DNA double strand breaks need to be repaired in an organized fashion to preserve genomic integrity. In the organization of faithful repair, histone ubiquitination plays a crucial role. Recent ...findings suggest an integrated model for DNA repair regulation through site-specific histone ubiquitination and crosstalk to other posttranslational modifications. Here we discuss how site-specific histone ubiquitination is achieved on a molecular level and how different multi-protein complexes work together to integrate different histone ubiquitination states. We propose a model where site-specific H2A ubiquitination organizes the spatio-temporal recruitment of DNA repair factors which will ultimately contribute to DNA repair pathway choice between homologous recombination and non-homologous end joining.
The ubiquitin-specific protease USP7/HAUSP regulates p53 and MDM2 levels, and cellular localization of FOXO4 and PTEN, and hence is critically important for their role in cellular processes. Here we ...show how the 64 kDa C-terminal region of USP7 can positively regulate deubiquitinating activity. We present the crystal structure of this USP7/HAUSP ubiquitin-like domain (HUBL) comprised of five ubiquitin-like (Ubl) domains organized in 2-1-2 Ubl units. The last di-Ubl unit, HUBL-45, is sufficient to activate USP7, through binding to a “switching” loop in the catalytic domain, which promotes ubiquitin binding and increases activity 100-fold. This activation can be enhanced allosterically by the metabolic enzyme GMPS. It binds to the first three Ubl domains (HUBL-123) and hyperactivates USP7 by stabilization of the HUBL-45-dependent active state.
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► USP7 needs its HUBL domain for activity and ubiquitin binding, in vitro and in vivo ► The HUBL crystal structure consists of five ubiquitin-like (Ubl) moieties ► The minimal activation domain is HUBL-45 including its C-terminal flexible peptide ► GMPS allosterically activates USP7, binding HUBL-123 and promoting HUBL-45 affinity
Ubiquitin and ubiquitin-like modifications are central to virtually all cellular signaling pathways. They occur primarily on lysine residues of target proteins and stimulate a large number of ...downstream signals. The diversity of these signals depends on the type, location and dynamics of the modification, but the role of the exact site of modification and the selectivity for specific lysines are poorly understood. Here we review the current literature on lysine specificity in these modifications, and we highlight the known signaling mechanisms and the open questions that pose future challenges to ubiquitin research.
Ubiquitin (Ub) conjugation is a critical signalling process in eukaryotic cells. The precise regulation of deubiquitination is an important component of this signalling cascade. Here, we discuss how ...USP7 (or Herpes-Associated Ubiquitin-Specific Protease, HAUSP), one of the most abundant deubiquitinating enzymes, is regulated by complex formation with regulatory proteins and targets.
Full activity of USP7 requires that its C-terminal Ub-like domains fold back onto the catalytic domain, to allow the remodelling of the active site to a catalytically competent state by the very C-terminal peptide. This regulatory mode can be modulated by complex formation with other proteins.
USP7 is found in a large number of relatively stable complexes with different possible functions. Complex formation can provide recruitment of a target, bring in an E3 Ub ligase, or modulate the activation of the deubiquitinating enzyme activity. These complexes make up potential cellular “switches”, using their (de)ubiquitination ability to switch pathways on or off upon cellular signals. Here, we summarize what is known for USP7 complexes, focussing on the prevalence of E3 Ub ligases and how complex formation can affect Ub switches.
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•USP7 activity is regulated by itself and interacting proteins.•Many of the USP7 interacting proteins are E3 ubiquitin ligases.•E3/USP7 complexes can form cellular switches.
Deubiquitinating enzymes (DUBs) control vital processes in eukaryotes by hydrolyzing ubiquitin adducts. Their activities are tightly regulated, but the mechanisms remain elusive. In particular, the ...DUB UCH-L5 can be either activated or inhibited by conserved regulatory proteins RPN13 and INO80G, respectively. Here we show how the DEUBAD domain in RPN13 activates UCH-L5 by positioning its C-terminal ULD domain and crossover loop to promote substrate binding and catalysis. The related DEUBAD domain in INO80G inhibits UCH-L5 by exploiting similar structural elements in UCH-L5 to promote a radically different conformation, and employs molecular mimicry to block ubiquitin docking. In this process, large conformational changes create small but highly specific interfaces that mediate activity modulation of UCH-L5 by altering the affinity for substrates. Our results establish how related domains can exploit enzyme conformational plasticity to allosterically regulate DUB activity. These allosteric sites may present novel insights for pharmaceutical intervention in DUB activity.
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•The RPN13 DEUBAD domain activates UCH-L5 by positioning its CL and ULD domain•The INO80G DEUBAD domain inhibits UCH-L5 by blocking ubiquitin binding•The FRF hairpin in the DEUBAD domain of INO80G drives UCH-L5 inhibition•DEUBAD domains regulate UCH-L5 activity by tuning UCH-L5 substrate affinity
Deubiquitinating enzyme UCH-L5 (UCH37) is involved in DNA repair and the proteasome system. Sahtoe et al. uncover how two evolutionarily related DEUBAD domains in RPN13 (ADRM1) and INO80G (NFRKB) can either activate or inhibit UCH-L5. These remarkable regulatory modes exploit flexible structural elements in UCH-L5 to modulate activity.
The deubiquitinating enzyme BAP1 is an important tumor suppressor that has drawn attention in the clinic since its loss leads to a variety of cancers. BAP1 is activated by ASXL1 to deubiquitinate ...mono-ubiquitinated H2A at K119 in Polycomb gene repression, but the mechanism of this reaction remains poorly defined. Here we show that the BAP1 C-terminal extension is important for H2A deubiquitination by auto-recruiting BAP1 to nucleosomes in a process that does not require the nucleosome acidic patch. This initial encounter-like complex is unproductive and needs to be activated by the DEUBAD domains of ASXL1, ASXL2 or ASXL3 to increase BAP1's affinity for ubiquitin on H2A, to drive the deubiquitination reaction. The reaction is specific for Polycomb modifications of H2A as the complex cannot deubiquitinate the DNA damage-dependent ubiquitination at H2A K13/15. Our results contribute to the molecular understanding of this important tumor suppressor.
Ubiquitin-dependent signaling during the DNA damage response (DDR) to double-strand breaks (DSBs) is initiated by two E3 ligases, RNF8 and RNF168, targeting histone H2A and H2AX. RNF8 is the first ...ligase recruited to the damage site, and RNF168 follows RNF8-dependent ubiquitination. This suggests that RNF8 initiates H2A/H2AX ubiquitination with K63-linked ubiquitin chains and RNF168 extends them. Here, we show that RNF8 is inactive toward nucleosomal H2A, whereas RNF168 catalyzes the monoubiquitination of the histones specifically on K13-15. Structure-based mutagenesis of RNF8 and RNF168 RING domains shows that a charged residue determines whether nucleosomal proteins are recognized. We find that K63 ubiquitin chains are conjugated to RNF168-dependent H2A/H2AX monoubiquitination at K13-15 and not on K118-119. Using a mutant of RNF168 unable to target histones but still catalyzing ubiquitin chains at DSBs, we show that ubiquitin chains per se are insufficient for signaling, but RNF168 target ubiquitination is required for DDR.
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► Recruitment order of RNF8/RNF168 is uncoupled from activity on nucleosomal H2A/H2AX ► A charged site on these E3s affects histone ubiquitination, but not chain formation ► RNF168 ubiquitinates K13-15 of H2A/H2AX at DSBs, distinct from K119 PRC1 site ► Target modification by RNF168 rather than Ub chain formation drives DSB signaling
The RING domain of RNF168 recognizes H2A/H2AX at sites of double-strand DNA breaks. RNF168 ubiquitinates these histones at lysines 13–15 to enable the recruitment of downstream factors and drive DNA repair.
DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions that trigger non-proteolytic ubiquitylation of adjacent chromatin areas to generate binding sites for DNA repair factors. This depends ...on the sequential actions of the E3 ubiquitin ligases RNF8 and RNF168 (refs 1-6), and UBC13 (also known as UBE2N), an E2 ubiquitin-conjugating enzyme that specifically generates K63-linked ubiquitin chains. Whereas RNF168 is known to catalyse ubiquitylation of H2A-type histones, leading to the recruitment of repair factors such as 53BP1 (refs 8-10), the critical substrates of RNF8 and K63-linked ubiquitylation remain elusive. Here we elucidate how RNF8 and UBC13 promote recruitment of RNF168 and downstream factors to DSB sites in human cells. We establish that UBC13-dependent K63-linked ubiquitylation at DSB sites is predominantly mediated by RNF8 but not RNF168, and that H1-type linker histones, but not core histones, represent major chromatin-associated targets of this modification. The RNF168 module (UDM1) recognizing RNF8-generated ubiquitylations is a high-affinity reader of K63-ubiquitylated H1, mechanistically explaining the essential roles of RNF8 and UBC13 in recruiting RNF168 to DSBs. Consistently, reduced expression or chromatin association of linker histones impair accumulation of K63-linked ubiquitin conjugates and repair factors at DSB-flanking chromatin. These results identify histone H1 as a key target of RNF8-UBC13 in DSB signalling and expand the concept of the histone code by showing that posttranslational modifications of linker histones can serve as important marks for recognition by factors involved in genome stability maintenance, and possibly beyond.
Layers of DUB regulation Sahtoe, Danny D.; Sixma, Titia K.
Trends in biochemical sciences (Amsterdam. Regular ed.),
August 2015, 2015-Aug, 2015-08-00, 20150801, Letnik:
40, Številka:
8
Journal Article
Recenzirano
•Deubiquitylating enzymes (DUBs) are tightly regulated at different layers.•Internal domains and external proteins can contribute to regulation.•Mechanisms of DUB regulation involve PTMs, ...recruitment, and modulation of catalysis.•Multiple types of allosteric regulation can impinge on DUB activity simultaneously.
Proteolytic enzymes, such as (iso–)peptidases, are potentially hazardous for cells. To neutralize their potential danger, tight control of their activities has evolved. Deubiquitylating enzymes (DUBs) are isopeptidases involved in eukaryotic ubiquitylation. They reverse ubiquitin signals by hydrolyzing ubiquitin adducts, giving them control over all aspects of ubiquitin biology. The importance of DUB function is underscored by their frequent deregulation in human disease, making these enzymes potential drug targets. Here, we review the different layers of DUB enzyme regulation. We discuss how post-translational modification (PTM), regulatory domains within DUBs, and incorporation of DUBs into macromolecular complexes contribute to their activity. We conclude that most DUBs are likely to use a combination of these basic regulatory mechanisms.
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