Targeted interplay between bacterial pathogens and host autophagy

Due to the critical role played by autophagy in pathogen clearance, pathogens have developed diverse strategies to subvert autophagy. Despite previous key findings of bacteria-autophagy interplay, a systems level insight into selective targeting by the host and autophagy modulation by the pathogens is lacking. We predicted potential interactions between human autophagy proteins and effector proteins from 56 pathogenic bacterial species by identifying bacterial proteins predicted to have recognition motifs for selective autophagy receptors p62/NDP52 and LC3. Conversely, using structure-based interaction prediction methods, we identified bacterial effector proteins that could putatively modify core autophagy components. Our analysis revealed that autophagy receptors in general potentially target mostly genus specific proteins, and not those present in multiple genera. We also show that the complementarity between the predicted p62 and NDP52 targets, which has been shown for Salmonella, Listeria and Shigella, could be observed across other pathogens. Using literature evidence, we hypothesize that this complementarity potentially leave the host more susceptible to chronic infections upon the mutation of one of the autophagy receptors. To check any bias caused by our pathogenic protein selection criteria, control analysis using proteins derived from entero-toxigenic and non-toxigenic Bacillus outer membrane vesicles indicated that autophagy targets pathogenic proteins rather than non-pathogenic ones. We also observed a pathogen specific pattern as to which autophagy phase could be modulated by specific genera. We found intriguing examples of bacterial proteins which could modulate autophagy, and in turn capable of being targeted by the autophagy receptors and LC3 as a host defence mechanism. To demonstrate the validity of our predictions, we confirmed experimentally with in vitro Salmonella invasion assays the bi-directional interactions underlying the interplay between a Salmonella protease, YhjJ and autophagy. Our comparative meta-analysis points out key commonalities and differences in how pathogens could affect autophagy and how autophagy potentially recognises these pathogenic effectors

Autophagy in Microglia and Alzheimer's disease

Alzheimer’s disease (AD) is the most common neurodegenerative disease, characterized by amyloid-beta plaques, neurofibrillary tangles and neuroinflammation. Autophagy has been associated with several neurodegenerative diseases. Recently, autophagy has been linked to the regulation of the inflammatory response in macrophages. My thesis investigates how an impairment of autophagy influences the inflammatory response of microglia. We used Beclin1 heterozygous (Becn1+/-) mice as a model of impaired autophagy. Beclin1 plays a role in the initiation of autophagy and was shown to be decreased in microglia isolated from AD patients compared to healthy controls. In vitro, acutely stimulated microglia from neonatal Becn1+/- mice exhibited increased expression of the proinflammatory cytokines IL-1beta and IL-18 compared to wild type microglia. Both IL-1beta and IL-18 are processed by the NLRP3 inflammasome pathway. The investigation of this pathway showed an elevated number of cells with inflammasomes and increased levels of the inflammasome components NLRP3 and cleaved Caspase1 in Becn1+/- microglia. Super resolution microscopy revealed a very close association of NLRP3 aggregates and LC3-positive autophagosomes. Interestingly, despite suggestions that the murine CALCOCO2 does not function as an autophagic adaptor, we discovered CALCOCO2 colocalised with NLRP3 and that its downregulation by siRNA knockdown increased IL-1beta release. These data support the notion that selective autophagy can impact microglia activation by modulating IL-1beta and IL-18 production via NLRP3 degradation. These in vitro data present a mechanism how impaired autophagy could contribute to neuroinflammation in AD. In vivo analysis of Becn1+/-.APPPS1 mice also demonstrated enhanced IL-1beta levels, but no differences in amyloid beta pathology, nor phagocytic capacity. The constitutive heterozygosity of Beclin1 might be responsible for the milder effects in vivo. Therefore, we performed studies utilizing more sophisticated models targeting immune cells specifically. The first model, Aldh1l1-iCre.Becn1-flox, targets Becn1 deletion specifically in astrocytes in the central nervous system after injection with the drug tamoxifen. Peripherally, Aldh1l1 is also expressed by hepatocytes. The Aldh1l1-iCre.Becn1-flox mice suffered from peripheral damage in the liver 10 days after tamoxifen injection, and can therefore not be used in further studies. The second model, Cx3Cr1-iCre.Becn1-flox, targets Becn1 deletion specifically in microglia in the central nervous system, and will be crossed to the APPPS1 mice to create a tool to study the role of Beclin1 in microglia in neuroinflammation and neurodegeneration. This new tool and the data generated in this work will support a new direction of research, to unravel the therapeutic potential of autophagy-dependent inflammation in neurodegenerative diseases.Die Alzheimer-Krankheit (AD) ist die häufigste neurodegenerative Erkrankung, die durch Amyloid-Beta-Plaques, neurofibrilläre Verwicklungen und Neuroinflammation gekennzeichnet ist. Autophagie wurde mit mehreren neurodegenerativen Erkrankungen in Verbindung gebracht. Vor Kurzem wurde Autophagie mit der Regulierung der Entzündungsreaktion in Makrophagen in Verbindung gebracht. Meine Dissertation untersucht, wie eine Beeinträchtigung der Autophagie die Entzündungsreaktion von Mikroglia beeinflusst. Wir haben Beclin1-heterozygote (Becn1+/-) Mäuse als Modell für eingeschränkte Autophagie verwendet. Beclin1 spielt eine Rolle bei der Initiierung der Autophagie und es wurde gezeigt, dass es bei aus AD-Patienten isolierten Mikrogliazellen im Vergleich zu gesunden Kontrollen abnimmt. Akut stimulierte Mikroglia aus neonatalen Becn1+/– Mäusen zeigten in vitro eine erhöhte Expression der proinflammatorischen Zytokine IL-1beta und IL-18 im Vergleich zu Wildtyp-Mikroglia. Sowohl IL-1beta als auch IL-18 werden vom NLRP3-Inflammasom-Weg verarbeitet. Die Untersuchung dieses Weges zeigte eine erhöhte Anzahl von Zellen mit Inflammasomen und erhöhte Spiegel der Inflammasomenkomponenten NLRP3 und gespaltenen Caspase1 in Becn1+/– Mikroglia. Super-Resolution-Mikroskopie zeigte eine sehr enge Lokalisation von NLRP3-Aggregaten und LC3-positiven Autophagosomen. Interessanterweise haben wir trotz der Kritik, dass das murine CALCOCO2 nicht als autophagischer Adapter fungiert, entdeckt, dass CALCOCO2 mit NLRP3 kolokalisiert und dass die Herunterregulierung durch siRNA die IL-1beta-Freisetzung erhöhte. Diese Daten stützen die Ansicht, dass selektive Autophagie die Mikroglia-Aktivierung beeinflussen kann, indem die IL-1beta- und IL-18-Produktion durch NLRP3-Abbau moduliert wird. Diese in vitro Daten stellen einen Mechanismus dar, wie eine gestörte Autophagie zur Neuroinflammation bei AD beitragen kann. In vivo Analysen von Becn1+/–.APPPS1 Mäusen zeigten ebenfalls erhöhte IL-1beta-Spiegel, jedoch keine Unterschiede in der Amyloid-Beta-Pathologie und auch keine in Bezug auf die Phagozytosekapazität. Die konstitutive Heterozygotie von Beclin1 könnte für die geringen Auswirkungen in vivo verantwortlich sein. Daher etablierten zwei neue Modelle, die speziell auf Immunzellen abzielten. Das erste Modell, Aldh1l1-iCre.Becn1-Flox, zielt auf die Becn1-Deletion spezifisch in Astrozyten im zentralen Nervensystem nach Injektion des Arzneimittels Tamoxifen ab. In der Peripherie wird Aldh1l1 auch von Hepatozyten exprimiert. Die Aldh1l1-iCre.Becn1-Flox Mäuse erlitten 10 Tage nach Tamoxifen-Injektion eine periphere Schädigung der Leber und können daher nicht in weiteren Studien verwendet werden. Das zweite Modell, Cx3Cr1-iCre.Becn1-flox, zielt auf die Becn1-Deletion speziell in Mikroglia im Zentralnervensystem ab und wird mit den APPPS1-Mäusen gekreuzt, um ein Modell für die Untersuchung der Rolle von Beclin1 in Mikroglia bei Neuroinflammation und Neurodegeneration darzustellen. Dieses neue Mausmodell und die in dieser Arbeit generierten Daten werden eine neue Richtung der Forschung unterstützen, um das therapeutische Potenzial autophagieabhängiger Entzündungen bei neurodegenerativen Erkrankungen zu ermitteln

Genetic aberrations in macroautophagy genes leading to diseases

The catabolic process of macroautophagy, through the rapid degradation of unwanted cellular components, is involved in a multitude of cellular and organismal functions that are essential to maintain homeostasis. Those functions include adaptation to starvation, cell development and differentiation, innate and adaptive immunity, tumor suppression, autophagic cell death, and maintenance of stem cell stemness. Not surprisingly, an impairment or block of macroautophagy can lead to severe pathologies. A still increasing number of reports, in particular, have revealed that mutations in the autophagy-related (ATG) genes, encoding the key players of macroautophagy, are either the cause or represent a risk factor for the development of several illnesses. The aim of this review is to provide a comprehensive overview of the diseases and disorders currently known that are or could be caused by mutations in core ATG proteins but also in the so-called autophagy receptors, which provide specificity to the process of macroautophagy. Our compendium underlines the medical relevance of this pathway and underscores the importance of the eventual development of therapeutic approaches aimed at modulating macroautophagy

iLIR : a web resource for prediction of Atg8-family interacting proteins

Macroautophagy was initially considered to be a nonselective process for bulk breakdown of cytosolic material. However, recent evidence points toward a selective mode of autophagy mediated by the so-called selective autophagy receptors (SARs). SARs act by recognizing and sorting diverse cargo substrates (e.g., proteins, organelles, pathogens) to the autophagic machinery. Known SARs are characterized by a short linear sequence motif (LIR-, LRS-, or AIM-motif) responsible for the interaction between SARs and proteins of the Atg8 family. Interestingly, many LIR-containing proteins (LIRCPs) are also involved in autophagosome formation and maturation and a few of them in regulating signaling pathways. Despite recent research efforts to experimentally identify LIRCPs, only a few dozen of this class of—often unrelated—proteins have been characterized so far using tedious cell biological, biochemical, and crystallographic approaches. The availability of an ever-increasing number of complete eukaryotic genomes provides a grand challenge for characterizing novel LIRCPs throughout the eukaryotes. Along these lines, we developed iLIR, a freely available web resource, which provides in silico tools for assisting the identification of novel LIRCPs. Given an amino acid sequence as input, iLIR searches for instances of short sequences compliant with a refined sensitive regular expression pattern of the extended LIR motif (xLIR-motif) and retrieves characterized protein domains from the SMART database for the query. Additionally, iLIR scores xLIRs against a custom position-specific scoring matrix (PSSM) and identifies potentially disordered subsequences with protein interaction potential overlapping with detected xLIR-motifs. Here we demonstrate that proteins satisfying these criteria make good LIRCP candidates for further experimental verification. Domain architecture is displayed in an informative graphic, and detailed results are also available in tabular form. We anticipate that iLIR will assist with elucidating the full complement of LIRCPs in eukaryotes

Autophagosome content profiling reveals receptor-specific cargo candidates

Selective autophagy receptors have been implicated in the degradation of cellular constituents of various size and rigidity. However, the identity of protein cargo have largely remained elusive. In our recent study, we combined limited proteolysis-enhanced proximity biotinylation and organelle enrichment with quantitative proteomics to map the inventory of autophagosomes in a manner dependent on six different selective autophagy receptors, namely SQSTM1/p62, NBR1, CALCOCO2/NDP52, OPTN, TAX1BP1 and TOLLIP. Conducting this approach under basal and proteostasis-challenged conditions in mammalian cells led to the identification of various new autophagy substrates of which some were degraded through endosomal microautophagy rather than canonical autophagy dependent on the receptors TOLLIP and SQSTM1, respectively

The inflammation repressor TNIP1/ABIN-1 is degraded by autophagy following TBK1 phosphorylation of its LIR

The inflammatory repressor TNIP1/ABIN-1 is important for keeping in check inflammatory and cell-death pathways to avoid potentially dangerous sustained activation of these pathways. We have now found that TNIP1 is rapidly degraded by selective macroautophagy/autophagy early (0–4 h) after activation of TLR3 by poly(I:C)-treatment to allow expression of pro-inflammatory genes and proteins. A few hours later (6 h), TNIP1 levels rise again to counteract sustained inflammatory signaling. TBK1-mediated phosphorylation of a TNIP1 LIR motif regulates selective autophagy of TNIP1 by stimulating interaction with Atg8-family proteins. This is a novel level of regulation of TNIP1, whose protein level is crucial for controlling inflammatory signaling

Mycobacterium tuberculosis type VII secretion system effectors differentially impact the ESCRT endomembrane damage response

Mycobacterium tuberculosis causes tuberculosis, which kills more people than any other infection. M. tuberculosis grows in macrophages, cells that specialize in engulfing and degrading microorganisms. Like many intracellular pathogens, in order to cause disease, M. tuberculosis damages the membrane-bound compartment (phagosome) in which it is enclosed after macrophage uptake. Recent work showed that when chemicals damage this type of intracellular compartment, cells rapidly detect and repair the damage, using machinery called the endosomal sorting complex required for transport (ESCRT). Therefore, we hypothesized that ESCRT might also respond to pathogen-induced damage. At the same time, our previous work showed that the EsxG-EsxH heterodimer of M. tuberculosis can inhibit ESCRT, raising the possibility that M. tuberculosis impairs this host response. Here, we show that ESCRT is recruited to damaged M. tuberculosis phagosomes and that EsxG-EsxH undermines ESCRT-mediated endomembrane repair. Thus, our studies demonstrate a battle between host and pathogen over endomembrane integrity.Intracellular pathogens have varied strategies to breach the endolysosomal barrier so that they can deliver effectors to the host cytosol, access nutrients, replicate in the cytoplasm, and avoid degradation in the lysosome. In the case of Mycobacterium tuberculosis, the bacterium perforates the phagosomal membrane shortly after being taken up by macrophages. Phagosomal damage depends upon the mycobacterial ESX-1 type VII secretion system (T7SS). Sterile insults, such as silica crystals or membranolytic peptides, can also disrupt phagosomal and endolysosomal membranes. Recent work revealed that the host endosomal sorting complex required for transport (ESCRT) machinery rapidly responds to sterile endolysosomal damage and promotes membrane repair. We hypothesized that ESCRTs might also respond to pathogen-induced phagosomal damage and that M. tuberculosis could impair this host response. Indeed, we found that ESCRT-III proteins were recruited to M. tuberculosis phagosomes in an ESX-1-dependent manner. We previously demonstrated that the mycobacterial effectors EsxG/TB9.8 and EsxH/TB10.4, both secreted by the ESX-3 T7SS, can inhibit ESCRT-dependent trafficking of receptors to the lysosome. Here, we additionally show that ESCRT-III recruitment to sites of endolysosomal damage is antagonized by EsxG and EsxH, both within the context of M. tuberculosis infection and sterile injury. Moreover, EsxG and EsxH themselves respond within minutes to membrane damage in a manner that is independent of calcium and ESCRT-III recruitment. Thus, our study reveals that T7SS effectors and ESCRT participate in a series of measures and countermeasures for control of phagosome integrity

Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization

The PARKIN (PARK2) ubiquitin ligase and its regulatory kinase PINK1 (PARK6), often mutated in familial early onset Parkinson’s Disease (PD), play central roles in mitochondrial homeostasis and mitophagy.1–3 While PARKIN is recruited to the mitochondrial outer membrane (MOM) upon depolarization via PINK1 action and can ubiquitylate Porin, Mitofusin, and Miro proteins on the MOM,1,4–11 the full repertoire of PARKIN substrates – the PARKIN-dependent ubiquitylome - remains poorly defined. Here we employ quantitative diGLY capture proteomics12,13 to elucidate the ubiquitylation site-specificity and topology of PARKIN-dependent target modification in response to mitochondrial depolarization. Hundreds of dynamically regulated ubiquitylation sites in dozens of proteins were identified, with strong enrichment for MOM proteins, indicating that PARKIN dramatically alters the ubiquitylation status of the mitochondrial proteome. Using complementary interaction proteomics, we found depolarization-dependent PARKIN association with numerous MOM targets, autophagy receptors, and the proteasome. Mutation of PARKIN’s active site residue C431, which has been found mutated in PD patients, largely disrupts these associations. Structural and topological analysis revealed extensive conservation of PARKIN-dependent ubiquitylation sites on cytoplasmic domains in vertebrate and D. melanogaster MOM proteins. These studies provide a resource for understanding how the PINK1-PARKIN pathway re-sculpts the proteome to support mitochondrial homeostasis

The role of Nrf2 signaling in counteracting neurodegenerative diseases

The transcription factor Nrf2 (nuclear factor-erythroid 2 p45-related factor 2) functions at the interface of cellular redox and intermediary metabolism. Nrf2 target genes encode antioxidant enzymes, and proteins involved in xenobiotic detoxification, repair and removal of damaged proteins and organelles, inflammation, and mitochondrial bioenergetics. The function of Nrf2 is altered in many neurodegenerative disorders, such as Huntington's disease, Alzheimer's disease, amyotrophic lateral sclerosis, and Friedreich's ataxia. Nrf2 activation mitigates multiple pathogenic processes involved in these neurodegenerative disorders through upregulation of antioxidant defenses, inhibition of inflammation, improvement of mitochondrial function, and maintenance of protein homeostasis. Small molecule pharmacological activators of Nrf2 have shown protective effects in numerous animal models of neurodegenerative diseases, and in cultures of human cells expressing mutant proteins. Targeting Nrf2 signaling may provide a therapeutic option to delay onset, slow progression, and ameliorate symptoms of neurodegenerative disorders.</p