TY - JOUR A1 - Franke, Werner W. A1 - Scheer, Ulrich A1 - Trendelenburg, Michael F. A1 - Spring, Herbert A1 - Zentgraf, Hanswalter T1 - Absence of nucleosomes in transcriptionally active chromatin N2 - The ultrastructure of twO kinds of transcription ally active chromatin, the lampbrush chromosome loops and the nucleoli from amphibian oocytes and primary nuclei of the green alga Acetabularia, has been examined after manual isolation and dispersion in low salt media of slightly alkaline pH using various electron microscopic staining techniques (positive staining, metal shadowing, negative staining, preparation on positively charged films, etc.) and compared with the appearance of chromatin from various somatic cells (hen erythrocytes, rat hepatocytes, ClIltured murine sarcoma cells) prepared in parallel. While typical nucleosomes were revealed with all the techniques for chromatin from the latter three cell system, no nucleosomes were identified in either the lampbrush chromosome structures or the nucleolar chromatin. Nucleosomal arrays were absent not only in maximally fibril-covered matrix units but also in fibril-free regions between transcriptional complexes, including the apparent spacer intercepts between different transcriptional units. Moreover, comparisons of the length of the repeating units of rDNA in the transcribed state with those determined in the isolated rDNA and with the lengths of the first stable product of rDNA transcription, the pre-rRNA, demonstrated that the transcribed rDNA was not significantly shortened and/or condensed but rather extended in the transcriptional units. Distinct granules of about nucleosomal size which were sometimes found in apparent spacer regions as well as within matrix units of reduced fibril density were shown not to represent nucleosomes since their number per spacer unit was not inversely correlated with the length of the specific unit and also on the basis of their resistance to treatment with the detergent Sarkosyl NL-30. It is possible to structurally distinguish between transcriptionally active chromatin in which the DNA is extended in a non-nucleosomal form of chromatin and condensed, inactive chromatin within the typical nucleosomal package. The characteristic extended structure of transcriptionally active chromatin is found not only in the transcribed genes but also in non-transcribed regions within or between ("spacer") transcriptional units as well as in transcriptional units that are untranscribed amidst transcribed ones and/or have been inactivated for relatively short time. It is hypothesized that activation of transcription involves a transition from a nucleosomal to an extended chromatin organisation and that this structural transition is not specific for single "activated" genes but may involve larger chromatin regions, including adjacent untranscribed intercepts. KW - Cytologie KW - Chromatin structure KW - nucleosomes KW - transcription KW - electron microscopy Y1 - 1976 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-40646 ER - TY - THES A1 - Flegler, Vanessa Judith T1 - Application of electron cryomicroscopy for structural and functional studies on the mechanosensitive channels of small conductance T1 - Kryoelektronenmikroskopie zur strukturellen und funktionellen Untersuchung der mechanosensitiven Kanäle kleiner Leitfähigkeit N2 - Bacteria thrive and survive in many different environments, and as a result, they have developed robust mechanisms to adapt rapidly to alterations in their surroundings. The protection against osmotic forces is provided by mechanosensitive channels: their primary function is to maintain the integrity of the cell upon a hypoosmotic shock. The mechanosensitive channel of small conductance (MscS) is not only the smallest common structural unit of a diverse family that allows for a tailored response in osmoregulation; it is also the most intensively studied homologue. Mechanosensitive channels directly sense elevated membrane tension levels generated by increased pressure within the cell and open transiently. Escherichia coli has six paralogues that differ in their gating properties and the number of additional transmembrane (TM) helices. These TM helices, termed sensor paddles, are essential for sensing, as they directly contact the surrounding membrane; however, the role of the additional TM helices is still unclear. Furthermore, lipids occupy hydrophobic pockets far away from the membrane plane. A recent gating model for MscS states that increased membrane tension triggers the expulsion of lipids out of those pockets, modulating different conformational states of MscS. This model focuses on bound lipids, but it is still unclear to what extent the direct interaction with the membrane influences sensing and how relevant it is for the larger paralogues. In the herein described work, structural studies on two larger paralogues, the medium-sized channel YnaI and the large channel YbiO were realised using electron cryomicroscopy (cryo-EM). Lipids were identified in YnaI in the pockets in a similar position and orientation as in MscS, suggesting a conserved sensing mechanism. Moreover, the copolymer diisobutylene/maleic acid (DIBMA) allowed the extraction of artificially activated YnaI from plasma membranes, leading to an open-like form of this channel. This novel conformation indicated that the pore helices bend at a GGxGG motif during gating, which is unique among the Escherichia coli paralogues, concomitant with a structural reorganisation of the sensor paddles. Thus, despite a high similarity of their closed states, the gating mechanisms of MscS and YnaI are surprisingly different. Furthermore, the comparison of MscS, YnaI, and YbiO accentuates variations and similarities between the differently sized family members, implying fine-tuning of channel properties in the pore regions and the cytosolic lateral entry sides into the channel. Structural analyses of MscS reconstituted into different systems showed the advantages and disadvantages of certain polymers and detergents. The novel DIBMA copolymer and the more conventional amphiphilic polymers, so-called Amphipols, perturb contacting transmembrane helices or lead to their denaturation. Due to this observation, the obtained structures of YnaI must also be cautiously considered. The structures obtained in detergents resulted in unaffected channels; however, the applicability of detergents for MscS-like channels is limited by the increased required sample concentration. The role of lipids for gating MscS in the absence of a membrane was examined by deliberately removing coordinated lipid molecules from MscS using different amounts and kinds of detergent. The effects on the channel were inspected by cryo-EM. These experiments showed that closed MscS adopts the open conformation when it is enough delipidated by incubation with the detergent n-dodecyl-β-D-maltoside, and adding lipids to the open channel reverses this process. The results agree with the state-of-the-art model that the amount of lipid molecules in the pockets and grooves is responsible for the conformational state of MscS. Furthermore, incubation with the detergent lauryl maltose neopentyl glycol, which has stabilising and delipidating characteristics, resulted in a high-resolution structure of open MscS exhibiting an intricate network of ligands. Based on this structure, an updated gating model is proposed, which states that upon opening, lipids from the pockets migrate into the cytosolic membrane leaflet, while lipids from the periplasmic leaflet enter the grooves that arise between the sensor paddles. N2 - Bakterien gedeihen und überleben in vielen unterschiedlichen Umgebungen. Daher haben sie robuste Mechanismen entwickelt, um sich rasch an Veränderungen in ihrer Umgebung anzupassen. Den Schutz vor osmotischen Kräften gewährleisten mechanosensitive Kanäle: Ihre Hauptfunktion besteht darin, die Unversehrtheit der Zelle bei einem hypoosmotischen Schock zu erhalten. Der mechanosensitive Kanal geringer Leitfähigkeit (mechanosensitive channel of small conductance, MscS) stellt nicht nur die kleinste gemeinsame Struktureinheit einer Familie von Kanälen dar, die eine maßgeschneiderte Antwort auf hypoosmotischen Stress ermöglicht; er ist auch das intensivste untersuchte Familienmitglied. Mechanosensitive Kanäle registrieren erhöhte Membranspannungen, die durch steigenden Druck innerhalb der Zelle entstehen, und öffnen vorübergehend. In Escherichia coli gibt es sechs paraloge Kanäle, die sich in ihren Öffnungs-Eigenschaften und der Anzahl zusätzlicher transmembranen Helices unterscheiden. Diese Helices, die als sensor paddles bezeichnet werden, sind für das Erfassen ansteigender Membranspannung unerlässlich, da sie direkt mit der umgebenden Membran in Kontakt stehen; die Rolle der zusätzlichen transmembranen Helices ist jedoch noch nicht geklärt. Außerdem sitzen Lipide in hydrophoben Taschen weit entfernt von der Membran. Ei kürzlich vorgeschlagenes Öffnungs-Modell für MscS besagt, dass eine erhöhte Membranspannung zum Ausstoß der Lipide aus diesen Taschen führt, wodurch verschiedene Konformationszustände von MscS moduliert werden. Dieses Modell konzentriert sich auf die Rolle der Lipide, aber es ist noch immer unklar, inwieweit die direkte Wechselwirkung mit der Membran das Wahrnehmen der Membranspannung beeinflusst und welche Bedeutung sie für die größeren paralogen Kanäle hat. In der vorliegenden Arbeit wurden Strukturstudien an zwei größeren paralogen Kanälen, dem mittelgroßen Kanal YnaI und dem großen Kanal YbiO, mittels Kryoelektronenmikroskopie (Kryo-EM) durchgeführt. In YnaI wurden Lipide in den Taschen in ähnlicher Position und Ausrichtung wie in MscS gefunden, was auf einen konservierten Mechanismus zur Wahrnehmung der Membranspannung schließen lässt. Darüber hinaus ermöglichte das Copolymer Diisobutylen/Maleinsäure (DIBMA) die Isolation von artifiziell aktiviertem YnaI aus Plasmamembranen, was zur Struktur einer anscheinend offenen Form dieses Kanals führte. Diese neuartige Konformation deutet darauf hin, dass sich die Porenhelices während des Öffnens im Bereich eines GGxGG-Motiv biegen, das unter den paralogen Kanälen von Escherichia coli einzigartig ist und mit einer strukturellen Reorganisation der sensor paddles einhergeht. Trotz der großen Ähnlichkeit ihrer geschlossenen Zustände sind die Öffnungs-Mechanismen von MscS und YnaI also überraschend unterschiedlich. Darüber hinaus zeigte der Vergleich von MscS, YnaI und YbiO Unterschiede und Gemeinsamkeiten zwischen den unterschiedlich großen Familienmitgliedern. Diese Erkenntnissse deuten auf eine Feinabstimmung der Kanaleigenschaften im Bereich der Pore und an den zytosolischen seitlichen Eingängen der Kanäle hin. Strukturanalysen von MscS, in verschiedene Systeme rekonstituiert, zeigten die Vor- und Nachteile von ausgewählten Polymeren und Detergenzien. Das neuartige DIBMA-Copolymer und herkömmlichere amphiphile Polymere, die sogenannten Amphipole, stören die kontaktierenden transmembranen Helices oder führen zu deren Denaturierung. Im Zuge dieser Beobachtung müssen auch die erhaltenen Strukturen von YnaI vorsichtig betrachtet werden. Die in Detergenzien erhaltenen Strukturen zeigen unbeeinträchtigte Kanäle; die Anwendbarkeit von Detergenzien für MscS-ähnliche Kanäle wird jedoch durch die erhöhte erforderliche Proteinkonzentration eingeschränkt. Die Rolle der Lipide für das Öffnen von MscS wurde in Abwesenheit einer Membran untersucht, indem koordinierte Lipidmoleküle mit verschiedenen Mengen und Arten von Detergenzien bewusst von MscS entfernt wurden. Die Auswirkungen auf den Kanal wurden mittels Kryo-EM untersucht. Dabei zeigte sich, dass die geschlossene Form von MscS in die offene Konformation übergeht, wenn es durch Inkubation mit dem Detergenz n-Dodecyl-β-D-Maltosid ausreichend delipidiert wird, und dass die Zugabe von Lipiden zum offenen Kanal diesen Prozess wieder umkehrt. Die Ergebnisse stimmen mit dem Öffnungs-Modell überein, das besagt, dass die Menge der Lipidmoleküle in den Taschen und Furchen für den Konformationszustand von MscS verantwortlich ist. Darüber hinaus führte die Inkubation mit dem Detergenz Laurylmaltose-neopentylglykol, das sowohl stabilisierende als auch delipidierende Eigenschaften hat, zu einer hochaufgelösten Struktur des offenen MscS, die ein ausgeprägtes Netzwerk von Liganden zeigt. Auf der Grundlage dieser Struktur wird ein aktualisiertes Öffnungs-Modell vorgeschlagen, das besagt, dass bei der Öffnung Lipide aus den Taschen in die zytosolische Lipidschicht der Membran wandern, während Lipide aus der periplasmatischen Lipidschicht in die Furchen gelangen, die zwischen den sensor paddles entstehen. KW - mechanosensitive channels KW - electron cryomicroscopy KW - MscS KW - YnaI KW - protein-lipid interactions KW - delipidation KW - mechanosensing KW - electron microscopy Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-268979 ER - TY - JOUR A1 - Mostosi, Philipp A1 - Schindelin, Hermann A1 - Kollmannsberger, Philip A1 - Thorn, Andrea T1 - Haruspex: A Neural Network for the Automatic Identification of Oligonucleotides and Protein Secondary Structure in Cryo‐Electron Microscopy Maps JF - Angewandte Chemie International Edition N2 - In recent years, three‐dimensional density maps reconstructed from single particle images obtained by electron cryo‐microscopy (cryo‐EM) have reached unprecedented resolution. However, map interpretation can be challenging, in particular if the constituting structures require de‐novo model building or are very mobile. Herein, we demonstrate the potential of convolutional neural networks for the annotation of cryo‐EM maps: our network Haruspex has been trained on a carefully curated set of 293 experimentally derived reconstruction maps to automatically annotate RNA/DNA as well as protein secondary structure elements. It can be straightforwardly applied to newly reconstructed maps in order to support domain placement or as a starting point for main‐chain placement. Due to its high recall and precision rates of 95.1 % and 80.3 %, respectively, on an independent test set of 122 maps, it can also be used for validation during model building. The trained network will be available as part of the CCP‐EM suite. KW - DNA structures KW - electron microscopy KW - neural networks KW - protein structures KW - RNA structures Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-214763 VL - 59 IS - 35 SP - 14788 EP - 14795 ER - TY - JOUR A1 - Dogan, Leyla A1 - Scheuring, Ruben A1 - Wagner, Nicole A1 - Ueda, Yuichiro A1 - Schmidt, Sven A1 - Wörsdörfer, Philipp A1 - Groll, Jürgen A1 - Ergün, Süleyman T1 - Human iPSC-derived mesodermal progenitor cells preserve their vasculogenesis potential after extrusion and form hierarchically organized blood vessels JF - Biofabrication N2 - Post-fabrication formation of a proper vasculature remains an unresolved challenge in bioprinting. Established strategies focus on the supply of the fabricated structure with nutrients and oxygen and either rely on the mere formation of a channel system using fugitive inks or additionally use mature endothelial cells and/or peri-endothelial cells such as smooth muscle cells for the formation of blood vessels in vitro. Functional vessels, however, exhibit a hierarchical organization and multilayered wall structure that is important for their function. Human induced pluripotent stem cell-derived mesodermal progenitor cells (hiMPCs) have been shown to possess the capacity to form blood vessels in vitro, but have so far not been assessed for their applicability in bioprinting processes. Here, we demonstrate that hiMPCs, after formulation into an alginate/collagen type I bioink and subsequent extrusion, retain their ability to give rise to the formation of complex vessels that display a hierarchical network in a process that mimics the embryonic steps of vessel formation during vasculogenesis. Histological evaluations at different time points of extrusion revealed the initial formation of spheres, followed by lumen formation and further structural maturation as evidenced by building a multilayered vessel wall and a vascular network. These findings are supported by immunostainings for endothelial and peri-endothelial cell markers as well as electron microscopic analyses at the ultrastructural level. Moreover, endothelial cells in capillary-like vessel structures deposited a basement membrane-like matrix at the basal side between the vessel wall and the alginate-collagen matrix. After transplantation of the printed constructs into the chicken chorioallantoic membrane (CAM) the printed vessels connected to the CAM blood vessels and get perfused in vivo. These results evidence the applicability and great potential of hiMPCs for the bioprinting of vascular structures mimicking the basic morphogenetic steps of de novo vessel formation during embryogenesis. KW - vascular biofabrication KW - human iPSC-derived mesodermal cells (hiMPCs) KW - extrusion of hiMPC-containing bioinks alginate + collagen type I KW - multilayered vessel wall with intimate, media and adventitia KW - vascular network and hierarchical organized vessels KW - electron microscopy KW - serial block face EM Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-254046 VL - 13 IS - 4 ER - TY - JOUR A1 - Spring, Herbert A1 - Trendelenbrug, Michael F. A1 - Scheer, Ulrich A1 - Franke, Werner W. A1 - Herth, Werner T1 - Structural and biochemical studies of the primary nucleus of two green algal species, Acetabularia mediterranea and Acetabularia major N2 - Primary (giant) nuclei of the green algae Acetabularia mediterranea and A. major were studied by light and electron microscopy using in situ fixed material as well as manually isolated nuclear components. In addition, cytochemical reactions of nuclear structures and biochemical determinations of nuclear and cytoplasmic RNA and of genome DNA content were performed. The data obtained and the structures observed are interpreted as demonstralions of transcriptional activities of different gene classes. The most prominent class is the nucleolar cistrons of precursors of ribosomal RNA which occur highly repeated in clusters in the form of regularly alternating intercepts on deoxyribonucleoprotein axes of transcribed rDNA, the fibril-covered matrix units, and the fibril-free "spacer" segments. A description and a classification of the various structural complexes which seem to represent transcriptional activities is given. Quantitative evaluations of these arrangements are presented. The morphology and the dimensions of such structures are compared with the RNA molecular weight determinations and with the corresponding data reported from various animal cell systems. It is suggested that the formation of the giant nucleus is correlated with, and probably due to, an enormous amplification of transcriptionally active rDNA and packing of the extrachromosomal copies into the large nucleolar aggregate bodies. KW - Cytologie KW - Nucleolus KW - electron microscopy KW - Acetabularia KW - transcription KW - gene activity KW - ribosomes Y1 - 1974 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-40600 ER - TY - THES A1 - Song, Boyuan T1 - Structural and functional studies of \(Saccharomyces\) \(cerevisiae\) Ccr4-Not complex with Electron microscopy T1 - Strukturelle und funktionelle Untersuchungen von \(Saccharomyces\) \(cerevisiae\) Ccr4-Not Komplexen mittels Elektronenmikroskopie N2 - The degradation of poly-adenosine tails of messenger RNAs (mRNAs) in the eukaryotic cells is a determining step in controlling the level of gene expression. The highly conserved Ccr4-Not complex was identified as the major deadenylation complex in all eukaryotic organisms. Plenty of biochemical studies have shown that this complex is also involved in many aspects of the mRNA metabolism, but we are still lacking the detailed structural information about its overall architecture and conformational states that could help to elucidate its multifunction and the way it is coordinated in the cells. Such information can also provide a basis to finding a possible way of intervention since the complex is also involved in some diseases such as cancer and cardiovascular disorders in humans. Meanwhile, the single particle Cryo-EM method has been through a “resolution revolution” recently due to the use of the newly developed direct electron detectors and has since resolved the high-resolution structures of many macromolecular protein complexes in their near-native state. Therefore, it was employed as a suitable method for studying the Ccr4-Not complex here. In this work, the Falcon 3EC direct detector mounted on the 300kV Titan Krios G3i Cryo-EM was evaluated for its practical performance at obtaining high-quality Cryo-EM data from protein samples of different molecular sizes. This served as a proof of principle for this detector’s capabilities and as a data collection guidance for studying the macromolecular complexes, such as the Ccr4-Not, when using an advanced high-performance microscope system. Next, the endogenous yeast Ccr4-Not complex was also purified via the immunoaffinity purification method and evaluated using negative staining EM to assess the conditions of the complex before proceeding to sample preparation for Cryo-EM. This has shown that the complex had an unexpected inherently dynamic property in vitro and extra optimisation procedures were needed to stabilise the complex during the purification and sample preparation. In addition, by using the label-free quantitative Mass spectrometry to examine the coimmunoprecipitated complex via different tagged subunits, it was deduced that two of the subunits (Not3/Not5) that shared some sequence similarity might compete for association with the scaffold subunit of the complex. An uncharacterised protein was also identified coimmunoprecipitating with the Caf130 subunit of the yeast complex. Cryo-EM data from the purified complex provided a low-resolution map that represents a surprisingly smaller partial complex as compared to 3D structures from previous studies, although gel electrophoresis and Mass spectrometry data have identified all of the nine subunits of the Ccr4-Not core complex in the sample. It was concluded that due to the presence of many predicted unstructured regions VI in the subunits and their dynamic composition in solution, the native complex could have been spontaneously denatured at the air/water interface during the sample preparation thus limiting the resolution of the Cryo-EM reconstruction. The purified complex was also examined for its deadenylase and ubiquitin ligase activity by in vitro assays. It was shown that the native complex has a different rate of activity and possibly also a different mode of action compared to the recombinant complexes from other species under similar reaction conditions. The Not4 E3 ligase was also shown to be active in the complex and was likely auto-ubiquitinated in the absence of a substrate. Both types of assays have also shown that the conformational flexibility does not seem to affect the enzymatic reactions when using a chemically crosslinked form of the complex for the assay, which implies that there can be other underlying mechanisms coordinating its structural and functional relationship. The findings from this work have therefore moved our understanding of the Ccr4-Not complex forward by looking at the different structural and functional behaviours of the endogenous complex, especially highlighting the obstacles in sample preparation for the native complex in high-resolution Cryo-EM. This would serve as foundation for future studies on the mechanism of this complex’s catalytic functions and also for optimising the Cryo-EM sample to generate better data that could eventually resolve the structure to a high-resolution. N2 - Der Abbau des Poly(A)-Schwanzes von Messenger-RNAs (mRNA) in den eukaryotischen Zellen ist ein entscheidender Schritt bei der Kontrolle des Niveaus der Genexpression. Der hochkonservierte Ccr4-Not-Komplex wurde in allen eukaryotischen Organismen als der Hauptdeadenylierungskomplex identifiziert. Zahlreiche biochemische Studien haben gezeigt, dass dieser Komplex auch an vielen Aspekten des mRNA-Metabolismus beteiligt ist. Uns fehlen jedoch noch die detaillierten Strukturinformationen über seine Gesamtarchitektur und seine Konformationszustände, die zur Aufklärung seiner Multifunktion und seiner Koordinierung in den Zellen beitragen könnten. Solche Informationen können auch Grundlage für die Suche nach einem möglichen Interventionsweg bieten, da der Komplex auch an einigen Krankheiten wie Krebs und Herz-Kreislauf-Erkrankungen des Menschen beteiligt ist. In der Zwischenzeit hat die Einzelpartikel-Kryo-EM-Methode aufgrund der Verwendung der neu entwickelten direkten Elektronendetektoren kürzlich eine „Auflösungsrevolution“ durchlaufen und seitdem die hochauflösenden Strukturen vieler makromolekularer Proteinkomplexe in ihrem nahezu nativen Zustand aufgelöst. Daher wurde es hier als geeignete Methode zur Untersuchung des Ccr4-Not-Komplexes eingesetzt. In dieser Arbeit wurde der Falcon 3EC-Direktdetektor, der an das 300-kV-Titan Krios G3i Kryo-EM montiert ist, auf seine praktische Leistung bei der Gewinnung hochwertiger Kryo-EM-Daten aus Proteinproben unterschiedlicher Molekülgröße untersucht. Dies diente als Grundsatznachweis für die Fähigkeiten des Detektors und als Leitfaden für die Datenerfassung zur Untersuchung der makromolekularen Komplexe wie Ccr4-Not bei Verwendung eines fortschrittlichen Hochleistungsmikroskopsystems. Als nächstes wurde der endogene Hefe-Ccr4-Not-Komplex auch über das Immunaffinitäts-Reinigungsverfahren gereinigt und unter Verwendung einer negativ gefärbten EM bewertet, um die Bedingungen des Komplexes zu bewerten, bevor mit der Probenvorbereitung für Kryo-EM fortgefahren wurde. Dies hat gezeigt, dass der Komplex in vitro eine unerwartete inhärent dynamische Eigenschaft aufwies und zusätzliche Optimierungsverfahren erforderlich waren, um den Komplex während der Reinigung und Probenvorbereitung zu stabilisieren. Darüber hinaus wurde unter Verwendung der markierungsfreien quantitativen Massenspektrometrie zur Untersuchung des co-immunpräzipitierten Komplexes über verschiedene markierte Untereinheiten abgeleitet, dass zwei der Untereinheiten (Not3 / Not5), die eine gewisse Sequenzähnlichkeit teilen, um die Verbindung mit der Gerüstuntereinheit des Komplexes konkurrieren könnten. Es wurde auch ein nicht charakterisiertes Protein identifiziert, das zusammen mit der Caf130-Untereinheit des Hefekomplexes immunpräzipitiert. Kryo-EM-Daten aus dem gereinigten Komplex lieferten eine Karte mit niedriger Auflösung, die im Vergleich zu 3D-Strukturen aus früheren Studien einen überraschend kleineren Teilkomplex darstellt, obwohl Gelelektrophorese- und Massenspektrometriedaten gezeigt haben, dass alle neun Untereinheiten des Ccr4-Not Kernkomplexware in der Probe vorhanden waren. Daraus kann man schließen, dass aufgrund des Vorhandenseins vieler vorhergesagter unstrukturierter Regionen in den Untereinheiten und ihrer dynamischen Zusammensetzung in Lösung der native Komplex während der Probenvorbereitung an der Luft / Wasser-Grenzfläche spontan denaturiert werden konnte, wodurch die Auflösung des Kryo-EM Wiederaufbaus begrenzt wurde. Der gereinigte Komplex wurde auch durch In-vitro-Tests auf seine Deadenylase- und Ubiquitin-Ligase-Aktivität untersucht. Es wurde aufgezeigt, dass der native Komplex eine andere Aktivitätsrate und möglicherweise auch eine andere Wirkungsweise aufweist als die rekombinanten Komplexe anderer Spezies unter ähnlichen Reaktionsbedingungen. Es wurde auch dargestellt, dass die Not4 E3-Ligase in dem Komplex aktiv ist und wahrscheinlich in Abwesenheit eines Substrats automatisch ubiquitiniert wird. Beide Arten von Assays haben auch gezeigt, dass die Konformationsflexibilität die enzymatischen Reaktionen bei Verwendung einer chemisch vernetzten Form des Komplexes für den Assay nicht zu beeinflussen scheint, was impliziert, dass es andere zugrunde liegende Mechanismen geben kann, die seine strukturelle und funktionelle Beziehung koordinieren. Die Ergebnisse dieser Arbeit haben daher unser Verständnis des Ccr4-Not-Komplexes weiterentwickelt, indem wir die unterschiedlichen strukturellen und funktionellen Verhaltensweisen des endogenen Komplexes untersucht und insbesondere die Hindernisse bei der Probenvorbereitung für den nativen Komplex im hochauflösendem Kryo-EM hervorgehoben haben. Dies würde als Grundlage für zukünftige Forschungen dienen, die Mechanismen seiner katalytischen Funktionen weiter zu untersuchen und auch die Kryo-EM-Probe zu optimieren, um bessere Daten zu generieren, die die Struktur schließlich in eine hohe Auflösung auflösen könnten. KW - CCR4 KW - Ccr4-Not KW - biochemistry KW - electron microscopy Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-216527 ER - TY - JOUR A1 - Scheer, Ulrich T1 - Structure of lampbrush chromosome loops during different states of transcriptional activity as visualized in the presence of physiological salt concentrations N2 - Lampbrush chromosomes of amphibian oocytes were isolated in the presence of near-physiological salt concentrations, to preserve their native state, and studied by electron microscopy of ultrathin s~dions. The transcriptional state of the lampbrush chromosomes was experimentally modulated by incubating the oocytes for various time periods in medium containing actinomycin D. The observations show that the structure of the lateral loops changes rapidly in response to alterations in transcriptional activity. During decreasing transcriptional activity and reduced packing density of transcripts, the chromatin axis first condensed into nucleosomes and then into an approximately 30 nm thick higher order chromatin fiber. Packaging of the loop axis into supranucleosomal structures may contribute to the foreshortening and retraction of the loops observed during inhibition of transcription and in later stages of meiotic prophase. The increasing packing density of the DNA during the retraction process of the loops could also be visualized by immunofluorescence microscopy using antibodies to DNA. The dependence of the loop chromatin structure on transcriptional activity is discussed in relation to current views of mechanisms involved in gene activation. KW - lampbrush chromosomes KW - chromatin structure KW - electron microscopy KW - immunofluorescence microscopy KW - DNA antibodies Y1 - 1987 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-39304 ER -