The UBA domain of conjugating enzyme Ubc1/Ube2K facilitates assembly of K48/K63‐branched ubiquitin chains

The assembly of a specific polymeric ubiquitin chain on a target protein is a key event in the regulation of numerous cellular processes. Yet, the mechanisms that govern the selective synthesis of particular polyubiquitin signals remain enigmatic. The homologous ubiquitin-conjugating (E2) enzymes Ubc1 (budding yeast) and Ube2K (mammals) exclusively generate polyubiquitin linked through lysine 48 (K48). Uniquely among E2 enzymes, Ubc1 and Ube2K harbor a ubiquitin-binding UBA domain with unknown function. We found that this UBA domain preferentially interacts with ubiquitin chains linked through lysine 63 (K63). Based on structural modeling, in vitro ubiquitination experiments, and NMR studies, we propose that the UBA domain aligns Ubc1 with K63-linked polyubiquitin and facilitates the selective assembly of K48/K63-branched ubiquitin conjugates. Genetic and proteomics experiments link the activity of the UBA domain, and hence the formation of this unusual ubiquitin chain topology, to the maintenance of cellular proteostasis.Deutsche Forschungsgemeinschaft (DFG) http://dx.doi.org/10.13039/501100001659Max‐Planck‐Gesellschaft (MPG) http://dx.doi.org/10.13039/501100004189Peer Reviewe

Anti-Tumor Necrosis Factor α Therapeutics Differentially Affect Leishmania Infection of Human Macrophages

Tumor necrosis factor α (TNFα) drives the pathophysiology of human autoimmune diseases and consequently, neutralizing antibodies (Abs) or Ab-derived molecules directed against TNFα are essential therapeutics. As treatment with several TNFα blockers has been reported to entail a higher risk of infectious diseases such as leishmaniasis, we established an in vitro model based on Leishmania-infected human macrophages, co-cultured with autologous T-cells, for the analysis and comparison of anti-TNFα therapeutics. We demonstrate that neutralization of soluble TNFα (sTNFα) by the anti-TNFα Abs Humira®, Remicade®, and its biosimilar Remsima® negatively affects infection as treatment with these agents significantly reduces Leishmania-induced T-cell proliferation and increases the number of infected macrophages. By contrast, we show that blockade of sTNFα by Cimzia® does not affect T-cell proliferation and infection rates. Moreover, compared to Remicade®, treatment with Cimzia® does not impair the expression of cytolytic effector proteins in proliferating T-cells. Our data demonstrate that Cimzia® supports parasite control through its conjugated polyethylene glycol (PEG) moiety as PEGylation of Remicade® improves the clearance of intracellular Leishmania. This effect can be linked to complement activation, with levels of complement component C5a being increased upon treatment with Cimzia® or a PEGylated form of Remicade®. Taken together, we provide an in vitro model of human leishmaniasis that allows direct comparison of different anti-TNFα agents. Our results enhance the understanding of the efficacy and adverse effects of TNFα blockers and they contribute to evaluate anti-TNFα therapy for patients living in countries with a high prevalence of leishmaniasis

Impaired antibacterial autophagy links granulomatous intestinal inflammation in Niemann-Pick disease type C1 and XIAP deficiency with NOD2 variants in Crohn's disease

OBJECTIVE: Patients with Niemann-Pick disease type C1 (NPC1), a lysosomal lipid storage disorder that causes neurodegeneration and liver damage, can present with IBD, but neither the significance nor the functional mechanism of this association is clear. We studied bacterial handling and antibacterial autophagy in patients with NPC1. DESIGN: We characterised intestinal inflammation in 14 patients with NPC1 who developed IBD. We investigated bacterial handling and cytokine production of NPC1 monocytes or macrophages in vitro and compared NPC1-associated functional defects to those caused by IBD-associated nucleotide-binding oligomerization domain-containing protein 2 (NOD2) variants or mutations in X-linked inhibitor of apoptosis (XIAP). RESULTS: Patients with the lysosomal lipid storage disorder NPC1 have increased susceptibility to early-onset fistulising colitis with granuloma formation, reminiscent of Crohn's disease (CD). Mutations in NPC1 cause impaired autophagy due to defective autophagosome function that abolishes NOD2-mediated bacterial handling in vitro similar to variants in NOD2 or XIAP deficiency. In contrast to genetic NOD2 and XIAP variants, NPC1 mutations do not impair NOD2-receptor-interacting kinase 2 (RIPK2)-XIAP-dependent cytokine production. Pharmacological activation of autophagy can rescue bacterial clearance in macrophages in vitro by increasing the autophagic flux and bypassing defects in NPC1. CONCLUSIONS: NPC1 confers increased risk of early-onset severe CD. Our data support the concept that genetic defects at different checkpoints of selective autophagy cause a shared outcome of CD-like immunopathology linking monogenic and polygenic forms of IBD. Muramyl dipeptide-driven cytokine responses and antibacterial autophagy induction are parallel and independent signalling cascades downstream of the NOD2-RIPK2-XIAP complex

Aktivität Ubiquitin-konjugierender Enzyme an den RING-Ligasen des ERAD-Systems

Fehlerhafte sekretorische Proteine werden über einen speziellen Abbauweg, die ER-assoziierte Proteindegradation (ERAD), mit Lysin48-verknüpften Ubiquitinketten polyubiquitiniert und dem proteolytischen Abbau am 26S Proteasom zugeführt. In der Hefe Saccharomyces cerevisiae bilden die beiden ER-membranständigen RING-Ubiquitinligasen Hrd1 und Doa10 zentrale Komponenten im Ubiquitinierungsprozess. Das lösliche zytosolische Ubiquitin-konjugierende Enzym Ubc7, welches mit beiden Ligasen bei der Polyubiquitinierung von Substratproteinen zusammenwirkt, wird über den membranverankerten Co-Faktor Cue1 an die ER-Membran rekrutiert. Die in dieser Arbeit dargestellten Ergebnisse belegen zwei weitere Funktionen für Cue1 im Ubiquitinierungsprozess: Die Bindung von Ubc7 an einen carboxyterminalen Bereich in Cue1 führt zur Stimulation der Ubiquitinierungsaktivität von Ubc7 mit den RING-Ligasen. Darüber hinaus bewirkt die Ubiquitin-bindende CUE-Domäne in Cue1 eine Steigerung der Länge der Ubiquitinketten und deren Syntheserate, was zum effektiven Abbau einiger ER-membrangebundener Substratproteine beiträgt. Die durch Ubc7 synthetisierten Lysin48-verknüpften Ubiquitinketten werden in Abhängigkeit eines schleifenförmigen sauren Bereichs in Ubc7 gebildet. Entfernen dieses Bereichs resultiert im Abbruch der Ubiquitinierung nach Konjugation eines Monoubiquitins auf dem Substrat. An der Hrd1-Ligase werden durch Ubc7 polyubiquitinierte Proteine umgehend zum Proteasom transferiert. Für den Doa10-abhängigen Substratabbau ist die Funktion eines weiteren Ubiquitin-konjugierenden Enzyms, Ubc6, notwendig. Die hier gezeigten Daten weisen auf eine Ubc6-abhängige Verknüpfung von Ubiquitinmolekülen in einer Lysin11-abhängigen Weise hin. Eine Inhibition der Synthese Lysin11-verknüpfter Ubiquitinketten hatte jedoch keinen Effekt auf den Abbau von Substratproteinen. Stattdessen wurde der Abbau von Ubc6 selbst durch Unterbindung der Bildung Lysin27-verknüpfter Ubiquitinketten verhindert.Aberrant secretory proteins are removed from the cell in a process termed „endoplasmic reticulum-associated protein degradation" (ERAD), as it screens the endoplasmic reticulum for unwanted polypeptides and triggers their elimination via the 26S proteasome. To this end, client proteins of the ERAD pathway are polyubiquitinated with lysine48-linked ubiquitin chains at the ER membrane. Two ER membrane-integrated RING ubiquitin ligases, Hrd1 and Doa10, constitute central components of the ubiquitination machinery in Saccharomyces cerevisiae. To polyubiquitinate substrate proteins, both ligases interact with the ubiquitin-conjugating enzyme Ubc7. Since Ubc7 itself is a soluble cytosolic protein, it is recruited to the ER-membrane by is anchoring factor Cue1. Results in this study reveal two additional functions of Cue1 in the ubiquitination reaction: First, binding of Ubc7 to the Cue1-carboxyterminus stimulates the ubiquitin chain formation by Ubc7 and the ligases. Second, the CUE domain within Cue1 increases the chain length and accelerates the synthesis of the polyubiquitin chain, which results in efficient degradation of certain substrate proteins. Formation of lysine48-linked ubiquitin chains by Ubc7 depends on an acidic loop within Ubc7. Deletion of this structure leads to inhibition of ubiquitin chain elongation after the initial substrate monoubiquitination. Client proteins, ubiquitinated by Ubc7 and Hrd1, are immediately transferred to the proteasome. For Doa10-dependent substrate degradation, the activity of another ubiquitin-conjugating enzyme, Ubc6, is required. Data shown here indicate a function of Ubc6 in the formation of lysine11-linked polyubiquitin, since mutation of this lysine residue resulted in the prevention of ubiquitin chain synthesis. However, expression of this ubiquitin mutant had no effect on substrate degradation. Moreover, the proteolysis of Ubc6 itself is inhibited by prevention of lysin27-linked polyubiquitin chain formation

Data_Sheet_1_Anti-Tumor Necrosis Factor α Therapeutics Differentially Affect Leishmania Infection of Human Macrophages.PDF

<p>Tumor necrosis factor α (TNFα) drives the pathophysiology of human autoimmune diseases and consequently, neutralizing antibodies (Abs) or Ab-derived molecules directed against TNFα are essential therapeutics. As treatment with several TNFα blockers has been reported to entail a higher risk of infectious diseases such as leishmaniasis, we established an in vitro model based on Leishmania-infected human macrophages, co-cultured with autologous T-cells, for the analysis and comparison of anti-TNFα therapeutics. We demonstrate that neutralization of soluble TNFα (sTNFα) by the anti-TNFα Abs Humira^®, Remicade^®, and its biosimilar Remsima^® negatively affects infection as treatment with these agents significantly reduces Leishmania-induced T-cell proliferation and increases the number of infected macrophages. By contrast, we show that blockade of sTNFα by Cimzia^® does not affect T-cell proliferation and infection rates. Moreover, compared to Remicade^®, treatment with Cimzia^® does not impair the expression of cytolytic effector proteins in proliferating T-cells. Our data demonstrate that Cimzia^® supports parasite control through its conjugated polyethylene glycol (PEG) moiety as PEGylation of Remicade^® improves the clearance of intracellular Leishmania. This effect can be linked to complement activation, with levels of complement component C5a being increased upon treatment with Cimzia^® or a PEGylated form of Remicade^®. Taken together, we provide an in vitro model of human leishmaniasis that allows direct comparison of different anti-TNFα agents. Our results enhance the understanding of the efficacy and adverse effects of TNFα blockers and they contribute to evaluate anti-TNFα therapy for patients living in countries with a high prevalence of leishmaniasis.</p

Distinct single-component adjuvants steer human DC-mediated T-cell polarization via Toll-like receptor signaling toward a potent antiviral immune response

The COVID-19 pandemic highlights the importance of efficient and safe vaccine development. Vaccine adjuvants are essential to boost and tailor the immune response to the corresponding pathogen. To allow for an educated selection, we assessed the effect of different adjuvants on human monocyte-derived dendritic cells (DCs) and their ability to polarize innate and adaptive immune responses. In contrast to commonly used adjuvants, such as aluminum hydroxide, Toll-like receptor (TLR) agonists induced robust phenotypic and functional DC maturation. In a DC-lymphocyte coculture system, we investigated the ensuing immune reactions. While monophosphoryl lipid A synthetic, a TLR4 ligand, induced checkpoint inhibitors indicative for immune exhaustion, the TLR7/8 agonist Resiquimod (R848) induced prominent type-1 interferon and interleukin 6 responses and robust CTL, B-cell, and NK-cell proliferation, which is particularly suited for antiviral immune responses. The recently licensed COVID-19 vaccines, BNT162b and mRNA-1273, are both based on single-stranded RNA. Indeed, we could confirm that the cytokine profile induced by lipid-complexed RNA was almost identical to the pattern induced by R848. Although this awaits further investigation, our results suggest that their efficacy involves the highly efficient antiviral response pattern stimulated by the RNAs’ TLR7/8 activation

Human ZBP1 induces cell death-independent inflammatory signaling via RIPK3 and RIPK1

ZBP1 is an interferon-induced cytosolic nucleic acid sensor that facilitates antiviral responses via RIPK3. Although ZBP1-mediated programmed cell death is widely described, whether and how it promotes inflammatory signaling is unclear. Here, we report a ZBP1-induced inflammatory signaling pathway mediated by K63- and M1-linked ubiquitin chains, which depends on RIPK1 and RIPK3 as scaffolds independently of cell death. In human HT29 cells, ZBP1 associated with RIPK1 and RIPK3 as well as ubiquitin ligases cIAP1 and LUBAC. ZBP1-induced K63- and M1-linked ubiquitination of RIPK1 and ZBP1 to promote TAK1- and IKK-mediated inflammatory signaling and cytokine production. Inhibition of caspase activity suppressed ZBP1-induced cell death but enhanced cytokine production in a RIPK1- and RIPK3 kinase activity-dependent manner. Lastly, we provide evidence that ZBP1 signaling contributes to SARS-CoV-2-induced cytokine production. Taken together, we describe a ZBP1-RIPK3-RIPK1-mediated inflammatory signaling pathway relayed by the scaffolding role of RIPKs and regulated by caspases, which may induce inflammation when ZBP1 is activated below the threshold needed to trigger a cell death response

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges

The spike protein (S) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the primary focus for vaccine development. In this study, we combined cryo–electron tomography, subtomogram averaging, and molecular dynamics simulations to structurally analyze S in situ. Compared with the recombinant S, the viral S was more heavily glycosylated and occurred mostly in the closed prefusion conformation. We show that the stalk domain of S contains three hinges, giving the head unexpected orientational freedom. We propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat. The structure of native S contributes to our understanding of SARS-CoV-2 infection and potentially to the development of safe vaccines