Role of ubiquitin- and Ubl-binding proteins in cell signaling
Introduction
Ubiquitin (Ub) is a small versatile protein that has been a focus of active research during the past 30 years. Once freed from its precursor polypeptide by specific proteases, it is subjected to an enzymatic reaction cascade, which involves Ub-activating (E1), Ub-conjugating (E2) and Ub-ligating (E3) enzymes. This ultimately leads to the covalent attachment of Ub to a lysine (K) residue or the N-terminus of the target protein, referred to as ubiquitylation, or ubiquitination [1]. Through repeated conjugation to itself, Ub can form long chains that, in the case of K48-linkage, constitute a well-recognized proteasomal degradation signal [1]. Alternative Ub chain formation appears to play other important regulatory roles (e.g. K63-linkage in NF-κB signaling [2]). As well as forming polyubiquitin (polyUb) chains, single Ub moieties (monoUb) can also be covalently attached to various proteins. Monoubiquitylation has now surfaced as a major signaling event thought to mediate complex cellular processes, of which endocytosis and DNA repair are the best-studied examples [2]. The ability of different Ub chains and monoUb to signal in different ways seems to depend largely on the specificity and function of proteins that serve as Ub receptors. Ub-binding modules found within these proteins have co-evolved with Ub to recognize and bind their ligand, thereby mediating all known functions of Ub. So far >15 individual ubiquitin binding domains (UBDs) have been identified ([3, 4] and references therein) and this number is constantly growing (Table 1).
Besides Ub, 13 other small Ub-like protein modifiers (Ubls) have been described to date (Table 1). All of them share a characteristic β-grasp fold (the ‘ubiquitin fold’) and can be conjugated to proteins or lipids via their C-terminus [5, 6]. Attachment of Ubls to their substrate has been shown to have profound influence on various cellular processes, including transcription, DNA repair, signal transduction and autophagy [6]. By analogy to Ub, recognition of Ubls by specialized protein domains is predicted to drive these cellular responses. Indeed, recent results provide several examples of such novel recognition modules. This review covers major advances made in the last two years in understanding how Ub- and Ubl-binding proteins mediate and control cellular signaling networks.
Section snippets
Ub-binding proteins in proteolysis
The first recognized function of Ub was earmarking proteins for the proteasomal degradation pathway. Consequently, the first Ub-binding protein to be published was a proteasome subunit S5A/RPN10 [7]. In the meantime it has become quite clear that the few constitutive proteasome receptors do receive generous donations from multiple adaptors, such as yeast proteins rad23p and Dsk2p. They possess both UBDs and Ub-like (UBL) domains and, through binding both Ub and the proteasome, dock
Ubiquitin-binding proteins in endocytosis
The majority of cell-surface receptors undergo endocytosis either constitutively or as a result of their activation. Conjugation with monoUb [13] or oligo-Ub chains [14•] functions as an endosomal sorting signal for receptor tyrosine kinases (RTKs), G-protein-coupled receptors (GPCRs), transporters and ion channels [15, 16]. Elaborate molecular machinery is responsible for recognition and sorting of monoubiquitylated cargo from the cell membrane and, further along the endocytic route, for
Ub signaling in transcription and DNA repair
Gene transcription is a fundamental process whose regulation is the end point of many signaling pathways in the cell. Given the fact that histones were the first published substrate for Ub-conjugation, the role of Ub in chromatin regulation has long been suggested. Today it is largely believed that monoubiquitylation is able to influence transcription by causing changes in the other post-translational modifications of histones, such as methylation and acetylation, and hence altering chromatin
Signaling role of SUMO-binding proteins
Modification of proteins with SUMO has long been known to regulate various cellular processes, such as nuclear transport, cell cycle, transcription and DNA repair [40]. In a great number of cases, however, the exact mechanism by which sumoylation is translated into a biological effect is unknown. However, by analogy to Ub, it is safe to speculate that SUMO-binding proteins will act as sensors for this modification, thereby providing the basis for protein–protein interaction platforms. Indeed,
Conclusions and perspectives
Characterization of non-covalent interactions between Ub and Ub-binding proteins using both biochemical and structural analyses has provided an important insight into the mechanistic link between ubiquitylation and the processes it regulates. The variety and specificity of cellular responses to Ub can now be attributed to the diversity of UBD-containing proteins, each of which displays a unique binding repertoire. Although UBD–Ub interactions are typically weak (Kd>50 μM [4]), the latest
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
We are thankful to Kaisa Haglund and Daniela Hoeller for critical comments on the manuscript. We apologize to investigators whose important contributions were not included in this review due to space limitations. I.D. acknowledges support from the Deutsche Forschungsgemeinschaft, the German-Israeli Foundation and the Boehringer Ingelheim Foundation.
References (54)
- et al.
Characterization of two polyubiquitin binding sites in the 26 S protease subunit 5a
J Biol Chem
(1998) - et al.
NEDD8 ultimate buster-1L interacts with the ubiquitin-like protein FAT10 and accelerates its degradation
J Biol Chem
(2004) - et al.
The UBA domains of NUB1L are required for binding but not for accelerated degradation of the ubiquitin-like modifier FAT10
J Biol Chem
(2006) - et al.
Regulation of the NEDD8 conjugation system by a splicing variant, NUB1L
J Biol Chem
(2003) - et al.
Differential regulation of EGF receptor internalization and degradation by multiubiquitination within the kinase domain
Mol Cell
(2006) - et al.
Crystal structure of the ubiquitin binding domains of rabex-5 reveals two modes of interaction with ubiquitin
Cell
(2006) - et al.
The Rab5 guanine nucleotide exchange factor Rabex-5 binds ubiquitin (Ub) and functions as a Ub ligase through an atypical Ub-interacting motif and a zinc finger domain
J Biol Chem
(2006) - et al.
How the ubiquitin-proteasome system controls transcription
Nat Rev Mol Cell Biol
(2003) - et al.
Trading places: how do DNA polymerases switch during translesion DNA synthesis?
Mol Cell
(2005) - et al.
Molecular genetics of Xeroderma pigmentosum variant
Exp Dermatol
(2003)
Nuclear and unclear functions of SUMO
Nat Rev Mol Cell Biol
Covalent modification of p73alpha by SUMO-1. Two-hybrid screening with p73 identifies novel SUMO-1-interacting proteins and a SUMO-1 interaction motif
J Biol Chem
Something about SUMO inhibits transcription
Curr Opin Genet Dev
Autophagy: in sickness and in health
Trends Cell Biol
Ubiquitin and NEDD8: brothers in arms
Sci STKE
The ubiquitin system
Annu Rev Biochem
Ubiquitylation and cell signaling
EMBO J
Ubiquitin-binding domains
Nat Rev Mol Cell Biol
Ubiquitin-binding domains
Biochem J
Ubiquitin and ubiquitin-like proteins as multifunctional signals
Nat Rev Mol Cell Biol
Modification of proteins by ubiquitin and ubiquitin-like proteins
Annu Rev Cell Dev Biol
Delivery of ubiquitinated substrates to protein-unfolding machines
Nat Cell Biol
A novel ubiquitin-binding protein ZNF216 functioning in muscle atrophy
EMBO J
Multiple monoubiquitination of RTKs is sufficient for their endocytosis and degradation
Nat Cell Biol
Distinct monoubiquitin signals in receptor endocytosis
Trends Biochem Sci
Regulation of membrane protein transport by ubiquitin and ubiquitin-binding proteins
Annu Rev Cell Dev Biol
When ubiquitin meets ubiquitin receptors: a signalling connection
Nat Rev Mol Cell Biol
Cited by (169)
Ciliary disassembly
2023, The Chlamydomonas Sourcebook: Volume 3: Cell Motility and BehaviorAltered Protein Abundance and Localization Inferred from Sites of Alternative Modification by Ubiquitin and SUMO: Revealing new insights into protein function from Sites of Alternative Modifications (SAM)
2021, Journal of Molecular BiologyCitation Excerpt :However, we are far from understanding the full extent of their functions and involvement in cell physiology and pathology. Ubiquitination is one of the most studied PTMs and regulates fundamental cellular processes including proteolysis, signal transduction, cell division, and cell differentiation.2–5 Ubiquitin has seven lysine residues through which it may form different poly-ubiquitin chains on target proteins, each leading to different functional consequences.
Targeting kinases with thymoquinone: a molecular approach to cancer therapeutics
2020, Drug Discovery TodayDiscovery of a fluorescigenic pyrazoline derivative targeting ubiquitin
2020, Biochemical and Biophysical Research Communications