Linear ubiquitination: a newly discovered regulator of cell signalling

doi:10.1016/j.tibs.2012.11.007

Trends in Biochemical Sciences

Volume 38, Issue 2, February 2013, Pages 94-102

https://doi.org/10.1016/j.tibs.2012.11.007 Get rights and content

Ubiquitination is a post-translational modification that creates versatility in cell signalling, in part because eight biochemically different inter-ubiquitin linkages can be formed through the seven internal lysine residues of ubiquitin or its amino-terminal methionine. The latter, referred to as linear or M1 linkage, is created by the linear ubiquitin chain assembly complex (LUBAC). Previously, K63 linkages were thought to be exclusively responsible for ubiquitin-mediated nondegradative functions. It now emerges, however, that M1 ubiquitination is crucial in various pathways, and that generation of a physiological signalling output requires cooperation between different ubiquitin linkage types. Here, we review the currently known functions of LUBAC and M1 ubiquitination, discuss promising future research directions into their functions, and how this may reveal novel therapeutic opportunities for diseases with perturbed linear ubiquitination.

Section snippets

Ubiquitin system

Post-translational modifications regulate and fine tune signals induced by extracellular and intrinsic stimuli. Ubiquitination, along with phosphorylation, are arguably the two best-studied and perhaps main regulatory modifications. Phosphorylation is the covalent attachment of a phosphoryl group to a serine, threonine, or tyrosine residue of a target protein, thereby altering its electrostatic properties and allowing recruitment of downstream proteins and/or a change in activity.

Diversity of inter-ubiquitin linkages

How are differently linked di-ubiquitins different from each other? Each of the eight di-ubiquitin linkage types results in a distinct, unique overall structure with continuous surfaces and relative topologies between the two individual ubiquitin moieties. These structural differences are decoded by ubiquitin receptors that interact with high affinity with certain di-ubiquitin linkages and not others, thereby translating structural information into specific functions [5]. It is currently

Different classes of E3s act via distinct mechanisms

E2s are generally thought to determine linkage specificity, whereas E3s are thought to confer substrate specificity by facilitating the interaction between a particular substrate and an E2 [13]. However, although some E2s possess unique linkage specificity, others – including the UbcH5 family – are rather promiscuous and contribute to the generation of various ubiquitin linkages [14]. Based on their structure and function, E3s can be classified into HECT (homology to E6AP C terminus), RING

LUBAC: a novel RBR that promotes linear ubiquitin linkages

Heme-oxidised iron-responsive element-binding protein 2 (IRP2) ubiquitin ligase-1 [HOIL-1; also called RanBP-type and C3HC4-type zinc finger-containing protein 1 (RBCK1)] and HOIL-1-interacting protein (HOIP; also known as RNF31) are members of the RBR family. These two proteins have recently entered the spotlight because they form part of the LUBAC, a 600-kDa E3 complex capable of forming linear ubiquitin linkages, [20]. SH3 and multiple ankyrin repeat domains protein (SHANK)-associated RBCK1

Role of linear ubiquitination in TNF receptor 1 (TNFR1) signalling

The physiological function of LUBAC and linear ubiquitin linkages remained unclear for several years. It was initially proposed that M1 ubiquitination triggers proteasomal degradation [20]. Subsequently, however, it was discovered that LUBAC is implicated in various signalling pathways including those triggered by TNF, IL-1β, CD40 ligand (CD40L), various Toll-like receptors (TLRs), and NOD2 (nucleotide-binding oligomerisation domain-containing protein 2) 21, 23, 24, 25, 29, 30, 31 (Figure 5).

Implication of linear ubiquitination in other signalling pathways

Although the function of LUBAC is best characterised in TNFR1 signalling, it has also been implicated in a variety of other signalling pathways. CD40 is a TNFR superfamily member expressed on the surface of antigen-presenting cells and is required for various crucial steps in achieving adaptive immunity. Stimulation of CD40 by CD40L on B cells results in activation of MAPKs and canonical and noncanonical NF-κB signalling. LUBAC also forms part of the native CD40-RSC [21]. Interestingly,

Concluding remarks

It came as a surprise that LUBAC is a bona fide component of the TNF-RSC and that it functions to place M1 linkages on key signalling hubs, modifying the output of many different signalling pathways. Yet, it establishes LUBAC and the M1-ubiquitin linkage as crucial components in the cellular signalling repertoire. For most signalling complexes and pathways it remains to be determined how exactly LUBAC influences them, which factors are targeted by LUBAC, and how their function is thereby

References (64)

A. Hershko
Components of ubiquitin-protein ligase system. Resolution, affinity purification, and role in protein breakdown
J. Biol. Chem.
(1983)
C.M. Pickart et al.
Ubiquitin: structures, functions, mechanisms
Biochim. Biophys. Acta
(2004)
W.J. Cook
Structure of tetraubiquitin shows how multiubiquitin chains can be formed
J. Mol. Biol.
(1994)
R. Varadan
Structural properties of polyubiquitin chains in solution
J. Mol. Biol.
(2002)
P. Xu
Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation
Cell
(2009)
H.T. Kim
Certain pairs of ubiquitin-conjugating enzymes (E2s) and ubiquitin-protein ligases (E3s) synthesize nondegradable forked ubiquitin chains containing all possible isopeptide linkages
J. Biol. Chem.
(2007)
T.L. Haas
Recruitment of the linear ubiquitin chain assembly complex stabilizes the TNF-R1 signaling complex and is required for TNF-mediated gene induction
Mol. Cell
(2009)
B. Stieglitz
Structural analysis of SHARPIN, a subunit of a large multi-protein E3 ubiquitin ligase, reveals a novel dimerization function for the pleckstrin homology superfold
J. Biol. Chem.
(2012)
K.S. Inn
Linear ubiquitin assembly complex negatively regulates RIG-I- and TRIM25-mediated type I interferon induction
Mol. Cell
(2011)
R.B. Damgaard
The ubiquitin ligase XIAP recruits LUBAC for NOD2 signaling in inflammation and innate immunity
Mol. Cell
(2012)

O. Micheau et al.

Induction of TNF receptor I-mediated apoptosis via two sequential signaling complexes

Cell

(2003)

H. Hsu

TNF-dependent recruitment of the protein kinase RIP to the TNF receptor-1 signaling complex

Immunity

(1996)

H. Hsu

TRADD-TRAF2 and TRADD-FADD interactions define two distinct TNF receptor 1 signal transduction pathways

Cell

(1996)

H. Hsu

The TNF receptor 1-associated protein TRADD signals cell death and NF-kappa B activation

Cell

(1995)

D.H. Tsao

Solution structure of N-TRADD and characterization of the interaction of N-TRADD and C-TRAF2, a key step in the TNFR1 signaling pathway

Mol. Cell

(2000)

J.E. Vince

TRAF2 must bind to cellular inhibitors of apoptosis for tumor necrosis factor (tnf) to efficiently activate nf-{kappa}b and to prevent tnf-induced apoptosis

J. Biol. Chem.

(2009)

M. Rothe

The TNFR2-TRAF signaling complex contains two novel proteins related to baculoviral inhibitor of apoptosis proteins

Cell

(1995)

C.K. Ea

Activation of IKK by TNFalpha requires site-specific ubiquitination of RIP1 and polyubiquitin binding by NEMO

Mol. Cell

(2006)

M. Xu

A ubiquitin replacement strategy in human cells reveals distinct mechanisms of IKK activation by TNFalpha and IL-1beta

Mol. Cell

(2009)

Y.C. Lo

Structural basis for recognition of diubiquitins by NEMO

Mol. Cell

(2009)

S. Rahighi

Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation

Cell

(2009)

T. Kensche

Analysis of NF-kappaB essential modulator (NEMO) binding to linear and lysine-linked ubiquitin chains and its role in the activation of NF-kappaB

J. Biol. Chem.

(2012)

M.J. Gijbels

Maintenance of donor phenotype after full-thickness skin transplantation from mice with chronic proliferative dermatitis (cpdm/cpdm) to C57BL/Ka and nude mice and vice versa

J. Invest. Dermatol.

(1995)

F.M. Brennan et al.

Cytokines in autoimmunity

Curr. Opin. Immunol.

(1996)

J. Mazza

Innovative uses of tumor necrosis factor alpha inhibitors

Dermatol. Clin.

(2010)

S.J. van Wijk

Fluorescence-based sensors to monitor localization and functions of linear and k63-linked ubiquitin chains in cells

Mol. Cell

(2012)

K. Haglund et al.

Ubiquitylation and cell signaling

EMBO J.

(2005)

A. Hershko et al.

The ubiquitin system

Annu. Rev. Biochem.

(1998)

D. Komander et al.

The ubiquitin code

Annu. Rev. Biochem.

(2012)

K. Husnjak

Proteasome subunit Rpn13 is a novel ubiquitin receptor

Nature

(2008)

D. Meierhofer

Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry

J. Proteome Res.

(2008)

V. Chau

A multiubiquitin chain is confined to specific lysine in a targeted short-lived protein

Science

(1989)

Cited by (127)

The ubiquitin-proteasome system and learning-dependent synaptic plasticity – A 10 year update
2023, Neuroscience and Biobehavioral Reviews
Over 25 years ago, a seminal paper demonstrated that the ubiquitin-proteasome system (UPS) was involved in activity-dependent synaptic plasticity. Interest in this topic began to expand around 2008 following another seminal paper showing that UPS-mediated protein degradation controlled the “destabilization” of memories following retrieval, though we remained with only a basic understanding of how the UPS regulated activity- and learning-dependent synaptic plasticity. However, over the last 10 years there has been an explosion of papers on this topic that has significantly changed our understanding of how ubiquitin-proteasome signaling regulates synaptic plasticity and memory formation. Importantly, we now know that the UPS controls much more than protein degradation, is involved in plasticity underlying drugs of abuse and that there are significant sex differences in how ubiquitin-proteasome signaling is used for memory storage processes. Here, we aim to provide a critical 10-year update on the role of ubiquitin-proteasome signaling in synaptic plasticity and memory formation, including updated cellular models of how ubiquitin-proteasome activity could be regulating learning-dependent synaptic plasticity in the brain.
Neuroprotective effects of linear ubiquitin E3 ligase against aging-induced DNA damage and amyloid β neurotoxicity in the brain of Drosophila melanogaster
2022, Biochemical and Biophysical Research Communications
E3 ubiquitin ligase, HOIL1-interacting protein (HOIP), forms the linear ubiquitin chain assembly complex (LUBAC) with HOIL and SHANK-associated RH domain interactor and catalyzes linear ubiquitination, directly linking the N- and C-termini of ubiquitin. Recently, several studies have implicated linear ubiquitination in aging and Alzheimer disease (AD). However, little is currently known about the roles of HOIP in brain aging and AD pathology. Here, we investigated the role of linear ubiquitin E3 ligase (LUBEL), a Drosophila HOIP ortholog, in brain aging and amyloid β (Aβ) pathology in a Drosophila AD model. DNA double-strand breaks (DSBs) were increased in the aged brains of neuron-specific LUBEL-knockdown flies compared to the age-matched controls. Silencing of LUBEL in the neuron of AD model flies increased the neuronal apoptosis and neurodegeneration, whereas silencing in glial cells had no such effect. Aβ aggregation levels and DSBs were also increased in the LUBEL-silenced AD model fly brains, but autophagy and proteostasis were not affected by LUBEL silencing. Collectively, our results suggest that LUBEL protects neurons from aging-induced DNA damage and Aβ neurotoxicity.
Linkage reprogramming by tailor-made E3s reveals polyubiquitin chain requirements in DNA-damage bypass
2022, Molecular Cell
A polyubiquitin chain can adopt a variety of shapes, depending on how the ubiquitin monomers are joined. However, the relevance of linkage for the signaling functions of polyubiquitin chains is often poorly understood because of our inability to control or manipulate this parameter in vivo. Here, we present a strategy for reprogramming polyubiquitin chain linkage by means of tailor-made, linkage- and substrate-selective ubiquitin ligases. Using the polyubiquitylation of the budding yeast replication factor PCNA in response to DNA damage as a model case, we show that altering the features of a polyubiquitin chain in vivo can change the fate of the modified substrate. We also provide evidence for redundancy between distinct but structurally similar linkages, and we demonstrate by proof-of-principle experiments that the method can be generalized to targets beyond PCNA. Our study illustrates a promising approach toward the in vivo analysis of polyubiquitin signaling.
E2-E3 ubiquitin enzyme pairing - partnership in provoking or mitigating cancers
2022, Biochimica et Biophysica Acta - Reviews on Cancer
Citation Excerpt :
The most well-known function of ubiquitin (Ub) is degradation of targeted protein substrates. For example, the most common Ub linkage, UbK48 (Lys48-bridged Ub chains), is closely associated with degradation of the UbK48 linked protein by the proteasome [1]. On the other hand, as the second most abundant form of ubiquitination, the UbK63 (Lys63-bridged Ub chain)-linked target protein is associated with protein trafficking, DNA repair, and inflammation [2].
The ubiquitin-proteasome system (UPS) modulates carcinogenesis through ubiquitination of cancer-related target proteins, leading to their degradation in the proteasome. This may deactivate tumor suppressors or activate tumor promoters- either way causing homeostatic imbalance. As major components of the UPS, the E2 and E3 enzymes are recognized as pivotal determinants of substrate recognition and ubiquitination. Identification of E2-E3 pairing selectivity is particularly pertinent to early diagnosis and potential development of targeted cancer therapeutics. This review is motivated by recent findings and new insights into the molecular dynamics of ubiquitination triggered by specific E2-E3 pairing, leading to cancer initiation and progression if cancer suppressors are degraded or cancer suppression (if cancer promoters are degraded), respectively. We provide an overview of strategies employed in screening for E2-E3 interactions based on up-to-date studies focusing on the E2-E3 interface motifs. Of considerable recent interest is how E2 and E3 might switch their functional partnerships via UBE2O, which suggests an emerging significance on how UBE2O might influence E2-E3 pairing. Thus, a reflection on the role of UBE2O is included. Finally, we deliberate on the rational and cautious development of anti-cancer cocktail drugs which specifically target E2-E3 interacting residues for precision in cancer-killing with minimal side-effects. To this end, a list of potential future research is proposed.
Advancements in the analysis of protein post-translational modifications
2022, Advances in Protein Molecular and Structural Biology Methods
Post-translational modifications (PTMs) are the alteration of amino acids in proteins after their synthesis. Such alteration significantly affects the stability, function, and structure of proteins. These modifications, in turn, regulate diverse cellular processes. Ubiquitination is an important post-translational modification that involved in the regulation of many signaling pathways. It is a multi-step enzymatic reaction that leads to the attachment of ubiquitin molecules to the substrate proteins. Aberrant ubiquitin signaling is known to be a molecular causality of several immune, cancer, neurodegenerative, and cardiovascular diseases. Thus, detection and analysis of PTMs are of immense significance in understanding the pathological mechanism of the diseases and developing new therapeutic strategies. In this chapter, we describe the advancement of the methods for the detection of protein post-translational modifications with particular reference to ubiquitination.
Indole-3-carbinol ameliorates necroptosis and inflammation of intestinal epithelial cells in mice with ulcerative colitis by activating aryl hydrocarbon receptor
2021, Experimental Cell Research
Ulcerative colitis (UC) is a disease characterized by inflammation and disruption of the intestinal epithelial barrier. Necroptosis plays a critical role in disease progression. Indole-3-carbinol (I3C), a natural dietary agonist of aryl hydrocarbon receptor (AHR), has shown alleviating effects on UC. However, its mechanisms of action have not been comprehensively elucidated. Therefore, we aimed at investigating the protective role of I3C in DSS-induced colitis mice models. I3C significantly ameliorated body weight loss, colon length shortening and colonic pathological damage in colitis mice, reduced disease activity index (DAI) and histological (HI) scores, as well as alleviated colonic necroptosis and inflammation. In vitro, I3C attenuated necroptosis and inflammation of colonoids and NCM460 cells. AHR, activated by I3C, inhibits activation of receptor-interacting protein kinase 1 (RIPK1) and the subsequent assembly of necrosome in a time-dependent manner, as well as suppressing NF-κB activation and decreasing TNF-α, IL-1β, IL-6 and IL-8 expression. Silencing of AHR aggravated necroptosis and inflammation of NCM460 cells, and did not be ameliorated by I3C. Furthermore, AHR activation induces the expression of inhibitor of apoptosis proteins (IAPs) and the ubiquitination of RIPK1. In conclusion, I3C exerts a protective effect in DSS-induced colitis mice models by alleviating the necroptosis and inflammation of IECs through activating AHR.

View all citing articles on Scopus

View full text

Trends in Biochemical Sciences

ReviewLinear ubiquitination: a newly discovered regulator of cell signalling

Section snippets

Ubiquitin system

Diversity of inter-ubiquitin linkages

Different classes of E3s act via distinct mechanisms

LUBAC: a novel RBR that promotes linear ubiquitin linkages

Role of linear ubiquitination in TNF receptor 1 (TNFR1) signalling

Implication of linear ubiquitination in other signalling pathways

Concluding remarks

J. Biol. Chem.

Biochim. Biophys. Acta

J. Mol. Biol.

J. Mol. Biol.

Cell

J. Biol. Chem.

Mol. Cell

J. Biol. Chem.

Mol. Cell

Mol. Cell

Cell

Immunity

Cell

Cell

Mol. Cell

J. Biol. Chem.

Cell

Mol. Cell

Mol. Cell

Mol. Cell

Cell

J. Biol. Chem.

J. Invest. Dermatol.

Curr. Opin. Immunol.

Dermatol. Clin.

Mol. Cell

Ubiquitylation and cell signaling

EMBO J.

The ubiquitin system

Annu. Rev. Biochem.

The ubiquitin code

Annu. Rev. Biochem.

Proteasome subunit Rpn13 is a novel ubiquitin receptor

Nature

Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry

J. Proteome Res.

A multiubiquitin chain is confined to specific lysine in a targeted short-lived protein

Science

Review
Linear ubiquitination: a newly discovered regulator of cell signalling