TY - JOUR A1 - Tolay, Nazife A1 - Buchberger, Alexander T1 - Role of the ubiquitin system in stress granule metabolism JF - International Journal of Molecular Sciences N2 - Eukaryotic cells react to various stress conditions with the rapid formation of membrane-less organelles called stress granules (SGs). SGs form by multivalent interactions between RNAs and RNA-binding proteins and are believed to protect stalled translation initiation complexes from stress-induced degradation. SGs contain hundreds of different mRNAs and proteins, and their assembly and disassembly are tightly controlled by post-translational modifications. The ubiquitin system, which mediates the covalent modification of target proteins with the small protein ubiquitin (‘ubiquitylation’), has been implicated in different aspects of SG metabolism, but specific functions in SG turnover have only recently emerged. Here, we summarize the evidence for the presence of ubiquitylated proteins at SGs, review the functions of different components of the ubiquitin system in SG formation and clearance, and discuss the link between perturbed SG clearance and the pathogenesis of neurodegenerative disorders. We conclude that the ubiquitin system plays an important, medically relevant role in SG biology. KW - 26S proteasome KW - p97/VCP KW - Cdc48 KW - DUB KW - G3BP KW - granulostasis KW - granulophagy KW - ALS Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-284061 SN - 1422-0067 VL - 23 IS - 7 ER - TY - JOUR A1 - Tolay, Nazife A1 - Buchberger, Alexander T1 - Comparative profiling of stress granule clearance reveals differential contributions of the ubiquitin system JF - Life Science Alliance N2 - Stress granules (SGs) are cytoplasmic condensates containing untranslated mRNP complexes. They are induced by various proteotoxic conditions such as heat, oxidative, and osmotic stress. SGs are believed to protect mRNPs from degradation and to enable cells to rapidly resume translation when stress conditions subside. SG dynamics are controlled by various posttranslationalmodifications, but the role of the ubiquitin system has remained controversial. Here, we present a comparative analysis addressing the involvement of the ubiquitin system in SG clearance. Using high-resolution immuno-fluorescence microscopy, we found that ubiquitin associated to varying extent with SGs induced by heat, arsenite, H2O2, sorbitol, or combined puromycin and Hsp70 inhibitor treatment. SG-associated ubiquitin species included K48- and K63-linked conjugates, whereas free ubiquitin was not significantly enriched. Inhibition of the ubiquitin activating enzyme, deubiquitylating enzymes, the 26S proteasome and p97/VCP impaired the clearance of arsenite- and heat-induced SGs, whereas SGs induced by other stress conditions were little affected. Our data underline the differential involvement of the ubiquitin system in SG clearance, a process important to prevent the formation of disease-linked aberrant SGs. KW - phase transition KW - quality control KW - protein KW - inhibition KW - complexity KW - separation KW - diversity KW - autophagy KW - ALS KW - P97 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-259810 VL - 4 IS - 5 ER - TY - THES A1 - Reil, Lucy Honor T1 - The role of WASH complex subunit Strumpellin in platelet function T1 - Die Rolle der WASH-Komplexuntereinheit Strumpellin in der Thrombozytenfunktion N2 - Strumpellin is a member of the highly conserved pentameric WASH complex, which stimulates the Arp2/3 complex on endosomes and induces the formation of a branched actin network. The WASH complex is involved in the formation and stabilisation of endosomal retrieval subdomains and transport carriers, into which selected proteins are packaged and subsequently transported to their respective cellular destination, e.g. the plasma membrane. Up until now, the role of Strumpellin in platelet function and endosomal trafficking has not been researched. In order to examine its role, a conditional knockout mouse line was generated, which specifically lacked Strumpellin in megakaryocytes and platelets. Conditional knockout of Strumpellin resulted in only a mild platelet phenotype. Loss of Strumpellin led to a decreased abundance of the αIIbβ3 integrin in platelets, including a reduced αIIbβ3 surface expression by approximately 20% and an impaired αIIbβ3 activation after platelet activation. The reduced surface expression of αIIbβ3 was also detected in megakaryocytes. The expression of other platelet surface glycoproteins was not affected. Platelet count, size and morphology remained unaltered. The reduction of αIIbβ3 expression in platelets resulted in a reduced fibrinogen binding capacity after platelet activation. However, fibrinogen uptake under resting conditions, although slightly delayed, as well as overall fibrinogen content in Strumpellin-deficient platelets were comparable to controls. Most notably, reduced αIIbβ3 expression did not lead to any platelet spreading and aggregation defects in vitro. Furthermore, reduced WASH1 protein levels were detected in the absence of Strumpellin. In conclusion, loss of Strumpellin does not impair platelet function, at least not in vitro. However, the data demonstrates that Strumpellin plays a role in selectively regulating αIIbβ3 surface expression. As a member of the WASH complex, Strumpellin may regulate αIIbβ3 recycling back to the platelet surface. Furthermore, residual WASH complex subunits may still assemble and partially function in the absence of Strumpellin, which could explain the only 20% decrease in αIIbβ3 surface expression. Nonetheless, the exact mechanism still remains unclear. N2 - Strumpellin ist Teil des hoch konservierten, pentameren WASH-Komplexes, der den Arp2/3-Komplex auf Endosomen aktiviert und somit die Bildung eines verzweigten Aktinnetzwerkes ermöglicht. Der WASH-Komplex beteiligt sich an der Bildung und Sta-bilisierung von endosomalen Retrieval-Subdomänen und Transportvesikel. In letztere werden Proteine verpackt und anschließend zu ihrem Bestimmungsort innerhalb der Zelle, z.B. der Zellmembran, transportiert. Die Rolle von Strumpellin in der Thrombozytenfunktion und im endosomalen Transport wurde bislang noch nicht untersucht. Hierfür wurde eine konditionale Knockout-Mauslinie generiert, die weder in Megakaryozyten noch in Thrombozyten Strumpellin aufwies. Der konditionale Knockout von Strumpellin hatte nur einen milden Thrombozytenphänotyp zur Folge. Der Verlust von Strumpellin resultierte in einem verminderten Gesamt-proteingehalt von αIIbβ3-Integrin in Thrombozyten, einschließlich einer ca. 20-prozentigen Reduktion der Oberflächenexpression von αIIbβ3 und einer verringerten αIIbβ3-Aktivierung nach Thrombozytenaktivierung. Die reduzierte Oberflächenexpression von αIIbβ3 konnte auch in Megakaryozyten nachgewiesen werden. Die Expression anderer Oberflächenglykoproteine war nicht betroffen. Thrombozytenzahl, -größe und -morphologie blieben unverändert. Die reduzierte αIIbβ3-Expression in Thrombozyten führte zu einer verminderten Fibrinogenbindungskapazität nach Thrombozytenaktivierung. Die Fibrinogenaufnahme unter ruhenden Bedingungen, trotz initialer Verzögerung, und der Gesamtproteingehalt von Fibrinogen waren hingegen vergleichbar mit Kontrollproben. Interessanterweise verursachte die reduzierte αIIbβ3-Expression keine in vitro Spreading- und Aggregationsdefekte der Thrombozyten. Ein verminderter WASH1-Proteingehalt konnte ebenfalls nachgewiesen werden. Abschließend lässt sich sagen, dass der Verlust von Strumpellin die Thrombozytenfunktion, zumindest in vitro, nicht beeinträchtigt. Die Daten zeigen jedoch, dass Strumpellin eine selektive Rolle in der Regulierung der αIIbβ3-Oberflächenexpression spielt. Als WASH-Komplexuntereinheit könnte Strumpellin möglicherweise das Recycling von αIIbβ3 zurück zur Thrombozytenoberfläche regulieren. Zudem könnten verbleibende WASH-Komplexuntereinheiten trotz fehlendem Strumpellin weiterhin einen funktions- fähigen Komplex bilden. Dies könnte unter anderem die nur 20-prozentige Reduktion der αIIbβ3 Oberflächenexpression erklären. Der genaue Mechanismus ist jedoch noch nicht bekannt. KW - Strumpellin KW - WASH complex KW - endosomal trafficking KW - alpha-IIb beta-3 KW - platelet Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-242077 ER - TY - THES A1 - Klingler, Philipp T1 - Exploration of proteasome interactions with human platelet function T1 - Untersuchung von Proteasom-Wechselwirkungen mit der Funktion humaner Thrombozyten N2 - Platelets are anucleated cell fragments derived from megakaryocytes. They play a fundamental role in hemostasis, but there is rising evidence that they are also involved in immunological processes. Despite absence of a nucleus, human platelets are capable of de novo protein synthesis and contain a fully functional proteasome system, which is, in nucleated cells, involved in processes like cell cycle progression or apoptosis by its ability of protein degradation. The physiological significance of the proteasome system in human platelets is not yet fully understood and subject of ongoing research. Therefore, this study was conducted with the intention to outline the role of the proteasome system for functional characteristics of human platelets. For experimentation, citrated whole blood from healthy donors was obtained and preincubated with proteasome inhibitors. In addition to the commonly used bortezomib, the potent and selective proteasome inhibitor carfilzomib was selected as a second inhibitor to rule out agent-specific effects and to confirm that observed changes are related to proteasome inhibition. Irreversibly induced platelet activation and aggregation were not affected by proteasome blockade with bortezomib up to 24 hours. Conversely, proteasome inhibition led to enhanced threshold aggregation and agglutination up to 25 %, accompanied by partial alleviation of induced VASP phosphorylation of approximately 10-15 %. Expression of different receptors were almost unaffected. Instead, a significant increase of PP2A activity was observable in platelets after proteasome blockade, accompanied by facilitated platelet adhesion to coated surfaces in static experiments or flow chamber experiments. Carfilzomib, used for the first time in functional experimentation with human platelets in vitro, led to a dose-dependent decrease of proteasome activity with accumulation of poly ubiquitylated proteins. Like bortezomib, carfilzomib treatment resulted in enhanced threshold aggregation with attenuated VASP phosphorylation. As the main conclusion of this thesis, proteasome inhibition enhances the responsiveness of human platelets, provided by an alleviation of platelet inhibitory pathways and by an additional increase of PP2A activity, resulting in facilitated platelet adhesion under static and flow conditions. The proteasome system appears to be involved in the promotion of inhibitory counterregulation in platelets. The potential of proteasome inhibitors for triggering thromboembolic adverse events in patients must be clarified in further studies, in addition to their possible use for targeting platelet function to improve the hemostatic reactivity of platelets. N2 - Thrombozyten sind kernlose Zellfragmente, welche aus Megakaryozyten gebildet werden. Sie spielen eine fundamentale Rolle in der Hämostase, aber es gibt immer mehr Hinweise, dass Thrombozyten auch in immunologischen Prozessen involviert sind. Trotz Fehlen eines Zellkerns haben humane Thrombozyten die Fähigkeit zur de novo Proteinsynthese und besitzen außerdem ein voll funktionstüchtiges Proteasomsystem, welches in kernhaltigen Zellen über den Proteinabbau an Prozessen wie dem Fortschreiten des Zellzyklus oder der Apoptose beteiligt ist. Die physiologische Bedeutung des Proteasomsystems in humanen Thrombozyten ist nicht vollständig geklärt und ist aus diesem Grund Gegenstand aktueller Forschung. Daher war es Ziel dieser Studie, die Rolle des Proteasomsystems für die funktionellen Eigenschaften humaner Thrombozyten zu erforschen. Für die Experimente wurde Citrat-Vollblut von gesunden Spendern gewonnen und mit Proteasom-Hemmstoffen vorinkubiert. Es wurde neben dem gängigen Bortezomib der potente und selektive Proteasom-Inhibitor Carfilzomib als zweiter Inhibitor eingesetzt, um substanzspezifische Effekte auszuschließen und zu bestätigen, dass die beobachteten Veränderungen auf der Proteasom-Inhibition beruhen. Die irreversibel induzierte Thrombozytenaktivierung und -aggregation wurde durch die Hemmung des Proteasoms mit Bortezomib bis zu 24 Stunden nicht beeinflusst. Allerdings führte die Proteasom-Hemmung zu einer verstärkten Schwellenwertaggregation und -agglutination um bis zu 25 % sowie zu einer partiellen Abschwächung der induzierten VASP-Phosphorylierung um etwa 10-15 %. Die Expression verschiedener Rezeptoren blieb nahezu unbeeinflusst. Stattdessen konnte unter Proteasom-Inhibition eine erhöhte Enzymaktivität der PP2A beobachtet werden, begleitet von einer erleichterten Thrombozytenadhäsion an beschichteten Oberflächen bei statischen Versuchen ober bei Flusskammerversuchen. Carfilzomib, welches erstmals für funktionelle Experimente mit menschlichen Thrombozyten in vitro eingesetzt wurde, führte zu einer dosisabhängigen Abnahme der Proteasom-Aktivität mit einer Akkumulation von poly ubiquitylierten Proteinen. Wie Bortezomib mündete die Behandlung mit Carfilzomib in einer verstärkten Schwellenwertaggregation und abgeschwächter VASP-Phosphorylierung. Die wichtigste Schlussfolgerung dieser Arbeit ist, dass die Inhibition des Proteasoms die Reaktivität humaner Thrombozyten erhöht, gekennzeichnet durch eine Abschwächung der hemmenden Signalwege der Thrombozyten und durch eine zusätzliche Erhöhung der PP2A-Enzymaktivität, was zu einer erleichterten Thrombozytenadhäsion unter statischen Verhältnissen und unter Flussbedingungen führt. Das Proteasomsystem scheint an der Förderung der hemmenden Gegenregulation in Thrombozyten beteiligt zu sein. Das Potenzial von Proteasom Inhibitoren, thromboembolische Nebenwirkungen bei Patienten auszulösen, muss in weiteren Studien geklärt werden, ebenso wie ihr möglicher Einsatz für die gezielte Beeinflussung der Thrombozytenfunktion zur Verbesserung der hämostatischen Reaktivität der Thrombozyten. KW - Thrombozyt KW - Proteasom KW - Platelet KW - Proteasome KW - Bortezomib Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-321089 ER - TY - THES A1 - Huber, Hannes T1 - Biochemical and functional characterization of DHX30, an RNA helicase linked to neurodevelopmental disorder T1 - Biochemische und funktionelle Charakterisierung von DHX30, einer RNA Helikase assoziiert mit neurologischen Entwicklungsstörungen N2 - RNA helicases are key players in the regulation of gene expression. They act by remodeling local RNA secondary structures as well as RNA-protein interactions to enable the dynamic association of RNA binding proteins to their targets. The putative RNA helicase DHX30 is a member of the family of DEAH-box helicases with a putative role in the ATP-dependent unwinding of RNA secondary structures. Mutations in the DHX30 gene causes the autosomal dominant neuronal disease “Neurodevelopmental Disorder with severe Motor Impairment and Absent Language” (NEDMIAL;OMIM#617804). In this thesis, a strategy was established that enabled the large-scale purification of enzymatically active DHX30. Through enzymatic studies performed in vitro, DHX30 was shown to act as an ATP-dependent 3’ → 5’ RNA helicase that catalyzes the unwinding of RNA:RNA and RNA:DNA substrates. Using recombinant DHX30, it could be shown that disease-causing missense mutations in the conserved helicase core caused the disruption of its ATPase and helicase activity. The protein interactome of DHX30 however, was unchanged indicating that the pathogenic missense-mutations do not cause misfolding of DHX30, but rather specifically affect its catalytic activity. DHX30 localizes predominantly in the cytoplasm where it forms a complex with ribosomes and polysomes. Using a cross-linking mass spectrometry approach, a direct interaction of the N-terminal double strand RNA binding domain of DHX30 with sites next to the ribosome’s mRNA entry channel and the subunit interface was uncovered. RNA sequencing of DHX30 knockout cells revealed a strong de-regulation of mRNAs involved in neurogenesis and nervous system development, which is in line with the NEDMIAL disease phenotype. The knockdown of DHX30 results in a decreased 80S peak in polysome gradients, indicating that DHX30 has an effect on the translation machinery. Sequencing of the pool of active translating mRNAs revealed that upon DHX30 knockout mainly 5’TOP mRNAs are downregulated. These mRNAs are coding for proteins of the translational machinery and translation initiation factors. This study identified DHX30 as a factor of the translation machinery that selectively impacts the expression of a subset of proteins and provides insight on the etiology of NEDMIAL. N2 - RNA-Helikasen sind Schlüsselfaktoren bei der Regulierung der Genexpression. Sie remodellieren RNA-Sekundärstrukturen und RNA-Protein Interaktionen und dadurch die dynamische Interaktion von RNA-bindenden Proteinen mit deren Substraten. Die putative RNA-Helikase DHX30 ist Mitglied der DEAH-box Helikasen, welche in Abhängigkeit von ATP in der Lage sind, RNA-Sekundärstrukturen aufzulösen. Mutationen im DHX30 Gen verursachen die autosomal-dominante neuronale Krankheit “Neurodevelopmental Disorder with Severe Motor Impairment and Absent Language” (NEDMIAL; OMIM#617804). In dieser Arbeit wurde eine Aufreinigungs-Strategie etabliert, um im präparativen Maßstab enzymatisch-aktives DHX30 Protein zu gewinnen. Mit dem aufgereinigten Protein wurden enzymatische Experimente durchgeführt, wodurch DHX30 als ATP abhängige RNA-Helikase charakterisiert wurde. Es konnte gezeigt werden, dass es in der Lage ist RNA:RNA sowie RNA:DNA Substrate in einer 3’ → 5’ Richtung zu entwinden. Mithilfe des rekombinanten Proteins konnte weiter gezeigt werden, dass krankheitsverursachende Mutationen im hoch-konservierten Helikase-Kern von DHX30 zur Beeinträchtigung der ATPase und Helikase-Aktivität des Proteins führen. Des Weiteren ergab sich, dass das Protein-Interaktom der DHX30 Mutanten sich im Vergleich zum Wildtyp nicht verändert, was impliziert, dass die Mutationen nicht zu einer Missfaltung des Proteins, sondern dessen katalytische Aktivität inhibieren. DHX30 lokalisiert hauptsächlich im Cytoplasma und bildet dort einen Proteinkomplex mit Ribosomen und Polysomen. Mittels eines cross-linking mass spectrometry-Experiments konnte eine direkte Interaktion von DHX30 mit Stellen der ribosomalen mRNA Eintrittsstelle und dem Interface der ribosomalen Untereinheiten identifiziert werden. Die RNA Sequenzierung von DHX30-deletieren Zellen zeigte eine starke Deregulierung von mRNAs welche für die Entwicklung des Nervensystems und in der Neurogenese eine Rolle spielen, was mit dem Krankheits-Phänotyp von NEDMIAL korreliert. Weiter konnte gezeigt werden, dass es in DHX30-deletierten Zellen zur Abnahme von 80S Ribosomen in Polysomen-Gradienten kommt, was auf eine Funktion von DHX30 während der Translation schließen lässt. Durch das Sequenzieren aktiv translatierender mRNAs zeigte sich, dass der KO von DHX30 zur Abnahme von 5‘TOP mRNAs führt. Diese mRNAs kodieren für Proteine der Translations-Maschinerie und für Translations-Initiations Faktoren. Diese Studie identifiziert DHX30 als Faktor der Translations-Maschinerie, der selektiv die Expression einer mRNA-Untergruppe beeinflusst und Einblicke in die Ätiologie von NEDMIAL liefert. KW - DHX30 KW - NEDMIAL KW - Neurodevelopmental diseases KW - RNA helicase KW - RNA metabolism Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-280505 ER - TY - JOUR A1 - Benhalevy, Daniel A1 - Gupta, Sanjay K. A1 - Danan, Charles H. A1 - Ghosal, Suman A1 - Sun, Hong-Wei A1 - Kazemeier, Hinke G. A1 - Paeschke, Katrin A1 - Hafner, Markus A1 - Juranek, Stefan A. T1 - The Human CCHC-type Zinc Finger Nucleic Acid-Binding Protein Binds G-Rich Elements in Target mRNA Coding Sequences and Promotes Translation JF - Cell Reports N2 - The CCHC-type zinc finger nucleic acid-binding protein (CNBP/ZNF9) is conserved in eukaryotes and is essential for embryonic development in mammals. It has been implicated in transcriptional, as well as post-transcriptional, gene regulation; however, its nucleic acid ligands and molecular function remain elusive. Here, we use multiple systems-wide approaches to identify CNBP targets and function. We used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) to identify 8,420 CNBP binding sites on 4,178 mRNAs. CNBP preferentially bound G-rich elements in the target mRNA coding sequences, most of which were previously found to form G-quadruplex and other stable structures in vitro. Functional analyses, including RNA sequencing, ribosome profiling, and quantitative mass spectrometry, revealed that CNBP binding did not influence target mRNA abundance but rather increased their translational efficiency. Considering that CNBP binding prevented G-quadruplex structure formation in vitro, we hypothesize that CNBP is supporting translation by resolving stable structures on mRNAs. KW - PAR-CLIP KW - ribosome profiling KW - translational regulation KW - posttranscriptional gene regulation KW - zinc-finger KW - RNA binding protein KW - CLIP-seq Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-171122 VL - 18 IS - 12 ER - TY - JOUR A1 - Othman, Eman M. A1 - Fathy, Moustafa A1 - Bekhit, Amany Abdlrehim A1 - Abdel-Razik, Abdel-Razik H. A1 - Jamal, Arshad A1 - Nazzal, Yousef A1 - Shams, Shabana A1 - Dandekar, Thomas A1 - Naseem, Muhammad T1 - Modulatory and toxicological perspectives on the effects of the small molecule kinetin JF - Molecules N2 - Plant hormones are small regulatory molecules that exert pharmacological actions in mammalian cells such as anti-oxidative and pro-metabolic effects. Kinetin belongs to the group of plant hormones cytokinin and has been associated with modulatory functions in mammalian cells. The mammalian adenosine receptor (A2a-R) is known to modulate multiple physiological responses in animal cells. Here, we describe that kinetin binds to the adenosine receptor (A2a-R) through the Asn253 residue in an adenosine dependent manner. To harness the beneficial effects of kinetin for future human use, we assess its acute toxicity by analyzing different biochemical and histological markers in rats. Kinetin at a dose below 1 mg/kg had no adverse effects on the serum level of glucose or on the activity of serum alanine transaminase (ALT) or aspartate aminotransferase (AST) enzymes in the kinetin treated rats. Whereas, creatinine levels increased after a kinetin treatment at a dose of 0.5 mg/kg. Furthermore, 5 mg/kg treated kinetin rats showed normal renal corpuscles, but a mild degeneration was observed in the renal glomeruli and renal tubules, as well as few degenerated hepatocytes were also observed in the liver. Kinetin doses below 5 mg/kg did not show any localized toxicity in the liver and kidney tissues. In addition to unraveling the binding interaction between kinetin and A2a-R, our findings suggest safe dose limits for the future use of kinetin as a therapeutic and modulatory agent against various pathophysiological conditions. KW - cytokinin kinetin KW - modulatory effects KW - in vivo toxicity KW - A2a-R receptor Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-223064 SN - 1420-3049 VL - 26 IS - 3 ER - TY - JOUR A1 - Paknia, Elham A1 - Chari, Ashwin A1 - Stark, Holger A1 - Fischer, Utz T1 - The Ribosome Cooperates with the Assembly Chaperone pICln to Initiate Formation of snRNPs JF - Cell Reports N2 - The formation of macromolecular complexes within the crowded environment of cells often requires aid from assembly chaperones. PRMT5 and SMN complexes mediate this task for the assembly of the common core of pre-mRNA processing small nuclear ribonucleoprotein particles (snRNPs). Core formation is initiated by the PRMT5-complex subunit pICln, which pre-arranges the core proteins into spatial positions occupied in the assembled snRNP. The SMN complex then accepts these pICln-bound proteins and unites them with small nuclear RNA (snRNA). Here, we have analyzed how newly synthesized snRNP proteins are channeled into the assembly pathway to evade mis-assembly. We show that they initially remain bound to the ribosome near the polypeptide exit tunnel and dissociate upon association with pICln. Coincident with its release activity, pICln ensures the formation of cognate heterooligomers and their chaperoned guidance into the assembly pathway. Our study identifies the ribosomal quality control hub as a site where chaperone-mediated assembly of macromolecular complexes can be initiated. KW - ribosome KW - snRNPs KW - assembly chaperone KW - pICln Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-162420 VL - 16 IS - 12 ER - TY - JOUR A1 - Ye, Mingyu A1 - Wilhelm, Martina A1 - Gentschev, Ivaylo A1 - Szalay, Aladár T1 - A modified limiting dilution method for monoclonal stable cell line selection using a real-time fluorescence imaging system: A practical workflow and advanced applications JF - Methods and Protocols N2 - Stable cell lines are widely used in laboratory research and pharmaceutical industry. They are mainly applied in recombinant protein and antibody productions, gene function studies, drug screens, toxicity assessments, and for cancer therapy investigation. There are two types of cell lines, polyclonal and monoclonal origin, that differ regarding their homogeneity and heterogeneity. Generating a high-quality stable cell line, which can grow continuously and carry a stable genetic modification without alteration is very important for most studies, because polyclonal cell lines of multicellular origin can be highly variable and unstable and lead to inconclusive experimental results. The most commonly used technologies of single cell originate monoclonal stable cell isolation in laboratory are fluorescence-activated cell sorting (FACS) sorting and limiting dilution cloning. Here, we describe a modified limiting dilution method of monoclonal stable cell line selection using the real-time fluorescence imaging system IncuCyte\(^®\)S3. KW - monoclonal stable cell KW - limiting dilution cloning KW - ncuCyte\(^®\)S3 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-228896 VL - 4 IS - 1 ER - TY - CHAP A1 - Das, Hirakjyoti A1 - Zografakis, Alexandros A1 - Oeljeklaus, Silke A1 - Warscheid, Bettina T1 - Analysis of Yeast Peroxisomes via Spatial Proteomics T1 - Analyse von Hefeperoxisomen durch Spatial Proteomik T2 - Peroxisomes N2 - Peroxisomes are ubiquitous organelles with essential functions in numerous cellular processes such as lipid metabolism, detoxification of reactive oxygen species and signaling. Knowledge of the peroxisomal proteome including multi-localized proteins and, most importantly, changes of its composition induced by altering cellular conditions or impaired peroxisome biogenesis and function is of paramount importance for a holistic view on peroxisomes and their diverse functions in a cellular context. In this chapter, we provide a spatial proteomics protocol specifically tailored to the analysis of the peroxisomal proteome of baker's yeast that enables the definition of the peroxisomal proteome under distinct conditions and to monitor dynamic changes of the proteome including the relocation of individual proteins to a different cellular compartment. The protocol comprises subcellular fractionation by differential centrifugation followed by Nycodenz density gradient centrifugation of a crude peroxisomal fraction, quantitative mass spectrometric measurements of subcellular and density gradient fractions and advanced computational data analysis, resulting in the establishment of organellar maps on a global scale. KW - peroxisome purification KW - mass spectrometry KW - label-free quantification KW - protein localization KW - spatial proteomics KW - Saccharomyces cerevisiae KW - differential centrifugation KW - density gradient centrifugation KW - organellar mapping Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-327532 PB - Springer ET - accepted version ER -