | RNA binding domain | C-terminal domain | Biological functions | Key references |
|---|---|---|---|---|---|
| TRIM2 | BRAT, Mei-P26 (D. melanogaster), NHL-2, NCL-1 (C. elegans) | Unknown, NHL by homology | NHL | Neuronal development, long-term potentiation | Ohkawa et al. (2001); Balastik et al. (2008); Khazaei et al. (2011); Thompson et al. (2011); Chen et al. (2015); Tocchini and Ciosk (2015) |
| TRIM3 | BRAT, Mei-P26 (D. melanogaster), NHL-2, NCL-1 (C. elegans) | Unknown, NHL by homology | NHL | Neuronal development, long-term potentiation | Cheung et al. (2010); Chen et al. (2014); Schreiber et al. (2015); Tocchini and Ciosk (2015) |
| TRIM25 | N/A | PRY/SPRY and/or coiled coil | PRY/SPRY | Innate immunity, cell differentiation, morphogenesis, microRNA regulation | Orimo et al. (1999); Gack et al. (2007); Kwon et al. (2013); Choudhury et al. (2014); Sanchez et al. (2018) |
| TRIM26 | N/A | Unknown | PRY/SPRY | Innate immunity, DNA damage response | Wang et al. (2015); Treiber et al. (2017); Williams and Parsons (2018); Trendel et al. (2019) |
| TRIM28 | N/A | Unknown | Bromodomain | Regulation of histone modification, regulation of autophagy, DNA damage response, pluripotency maintenance | Czerwinska et al. (2017); Trendel et al. (2019) |
| TRIM32 | Abba (D. melanogaster), NHL-1 (C. elegans) | Unknown, NHL by homology | NHL | Cell differentiation, microRNA regulation | Frosk et al. (2002); Kudryashova et al. (2005, 2009); Schoser et al. (2005); Schwamborn et al. (2009); Tocchini and Ciosk (2015); Kumari et al. (2018) |
| TRIM33 | N/A | Unknown | Bromodomain | Cell differentiation, immune response, cell cycle regulation, DNA damage response | Kulkarni et al. (2013); Pommier et al. (2015); Gallouet et al. (2017); Tanaka et al. (2018); Ali et al. (2019); Trendel et al. (2019) |
| TRIM44 | N/A | Unknown | None | Occular development, innate immunity | Yang et al. (2013); Zhang et al. (2015b); Trendel et al. (2019) |
| TRIM56 | N/A | Unknown, NHL by homology | NHL-like | Innate immunity | Shen et al. (2012); Kwon et al. (2013); Tocchini and Ciosk (2015); Liu et al. (2016); Garcia-Moreno et al. (2018); Kumari et al. (2018); Trendel et al. (2019) |
| TRIM65 | N/A | Unknown | PRY/SPRY | microRNA regulation, innate immunity | Li et al. (2014); Lang et al. (2017) |
| TRIM71 | Wech (D. melanogaster), LIN41 (C. elegans) | NHL domain | NHL | Cell differentiation, miRNA regulation | Slack et al. (2000); Rybak et al. (2009); Loedige et al. (2013); Zou et al. (2013); Tocchini et al. (2014); Mitschka et al. (2015); Tocchini and Ciosk (2015); Nguyen et al. (2017); Kumari et al. (2018) |
TRIM proteins have roles in a wide range of biological processes such as cellular differentiation, autophagy, apoptosis, DNA repair and tumour suppression (Hatakeyama, 2017). Notably, over 20 members have been implicated in cell signalling pathways involved in innate immunity, having both positive and negative regulatory roles in the transcriptional activation of nuclear factor kappa-B (NF-κB) and interferon regulatory factors (IRFs) 3/7 required for the production of antiviral cytokines and interferons (van Gent et al., 2018). Some TRIM proteins can also target viral particles directly, as has been shown for TRIM5α in response to HIV infection (Pertel et al., 2011), or indirectly, in the case of TRIM21/Ro52 through association with antibody-coated virions (McEwan et al., 2011). The latter has implications in diseases such as Sjögren’s syndrome and congenital heart block in which autoantibodies against TRIM21/Ro52 are pathogenic (Ambrosi et al., 2014; Ambrosi and Wahren-Herlenius, 2015).
In addition, a number of family members are crucial in neuronal development, with specific roles in neurite growth (Hung et al., 2010), as well as axon guidance and polarisation (Khazaei et al., 2011; Menon et al., 2015; van Beuningen et al., 2015). These include members of the TRIM-NHL subfamily TRIM2, TRIM3 and TRIM32, as well as the SPRY-containing TRIM9, TRIM46 and TRIM67 (Schwamborn et al., 2009; Boyer et al., 2018). Transcriptional regulation has also been shown to be mediated by several TRIM proteins, specifically TRIM19/PML, TRIM24/TIF1α, TRIM28/TIF1β/KAP1, TRIM33 and TRIM66 (Cammas et al., 2012). Thus, the conserved RBCC motif is rather versatile and involved in a wide array of cellular pathways. Not surprisingly, members of the TRIM family have been implicated in both congenital and hereditary diseases. Mutations in TRIM18/MID1, for example, cause X-linked Opitz syndrome (De Falco et al., 2003). In addition, many different TRIM proteins have been connected to inflammatory diseases and cancer [reviewed in Hatakeyama (2011)]. In some cases, increased protein expression is associated with malignancy, while other TRIM proteins (e.g. TRIM3) promote cellular differentiation and have tumour suppressor roles (Hatakeyama, 2011; Chen et al., 2014).
The RBCC motif mediates ubiquitination
The most well-established biochemical function of TRIM proteins is the catalysis of the third step in the ubiquitination cascade, acting as RING E3 ligases to covalently modify protein substrates with ubiquitin (Ub) (Chu and Yang, 2010; Buetow and Huang, 2016) (Figure 3A, B). The RING domain mediates this reaction by binding the Ub-loaded E2 conjugating enzyme and positioning the Ub moiety in the correct orientation (Buetow and Huang, 2016) (Figure 3C). Upon association of the RING domain and the E2 Ub conjugate, a conserved cysteine in the E2 is poised for catalysis. The reaction typically results in the formation of an isopeptide bond between the carboxy-terminal glycine residue of Ub and a lysine residue on the substrate, although other residues can be involved (Buetow and Huang, 2016). In addition, TRIM proteins have been shown to become auto-ubiquitinated in a functionally relevant manner, such as in the case of TRIM5α and TRIM25 (Diaz-Griffero et al., 2006; Choudhury et al., 2017).
![Figure 3: Ubiquitination in the TRIM family.(A) The ubiquitination cascade involves an E1 activating enzyme that binds ATP and catalyses the formation of a thioester bond (represented by ~) with ubiquitin (Ub). The E2 conjugating enzyme transfers Ub to its cysteine active site to form a second thioester linkage. In the presence of a substrate (S) and a RING-containing TRIM protein, the latter can act as an E3 ligase to modify residues such as lysine on the substrate. (B) Different types of Ub linkages result in a range of chain lengths and topologies, which can have different downstream effects [see Akutsu et al. (2016) for a comprehensive review]. (C) RING-containing E3s associate with the Ub-conjugated E2 to aid catalysis. Shown is the crystal structure of the RING domain of TRIM25 in complex with Ub~UBCH5A (E2) (Koliopoulos et al., 2016) (PDB:5FER).](/document/doi/10.1515/hsz-2019-0158/asset/graphic/j_hsz-2019-0158_fig_003.jpg)
Ubiquitination in the TRIM family.
(A) The ubiquitination cascade involves an E1 activating enzyme that binds ATP and catalyses the formation of a thioester bond (represented by ~) with ubiquitin (Ub). The E2 conjugating enzyme transfers Ub to its cysteine active site to form a second thioester linkage. In the presence of a substrate (S) and a RING-containing TRIM protein, the latter can act as an E3 ligase to modify residues such as lysine on the substrate. (B) Different types of Ub linkages result in a range of chain lengths and topologies, which can have different downstream effects [see Akutsu et al. (2016) for a comprehensive review]. (C) RING-containing E3s associate with the Ub-conjugated E2 to aid catalysis. Shown is the crystal structure of the RING domain of TRIM25 in complex with Ub~UBCH5A (E2) (Koliopoulos et al., 2016) (PDB:5FER).
With multiple ligation cycles, the target protein can become multi-mono-ubiquitinated and poly-ubiquitinated, resulting in chains of various topologies and lengths (Figure 3B) [see Akutsu et al. (2016) for a comprehensive review]. The diversity in the locations and types of ubiquitin linkages makes this post-translational modification highly versatile. Lysine 48 (K48) ubiquitination, for instance, normally targets proteins for degradation through the proteasome system. Sequence motifs present in a protein substrate that regulate its stability through ubiquitin-mediated degradation or ubiquitin-independent pathways are called degrons. These are short linear motifs that are important for substrate targeting but are not themselves ubiquitinated (Meszaros et al., 2017). Due to the lack of sufficient data it is difficult, however, to define a degron motif for TRIM family members at this point. In contrast to K48 linkages, ubiquitination through lysine 63 (K63) forms more linear ubiquitin chains with roles in DNA repair and endocytosis (Akutsu et al., 2016). Additionally, a relatively high number of TRIM members can add the Small Ubiquitin-like Modifier (SUMO) through interaction with the corresponding conjugating enzyme UBC9 (Chu and Yang, 2010). TRIM28, for instance, is able to modify IRF7 with SUMO, thereby inhibiting its activity (Liang et al., 2011). Additionally, TRIM25 can ligate the ubiquitin-like ISG15 protein to several substrates in response to viral infection (Martin-Vicente et al., 2017). Therefore, the TRIM family is able to catalyse a wide variety of modification and linkage types, consistent with its extensive involvement in many different biological pathways. Notably, some TRIM proteins like Drosophila BRAT do not contain a RING domain and it is unclear whether these can act as E3 ligases (Figure 2). However, in the case of TRIM16, co-immunoprecipitation studies showed that it can homo- and hetero-oligomerize with other TRIM members and have ubiquitination activity despite lacking a classical RING domain (Bell et al., 2012).
Higher order oligomerisation of the RING finger may be a general feature of this type of domain (Kentsis et al., 2002a,b). In the case of TRIM proteins, RING self-association has been demonstrated to be important for TRIM5α, TRIM25, TRIM32 and TRIM19/PML catalytic function (Ganser-Pornillos et al., 2011; Koliopoulos et al., 2016; Fletcher et al., 2018; Wang et al., 2018). In contrast to the cullin RING ligases that form multi-subunit ubiquitination complexes (Buetow and Huang, 2016), the TRIM family has been referred to as ‘single protein RING fingers’, alluding to the fact that substrate recruitment and catalysis occur through domains located on the same polypeptide chain (Meroni and Diez-Roux, 2005). However, the formation of multimeric structures observed with monomers of TRIM5α and TRIM32, for example, indicates that ordered aggregation may be necessary for full activity (Albor et al., 2006; Ganser-Pornillos et al., 2011). This is consistent with the observations that many TRIM members form subcellular compartments (Reymond et al., 2001).
Bioinformatic studies on the RBCC motif showed that it evolved as a functional unit rather than three separate domains, strongly suggesting that the RING domain is intricately linked structurally and functionally to the B-box (BB) and coiled-coil (CC) regions (Sardiello et al., 2008). The conservation of linker residues separating the different domains and the observation that the RBCC motif is often encoded by a single exon support this idea (Hennig et al., 2008; Sardiello et al., 2008). In addition, although the RING and first BB motifs have been lost in some TRIM members, the second BB and CC regions are highly conserved (Sardiello et al., 2008). The BB and CC domains are thought to enhance ubiquitination by promoting multimerisation and aiding in substrate recognition, as has been shown for TRIM5α and TRIM21 (Diaz-Griffero et al., 2006; Li and Sodroski, 2008). However, multimerisation may be context dependent: recent preprints describe the characterisation of the RBCC motif of TRIM28 in its entirety (Lim et al., 2018; Stoll et al., 2018). In both structural models, the RING and BB domains are in close proximity to the CC domain, which mediates dimerisation. One of the studies found that although the first BB of TRIM28 promoted oligomerisation, this was not essential for transcriptional silencing of retrotranposons in cell-based assays (Stoll et al., 2018). Thus, high order self-association through the RING and BB regions may only be necessary in some contexts and/or depend on additional factors (e.g. viruses) to occur (Ganser-Pornillos et al., 2011).
Diversity in the C-terminal domains
Although the N-terminal RBCC architecture is highly conserved and specific to the TRIM family, the C-terminal region contains a variety of domain organisations not specific to the group. These domains are involved in substrate recruitment by association with targets through both protein-protein and protein-RNA interactions, thereby localising ubiquitination substrates to the Ub-conjugated E2 bound by the RING domain (Gack et al., 2007; Biris et al., 2013; Zhang et al., 2017). Several classifications of the TRIM proteins have been conducted based on structural similarities and sequence homology of the RBCC and C-terminal regions, resulting in the establishment of up to 11 distinct subclasses (I to XI) (Figure 2) (Reymond et al., 2001; Short and Cox, 2006; Hennig et al., 2008; Ozato et al., 2008; Sardiello et al., 2008; Marín, 2012).
The most common C-terminal domain, found in subfamilies I and IV, is the Sp1A kinase and Ryanodine receptors (SPRY) domain present in ~50% of the family members (Figure 2). This region comprises ~140 residues that fold into a β-sandwich structure (Ozato et al., 2008). In many cases, N-terminal to this domain is the SPRY-associated (PRY) region that extends the domain to form a PRY/SPRY fusion, also known as the B30.2 or RFP-like domain (D’Cruz et al., 2013). Proteins lacking the PRY region also contain N-terminal extensions which, analogous to the PRY motif, form an integral part of the SPRY domain architecture (D’Cruz et al., 2013). The PRY/SPRY and related folds are classically known for mediating protein-protein interactions, having various roles in innate immune responses (see TRIM25 below) (D’Cruz et al., 2013). Often associated with the PRY/SPRY domain are the C-terminal subgroup One Signature (COS) domain, which associates with microtubules, and the fibronectin type III (FN3) domain, found in many extracellular matrix proteins (Ozato et al., 2008).
A smaller number of TRIM proteins contain the NCL-1, H2A, LIN-41 (NHL) domain, found in many proteins in eukaryotes and prokaryotes, and serving as binding interfaces for various interactions (Slack and Ruvkun, 1998). This domain folds into a β-propeller structure resembling the well-studied tryptophan-aspartic acid WD40 domain (Edwards et al., 2003). Studies on BRAT demonstrated association of its NHL domain with single-stranded RNA, and currently all members of the TRIM-NHL subfamily are thought to bind RNA (see below for details) (Loedige et al., 2013, 2014). Often associated with the NHL domain is the filamin (FIL) domain, which may localise the protein to the cytoskeleton through interactions with actin (Ozato et al., 2008). In a few members of the TRIM family there are also zinc-binding PHD finger and bromodomains known for their interaction with modified chromatin-associated histones during gene regulation (Ragvin et al., 2004). In addition, a few members contain the meprin and TRAF homology (MATH) and ADP ribosylation factor (ARF) domains, among others. Thus, the C-terminal domains mediate substrate specificity and confer TRIM proteins with a rich diversity of biological functions.
Several salient reviews on TRIM proteins have highlighted their role in immunity during viral infection (Nisole et al., 2005; Gack et al., 2007; Ozato et al., 2008; Sparrer and Gack, 2018; van Gent et al., 2018) and in disease processes (Hatakeyama, 2011; Tocchini and Ciosk, 2015; Hatakeyama, 2017; Watanabe and Hatakeyama, 2017; Crawford et al., 2018). For more focussed syntheses of TRIM protein function as ubiquitin E3 ligases, the reader is referred to overviews by Ikeda and Inoue (2012) and Ebner et al. (2017). In this review, we will focus on TRIM family members for which there exists clear evidence of RNA binding such as those containing the PRY/SPRY and NHL domains, and discuss potential functional and structural links between their ligase function and association with RNA.
TRIM-NHL proteins
The TRIM-NHL family is a relatively small subfamily which is defined by the presence of an NHL domain at the C-terminus (see Figure 4A). This family includes five members in humans (TRIM2, TRIM3, TRIM32, TRIM56 and TRIM71). Almost all of these proteins have six NHL repeat regions which together form an NHL domain.
Structure of the NHL domain and its RNA-binding site.
(A) Structure of the BRAT NHL domain from Edwards et al. (2003) with NHL repeats coloured according to their order from red to purple with a ‘top’ view on the left and a side view on the right. Blades and β-strands are also numbered according to convention. (B) Structure of UUGUUG bound BRAT-NHL from Loedige et al. (2015) (PDB:4ZLR). (C) Structure of TRIM71-NHL bound to a 13mer from the mab-10 3′UTR from Kumari et al. (2018) (PDB:6FQL).
The NHL domain is a β-propeller containing six blades each made up of four anti-parallel β-sheets named β-a to β-d (Figure 4A). Each blade is made up of three β-strands from one NHL repeat plus one β-strand from the previous NHL repeat, with the exception of the first blade which brings the N-terminal and C-terminal amino acids of the domain into contact. Blade I is made up of one β-strand from the N-terminus and three β-strands from the C-terminus. In the case of TRIM32, the fourth NHL repeat region is replaced with a sequence which, although compatible with β-strand formation, is not an NHL repeat (Slack and Ruvkun, 1998). However, it is not clear what effect this has on the structure of the domain.
The canonical NHL domain has a ‘top’ defined as the side on which the β-b to β-c loop is located (Edwards et al., 2003). So far, all known interactions of the NHL domain with RNA have been mediated by this ‘top’ surface (Loedige et al., 2015; Kumari et al., 2018). However, protein ligands can bind either the ‘top’ (Lee et al., 2006) or ‘bottom’ surface (Cho et al., 2006).
It has been noted that all TRIM-NHLs possess a positively charged ‘top’ surface, suggesting that RNA binding is a conserved feature of this protein family (Loedige et al., 2014). However, it has been proposed that the RNA targets and binding modes may vary widely between NHL domains (Kumari et al., 2018) as there are large differences in charge distributions and a general lack of conservation between most TRIM-NHL paralogs present in a given organism.
It has previously been noted that NHL domains bear a marked similarity to WD40 domains (Edwards et al., 2003). These were found to be enriched within the mESC mRNA interactome (Kwon et al., 2013) and display remarkable versatility in their interactions, including RNA binding (Lau et al., 2009; Stirnimann et al., 2010). It may therefore be helpful to consider the NHL domains within the broader context of RNA binding β-propellers.
RNA sequence preferences of TRIM-NHL proteins
The best understood TRIM-NHL protein, BRAT, was initially thought to bind RNA indirectly through its interaction with Pumilio (Pum) (Arama et al., 2000; Sonoda and Wharton, 2001) but has since been demonstrated to bind RNA directly (Loedige et al., 2014). NHL domains are now seen as crucial for RNA binding; for example, it was shown that swapping the NHL domains of TRIM71 and TRIM32 swapped their mRNA targets (Loedige et al., 2013).
RNAcompete (Ray et al., 2009) experiments identified UU[G/A]UU[G/A] and UUUACA as the RNA motifs for BRAT and its paralog Mei-P26 (both D. melanogaster proteins), respectively, (Loedige et al., 2015) while Davis et al. (2018) found that the C. elegans ortholog of Mei-P26, NHL-2, preferentially binds poly-uridine.
Binding motifs for TRIM71, LIN-41 and Wech (human, C. elegans and D. melanogaster orthologs, respectively) deviate substantially from those of the BRAT orthologues and are characterised by a single highly conserved adenine (Loedige et al., 2015). The lack of clear binding motifs found for TRIM71/LIN41 in this study may be explained by (Kumari et al., 2018)’s observation that binding to TRIM71 is dependent on the formation of a stem loop. Based on data from Loedige et al. (2015) and Laver et al. (2015), they demonstrated that while most NHL domains specify an RNA sequence motif, the NHL domain of LIN41/TRIM71 has a mixed motif dependent both on structure and sequence. Binding necessitates a stem-loop containing a three nucleotide loop with a strong preference for those containing a U-A base pair at the end of the stem and a purine at the third position in the loop. The importance of the interactions was confirmed by the subsequent finding that mutations in residues that interact with the adenine and the purine are linked to congenital hydrocephalus (Furey et al., 2018).
The two structurally characterised NHL domains BRAT and TRIM71 show very different RNA binding modes: the ‘top’ surface of BRAT-NHL has a sequence of grooves and clefts that accommodate specific bases lying flat along the NHL domain (six bases length total), whereas TRIM71 binds the trinucleotide loop of the stem loop end-on through a positively charged shallow central cavity (Loedige et al., 2015; Kumari et al., 2018) (Figure 4B and C). Thus, as for many other RBDs, for example, RRMs (Daubner et al., 2013), the adaptability of this domain architecture allows for a wide variety of RNA binding specificities and makes it currently impossible to predict this selectivity based on protein sequence or structure alone.
The NHL domain mediates both protein-protein and protein-RNA interactions. RNA binding to the NHL may be regulated by protein binding at nearby or overlapping sites. For example, the binding site for the protein Miranda on BRAT-NHL overlaps with that of RNA (Lee et al., 2006; Loedige et al., 2015). Miranda binding was shown to be inhibitory of RNA binding and is thought to be important in regulating mRNA transcriptional downregulation by BRAT.
Despite the sequence and structure specificity of NHL domains, binding can be relatively weak, with affinities in the lower micromolar range (Davis et al., 2018; Kumari et al., 2018). This is similar to RNA affinities of many other RBDs in isolation, like RRMs or CSDs, which also bind RNA in the low micromolar range (Maris et al., 2005; Hennig et al., 2014a) but increase affinity up to 1000-fold in the context of neighbouring domains or multi-RBP-RNA complexes due to cooperative binding (Hennig et al., 2014b). Similarly, for TRIM proteins the coiled-coil domain mediates dimerisation and thus each complex features two NHL domains. These could, for instance, reach across long stretches of RNA to bind to their preferred motifs on a single mRNA, which would in turn increase binding affinity of TRIM proteins to their respective RNA targets. This effect could be even further increased if, as suggested in (Koliopoulos et al., 2016), further RING-B-box mediated oligomerisation occurred (Figure 5). The functional consequence of TRIM-NHL mediated RNA binding will be reviewed and discussed in the next section.
Diagram showing how dimerisation and potentially oligomerisation as discussed in Koliopoulos et al. (2016) can drive higher affinity and selectivity in TRIM-NHL protein binding to RNA.
RNA-dependent functions of TRIM-NHL proteins
TRIM-NHL proteins carry out a variety of roles, many of them relating to the acquisition and maintenance of differentiated cellular identity as well as translation regulation (Tocchini and Ciosk, 2015). We will focus on roles that relate to RNA binding and regulation, as well as some of the functional parallels between paralogous and orthologous TRIM-NHL proteins.
BRAT, Mei-P26 and their orthologs
One of the best understood TRIM-NHL proteins is the D. melanogaster BRAT, which notably lacks an N-terminal RING domain and is involved in a variety of translational repression roles (Arvola et al., 2017). BRAT interference causes an increase in the levels of active Notch (NICD, Notch intra-cellular domain) and leads to cells with a more proliferative phenotype (Mukherjee et al., 2016).
BRAT segregates asymmetrically between D. melanogaster larval neuronal stem cells, leading to post-transcriptional dMyc inhibition through direct RNA binding and differentiation into a ganglion mother cell (Betschinger et al., 2006; Lee et al., 2006; Laver et al., 2015). During differentiation of ovarian germline stem cells into cytoblasts, BRAT interacts with Pum to repress Mad and cMyc (Harris et al., 2011). BRAT also drives the differentiation from neuroblasts to intermediate neural precursors through binding of deadpan and zelda mRNA at their 3′UTR and exploits the different affinities of these 3′UTRs to achieve different levels of repression (Reichardt et al., 2018). Furthermore, BRAT is involved in axon maintenance through translational repression of src64B, possibly by direct binding, and regulates neuromuscular synapse size and density by repressing Mad translation (Shi et al., 2013; Marchetti et al., 2014).
The earliest known function was discovered in Drosophila embryos, where BRAT controls body patterning by generating a gradient of the protein morphogen Hunchback. The fly embryo contains a uniform distribution of hunchback mRNA (Tautz, 1988) but has an anterior-posterior gradient in Nanos (Wang and Lehmann, 1991). BRAT interacts with Nanos and Pum to repress hunchback translation (Sonoda and Wharton, 2001; Arvola et al., 2017). The complex forms on the 3′UTR of hunchback mRNA through binding of Nanos response elements, themselves composed of two conserved boxes that bind BRAT and Pum-Nanos (Wharton and Struhl, 1991; Murata and Wharton, 1995; Loedige et al., 2014; Weidmann et al., 2016; Arvola et al., 2017).
The BRAT orthologs in humans are TRIM2 and TRIM3, two closely related proteins (67% identity). Although they are only distantly related to BRAT and have kept their RING domain, they play similar roles including regulating neuron polarisation, switching cells to asymmetric division and regulating NICD and cMyc [see Figure 2; Balastik et al. (2008); Khazaei et al. (2011); Chen et al. (2014); Tocchini and Ciosk (2015); Mukherjee et al. (2016); Kumari et al. (2018)].
Although little is known about the role of RNA binding in the function of TRIM2 and TRIM3, both are abundant constituents of mRNPs. They bind myosin V, which transports mRNPs to the synapse (Ohkawa et al., 2001; Kanai et al., 2004), but do not ubiquitinate myosin and are not essential for mRNP trafficking (Balastik et al., 2008; Schreiber et al., 2015). Both TRIM2 and TRIM3 have been linked to the regulation of long-term potentiation (Ohkawa et al., 2001; Cheung et al., 2010; Schreiber et al., 2015). The rapid changes in protein expression and stability involved in this synaptic plasticity could implicate both post-transcriptional and ubiquitination mediated regulation.
More closely related to BRAT but absent in vertebrates are Mei-P26 (D. melanogaster) and NHL-2 (C. elegans). Mei-P26 is a cofactor of the microRNA induced silencing complex (miRISC) where it interacts with Argonaute-1 to inhibit a variety of miRNAs, in particular bantam, a regulator of proliferation and apoptosis. Mei-P26 drives differentiation, suppresses mitotic proliferation and, like BRAT, suppresses dMyc expression (Neumuller et al., 2008). NHL-2 is also a cofactor of the miRISC (Hammell et al., 2009) but can also localise to peri-nuclear granules (P-granules) present in germline cells involved in mRNA regulation and potentially in totipotency maintenance (Wang and Seydoux, 2014; Davis et al., 2018), where it interacts with 22G-RNAs involved in the CSR and WAGO pathways, possibly determining the fate of a subset of 22Gs (Davis et al., 2018).
TRIM71, LIN41 and Wech
TRIM71 and its C. elegans ortholog LIN41 are enriched in processing bodies (P-bodies). There, they form part of the RISC complex and ubiquitinate Argonaute-2 as well as interacting with Dicer and regulating AGO-1 (Rybak et al., 2009; Zou et al., 2013). These interactions are decreased upon RNAse treatment indicating that it is at least partially mediated by RNA binding (Loedige et al., 2013). Once RNA binding has occurred, TRIM71 acts as a translational repressor through its CC-Filamin domain; this repression can occur independently of the RISC complex (Loedige et al., 2013). Similarly, LIN41 participates in both transcript degradation and translational repression. Interestingly, positioning of the LIN41 binding site at either the 5′UTR or 3′UTR was shown to regulate whether translational repression or transcript degradation, respectively, occurred (Aeschimann et al., 2017).
TRIM71/LIN41 acts as a ‘roadblock’ to differentiation. This activity is exercised, similarly to other TRIM-NHL proteins, in neuronal and germline cells (Tocchini et al., 2014; Mitschka et al., 2015). It represses various differentiation markers such as the transcription factor EGR1 and ccnd2 in neurons, in many cases through interactions with the 3′UTR, but does not appear to drive stem cell marker maintenance (Slack et al., 2000; Loedige et al., 2013; Worringer et al., 2014; Mitschka et al., 2015).
In adult neurons, LIN-41 promotes axon regeneration after injury and was shown to be involved in a negative regulation loop with its well established repressor let-7 through its regulation of the argonaute protein Alg-1 (Zou et al., 2013).
The TRIM71 D. melanogaster ortholog, Wech, has mostly been studied in relation to a potential role as a scaffolding protein at muscle attachment sites (Loer and Hoch, 2008; Loer et al., 2008) but, interestingly, has been shown to be protective against CAG-repeat based RNA toxicity (Shieh and Bonini, 2011).
TRIM32, NHL-1 and Abba
In mouse neurons, TRIM32 plays a crucial role in neuronal differentiation by becoming polarised between progenitor and daughter cells and determining cell differentiation fate by down-regulating cMyc and binding AGO1 to activate let-7a (Schwamborn et al., 2009).
Similar to TRIM2 and TRIM3, TRIM32 binds myosin through its NHL domain as part of its role in muscle remodelling (Kudryashova et al., 2005). TRIM32 orthologs are relatively poorly studied: Abba (D. melanogaster) is involved in sarcomere organisation (LaBeau-DiMenna et al., 2012; Domsch et al., 2013) while NHL-1 (C. elegans) is involved in stress responses in neuronal cells (Volovik et al., 2014).
TRIM56
Finally, TRIM56, which is often not included in discussions of NHL-TRIM proteins but is closely related and possesses NHL-like repeats (Liu et al., 2016), has been identified to be part of the human RNA interactome (Kwon et al., 2013). It is a key component of the Toll like receptor 3 (dsRNA sensing) pathway and inhibits the replication of influenza viruses, however this activity is dependent only on a 63 amino acid-long segment of the C-terminus, not on a fully formed NHL domain (Shen et al., 2012; Liu et al., 2016). However, in the case of bovine diarrhoea virus, the entire C-terminus as well as the E3 ubiquitin ligase activity were necessary to restrict viral RNA replication (Wang et al., 2011). A review by Garcia-Moreno et al. (2018) drew parallels between the RNA binding dependence of E3 ligase activity observed in TRIM25 by Choudhury et al. (2017) and the potential for a similar mechanism for TRIM56.
In summary, TRIM-NHL proteins play crucial roles during cell differentiation, especially in neuronal and germline cells. Their ability to act both post-transcriptionally and post-translationally is ideally suited to these steps during which cellular states must undergo rapid and dramatic changes. All the described functions are directly or at least indirectly related to RNA binding. A more in-depth study of these proteins can shed light on networks and checkpoints involved (Mitschka et al., 2015) as well as how they came to evolve. A detailed understanding of the interplay between these proteins’ ubiquitination and RNA binding activities will most likely be crucial to a more complete understanding of their biological roles.
Although most direct TRIM-RNA interactions described to date are mediated by the NHL domain, new work is starting to uncover a role for non-NHL mediated TRIM protein-RNA interactions, particularly the so far unique case of RNA binding by TRIM25 through its PRY/SPRY domain (Kwon et al., 2013; Choudhury et al., 2017).
RNA-binding of the PRY/SPRY containing TRIM25
So far RNA-binding has only been shown for a single member of the TRIM-SPRY family, TRIM25, which exhibits diverse functions in innate immunity, morphogenesis and cell proliferation (Orimo et al., 1999; Gack et al., 2007; Castanier et al., 2012; Qin et al., 2015; Takayama et al., 2018). TRIM25 was identified by RNA interactome capture studies from mESCs (Kwon et al., 2013). Meanwhile, it has been shown that TRIM25 interacts with a wide variety of RNAs, including the 3′-UTRs and exons of mRNAs (Kwon et al., 2013; Choudhury et al., 2017), lincRNAs (Choudhury et al., 2017), miRNAs (Choudhury et al., 2014), viral RNAs and their corresponding RNPs (Manokaran et al., 2015; Meyerson et al., 2017). No clear consensus motif for RNA-binding has been identified, although G- and C-rich sequences are overrepresented in CLIP-data (Choudhury et al., 2017). In vitro assays found no clear preference for single or double stranded RNA (Sanchez et al., 2018).
This broad range of RNA targets in part reflects TRIM25’s broad and often poorly understood range of functions. The case of precursor-of-microRNA let-7 (pre-let-7a-1) might give insights into the general principle behind these interactions: TRIM25 recruits the pluripotency promoting factor Lin28 and the terminal uridylyltransferase 4 (TUT4). TUT4, possibly after activation through ubiquitination by TRIM25, poly-uridylates pre-let-7 and marks it for RNA degradation (Choudhury et al., 2014).
Efforts have been made to identify the regions responsible for RNA binding. Kwon et al. (2013) originally mapped the RNA-binding of TRIM25 to the CC region based on co-purification experiments. Later work identified an amino acid stretch in the PRY motif as crosslinking to RNA (Castello et al., 2016). Deletion of this peptide abolished RNA-binding of the full-length protein in electrophoretic mobility shift assays (EMSAs) (Choudhury et al., 2017).
Neither the isolated PRY/SPRY domain nor TRIM25ΔCC bound in these assays, indicating a critical role of the CC, either through direct interaction or by mediating dimerisation. In addition, the linker connecting the PRY/SPRY and CC domains (referred to as L2 linker) contains a short lysine-rich motif that contributes to RNA-binding (Sanchez et al., 2018).
Together, these results suggest that although several regions in the protein are likely involved in RNA-binding, the PRY/SPRY domain plays a critical role. This would be the first example of RNA-binding by a PRY/SPRY domain. Most PRY/SPRY domains are protein-protein interaction domains, with a few examples adapted to binding of large supramolecular assemblies like viral capsids or antibodies (Woo et al., 2006; Keeble et al., 2008; Biris et al., 2012). Although the fold of the core domain is highly conserved, the varying length and amino acid composition of the four flexible regions v1–v4 allow for binding of this remarkably broad variety of substrates (Song et al., 2005) (Figure 6A). It is therefore not surprising that several of the mutants described by Sanchez et al. (2018) as affecting RNA-binding cluster in the v1 and v2 region, and the proposed RNA-binding region from Choudhury et al. (2017) contains the complete v1 region (Figure 6B and C).
![Figure 6: Charge distribution and conservation of TRIM-PRY/SPRY domains and the likely RNA-binding site.(A) Sequence alignment of several human TRIM-SPRY domains reveals variable regions v1-v4 (numbering corresponds to TRIM25). (B) Structural alignment of all published structures of primate TRIM-SPRY domains [TRIM5α (PDB:2LM3), TRIM20(PDB:4CG4), TRIM21(PDB:2IWG), TRIM25(PDB:6FLM), TRIM72(PDB:3KB5)]. The variable regions are highlighted in the same colour scheme as in A. (C) Comparison with the postulated RNA-binding region (Choudhury et al., 2017) in yellow and mutants described to affect the RNA-binding of TRIM25 (Sanchez et al., 2018) in red shows that they cluster in the variable region, possibly indicating that RNA-binding is not a conserved feature of TRIM-PRY/SPRY domains. (D) The PRY/SPRY domain of TRIM25 (PDB:6FLN) interacts weakly with the CC and the two domains form a shared, strongly positively charged surface (in blue), that may allow for cooperative RNA-binding.](/document/doi/10.1515/hsz-2019-0158/asset/graphic/j_hsz-2019-0158_fig_006.jpg)
Charge distribution and conservation of TRIM-PRY/SPRY domains and the likely RNA-binding site.
(A) Sequence alignment of several human TRIM-SPRY domains reveals variable regions v1-v4 (numbering corresponds to TRIM25). (B) Structural alignment of all published structures of primate TRIM-SPRY domains [TRIM5α (PDB:2LM3), TRIM20(PDB:4CG4), TRIM21(PDB:2IWG), TRIM25(PDB:6FLM), TRIM72(PDB:3KB5)]. The variable regions are highlighted in the same colour scheme as in A. (C) Comparison with the postulated RNA-binding region (Choudhury et al., 2017) in yellow and mutants described to affect the RNA-binding of TRIM25 (Sanchez et al., 2018) in red shows that they cluster in the variable region, possibly indicating that RNA-binding is not a conserved feature of TRIM-PRY/SPRY domains. (D) The PRY/SPRY domain of TRIM25 (PDB:6FLN) interacts weakly with the CC and the two domains form a shared, strongly positively charged surface (in blue), that may allow for cooperative RNA-binding.
The TRIM25 PRY/SPRY domain is necessary and sufficient for the interaction with substrates such as Retinoic Acid Inducible Gene I (RIG-I) or Zinc finger antiviral protein (ZAP), two well-known RBPs involved in innate immunity (Gack et al., 2007; Li et al., 2017).
The link between RNA binding and ubiquitination
An influence of RNA-binding on ubiquitination was first reported by Choudhury et al. (2017). RNAse I treatment strongly decreased auto-ubiquitination of TRIM25 as well as TRIM25-mediated ubiquitination of ZAP in vitro. Deletion of its proposed RNA-binding region showed a similar phenotype, in addition to abolishing RNA-binding. However, parts of this deletion were shown to be involved in the interaction between the PRY/SPRY and CC domains, which proved to be crucial for ubiquitination of RIG-I in vivo (Koliopoulos et al., 2018) and a similar role in ZAP ubiquitination appears likely, possibly explaining the observed phenotype in an RNA-independent way.
The RNA dependence of TRIM25’s catalytic activity was, however, also reported elsewhere (Sanchez et al., 2018). Mutation of a lysine-rich stretch in the L2 linker region reduced not only RNA-binding, but also ubiquitination of RIG-I in vivo and therefore suppression of viral replication.
RNA-binding might enhance ubiquitination activity by at least two different mechanisms: either by facilitating substrate recruitment through binding to the same RNA or by directly increasing catalytic activity through allosteric changes of TRIM25 (Choudhury et al., 2017). In support of the first mechanism, both ZAP and RIG-I are well-known RNA-binding molecules and co-localisation of TRIM25 and RIG-I in stress granules is RNA-dependent (Sanchez et al., 2018). Although TRIM25 and RIG-I co-purify when either of them is immuno-precipitated from cells (Gack et al., 2007), there is no clear evidence for a direct interaction in vitro, suggesting that additional factors like RNA might be needed for the interaction. There is no indication of preferential binding of TRIM25 to RIG-I bound RNA over free RNA (Sanchez et al., 2018).
An allosteric effect of RNA-binding on ubiquitin E3 ligase activity would most likely be accomplished by facilitating interactions between the substrate which recognises the PRY/SPRY domain and the catalytic RING finger. Sanchez et al. (2018) propose that this is achieved through rearrangement of the disordered L2 linker upon RNA-binding. Alternatively, RNA might stabilise the weak CC:PRY/SPRY interaction, either through direct interactions with both domains or by allosterically modulating binding of the PRY/SPRY to the CC. Interestingly, the crystal structure of a CC-PRY/SPRY construct of TRIM25 shows the PRY/SPRY domain interacting with the CC region (Koliopoulos et al., 2018). However, in solution this interaction between both domains is rather weak (Koliopoulos et al., 2018). The PRY/SPRY domain being dissociated from the CC with the long flexible linker being distal to the E2-Ub bound RING would make ubiquitination of substrates difficult. Intriguingly, both domains together form a larger positively charged surface (Figure 6D), which could accommodate RNA. This RNA could decrease the average distance of the substrate to the E2-Ub conjugate significantly. Allosteric effects could also directly enhance interactions with the substrate.
RIG-I binds double-stranded RNA with a 5′-triphosphate (5′ ppp) moiety through its helicase and C-terminal domains (Hornung et al., 2006). It is likely that TRIM25 and RIG-I will bind the same RNA molecule, thereby facilitating the interaction between E3 ligase and substrate. RNA-binding could not only increase the ubiquitination activity of TRIM25 by facilitating CC:PRY/SPRY interactions, but will also lead to a conformational change of RIG-I that makes the N-terminal CARD domains, that are otherwise bound to the helicase domain in an auto-inhibited state, accessible for ubiquitination by TRIM25 (Kolakofsky et al., 2012) (Figure 7). Poly-ubiquitination of the CARD domains and release of unanchored K63-linked ubiquitin chains triggers filament formation of the mitochondrial antiviral signalling protein (MAVS) and causes IFN expression (Hou et al., 2011). A recent report identifies the long non-coding RNA Lnczc3h7a as binding both the TRIM25 PRY/SPRY and RIG-I helicase domain, thereby facilitating their interaction and TRIM25-dependent ubiquitination of RIG-I. Interestingly, Lnczc3h7a does not activate RIG-I and might bind the helicase domain via a novel interaction site independent of the known binding site for double-stranded RNAs (Lin et al., 2019).
One potential, albeit speculative mechanism of RNA-assisted RIG-I ubiquitination in accordance with experimental evidence.
(A) In the absence of RNA the substrate-binding PRY/SPRY domain interacts only transiently with the CC (Koliopoulos et al., 2018). (B) RNA-binding induces a conformational change of TRIM25 through remodulation of the linker connecting the CC and PRY/SPRY domain (Sanchez et al., 2018) or direct interaction with both domains (Kwon et al., 2013; Choudhury et al., 2017), leading to its activation. (C) RIG-I binds the same RNA-strand via its helicase and C-terminal domain (CTD), leading to opening of the auto-inhibited state (Kolakofsky et al., 2012). (D) TRIM25 poly-ubiquitinates the RIG-I CARD domains, triggering RIG-I signalling. This mechanism is, of course, speculative and other mechanisms are possible, for example, other factors might be included to mediate RIG-I-CARD domain interactions with the TRIM25 PRY/SPRY domain. An example for such a factor might be the long non-coding RNA Lnczc3h7a, that binds both TRIM25 and RIG-I, but does not remove auto-inhibition of RIG-I (Lin et al., 2019).
Despite the clear evidence for an activating function of RNA on TRIM25 in vitro, the example of the Dengue virus subgenomic RNA (sfRNA) shows that the situation is less clear in vivo. Mutations in the sfRNA of the Dengue virus not only increased affinity of this RNA to TRIM25, but also decreased IFN-β expression, possibly indicating reduced RIG-I signalling (Manokaran et al., 2015). Immunoprecipitation of RIG-I from sfRNA-transfected cells still co-purified TRIM25, indicating that the interaction with RIG-I is not impaired, but showed a higher proportion of ubiquitinated TRIM25. This may indicate that sustained activation of TRIM25 E3 ligase activity by sfRNA facilitates auto-ubiquitination and increased proteasomal degradation of TRIM25, thereby decreasing RIG-I signalling.
RNA binding in other PRY/SPRY TRIM proteins
The role of the PRY/SPRY domain in RNA-binding of TRIM25 has led to the suggestion that RNA-binding might be a conserved feature of TRIM-PRY/SPRY domains and that other members of the PRY/SPRY-carrying TRIM family might bind RNA. So far evidence for this is sparse. Replacement of the proposed RNA-binding peptide in the TRIM25 PRY/SPRY domain with homologous sequences from other TRIM proteins (TRIM5α, TRIM21, TRIM27 and TRIM65) preserves both RNA binding and auto-ubiquitination activity (Choudhury et al., 2017). However, the interpretation that RNA binding is found in more PRY/SPRY domains is controversial, as the results can also be explained by preserved interactions between PRY/SPRY and CC domains. Given the broad spectrum of interaction partners of PRY/SPRY domains and the fact that published mutants affecting RNA binding are mostly located in the poorly conserved loop regions, it is unlikely that RNA binding is a broadly conserved feature of PRY/SPRY domains.
Nevertheless, TRIM65, a close relative of TRIM25, was found in the interactome of miRNAs, although it is likely that interaction with the known RNA-binding TNRC6 proteins accounts for this observation rather than direct protein-RNA interactions (Li et al., 2014). Another recently described RNA-binding TRIM is TRIM26, which seems to interact specifically with the microRNA miR-18b (Treiber et al., 2017; Trendel et al., 2019). Unlike TRIM25 and TRIM65, which are ancient proteins with homologs in all vertebrates, TRIM26 is part of a younger, mammalian specific and more rapidly evolving subgroup of TRIM proteins (Sardiello et al., 2008). The large evolutionary distance and the absence of reported RNA-binding for other PRY/SPRY domains suggest, that RNA-binding in PRY/SPRY domains might have evolved more than once.
Co-localisation of substrates on the RNA and phase separation
The case of TRIM25 suggests that RNA-binding in TRIM proteins might generally play a role in substrate recruitment, with binding of both substrate and E3 ligase to the same RNA facilitating their interaction. While other TRIM proteins have been less studied in this context, TRIM25 and TRIM71 give insights into the links between RNA binding, RNP formation and ubiquitination.
In extension of this idea, RNA-induced biological condensation might lead to enrichment of TRIM proteins and their substrates in ‘membrane-less organelles’. This phase separation is usually strongly coupled to multivalency (Li et al., 2012) and RNA-binding in addition often promotes macromolecular condensation (Lin et al., 2015). Given that TRIM proteins with their diverse and redundant interaction sites distributed over several domains are archetypal multivalent proteins, it is not surprising that phase separation is a common theme in TRIM proteins with TRIM19 (PML) condensation into nuclear bodies being the prime example (Dyck et al., 1994). TRIM proteins also feature large intrinsically disordered regions (Uversky, 2014) that have been implicated in phase-separation (Malinovska et al., 2013). Formation of TRIM containing cell compartments in response to overexpression was shown for most TRIM proteins (Reymond et al., 2001). Among those proteins are also RNA-binding TRIM proteins and, at least in the case of TRIM25, an RNA-dependence for the formation of these stress granules was shown (Sanchez et al., 2018). Redundant TRIM binding sites are found in several RNA targets, possibly supporting RNA-induced phase-separation (Kumari et al., 2018). Macromolecular condensates remain liquid and as such allow for free diffusion of moderately large molecules, including proteins, and exchange with the surrounding liquid while at the same time featuring very high protein concentrations and frequent encounters between proteins (Banani et al., 2017). The catalytic activity of TRIM proteins opens up the possibility of a fine-tuned regulation of macromolecular condensation, as post-translational modifications (PTMs) often act as switches to induce or repress phase separation and ubiquitination regulates the formation of some membrane-less organelles (Mittag et al., 2017; Dao et al., 2018; Herhaus and Dikic, 2018). Although so far, no TRIM protein was shown to directly regulate phase separation by ubiquitination, TRIM19 auto-sumoylation facilitates nuclear body formation (Shen et al., 2006). While auto-ubiquitination of TRIM proteins in the cytosol promotes proteasomal degradation, resulting in short life-times (Diaz-Griffero et al., 2006; Versteeg et al., 2013), poly-ubiquitinated proteins are likely protected from proteasomal degradation in phase-separated droplets. Phase-separation in addition to facilitating substrate recruitment by increasing local concentration might therefore also regulate stability. TRIM proteins are also subject to other PTMs that might have an influence on phase-separation (Stacey et al., 2012; Lee et al., 2018). This might explain why the RNA-binding of some TRIM proteins’ changes upon stress (Garcia-Moreno et al., 2019; Trendel et al., 2019). Macromolecular condensation into membrane-less organelles provides a powerful and elegant hypothesis to explain localisation of low-abundance proteins with their substrates and enable another layer of post-translational regulation, but it should not be forgotten that most proteins will phase-separate given the right condition (Dumetz et al., 2008). It is therefore not always clear if results from over-expressed proteins or in vitro reconstituted systems reflect the situation at much lower physiological concentrations. While phase separation is a relatively new concept in biology (Li et al., 2012), in the context of TRIM proteins it can be seen as the newest evolution of the idea of functional multimerisation. The clearest example of functional multimerisation in TRIM proteins are the highly ordered hexagonal lattices that TRIM5α forms on retroviral capsids (Ganser-Pornillos et al., 2011) and even spontaneously (Li et al., 2016). Trimeric BB structures form the junctions of these networks, connected by the CC dimers (Li and Sodroski, 2008). The PRY/SPRY domains are found on one side of the network, where they are prearranged for interaction with the viral capsid, while the RING domains form trimers on the other side of the network (Biris et al., 2013; Fletcher et al., 2018). While it was a popular hypothesis that similar forms of oligomerisation might be a common feature of other TRIM proteins, the highly ordered two-dimensional (2D) crystals formed by TRIM5α through well-defined interactions between B-boxes are structurally and functionally different from liquid-like macromolecular condensates held together by numerous, weak, often unspecific, interactions. To the best of our knowledge, TRIM5α remains the only member of the TRIM family to form these kind of well-ordered oligomers and generalisations from TRIM5α to other TRIM proteins are therefore difficult.
miRNA regulation
The most obvious case in which TRIM proteins are involved in phase separation is the role they play within the miRISC complex which is segregated into P-bodies. It was established relatively early on that miRNA regulation was central to the role of many TRIM proteins (Loedige and Filipowicz, 2009; Wulczyn et al., 2011). This is most heavily studied in the case of TRIM71, itself a target of the miRNA let-7, which also localises to P-bodies where it ubiquitinates AGO2 and leads to reduced silencing efficiency (Rybak et al., 2009). TRIM71 also negatively regulates let-7 levels through its binding and regulation of the argonaute protein ALG-1 (Zou et al., 2013) and was demonstrated to bind pri-miR-29a through its apical loop, driving its downstream processing and repression of proteins TET2 and TET3 (Treiber et al., 2017). TRIM25 has also been postulated to regulate pre-let-7 as described above (Choudhury et al., 2014).
The homologs Mei-P26, and NHL-2 are also members of the miRISC complex as discussed above (Neumuller et al., 2008; Hammell et al., 2009; Davis et al., 2018). BRAT, Mei-P26 and TRIM32 all bind AGO1 (Neumuller et al., 2008; Schwamborn et al., 2009). While NHL-2 binds ALG-1 and upregulates let-7 and lsy-6 activity (Hammell et al., 2009) and TRIM32 upregulates let-7, Mei-P26 was reported to globally decrease miRNA levels (Neumuller et al., 2008; Schwamborn et al., 2009).
A common observation in most of these studies is that the regulation exercised by TRIM-NHL proteins is highly specific to particular miRNAs, presumably achieved via direct TRIM-RNA interactions, suggesting they may play a crucial role in regulating specificity of miRNA network changes.
Comparison with other RNA-binding E3-ligases
The TRIM proteins discussed above are a significant addition to the list of known proteins that combine RNA-binding and E3-ubiquitin ligase activity. Previously, only around thirty out of the approximately 600 human Ubiquitin E3 ligases were known to bind RNA (Cano et al., 2010). As in the case of TRIM25, several of these have ubiquitination activity regulated by RNA-binding (Cano et al., 2012; Zhang et al., 2015a). A particularly interesting case is Roquin, which promotes mRNA decay (Leppek et al., 2013) by binding stem-loop motifs known as constitutive decay elements (CDEs) (Schlundt et al., 2014). Roquin-mediated RNA-binding can either up- or down-regulate the E3 ligase activity dependent on the E2 bound, allowing for regulation of the linkage type of poly-ubiquitin chains (Zhang et al., 2015a). This is achieved by a bipartite architecture with two rigid modules connected by flexible linkers. Both modules contain RNA-binding sites and RNA-binding causes major domain rearrangements also involving the catalytic RING domain (Zhang et al., 2015a). This situation might resemble the architecture of TRIM proteins with the rigid tripartite motif and the additional C-terminal domains.
Concluding remarks
In this review we hope to have demonstrated that RNA interaction is crucial to understanding the role of many TRIM proteins. Current knowledge prompts us to postulate two hypotheses about TRIM-RNA interaction. (i) TRIM proteins bind RNAs to regulate their fate, whether it will be RNA decay, translation regulation or other functions around the central dogma. (ii) Regulatory RNAs and RNA pathogens bind TRIM proteins to regulate their ubiquitination efficiency. These aspects of the field have opened up many exciting lines of enquiry: how are the RNA binding functions of these proteins coupled to their more classical ubiquitination roles? Can RNA binding sites act as TRIM-specific degrons? How does the inherently dimeric and potentially multimeric nature of these proteins impact how they recognise and recruit their RNA targets? How can we reconcile the variability observed in the domain architecture of certain orthologous TRIMs with their relatively well-conserved biological roles? How can we develop a solid understanding of the specific cellular environments such as membraneless organelles in which these proteins operate?
Many of these questions could not be tackled without the recent developments in RNA specific methods, ‘omics’ techniques and structural biology methods capable of addressing large and flexible complexes. These developments make RNA-TRIM interactions a challenging yet manageable field of study and, given the biologically central role played by many of these proteins, exciting developments are to be expected.
Funding source: Marie Sklodowska-Curie Actions COFUND
Award Identifier / Grant number: 664726
Funding source: Deutsche Forschungsgemeinschaft
Award Identifier / Grant number: SPP1935
Funding statement: C.P.B. thanks the EMBL Interdisciplinary Postdoc (EI3POD) Programme fellowship under Marie Sklodowska-Curie Actions COFUND (grant number 664726) for support. J.H. gratefully acknowledges the German Research Council (Deutsche Forschungsgemeinschaft) DFG for funding via the Emmy-Noether Programme and the Priority Programme, Funder Id: http://dx.doi.org/10.13039/501100001659, SPP1935.
References
Aeschimann, F., Kumari, P., Bartake, H., Gaidatzis, D., Xu, L., Ciosk, R., and Grosshans, H. (2017). LIN41 post-transcriptionally silences mRNAs by two distinct and position-dependent mechanisms. Mol. Cell 65, 476–489.10.1016/j.molcel.2016.12.010Search in Google Scholar PubMed
Ahmad, Y. and Lamond, A.I. (2014). A perspective on proteomics in cell biology. Trends Cell Biol. 24, 257–264.10.1016/j.tcb.2013.10.010Search in Google Scholar PubMed PubMed Central
Akutsu, M., Dikic, I., and Bremm, A. (2016). Ubiquitin chain diversity at a glance. J. Cell Sci. 129, 875.10.1242/jcs.183954Search in Google Scholar PubMed
Albor, A., El-Hizawi, S., Horn, E.J., Laederich, M., Frosk, P., Wrogemann, K., and Kulesz-Martin, M. (2006). The interaction of piasy with TRIM32, an E3-ubiquitin ligase mutated in limb-girdle muscular dystrophy type 2H, promotes Piasy degradation and regulates UVB-induced keratinocyte apoptosis through NFkappaB. J. Biol. Chem. 281, 25850–25866.10.1074/jbc.M601655200Search in Google Scholar PubMed
Ali, H., Mano, M., Braga, L., Naseem, A., Marini, B., Vu, D.M., Collesi, C., Meroni, G., Lusic, M., and Giacca, M. (2019). Cellular TRIM33 restrains HIV-1 infection by targeting viral integrase for proteasomal degradation. Nat. Commun. 10, 926.10.1038/s41467-019-08810-0Search in Google Scholar PubMed PubMed Central
Ambrosi, A. and Wahren-Herlenius, M. (2015). Update on the immunobiology of Sjogren’s syndrome. Curr. Opin. Rheumatol. 27, 468–475.10.1097/BOR.0000000000000195Search in Google Scholar PubMed
Ambrosi, A., Sonesson, S.E., and Wahren-Herlenius, M. (2014). Molecular mechanisms of congenital heart block. Exp. Cell Res. 325, 2–9.10.1016/j.yexcr.2014.01.003Search in Google Scholar PubMed
Angerer, P., Simon, L., Tritschler, S., Wolf, F.A., Fischer, D., and Theis, F.J. (2017). Single cells make big data: new challenges and opportunities in transcriptomics. Curr. Opin. Syst. Biol. 4, 85–91.10.1016/j.coisb.2017.07.004Search in Google Scholar
Arama, E., Dickman, D., Kimchie, Z., Shearn, A., and Lev, Z. (2000). Mutations in the beta-propeller domain of the Drosophila brain tumor (brat) protein induce neoplasm in the larval brain. Oncogene 19, 3706–3716.10.1038/sj.onc.1203706Search in Google Scholar PubMed
Arvola, R.M., Weidmann, C.A., Tanaka Hall, T.M., and Goldstrohm, A.C. (2017). Combinatorial control of messenger RNAs by Pumilio, Nanos and brain tumor proteins. RNA Biol. 14, 1445–1456.10.1080/15476286.2017.1306168Search in Google Scholar PubMed PubMed Central
Balastik, M., Ferraguti, F., Pires-da Silva, A., Lee, T.H., Alvarez-Bolado, G., Lu, K.P., and Gruss, P. (2008). Deficiency in ubiquitin ligase TRIM2 causes accumulation of neurofilament light chain and neurodegeneration. Proc. Natl. Acad. Sci. U.S.A. 105, 12016–12021.10.1073/pnas.0802261105Search in Google Scholar PubMed PubMed Central
Baltz, A.G., Munschauer, M., Schwanhäusser, B., Vasile, A., Murakawa, Y., Schueler, M., Youngs, N., Penfold-Brown, D., Drew, K., Milek, M., et al. (2012). The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol. Cell 46, 674–690.10.1016/j.molcel.2012.05.021Search in Google Scholar PubMed
Banani, S.F., Lee, H.O., Hyman, A.A., and Rosen, M.K. (2017). Biomolecular condensates: organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol. 18, 285–298.10.1038/nrm.2017.7Search in Google Scholar PubMed PubMed Central
Bell, J.L., Malyukova, A., Holien, J.K., Koach, J., Parker, M.W., Kavallaris, M., Marshall, G.M., and Cheung, B.B. (2012). TRIM16 acts as an E3 ubiquitin ligase and can heterodimerize with other TRIM family members. PLoS One 7, 1–9.10.1371/journal.pone.0037470Search in Google Scholar PubMed PubMed Central
Betschinger, J., Mechtler, K., and Knoblich, J.A. (2006). Asymmetric segregation of the tumor suppressor Brat regulates self-renewal in Drosophila neural stem cells. Cell 124, 1241–1253.10.1016/j.cell.2006.01.038Search in Google Scholar PubMed
Biris, N., Tomashevski, A., Bhattacharya, A., Diaz-Griffero, F., and Ivanov, D.N. (2013). Rhesus monkey TRIM5alpha SPRY domain recognizes multiple epitopes that span several capsid monomers on the surface of the HIV-1 mature viral core. J. Mol. Biol. 425, 5032–5044.10.1016/j.jmb.2013.07.025Search in Google Scholar PubMed PubMed Central
Biris, N., Yang, Y., Taylor, A.B., Tomashevski, A., Guo, M., Hart, P.J., Diaz-Griffero, F., and Ivanov, D.N. (2012). Structure of the rhesus monkey TRIM5alpha PRYSPRY domain, the HIV capsid recognition module. Proc. Natl. Acad. Sci. U.S.A. 109, 13278–13283.10.1073/pnas.1203536109Search in Google Scholar PubMed PubMed Central
Boyer, N.P., Monkiewicz, C., Menon, S., Moy, S.S., and Gupton, S.L. (2018). Mammalian TRIM67 functions in brain development and behavior. eNeuro 5, e0186–18.10.1523/ENEURO.0186-18.2018Search in Google Scholar PubMed PubMed Central
Buetow, L. and Huang, D.T. (2016). Structural insights into the catalysis and regulation of E3 ubiquitin ligases. Nat. Rev. Mol. Cell Biol. 17, 626–642.10.1038/nrm.2016.91Search in Google Scholar PubMed PubMed Central
Cammas, F., Khetchoumian, K., Chambon, P., and Losson, R. (2012). TRIM involvement in transcriptional regulation. Adv. Exp. Med. Biol. 770, 59–76.10.1007/978-1-4614-5398-7_5Search in Google Scholar PubMed
Cano, F., Bye, H., Duncan, L.M., Buchet-Poyau, K., Billaud, M., Wills, M.R., and Lehner, P.J. (2012). The RNA-binding E3 ubiquitin ligase MEX-3C links ubiquitination with MHC-I mRNA degradation. EMBO J. 31, 3596–3606.10.1038/emboj.2012.218Search in Google Scholar PubMed PubMed Central
Cano, F., Miranda-Saavedra, D., and Lehner, P.J. (2010). RNA-binding E3 ubiquitin ligases: novel players in nucleic acid regulation. Biochem. Soc. Trans. 38, 1621–1626.10.1042/BST0381621Search in Google Scholar PubMed
Castanier, C., Zemirli, N., Portier, A., Garcin, D., Bidere, N., Vazquez, A., and Arnoult, D. (2012). MAVS ubiquitination by the E3 ligase TRIM25 and degradation by the proteasome is involved in type I interferon production after activation of the antiviral RIG-I-like receptors. BMC Biol. 10, 44.10.1186/1741-7007-10-44Search in Google Scholar PubMed PubMed Central
Castello, A., Fischer, B., Eichelbaum, K., Horos, R., Beckmann, B.M., Strein, C., Davey, N.E., Humphreys, D.T., Preiss, T., Steinmetz, L.M., et al. (2012). Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 149, 1393–1406.10.1016/j.cell.2012.04.031Search in Google Scholar PubMed
Castello, A., Fischer, B., Frese, C.K., Horos, R., Alleaume, A.M., Foehr, S., Curk, T., Krijgsveld, J., and Hentze, M.W. (2016). Comprehensive identification of RNA-binding domains in human cells. Mol. Cell 63, 696–710.10.1016/j.molcel.2016.06.029Search in Google Scholar PubMed PubMed Central
Chen, G., Kong, J., Tucker-Burden, C., Anand, M., Rong, Y., Rahman, F., Moreno, C.S., Van Meir, E.G., Hadjipanayis, C.G., and Brat, D.J. (2014). Human Brat ortholog TRIM3 is a tumor suppressor that regulates asymmetric cell division in glioblastoma. Cancer Res. 74, 4536–4548.10.1158/0008-5472.CAN-13-3703Search in Google Scholar PubMed PubMed Central
Chen, X., Dong, C., Law, P.T.Y., Chan, M.T.V., Su, Z., Wang, S., Wu, W.K.K., and Xu, H. (2015). MicroRNA-145 targets TRIM2 and exerts tumor-suppressing functions in epithelial ovarian cancer. Gynecol. Oncol. 139, 513–519.10.1016/j.ygyno.2015.10.008Search in Google Scholar PubMed
Cheung, C.C., Yang, C., Berger, T., Zaugg, K., Reilly, P., Elia, A.J., Wakeham, A., You-Ten, A., Chang, N., Li, L., et al. (2010). Identification of BERP (brain-expressed RING finger protein) as a p53 target gene that modulates seizure susceptibility through interacting with GABA(A) receptors. Proc. Natl. Acad. Sci. U.S.A. 107, 11883–11888.10.1073/pnas.1006529107Search in Google Scholar PubMed PubMed Central
Cho, P.F., Gamberi, C., Cho-Park, Y.A., Cho-Park, I.B., Lasko, P., and Sonenberg, N. (2006). Cap-dependent translational inhibition establishes two opposing morphogen gradients in Drosophila embryos. Curr. Biol. 16, 2035–2041.10.1016/j.cub.2006.08.093Search in Google Scholar PubMed PubMed Central
Choudhury, N.R., Heikel, G., Trubitsyna, M., Kubik, P., Nowak, J.S., Webb, S., Granneman, S., Spanos, C., Rappsilber, J., Castello, A., et al. (2017). RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. BMC Biol. 15, 105.10.1186/s12915-017-0444-9Search in Google Scholar PubMed PubMed Central
Choudhury, N.R., Nowak, J.S., Zuo, J., Rappsilber, J., Spoel, S.H., and Michlewski, G. (2014). TRIM25 is an RNA-specific activator of Lin28a/TuT4-mediated uridylation. Cell Rep. 9, 1265–1272.10.1016/j.celrep.2014.10.017Search in Google Scholar PubMed PubMed Central
Chu, Y. and Yang, X. (2010). SUMO E3 ligase activity of TRIM proteins. Oncogene 30, 1108.10.1038/onc.2010.462Search in Google Scholar PubMed PubMed Central
Cooper, T.A., Wan, L., and Dreyfuss, G. (2009). RNA and disease. Cell 136, 777–793.10.1016/j.cell.2009.02.011Search in Google Scholar PubMed PubMed Central
Crawford, L.J., Johnston, C.K., and Irvine, A.E. (2018). TRIM proteins in blood cancers. J. Cell Commun. Signal. 12, 21–29.10.1007/s12079-017-0423-5Search in Google Scholar PubMed PubMed Central
Czerwinska, P., Mazurek, S., and Wiznerowicz, M. (2017). The complexity of TRIM28 contribution to cancer. J. Biomed. Sci. 24, 63.10.1186/s12929-017-0374-4Search in Google Scholar PubMed PubMed Central
Dao, T.P., Kolaitis, R.M., Kim, H.J., O’Donovan, K., Martyniak, B., Colicino, E., Hehnly, H., Taylor, J.P., and Castaneda, C.A. (2018). Ubiquitin modulates liquid-liquid phase separation of UBQLN2 via disruption of multivalent interactions. Mol. Cell 69, 965–978.10.1016/j.molcel.2018.02.004Search in Google Scholar PubMed PubMed Central
Daubner, G.M., Clery, A., and Allain, F.H.T. (2013). RRM-RNA recognition: NMR or crystallography…and new findings. Curr. Opin. Struct. Biol. 23, 100–108.10.1016/j.sbi.2012.11.006Search in Google Scholar PubMed
Davis, G.M., Tu, S., Anderson, J.W.T., Colson, R.N., Gunzburg, M.J., Francisco, M.A., Ray, D., Shrubsole, S.P., Sobotka, J.A., Seroussi, U., et al. (2018). The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans. Elife 7, e35478.10.7554/eLife.35478.032Search in Google Scholar
D’Cruz, A.A., Babon, J.J., Norton, R.S., Nicola, N.A., and Nicholson, S.E. (2013). Structure and function of the SPRY/B30.2 domain proteins involved in innate immunity. Protein Sci. 22, 1–10.10.1002/pro.2185Search in Google Scholar PubMed PubMed Central
De Falco, F., Cainarca, S., Andolfi, G., Ferrentino, R., Berti, C., Rodriguez Criado, G., Rittinger, O., Dennis, N., Odent, S., Rastogi, A., et al. (2003). X-linked Opitz syndrome: novel mutations in the MID1 gene and redefinition of the clinical spectrum. Am. J. Med. Genet. A 120A, 222–228.10.1002/ajmg.a.10265Search in Google Scholar PubMed
Diaz-Griffero, F., Li, X., Javanbakht, H., Song, B., Welikala, S., Stremlau, M., and Sodroski, J. (2006). Rapid turnover and polyubiquitylation of the retroviral restriction factor TRIM5. Virology 349, 300–315.10.1016/j.virol.2005.12.040Search in Google Scholar
Dominguez, D., Freese, P., Alexis, M.S., Su, A., Hochman, M., Palden, T., Bazile, C., Lambert, N.J., Van Nostrand, E.L., Pratt, G.A., et al. (2018). Sequence, structure, and context preferences of human RNA binding proteins. Mol. Cell 70, 854–867.e9.10.1016/j.molcel.2018.05.001Search in Google Scholar
Domsch, K., Ezzeddine, N., and Nguyen, H.T. (2013). Abba is an essential TRIM/RBCC protein to maintain the integrity of sarcomeric cytoarchitecture. J. Cell Sci. 126, 3314–3323.Search in Google Scholar
Dumetz, A.C., Chockla, A.M., Kaler, E.W., and Lenhoff, A.M. (2008). Protein phase behavior in aqueous solutions: crystallization, liquid-liquid phase separation, gels, and aggregates. Biophys. J. 94, 570–583.10.1529/biophysj.107.116152Search in Google Scholar
Dyck, J.A., Maul, G.G., Miller, W.H.J., Chen, J.D., Kakizuka, A., and Evans, R.M. (1994). A novel macromolecular structure is a target of the promyelocyte-retinoic acid receptor oncoprotein. Cell 76, 333–343.10.1016/0092-8674(94)90340-9Search in Google Scholar
Ebner, P., Versteeg, G.A., and Ikeda, F. (2017). Ubiquitin enzymes in the regulation of immune responses. Crit. Rev. Biochem. Mol. Biol. 52, 425–460.10.1080/10409238.2017.1325829Search in Google Scholar PubMed PubMed Central
Edwards, T.A., Wilkinson, B.D., Wharton, R.P., and Aggarwal, A.K. (2003). Model of the brain tumor-Pumilio translation repressor complex. Genes Dev. 17, 2508–2513.10.1101/gad.1119403Search in Google Scholar PubMed PubMed Central
Falkenberg, C.V., Carson, J.H., and Blinov, M.L. (2017). Multivalent molecules as modulators of RNA granule size and composition. Biophys. J. 113, 235–245.10.1016/j.bpj.2017.01.031Search in Google Scholar PubMed PubMed Central
Fletcher, A.J., Vaysburd, M., Maslen, S., Zeng, J., Skehel, J.M., Towers, G.J., and James, L.C. (2018). Trivalent RING assembly on retroviral capsids activates TRIM5 ubiquitination and innate immune signaling. Cell Host Microbe 24, 761–775.e6.10.1016/j.chom.2018.10.007Search in Google Scholar PubMed PubMed Central
Frank, D.J. and Roth, M.B. (1998). ncl-1 is required for the regulation of cell size and ribosomal RNA synthesis in Caenorhabditis elegans. J. Cell Biol. 140, 1321–1329.10.1083/jcb.140.6.1321Search in Google Scholar PubMed PubMed Central
Fridell, R.A., Harding, L.S., Bogerd, H.P., and Cullen, B.R. (1995). Identification of a novel human zinc finger protein that specifically interacts with the activation domain of lentiviral Tat proteins. Virology 209, 347–357.10.1006/viro.1995.1266Search in Google Scholar PubMed
Frosk, P., Weiler, T., Nylen, E., Sudha, T., Greenberg, C.R., Morgan, K., Fujiwara, T.M., and Wrogemann, K. (2002). Limb-girdle muscular dystrophy type 2H associated with mutation in TRIM32, a putative E3-ubiquitin-ligase gene. Am. J. Hum. Genet. 70, 663–672.10.1086/339083Search in Google Scholar PubMed PubMed Central
Furey, C.G., Choi, J., Jin, S.C., Zeng, X., Timberlake, A.T., Nelson-Williams, C., Mansuri, M.S., Lu, Q., Duran, D., Panchagnula, S., et al. (2018). De novo mutation in genes regulating neural stem cell fate in human congenital hydrocephalus. Neuron 99, 302–314.10.1016/j.neuron.2018.06.019Search in Google Scholar PubMed PubMed Central
Gack, M.U., Shin, Y.C., Joo, C.H., Urano, T., Liang, C., Sun, L., Takeuchi, O., Akira, S., Chen, Z., Inoue, S., et al. (2007). TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity. Nature 446, 916.10.1038/nature05732Search in Google Scholar PubMed
Gallouet, A.S., Ferri, F., Petit, V., Parcelier, A., Lewandowski, D., Gault, N., Barroca, V., Le Gras, S., Soler, E., Grosveld, F., et al. (2017). Macrophage production and activation are dependent on TRIM33. Oncotarget 8, 5111–5122.10.18632/oncotarget.13872Search in Google Scholar PubMed PubMed Central
Ganser-Pornillos, B.K., Chandrasekaran, V., Pornillos, O., Sodroski, J.G., Sundquist, W.I., and Yeager, M. (2011). Hexagonal assembly of a restricting TRIM5alpha protein. Proc. Natl. Acad. Sci. U.S.A. 108, 534.10.1073/pnas.1013426108Search in Google Scholar PubMed PubMed Central
Garcia-Moreno, M., Jarvelin, A.I., and Castello, A. (2018). Unconventional RNA-binding proteins step into the virus-host battlefront. Wiley Interdiscip. Rev. RNA 9, e1498.10.1002/wrna.1498Search in Google Scholar PubMed PubMed Central
Garcia-Moreno, M., Noerenberg, M., Ni, S., Jarvelin, A.I., Gonzalez-Almela, E., Lenz, C.E., Bach-Pages, M., Cox, V., Avolio, R., Davis, T., et al. (2019). System-wide profiling of RNA-binding proteins uncovers key regulators of virus infection. Mol. Cell 74, 196–211.10.1016/j.molcel.2019.01.017Search in Google Scholar PubMed PubMed Central
Gerstberger, S., Hafner, M., and Tuschl, T. (2014). A census of human RNA-binding proteins. Nat. Rev. Genet. 15, 829.10.1038/nrg3813Search in Google Scholar PubMed
Hammell, C.M., Lubin, I., Boag, P.R., Blackwell, T.K., and Ambros, V. (2009). nhl-2 modulates microRNA activity in Caenorhabditis elegans. Cell 136, 926–938.10.1016/j.cell.2009.01.053Search in Google Scholar PubMed PubMed Central
Harris, R.E., Pargett, M., Sutcliffe, C., Umulis, D., and Ashe, H.L. (2011). Brat promotes stem cell differentiation via control of a bistable switch that restricts bmp signaling. Dev. Cell 20, 72–83.10.1016/j.devcel.2010.11.019Search in Google Scholar PubMed PubMed Central
Hatakeyama, S. (2011). TRIM proteins and cancer. Nat. Rev. Cancer 11, 792–804.10.1038/nrc3139Search in Google Scholar PubMed
Hatakeyama, S. (2017). TRIM family proteins: roles in autophagy, immunity, and carcinogenesis. Trends Biochem. Sci. 42, 297–311.10.1016/j.tibs.2017.01.002Search in Google Scholar PubMed
Hennig, J., Bresell, A., Sandberg, M., Hennig, K.D.M., Wahren-Herlenius, M., Persson, B., and Sunnerhagen, M. (2008). The fellowship of the RING: the RING-B-box linker region interacts with the RING in TRIM21/ro52, contains a native autoantigenic epitope in sjogren syndrome, and is an integral and conserved region in TRIM proteins. J. Mol. Biol. 377, 431–449.10.1016/j.jmb.2008.01.005Search in Google Scholar PubMed
Hennig, J., Gebauer, F., and Sattler, M. (2014a). Breaking the protein-RNA recognition code. Cell Cycle 13, 3619–3620.10.4161/15384101.2014.986625Search in Google Scholar PubMed PubMed Central
Hennig, J., Militti, C., Popowicz, G.M., Wang, I., Sonntag, M., Geerlof, A., Gabel, F., Gebauer, F., and Sattler, M. (2014b). Structural basis for the assembly of the sxl-unr translation regulatory complex. Nature 515, 287–290.10.1038/nature13693Search in Google Scholar PubMed
Hentze, M.W., Castello, A., Schwarzl, T., and Preiss, T. (2018). A brave new world of RNA-binding proteins. Nat. Rev. Mol. Cell Biol. 19, 327.10.1038/nrm.2017.130Search in Google Scholar PubMed
Herhaus, L. and Dikic, I. (2018). Ubiquitin-induced phase separation of p62/sqstm1. Cell Res. 28, 389–390.10.1038/s41422-018-0030-xSearch in Google Scholar PubMed PubMed Central
Hornung, V., Ellegast, J., Kim, S., Brzozka, K., Jung, A., Kato, H., Poeck, H., Akira, S., Conzelmann, K.K., Schlee, M., et al. (2006). 5′-Triphosphate RNA is the ligand for RIG-I. Science 314, 994–997.10.1126/science.1132505Search in Google Scholar PubMed
Hou, F., Sun, L., Zheng, H., Skaug, B., Jiang, Q.X., and Chen, Z.J. (2011). MAVS forms functional prion-like aggregates to activate and propagate antiviral innate immune response. Cell 146, 448–461.10.1016/j.cell.2011.06.041Search in Google Scholar PubMed PubMed Central
Hung, A.Y., Sung, C.C., Brito, I.L., and Sheng, M. (2010). Degradation of postsynaptic scaffold gkap and regulation of dendritic spine morphology by the TRIM3 ubiquitin ligase in rat hippocampal neurons. PLoS One 5, 1–11.10.1371/journal.pone.0009842Search in Google Scholar PubMed PubMed Central
Ikeda, K. and Inoue, S. (2012). TRIM proteins as RING finger E3 ubiquitin ligases. Adv. Exp. Med. Biol. 770, 27–37.10.1007/978-1-4614-5398-7_3Search in Google Scholar PubMed
Jankowsky, E. and Harris, M.E. (2015). Specificity and nonspecificity in RNA-protein interactions. Nat. Rev. Mol. Cell Biol. 16, 533–544.10.1038/nrm4032Search in Google Scholar PubMed PubMed Central
Kanai, Y., Dohmae, N., and Hirokawa, N. (2004). Kinesin transports RNA: isolation and characterization of an RNA-transporting granule. Neuron 43, 513–525.10.1016/j.neuron.2004.07.022Search in Google Scholar PubMed
Keeble, A.H., Khan, Z., Forster, A., and James, L.C. (2008). TRIM21 is an igg receptor that is structurally, thermodynamically, and kinetically conserved. Proc. Natl. Acad. Sci. U.S.A. 105, 6045–6050.10.1073/pnas.0800159105Search in Google Scholar PubMed PubMed Central
Kentsis, A., Gordon, R.E., and Borden, K.L.B. (2002a). Control of biochemical reactions through supramolecular RING domain self-assembly. Proc. Natl. Acad. Sci. U.S.A. 99, 15404.10.1073/pnas.202608799Search in Google Scholar PubMed PubMed Central
Kentsis, A., Gordon, R.E., and Borden, K.L.B. (2002b). Self-assembly properties of a model RING domain. Proc. Natl. Acad. Sci. U.S.A. 99, 667.10.1073/pnas.012317299Search in Google Scholar PubMed PubMed Central
Khazaei, M.R., Bunk, E.C., Hillje, A.L., Jahn, H.M., Riegler, E.M., Knoblich, J.A., Young, P., and Schwamborn, J.C. (2011). The E3-ubiquitin ligase TRIM2 regulates neuronal polarization. J. Neurochem. 117, 29–37.10.1111/j.1471-4159.2010.06971.xSearch in Google Scholar PubMed
Kolakofsky, D., Kowalinski, E., and Cusack, S. (2012). A structure-based model of RIG-I activation. RNA 18, 2118–2127.10.1261/rna.035949.112Search in Google Scholar PubMed PubMed Central
Koliopoulos, M.G., Esposito, D., Christodoulou, E., Taylor, I.A., and Rittinger, K. (2016). Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity. EMBO J. 35, 1204–1218.10.15252/embj.201593741Search in Google Scholar PubMed PubMed Central
Koliopoulos, M.G., Lethier, M., van der Veen, A.G., Haubrich, K., Hennig, J., Kowalinski, E., Stevens, R.V., Martin, S.R., Reis e Sousa, C., Cusack, S., et al. (2018). Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition. Nat. Commun. 9, 1820.10.1038/s41467-018-04214-8Search in Google Scholar PubMed PubMed Central
Kudryashova, E., Kudryashov, D., Kramerova, I., and Spencer, M.J. (2005). TRIM32 is a ubiquitin ligase mutated in limb girdle muscular dystrophy type 2H that binds to skeletal muscle myosin and ubiquitinates actin. J. Mol. Biol. 354, 413–424.10.1016/j.jmb.2005.09.068Search in Google Scholar PubMed
Kudryashova, E., Wu, J., Havton, L.A., and Spencer, M.J. (2009). Deficiency of the E3 ubiquitin ligase TRIM32 in mice leads to a myopathy with a neurogenic component. Hum. Mol. Genet. 18, 1353–1367.10.1093/hmg/ddp036Search in Google Scholar PubMed PubMed Central
Kulkarni, A., Oza, J., Yao, M., Sohail, H., Ginjala, V., Tomas-Loba, A., Horejsi, Z., Tan, A.R., Boulton, S.J., and Ganesan, S. (2013). Tripartite motif-containing 33 (TRIM33) protein functions in the poly(ADP-ribose) polymerase (PARP)-dependent DNA damage response through interaction with amplified in liver cancer 1 (ALC1) protein. J. Biol. Chem. 288, 32357–32369.10.1074/jbc.M113.459164Search in Google Scholar PubMed PubMed Central
Kumari, P., Aeschimann, F., Gaidatzis, D., Keusch, J.J., Ghosh, P., Neagu, A., Pachulska-Wieczorek, K., Bujnicki, J.M., Gut, H., Grosshans, H., et al. (2018). Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition. Nat. Commun. 9, 1549.10.1038/s41467-018-03920-7Search in Google Scholar PubMed PubMed Central
Kwon, S.C., Yi, H., Eichelbaum, K., Föhr, S., Fischer, B., You, K.T., Castello, A., Krijgsveld, J., Hentze, M.W., and Kim, V.N. (2013). The RNA-binding protein repertoire of embryonic stem cells. Nat. Struct. Mol. Biol. 20, 1122.10.1038/nsmb.2638Search in Google Scholar PubMed
LaBeau-DiMenna, E.M., Clark, K.A., Bauman, K.D., Parker, D.S., Cripps, R.M., and Geisbrecht, E.R. (2012). Thin, a TRIM32 ortholog, is essential for myofibril stability and is required for the integrity of the costamere in Drosophila. Proc. Natl. Acad. Sci. U.S.A. 109, 17983–17988.10.1073/pnas.1208408109Search in Google Scholar PubMed PubMed Central
Lang, X., Tang, T., Jin, T., Ding, C., Zhou, R., and Jiang, W. (2017). TRIM65-catalized ubiquitination is essential for MDA5- mediated antiviral innate immunity. J. Exp. Med. 214, 459–473.10.1084/jem.20160592Search in Google Scholar PubMed PubMed Central
Langevin, C., Levraud, J.P., and Boudinot, P. (2019). Fish antiviral tripartite motif (TRIM) proteins. Fish Shellfish Immunol. 86, 724 – 733.10.1016/j.fsi.2018.12.008Search in Google Scholar PubMed
Lau, C.k., Bachorik, J.L., and Dreyfuss, G. (2009). Gemin5-snRNA interaction reveals an RNA binding function for WD repeat domains. Nat. Struct. Mol. Biol. 16, 486–491.10.1038/nsmb.1584Search in Google Scholar PubMed
Laver, J.D., Li, X., Ray, D., Cook, K.B., Hahn, N.A., Nabeel-Shah, S., Kekis, M., Luo, H., Marsolais, A.J., Fung, K.Y., et al. (2015). Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition. Genome Biol. 16, 94.10.1186/s13059-015-0659-4Search in Google Scholar PubMed PubMed Central
Lee, C.Y., Wilkinson, B.D., Siegrist, S.E., Wharton, R.P., and Doe, C.Q. (2006). Brat is a Miranda cargo protein that promotes neuronal differentiation and inhibits neuroblast self-renewal. Dev. Cell 10, 441–449.10.1016/j.devcel.2006.01.017Search in Google Scholar PubMed
Lee, N.R., Choi, J.Y., Yoon, I.H., Lee, J.K., and Inn, K.S. (2018). Positive regulatory role of c-Src-mediated TRIM25 tyrosine phosphorylation on RIG-I ubiquitination and RIG-I-mediated antiviral signaling pathway. Cell. Immunol. 332, 94–100.10.1016/j.cellimm.2018.08.004Search in Google Scholar PubMed
Leppek, K., Schott, J., Reitter, S., Poetz, F., Hammond, M.C., and Stoecklin, G. (2013). Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs. Cell 153, 869–881.10.1016/j.cell.2013.04.016Search in Google Scholar PubMed
Li, X. and Sodroski, J. (2008). The TRIM5alpha B-box 2 domain promotes cooperative binding to the retroviral capsid by mediating higher-order self-association. J. Virol. 82, 11495–11502.10.1128/JVI.01548-08Search in Google Scholar PubMed PubMed Central
Li, P., Banjade, S., Cheng, H.C., Kim, S., Chen, B., Guo, L., Llaguno, M., Hollingsworth, J.V., King, D.S., Banani, S.F., et al. (2012). Phase transitions in the assembly of multivalent signalling proteins. Nature 483, 336–340.10.1038/nature10879Search in Google Scholar PubMed PubMed Central
Li, S., Wang, L., Fu, B., and Dorf, M.E. (2014). TRIM65: A cofactor for regulation of the microRNA pathway. RNA Biol. 11, 1113–1121.10.4161/rna.36179Search in Google Scholar PubMed PubMed Central
Li, Y.L., Chandrasekaran, V., Carter, S.D., Woodward, C.L., Christensen, D.E., Dryden, K.A., Pornillos, O., Yeager, M., Ganser-Pornillos, B.K., Jensen, G.J., et al. (2016). Primate TRIM5 proteins form hexagonal nets on HIV-1 capsids. Elife 5, e16269.10.7554/eLife.16269Search in Google Scholar PubMed PubMed Central
Li, M.M.H., Lau, Z., Cheung, P., Aguilar, E.G., Schneider, W.M., Bozzacco, L., Molina, H., Buehler, E., Takaoka, A., Rice, C.M., et al. (2017). TRIM25 enhances the antiviral action of Zinc-Finger Antiviral Protein (ZAP). PLoS Pathog. 13, e1006145.10.1371/journal.ppat.1006145Search in Google Scholar PubMed PubMed Central
Liang, Q., Deng, H., Li, X., Wu, X., Tang, Q., Chang, T.H., Peng, H., Rauscher 3rd, F.J., Ozato, K., and Zhu, F. (2011). Tripartite motif-containing protein 28 is a small ubiquitin-related modifier E3 ligase and negative regulator of IFN regulatory factor 7. J. Immunol. 187, 4754–4763.10.4049/jimmunol.1101704Search in Google Scholar PubMed PubMed Central
Lim, M., Newman, J.A., Williams, H.L., Aitkenhead, H., Gileadi, O., and Svejstrup, J. (2018). A ubiquitin-binding domain that does not bind ubiquitin. bioRxiv, 375832.10.1101/375832Search in Google Scholar
Lin, Y., Protter, D.S.W., Rosen, M.K., and Parker, R. (2015). Formation and maturation of phase-separated liquid droplets by RNA-binding proteins. Mol. Cell 60, 208–219.10.1016/j.molcel.2015.08.018Search in Google Scholar PubMed PubMed Central
Lin, H., Jiang, M., Liu, L., Yang, Z., Ma, Z., Liu, S., Ma, Y., Zhang, L., and Cao, X. (2019). The long noncoding RNA Lnczc3h7a promotes a TRIM25-mediated RIG-I antiviral innate immune response. Nat. Immunol. doi: 10.1038/s41590-019-0379-0. [Epub ahead of print].10.1038/s41590-019-0379-0Search in Google Scholar PubMed
Liu, B., Li, N.L., Shen, Y., Bao, X., Fabrizio, T., Elbahesh, H., Webby, R.J., and Li, K. (2016). The C-terminal tail of TRIM56 dictates antiviral restriction of influenza a and b viruses by impeding viral RNA synthesis. J. Virol. 90, 4369–4382.10.1128/JVI.03172-15Search in Google Scholar PubMed PubMed Central
Loedige, I. and Filipowicz, W. (2009). TRIM-NHL proteins take on miRNA regulation. Cell 136, 818–820.10.1016/j.cell.2009.02.030Search in Google Scholar PubMed
Loedige, I., Gaidatzis, D., Sack, R., Meister, G., and Filipowicz, W. (2013). The mammalian TRIM-NHL protein TRIM71/LIN-41 is a repressor of mRNA function. Nucleic Acids Res. 41, 518–532.10.1093/nar/gks1032Search in Google Scholar PubMed PubMed Central
Loedige, I., Stotz, M., Qamar, S., Kramer, K., Hennig, J., Schubert, T., Loffler, P., Langst, G., Merkl, R., Urlaub, H., et al. (2014). The NHL domain of BRAT is an RNA-binding domain that directly contacts the hunchback mRNA for regulation. Genes Dev. 28, 749–764.10.1101/gad.236513.113Search in Google Scholar PubMed PubMed Central
Loedige, I., Jakob, L., Treiber, T., Ray, D., Stotz, M., Treiber, N., Hennig, J., Cook, K.B., Morris, Q., Hughes, T.R., et al. (2015). The crystal structure of the NHL domain in complex with RNA reveals the molecular basis of Drosophila brain-tumor-mediated gene regulation. Cell Rep. 13, 1206–1220.10.1016/j.celrep.2015.09.068Search in Google Scholar PubMed
Loer, B. and Hoch, M. (2008). Wech proteins: roles in integrin functions and beyond. Cell Adh. Migr. 2, 177–179.10.4161/cam.2.3.6579Search in Google Scholar PubMed PubMed Central
Loer, B., Bauer, R., Bornheim, R., Grell, J., Kremmer, E., Kolanus, W., and Hoch, M. (2008). The NHL-domain protein Wech is crucial for the integrin-cytoskeleton link. Nat. Cell Biol. 10, 422–428.10.1038/ncb1704Search in Google Scholar PubMed
Malinovska, L., Kroschwald, S., and Alberti, S. (2013). Protein disorder, prion propensities, and self-organizing macromolecular collectives. Biochim. Biophys. Acta 1834, 918–931.10.1016/j.bbapap.2013.01.003Search in Google Scholar PubMed
Manokaran, G., Finol, E., Wang, C., Gunaratne, J., Bahl, J., Ong, E.Z., Tan, H.C., Sessions, O.M., Ward, A.M., Gubler, D.J., et al. (2015). Dengue subgenomic RNA binds TRIM25 to inhibit interferon expression for epidemiological fitness. Science 350, 217–221.10.1126/science.aab3369Search in Google Scholar PubMed PubMed Central
Marchetti, G., Reichardt, I., Knoblich, J.A., and Besse, F. (2014). The TRIM-NHL protein Brat promotes axon maintenance by repressing src64b expression. J. Neurosci. 34, 13855–13864.10.1523/JNEUROSCI.3285-13.2014Search in Google Scholar PubMed PubMed Central
Marín, I. (2012). Origin and diversification of TRIM ubiquitin ligases. PLoS One 7, e50030.10.1371/journal.pone.0050030Search in Google Scholar PubMed PubMed Central
Maris, C., Dominguez, C., and Allain, F.H.T. (2005). The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J. 272, 2118–2131.10.1111/j.1742-4658.2005.04653.xSearch in Google Scholar PubMed
Martin-Vicente, M., Medrano, L.M., Resino, S., Garcia-Sastre, A., and Martinez, I. (2017). TRIM25 in the regulation of the antiviral innate immunity. Front. Immunol. 8, 1187.10.3389/fimmu.2017.01187Search in Google Scholar PubMed PubMed Central
McEwan, W.A., Mallery, D.L., Rhodes, D.A., Trowsdale, J., and James, L.C. (2011). Intracellular antibody-mediated immunity and the role of TRIM21. Bioessays 33, 803–809.10.1002/bies.201100093Search in Google Scholar PubMed
Menon, S., Boyer, N.P., Winkle, C.C., McClain, L.M., Hanlin, C.C., Pandey, D., Rothenfußer, S., Taylor, A.M., and Gupton, S.L. (2015). The E3 ubiquitin ligase TRIM9 is a filopodia off switch required for Netrin-dependent axon guidance. Dev. Cell 35, 698–712.10.1016/j.devcel.2015.11.022Search in Google Scholar PubMed PubMed Central
Meroni, G. and Diez-Roux, G. (2005). TRIM/RBCC, a novel class of ‘single protein RING finger’ E3 ubiquitin ligases. Bioessays 27, 1147–1157.10.1002/bies.20304Search in Google Scholar PubMed
Meszaros, B., Kumar, M., Gibson, T.J., Uyar, B., and Dosztanyi, Z. (2017). Degrons in cancer. Sci. Signal. 10, pii: eaak9982.Search in Google Scholar
Meyerson, N.R., Zhou, L., Guo, Y.R., Zhao, C., Tao, Y.J., Krug, R.M., and Sawyer, S.L. (2017). Nuclear TRIM25 specifically targets influenza virus ribonucleoproteins to block the onset of RNA chain elongation. Cell Host Microbe 22, 627–638.10.1016/j.chom.2017.10.003Search in Google Scholar PubMed PubMed Central
Mitschka, S., Ulas, T., Goller, T., Schneider, K., Egert, A., Mertens, J., Brustle, O., Schorle, H., Beyer, M., Klee, K., et al. (2015). Co-existence of intact stemness and priming of neural differentiation programs in mES cells lacking TRIM71. Sci. Rep. 5, 11126.10.1038/srep11126Search in Google Scholar PubMed PubMed Central
Mittag, T., Bouchard, J., Martin, E., Otero, J., Marada, S., and Ogden, S. (2017). Multivalent interactions between a ubiquitin ligase and its substrates mediate their recruitment to liquid membrane-less organelles. FASEB J. 31, 916.3.Search in Google Scholar
Mukherjee, S., Tucker-Burden, C., Zhang, C., Moberg, K., Read, R., Hadjipanayis, C., and Brat, D.J. (2016). Drosophila Brat and human ortholog TRIM3 maintain stem cell equilibrium and suppress brain tumorigenesis by attenuating Notch nuclear transport. Cancer Res. 76, 2443–2452.10.1158/0008-5472.CAN-15-2299Search in Google Scholar
Murata, Y. and Wharton, R.P. (1995). Binding of pumilio to maternal hunchback mRNA is required for posterior patterning in Drosophila embryos. Cell 80, 747–756.10.1016/0092-8674(95)90353-4Search in Google Scholar
Neumuller, R.A., Betschinger, J., Fischer, A., Bushati, N., Poernbacher, I., Mechtler, K., Cohen, S.M., and Knoblich, J.A. (2008). Mei-P26 regulates microRNAs and cell growth in the Drosophila ovarian stem cell lineage. Nature 454, 241–245.10.1038/nature07014Search in Google Scholar PubMed PubMed Central
Nguyen, D.T.T., Richter, D., Michel, G., Mitschka, S., Kolanus, W., Cuevas, E., and Wulczyn, F.G. (2017). The ubiquitin ligase LIN41/TRIM71 targets p53 to antagonize cell death and differentiation pathways during stem cell differentiation. Cell Death Differ. 24, 1063–1078.10.1038/cdd.2017.54Search in Google Scholar PubMed PubMed Central
Nisole, S., Stoye, J.P., and Saib, A. (2005). TRIM family proteins: retroviral restriction and antiviral defence. Nat. Rev. Microbiol. 3, 799–808.10.1038/nrmicro1248Search in Google Scholar PubMed
Ohkawa, N., Kokura, K., Matsu-Ura, T., Obinata, T., Konishi, Y., and Tamura, T.A. (2001). Molecular cloning and characterization of neural activity-related RING finger protein (NARF): a new member of the RBCC family is a candidate for the partner of myosin V. J. Neurochem. 78, 75–87.10.1046/j.1471-4159.2001.00373.xSearch in Google Scholar PubMed
Orimo, A., Inoue, S., Minowa, O., Tominaga, N., Tomioka, Y., Sato, M., Kuno, J., Hiroi, H., Shimizu, Y., Suzuki, M., et al. (1999). Underdeveloped uterus and reduced estrogen responsiveness in mice with disruption of the estrogen-responsive finger protein gene, which is a direct target of estrogen receptor alpha. Proc. Natl. Acad. Sci. U.S.A. 96, 12027–12032.10.1073/pnas.96.21.12027Search in Google Scholar PubMed PubMed Central
Ozato, K., Shin, D.M., Chang, T.H., and Morse, H.C. 3rd. (2008). TRIM family proteins and their emerging roles in innate immunity. Nat. Rev. Immunol. 8, 849–860.10.1038/nri2413Search in Google Scholar PubMed PubMed Central
Pertel, T., Hausmann, S., Morger, D., Züger, S., Guerra, J., Lascano, J., Reinhard, C., Santoni, F.A., Uchil, P.D., Chatel, L., et al. (2011). TRIM5 is an innate immune sensor for the retrovirus capsid lattice. Nature 472, 361.10.1038/nature09976Search in Google Scholar PubMed PubMed Central
Pommier, R.M., Gout, J., Vincent, D.F., Alcaraz, L.B., Chuvin, N., Arfi, V., Martel, S., Kaniewski, B., Devailly, G., Fourel, G., et al. (2015). TIF1gamma suppresses tumor progression by regulating mitotic checkpoints and chromosomal stability. Cancer Res. 75, 4335–4350.10.1158/0008-5472.CAN-14-3426Search in Google Scholar PubMed
Qin, Y., Cui, H., and Zhang, H. (2015). Overexpression of TRIM25 in lung cancer regulates tumor cell progression. Technol. Cancer Res. Treat. 15, 707–715.10.1177/1533034615595903Search in Google Scholar PubMed
Ragvin, A., Valvatne, H., Erdal, S., Arskog, V., Tufteland, K.R., Breen, K., OYan, A.M., Eberharter, A., Gibson, T.J., Becker, P.B., et al. (2004). Nucleosome binding by the bromodomain and PHD finger of the transcriptional cofactor p300. J. Mol. Biol. 337, 773–788.10.1016/j.jmb.2004.01.051Search in Google Scholar PubMed
Ray, D., Kazan, H., Chan, E.T., Pena Castillo, L., Chaudhry, S., Talukder, S., Blencowe, B.J., Morris, Q., and Hughes, T.R. (2009). Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat. Biotechnol. 27, 667–670.10.1038/nbt.1550Search in Google Scholar PubMed
Reichardt, I., Bonnay, F., Steinmann, V., Loedige, I., Burkard, T.R., Meister, G., and Knoblich, J.A. (2018). The tumor suppressor Brat controls neuronal stem cell lineages by inhibiting Deadpan and Zelda. EMBO Rep. 19, 102–117.10.15252/embr.201744188Search in Google Scholar PubMed PubMed Central
Reymond, A., Meroni, G., Fantozzi, A., Merla, G., Cairo, S., Luzi, L., Riganelli, D., Zanaria, E., Messali, S., Cainarca, S., et al. (2001). The tripartite motif family identifies cell compartments. EMBO J. 20, 2140–2151.10.1093/emboj/20.9.2140Search in Google Scholar PubMed PubMed Central
Rybak, A., Fuchs, H., Hadian, K., Smirnova, L., Wulczyn, E.A., Michel, G., Nitsch, R., Krappmann, D., and Wulczyn, F.G. (2009). The let-7 target gene mouse lin-41 is a stem cell specific E3 ubiquitin ligase for the miRNA pathway protein Ago2. Nat. Cell Biol. 11, 1411–1420.10.1038/ncb1987Search in Google Scholar PubMed
Sanchez, J.G., Sparrer, K.M.J., Chiang, C., Reis, R.A., Chiang, J.J., Zurenski, M.A., Wan, Y., Gack, M.U., and Pornillos, O. (2018). TRIM25 binds RNA to modulate cellular anti-viral defense. J. Mol. Biol. 430, 5280–5293.10.1016/j.jmb.2018.10.003Search in Google Scholar PubMed PubMed Central
Sardiello, M., Cairo, S., Fontanella, B., Ballabio, A., and Meroni, G. (2008). Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties. BMC Evol. Biol. 8, 225.10.1186/1471-2148-8-225Search in Google Scholar PubMed PubMed Central
Schlundt, A., Heinz, G.A., Janowski, R., Geerlof, A., Stehle, R., Heissmeyer, V., Niessing, D., and Sattler, M. (2014). Structural basis for RNA recognition in roquin-mediated post-transcriptional gene regulation. Nat. Struct. Mol. Biol. 21, 671.10.1038/nsmb.2855Search in Google Scholar PubMed
Schoser, B.G.H., Frosk, P., Engel, A.G., Klutzny, U., Lochmuller, H., and Wrogemann, K. (2005). Commonality of TRIM32 mutation in causing sarcotubular myopathy and LGMD2H. Ann. Neurol. 57, 591–595.10.1002/ana.20441Search in Google Scholar PubMed
Schreiber, J., Vegh, M.J., Dawitz, J., Kroon, T., Loos, M., Labonte, D., Li, K.W., Van Nierop, P., Van Diepen, M.T., De Zeeuw, C.I., et al. (2015). Ubiquitin ligase TRIM3 controls hippocampal plasticity and learning by regulating synaptic gamma-actin levels. J. Cell Biol. 211, 569–586.10.1083/jcb.201506048Search in Google Scholar
Schwamborn, J.C., Berezikov, E., and Knoblich, J.A. (2009). The TRIM-NHL protein TRIM32 activates microRNAs and prevents self-renewal in mouse neural progenitors. Cell 136, 913–925.10.1016/j.cell.2008.12.024Search in Google Scholar
Shen, T.H., Lin, H.K., Scaglioni, P.P., Yung, T.M., and Pandolfi, P.P. (2006). The mechanisms of PML-nuclear body formation. Mol. Cell 24, 331–339.10.1016/j.molcel.2006.09.013Search in Google Scholar
Shen, Y., Li, N.L., Wang, J., Liu, B., Lester, S., and Li, K. (2012). TRIM56 is an essential component of the TLR3 antiviral signaling pathway. J. Biol. Chem. 287, 36404–36413.10.1074/jbc.M112.397075Search in Google Scholar
Shi, W., Chen, Y., Gan, G., Wang, D., Ren, J., Wang, Q., Xu, Z., Xie, W., and Zhang, Y.Q. (2013). Brain tumor regulates neuromuscular synapse growth and endocytosis in Drosophila by suppressing mad expression. J. Neurosci. 33, 12352–12363.10.1523/JNEUROSCI.0386-13.2013Search in Google Scholar
Shieh, S.Y. and Bonini, N.M. (2011). Genes and pathways affected by CAG-repeat RNA-based toxicity in Drosophila. Hum. Mol. Genet. 20, 4810–4821.10.1093/hmg/ddr420Search in Google Scholar
Short, K.M. and Cox, T.C. (2006). Subclassification of the RBCC/TRIM superfamily reveals a novel motif necessary for microtubule binding. J. Biol. Chem. 281, 8970–8980.10.1074/jbc.M512755200Search in Google Scholar
Slack, F.J. and Ruvkun, G. (1998). A novel repeat domain that is often associated with RING finger and B-box motifs. Trends Biochem. Sci. 23, 474–475.10.1016/S0968-0004(98)01299-7Search in Google Scholar
Slack, F.J., Basson, M., Liu, Z., Ambros, V., Horvitz, H.R., and Ruvkun, G. (2000). The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol. Cell 5, 659–669.10.1016/S1097-2765(00)80245-2Search in Google Scholar
Song, B., Gold, B., O’hUigin, C., Javanbakht, H., Li, X., Stremlau, M., Winkler, C., Dean, M., and Sodroski, J. (2005). The B30.2(SPRY) domain of the retroviral restriction factor TRIM5alpha exhibits lineage-specific length and sequence variation in primates. J. Virol. 79, 6111–6121.10.1128/JVI.79.10.6111-6121.2005Search in Google Scholar PubMed PubMed Central
Sonoda, J. and Wharton, R.P. (2001). Drosophila brain tumor is a translational repressor. Genes Dev. 15, 762–773.10.1101/gad.870801Search in Google Scholar PubMed PubMed Central
Sparrer, K.M.J. and Gack, M.U. (2018). TRIM proteins: New players in virus-induced autophagy. PLoS Pathog. 14, e1006787.10.1371/journal.ppat.1006787Search in Google Scholar PubMed PubMed Central
Stacey, K.B., Breen, E., and Jefferies, C.A. (2012). Tyrosine phosphorylation of the E3 ubiquitin ligase TRIM21 positively regulates interaction with IRF3 and hence TRIM21 activity. PLoS One 7, e34041.10.1371/journal.pone.0034041Search in Google Scholar PubMed PubMed Central
Stirnimann, C.U., Petsalaki, E., Russell, R.B., and Muller, C.W. (2010). WD40 proteins propel cellular networks. Trends Biochem. Sci. 35, 565–574.10.1016/j.tibs.2010.04.003Search in Google Scholar PubMed
Stoll, G.A., Oda, S.i., Chong, Z.S., Yu, M., McLaughlin, S.H., and Modis, Y. (2018). Structure of the tripartite motif of KAP1/TRIM28 identifies molecular interfaces required for transcriptional silencing of retrotransposons. bioRxiv, 505677.10.1101/505677Search in Google Scholar
Takayama, K.I., Suzuki, T., Tanaka, T., Fujimura, T., Takahashi, S., Urano, T., Ikeda, K., and Inoue, S. (2018). TRIM25 enhances cell growth and cell survival by modulating p53 signals via interaction with G3BP2 in prostate cancer. Oncogene 37, 2165–2180.10.1038/s41388-017-0095-xSearch in Google Scholar PubMed
Tanaka, S., Jiang, Y., Martinez, G.J., Tanaka, K., Yan, X., Kurosaki, T., Kaartinen, V., Feng, X.H., Tian, Q., Wang, X., et al. (2018). TRIM33 mediates the proinflammatory function of Th17 cells. J. Exp. Med. 215, 1853–1868.10.1084/jem.20170779Search in Google Scholar PubMed PubMed Central
Tautz, D. (1988). Regulation of the Drosophila segmentation gene hunchback by two maternal morphogenetic centres. Nature 332, 281–284.10.1038/332281a0Search in Google Scholar PubMed
Thompson, S., Pearson, A.N., Ashley, M.D., Jessick, V., Murphy, B.M., Gafken, P., Henshall, D.C., Morris, K.T., Simon, R.P., and Meller, R. (2011). Identification of a novel Bcl-2-interacting mediator of cell death (Bim) E3 ligase, tripartite motif-containing protein 2 (TRIM2), and its role in rapid ischemic tolerance-induced neuroprotection. J. Biol. Chem. 286, 19331–19339.10.1074/jbc.M110.197707Search in Google Scholar PubMed PubMed Central
Tocchini, C. and Ciosk, R. (2015). TRIM-NHL proteins in development and disease. Semin. Cell Dev. Biol. 47–48, 52–59.10.1016/j.semcdb.2015.10.017Search in Google Scholar PubMed
Tocchini, C., Keusch, J.J., Miller, S.B., Finger, S., Gut, H., Stadler, M.B., and Ciosk, R. (2014). The TRIM-NHL protein LIN-41 controls the onset of developmental plasticity in Caenorhabditis elegans. PLoS Genet. 10, 1–13.10.1371/journal.pgen.1004533Search in Google Scholar
Treiber, T., Treiber, N., Plessmann, U., Harlander, S., Daiß, J.L., Eichner, N., Lehmann, G., Schall, K., Urlaub, H., and Meister, G. (2017). A compendium of RNA-binding proteins that regulate microRNA biogenesis. Mol. Cell 66, 270–284.e13.10.1016/j.molcel.2017.03.014Search in Google Scholar
Trendel, J., Schwarzl, T., Horos, R., Prakash, A., Bateman, A., Hentze, M.W., and Krijgsveld, J. (2019). The human RNA-binding proteome and its dynamics during translational arrest. Cell 176, 391–403.e19.10.1016/j.cell.2018.11.004Search in Google Scholar
Uversky, V.N. (2014). Unreported intrinsic disorder in proteins: building connections to the literature on IDPs. Intrinsically Disord. Proteins 2, e970499.10.4161/21690693.2014.970499Search in Google Scholar
van Beuningen, S.F., Will, L., Harterink, M., Chazeau, A., van Battum, E.Y., Frias, C.P., Franker, M.A., Katrukha, E.A., Stucchi, R., Vocking, K., et al. (2015). TRIM46 controls neuronal polarity and axon specification by driving the formation of parallel microtubule arrays. Neuron 88, 1208–1226.10.1016/j.neuron.2015.11.012Search in Google Scholar
van Gent, M., Sparrer, K.M.J., and Gack, M.U. (2018). TRIM proteins and their roles in antiviral host defenses. Annu. Rev. Virol. 5, 385–405.10.1146/annurev-virology-092917-043323Search in Google Scholar
Versteeg, G.A., Rajsbaum, R., Sánchez-Aparicio, M.T., Maestre, A.M., Valdiviezo, J., Shi, M., Inn, K.S., Fernandez-Sesma, A., Jung, J., and Garca-Sastre, A. (2013). The E3-ligase TRIM family of proteins regulates signaling pathways triggered by innate immune pattern-recognition receptors. Immunity 38, 384–398.10.1016/j.immuni.2012.11.013Search in Google Scholar
Volovik, Y., Moll, L., Marques, F.C., Maman, M., Bejerano-Sagie, M., and Cohen, E. (2014). Differential regulation of the heat shock factor 1 and DAF-16 by neuronal nhl-1 in the nematode C. elegans. Cell Rep. 9, 2192–2205.10.1016/j.celrep.2014.11.028Search in Google Scholar
Wang, C. and Lehmann, R. (1991). Nanos is the localized posterior determinant in Drosophila. Cell 66, 637–647.10.1016/0092-8674(91)90110-KSearch in Google Scholar
Wang, J.T. and Seydoux, G. (2014). P granules. Curr. Biol. 24, R637–R638.10.1016/j.cub.2014.06.018Search in Google Scholar PubMed PubMed Central
Wang, P., Benhenda, S., Wu, H., Lallemand-Breitenbach, V., Zhen, T., Jollivet, F., Peres, L., Li, Y., Chen, S.J., Chen, Z., et al. (2018). RING tetramerization is required for nuclear body biogenesis and PML sumoylation. Nat. Commun. 9, 1277.10.1038/s41467-018-03498-0Search in Google Scholar
Wang, J., Liu, B., Wang, N., Lee, Y.M., Liu, C., and Li, K. (2011). TRIM56 is a virus- and interferon-inducible E3 ubiquitin ligase that restricts pestivirus infection. J. Virol. 85, 3733–3745.10.1128/JVI.02546-10Search in Google Scholar
Wang, P., Zhao, W., Zhao, K., Zhang, L., and Gao, C. (2015). TRIM26 negatively regulates interferon-beta production and antiviral response through polyubiquitination and degradation of nuclear IRF3. PLoS Pathog. 11, e1004726.10.1371/journal.ppat.1004726Search in Google Scholar
Watanabe, M. and Hatakeyama, S. (2017). TRIM proteins and diseases. J. Biochem. 161, 135–144.10.1093/jb/mvw087Search in Google Scholar
Weidmann, C.A., Qiu, C., Arvola, R.M., Lou, T.F., Killingsworth, J., Campbell, Z.T., Tanaka Hall, T.M., and Goldstrohm, A.C. (2016). Drosophila Nanos acts as a molecular clamp that modulates the RNA-binding and repression activities of Pumilio. Elife 5, pii: e17096.10.7554/eLife.17096.041Search in Google Scholar
Wharton, R.P. and Struhl, G. (1991). RNA regulatory elements mediate control of Drosophila body pattern by the posterior morphogen nanos. Cell 67, 955–967.10.1016/0092-8674(91)90368-9Search in Google Scholar
Williams, S.C. and Parsons, J.L. (2018). NTH1 is a new target for ubiquitylation-dependent regulation by TRIM26 required for the cellular response to oxidative stress. Mol. Cell. Biol. 38, pii: e00616-7.10.1128/MCB.00616-17Search in Google Scholar PubMed PubMed Central
Woo, J.S., Suh, H.Y., Park, S.Y., and Oh, B.H. (2006). Structural basis for protein recognition by B30.2/SPRY domains. Mol. Cell 24, 967–976.10.1016/j.molcel.2006.11.009Search in Google Scholar PubMed
Worringer, K.A., Rand, T.A., Hayashi, Y., Sami, S., Takahashi, K., Tanabe, K., Narita, M., Srivastava, D., and Yamanaka, S. (2014). The let-7/LIN-41 pathway regulates reprogramming to human induced pluripotent stem cells by controlling expression of prodifferentiation genes. Cell Stem Cell 14, 40–52.10.1016/j.stem.2013.11.001Search in Google Scholar PubMed PubMed Central
Wulczyn, F.G., Cuevas, E., Franzoni, E., and Rybak, A. (2011). miRNAs need a TRIM: regulation of miRNA activity by TRIM-NHL proteins. Adv. Exp. Med. Biol. 700, 85–105.10.1007/978-1-4419-7823-3_9Search in Google Scholar PubMed
Yang, B., Wang, J., Wang, Y., Zhou, H., Wu, X., Tian, Z., and Sun, B. (2013). Novel function of TRIM44 promotes an antiviral response by stabilizing VISA. J. Immunol. 190, 3613–3619.10.4049/jimmunol.1202507Search in Google Scholar PubMed
Zhang, Q., Fan, L., Hou, F., Dong, A., Wang, Y.X., and Tong, Y. (2015a). New insights into the RNA-binding and E3 ubiquitin ligase activities of Roquins. Sci. Rep. 5, 15660.10.1038/srep15660Search in Google Scholar PubMed PubMed Central
Zhang, X., Qin, G., Chen, G., Li, T., Gao, L., Huang, L., Zhang, Y., Ouyang, K., Wang, Y., Pang, Y., Zeng, B., and Yu, L. (2015b). Variants in TRIM44 cause aniridia by impairing PAX6 expression. Hum. Mutat. 36, 1164–1167.10.1002/humu.22907Search in Google Scholar PubMed
Zhang, J., Zhang, C., Cui, J., Ou, J., Han, J., Qin, Y., Zhi, F., and Wang, R.F. (2017). TRIM45 functions as a tumor suppressor in the brain via its E3 ligase activity by stabilizing p53 through K63-linked ubiquitination. Cell Death Dis. 8, e2831.10.1038/cddis.2017.149Search in Google Scholar PubMed PubMed Central
Zou, Y., Chiu, H., Zinovyeva, A., Ambros, V., Chuang, C.F., and Chang, C. (2013). Developmental decline in neuronal regeneration by the progressive change of two intrinsic timers. Science 340, 372–376.10.1126/science.1231321Search in Google Scholar PubMed PubMed Central
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