Podcasts about ubiquitin ligase

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.16.533063v1?rss=1 Authors: Farrukh, A., Musabyimana, J.-P., Distler, U., Tenzer, S., Pradel, G., Julius Ngwa, C. Abstract: Some proteins have acquired both ubiquitin ligase activity and RNA-binding properties and are therefore known as RNA-binding Ubiquitin ligases (RBULs). These proteins provide a link between the RNA metabolism and the ubiquitin proteasome system (UPS). The UPS is a crucial protein surveillance system of eukaryotes primarily involved in the selective proteolysis of proteins which are covalently marked with ubiquitin through a series of steps involving ubiquitin E1 activating, E2 conjugating and E3 ligating enzymes. The UPS also regulates other key cellular processes such as cell cycle, proliferation, cell differentiation, transcription and signal transduction. While RBULs have been characterized in other organisms, little is known about their role in Plasmodium falciparum, the causative agent of the deadliest human malaria, malaria tropica. In this study, we characterized a previously identified putative P. falciparum RING finger E3 ligase PfRNF1. We show that the protein is highly expressed in sexual stage parasites and mainly present in immature male gametocytes. Using proximity interaction studies with parasite lines expressing PfRNF1 tagged with the Biotin ligase BirA, we identified an interaction network of PfRNF1 in both the asexual blood stages and gametocytes composed mainly of ribosomal proteins, RNA-binding proteins including translational repressors such DOZI, CITH, PUF1 and members of the CCR4-NOT complex, as well as proteins of the UPS such as RPN11, RPT1 and RPT6. Our interaction network analysis reveals PfRNF1 as a potential RNA-binding E3 ligase which links RNA dependent processes with protein ubiquitination to regulate gene expression. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.11.01.514535v1?rss=1 Authors: Lavie, J., Lalou, C., Mahouf, W., Dupuy, J.-W., Lacaule, A., Ars, A., Lacombe, D., Duchene, A.-M., Raymond, A.-A., Rezvani, H. R., Ngondo, P., Benard, G. Abstract: The large majority of mitochondrial proteins is synthesized in the cytosol and then imported to the organelle. To ensure proper mitochondrial functions, the quality of these proteins needs to be guaranteed. Here, we show that the E3 ubiquitin ligase F-box/LRR-repeat protein 6 (FBXL6) participates to the quality of these mitochondrial proteins at the level of the cytosolic translation. We found that lack of FBXL6 has severe effects including mitochondrial ribosomal protein aggregations, altered mitochondrial metabolism and inhibited cell cycle progression in oxidative conditions. FBXL6 was found to interact specifically with ribosomal-associated quality control proteins and chaperones involved in the regulation of newly synthesized proteins and also it preferentially binds newly synthesized mitochondrial ribosomal proteins. Consistently, deletion of the RQC protein, NEMF or HSP70-family chaperone HSPA1A impedes FBXL6 interaction with its substrate. In addition, cells lacking FBXL6 display altered degradation of defective mitochondrial ribosomal protein containing C-terminal alanyl-threonyl extension. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.02.324285v1?rss=1 Authors: Song, J., Merrill, R. A., Usachev, A. Y., Strack, S. Abstract: Proper brain development and function requires finely controlled mechanisms for protein turnover and disruption of genes involved in proteostasis is a common cause of neurodevelopmental disorders. Kelch-like 15 (KLHL15) is a substrate adaptor for cullin3 (Cul3)-containing E3 ubiquitin ligases and KLHL15 gene mutations were recently described as a cause of severe X-linked intellectual disability. Here, we used a bioinformatics approach to identify a family of neuronal microtubule-associated proteins (MAPs) as KLHL15 substrates, which are themselves critical for early brain development. We biochemically validated doublecortin (DCX), also an X-linked disease gene, and doublecortin-like kinases 1 and 2 (DCLK1/2) as bona fide KLHL15 interactors and mapped KLHL15 interaction regions to their tandem DCX domains. Shared with two previously identified KLHL15 substrates, a FRY tripeptide at the C-terminal edge of the second DCX domain is necessary for KLHL15-mediated ubiquitination of DCX and DCLK1/2 and subsequent proteasomal degradation. Conversely, silencing endogenous KLHL15 markedly stabilizes these DCX domain-containing proteins and prolongs their half-life. Functionally, overexpression of KLHL15 in the presence of wild-type DCX reduces dendritic complexity of cultured hippocampal neurons, whereas neurons expressing FRY-mutant DCX are resistant to KLHL15. Collectively, our findings highlight the critical importance of the E3 ubiquitin ligase adaptor KLHL15 in proteostasis of neuronal MAPs and identify a regulatory network important for development of the mammalian nervous system. Copy rights belong to original authors. Visit the link for more info

Jane Ferguson:                Hi, everyone. Welcome to Getting Personal: Omics of the Heart, the monthly podcast from Circulation: Genomic and Precision Medicine. I'm Jane Ferguson, an assistant professor of medicine at Vanderbilt University Medical Center and an associate editor at CircGen. This is episode 32 from September 2019. Starting off this month, we have a paper on Genetic Mosaicism in Calmodulinopathy brought to us by Lisa Wren, Alfred George and colleagues from Northwestern University. They were interested in exploring the disease phenotypes that result from variation in the calmodulin genes, CALM1, 2 and 3.                                            Mutations in calmodulin are known to associate with congenital arrhythmia, but the group hypothesized that there may be a broader range of phenotypes associated with calmodulin mutations. They report on four unrelated families all with pro bands exhibiting symptoms of prolonged QTC interval and documented ventricular arrhythmia. They conducted targeted exome sequencing in these individuals and in their families and identified mutations in calmodulin genes, including two novel mutations. In one family with multiple occurrences of intrauterine fetal demise, there was evidence for sematic mosaicism in both parents.                                            The team studied the two novel mutations and found that the variants led to alterations in a calcium binding site resulting in impaired calcium binding. In human induced pluripotent stem cell derived cardiomyocytes, the team showed that the mutations impaired calcium dependent inactivation of L-type calcium channels and prolonged action potential duration. Their study not only demonstrates that mutations in calmodulins can cause dysregulation of L-type calcium channels, but that parental mosaicism maybe a factor in families with unexplained fetal arrhythmia or fetal demise.                                            Our next paper come from Wan G Pang, Christiana Kartsonaki, Michael Holmes and Zing Min Chen from the University of Oxford and Peking University Health Science Center and is entitled Physical Activity, Sedentary Leisure Time, Circulating Metabolic Markers, and Risk of Major Vascular Diseases. In this study, the authors were interested in finding out whether circulating metabolites are associated with the relationship between physical inactivity or sedentary behavior and increased risk of cardiovascular disease. They identified over 3000 cases of incident CVD from the China Kadoorie Biobank and included over 1400 controls without CVD. They measured 225 different metabolites and baseline plasma samples using NMR.                                            They used measures of self-reported physical activity and sedentary leisure time to associate physical activity with circulating metabolites, and then they ran analysis to relate the metabolites to CVD. Physical activity and sedentary leisure time were associated with over 100 metabolic markers. In general, the patterns of associations were similar using either activity measure. Physical activity was inversely related to very low and low density HDL particles, but positively related to large and very large HDL particle concentrations. Physical activity was also inversely associated with alanine, glucose, lactate, acetoacetate, and glycoprotein acetyls.                                            When they examined the associations of these same metabolites with CVD, the directions were generally consistent with expectation, going on the premise that physical activity is protective, and that sedentary behavior is a risk factor for CVD. Their analyses suggests that metabolite markers could explain about 70% of the protective associations of physical activity and around 50% of the risk associations of sedentary leisure time with cardiovascular disease. Next up, we have a paper on Biallelic Variants in ASNA1, Encoding a Cytosolic Targeting Factor of Tail-Anchored Proteins, Cause Rapidly Progressive Pediatric Cardiomyopathy, coming from Judith Verhagen, Ingrid van de Laar and colleagues from University Medical Center Rotterdam.                                            Their focus was on pediatric cardiomyopathies, which are both clinically and genetically heterogeneous. They had identified a family where two siblings had died during early infancy of rapidly progressive dilated cardiomyopathy. Through exome sequencing, they identified variants in the ASNA-1 gene and established that the children were compound heterozygotes for the variants. This highly conserved gene encodes an ATPase, which is required for post-translational membrane insertion of tail-anchored proteins. The team looked at expression of this protein in patient samples and then followed this up with functional analyses using cells and zebrafish. They found that one of the variants was predicted to result in a premature stop codon.                                            In support of this, they observed decreased protein expression in myocardial tissue and skin fibroblasts. The other variant caused a missense mutation, and the team found that this resulted in protein misfolding, as well as less effective tail-anchored protein insertion. In zebrafish, knock out of the ASNA1 gene resulted in reduced cardiac contractility and early lethality, which could not be rescued by either version of the variant mRNA. This translational study highlights the importance of the ASNA1 gene as a cardiomyopathy susceptibility gene and further reveals the importance of tail-anchored membrane protein insertion pathways in cardiac function.                                            The next paper from Karni Moshal, Gideon Koren and colleagues from Brown University is entitled LITAF Regulates Cardiac L-Type Calcium Channels by Modulating NEDD 4-1 Ubiquitin Ligase. In this paper, the authors report on the role of ubiquitination as a crucial component in cardiac ion channel turnover and action potential duration. Previous genome wide association studies of QT interval had identified snips in or near genes regulating protein ubiquitination, particularly the LITAF or lipopolysaccharide-induced tumor necrosis factor gene. Using zebrafish, the team performed optical mapping in hearts to identify calcium and found that knocked down of LITAF resulted in an increase in calcium transients.                                            They studied intracellular calcium handling and rapid derived cardiomyocytes and found that over expression of LITAF caused a decrease in L-type calcium channel current and abundance of the L-type calcium channel alpha1c sub unit or Cava1c, whereas LITAF knocked down increased calcium channel current and Cava1c protein. LITAF downregulated total and surface pools of Cava1c via increased Cava1c ubiquitination and lysosomal degradation in tsA201 kidney cells. There was evidence of colocalization between LITAF and L-type calcium channel, or LTCC, in the tsA201 kidney cells and in cardiomyocytes. In the tsA201 cells, NEDD4-1 protein increased Cava1c ubiquitination, but a catalytically inactive form of NEDD4-1 had no effect.                                            Cava1c ubiquitination was further increased by co-expressed LITAF NEDD4-1, but not the inactive version of NeNEDD4-1. NEDD4-1 knockdown abolished the negative effect of LITAF on L-type calcium channel current and Cava1c levels in three week old rapid cardiomyocytes. Taken together, these data show that LITAF acts as an adapter protein promoting NEDD4-1 mediated ubiquitination and subsequent degradation of LTCC, highlighting LITAF as a novel regulator of cardiac excitation. Rounding out this issue is a review on the Gut Microbiome and Response to Cardiovascular Drugs from Sony Tuteja and Jane Ferguson from the University of Pennsylvania and Vanderbilt University Medical Center.                                            Since that last author is me, I'm sure I have a biased view of the importance of the topic, but the increasing awareness of the microbiome in every aspect of health has also led to increased awareness of the role of commensal microbiota in drug metabolism, including in the metabolism of drugs used to treat cardiovascular diseases. In this article, we aim to review what is currently known about how the gut microbiome interacts with cardiovascular drugs and to summarize some of the mechanisms whereby gut microbiota might affect drug metabolism. Early evidence suggests that the gut microbiome modulates response to statins and antihypertensive medications, but there may be many other drugs that are susceptible to interaction with microbiota.                                            Drug metabolism by the gut microbiome can result in altered drug pharmacokinetics and pharmacodynamics or in the formation of toxic metabolites which can interfere with drug response. While we are still in a relatively early stage in this field, we suggest that a better understanding of the complex interactions of the gut microbiome, host factors and response to medications will be important for the development of novel precision therapeutics in cardiovascular disease prevention and treatment. That's all for the September issue of Circulation: Genomic and Precision Medicine. Come back next month for the next installment. Thanks for listening.                                            This podcast was brought to you by Circulation: Genomic and Precision Medicine and the American Heart Association Council on Genomic and Precision Medicine. This program is copyright American Heart Association 2019.  

Markus Gerhard explains how the E3 ubiquitin ligase RNF43 inhibits a transcription factor that mediates Wnt-β-catenin signaling without ubiquitylating it.

Vitezslav Bryja, Reinoud de Groot, and Rik Korswagen discovered that Huwe1 ubiquitylates Dishevelled to negatively regulate Wnt signaling.

Fri, 6 Jul 2012 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/15328/ https://edoc.ub.uni-muenchen.de/15328/1/Pilsl_Anna.pdf Pilsl, Anna

Um eine Parthenogenese zu verhindern, arretieren reife Oozyten von Wirbeltieren in der Metaphase der Meiose II. Diese biochemische Aktivität wurde 1971 als Zytostatischer Faktor (engl. Cytostatic Factor; CSF) beschrieben. Einzelne wichtige Komponenten wurden im Laufe der Zeit identifiziert, aber deren Zusammenspiel noch nicht aufgeklärt. Eine wichtige Rolle spielt dabei der Anaphase Fördernder Komplex (engl.Anaphase promoting complex/Cyclosome;APC/C), eine Ubiquitin-Ligase welche Zellzyklus regulierende Proteine dem Abbau zuführt und somit den Beginn der Anaphase ermöglicht. Der APC/C ist in reifen Oozyten inaktiv und wird nach der Befruchtung aktiviert, so dass der Arrest aufgehoben wird. Des Weiteren sind für den Eintritt in die Anaphase II die Aktivitäten zweier Kinasen nötig. Erstens erfolgt während der Befruchtung ein Anstieg der Konzentration des intrazellulären Calciums, dies führt zur Aktivierung der Calmodulin-abhängigen-kinase-II (CaMKII). Allerdings waren die Substrate dieser Kinase bis jetzt unbekannt. Zweitens ist die Polo-like-kinase-1 (Plk1) essentiell für die Aufhebung des Metaphase II - Arrests. In Xenopus Eiextrakt konnte gezeigt werden, dass die Aktivität der Xenopus Plk1 (Plx1) essentiell für den Eintritt in die Anaphase ist. Kürzlich wurde ein Inhibitor des APC/C in einem Yeast-Two-Hybrid-Screen mit inaktiver Plx1 als bait gefunden – Xenopus-Emi1-verwandtes-Protein-1 (engl. Xenopus-Emi1-related protein-1; XErp1). Die Depletion dieses Proteins in Xenopus-Ei-Extrakt führt zu einem verfrühten Eintritt in die Anaphase. Im Rahmen meiner Doktorarbeit konnte gezeigt werden, dass CaMKII und Plx1 kooperieren, um XErp1 nach der Befruchtung zu inaktivieren, indem sie XErp1 für den Abbau markieren. Auch das humane Protein wurde kloniert und es wurde damit begonnen Versuche in Säugetierzelllinien durchzuführen. Erste Hinweise lassen darauf schließen, dass das humane Protein in gleicher Weise reguliert wird wie XErp1.

Die Inaktivierung des von Hippel-Lindau (VHL) Tumorsuppressors spielt eine Rolle in der Entstehung von verschiedenen gut- und bösartigen Tumoren mit hoher Gewebespezifität. Als substraterkennende Untereinheit des CBCVHL Ubiquitin Ligase Komplexes steuert VHL den sauerstoffabhängigen Abbau des Transkriptionsfaktors HIF1/2α. HIF1/2α aktiviert die Transkription einer Vielzahl von Faktoren, die für den Energiehaushalt der Zelle und die Blutgefäßneubildung von entscheidender Bedeutung sind. Die Akkumulation von HIF1/2α führt zu deren konstitutiver Expression und fördert somit das Wachstum von Tumoren durch eine verbesserte Nährstoffversorgung. Der sauerstoffabhängige Mechanismus der HIF-Erkennung wird durch die Aktivität einer neuen Familie von Prolylhydroxylasen reguliert, die möglicherweise ihrerseits eine Reihe von zellulären Substraten haben. Trotz der guten Korrelation zwischen bestimmten, den HIF-Abbau beeinflussenden VHL-Mutationen und dem Auftreten von verschiedenen Krankheitssubtypen sind noch nicht alle Phänotypen im Zusammenhang mit VHL erklärbar. Vor allem die Identifizierung neuer Substrate für den CBCVHL Komplex ist für ein umfassendes Verständnis der VHL-Krankheit von Interesse. In dieser Arbeit wurden unterschiedliche Methoden zur Identifizierung neuer Substrate von VHL angewendet. Durch Affinitätschromatographie mit einem rekombinanten Komplex aus VHL, Elongin B und Elongin C (VCB) konnte Daxx als neuer Interaktor von VHL identifiziert werden. Daxx bindet Elongin B/C-unabhängig an VHL, und seine Stabilität wird nicht durch VHL reguliert. Zudem bildet Daxx einen Komplex mit dem VHL-Substrat HIF1α. Dies weist auf eine mögliche Funktion von VHL neben seiner Rolle als Ubiquitin Ligase hin, z.B. in der Regulation von Daxx als transkriptionellem Repressor. In einem funktionalisierten „TwoHybrid“-Screen konnte der Mechanismus der HIF-Regulation in S. cerevisiae rekonstituiert werden. Dies ermöglichte die Identifizierung weiterer potentieller VHL-Substrate, unter anderem Diacylglycerol Kinase iota (DGKι). DGKι weist zwei Erkennungsmotive für Prolylhydroxylasen auf und wird in Gehirn und Retina exprimiert. In diesem Organen kommt es bei VHL-Patienten zur Entstehung von Hämangioblastomen. DGKι wird in vivo ubiquityliert und bindet sowohl an VHL, als auch an zwei der drei bekannten Prolylhydroxylasen. Mit Mutanten von DGKι konnte allerdings gezeigt werden, dass Bindung und Ubiquitylierung nicht über den gleichen Mechanismus erfolgen wie bei HIF1α. Möglicherweise spielen Ubiquitylierung und VHL-Bindung getrennte Rollen in unterschiedlichen zellulären Prozessen. Es wird zunehmend deutlicher, dass VHL nicht nur eine Komponente des CBCVHL Komplexes bildet, sondern weitere Funktionen in der Zelle erfüllt. VHL spielt eine Rolle in der Assemblierung der Fibronektinmatrix, der Regulation von Mikrotubulistabilität und –dynamik und der Transkriptionskontrolle. Eine weitere Charakterisierung des nicht-degradativen Einflusses von VHL auf die in dieser Arbeit beschriebenen Bindungspartner ist nötig, um die zelluläre Wirkungsweise von VHL vollständig zu verstehen.