RING Dimerization Links Higher-Order Assembly of TRIM5α to Synthesis of K63-Linked Polyubiquitin

Yudina, Zinaida; Roa, Amanda; Johnson, Rory; Biris, Nikolaos; Vieira, Daniel A. de Souza Aranha; Tsiperson, Vladislav; Reszka, Natalia; Taylor, Alexander B.; Hart, P. John; Demeler, Borries; Díaz-Griffero, Felipe; Ivanov, Dmitri N.

doi:10.1016/j.celrep.2015.06.072

Cited by 78 publications

(141 citation statements)

References 51 publications

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“…RING dimerization through a four‐helix bundle employing regions outside the RING has been observed in a number of dimeric RINGs such as the BRCA1/BARD1 heterodimer or the Rad18 homodimer (Brzovic et al , 2001; Huang et al , 2011). Furthermore, this arrangement is similar to that recently reported in the crystal structures of the RING domains of the retroviral restriction factor TRIM5α (Yudina et al , 2015) (Fig 3B) and TRIM37 (Northeast Structural Genomics Consortium, 3LRQ.pdb).…”

Section: Resultssupporting

confidence: 88%

“…This effect is similar to the mutation of I85R, which interferes with dimerization, similar to V72R in TRIM25 (Figs 5C and E, and EV2). Moreover, structural and sequence comparison of the RINGs of TRIM25 and TRIM5α shows that E11 and E12 occupy similar positions (Yudina et al , 2015). Intriguingly, structural alignment of the RINGs of TRIM25 and monomeric Cbl‐b shows that Y363 of Cbl‐b, which needs to become phosphorylated for full ligase activity, is in the equivalent position of E10, although the residues come from different structural elements (Dou et al , 2013).…”

Section: Resultsmentioning

confidence: 99%

“…In addition, there have been suggestions that substrate binding might induce higher order oligomers that may further enhance activity (Yudina et al , 2015). Though structural details of the mechanistic features that could explain oligomerization‐dependent activity are currently sparse, coiled‐coil‐mediated RING dimerization and subsequent stabilization of a closed E2~ubiquitin intermediate could explain this observation.…”

Section: Introductionmentioning

confidence: 99%

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Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity

et al. 2016

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TRIM E3 ubiquitin ligases regulate a wide variety of cellular processes and are particularly important during innate immune signalling events. They are characterized by a conserved tripartite motif in their N‐terminal portion which comprises a canonical RING domain, one or two B‐box domains and a coiled‐coil region that mediates ligase dimerization. Self‐association via the coiled‐coil has been suggested to be crucial for catalytic activity of TRIMs; however, the precise molecular mechanism underlying this observation remains elusive. Here, we provide a detailed characterization of the TRIM ligases TRIM25 and TRIM32 and show how their oligomeric state is linked to catalytic activity. The crystal structure of a complex between the TRIM25 RING domain and an ubiquitin‐loaded E2 identifies the structural and mechanistic features that promote a closed E2~Ub conformation to activate the thioester for ubiquitin transfer allowing us to propose a model for the regulation of activity in the full‐length protein. Our data reveal an unexpected diversity in the self‐association mechanism of TRIMs that might be crucial for their biological function.

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Section: Resultssupporting

confidence: 88%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity

et al. 2016

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“…One possibility is that N-terminal tags alter the turnover of TRIM5␣, potentially by perturbing the N-terminal acetylation observed in other studies (9,43). Alternatively, N-terminal tags may alter the ubiquitination of TRIM5␣ by perturbing the dimerization of the RING domains (44). Either of these possibilities might shift the degradative fate toward autophagic degradation pathways.…”

Section: Discussionmentioning

confidence: 96%

TRIM5α Degradation via Autophagy Is Not Required for Retroviral Restriction

Imam

Talley

Nelson

et al. 2016

J Virol

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TRIM5␣ is an interferon-inducible retroviral restriction factor that prevents infection by inducing the abortive disassembly of capsid cores recognized by its C-terminal PRY/SPRY domain. The mechanism by which TRIM5␣ mediates the disassembly of viral cores is poorly understood. Previous studies demonstrated that proteasome inhibitors abrogate the ability of TRIM5␣ to induce premature core disassembly and prevent reverse transcription; however, viral infection is still inhibited, indicating that the proteasome is partially involved in the restriction process. Alternatively, we and others have observed that TRIM5␣ associates with proteins involved in autophagic degradation pathways, and one recent study found that autophagic degradation is required for the restriction of retroviruses by TRIM5␣. Here, we show that TRIM5␣ is basally degraded via autophagy in the absence of restriction-sensitive virus. We observe that the autophagy markers LC3b and lysosome-associated membrane protein 2A (LAMP2A) localize to a subset of TRIM5␣ cytoplasmic bodies, and inhibition of lysosomal degradation with bafilomycin A1 increases this association. To test the requirement for macroautophagy in restriction, we examined the ability of TRIM5␣ to restrict retroviral infection in cells depleted of the autophagic mediators ATG5, Beclin1, and p62. In all cases, restriction of retroviruses by human TRIM5␣, rhesus macaque TRIM5␣, and owl monkey TRIM-Cyp remained potent in cells depleted of these autophagic effectors by small interfering RNA (siRNA) knockdown or clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 genome editing. Collectively, these results are consistent with observations that the turnover of TRIM5␣ proteins is sensitive to autophagy inhibition; however, the data presented here do not support observations that the inhibition of autophagy abrogates retroviral restriction by TRIM5 proteins. IMPORTANCERestriction factors are a class of proteins that inhibit viral replication. Following fusion of a retrovirus with a host cell membrane, the retroviral capsid is released into the cytoplasm of the target cell. TRIM5␣ inhibits retroviral infection by promoting the abortive disassembly of incoming retroviral capsid cores; as a result, the retroviral genome is unable to traffic to the nucleus, and the viral life cycle is extinguished. In the process of restriction, TRIM5␣ itself is degraded by the proteasome. However, in the present study, we have shown that in the absence of a restriction-sensitive virus, TRIM5␣ is degraded by both proteasomal and autophagic degradation pathways. Notably, we observed that restriction of retroviruses by TRIM5␣ does not require autophagic machinery. These data indicate that the effector functions of TRIM5␣ can be separated from its degradation and may have further implications for understanding the mechanisms of other TRIM family members.

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“…Further biochemical analysis of TRIM5α and homologous TRIMs, reveal that the RING domain is a prerequisite for efficient higher-order oligomer formations 189 . The most recent structure of the RING domain from TRIM5α in complex with Ubc13 suggests that RING dimerization is essential for mediating Lys63-linked ubiquitination 143 . To conclude, while the most recent structural findings have revealed the conserved structural signature of TRIM proteins forming anti-parallel dimerization mediated by the Coiled-coil region 177 , the formation of higher-order oligomers in other TRIMs remains to be explored.…”

Section: Trims Higher-order Oligomer Formationsmentioning

confidence: 99%

Structural insights into protein-protein interactions governing regulation in transcription initiation and ubiquitination

Anandapadamanaban¹

2015

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Front cover:Surface representation of the protein-protein complexes of E2~Ub-TRIM E3 ligase, which I have embellished with interacting proteins/domains in a range of colors.The author apologizes to those whose work could not be cited directly as original research articles but rather cited the recent reviews, due to space limitations.All previously published original peer reviewed articles are reprinted with permissions from the publisher.© Copyright 2015 Madhanagopal Anandapadamanaban, unless otherwise mentioned. Linkoping studies in Science and Technology. Dissertation No. 1694 Printed in Sweden by LiU-Tryck, 2015 Madhanagopal Anandapadamanaban Structural insights into protein-protein interactions governing regulation in transcription initiation and ubiquitination AbstractVirtually every aspect of the cellular processes in eukaryotes requires that the interactions between protein molecules are well coordinated in different regulatory pathways. Any protein dysfunction involved in these regulatory pathways might lead to various pathological conditions. Understanding the structural and functional peculiarities of these proteins molecular machineries will help in formulating structure-based drug design.The first regulatory process studied here is the RNA polymerase-II mediated transcription of the eukaryotic protein-coding genes to produce mRNAs. This process requires the formation of the 'transcription initiation' by the assembly of Pre-Initiation Complex (PIC) formation at a core promoter region. Regulation at this initiation level is a key mechanism for the control of gene expression that governs cellular growth and differentiation. The transcription Factor IID (TFIID) is a conserved multiprotein general transcription factor with an essential role in nucleating the PIC formation, composed of TATA Binding Protein (TBP) and about 14 TBP Associated Factors (TAFs). The here presented crystal structure (1.97 Å) of TBP bound to TAND1 and TAND2 domains from TAF1 reveals a detailed molecular pattern of interactions involving both transcriptionally activating and repressing regions in TBP, thereby uncovering central principles for anchoring of TBP-binding motifs. Together with NMR and cellular analysis, this work provides the structural basis of competitive binding with TFIIA to modulate TBP in promoter recognition.In eukaryotes, another fundamental mechanism in the regulation of cellular physiology is the post-translational modification of substrate proteins by ubiquitin, termed 'ubiquitination'. Important actors in this mechanism are the ubiquitin-ligases (E3s) that culminate the transfer of ubiquitin to the substrate and govern the specificity of this system. One E3 ligase in particular, TRIM21, defines a subgroup of the Tripartite Motif (TRIM) family, which belongs to the major RING-type of E3 ubiquitin ligases, and plays an important role in pathogenesis of autoimmunity by mediating ubiquitination of transcription factors. The crystal structure (2.86 Å) of the RING domain from TRIM21 ...

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RING Dimerization Links Higher-Order Assembly of TRIM5α to Synthesis of K63-Linked Polyubiquitin

Cited by 78 publications

References 51 publications

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity

TRIM5α Degradation via Autophagy Is Not Required for Retroviral Restriction

Structural insights into protein-protein interactions governing regulation in transcription initiation and ubiquitination

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