Identification of quinazolinyloxy biaryl urea as a new class of SUMO activating enzyme 1 inhibitors

SUMO activating enzyme 1 (SUMO E1) is the first enzyme in sumoylation pathway and an important cancer drug target. However, only a few inhibitors were reported up to now that includes three natural products, semi-synthetic protein inhibitors and one AMP mimic. Here, we report the identification of quinazolinyloxy biaryl urea as a new class of SUMO E1 inhibitors. The most active compound of this class inhibited the in vitro sumoylation with an IC₅₀ of 13.4 μM. This compound inhibits sumoylation by blocking the formation of SUMOE1-SUMO thioester intermediate. The biological activity of the most active compound is comparable to previously reported inhibitors with properties suitable for medicinal chemistry optimization for potency and druggability.     

β-Sheet Augmentation Is a Conserved Mechanism of Priming HECT E3 Ligases for Ubiquitin Ligation

Ubiquitin (Ub) ligases (E3s) catalyze the attachment of Ub chains to target proteins and thereby regulate a wide array of signal transduction pathways in eukaryotes. In HECT-type E3s, Ub first forms a thioester intermediate with a strictly conserved Cys in the C-lobe of the HECT domain and is then ligated via an isopeptide bond to a Lys residue in the substrate or a preceding Ub in a poly-Ub chain. To date, many key aspects of HECT-mediated Ub transfer have remained elusive. Here, we provide structural and functional insights into the catalytic mechanism of the HECT-type ligase Huwe1 and compare it to the unrelated, K63-specific Smurf2 E3, a member of the Nedd4 family. We found that the Huwe1 HECT domain, in contrast to Nedd4-family E3s, prioritizes K6- and K48-poly-Ub chains and does not interact with Ub in a non-covalent manner. Despite these mechanistic differences, we demonstrate that the architecture of the C-lobe ~ Ub intermediate is conserved between Huwe1 and Smurf2 and involves a reorientation of the very C-terminal residues. Moreover, in Nedd4 E3s and Huwe1, the individual sequence composition of the Huwe1 C-terminal tail modulates ubiquitination activity, without affecting thioester formation. In sum, our data suggest that catalysis of HECT ligases hold common features, such as the β-sheet augmentation that primes the enzymes for ligation, and variable elements, such as the sequence of the HECT C-terminal tail, that fine-tune ubiquitination activity and may aid in determining Ub chain specificity by positioning the substrate or acceptor Ub.     

Role of SUMO in RNF4-mediated Promyelocytic Leukemia Protein (PML) Degradation: Sumoylation of pml and phospho-switch control of its sumo binding domain dissected in living cells*

Promyelocytic leukemia protein (PML) is a tumor suppressor acting as the organizer of subnuclear structures called PML nuclear bodies (NBs). Both covalent modification of PML by the small ubiquitin-like modifier (SUMO) and non-covalent binding of SUMO to the PML SUMO binding domain (SBD) are necessary for PML NB formation and maturation. PML sumoylation and proteasome-dependent degradation induced by the E3 ubiquitin ligase, RNF4, are enhanced by the acute promyelocytic leukemia therapeutic agent, arsenic trioxide (As₂O₃). Here, we established a novel bioluminescence resonance energy transfer (BRET) assay to dissect and monitor PML/SUMO interactions dynamically in living cells upon addition of therapeutic agents. Using this sensitive and quantitative SUMO BRET assay that distinguishes PML sumoylation from SBD-mediated PML/SUMO non-covalent interactions, we probed the respective roles of covalent and non-covalent PML/SUMO interactions in PML degradation and interaction with RNF4. We found that, although dispensable for As₂O₃-enhanced PML sumoylation and RNF4 interaction, PML SBD core sequence was required for As₂O₃- and RNF4-induced PML degradation. As confirmed with a phosphomimetic mutant, phosphorylation of a stretch of serine residues, contained within PML SBD was needed for PML interaction with SUMO-modified protein partners and thus for NB maturation. However, mutation of these serine residues did not impair As₂O₃- and RNF4-induced PML degradation, contrasting with the known role of these phosphoserine residues for casein kinase 2-promoted PML degradation. Altogether, these data suggest a model whereby sumoylation- and SBD-dependent PML oligomerization within NBs is sufficient for RNF4-mediated PML degradation and does not require the phosphorylation-dependent association of PML with other sumoylated partners.Promyelocytic leukemia protein (PML)⁵ is a tumor suppressor (1) whose gene is translocated in cases of acute promyelocytic leukemia (2). PML functions as the organizer of PML NBs, which are dynamic structures harboring numerous transiently and permanently localized proteins (3). The importance of PML NB structural integrity was first revealed in acute promyelocytic leukemia because, in this malignancy, the abnormal fusion protein PML/RARα leads to NB disruption. Patient treatment with As₂O₃ induces the reversion of the acute promyelocytic leukemia phenotype as well as PML/RARα degradation and PML NB reformation (4).PML is a target for the post-translational modification by SUMO, an ubiquitin-like protein that is covalently coupled to PML lysine residues 65, 160, and 490 via a process called sumoylation (5, 6). Among the four human SUMO paralogs identified, SUMO1, -2, and -3 were found to be conjugated to target proteins. It involves an enzymatic cascade for the transfer of the mature SUMO and the formation of an isopeptide bond between the COOH-terminal glycine of SUMO and a lysine from the target protein. Sumoylation is a reversible process due to the existence of several deconjugating enzymes.PML NB formation requires both the covalent linkage (sumoylation) (reviewed in Ref. 7) and the non-covalent interactions of SUMO with PML through a SUMO binding domain (SBD also named SIM for SUMO interacting motif) (8). Interestingly, PML SBD contains specific serines, acting as substrates for the caseine kinase-2 (CK2), which are implicated in PML ubiquitination and degradation (9) and which phosphorylation status could regulate the function of the SBD.Because sumoylation of proteins is dynamic and reversible, this post-translational modification is difficult to follow in vivo and its detection mainly relies on the identification of sumoylated protein species by Western blot following cell lysis. Recently, we used bioluminescence resonance energy transfer (BRET) to detect covalent linkage of ubiquitin (ubiquitination) in living mammalian cells and in real time (10). In brief, BRET monitors the interaction between a protein fused to a luciferase and a protein fused to yellow or green fluorescent protein (YFP or GFP), upon addition of a luciferase substrate; it is a proximity-based assay that requires that the donor of energy (luciferase fusion) and the acceptor (YFP or GFP fusions) are within 50 to 100 Å for an efficient energy transfer (11–13). However, a demonstration that BRET may provide a method of choice to follow the dynamics of protein sumoylation in living cells is lacking. Here, we developed a sensitive and quantitative SUMO BRET assay for the detection of PML interactions with SUMO in living cells. We proved that BRET can be used to detect both SUMO covalent and non-covalent interactions with PML (model, Fig. 1H). For this purpose, we used the PMLIII isoform in which sumoylation is induced by As₂O₃ and triggers a proteasome-dependent PML degradation (14); the degradation process involves the ubiquitination of poly-SUMO covalently coupled to PML by the poly-SUMO-specific E3 ubiquitin ligase RNF4 (15–17). Altogether, our BRET results indicate that, As₂O₃ and/or RNF4-induced PML degradation are dependent on the integrity of both PML sumoylation target sites and the PML SBD core sequence but not on the CK2 serine phosphorylation sites within the SBD. However, phosphorylation of these serines is required for most PML SBD-dependent non-covalent interactions. This phospho-regulation of PML SBD (“SBD phospho-switch”) establishes another link between the phosphorylation and SUMO, different from the phospho-sumoyl switch (18).Open in a separate windowFIGURE 1.BRET reveals both covalent and non-covalent PML/SUMO1 interactions as well as As₂O₃-induced PML sumoylation in living cells. A and B, detection of PML/SUMO1 interactions by BRET¹ (A) or BRET² (B) titration assays using HEK293T cells transfected for expression of increasing amounts of YFP-SUMO1 (BRET¹) or GFP-SUMO1 (BRET²) and a fixed amount of Luc fusion. Negative controls: BRET pairs including PML_C57,60A-Luc (a non-sumoylatable mutant with Cys⁵⁷ and Cys⁶⁰ mutated to Ala) or YFP-SUMO1G (a SUMO1 that cannot be processed) (dotted line) (A) and Luc fused to a NLS (B). C and D, detection of covalent and non-covalent PML/SUMO1 interactions by BRET¹ (C) or BRET² (D) titration assays in the presence (dotted lines, empty symbols) or absence (solid lines and symbols) of As₂O₃ in HEK293T cells transfected for expression of PML_WT-Luc or its sumoylation deficient mutant PML_3K-Luc in pairs with either YFP-SUMO1 (BRET¹) or GFP-SUMO1 (BRET²). Negative control: PML_WT-Luc in pairs with YFP-SUMO1G. E, kinetics of As₂O₃-induced PML_WT-Luc sumoylation revealed by BRET¹ (assay on attached cells) and BRET² (cells in suspension). F, dose-response curve to As₂O₃ treatment for PML_WT-Luc or PML_3KR-Luc/YFP-SUMO1 BRET¹ pairs. Negative control: PML_C57,60A-Luc/YFP-SUMO1. G, comparison of As₂O₃-induced sumoylation of PML_WT, PML_3KR, and its single lysine mutants at an identical YFP acceptor/Luc donor expression ratio as derived from titration curves. As₂O₃ treatment (C–G): 5 μm, 4 h exposure for BRET¹ and Western blot or 10 μm, 70-min exposure for BRET². H, model for the covalent (sumoylation) and non-covalent interactions between a tested protein fused to Luc and SUMO fused to a fluorescent protein (YFP) that generates a BRET signal. The black arrows indicate the bioluminescent transfer of energy (or BRET) that occurs between Luc and GFP fusion upon exposure to the cell-permeable luciferase substrate.     

SUMO E3连接酶在植物适应非生物胁迫中的作用研究进展

SUMO化(Sumoylation)作为一种广泛存在于真核生物的重要翻译后修饰,在调控植物生长、发育和逆境应答等方面发挥着重要作用。SUMO E3连接酶具有底物识别和选择的作用,直接促进SUMO蛋白与靶蛋白的结合。目前,在植物中已经鉴定出多种SUMO E3连接酶。综述了SUMO E3连接酶在植物适应干旱、盐害、高/低温、营养元素匮缺和重金属毒害等非生物胁迫过程中的作用,并展望了未来植物SUMO化研究的方向,以期为今后植物SUMO化方面的研究提供参考。     

DNA activates the Nse2/Mms21 SUMO E3 ligase in the Smc5/6 complex

Modification of chromosomal proteins by conjugation to SUMO is a key step to cope with DNA damage and to maintain the integrity of the genome. The recruitment of SUMO E3 ligases to chromatin may represent one layer of control on protein sumoylation. However, we currently do not understand how cells upregulate the activity of E3 ligases on chromatin. Here we show that the Nse2 SUMO E3 in the Smc5/6 complex, a critical player during recombinational DNA repair, is directly stimulated by binding to DNA. Activation of sumoylation requires the electrostatic interaction between DNA and a positively charged patch in the ARM domain of Smc5, which acts as a DNA sensor that subsequently promotes a stimulatory activation of the E3 activity in Nse2. Specific disruption of the interaction between the ARM of Smc5 and DNA sensitizes cells to DNA damage, indicating that this mechanism contributes to DNA repair. These results reveal a mechanism to enhance a SUMO E3 ligase activity by direct DNA binding and to restrict sumoylation in the vicinity of those Smc5/6‐Nse2 molecules engaged on DNA.     

The yeast homologue of the microtubule-associated protein Lis1 interacts with the sumoylation machinery and a SUMO-targeted ubiquitin ligase

Microtubules and microtubule-associated proteins are fundamental for multiple cellular processes, including mitosis and intracellular motility, but the factors that control microtubule-associated proteins (MAPs) are poorly understood. Here we show that two MAPs—the CLIP-170 homologue Bik1p and the Lis1 homologue Pac1p—interact with several proteins in the sumoylation pathway. Bik1p and Pac1p interact with Smt3p, the yeast SUMO; Ubc9p, an E2; and Nfi1p, an E3. Bik1p interacts directly with SUMO in vitro, and overexpression of Smt3p and Bik1p results in its in vivo sumoylation. Modified Pac1p is observed when the SUMO protease Ulp1p is inactivated. Both ubiquitin and Smt3p copurify with Pac1p. In contrast to ubiquitination, sumoylation does not directly tag the substrate for degradation. However, SUMO-targeted ubiquitin ligases (STUbLs) can recognize a sumoylated substrate and promote its degradation via ubiquitination and the proteasome. Both Pac1p and Bik1p interact with the STUbL Nis1p-Ris1p and the protease Wss1p. Strains deleted for RIS1 or WSS1 accumulate Pac1p conjugates. This suggests a novel model in which the abundance of these MAPs may be regulated via STUbLs. Pac1p modification is also altered by Kar9p and the dynein regulator She1p. This work has implications for the regulation of dynein''s interaction with various cargoes, including its off-loading to the cortex.     

UHRF2, a Ubiquitin E3 Ligase,Acts as a Small Ubiquitin-like Modifier E3 Ligase for Zinc Finger Protein 131

Small ubiquitin-like modifier (SUMO), a member of the ubiquitin-related protein family, is covalently conjugated to lysine residues of its substrates in a process referred to as SUMOylation. SUMOylation occurs through a series of enzymatic reactions analogous to that of the ubiquitination pathway, resulting in modification of the biochemical and functional properties of substrates. To date, four mammalian SUMO isoforms, a single heterodimeric SUMO-activating E1 enzyme SAE1/SAE2, a single SUMO-conjugating E2 enzyme ubiquitin-conjugating enzyme E2I (UBC9), and a few subgroups of SUMO E3 ligases have been identified. Several SUMO E3 ligases such as topoisomerase I binding, arginine/serine-rich (TOPORS), TNF receptor-associated factor 7 (TRAF7), and tripartite motif containing 27 (TRIM27) have dual functions as ubiquitin E3 ligases. Here, we demonstrate that the ubiquitin E3 ligase UHRF2 also acts as a SUMO E3 ligase. UHRF2 effectively enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. In addition, the SUMO E3 activity of UHRF2 on ZNF131 depends on the presence of SET and RING finger-associated and nuclear localization signal-containing region domains, whereas the critical ubiquitin E3 activity RING domain is dispensable. Our findings suggest that UHRF2 has independent functional domains and regulatory mechanisms for these two distinct enzymatic activities.     

A Role for Non-Covalent SUMO Interaction Motifs in Pc2/CBX4 E3 Activity

Background

Modification of proteins by the small ubiquitin like modifier (SUMO) is an essential process in mammalian cells. SUMO is covalently attached to lysines in target proteins via an enzymatic cascade which consists of E1 and E2, SUMO activating and conjugating enzymes. There is also a variable requirement for non-enzymatic E3 adapter like proteins, which can increase the efficiency and specificity of the sumoylation process. In addition to covalent attachment of SUMO to target proteins, specific non-covalent SUMO interaction motifs (SIMs) that are generally short hydrophobic peptide motifs have been identified.

Methodology/Principal Findings

Intriguingly, consensus SIMs are present in most SUMO E3s, including the polycomb protein, Pc2/Cbx4. However, a role for SIMs in SUMO E3 activity remains to be shown. We show that Pc2 contains two functional SIMs, both of which contribute to full E3 activity in mammalian cells, and are also required for sumoylation of Pc2 itself. Pc2 forms distinct sub-nuclear foci, termed polycomb bodies, and can recruit partner proteins, such as the corepressor CtBP. We demonstrate that mutation of the SIMs in Pc2 prevents Pc2-dependent CtBP sumoylation, and decreases enrichment of SUMO1 and SUMO2 at polycomb foci. Furthermore, mutational analysis of both SUMO1 and SUMO2 reveals that the SIM-interacting residues of both SUMO isoforms are required for Pc2-mediated sumoylation and localization to polycomb foci.

Conclusions/Significance

This work provides the first clear evidence for a role for SIMs in SUMO E3 activity.     

Positively charged amino acids flanking a sumoylation consensus tetramer on the 110 kDa tri-snRNP component SART1 enhance sumoylation efficiency

Covalent attachment of Small Ubiquitin-like MOdifiers (SUMOs) to the ε-amino group of lysine residues in target proteins regulates many cellular processes. Previously, we have identified the 110 kDa U4/U6.U5 tri-snRNP component SART1 as a target protein for SUMO-1 and SUMO-2. SART1 contains lysines on positions 94, 141, 709 and 742 that are situated in tetrameric sumoylation consensus sites. Recombinant SART1 was produced in E. coli, conjugated to SUMO-2 in vitro, digested by trypsin and analysed by MALDI-ToF, MALDI-FT-ICR or nanoLC-iontrap MS/MS. We found that Lys⁹⁴ and Lys¹⁴¹ of SART1 were preferentially conjugated to SUMO-2 monomers and multimers in vitro. In agreement with these results, mutation of Lys⁹⁴ and Lys¹⁴¹, but not Lys⁷⁰⁹ and Lys⁷⁴², resulted in a reduced sumoylation of SART1 in HeLa cells. A detailed characterization of the four sumoylation sites of SART1 using full-length recombinant SART1 and a peptide sumoylation approach indicated that positively charged amino acids adjacent to the tetrameric sumoylation consensus site enhance the sumoylation of Lys⁹⁴. These results show that amino acids surrounding the classic tetrameric SUMO consensus site can regulate sumoylation efficiency and validate the use of an in vitro sumoylation-mass spectrometry approach for the identification of sumoylation sites.     

Upregulation of MuRF1 and MAFbx participates to muscle wasting upon gentamicin-induced acute kidney injury

Acute Kidney Injury (AKI) is frequently encountered in hospitalized patients where it is associated with increased mortality and morbidity notably affecting muscle wasting. Increased protein degradation has been shown to be the main actor of AKI-induced muscle atrophy, but the proteolytic pathways involved are poorly known. The Ubiquitin Proteasome System (UPS) is almost systematically activated in various catabolic situations, and the E3 ligases MuRF1 and MAFbx are generally up regulated in atrophying muscles. We hypothesized that the UPS may be one of the main actors in catabolic skeletal muscles from AKI animals. We used gentamicin-induced acute kidney disease (G-AKI) in rats fed a high protein diet to promote acidosis. We first addressed the impact of G-AKI in the development of mild catabolic conditions. We found that both muscle atrophy and UPS activation were induced with the development of G-AKI. In addition, the phasic muscles were more sensitive to 7-days G-AKI (−11 to −17%, P < 0.05) than the antigravity soleus muscle (−11%, NS), indicating a differential impact of AKI in the musculature. We observed an increased expression of the muscle-specific E3 ligases MuRF1 and MAFbx in phasic muscles that was highly correlated to the G-AKI severity (R² = 0.64, P < 0.01 and R² = 0.71, P < 0.005 respectively). Conversely, we observed no variation in the expression of three other E3 ligases (Nedd4, Trim32 and Fbxo30/MUSA1). Altogether, our data indicate that MuRF1 and MAFbx are sensitive markers and potential targets to prevent muscle atrophy during G-AKI.     

A Chemical and Enzymatic Approach to Study Site-Specific Sumoylation

A variety of cellular pathways are regulated by protein modifications with ubiquitin-family proteins. SUMO, the Small Ubiquitin-like MOdifier, is covalently attached to lysine on target proteins via a cascade reaction catalyzed by E1, E2, and E3 enzymes. A major barrier to understanding the diverse regulatory roles of SUMO has been a lack of suitable methods to identify protein sumoylation sites. Here we developed a mass-spectrometry (MS) based approach combining chemical and enzymatic modifications to identify sumoylation sites. We applied this method to analyze the auto-sumoylation of the E1 enzyme in vitro and compared it to the GG-remnant method using Smt3-I96R as a substrate. We further examined the effect of smt3-I96R mutation in vivo and performed a proteome-wide analysis of protein sumoylation sites in Saccharomyces cerevisiae. To validate these findings, we confirmed several sumoylation sites of Aos1 and Uba2 in vivo. Together, these results demonstrate that our chemical and enzymatic method for identifying protein sumoylation sites provides a useful tool and that a combination of methods allows a detailed analysis of protein sumoylation sites.     

Cryoprotectant effect of trehalose and low-density lipoprotein in extenders for frozen ram semen

This study tested trehalose and low-density lipoprotein (LDL) as cryoprotectants in extenders for frozen ram semen. In the first experiment, the extenders were Tris, with 20% egg yolk (E1-1); E1-1 with 5% glycerol (E1-2); E1-1 with 100 mM trehalose (E1-3); and E1-1 with 100 mM trehalose and 5% glycerol (E1-4). Sperm motility and membrane integrity of the E1-2, E1-3 and E1-4 extenders were greater than for E1-1 (P < 0.05), but acrosome integrity following cryopreservation did not differ. In the second experiment, the extenders were Tris, with 20% egg yolk and 100 mM trehalose (E2-1); Tris with 8% LDL and 5% glycerol (E2-2); Tris with 8% LDL and 100 mM trehalose (E2-3); and Tris with 8% LDL, 100 mM trehalose and 5% glycerol (E2-4). Sperm membrane integrity was lowest for the E2-1 extender (P < 0.05), but similar for extenders including LDL. Sperm motility post-thawing was highest for E2-2 and E2-3 extenders (P < 0.05), but acrosome integrity did not differ. Thus, extenders including trehalose and LDL as cryoprotectants recorded a post-thawing ram sperm quality similar to that achieved when using conventional cryoprotectants.     

A new complex triterpenoid saponin from Calliandra pulcherrima with haemolytic activity and adjuvant effect

A new complex triterpenoid saponin was isolated from the leaves of Calliandra pulcherrima by using chromatographic methods. On the basis of chemical evidence, spectroscopic analyses and comparison of known compounds its structure was established as 3-[(O-α-l-arabinopyranosyl-(1 → 2)-O-α-l-arabinopyranosyl-(1 → 6)-2-(acetylamino)-2-deoxy-β-d-glucopyranosyl)oxy]-(3β)-olean-12-en-28-oic acid O-β-d-xylopyranosyl-(1 → 3)-O-β-d-xylopyranosyl-(1 → 4)-O-[(β-d-glucopyranosyl-(1 → 3)]-O-6-deoxy-α-l-mannopyranosyl-(1 → 2)-6-O-[(2E,6S)-6-[[2-O-[(2E,6S)-6-[[6-deoxy-2-O-[(2E,6S)-2,6-dimethyl-1-oxo-6-(β-d-xylopyranosyloxy)-2,7-octadienyl]-β-d-glucopyranosyl]oxy]-2,6-dimethyl-1-oxo-2,7-octadienyl]-β-d-xylopyranosyl]oxy]-2,6-dimethyl-1-oxo-2,7-octadienyl]-β-d-glucopyranosyl ester (1). The haemolytic activity of the saponin was evaluated using in vitro assays, and its adjuvant potential on the cellular immune response against ovalbumin antigen was investigated using in vivo models     

Triterpene saponins from Antonia ovata leaves

Six pentacyclic triterpenoid saponins, named antoniosides E–J along with two known alkaloids, were isolated from the leaves of Antonia ovata. Their structures were determined by the extensive use of 1D and 2D-NMR experiments along with HRESIMS analysis and acid hydrolysis. All isolated saponins contained the same pentasaccharide chain: 3-O-[β-d-glucopyranosyl-(1 → 2)]-[β-d-glucopyranosyl-(1 → 4)]-[β-d-glucopyranosyl-(1 → 3)-α-l-arabinopyranosyl(1 → 6)]-β-d-glucopyranoside, linked at C-3 of esterified derivatives of polyhydroxyoleanene triterpenoids (theasapogenol A and 15α-hydroxy-theasapogenol A). Isolated compounds were evaluated for their cytotoxic activity against KB cell line by a WST-1 assay, and the IC₅₀ values ranged from 3.3 to 5.3 μM.     

Chemoenzymatic synthesis of (S)-duloxetine using carbonyl reductase from Rhodosporidium toruloides

A chemoenzymatic strategy was developed for (S)-duloxetine production employing carbonyl reductases from newly isolated Rhodosporidium toruloides into the enantiodetermining step. Amongst the ten most permissive enzymes identified, cloned, and overexpressed in Escherichia coli, RtSCR9 exhibited excellent activity and enantioselectivity. Using co-expressed E. coli harboring both RtSCR9 and glucose dehydrogenase, (S)-3-(dimethylamino)-1-(2-thienyl)-1-propanol 3a was fabricated with so far the highest substrate loading (1000 mM) in a space-time yield per gram of biomass (DCW) of 22.9 mmol L⁻¹ h⁻¹ g DCW⁻¹ at a 200-g scale. The subsequent synthetic steps from RtSCR9-catalyzed (S)-3a were further performed, affording (S)-duloxetine with 60.2% overall yield from 2-acethylthiophene in >98.5% ee.