immuno-fluorescent-labeling-microtubules-centrosomal-proteins-ex-vivo

Immuno-fluorescent Labeling of Microtubules and Centrosomal Proteins in <em>Ex Vivo</em> Intestinal Tissue and 3D <em>In Vitro</em> Intestinal Organoids

The advent of 3D in vitro organoids that mimic the in vivo tissue architecture and morphogenesis has greatly advanced the ability to study key biological ...

The replication of many viruses is associated with specific intracellular compartments called virus factories or virioplasm. These are thought to provide a physical scaffold to concentrate viral components and thereby increase the efficiency of replication. The formation of virus replication sites often results in rearrangement of cellular membranes and reorganization of the cytoskeleton. Similar rearrangements are seen in cells in response to protein aggregation, where aggresomes and autophagosomes are produced to facilitate protein degradation. Here I review the evidence that some viruses induce aggresomes and autophagosomes to generate sites of replication.

Aggresomes and autophagy generate sites for virus replication.

Virus replication and virus assembly often occur in virus inclusions or virus factories that form at pericentriolar sites close to the microtubule organizing center or in specialized nuclear domains called ND10/PML bodies. Similar inclusions called aggresomes form in response to protein aggregation. Protein aggregates are toxic to cells and are transported along microtubules to aggresomes for immobilization and subsequent degradation by proteasomes and/or autophagy. The similarity between aggresomes and virus inclusions raises the possibility that viruses use aggresome pathways to concentrate cellular and viral proteins to facilitate replication and assembly. Alternatively, aggresomes may be part of an innate cellular response that recognizes virus components as foreign or misfolded and targets them for storage and degradation. Insights into the possible roles played by aggresomes during virus assembly are emerging from an understanding of how virus inclusions form and how viral proteins are targeted to them.

Aggresomes and pericentriolar sites of virus assembly: cellular defense or viral design?

Autophagy is a cellular response to starvation which generates autophagosomes to carry cellular organelles and long-lived proteins to lysosomes for degradation. Degradation through autophagy can provide an innate defence against virus infection, or conversely autophagosomes can promote infection by facilitating assembly of replicase proteins. We demonstrate that the avian coronavirus, Infectious Bronchitis Virus (IBV) activates autophagy. A screen of individual IBV non-structural proteins (nsps) showed that autophagy was activated by IBV nsp6. This property was shared with nsp6 of mammalian coronaviruses Mouse Hepatitis Virus, and Severe Acute Respiratory Syndrome Virus, and the equivalent nsp5-7 of the arterivirus Porcine Reproductive and Respiratory Syndrome Virus. These multiple-spanning transmembrane proteins located to the endoplasmic reticulum (ER) where they generated Atg5 and LC3II-positive vesicles, and vesicle formation was dependent on Atg5 and class III PI3 kinase. The vesicles recruited double FYVE-domain containing protein (DFCP) indicating localised concentration of phosphatidylinositol 3 phosphate, and therefore shared many features with omegasomes formed from the ER in response to starvation. Omegasomes induced by viral nsp6 matured into autophagosomes that delivered LC3 to lysosomes and therefore recruited and recycled the proteins needed for autophagosome nucleation, expansion, cellular trafficking and delivery of cargo to lysosomes. The coronavirus nsp6 proteins activated omegasome and autophagosome formation independently of starvation, but activation did not involve direct inhibition of mTOR signalling, activation of sirtuin1 or induction of ER stress.

Coronavirus nsp6 proteins generate autophagosomes from the endoplasmic reticulum via an omegasome intermediate.

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

Guidelines for the use and interpretation of assays for monitoring autophagy.

Im Jahr 2008 haben wir den ersten Satz von Richtlinien f&uuml;r die Standardisierung der Forschung in Autophagy ver&ouml;ffentlicht. Seitdem Forschung zu diesem Thema hat sich weiter beschleunigen, und viele neue Wissenschaftler haben das Spielfeld betreten. Unsere Wissensdatenbank und relevante neue Technologien haben auch erweitert. Dementsprechend ist es wichtig, diese Leitlinien f&uuml;r die &Uuml;berwachung Autophagy in verschiedenen Organismen zu aktualisieren. Verschiedene Meinungen haben die Proben beschrieben, die f&uuml;r diesen Zweck verwendet wurden. Dennoch weiterhin besteht Verwirrung in Bezug auf akzeptierte, Autophagy, vor allem bei mehrzelligen Eukaryoten zu messen. Ein wesentlicher Punkt, der betont werden muss ist, dass es ein Unterschied zwischen Messungen, die &Uuml;berwachung der Zahlen oder Volume autophagic Elemente (z. B. Autophagosomes oder Autolysosomes) in jedem Stadium des Prozesses gegen die autophagic dieser Ma&szlig;nahme-Fluss durch den Autophagy Pathway (d. h. der vollst&auml;ndige Proze&szlig;); so ein Block in Macroautophagy, Ergebnisse in Autophagosomen Anh&auml;ufung von Reize unterschieden werden, die erh&ouml;hte autophagic Aktivit&auml;t, f&uuml;hren die definiert als erh&ouml;hte Autophagy Induktion gepaart mit erh&ouml;hter Lieferung an und Verschlechterung in Lysosomen (in den meisten h&ouml;heren Eukaryotes und einigen Einzellern wie Dictyostelium) oder die Vakuole (in Pflanzen und Pilzen). Mit anderen Worten, ist es besonders wichtig, dass die Ermittler in das Feld neue verstehen, dass die Darstellung des mehr Autophagosomes nicht unbedingt mit mehr Autophagy gleichzusetzen ist. In der Tat sammeln in vielen F&auml;llen Autophagosomes wegen einen Block in den Handel zu Lysosomen ohne eine damit einhergehende &Auml;nderung in Autophagosomen Biogenese, w&auml;hrend eine Zunahme der Autolysosomes eine Verringerung in Degradations-Aktivit&auml;t widerspiegeln kann. Hier pr&auml;sentieren wir eine Reihe von Leitlinien f&uuml;r die Auswahl und Interpretation der Methoden f&uuml;r die Verwendung von Ermittlern, die Macroautophagy und die damit verbundenen Prozesse untersuchen wollen, sowie f&uuml;r Pr&uuml;fer, die realistische und vern&uuml;nftige Kritiken von Papier bereitstellen, die auf diese Prozesse gerichtet werden m&uuml;ssen. Diese Richtlinien sollen kein formelhaften Satz von Regeln, weil die entsprechenden Assays teilweise auf die Frage und das System verwendet wird. Dar&uuml;ber hinaus betonen wir, dass keine einzelne Assay ist garantiert das passende Produkt in jeder Situation, und wir empfehlen die Verwendung von mehreren Proben Autophagy &uuml;berwachen. In diesen Leitlinien halten wir diese verschiedenen Methoden zur Bewertung Autophagy und welche Informationen kann, oder nicht, von ihnen abgerufen werden. Abschlie&szlig;end diskutieren die Vorz&uuml;ge und Grenzen von bestimmten Autophagy Assays, hoffen wir auf technische Innovationen im Bereich zu f&ouml;rdern.

Richtlinien f&uuml;r die Verwendung und Interpretation von Assays zur &Uuml;berwachung Autophagy in Verbindung.

Photoinduced electron transfer (PET)-based molecular probes have been successfully used for the intracellular imaging of the pH of acidic organelles. In this study, we describe the synthesis and characterization of a novel PET-based pH nanoprobe and its biological application for the signaling of acidic organelles in mammalian cells. A fluorescent ligand sensitive to pH via the PET mechanism that incorporates a thiolated moiety was synthesized and used to stabilize gold nanoparticles (2.4 ± 0.6 nm), yielding a PET-based nanoprobe. The PET nanoprobe was unambiguously characterized by transmission electron microscopy, proton nuclear magnetic resonance, Fourier transform infrared, ultraviolet-visible absorption, and steady-state/time-resolved fluorescence spectroscopies which confirmed the functionalization of the gold nanoparticles with the PET-based ligand. Following a classic PET behavior, the fluorescence emission of the PET-based nanoprobe was quenched in alkaline conditions and enhanced in an acidic environment. The PET-based nanoprobe was used for the intracellular imaging of acidic environments within Chinese hamster ovary cells by confocal laser scanning microscopy. The internalization of the nanoparticles by the cells was confirmed by confocal fluorescence images and also by recording the fluorescence emission spectra of the intracellular PET-based nanoprobe from within the cells. Co-localization experiments using a marker of acidic organelles, LysoTracker Red DND-99, and a marker of autophagosomes, GFP-LC3, confirm that the PET-based nanoprobe acts as marker of acidic organelles and autophagosomes within mammalian cells.

A photoinduced electron transfer-based nanoprobe as a marker of acidic organelles in mammalian cells.

Autophagy is a membrane trafficking pathway that results in the formation of autophagosomes which deliver portions of the cytosol to lysosomes for degradation. When autophagosomes engulf intracellular pathogens, the pathway is called 'xenophagy' because it leads to the removal of foreign material. Autophagy is activated during infection by Toll-like receptors that recognize pathogen-associated molecular patterns. This allows autophagy to kill micro-organisms and present pathogen components to the innate and acquired immune systems. The targeting of pathogens by autophagy is selective and involves a growing family of autophagy receptors that bind to the autophagosome membrane protein LC3 (light-chain 3)/Atg8 (autography-related protein 8). Ubiquitination of microbes identifies them as substrates for autophagy and they are delivered to autophagosomes by autophagy receptors that bind both ubiquitin and LC3/Atg8. Bacteria can also be detected before they enter the cytosol by autophagy receptors that scan the surface of membrane compartments for evidence of damage. The observation that some pathogens survive in cells suggests they can evade complete destruction by autophagy. For some bacteria this involves proteins that shield the surface of the bacteria from recognition by autophagy receptors. Other viruses and bacteria are resistant to degradation in lysosomes and use autophagosomes and/or lysosomes as sites for replication. Most of our current understanding of the role played by autophagy during microbial infection has come from studies of bacteria and viruses in tissue culture cell lines. Future work will focus on understanding how autophagy determines the outcome of infection 'in vivo', and how autophagy pathways can be exploited therapeutically.

Autophagy as a defence against intracellular pathogens.

Replication of positive-sense RNA viruses is associated with the rearrangement of cellular membranes. Previous work on the infection of tissue culture cell lines with the betacoronaviruses mouse hepatitis virus and severe acute respiratory syndrome coronavirus (SARS-CoV) showed that they generate double-membrane vesicles (DMVs) and convoluted membranes as part of a reticular membrane network. Here we describe a detailed study of the membrane rearrangements induced by the avian gammacoronavirus infectious bronchitis virus (IBV) in a mammalian cell line but also in primary avian cells and in epithelial cells of ex vivo tracheal organ cultures. In all cell types, structures novel to IBV infection were identified that we have termed zippered endoplasmic reticulum (ER) and spherules. Zippered ER lacked luminal space, suggesting zippering of ER cisternae, while spherules appeared as uniform invaginations of zippered ER. Electron tomography showed that IBV-induced spherules are tethered to the zippered ER and that there is a channel connecting the interior of the spherule with the cytoplasm, a feature thought to be necessary for sites of RNA synthesis but not seen previously for membrane rearrangements induced by coronaviruses. We also identified DMVs in IBV-infected cells that were observed as single individual DMVs or were connected to the ER via their outer membrane but not to the zippered ER. Interestingly, IBV-induced spherules strongly resemble confirmed sites of RNA synthesis for alphaviruses, nodaviruses, and bromoviruses, which may indicate similar strategies of IBV and these diverse viruses for the assembly of RNA replication complexes.

Infectious bronchitis virus generates spherules from zippered endoplasmic reticulum membranes.

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a heterogeneous disorder of significant societal impact that is proposed to involve both host and environmentally derived aetiologies that may be autoimmune in nature. Immune-related symptoms of at least moderate severity persisting for prolonged periods of time are common in ME/CFS patients and B cell depletion therapy is of significant therapeutic benefit. The origin of these symptoms and whether it is infectious or inflammatory in nature is not clear, with seeking evidence of acute or chronic virus infections contributing to the induction of autoimmune processes in ME/CFS being an area of recent interest. This article provides a comprehensive review of the current evidence supporting an infectious aetiology for ME/CFS leading us to propose the novel concept that the intestinal microbiota and in particular members of the virome are a source of the "infectious" trigger of the disease. Such an approach has the potential to identify disease biomarkers and influence therapeutics, providing much-needed approaches in preventing and managing a disease desperately in need of confronting.

A Role for the Intestinal Microbiota and Virome in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)?

Differentiation of columnar epithelial cells involves a dramatic reorganization of the microtubules (MTs) and centrosomal components into an apico-basal array no longer anchored at the centrosome. Instead, the minus-ends of the MTs become anchored at apical non-centrosomal microtubule organizing centres (n-MTOCs). Formation of n-MTOCs is critical as they determine the spatial organization of MTs, which in turn influences cell shape and function. However, how they are formed is poorly understood. We have previously shown that the centrosomal anchoring protein ninein is released from the centrosome, moves in a microtubule-dependent manner and accumulates at n-MTOCs during epithelial differentiation. Here, we report using depletion and knockout (KO) approaches that ninein expression is essential for apico-basal array formation and epithelial elongation and that CLIP-170 is required for its redeployment to n-MTOCs. Functional inhibition also revealed that IQGAP1 and active Rac1 coordinate with CLIP-170 to facilitate microtubule plus-end cortical targeting and ninein redeployment. Intestinal tissue and in vitro organoids from the Clip1/Clip2 double KO mouse with deletions in the genes encoding CLIP-170 and CLIP-115, respectively, confirmed requirement of CLIP-170 for ninein recruitment to n-MTOCs, with possible compensation by other anchoring factors such as p150Glued and CAMSAP2 ensuring apico-basal microtubule formation despite loss of ninein at n-MTOCs.

Article	Year
Aggresomes and autophagy generate sites for virus replication. Science (New York, N.Y.)\| PubMed ID: 16690857	2006
Aggresomes and pericentriolar sites of virus assembly: cellular defense or viral design? Annual review of microbiology\| PubMed ID: 17896875	2007
Coronavirus nsp6 proteins generate autophagosomes from the endoplasmic reticulum via an omegasome intermediate. Autophagy\| PubMed ID: 21799305	2011
Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy\| PubMed ID: 22966490	2012
A photoinduced electron transfer-based nanoprobe as a marker of acidic organelles in mammalian cells. Analytical and bioanalytical chemistry\| PubMed ID: 23552971	2013
Autophagy as a defence against intracellular pathogens. Essays in biochemistry\| PubMed ID: 24070478	2013
Infectious bronchitis virus generates spherules from zippered endoplasmic reticulum membranes. mBio\| PubMed ID: 24149513	2013
A Role for the Intestinal Microbiota and Virome in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)? Journal of clinical medicine\| PubMed ID: 27275835	2016
Ninein is essential for apico-basal microtubule formation and CLIP-170 facilitates its redeployment to non-centrosomal microtubule organizing centres. Open biology\| PubMed ID: 28179500	2017

Tom Wileman

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